Chem 121: Concepts For A Molecular View of Biology Ii: Krista Cunningham

CHEM 121: CONCEPTS
FOR A MOLECULAR
VIEW OF BIOLOGY II
Krista Cunningham
Case Western Reserve University
CHEM 121: Concepts for a Molecular View
of Biology II (Cunningham)
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This text was compiled on 01/11/2024
TABLE OF CONTENTS
Licensing
1: Organic Chemistry Basics

1.1: Organic Chemistry
1.2: Structures and Names of Alkanes
1.3: Branched-Chain Alkanes
1.4: Condensed Structural and Line-Angle Formulas
1.5: IUPAC Nomenclature
1.6: Physical Properties of Alkanes
1.7: Chemical Properties of Alkanes
1.8: Cycloalkanes
1.9: Organic Chemistry: Alkanes
1.10: Alkenes: Structures and Names
1.11: Cis-Trans Isomers (Geometric Isomers)
1.12: Physical Properties of Alkenes
1.13: Chemical Properties of Alkenes
1.14: Alkynes
1.15: Aromatic Compounds: Benzene
1.16: Structure and Nomenclature of Aromatic Compounds
1.17: Unsaturated and Aromatic Hydrocarbons (Summary)
1.18: Chirality and Stereoisomers
1.19: R-S Sequence Rules
1.21: Unsaturated and Aromatic Hydrocarbons (Exercises)
2: Carbohydrates
2.1: Prelude to Carbohydrates
2.2: Carbohydrates
2.3: Classes of Monosaccharides
2.4: Important Hexoses
2.5: Cyclic Structures of Monosaccharides
2.6: Properties of Monosaccharides
2.7: Disaccharides
2.8: Polysaccharides
2.9: Carbohydrates (Summary)
3: Lipids
3.1: Prelude to Lipids
3.2: Fatty Acids
3.3: Fats and Oils
3.4: Membranes and Membrane Lipids
3.5: Steroids
3.6: Lipids (Summary)
3.7: Exercises
1 https://chem.libretexts.org/@go/page/182167
4: Amino Acids, Proteins, and Enzymes
4.1: Prelude to Amino Acids, Proteins, and Enzymes
4.2: Properties of Amino Acids
4.3: Reactions of Amino Acids
4.4: Peptides
4.5: Proteins
4.6: Enzymes
4.7: Enzyme Action
4.8: Enzyme Activity
4.9: Enzyme Inhibition
4.10: Enzyme Cofactors and Vitamins
4.11: Amino Acids, Proteins, and Enzymes (Summary)
4.12: Amino Acids, Proteins, and Enzymes (Exercises)
5: Nucleic Acids
5.1: Prelude to Nucleic Acids
5.2: Nucleotides
5.3: Nucleic Acid Structure
5.4: Replication and Expression of Genetic Information
5.5: Protein Synthesis and the Genetic Code
5.6: Mutations and Genetic Diseases
5.7: Viruses
5.8: Nucleic Acids (Summary)
5.9: Nucleic Acids (Exercises)
6: Energy Metabolism
6.1: Prelude to Energy Metabolism
6.2: ATP: the Universal Energy Currency
6.3: Stage I of Catabolism
6.4: Overview of Stage II of Catabolism
6.5: Stage III of Catabolism
6.6: Stage II of Carbohydrate Catabolism
6.7: Stage II of Lipid Catabolism
6.8: Stage II of Protein Catabolism
6.9: Energy Metabolism (Summary)
6.10: Energy Metabolism (Exercises)
7: Chemical Messengers: Hormones, Neurotransmitters, and Drugs

7.1: Messenger Molecules
7.2: Hormones and the Endocrine System
7.3: How Hormones Work - Epinephrine and Fight-or-Flight
7.4: Amino Acid Derivatives and Polypeptides as Hormones
7.5: Steroid Hormones
7.6: Neurotransmitters
7.7: How Neurotransmitters Work: Acetylcholine, Its Agonists and Antagonists
7.8: Histamine and Antihistamines
7.9: Serotonin, Norepinephrine, and Dopamine
7.10: Neuropeptides and Pain Relief
7.11: Drug Discovery and Drug Design
Index
Glossary
Detailed Licensing
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CHAPTER OVERVIEW
1: Organic Chemistry Basics

1.8: Cycloalkanes
1.14: Alkynes
1: Organic Chemistry Basics is shared under a CC BY-NC-SA 4.0 license and was authored, remixed, and/or curated by LibreTexts.
1
Learning Objectives
To recognize the composition and properties typical of organic and inorganic compounds.
Scientists of the 18th and early 19th centuries studied compounds obtained from plants and animals and labeled them organic
because they were isolated from “organized” (living) systems. Compounds isolated from nonliving systems, such as rocks and ores,
the atmosphere, and the oceans, were labeled inorganic. For many years, scientists thought organic compounds could be made by
only living organisms because they possessed a vital force found only in living systems. The vital force theory began to decline in
1828, when the German chemist Friedrich Wöhler synthesized urea from inorganic starting materials. He reacted silver cyanate
(AgOCN) and ammonium chloride (NH4Cl), expecting to get ammonium cyanate (NH4OCN). What he expected is described by
the following equation.
AgOC N + N H4 C l → AgC l + N H4 OC N (1.1.1)
Instead, he found the product to be urea (NH2CONH2), a well-known organic material readily isolated from urine. This result led to
a series of experiments in which a wide variety of organic compounds were made from inorganic starting materials. The vital force
theory gradually went away as chemists learned that they could make many organic compounds in the laboratory.
Today organic chemistry is the study of the chemistry of the carbon compounds, and inorganic chemistry is the study of the
chemistry of all other elements. It may seem strange that we divide chemistry into two branches—one that considers compounds of
only one element and one that covers the 100-plus remaining elements. However, this division seems more reasonable when we
consider that of tens of millions of compounds that have been characterized, the overwhelming majority are carbon compounds.
The word organic has different meanings. Organic fertilizer, such as cow manure, is organic in the original sense; it is derived
from living organisms. Organic foods generally are foods grown without synthetic pesticides or fertilizers. Organic chemistry is
the chemistry of compounds of carbon.
Carbon is unique among the other elements in that its atoms can form stable covalent bonds with each other and with atoms of
other elements in a multitude of variations. The resulting molecules can contain from one to millions of carbon atoms. We
previously surveyed organic chemistry by dividing its compounds into families based on functional groups. We begin with the
simplest members of a family and then move on to molecules that are organic in the original sense—that is, they are made by and
found in living organisms. These complex molecules (all containing carbon) determine the forms and functions of living systems
and are the subject of biochemistry.
Organic compounds, like inorganic compounds, obey all the natural laws. Often there is no clear distinction in the chemical or
physical properties among organic and inorganic molecules. Nevertheless, it is useful to compare typical members of each class, as
in Table 1.1.1.
1.1.1 https://chem.libretexts.org/@go/page/178734
Table 1.1.1 : General Contrasting Properties and Examples of Organic and Inorganic Compounds
Organic Hexane Inorganic NaCl
low melting points −95°C high melting points 801°C
low boiling points 69°C high boiling points 1,413°C
low solubility in water; greater solubility in water;

insoluble in water; soluble soluble in water; insoluble
high solubility in nonpolar low solubility in nonpolar
in gasoline in gasoline
solvents solvents
flammable highly flammable nonflammable nonflammable
aqueous solutions do not aqueous solutions conduct conductive in aqueous

nonconductive
conduct electricity electricity solution
exhibit covalent bonding covalent bonds exhibit ionic bonding ionic bonds
Keep in mind, however, that there are exceptions to every category in this table. To further illustrate typical differences among
organic and inorganic compounds, Table 1.1.1 also lists properties of the inorganic compound sodium chloride (common table salt,
NaCl) and the organic compound hexane (C6H14), a solvent that is used to extract soybean oil from soybeans (among other uses).
Many compounds can be classified as organic or inorganic by the presence or absence of certain typical properties, as illustrated in
Table 1.1.1.
1.1: Organic Chemistry is shared under a CC BY-NC-SA 4.0 license and was authored, remixed, and/or curated by LibreTexts.
Learning Objectives
To identify and name simple (straight-chain) alkanes given formulas and write formulas for straight-chain alkanes given
their names.
We begin our study of organic chemistry with the hydrocarbons, the simplest organic compounds, which are composed of carbon
and hydrogen atoms only. As we noted, there are several different kinds of hydrocarbons. They are distinguished by the types of
bonding between carbon atoms and the properties that result from that bonding. Hydrocarbons with only carbon-to-carbon single
bonds (C–C) and existing as a continuous chain of carbon atoms also bonded to hydrogen atoms are called alkanes (or saturated
hydrocarbons). Saturated, in this case, means that each carbon atom is bonded to four other atoms (hydrogen or carbon)—the most
possible; there are no double or triple bonds in the molecules.
The word saturated has the same meaning for hydrocarbons as it does for the dietary fats and oils: the molecule has no carbon-
to-carbon double bonds (C=C).
We previously introduced the three simplest alkanes—methane (CH4), ethane (C2H6), and propane (C3H8) and they are shown
again in Figure 1.2.1.
Figure 1.2.1 : The Three Simplest Alkanes

The flat representations shown do not accurately portray bond angles or molecular geometry. Methane has a tetrahedral shape that
chemists often portray with wedges indicating bonds coming out toward you and dashed lines indicating bonds that go back away
from you. An ordinary solid line indicates a bond in the plane of the page. Recall that the VSEPR theory correctly predicts a
tetrahedral shape for the methane molecule (Figure 1.2.2).
Figure 1.2.2 : The Tetrahedral Methane Molecule

Methane (CH4), ethane (C2H6), and propane (C3H8) are the beginning of a series of compounds in which any two members in a
sequence differ by one carbon atom and two hydrogen atoms—namely, a CH2 unit. The first 10 members of this series are given in
Table 1.2.1.
Table 1.2.1 : The First 10 Straight-Chain Alkanes
Name Molecular Formula (CnH2n + 2) Condensed Structural Formula Number of Possible Isomers
methane CH4 CH4 —
ethane C2H6 CH3CH3 —
propane C3H8 CH3CH2CH3 —
butane C4H10 CH3CH2CH2CH3 2
pentane C5H12 CH3CH2CH2CH2CH3 3
hexane C6H14 CH3CH2CH2CH2CH2CH3 5
heptane C7H16 CH3CH2CH2CH2CH2CH2CH3 9
Name Molecular Formula (CnH2n + 2) Condensed Structural Formula Number of Possible Isomers
CH3CH2CH2CH2CH2CH2CH2CH
octane C8H18 18
3
nonane C9H20 35
2CH3
decane C10H22 75
2CH2CH3
Consider the series in Figure 1.2.3. The sequence starts with C3H8, and a CH2 unit is added in each step moving up the series. Any
family of compounds in which adjacent members differ from each other by a definite factor (here a CH2 group) is called a
homologous series. The members of such a series, called homologs, have properties that vary in a regular and predictable manner.
The principle of homology gives organization to organic chemistry in much the same way that the periodic table gives organization
to inorganic chemistry. Instead of a bewildering array of individual carbon compounds, we can study a few members of a
homologous series and from them deduce some of the properties of other compounds in the series.
Figure 1.2.3 : Members of a Homologous Series. Each succeeding formula incorporates one carbon atom and two hydrogen atoms
more than the previous formula.
The principle of homology allows us to write a general formula for alkanes: CnH2n + 2. Using this formula, we can write a
molecular formula for any alkane with a given number of carbon atoms. For example, an alkane with eight carbon atoms has the
molecular formula C8H(2 × 8) + 2 = C8H18.
Key Takeaway
Simple alkanes exist as a homologous series, in which adjacent members differ by a CH2 unit.
1.2: Structures and Names of Alkanes is shared under a CC BY-NC-SA 4.0 license and was authored, remixed, and/or curated by LibreTexts.
Learning Objectives
To learn how alkane molecules can have branched chains and recognize compounds that are isomers.
We can write the structure of butane (C4H10) by stringing four carbon atoms in a row,
–C–C–C–C–
and then adding enough hydrogen atoms to give each carbon atom four bonds:
The compound butane has this structure, but there is another way to put 4 carbon atoms and 10 hydrogen atoms together. Place 3 of
the carbon atoms in a row and then branch the fourth one off the middle carbon atom:
Now we add enough hydrogen atoms to give each carbon four bonds.
Figure 1.3.1 ).
Figure 1.3.1 : Butane and Isobutane. The ball-and-stick models of these two compounds show them to be isomers; both have the
molecular formula C4H10.
Notice that C4H10 is depicted with a bent chain in Figure 1.3.1. The four-carbon chain may be bent in various ways because the
groups can rotate freely about the C–C bonds. However, this rotation does not change the identity of the compound. It is important
to realize that bending a chain does not change the identity of the compound; all of the following represent the same compound,
butane:
The structure of isobutane shows a continuous chain of three carbon atoms only, with the fourth attached as a branch off the middle
carbon atom of the continuous chain, which is different from the structures of butane (compare the two structures in Figure 1.3.1.
Unlike C4H10, the compounds methane (CH4), ethane (C2H6), and propane (C3H8) do not exist in isomeric forms because there is
only one way to arrange the atoms in each formula so that each carbon atom has four bonds.
Next beyond C4H10 in the homologous series is pentane. Each compound has the same molecular formula: C5H12. (Table 12.2 has a
column identifying the number of possible isomers for the first 10 straight-chain alkanes.) The compound at the far left is pentane
because it has all five carbon atoms in a continuous chain. The compound in the middle is isopentane; like isobutane, it has a one
CH3 branch off the second carbon atom of the continuous chain. The compound at the far right, discovered after the other two, was
named neopentane (from the Greek neos, meaning “new”). Although all three have the same molecular formula, they have different
properties, including boiling points: pentane, 36.1°C; isopentane, 27.7°C; and neopentane, 9.5°C.
A continuous (unbranched) chain of carbon atoms is often called a straight chain even though the tetrahedral arrangement about
each carbon gives it a zigzag shape. Straight-chain alkanes are sometimes called normal alkanes, and their names are given the
prefix n-. For example, butane is called n-butane. We will not use that prefix here because it is not a part of the system
established by the International Union of Pure and Applied Chemistry.
1.3: Branched-Chain Alkanes is shared under a CC BY-NC-SA 4.0 license and was authored, remixed, and/or curated by LibreTexts.
Learning Objectives
Write condensed structural formulas for alkanes given complete structural formulas.
Draw line-angle formulas given structural formulas.
We use several kinds of formulas to describe organic compounds. A molecular formula shows only the kinds and numbers of atoms
in a molecule. For example, the molecular formula C4H10 tells us there are 4 carbon atoms and 10 hydrogen atoms in a molecule,
but it doesn’t distinguish between butane and isobutane. A structural formula shows all the carbon and hydrogen atoms and the
bonds attaching them. Thus, structural formulas identify the specific isomers by showing the order of attachment of the various
atoms.
Unfortunately, structural formulas are difficult to type/write and take up a lot of space. Chemists often use condensed structural
formulas to alleviate these problems. The condensed formulas show hydrogen atoms right next to the carbon atoms to which they
are attached, as illustrated for butane:
The ultimate condensed formula is a line-angle formula, in which carbon atoms are implied at the corners and ends of lines, and
each carbon atom is understood to be attached to enough hydrogen atoms to give each carbon atom four bonds. For example, we
can represent pentane (CH3CH2CH2CH2CH3) and isopentane [(CH3)2CHCH2CH3] as follows:
Parentheses in condensed structural formulas indicate that the enclosed grouping of atoms is attached to the adjacent carbon
atom.
Key Takeaways
Condensed chemical formulas show the hydrogen atoms (or other atoms or groups) right next to the carbon atoms to which they
are attached.
Line-angle formulas imply a carbon atom at the corners and ends of lines. Each carbon atom is understood to be attached to
enough hydrogen atoms to give each carbon atom four bonds.
1.4: Condensed Structural and Line-Angle Formulas is shared under a CC BY-NC-SA 4.0 license and was authored, remixed, and/or curated by
LibreTexts.
Learning Objectives
To name alkanes by the IUPAC system and write formulas for alkanes given IUPAC names
As noted in previously, the number of isomers increases rapidly as the number of carbon atoms increases. There are 3 pentanes, 5
hexanes, 9 heptanes, and 18 octanes. It would be difficult to assign unique individual names that we could remember. A systematic
way of naming hydrocarbons and other organic compounds has been devised by the International Union of Pure and Applied
Chemistry (IUPAC). These rules, used worldwide, are known as the IUPAC System of Nomenclature. (Some of the names we used
earlier, such as isobutane, isopentane, and neopentane, do not follow these rules and are called common names.) A stem name
(Table 1.5.1) indicates the number of carbon atoms in the longest continuous chain (LCC). Atoms or groups attached to this carbon
chain, called substituents, are then named, with their positions indicated by numbers. For now, we will consider only those
substituents called alkyl groups.
Table 1.5.1 : Stems That Indicate the Number of Carbon Atoms in Organic Molecules
Stem Number
meth- 1
eth- 2
prop- 3
but- 4
pent- 5
hex- 6
hept- 7
oct- 8
non- 9
dec- 10
An alkyl group is a group of atoms that results when one hydrogen atom is removed from an alkane. The group is named by
replacing the -ane suffix of the parent hydrocarbon with -yl. For example, the -CH3 group derived from methane (CH4) results from
subtracting one hydrogen atom and is called a methyl group. The alkyl groups we will use most frequently are listed in Table 1.5.2.
Alkyl groups are not independent molecules; they are parts of molecules that we consider as a unit to name compounds
systematically.
Table 1.5.2 : Common Alkyl Groups
Condensed Structural
Parent Alkane Alkyl Group
Formula
methane methyl CH3–
*There are four butyl groups, two derived from butane and two from isobutane. We will introduce the other three where appropriate.
Parent Alkane Alkyl Group
Formula
ethane ethyl CH3CH2–
propane propyl CH3CH2CH2–
isopropyl (CH3)2CH–
butane butyl* CH3CH2CH2CH2–
*There are four butyl groups, two derived from butane and two from isobutane. We will introduce the other three where appropriate.
Simplified IUPAC rules for naming alkanes are as follows (demonstrated in Example 1.5.1).
1. Name alkanes according to the LCC (longest continuous chain) of carbon atoms in the molecule (rather than the total
number of carbon atoms). This LCC, considered the parent chain, determines the base name, to which we add the suffix -ane to
indicate that the molecule is an alkane.
2. If the hydrocarbon is branched, number the carbon atoms of the LCC. Numbers are assigned in the direction that gives the
lowest numbers to the carbon atoms with attached substituents. Hyphens are used to separate numbers from the names of
substituents; commas separate numbers from each other. (The LCC need not be written in a straight line; for example, the LCC in
the following has five carbon atoms.)
3. Place the names of the substituent groups in alphabetical order before the name of the parent compound. If the same alkyl
group appears more than once, the numbers of all the carbon atoms to which it is attached are expressed. If the same group appears
more than once on the same carbon atom, the number of that carbon atom is repeated as many times as the group appears.
Moreover, the number of identical groups is indicated by the Greek prefixes di-, tri-, tetra-, and so on. These prefixes are not
considered in determining the alphabetical order of the substituents. For example, ethyl is listed before dimethyl; the di- is simply
ignored. The last alkyl group named is prefixed to the name of the parent alkane to form one word.
When these rules are followed, every unique compound receives its own exclusive name. The rules enable us to not only name a
compound from a given structure but also draw a structure from a given name. The best way to learn how to use the IUPAC system
is to put it to work, not just memorize the rules. It’s easier than it looks.
Example 1.5.1
Name each compound.
1.
2.
3.
SOLUTION
1. The LCC has five carbon atoms, and so the parent compound is pentane (rule 1). There is a methyl group (rule 2) attached to
the second carbon atom of the pentane chain. The name is therefore 2-methylpentane.
2. The LCC has six carbon atoms, so the parent compound is hexane (rule 1). Methyl groups (rule 2) are attached to the second
and fifth carbon atoms. The name is 2,5-dimethylhexane.
3. The LCC has eight carbon atoms, so the parent compound is octane (rule 1). There are methyl and ethyl groups (rule 2), both
attached to the fourth carbon atom (counting from the right gives this carbon atom a lower number; rule 3). The correct
name is thus 4-ethyl-4-methyloctane.
Exercise 1.5.1
Name each compound.
1.
2.
3.
Example 1.5.2
Draw the structure for each compound.
a. 2,3-dimethylbutane
b. 4-ethyl-2-methylheptane
SOLUTION
In drawing structures, always start with the parent chain.
a. The parent chain is butane, indicating four carbon atoms in the LCC.
Then add the groups at their proper positions. You can number the parent chain from either direction as long as you are
consistent; just don’t change directions before the structure is done. The name indicates two methyl (CH3) groups, one on the
second carbon atom and one on the third.
Finally, fill in all the hydrogen atoms, keeping in mind that each carbon atom must have four bonds.
b. The parent chain is heptane in this case, indicating seven carbon atoms in the LCC.
–C–C–C–C–C–C–C–
Adding the groups at their proper positions gives
Filling in all the hydrogen atoms gives the following condensed structural formulas:
Note that the bonds (dashes) can be shown or not; sometimes they are needed for spacing.
Exercise 1.5.2
a. 4-ethyloctane
b. 3-ethyl-2-methylpentane
c. 3,3,5-trimethylheptane
Key Takeaway
Alkanes have both common names and systematic names, specified by IUPAC.
1.5: IUPAC Nomenclature is shared under a CC BY-NC-SA 4.0 license and was authored, remixed, and/or curated by LibreTexts.
Learning Objectives
To identify the physical properties of alkanes and describe trends in these properties.
Because alkanes have relatively predictable physical properties and undergo relatively few chemical reactions other than
combustion, they serve as a basis of comparison for the properties of many other organic compound families. Let’s consider their
physical properties first.
Table 1.6.1 describes some of the properties of some of the first 10 straight-chain alkanes. Because alkane molecules are nonpolar,
they are insoluble in water, which is a polar solvent, but are soluble in nonpolar and slightly polar solvents. Consequently, alkanes
themselves are commonly used as solvents for organic substances of low polarity, such as fats, oils, and waxes. Nearly all alkanes
have densities less than 1.0 g/mL and are therefore less dense than water (the density of H2O is 1.00 g/mL at 20°C). These
properties explain why oil and grease do not mix with water but rather float on its surface.
Table 1.6.1 : Physical Properties of Some Alkanes
Physical State (at
Molecular Name Formula Melting Point (°C) Boiling Point (°C) Density (20°C)*
20°C)
methane CH4 –182 –164 0.668 g/L gas
ethane C2H6 –183 –89 1.265 g/L gas
propane C3H8 –190 –42 1.867 g/L gas
butane C4H10 –138 –1 2.493 g/L gas
pentane C5H12 –130 36 0.626 g/mL liquid
hexane C6H14 –95 69 0.659 g/mL liquid
octane C8H18 –57 125 0.703 g/mL liquid
decane C10H22 –30 174 0.730 g mL liquid
*Note the change in units going from gases (grams per liter) to liquids (grams per milliliter). Gas densities are at 1 atm pressure.
Figure 1.6.1 : Oil Spills. Crude oil coats the water’s surface in the Gulf of Mexico after the Deepwater Horizon oil rig sank
following an explosion. The leak was a mile below the surface, making it difficult to estimate the size of the spill. One liter of oil
can create a slick 2.5 hectares (6.3 acres) in size. This and similar spills provide a reminder that hydrocarbons and water don’t mix.
Source: Photo courtesy of NASA Goddard / MODIS Rapid Response Team, http://www.nasa.gov/topics/earth/features/oilspill/oil-
20100519a.html.
Looking Closer: Gas Densities and Fire Hazards

Table 1.6.1 indicates that the first four members of the alkane series are gases at ordinary temperatures. Natural gas is composed
chiefly of methane, which has a density of about 0.67 g/L. The density of air is about 1.29 g/L. Because natural gas is less dense
than air, it rises. When a natural-gas leak is detected and shut off in a room, the gas can be removed by opening an upper window.
On the other hand, bottled gas can be either propane (density 1.88 g/L) or butanes (a mixture of butane and isobutane; density about
2.5 g/L). Both are much heavier than air (density 1.2 g/L). If bottled gas escapes into a building, it collects near the floor. This
presents a much more serious fire hazard than a natural-gas leak because it is more difficult to rid the room of the heavier gas.
Also shown in Table 1.6.1 are the boiling points of the straight-chain alkanes increase with increasing molar mass. This general
rule holds true for the straight-chain homologs of all organic compound families. Larger molecules have greater surface areas and
consequently interact more strongly; more energy is therefore required to separate them. For a given molar mass, the boiling points
of alkanes are relatively low because these nonpolar molecules have only weak dispersion forces to hold them together in the liquid
state.
Looking Closer: An Alkane Basis for Properties of Other Compounds

An understanding of the physical properties of the alkanes is important in that petroleum and natural gas and the many products
derived from them—gasoline, bottled gas, solvents, plastics, and more—are composed primarily of alkanes. This understanding is
also vital because it is the basis for describing the properties of other organic and biological compound families. For example, large
portions of the structures of lipids consist of nonpolar alkyl groups. Lipids include the dietary fats and fatlike compounds called
phospholipids and sphingolipids that serve as structural components of living tissues. These compounds have both polar and
nonpolar groups, enabling them to bridge the gap between water-soluble and water-insoluble phases. This characteristic is essential
for the selective permeability of cell membranes.
Figure 1.6.2 : Tripalmitin (a), a typical fat molecule, has long hydrocarbon chains typical of most lipids. Compare these chains to
hexadecane (b), an alkane with 16 carbon atoms.
Concept Review Exercises

1. Without referring to a table, predict which has a higher boiling point—hexane or octane. Explain.
2. If 25 mL of hexane were added to 100 mL of water in a beaker, which of the following would you expect to happen? Explain.
a. Hexane would dissolve in water.
b. Hexane would not dissolve in water and would float on top.
c. Hexane would not dissolve in water and would sink to the bottom of the container.
Answers
1. octane because of its greater molar mass
2. b; hexane is insoluble in water and less dense than water.
Key Takeaway
Alkanes are nonpolar compounds that are low boiling and insoluble in water.
Exercises
1. Without referring to a table or other reference, predict which member of each pair has the higher boiling point.
a. pentane or butane
b. heptane or nonane
2. For which member of each pair is hexane a good solvent?
a. pentane or water
b. sodium chloride or soybean oil
Answer
1. a. pentane
b. nonane
1.6: Physical Properties of Alkanes is shared under a CC BY-NC-SA 4.0 license and was authored, remixed, and/or curated by LibreTexts.
Learning Objectives
To identify the main chemical properties of alkanes.
Alkane molecules are nonpolar and therefore generally do not react with ionic compounds such as most laboratory acids, bases,
oxidizing agents, or reducing agents. Consider butane as an example:
Neither positive ions nor negative ions are attracted to a nonpolar molecule. In fact, the alkanes undergo so few reactions that they
are sometimes called paraffins, from the Latin parum affinis, meaning “little affinity.”
Two important reactions that the alkanes do undergo are combustion and halogenation. Nothing happens when alkanes are merely
mixed with oxygen (O ) at room temperature, but when a flame or spark provides the activation energy, a highly exothermic
2
combustion reaction proceeds vigorously. For methane (CH4), the reaction is as follows:
C H4 + 2 O2 → C O2 + 2 H2 O + heat (1.7.1)
If the reactants are adequately mixed and there is sufficient oxygen, the only products are carbon dioxide (C O ), water (H O), and
2 2
heat—heat for cooking foods, heating homes, and drying clothes. Because conditions are rarely ideal, however, other products are
frequently formed. When the oxygen supply is limited, carbon monoxide (C O) is a by-product:
2C H4 + 3 O2 → 2C O + 4 H2 O (1.7.2)
This reaction is responsible for dozens of deaths each year from unventilated or improperly adjusted gas heaters. (Similar reactions
with similar results occur with kerosene heaters.)
Alkanes also react with the halogens chlorine (C l ) and bromine (Br ) in the presence of ultraviolet light or at high temperatures
2 2
to yield chlorinated and brominated alkanes. For example, chlorine reacts with excess methane (C H ) to give methyl chloride (
4
C H C l).
3
C H4 + C l2 → C H3 C l + H C l (1.7.3)
With more chlorine, a mixture of products is obtained: CH3Cl, CH2Cl2, CHCl3, and CCl4. Fluorine (F ), the lightest halogen,
2
combines explosively with most hydrocarbons. Iodine (I ) is relatively unreactive. Fluorinated and iodinated alkanes are produced
2
by indirect methods.

1. Why are alkanes sometimes called paraffins?
2. Which halogen reacts most readily with alkanes? Which reacts least readily?
Answers
1. Alkanes do not react with many common chemicals. They are sometimes called paraffins, from the Latin parum affinis,
meaning “little affinity.”
2. most readily: F ; least readily: I
2 2
Key Takeaway
Alkanes react with oxygen (combustion) and with halogens (halogenation).
Exercises
1. Why do alkanes usually not react with ionic compounds such as most laboratory acids, bases, oxidizing agents, or reducing
agents?
2. Write an equation for the complete combustion of methane (C H ), the main component of natural gas).
4
3. What is the most important reaction of alkanes?

4. Name some substances other than oxygen that react readily with alkanes.
Answers
1. Alkanes are nonpolar; they do not attract ions.
1.7: Chemical Properties of Alkanes is shared under a CC BY-NC-SA 4.0 license and was authored, remixed, and/or curated by LibreTexts.
1.8: Cycloalkanes
Learning Objectives
To name cycloalkanes given their formulas and write formulas for these compounds given their names.
The hydrocarbons we have encountered so far have been composed of molecules with open-ended chains of carbon atoms. When a
chain contains three or more carbon atoms, the atoms can join to form ring or cyclic structures. The simplest of these cyclic
hydrocarbons has the formula C3H6. Each carbon atom has two hydrogen atoms attached (Figure 1.8.1) and is called cyclopropane.
Figure 1.8.1 : Ball-and-Spring Model of Cyclopropane. The springs are bent to join the carbon atoms.
To Your Health: Cyclopropane as an Anesthetic

With its boiling point of −33°C, cyclopropane is a gas at room temperature. It is also a potent, quick-acting anesthetic with few
undesirable side effects in the body. It is no longer used in surgery, however, because it forms explosive mixtures with air at nearly
all concentrations.
The cycloalkanes—cyclic hydrocarbons with only single bonds—are named by adding the prefix cyclo- to the name of the open-
chain compound having the same number of carbon atoms as there are in the ring. Thus the name for the cyclic compound C4H8 is
cyclobutane. The carbon atoms in cyclic compounds can be represented by line-angle formulas that result in regular geometric
figures. Keep in mind, however, that each corner of the geometric figure represents a carbon atom plus as many hydrogen atoms as
needed to give each carbon atom four bonds.
Some cyclic compounds have substituent groups attached. Example 1.8.1 interprets the name of a cycloalkane with a single
substituent group.
Example 1.8.1
a. cyclopentane
b. methylcyclobutane
SOLUTION
a. The name cyclopentane indicates a cyclic (cyclo) alkane with five (pent-) carbon atoms. It can be represented as a pentagon.
b. The name methylcyclobutane indicates a cyclic alkane with four (but-) carbon atoms in the cyclic part. It can be represented
as a square with a CH3 group attached.
Exercise 1.8.1
a. cycloheptane
b. ethylcyclohexane
The properties of cyclic hydrocarbons are generally quite similar to those of the corresponding open-chain compounds. So
cycloalkanes (with the exception of cyclopropane, which has a highly strained ring) act very much like noncyclic alkanes. Cyclic
structures containing five or six carbon atoms, such as cyclopentane and cyclohexane, are particularly stable. We will see later that
some carbohydrates (sugars) form five- or six-membered rings in solution.
The cyclopropane ring is strained because the C–C–C angles are 60°, and the preferred (tetrahedral) bond angle is 109.5°. (This
strain is readily evident when you try to build a ball-and-stick model of cyclopropane; see Figure 1.8.1.) Cyclopentane and
cyclohexane rings have little strain because the C–C–C angles are near the preferred angles.

1. What is the molecular formula of cyclooctane?
2. What is the IUPAC name for this compound?
Answers
1. C8H16
2. ethylcyclopropane
Key Takeaway
Many organic compounds have cyclic structures.
Exercises
1. Draw the structure for each compound.
a. ethylcyclobutane
b. propylcyclopropane
a. methylcyclohexane
b. butylcyclobutane
3. Cycloalkyl groups can be derived from cycloalkanes in the same way that alkyl groups are derived from alkanes. These groups
are named as cyclopropyl, cyclobutyl, and so on. Name each cycloalkyl halide.
a.
b.
4. Halogenated cycloalkanes can be named by the IUPAC system. As with alkyl derivatives, monosubstituted derivatives need no
number to indicate the position of the halogen. To name disubstituted derivatives, the carbon atoms are numbered starting at the
position of one substituent (C1) and proceeding to the second substituted atom by the shortest route. Name each compound.
a.
b.
Answers
1. a.
b.
3. a. cyclopentyl bromide
b. cyclohexyl chloride
1.8: Cycloalkanes is shared under a CC BY-NC-SA 4.0 license and was authored, remixed, and/or curated by LibreTexts.
To ensure that you understand the material in this chapter, you should review the meanings of the following bold terms in the
summary and ask yourself how they relate to the topics in the chapter.
Organic chemistry is the chemistry of carbon compounds, and inorganic chemistry is the chemistry of all the other elements.
Carbon atoms can form stable covalent bonds with other carbon atoms and with atoms of other elements, and this property allows
the formation the tens of millions of organic compounds. Hydrocarbons contain only hydrogen and carbon atoms.
Hydrocarbons in which each carbon atom is bonded to four other atoms are called alkanes or saturated hydrocarbons. They have
the general formula CnH2n + 2. Any given alkane differs from the next one in a series by a CH2 unit. Any family of compounds in
which adjacent members differ from each other by a definite factor is called a homologous series.
Carbon atoms in alkanes can form straight chains or branched chains. Two or more compounds having the same molecular formula
but different structural formulas are isomers of each other. There are no isomeric forms for the three smallest alkanes; beginning
with C4H10, all other alkanes have isomeric forms.
A structural formula shows all the carbon and hydrogen atoms and how they are attached to one another. A condensed
structural formula shows the hydrogen atoms right next to the carbon atoms to which they are attached. A line-angle formula is
a formula in which carbon atoms are implied at the corners and ends of lines. Each carbon atom is understood to be attached to
enough hydrogen atoms to give each carbon atom four bonds.
The IUPAC System of Nomenclature provides rules for naming organic compounds. An alkyl group is a unit formed by
removing one hydrogen atom from an alkane.
The physical properties of alkanes reflect the fact that alkane molecules are nonpolar. Alkanes are insoluble in water and less dense
than water.
Alkanes are generally unreactive toward laboratory acids, bases, oxidizing agents, and reducing agents. They do burn (undergo
combustion reactions).
Alkanes react with halogens by substituting one or more halogen atoms for hydrogen atoms to form halogenated hydrocarbons.
An alkyl halide (haloalkane) is a compound resulting from the replacement of a hydrogen atom of an alkane with a halogen atom.
Cycloalkanes are hydrocarbons whose molecules are closed rings rather than straight or branched chains. A cyclic hydrocarbon is
a hydrocarbon with a ring of carbon atoms
1.9: Organic Chemistry: Alkanes is shared under a CC BY-NC-SA 4.0 license and was authored, remixed, and/or curated by LibreTexts.
Learning Objectives
To name alkenes given formulas and write formulas for alkenes given names.
As noted before, alkenes are hydrocarbons with carbon-to-carbon double bonds (R2C=CR2) and alkynes are hydrocarbons with
carbon-to-carbon triple bonds (R–C≡C–R). Collectively, they are called unsaturated hydrocarbons because they have fewer
hydrogen atoms than does an alkane with the same number of carbon atoms, as is indicated in the following general formulas:
Some representative alkenes—their names, structures, and physical properties—are given in Table 1.10.1.
Table 1.10.1: Physical Properties of Some Selected Alkenes
IUPAC Name Molecular Formula Melting Point (°C) Boiling Point (°C)
Formula
ethene C2H4 CH2=CH2 –169 –104
propene C3H6 CH2=CHCH3 –185 –47
1-butene C4H8 CH2=CHCH2CH3 –185 –6
1-pentene C5H10 CH2=CH(CH2)2CH3 –138 30
1-hexene C6H12 CH2=CH(CH2)3CH3 –140 63
1-heptene C7H14 CH2=CH(CH2)4CH3 –119 94
1-octene C8H16 CH2=CH(CH2)5CH3 –102 121
We used only condensed structural formulas in Table 1.10.1. Thus, CH2=CH2 stands for
The double bond is shared by the two carbonnd does not involve the hydrogen atoms, although the condensed formula does not
make this point obvious. Note that the molecular formula for ethene is C2H4, whereas that for ethane is C2H6.
The first two alkenes in Table 1.10.1, ethene and propene, are most often called by their common names—ethylene and propylene,
respectively (Figure 1.10.1). Ethylene is a major commercial chemical. The US chemical industry produces about 25 billion
kilograms of ethylene annually, more than any other synthetic organic chemical. More than half of this ethylene goes into the
manufacture of polyethylene, one of the most familiar plastics. Propylene is also an important industrial chemical. It is converted to
plastics, isopropyl alcohol, and a variety of other products.
Figure 1.10.1: Ethene and Propene. The ball-and-spring models of ethene/ethylene (a) and propene/propylene (b) show their
respective shapes, especially bond angles.
Although there is only one alkene with the formula C2H4 (ethene) and only one with the formula C3H6 (propene), there are
several alkenes with the formula C4H8.
Here are some basic rules for naming alkenes from the International Union of Pure and Applied Chemistry (IUPAC):
1. The longest chain of carbon atoms containing the double bond is considered the parent chain. It is named using the same stem
as the alkane having the same number of carbon atoms but ends in -ene to identify it as an alkene. Thus the compound
CH2=CHCH3 is propene.
2. If there are four or more carbon atoms in a chain, we must indicate the position of the double bond. The carbons atoms are
numbered so that the first of the two that are doubly bonded is given the lower of the two possible numbers.The compound
CH3CH=CHCH2CH3, for example, has the double bond between the second and third carbon atoms. Its name is 2-pentene (not
3-pentene).
3. Substituent groups are named as with alkanes, and their position is indicated by a number. Thus,
is 5-methyl-2-hexene. Note that the numbering of the parent chain is always done in such a way as to give the double bond
the lowest number, even if that causes a substituent to have a higher number. The double bond always has priority in
numbering.
Example 1.10.1
Name each compound.
a.
b.
SOLUTION
a. The longest chain containing the double bond has five carbon atoms, so the compound is a pentene (rule 1). To give the first
carbon atom of the double bond the lowest number (rule 2), we number from the left, so the compound is a 2-pentene. There
is a methyl group on the fourth carbon atom (rule 3), so the compound’s name is 4-methyl-2-pentene.
b. The longest chain containing the double bond has five carbon atoms, so the parent compound is a pentene (rule 1). To give
the first carbon atom of the double bond the lowest number (rule 2), we number from the left, so the compound is a 2-
pentene. There is a methyl group on the third carbon atom (rule 3), so the compound’s name is 3-methyl-2-pentene.
Exercise 1.10.1
Name each compound.
1. CH3CH2CH2CH2CH2CH=CHCH3
2.
Just as there are cycloalkanes, there are cycloalkenes. These compounds are named like alkenes, but with the prefix cyclo- attached
to the beginning of the parent alkene name.
Example 1.10.2
1. 3-methyl-2-pentene
2. cyclohexene
SOLUTION
1. First write the parent chain of five carbon atoms: C–C–C–C–C. Then add the double bond between the second and third
carbon atoms:
Now place the methyl group on the third carbon atom and add enough hydrogen atoms to give each carbon atom a total of
four bonds.
2. First, consider what each of the three parts of the name means. Cyclo means a ring compound, hex means 6 carbon atoms,
and -ene means a double bond.
Exercise 1.10.2
a. 2-ethyl-1-hexene
b. cyclopentene

1. Briefly identify the important distinctions between a saturated hydrocarbon and an unsaturated hydrocarbon.
2. Briefly identify the important distinctions between an alkene and an alkane.
3. Classify each compound as saturated or unsaturated. Identify each as an alkane, an alkene, or an alkyne.
a.
b. CH3CH2C≡CCH3
c.
Answers
1. Unsaturated hydrocarbons have double or triple bonds and are quite reactive; saturated hydrocarbons have only single bonds
and are rather unreactive.
2. An alkene has a double bond; an alkane has single bonds only.
3. a. saturated; alkane
b. unsaturated; alkyne
c. unsaturated; alkene
Key Takeaway
Alkenes are hydrocarbons with a carbon-to-carbon double bond.
Exercises
a. 2-methyl-2-pentene
b. 2,3-dimethyl-1-butene
c. cyclohexene
a. 5-methyl-1-hexene
b. 3-ethyl-2-pentene
c. 4-methyl-2-hexene
3. Name each compound according to the IUPAC system.
a.
b.
c.
a.
b.
c.
Answers
1. a.
b.
c.
3. a. 2-methyl-2-pentene
b. 3-methyl-2-heptene
c. 2,5-dimethyl-2-hexene
1.10: Alkenes: Structures and Names is shared under a CC BY-NC-SA 4.0 license and was authored, remixed, and/or curated by LibreTexts.
Learning Objectives
Recognize that alkenes that can exist as cis-trans isomers.
Classify isomers as cis or trans.
Draw structures for cis-trans isomers given their names.
There is free rotation about the carbon-to-carbon single bonds (C–C) in alkanes. In contrast, the structure of alkenes requires that
the carbon atoms of a double bond and the two atoms bonded to each carbon atom all lie in a single plane, and that each doubly
bonded carbon atom lies in the center of a triangle. This part of the molecule’s structure is rigid; rotation about doubly bonded
carbon atoms is not possible without rupturing the bond. Look at the two chlorinated hydrocarbons in Figure 1.11.1.
Table 1.11.1 : Rotation about Bonds. In 1,2-dichloroethane (a), free rotation about the C–C bond allows the two structures to be
interconverted by a twist of one end relative to the other. In 1,2-dichloroethene (b), restricted rotation about the double bond means
that the relative positions of substituent groups above or below the double bond are significant.
In 1,2-dichloroethane (part (a) of Figure 1.11.1), there is free rotation about the C–C bond. The two models shown represent
exactly the same molecule; they are not isomers. You can draw structural formulas that look different, but if you bear in mind the
possibility of this free rotation about single bonds, you should recognize that these two structures represent the same molecule:
In 1,2-dichloroethene (Figure 1.11.1b), however, restricted rotation about the double bond means that the relative positions of
substituent groups above or below the double bond become significant. This leads to a special kind of isomerism. The isomer in
which the two chlorine (Cl) atoms lie on the same side of the molecule is called the cis isomer (Latin cis, meaning “on this side”)
and is named cis-1,2-dichloroethene. The isomer with the two Cl atoms on opposite sides of the molecule is the trans isomer (Latin
trans, meaning “across”) and is named trans-1,2-dichloroethene. These two compounds are cis-trans isomers (or geometric
isomers), compounds that have different configurations (groups permanently in different places in space) because of the presence
of a rigid structure in their molecule.
Consider the alkene with the condensed structural formula CH3CH=CHCH3. We could name it 2-butene, but there are actually two
such compounds; the double bond results in cis-trans isomerism (Figure 1.11.2).
Figure 1.11.2: Ball-and-Spring Models of (a) Cis-2-Butene and (b) Trans-2-Butene. Cis-trans isomers have different physical,
chemical, and physiological properties.
Cis-2-butene has both methyl groups on the same side of the molecule. Trans-2-butene has the methyl groups on opposite sides of
the molecule. Their structural formulas are as follows:
Figure 1.11.3 : Models of (left) Cis-2-Butene and (right) Trans-2-Butene.
Note, however, that the presence of a double bond does not necessarily lead to cis-trans isomerism (Figure 1.11.4 ). We can draw
two seemingly different propenes:
Figure 1.11.4 : Different views of the propene molecule (flip vertically). These are not isomers.
However, these two structures are not really different from each other. If you could pick up either molecule from the page and flip
it over top to bottom, you would see that the two formulas are identical. Thus there are two requirements for cis-trans isomerism:
1. Rotation must be restricted in the molecule.
2. There must be two nonidentical groups on each doubly bonded carbon atom.
In these propene structures, the second requirement for cis-trans isomerism is not fulfilled. One of the doubly bonded carbon atoms
does have two different groups attached, but the rules require that both carbon atoms have two different groups. In general, the
following statements hold true in cis-trans isomerism:
Alkenes with a C=CH2 unit do not exist as cis-trans isomers.
Alkenes with a C=CR2 unit, where the two R groups are the same, do not exist as cis-trans isomers.
Alkenes of the type R–CH=CH–R can exist as cis and trans isomers; cis if the two R groups are on the same side of the carbon-
to-carbon double bond, and trans if the two R groups are on opposite sides of the carbon-to-carbon double bond.
Advanced Note: E/Z Isomerization
If a molecule has a C=C bond with one non-hydrogen group attached to each of the carbons, cis/trans nomenclature descried
above is enough to describe it. However, if you have three different groups (or four), then the cis/trans approach is insufficient
to describe the different isomers, since we do not know which two of the three groups are being described. For example, if you
have a C=C bond, with a methyl group and a bromine on one carbon , and an ethyl group on the other, it is neither trans nor cis,
since it is not clear whether the ethyl group is trans to the bromine or the methyl. This is addressed with a more advanced E/Z
nomenclature discussed elsewhere.
Cis-trans isomerism also occurs in cyclic compounds. In ring structures, groups are unable to rotate about any of the ring carbon–
carbon bonds. Therefore, groups can be either on the same side of the ring (cis) or on opposite sides of the ring (trans). For our
purposes here, we represent all cycloalkanes as planar structures, and we indicate the positions of the groups, either above or below
the plane of the ring.
Example 1.11.1
Which compounds can exist as cis-trans (geometric) isomers? Draw them.
1. CHCl=CHBr
2. CH2=CBrCH3
3. (CH3)2C=CHCH2CH3
4. CH3CH=CHCH2CH3
SOLUTION
All four structures have a double bond and thus meet rule 1 for cis-trans isomerism.
1. This compound meets rule 2; it has two nonidentical groups on each carbon atom (H and Cl on one and H and Br on the
other). It exists as both cis and trans isomers:
2. This compound has two hydrogen atoms on one of its doubly bonded carbon atoms; it fails rule 2 and does not exist as cis
and trans isomers.
3. This compound has two methyl (CH3) groups on one of its doubly bonded carbon atoms. It fails rule 2 and does not exist as
cis and trans isomers.
4. This compound meets rule 2; it has two nonidentical groups on each carbon atom and exists as both cis and trans isomers:
Exercise 1.11.1
Which compounds can exist as cis-trans isomers? Draw them.
a. CH2=CHCH2CH2CH3
b. CH3CH=CHCH2CH3
c. CH3CH2CH=CHCH2CH3
d.
e.

1. What are cis-trans (geometric) isomers? What two types of compounds can exhibit cis-trans isomerism?
2. Classify each compound as a cis isomer, a trans isomer, or neither.
a.
b.
c.
d.
Answers
1. Cis-trans isomers are compounds that have different configurations (groups permanently in different places in space) because of
the presence of a rigid structure in their molecule. Alkenes and cyclic compounds can exhibit cis-trans isomerism.
2. a. trans (the two hydrogen atoms are on opposite sides)
b. cis (the two hydrogen atoms are on the same side, as are the two ethyl groups)
c. cis (the two ethyl groups are on the same side)
d. neither (fliping the bond does not change the molecule. There are no isomers for this molecule)
Key Takeaway
Cis-trans (geometric) isomerism exists when there is restricted rotation in a molecule and there are two nonidentical groups on
each doubly bonded carbon atom.
Exercises
1. Draw the structures of the cis-trans isomers for each compound. Label them cis and trans. If no cis-trans isomers exist, write
none.
a. 2-bromo-2-pentene
b. 3-hexene
c. 4-methyl-2-pentene
d. 1,1-dibromo-1-butene
e. 2-butenoic acid (CH3CH=CHCOOH)
none.
a. 2,3-dimethyl-2-pentene
b. 1,1-dimethyl-2-ethylcyclopropane
c. 1,2-dimethylcyclohexane
d. 5-methyl-2-hexene
e. 1,2,3-trimethylcyclopropane
Answer
1. a: none. There are two distinct geometric isomers, but since there are there are four different groups off the double bond, these
are both cis/trans isomers (they are technically E/Z isomers discussed elsewhere).
b:
c:
d:
e:
1.11: Cis-Trans Isomers (Geometric Isomers) is shared under a CC BY-NC-SA 4.0 license and was authored, remixed, and/or curated by
LibreTexts.
Learning Objectives
To identify the physical properties of alkenes and describe trends in these properties.
The physical properties of alkenes are similar to those of the alkanes. The table at the start of the chapter shows that the boiling
points of straight-chain alkenes increase with increasing molar mass, just as with alkanes. For molecules with the same number of
carbon atoms and the same general shape, the boiling points usually differ only slightly, just as we would expect for substances
whose molar mass differs by only 2 u (equivalent to two hydrogen atoms). Like other hydrocarbons, the alkenes are insoluble in
water but soluble in organic solvents.
Looking Closer: Environmental Note

Alkenes occur widely in nature. Ripening fruits and vegetables give off ethylene, which triggers further ripening. Fruit processors
artificially introduce ethylene to hasten the ripening process; exposure to as little as 0.1 mg of ethylene for 24 h can ripen 1 kg of
tomatoes. Unfortunately, this process does not exactly duplicate the ripening process, and tomatoes picked green and treated this
way don’t taste much like vine-ripened tomatoes fresh from the garden.
The bright red color of tomatoes is due to lycopene—a polyene.

Other alkenes that occur in nature include 1-octene, a constituent of lemon oil, and octadecene (C18H36) found in fish liver. Dienes
(two double bonds) and polyenes (three or more double bonds) are also common. Butadiene (CH2=CHCH=CH2) is found in coffee.
Lycopene and the carotenes are isomeric polyenes (C40H56) that give the attractive red, orange, and yellow colors to watermelons,
tomatoes, carrots, and other fruits and vegetables. Vitamin A, essential to good vision, is derived from a carotene. The world would
be a much less colorful place without alkenes.

1. Briefly describe the physical properties of alkenes. How do these properties compare to those of the alkanes?
2. Without consulting tables, arrange the following alkenes in order of increasing boiling point: 1-butene, ethene, 1-hexene, and
propene.
Answers
1. Alkenes have physical properties (low boiling points, insoluble in water) quite similar to those of their corresponding alkanes.
2. ethene < propene < 1-butene < 1-hexene
Key Takeaway
The physical properties of alkenes are much like those of the alkanes: their boiling points increase with increasing molar mass,
and they are insoluble in water.
Exercises
a. 1-pentene or 1-butene
b. 3-heptene or 3-nonene
2. Which is a good solvent for cyclohexene, pentane or water?
Answer
1. a. 1-pentene
b. 3-nonene
1.12: Physical Properties of Alkenes is shared under a CC BY-NC-SA 4.0 license and was authored, remixed, and/or curated by LibreTexts.
Learning Objectives
To write equations for the addition reactions of alkenes with hydrogen, halogens, and water
Alkenes are valued mainly for addition reactions, in which one of the bonds in the double bond is broken. Each of the carbon atoms
in the bond can then attach another atom or group while remaining joined to each other by a single bond. Perhaps the simplest
addition reaction ishydrogenation—a reaction with hydrogen (H2) in the presence of a catalyst such as nickel (Ni) or platinum (Pt).
The product is an alkane having the same carbon skeleton as the alkene.
Alkenes also readily undergo halogenation—the addition of halogens. Indeed, the reaction with bromine (Br2) can be used to test
for alkenes. Bromine solutions are brownish red. When we add a Br2 solution to an alkene, the color of the solution disappears
because the alkene reacts with the bromine:
Another important addition reaction is that between an alkene and water to form an alcohol. This reaction, called hydration,
requires a catalyst—usually a strong acid, such as sulfuric acid (H2SO4):
The hydration reaction is discussed later, where we deal with this reaction in the synthesis of alcohols.
Example 1.13.1
Write the equation for the reaction between CH3CH=CHCH3 and each substance.
a. H2 (Ni catalyst)
b. Br2
c. H2O (H2SO4 catalyst)
SOLUTION
In each reaction, the reagent adds across the double bond.
a.
b.
c.
Exercise 1.13.1
Write the equation for each reaction.
a. CH3CH2CH=CH2 with H2 (Ni catalyst)
b. CH3CH=CH2 with Cl2
c. CH3CH2CH=CHCH2CH3 with H2O (H2SO4 catalyst)

1. What is the principal difference in properties between alkenes and alkanes? How are they alike?
2. If C12H24 reacts with HBr in an addition reaction, what is the molecular formula of the product?
Answers
1. Alkenes undergo addition reactions; alkanes do not. Both burn.
2. C12H24Br2
Key Takeaway
Alkenes undergo addition reactions, adding such substances as hydrogen, bromine, and water across the carbon-to-carbon
double bond.
Exercises
1. Complete each equation.
a. (CH3) 2C=CH2 + Br2 →
Ni
b. C H2 =C(C H3 )C H2 C H3 + H2 −→
c.
Ni
a. C H2 =CHCH=C H2 + 2 H2 −→
H2 SO4
b. (C H3 )2 C=C(C H3 )2 + H2 O −−−−→
c.
Answer
1. a. (CH3)2CBrCH2Br
b. CH3CH(CH3)CH2CH3
c.
1.13: Chemical Properties of Alkenes is shared under a CC BY-NC-SA 4.0 license and was authored, remixed, and/or curated by LibreTexts.
1.14: Alkynes
Learning Objectives
Describe the general physical and chemical properties of alkynes.
Name alkynes given formulas and write formulas for alkynes given names.
The simplest alkyne—a hydrocarbon with carbon-to-carbon triple bond—has the molecular formula C2H2 and is known by its
common name—acetylene (Figure 1.14.1). Its structure is H–C≡C–H.
Figure 1.14.1 : Ball-and-Spring Model of Acetylene. Acetylene (ethyne) is the simplest member of the alkyne family.
Acetylene is used in oxyacetylene torches for cutting and welding metals. The flame from such a torch can be very hot. Most
acetylene, however, is converted to chemical intermediates that are used to make vinyl and acrylic plastics, fibers, resins, and a
variety of other products.
Alkynes are similar to alkenes in both physical and chemical properties. For example, alkynes undergo many of the typical addition
reactions of alkenes. The International Union of Pure and Applied Chemistry (IUPAC) names for alkynes parallel those of alkenes,
except that the family ending is -yne rather than -ene. The IUPAC name for acetylene is ethyne. The names of other alkynes are
illustrated in the following exercises.

1. Briefly identify the important differences between an alkene and an alkyne. How are they similar?
2. The alkene (CH3)2CHCH2CH=CH2 is named 4-methyl-1-pentene. What is the name of (CH3)2CHCH2C≡CH?
3. Do alkynes show cis-trans isomerism? Explain.
Answers
1. Alkenes have double bonds; alkynes have triple bonds. Both undergo addition reactions.
2. 4-methyl-1-pentyne
3. No; a triply bonded carbon atom can form only one other bond. It would have to have two groups attached to show cis-trans
isomerism.
Key Takeaway
Alkynes are hydrocarbons with carbon-to-carbon triple bonds and properties much like those of alkenes.
Exercises
a. acetylene
b. 3-methyl-1-hexyne
a. 4-methyl-2-hexyne
b. 3-octyne
3. Name each alkyne.
a. CH3CH2CH2C≡CH
b. CH3CH2CH2C≡CCH3
Answers
1. a. H–C≡C–H
b.
3. a. 1-pentyne
b. 2-hexyne
1.14: Alkynes is shared under a CC BY-NC-SA 4.0 license and was authored, remixed, and/or curated by LibreTexts.
Learning Objectives
To describe the bonding in benzene and the way typical reactions of benzene differ from those of the alkenes.
Next we consider a class of hydrocarbons with molecular formulas like those of unsaturated hydrocarbons, but which, unlike the
alkenes, do not readily undergo addition reactions. These compounds comprise a distinct class, called aromatic hydrocarbons, with
unique structures and properties. We start with the simplest of these compounds. Benzene (C6H6) is of great commercial
importance, but it also has noteworthy health effects.
The formula C6H6 seems to indicate that benzene has a high degree of unsaturation. (Hexane, the saturated hydrocarbon with six
carbon atoms has the formula C6H14—eight more hydrogen atoms than benzene.) However, despite the seeming low level of
saturation, benzene is rather unreactive. It does not, for example, react readily with bromine, which, is a test for unsaturation.
Benzene is a liquid that smells like gasoline, boils at 80°C, and freezes at 5.5°C. It is the aromatic hydrocarbon produced in the
largest volume. It was formerly used to decaffeinate coffee and was a significant component of many consumer products, such
as paint strippers, rubber cements, and home dry-cleaning spot removers. It was removed from many product formulations in the
1950s, but others continued to use benzene in products until the 1970s when it was associated with leukemia deaths. Benzene is
still important in industry as a precursor in the production of plastics (such as Styrofoam and nylon), drugs, detergents, synthetic
rubber, pesticides, and dyes. It is used as a solvent for such things as cleaning and maintaining printing equipment and for
adhesives such as those used to attach soles to shoes. Benzene is a natural constituent of petroleum products, but because it is a
known carcinogen, its use as an additive in gasoline is now limited.
To explain the surprising properties of benzene, chemists suppose the molecule has a cyclic, hexagonal, planar structure of six
carbon atoms with one hydrogen atom bonded to each. We can write a structure with alternate single and double bonds, either as a
full structural formula or as a line-angle formula:
However, these structures do not explain the unique properties of benzene. Furthermore, experimental evidence indicates that all
the carbon-to-carbon bonds in benzene are equivalent, and the molecule is unusually stable. Chemists often represent benzene as a
hexagon with an inscribed circle:
The inner circle indicates that the valence electrons are shared equally by all six carbon atoms (that is, the electrons are delocalized,
or spread out, over all the carbon atoms). It is understood that each corner of the hexagon is occupied by one carbon atom, and each
carbon atom has one hydrogen atom attached to it. Any other atom or groups of atoms substituted for a hydrogen atom must be
shown bonded to a particular corner of the hexagon. We use this modern symbolism, but many scientists still use the earlier
structure with alternate double and single bonds.
To Your Health: Benzene and Us
Most of the benzene used commercially comes from petroleum. It is employed as a starting material for the production of
detergents, drugs, dyes, insecticides, and plastics. Once widely used as an organic solvent, benzene is now known to have both
short- and long-term toxic effects. The inhalation of large concentrations can cause nausea and even death due to respiratory or
heart failure, while repeated exposure leads to a progressive disease in which the ability of the bone marrow to make new blood
cells is eventually destroyed. This results in a condition called aplastic anemia, in which there is a decrease in the numbers of
both the red and white blood cells.
1. How do the typical reactions of benzene differ from those of the alkenes?
2. Briefly describe the bonding in benzene.
3. What does the circle mean in the chemist’s representation of benzene?
Answers
1. Benzene is rather unreactive toward addition reactions compared to an alkene.
2. Valence electrons are shared equally by all six carbon atoms (that is, the electrons are delocalized).
3. The six electrons are shared equally by all six carbon atoms.
Exercises
1. Draw the structure of benzene as if it had alternate single and double bonds.
2. Draw the structure of benzene as chemists usually represent it today.
Answer
1.
1.15: Aromatic Compounds: Benzene is shared under a CC BY-NC-SA 4.0 license and was authored, remixed, and/or curated by LibreTexts.
Learning Objectives
Recognize aromatic compounds from structural formulas.
Name aromatic compounds given formulas.
Write formulas for aromatic compounds given their names.
Historically, benzene-like substances were called aromatic hydrocarbons because they had distinctive aromas. Today, an aromatic
compound is any compound that contains a benzene ring or has certain benzene-like properties (but not necessarily a strong
aroma). You can recognize the aromatic compounds in this text by the presence of one or more benzene rings in their structure.
Some representative aromatic compounds and their uses are listed in Table 1.16.1, where the benzene ring is represented as C6H5.
Table 1.16.1: Some Representative Aromatic Compounds
Name Structure Typical Uses
starting material for the synthesis of dyes,

aniline C6H5–NH2 drugs, resins, varnishes, perfumes; solvent;
vulcanizing rubber
food preservative; starting material for the
benzoic acid C6H5–COOH synthesis of dyes and other organic
compounds; curing of tobacco
starting material for the synthesis of many
bromobenzene C6H5–Br other aromatic compounds; solvent; motor oil
additive
starting material for the synthesis of aniline;
nitrobenzene C6H5–NO2 solvent for cellulose nitrate; in soaps and shoe
polish
disinfectant; starting material for the synthesis
phenol C6H5–OH
of resins, drugs, and other organic compounds
solvent; gasoline octane booster; starting
material for the synthesis of benzoic acid,
toluene C6H5–CH3
benzaldehyde, and many other organic
compounds
Example 1.16.1
Which compounds are aromatic?
1.
2.
3.
4.
SOLUTION
1. The compound has a benzene ring (with a chlorine atom substituted for one of the hydrogen atoms); it is aromatic.
2. The compound is cyclic, but it does not have a benzene ring; it is not aromatic.
3. The compound has a benzene ring (with a propyl group substituted for one of the hydrogen atoms); it is aromatic.
4. The compound is cyclic, but it does not have a benzene ring; it is not aromatic.
Exercise 1.16.1
Which compounds are aromatic?
1.
2.
3.
In the International Union of Pure and Applied Chemistry (IUPAC) system, aromatic hydrocarbons are named as derivatives of
benzene. Figure 1.16.1 shows four examples. In these structures, it is immaterial whether the single substituent is written at the top,
side, or bottom of the ring: a hexagon is symmetrical, and therefore all positions are equivalent.
Figure 1.16.1 : Some Benzene Derivatives. These compounds are named in the usual way with the group that replaces a hydrogen
atom named as a substituent group: Cl as chloro, Br as bromo, I as iodo, NO2 as nitro, and CH3CH2 as ethyl.
Although some compounds are referred to exclusively by IUPAC names, some are more frequently denoted by common names, as
is indicated in Table 1.16.1.
When there is more than one substituent, the corners of the hexagon are no longer equivalent, so we must designate the relative
positions. There are three possible disubstituted benzenes, and we can use numbers to distinguish them (Figure 1.16.2). We start
numbering at the carbon atom to which one of the groups is attached and count toward the carbon atom that bears the other
substituent group by the shortest path.
Figure 1.16.2: The Three Isomeric Dichlorobenzenes
In Figure 1.16.2, common names are also used: the prefix ortho (o-) for 1,2-disubstitution, meta (m-) for 1,3-disubstitution, and
para (p-) for 1,4-disubstitution. The substituent names are listed in alphabetical order. The first substituent is given the lowest
number. When a common name is used, the carbon atom that bears the group responsible for the name is given the number 1:
Example 1.16.2
Name each compound using both the common name and the IUPAC name.
1.
2.
3.
SOLUTION
1. The benzene ring has two chlorine atoms (dichloro) in the first and second positions. The compound is o-dichlorobenzene or
1,2-dichlorobenzene.
2. The benzene ring has a methyl (CH3) group. The compound is therefore named as a derivative of toluene. The bromine atom
is on the fourth carbon atom, counting from the methyl group. The compound is p-bromotoluene or 4-bromotoluene.
3. The benzene ring has two nitro (NO2) groups in the first and third positions. It is m-dinitrobenzene or 1,3-dinitrobenzene.
Note: The nitro (NO2) group is a common substituent in aromatic compounds. Many nitro compounds are explosive, most
notably 2,4,6-trinitrotoluene (TNT).
Exercise 1.16.2
Name each compound using both the common name and the IUPAC name.
1.
2.
3.
Sometimes an aromatic group is found as a substituent bonded to a nonaromatic entity or to another aromatic ring. The group of
atoms remaining when a hydrogen atom is removed from an aromatic compound is called an aryl group. The most common aryl
group is derived from benzene (C6H6) by removing one hydrogen atom (C6H5) and is called a phenyl group, from pheno, an old
name for benzene.
Polycyclic Aromatic Hydrocarbons

Some common aromatic hydrocarbons consist of fused benzene rings—rings that share a common side. These compounds are
called polycyclic aromatic hydrocarbons (PAHs).
The three examples shown here are colorless, crystalline solids generally obtained from coal tar. Naphthalene has a pungent odor
and is used in mothballs. Anthracene is used in the manufacture of certain dyes. Steroids, a large group of naturally occurring
substances, contain the phenanthrene structure.
To Your Health: Polycyclic Aromatic Hydrocarbons and Cancer

The intense heating required for distilling coal tar results in the formation of PAHs. For many years, it has been known that workers
in coal-tar refineries are susceptible to a type of skin cancer known as tar cancer. Investigations have shown that a number of PAHs
are carcinogens. One of the most active carcinogenic compounds, benzopyrene, occurs in coal tar and has also been isolated from
cigarette smoke, automobile exhaust gases, and charcoal-broiled steaks. It is estimated that more than 1,000 t of benzopyrene are
emitted into the air over the United States each year. Only a few milligrams of benzopyrene per kilogram of body weight are
required to induce cancer in experimental animals.
Biologically Important Compounds with Benzene Rings

Substances containing the benzene ring are common in both animals and plants, although they are more abundant in the latter.
Plants can synthesize the benzene ring from carbon dioxide, water, and inorganic materials. Animals cannot synthesize it, but they
are dependent on certain aromatic compounds for survival and therefore must obtain them from food. Phenylalanine, tyrosine, and
tryptophan (essential amino acids) and vitamins K, B2 (riboflavin), and B9 (folic acid) all contain the benzene ring. Many important
drugs, a few of which are shown in Table 1.16.2, also feature a benzene ring.
So far we have studied only aromatic compounds with carbon-containing rings. However, many cyclic compounds have an
element other than carbon atoms in the ring. These compounds, called heterocyclic compounds, are discussed later. Some of
these are heterocyclic aromatic compounds.
Table 1.16.2 : Some Drugs That Contain a Benzene Ring

Name Structure
aspirin
acetaminophen
ibuprofen
amphetamine
sulfanilamide

1. Briefly identify the important characteristics of an aromatic compound.
2. What is meant by the prefixes meta, ortho, or para? Give the name and draw the structure for a compound that illustrates each.
3. What is a phenyl group? Give the structure for 3-phenyloctane.
Answers
1. An aromatic compound is any compound that contains a benzene ring or has certain benzene-like properties.
2. meta = 1,3 disubstitution; (answers will vary)
ortho = 1,2 disubstitution
para = 1,4 disubstitution or 1-bromo-4-chlorobenzene
3. phenyl group: C6H5 or
3-phenyloctane:
Key Takeaway
Aromatic compounds contain a benzene ring or have certain benzene-like properties; for our purposes, you can recognize
aromatic compounds by the presence of one or more benzene rings in their structure.
Exercises
1. Is each compound aromatic?
a.
b.
a.
b.
a. toluene
b. m-diethylbenzene
c. 3,5-dinitrotoluene
a. p-dichlorobenzene
b. naphthalene
c. 1,2,4-trimethylbenzene
5. Name each compound with its IUPAC name.
a.
b.
c.
d.
a.
b.
c.
d.
Answers
1. a. yes
b. no
3. a.
b.
c.
5. a. ethylbenzene
b. isopropylbenzene
c. o-bromotoluene
d. 3,5-dichlorotoluene
1.16: Structure and Nomenclature of Aromatic Compounds is shared under a CC BY-NC-SA 4.0 license and was authored, remixed, and/or
curated by LibreTexts.
To ensure that you understand the material in this chapter, you should review the meanings of the bold terms in the following
Any hydrocarbon containing either a double or triple bond is an unsaturated hydrocarbon. Alkenes have a carbon-to-carbon
double bond. The general formula for alkenes with one double bond is CnH2n. Alkenes can be straight chain, branched chain, or
cyclic. Simple alkenes often have common names, but all alkenes can be named by the system of the International Union of Pure
and Applied Chemistry.
Cis-trans isomers (or geometric isomers) are characterized by molecules that differ only in their configuration around a rigid part
of the structure, such as a carbon–to-carbon double bond or a ring. The molecule having two identical (or closely related) atoms or
groups on the same side is the cis isomer; the one having the two groups on opposite sides is the trans isomer.
The physical properties of alkenes are quite similar to those of alkanes. Like other hydrocarbons, alkenes are insoluble in water but
soluble in organic solvents.
More reactive than alkanes, alkenes undergo addition reactions across the double bond:
Addition of hydrogen (hydrogenation):
CH2=CH2 + H2 → CH3CH3
Addition of halogen (halogenation):
CH2=CH2 + X2 → XCH2CH2X
where X = F, Cl, Br, or I.
Addition of water (hydration):
CH2=CH2 + HOH → HCH2CH2OH
Alkenes also undergo addition polymerization, molecules joining together to form long-chain molecules.
…CH2=CH2 + CH2=CH2 + CH2=CH2 +…→…CH2CH2–CH2CH2–CH2CH2–…
The reactant units are monomers, and the product is a polymer.
Alkynes have a carbon-to-carbon triple bond. The general formula for alkynes is CnH2n − 2. The properties of alkynes are quite
similar to those of alkenes. They are named much like alkenes but with the ending -yne.
The cyclic hydrocarbon benzene (C6H6) has a ring of carbon atoms. The molecule seems to be unsaturated, but it does not undergo
the typical reactions expected of alkenes. The electrons that might be fixed in three double bonds are instead delocalized over all
six carbon atoms.
A hydrocarbon containing one or more benzene rings (or other similarly stable electron arrangements) is an aromatic
hydrocarbon, and any related substance is an aromatic compound. One or more of the hydrogen atoms on a benzene ring can be
replaced by other atoms. When two hydrogen atoms are replaced, the product name is based on the relative position of the
replacement atoms (or atom groups). A 1,2-disubstituted benzene is designated as an ortho (o-) isomer; 1,3-, a meta (m-) isomer;
and 1,4-, a para (p-) isomer. An aromatic group as a substituent is called an aryl group.
A polycyclic aromatic hydrocarbon (PAH) has fused benzene rings sharing a common side.
1.17: Unsaturated and Aromatic Hydrocarbons (Summary) is shared under a CC BY-NC-SA 4.0 license and was authored, remixed, and/or
Stereoisomers are isomers that differ in spatial arrangement of atoms, rather than order of atomic connectivity. One of their most
interesting type of isomer is the mirror-image stereoisomers, a non-superimposable set of two molecules that are mirror image of
one another. The existence of these molecules are determined by concept known as chirality.
Introduction
Organic compounds, molecules created around a chain of carbon atom (more commonly known as carbon backbone), play an
essential role in the chemistry of life. These molecules derive their importance from the energy they carry, mainly in a form of
potential energy between atomic molecules. Since such potential force can be widely affected due to changes in atomic placement,
it is important to understand the concept of an isomer, a molecule sharing same atomic make up as another but differing in
structural arrangements. This article will be devoted to a specific isomers called stereoisomers and its property of chirality (Figure
1).
Figure 1: Two enantiomers of a tetrahedral complex.

The concepts of steroisomerism and chirality command great deal of importance in modern organic chemistry, as these ideas helps
to understand the physical and theoretical reasons behind the formation and structures of numerous organic molecules, the main
reason behind the energy embedded in these essential chemicals. In contrast to more well-known constitutional isomerism, which
develops isotopic compounds simply by different atomic connectivity, stereoisomerism generally maintains equal atomic
connections and orders of building blocks as well as having same numbers of atoms and types of elements.
What, then, makes stereoisomers so unique? To answer this question, the learner must be able to think and imagine in not just two-
dimensional images, but also three-dimensional space. This is due to the fact that stereoisomers are isomers because their atoms are
different from others in terms of spatial arrangement.
Spatial Arrangement
First and foremost, one must understand the concept of spatial arrangement in order to understand stereoisomerism and chirality.
Spatial arrangement of atoms concern how different atomic particles and molecules are situated about in the space around the
organic compound, namely its carbon chain. In this sense, spatial arrangement of an organic molecule are different another if an
atom is shifted in any three-dimensional direction by even one degree. This opens up a very broad possibility of different
molecules, each with their unique placement of atoms in three-dimensional space .
Stereoisomers
Stereoisomers are, as mentioned above, contain different types of isomers within itself, each with distinct characteristics that
further separate each other as different chemical entities having different properties. Type called entaniomer are the previously-
mentioned mirror-image stereoisomers, and will be explained in detail in this article. Another type, diastereomer, has different
properties and will be introduced afterwards.
Enantiomers
This type of stereoisomer is the essential mirror-image, non-superimposable type of stereoisomer introduced in the beginning of the
article. Figure 3 provides a perfect example; note that the gray plane in the middle demotes the mirror plane.
Figure 2: Comparison of Chiral and Achiral Molecules. (a) Bromochlorofluoromethane is a chiral molecule whose stereocenter is
designated with an asterisk. Rotation of its mirror image does not generate the original structure. To superimpose the mirror
images, bonds must be broken and reformed. (b) In contrast, dichlorofluoromethane and its mirror image can be rotated so they are
superimposable.
Note that even if one were to flip over the left molecule over to the right, the atomic spatial arrangement will not be equal. This is
equivalent to the left hand - right hand relationship, and is aptly referred to as 'handedness' in molecules. This can be somewhat
counter-intuitive, so this article recommends the reader try the 'hand' example. Place both palm facing up, and hands next to each
other. Now flip either side over to the other. One hand should be showing the back of the hand, while the other one is showing the
palm. They are not same and non-superimposable.
This is where the concept of chirality comes in as one of the most essential and defining idea of stereoisomerism.
Chirality
Chirality essentially means 'mirror-image, non-superimposable molecules', and to say that a molecule is chiral is to say that its
mirror image (it must have one) is not the same as it self. Whether a molecule is chiral or achiral depends upon a certain set of
overlapping conditions. Figure 4 shows an example of two molecules, chiral and achiral, respectively. Notice the distinct
characteristic of the achiral molecule: it possesses two atoms of same element. In theory and reality, if one were to create a plane
that runs through the other two atoms, they will be able to create what is known as bisecting plane: The images on either side of the
plan is the same as the other (Figure 4).
Figure 4.
In this case, the molecule is considered 'achiral'. In other words, to distinguish chiral molecule from an achiral molecule, one must
search for the existence of the bisecting plane in a molecule. All chiral molecules are deprive of bisecting plane, whether simple or
complex.
As a universal rule, no molecule with different surrounding atoms are achiral. Chirality is a simple but essential idea to support the
concept of stereoisomerism, being used to explain one type of its kind. The chemical properties of the chiral molecule differs from
its mirror image, and in this lies the significance of chilarity in relation to modern organic chemistry.
Compounds with Multiple Chiral Centers
We turn our attention next to molecules which have more than one stereocenter. We will start with a common four-carbon sugar
called D-erythrose.
A note on sugar nomenclature: biochemists use a special system to refer to the stereochemistry of sugar molecules, employing
names of historical origin in addition to the designators 'D' and 'L'. You will learn about this system if you take a biochemistry
class. We will use the D/L designations here to refer to different sugars, but we won't worry about learning the system.
As you can see, D-erythrose is a chiral molecule: C2 and C3 are stereocenters, both of which have the R configuration. In addition,
you should make a model to convince yourself that it is impossible to find a plane of symmetry through the molecule, regardless of
the conformation. Does D-erythrose have an enantiomer? Of course it does – if it is a chiral molecule, it must. The enantiomer of
erythrose is its mirror image, and is named L-erythrose (once again, you should use models to convince yourself that these mirror
images of erythrose are not superimposable).
Notice that both chiral centers in L-erythrose both have the S configuration. In a pair of enantiomers, all of the chiral centers are of
the opposite configuration.
What happens if we draw a stereoisomer of erythrose in which the configuration is S at C2 and R at C3? This stereoisomer, which is
a sugar called D-threose, is not a mirror image of erythrose. D-threose is a diastereomer of both D-erythrose and L-erythrose.
The definition of diastereomers is simple: if two molecules are stereoisomers (same molecular formula, same connectivity, different
arrangement of atoms in space) but are not enantiomers, then they are diastereomers by default. In practical terms, this means that
at least one - but not all - of the chiral centers are opposite in a pair of diastereomers. By definition, two molecules that are
diastereomers are not mirror images of each other.
L-threose, the enantiomer of D-threose, has the R configuration at C2 and the S configuration at C3. L-threose is a diastereomer of
both erythrose enantiomers.
In general, a structure with n stereocenters will have 2n different stereoisomers. (We are not considering, for the time being, the
stereochemistry of double bonds – that will come later). For example, let's consider the glucose molecule in its open-chain form
(recall that many sugar molecules can exist in either an open-chain or a cyclic form). There are two enantiomers of glucose, called
D-glucose and L-glucose. The D-enantiomer is the common sugar that our bodies use for energy. It has n = 4 stereocenters, so
therefore there are 2n = 24 = 16 possible stereoisomers (including D-glucose itself).
In L-glucose, all of the stereocenters are inverted relative to D-glucose. That leaves 14 diastereomers of D-glucose: these are
molecules in which at least one, but not all, of the stereocenters are inverted relative to D-glucose. One of these 14 diastereomers, a
sugar called D-galactose, is shown above: in D-galactose, one of four stereocenters is inverted relative to D-glucose. Diastereomers
which differ in only one stereocenter (out of two or more) are called epimers. D-glucose and D-galactose can therefore be refered
to as epimers as well as diastereomers.
Example 3.10
Draw the structure of L-galactose, the enantiomer of D-galactose.
Solution
Example 3.11
Draw the structure of two more diastereomers of D-glucose. One should be an epimer.
Solution
Erythronolide B, a precursor to the 'macrocyclic' antibiotic erythromycin, has 10 stereocenters. It’s enantiomer is that molecule in
which all 10 stereocenters are inverted.
In total, there are 210 = 1024 stereoisomers in the erythronolide B family: 1022 of these are diastereomers of the structure above,
one is the enantiomer of the structure above, and the last is the structure above.
We know that enantiomers have identical physical properties and equal but opposite degrees of specific rotation. Diastereomers, in
theory at least, have different physical properties – we stipulate ‘in theory’ because sometimes the physical properties of two or
more diastereomers are so similar that it is very difficult to separate them. In addition, the specific rotations of diastereomers are
unrelated – they could be the same sign or opposite signs, and similar in magnitude or very dissimilar.
Constitutional isomers
Constitutational isomers or structural isomers are molecules with the same chemical formula but different structures of atoms
and bonds. For example, both 3-methylpentane and hexane have the same chemical formula, C6H14, yet they clearly have different
structures:
3-methylpentane hexane
Another example involves functional groups. Methoxy methane, an ether, and ethanol, an alcohol, both have the chemical formula
C2H6O:
Methoxy methane Ethanol
External Resources
1. Further Details of Stereochemistry: For those interested in the topic further!
2. MIT Online-Lecture including basic Organic Chemistry : Good background lecture to introduce Organic Chemistry.
3. Chirality Rap: Good way to understand the concept? Decide for yourself!
References
1. Anslyn, Eric V. and Dougherty, Dennis A. Modern Physical Organic Chemistry. Chicago, IL.: University Science. 2005
2. Hick, Janice M. The Physical Chemistry of Chirality. New York, N.Y.: An American Chemical Society Publication. 2001.
3. Vollhardt, K. Peter C. and Schore, Neil E. Organic Chemistry: Structure and Function. Fifth Edition. New York, N.Y.: W. H.
Freeman Company, 2007.
Problems
Identify the following as either a constitutional isomer or stereoisomer. If stereoisomer, determine if it is an enantiomer or
diastereomer. Explain the reason behind the answer. Also mark chirality for each molecule.
1. 2. 3.
Contributors
Dan Chong
Jonathan Mooney (McGill University)
1.18: Chirality and Stereoisomers is shared under a CC BY-NC-SA 4.0 license and was authored, remixed, and/or curated by LibreTexts.
To name the enantiomers of a compound unambiguously, their names must include the "handedness" of the molecule. The method
for this is formally known as R/S nomenclature.
Introduction
The method of unambiguously assigning the handedness of molecules was originated by three chemists: R.S. Cahn, C. Ingold, and
V. Prelog and, as such, is also often called the Cahn-Ingold-Prelog rules. In addition to the Cahn-Ingold system, there are two ways
of experimentally determining the absolute configuration of an enantiomer:
1. X-ray diffraction analysis. Note that there is no correlation between the sign of rotation and the structure of a particular
enantiomer.
2. Chemical correlation with a molecule whose structure has already been determined via X-ray diffraction.
However, for non-laboratory purposes, it is beneficial to focus on the R/S system. The sign of optical rotation, although different
for the two enantiomers of a chiral molecule,at the same temperature, cannot be used to establish the absolute configuration of an
enantiomer; this is because the sign of optical rotation for a particular enantiomer may change when the temperature changes.
Stereocenters are labeled R or S

The "right hand" and "left hand" nomenclature is used to name the enantiomers of a chiral compound. The stereocenters are labeled
as R or S.
Consider the first picture: a curved arrow is drawn from the highest priority (1) substituent to the lowest priority (4) substituent. If
the arrow points in a counterclockwise direction (left when leaving the 12 o' clock position), the configuration at stereocenter is
considered S ("Sinister" → Latin= "left"). If, however, the arrow points clockwise,(Right when leaving the 12 o' clock position)
then the stereocenter is labeled R ("Rectus" → Latin= "right"). The R or S is then added as a prefix, in parenthesis, to the name of
the enantiomer of interest.
Example 1
(R)-2-Bromobutane
(S)-2,3- Dihydroxypropanal
Sequence rules to assign priorities to substituents

Before applying the R and S nomenclature to a stereocenter, the substituents must be prioritized according to the following rules:
Rule 1
First, examine at the atoms directly attached to the stereocenter of the compound. A substituent with a higher atomic number takes
precedence over a substituent with a lower atomic number. Hydrogen is the lowest possible priority substituent, because it has the
lowest atomic number.
1. When dealing with isotopes, the atom with the higher atomic mass receives higher priority.
2. When visualizing the molecule, the lowest priority substituent should always point away from the viewer (a dashed line
indicates this). To understand how this works or looks, imagine that a clock and a pole. Attach the pole to the back of the clock,
so that when when looking at the face of the clock the pole points away from the viewer in the same way the lowest priority
substituent should point away.
3. Then, draw an arrow from the highest priority atom to the 2nd highest priority atom to the 3rd highest priority atom. Because
the 4th highest priority atom is placed in the back, the arrow should appear like it is going across the face of a clock. If it is
going clockwise, then it is an R-enantiomer; If it is going counterclockwise, it is an S-enantiomer.
When looking at a problem with wedges and dashes, if the lowest priority atom is not on the dashed line pointing away, the
molecule must be rotated.
Remember that
Wedges indicate coming towards the viewer.
Dashes indicate pointing away from the viewer.
Rule 2
If there are two substituents with equal rank, proceed along the two substituent chains until there is a point of difference. First,
determine which of the chains has the first connection to an atom with the highest priority (the highest atomic number). That chain
has the higher priority.
If the chains are similar, proceed down the chain, until a point of difference.
For example: an ethyl substituent takes priority over a methyl substituent. At the connectivity of the stereocenter, both have a
carbon atom, which are equal in rank. Going down the chains, a methyl has only has hydrogen atoms attached to it, whereas the
ethyl has another carbon atom. The carbon atom on the ethyl is the first point of difference and has a higher atomic number than
hydrogen; therefore the ethyl takes priority over the methyl.
Rule 3
If a chain is connected to the same kind of atom twice or three times, check to see if the atom it is connected to has a greater atomic
number than any of the atoms that the competing chain is connected to.
If none of the atoms connected to the competing chain(s) at the same point has a greater atomic number: the chain bonded to the
same atom multiple times has the greater priority
If however, one of the atoms connected to the competing chain has a higher atomic number: that chain has the higher priority.
Example 2
A 1-methylethyl substituent takes precedence over an ethyl substituent. Connected to the first carbon atom, ethyl only has one
other carbon, whereas the 1-methylethyl has two carbon atoms attached to the first; this is the first point of difference.
Therefore, 1-methylethyl ranks higher in priority than ethyl, as shown below:
However:
Remember that being double or triple bonded to an atom means that the atom is connected to the same atom twice. In such a
case, follow the same method as above.
Caution!!
Keep in mind that priority is determined by the first point of difference along the two similar substituent chains. After the first
point of difference, the rest of the chain is irrelevant.
When looking for the first point of difference on similar substituent chains, one may encounter branching. If there is branching,
choose the branch that is higher in priority. If the two substituents have similar branches, rank the elements within the branches
until a point of difference.
After all your substituents have been prioritized in the correct manner, you can now name/label the molecule R or S.
1. Put the lowest priority substituent in the back (dashed line).
2. Proceed from 1 to 2 to 3. (it is helpful to draw or imagine an arcing arrow that goes from 1--> 2-->3)
3. Determine if the direction from 1 to 2 to 3 clockwise or counterclockwise.
i) If it is clockwise it is R.
ii) if it is counterclockwise it is S.
USE YOUR MODELING KIT: Models assist in visualizing the structure. When using a model, make sure the lowest priority is
pointing away from you. Then determine the direction from the highest priority substituent to the lowest: clockwise (R) or
counterclockwise (S).
IF YOU DO NOT HAVE A MODELING KIT: remember that the dashes mean the bond is going into the screen and the wedges
means that bond is coming out of the screen. If the lowest priority bond is not pointing to the back, mentally rotate it so that it is.
However, it is very useful when learning organic chemistry to use models.
If you have a modeling kit use it to help you solve the following practice problems.
Problems
Are the following R or S?
Solutions
1. S: I > Br > F > H. The lowest priority substituent, H, is already going towards the back. It turns left going from I to Br to F, so
it's a S.
2. R: Br > Cl > CH3 > H. You have to switch the H and Br in order to place the H, the lowest priority, in the back. Then, going
from Br to Cl, CH3 is turning to the right, giving you a R.
3. Neither R or S: This molecule is achiral. Only chiral molecules can be named R or S.
4. R: OH > CN > CH2NH2 > H. The H, the lowest priority, has to be switched to the back. Then, going from OH to CN to
CH2NH2, you are turning right, giving you a R.
5. (5) S: −COOH > −CH OH > C≡CH > H . Then, going from −COOH to −CH OH to −C≡CH you are turning left,
2 2
giving you a S configuration.
References
1. Schore and Vollhardt. Organic Chemistry Structure and Function. New York:W.H. Freeman and Company, 2007.
2. McMurry, John and Simanek, Eric. Fundamentals of Organic Chemistry. 6th Ed. Brooks Cole, 2006.
Contributors
Ekta Patel (UCD), Ifemayowa Aworanti (University of Maryland Baltimore County)
1.19: R-S Sequence Rules is shared under a CC BY-NC-SA 4.0 license and was authored, remixed, and/or curated by LibreTexts.
1. Classify each compound as organic or inorganic.
a. C3H8O
b. CaCl2
c. Cr(NH3)3Cl3
d. C30H48O3N
2. Which compound is likely organic and which is likely inorganic?
a. a flammable compound that boils at 80°C and is insoluble in water
b. a compound that does not burn, melts at 630°C, and is soluble in water
Answers
1.
a. organic
b. inorganic
c. inorganic
d. organic
2.
a. organic
b. inorganic
a. C6H10
b. CoCl2
c. C12H22O11
a. CH3NH2
b. NaNH2
c. Cu(NH3)6Cl2
3. Which member of each pair has a higher melting point?
a. CH3OH and NaOH
b. CH3Cl and KCl
4. Which member of each pair has a higher melting point?
a. C2H6 and CoCl2
b. CH4 and LiH
Answers
1.
a. organic
b. inorganic
c. organic
3.
a. NaOH
b. KCl

1. In the homologous series of alkanes, what is the molecular formula for the member just above C8H18?
2. Use the general formula for alkanes to write the molecular formula of the alkane with 12 carbon atoms.
Answers
1. C9H20
2. C12H26
Exercises
1. What compounds contain fewer carbon atoms than C3H8 and are its homologs?
2. What compounds contain five to eight carbon atoms and are homologs of C4H10?
Answer
1. CH4 and C2H6

1. In alkanes, can there be a two-carbon branch off the second carbon atom of a four-carbon chain? Explain.
2. A student is asked to write structural formulas for two different hydrocarbons having the molecular formula C5H12. She writes
one formula with all five carbon atoms in a horizontal line and the other with four carbon atoms in a line, with a CH3 group
extending down from the first attached to the third carbon atom. Do these structural formulas represent different molecular
formulas? Explain why or why not.
Answers
1. No; the branch would make the longest continuous chain of five carbon atoms.
2. No; both are five-carbon continuous chains.
Key Takeaway
Alkanes with four or more carbon atoms can exist in isomeric forms.
Exercises
1. Briefly identify the important distinctions between a straight-chain alkane and a branched-chain alkane.
2. How are butane and isobutane related? How do they differ?
3. Name each compound.
a.
b.
4. Write the structural formula for each compound.
a. hexane
b. octane
5. Indicate whether the structures in each set represent the same compound or isomers.
a. CH3CH2CH2CH3 and
b. CH3CH2CH2CH2CH3 and
Answers
1. Straight-chain alkanes and branched-chain alkanes have different properties as well as different structures.
3.
a. pentane
b. heptane
5.
a. no
b. yes
Exercises
1. Write the condensed structural formula for each structural formula.
a.
b.
c.
2. A condensed structural formula for isohexane can be written as (CH3)2CHCH2CH2CH3. Draw the line-angle formula for
isohexane.
3. Draw a line-angle formula for the compound CH3CH2CH(CH3)CH2CH2CH3.
4. Give the structural formula for the compound represented by this line-angle formula:
Answers
1.
a. CH3CH3
b. CH3CH2CH3
c. CH3CH2CH2CH2CH3
3.

1. What is a CH3 group called when it is attached to a chain of carbon atoms—a substituent or a functional group?
2. Which type of name uses numbers to locate substituents—common names or IUPAC names?
Answers
1. substituent
2. IUPAC names
Exercises
1. Briefly identify the important distinctions between an alkane and an alkyl group.
2. How many carbon atoms are present in each molecule?
a. 2-methylbutane
b. 3-ethylpentane
3. How many carbon atoms are present in each molecule?
a. 2,3-dimethylbutane
b. 3-ethyl-2-methylheptane
a. 3-methylpentane
b. 2,2,5-trimethylhexane
c. 4-ethyl-3-methyloctane
a. 2-methylpentane
b. 4-ethyl-2-methylhexane
c. 2,2,3,3-tetramethylbutane
a.
b.
a.
b.
8. What is a substituent? How is the location of a substituent indicated in the IUPAC system?
9. Briefly identify the important distinctions between a common name and an IUPAC name.
Answers
1. An alkane is a molecule; an alkyl group is not an independent molecule but rather a part of a molecule that we consider as a
unit.
3.
a. 6
b. 10
5.
a.
b.
c.
7.
a. 2,2,4,4-tetramethylpentane
b. 3-ethylhexane
9. Common names are widely used but not very systematic; IUPAC names identify a parent compound and name other groups as
substituents.

1. Without referring to a table, predict which has a higher boiling point—hexane or octane. Explain.
2. If 25 mL of hexane were added to 100 mL of water in a beaker, which of the following would you expect to happen? Explain.
a. Hexane would dissolve in water.
b. Hexane would not dissolve in water and would float on top.
c. Hexane would not dissolve in water and would sink to the bottom of the container.
Answers
1. octane because of its greater molar mass
2. b; hexane is insoluble in water and less dense than water.
Exercises
a. pentane or butane
b. heptane or nonane
2. For which member of each pair is hexane a good solvent?
a. pentane or water
b. sodium chloride or soybean oil
Answer
1. a. pentane
b. nonane

1. Why are alkanes sometimes called paraffins?
2. Which halogen reacts most readily with alkanes? Which reacts least readily?
Answers
1. Alkanes do not react with many common chemicals. They are sometimes called paraffins, from the Latin parum affinis,
meaning “little affinity.”
2. most readily: F ; least readily: I
2 2
Exercises
1. Why do alkanes usually not react with ionic compounds such as most laboratory acids, bases, oxidizing agents, or reducing
agents?
2. Write an equation for the complete combustion of methane (C H ), the main component of natural gas).
4
3. What is the most important reaction of alkanes?

4. Name some substances other than oxygen that react readily with alkanes.
Answers
1. Alkanes are nonpolar; they do not attract ions.
12.8: Halogenated Hydrocarbons

1. What is the IUPAC name for the HFC that has the formula CH2FCF3? (Hint: you must use a number to indicate the location of
each substituent F atom.)
2. What is the IUPAC name for the HCFC that has the formula CHCl2CF3?
Answers
1. 1,1,1,2-tetrafluoroethane
2. 1,1,1-trifluoro-2,2-dichloroethane
Exercises
1. Write the condensed structural formula for each compound.
a. methyl chloride
b. chloroform
2. Write the condensed structural formula for each compound.
a. ethyl bromide
b. carbon tetrachloride
3. Write the condensed structural formulas for the two isomers that have the molecular formula C3H7Br. Give the common name
and the IUPAC name of each.
4. Write the condensed structural formulas for the four isomers that have the molecular formula C4H9Br. Give the IUPAC name of
each.
5. What is a CFC? How are CFCs involved in the destruction of the ozone layer?
6. Explain why each compound is less destructive to the ozone layer than are CFCs.
a. fluorocarbons
b. HCFCs
Answers
1. a. CH3Cl
b. CHCl3
3. CH3CH2CH2Br, propyl bromide, 1-bromopropane; CH3CHBrCH3, isopropyl bromide, 2-bromopropane
5. compounds containing Cl, F, and C; by releasing Cl atoms in the stratosphere
12.9: Cycloalkanes
1. What is the molecular formula of cyclooctane?
2. What is the IUPAC name for this compound?
Answers
1. C8H16
2. ethylcyclopropane
Exercises
a. ethylcyclobutane
b. propylcyclopropane
a. methylcyclohexane
b. butylcyclobutane
3. Cycloalkyl groups can be derived from cycloalkanes in the same way that alkyl groups are derived from alkanes. These groups
are named as cyclopropyl, cyclobutyl, and so on. Name each cycloalkyl halide.
a.
b.
4. Halogenated cycloalkanes can be named by the IUPAC system. As with alkyl derivatives, monosubstituted derivatives need no
number to indicate the position of the halogen. To name disubstituted derivatives, the carbon atoms are numbered starting at the
position of one substituent (C1) and proceeding to the second substituted atom by the shortest route. Name each compound.
a.
b.
Answers
1. a.
b.
3. a. cyclopentyl bromide
b. cyclohexyl chloride
12.10: Chapter Summary
Additional Exercises
1. You find an unlabeled jar containing a solid that melts at 48°C. It ignites readily and burns readily. The substance is insoluble in
water and floats on the surface. Is the substance likely to be organic or inorganic?
2. Give the molecular formulas for methylcyclopentane, 2-methylpentane, and cyclohexane. Which are isomers?
3. What is wrong with each name? (Hint: first write the structure as if it were correct.) Give the correct name for each compound.
a. 2-dimethylpropane
b. 2,3,3-trimethylbutane
c. 2,4-diethylpentane
d. 3,4-dimethyl-5-propylhexane
4. What is the danger in swallowing a liquid alkane?
5. Distinguish between lighter and heavier liquid alkanes in terms of their effects on the skin.
6. Following is the line formula for an alkane. Draw its structure and give its name.
7. Write equations for the complete combustion of each compound.

a. propane (a bottled gas fuel)
b. octane (a typical hydrocarbon in gasoline).
8. The density of a gasoline sample is 0.690 g/mL. On the basis of the complete combustion of octane, calculate the amount in
grams of carbon dioxide (CO2) and water (H2O) formed per gallon (3.78 L) of the gasoline when used in an automobile.
9. Draw the structures for the five isomeric hexanes (C6H14). Name each by the IUPAC system.
10. Indicate whether the structures in each set represent the same compound or isomers.
a.
b.
c.
11. Consider the line-angle formulas shown here and answer the questions.
a. Which pair of formulas represents isomers? Draw each structure.
b. Which formula represents an alkyl halide? Name the compound and write its condensed structural formula.
c. Which formula represents a cyclic alkane? Name the compound and draw its structure.
d. What is the molecular formula of the compound represented by (i)?
Answers
1. organic
3.
a. Two numbers are needed to indicate two substituents; 2,2-dimethylpropane.
b. The lowest possible numbers were not used; 2,2,3-trimethylbutane.
c. An ethyl substituent is not possible on the second carbon atom; 3,5-dimethylheptane.
d. A propyl substituent is not possible on the fifth carbon atom; 3,4,5-trimethyloctane.
5. Lighter alkanes wash away protective skin oils; heavier alkanes form a protective layer.
7.
a. C3H8 + 5O2 → 3CO2 + 4H2O
b. 2C8H18 + 25O2 → 16CO2 + 18H2O
9. CH3CH2CH2CH2CH2CH3; hexane
11.
a. ii and iii; CH3CH2CH2CH2CH2CH2CH3 and
b. iv; 3-chloropentane; CH3CH2CHClCH2CH3
c. i; ethylcyclopentane;
d. C7H14
1.20: Organic Chemistry: Alkanes is shared under a CC BY-NC-SA 4.0 license and was authored, remixed, and/or curated by LibreTexts.
12.6: Physical Properties of Alkanes by Anonymous is licensed CC BY-NC-SA 4.0. Original source:
https://2012books.lardbucket.org/books/introduction-to-chemistry-general-organic-and-biological.
12.7: Chemical Properties of Alkanes by Anonymous is licensed CC BY-NC-SA 4.0. Original source:
12.8: Halogenated Hydrocarbons by Anonymous is licensed CC BY-NC-SA 4.0. Original source:
12.9: Cycloalkanes by Anonymous is licensed CC BY-NC-SA 4.0. Original source: https://2012books.lardbucket.org/books/introduction-to-
chemistry-general-organic-and-biological.
13.1: Alkenes- Structures and Names
1. Briefly identify the important distinctions between a saturated hydrocarbon and an unsaturated hydrocarbon.
2. Briefly identify the important distinctions between an alkene and an alkane.
3. Classify each compound as saturated or unsaturated. Identify each as an alkane, an alkene, or an alkyne.
a.
b. CH3CH2C≡CCH3
c.
Answers
1. Unsaturated hydrocarbons have double or triple bonds and are quite reactive; saturated hydrocarbons have only single bonds
and are rather unreactive.
2. An alkene has a double bond; an alkane has single bonds only.
3. a. saturated; alkane
b. unsaturated; alkyne
c. unsaturated; alkene
Exercises
a. 2-methyl-2-pentene
b. 2,3-dimethyl-1-butene
c. cyclohexene
a. 5-methyl-1-hexene
b. 3-ethyl-2-pentene
c. 4-methyl-2-hexene
a.
b.
c.
a.
b.
c.
Answers
1. a.
b.
c.
3. a. 2-methyl-1-pentene
b. 2-methyl-2-pentene
c. 2,5-dimethyl-2-hexene

1. What are cis-trans (geometric) isomers? What two types of compounds can exhibit cis-trans isomerism?
2. Classify each compound as a cis isomer, a trans isomer, or neither.
a.
b.
c.
d.
Answers
1. Cis-trans isomers are compounds that have different configurations (groups permanently in different places in space) because of
the presence of a rigid structure in their molecule. Alkenes and cyclic compounds can exhibit cis-trans isomerism.
2. a. trans (the two hydrogen atoms are on opposite sides)
b. cis (the two hydrogen atoms are on the same side, as are the two ethyl groups)
c. cis (the two ethyl groups are on the same side)
d. neither (flipping the bond does not change the molecule. There are no isomers for this molecule)
Exercises
none.
a. 2-bromo-2-pentene
b. 3-hexene
c. 4-methyl-2-pentene
d. 1,1-dibromo-1-butene
e. 2-butenoic acid (CH3CH=CHCOOH)
none.
a. 2,3-dimethyl-2-pentene
b. 1,1-dimethyl-2-ethylcyclopropane
c. 1,2-dimethylcyclohexane
d. 5-methyl-2-hexene
e. 1,2,3-trimethylcyclopropane
Answer
1. a: none. There are two distinct geometric isomers, but since there are there are four different groups off the double bond, these
are both cis/trans isomers (they are technically E/Z isomers discussed elsewhere).
b:
c:
d:
e:

1. Briefly describe the physical properties of alkenes. How do these properties compare to those of the alkanes?
2. Without consulting tables, arrange the following alkenes in order of increasing boiling point: 1-butene, ethene, 1-hexene, and
propene.
Answers
1. Alkenes have physical properties (low boiling points, insoluble in water) quite similar to those of their corresponding alkanes.
2. ethene < propene < 1-butene < 1-hexene
Exercises
a. 1-pentene or 1-butene
b. 3-heptene or 3-nonene
2. Which is a good solvent for cyclohexene, pentane or water?
Answer
1. a. 1-pentene
b. 3-nonene

1. What is the principal difference in properties between alkenes and alkanes? How are they alike?
2. If C12H24 reacts with HBr in an addition reaction, what is the molecular formula of the product?
Answers
1. Alkenes undergo addition reactions; alkanes do not. Both burn.
2. C12H24Br2
Exercises
a. (CH3) 2C=CH2 + Br2 →
Ni
b. C H2 =C(C H3 )C H2 C H3 + H2 −→
c.
Ni
a. C H2 =CHCH=C H2 + 2 H2 −→
H2 SO4
b. (C H3 )2 C=C(C H3 )2 + H2 O −−−−→
c.
Answer
1. a. (CH3)2CBrCH2Br
b. CH3CH(CH3)CH2CH3
c.
13.5: Polymers

1. What is a monomer? What is a polymer? How do polymer molecules differ from the molecules we have discussed in earlier
sections of this chapter?
2. What is addition polymerization? What structural feature usually characterizes molecules used as monomers in addition
polymerization?
3. What is the molecular formula of a polymer molecule formed by the addition polymerization of 175 molecules of vinyl chloride
(CH2=CHCl)?
Answers
1. Monomers are small molecules that can be assembled into giant molecules referred to as polymers, which are much larger than
the molecules we discussed earlier in this chapter.
2. In addition polymerization, the monomers add to one another in such a way that the polymer contains all the atoms of the
starting monomers.
3. C350H525Cl175
Exercises
1. Write the condensed structural formula of the monomer from which Saran is formed. A segment of the Saran molecule has the
following structure: CH2CCl2CH2CCl2CH2CCl2CH2CCl2.
2. Write the condensed structural formula for the section of a molecule formed from four units of the monomer CH2=CHF.
Answer
1. H2C=CCl2
13.6: Alkynes

1. Briefly identify the important differences between an alkene and an alkyne. How are they similar?
2. The alkene (CH3)2CHCH2CH=CH2 is named 4-methyl-1-pentene. What is the name of (CH3)2CHCH2C≡CH?
3. Do alkynes show cis-trans isomerism? Explain.
Answers
1. Alkenes have double bonds; alkynes have triple bonds. Both undergo addition reactions.
2. 4-methyl-1-pentyne
3. No; a triply bonded carbon atom can form only one other bond. It would have to have two groups attached to show cis-trans
isomerism.
Exercises
a. acetylene
b. 3-methyl-1-hexyne
a. 4-methyl-2-hexyne
b. 3-octyne
3. Name each alkyne.
a. CH3CH2CH2C≡CH
b. CH3CH2CH2C≡CCH3
Answers
1. a. H–C≡C–H
b.
3. a. 1-pentyne
b. 2-hexyne
13.7: Aromatic Compounds- Benzene

1. How do the typical reactions of benzene differ from those of the alkenes?
2. Briefly describe the bonding in benzene.
3. What does the circle mean in the chemist’s representation of benzene?
Answers
1. Benzene is rather unreactive toward addition reactions compared to an alkene.
2. Valence electrons are shared equally by all six carbon atoms (that is, the electrons are delocalized).
3. The six electrons are shared equally by all six carbon atoms.
Exercises
1. Draw the structure of benzene as if it had alternate single and double bonds.
2. Draw the structure of benzene as chemists usually represent it today.
Answer
1.
1. Briefly identify the important characteristics of an aromatic compound.
2. What is meant by the prefixes meta, ortho, or para? Give the name and draw the structure for a compound that illustrates each.
3. What is a phenyl group? Give the structure for 3-phenyloctane.
Answers
1. An aromatic compound is any compound that contains a benzene ring or has certain benzene-like properties.
2. meta = 1,3 disubstitution; (answers will vary)
ortho = 1,2 disubstitution
para = 1,4 disubstitution or 1-bromo-4-chlorobenzene
3. phenyl group: C6H5 or
3-phenyloctane:
Exercises
a.
b.
a.
b.
a. toluene
b. m-diethylbenzene
c. 3,5-dinitrotoluene
a. p-dichlorobenzene
b. naphthalene
c. 1,2,4-trimethylbenzene
a.
b.
c.
d.
a.
b.
c.
d.
Answers
1. a. yes
b. no
3. a.
b.
c.
5. a. ethylbenzene
b. isopropylbenzene
c. o-bromotoluene
d. 3,5-dichlorotoluene
1. Classify each compound as saturated or unsaturated.
a.
b. CH3C≡CCH3
2. Classify each compound as saturated or unsaturated.
a.
b.
3. Give the molecular formula for each compound.
a.
b.
4. When three isomeric pentenes—X, Y, and Z—are hydrogenated, all three form 2-methylbutane. The addition of Cl2 to Y gives
1,2-dichloro-3-methylbutane, and the addition of Cl2 to Z gives 1,2-dichloro-2-methylbutane. Draw the original structures for
X, Y, and Z.
5. Pentane and 1-pentene are both colorless, low-boiling liquids. Describe a simple test that distinguishes the two compounds.
Indicate what you would observe.
6. Draw and name all the alkene cis-trans isomers corresponding to the molecular formula C5H10. (Hint: there are only two.)
7. The complete combustion of benzene forms carbon dioxide and water:
C6H6 + O2 → CO2 + H2O
Balance the equation. What mass, in grams, of carbon dioxide is formed by the complete combustion of 39.0 g of benzene?
8. Describe a physiological effect of some PAHs.
9. What are some of the hazards associated with the use of benzene?
10. What is wrong with each name? Draw the structure and give the correct name for each compound.
a. 2-methyl-4-heptene
b. 2-ethyl-2-hexene
c. 2,2-dimethyl-3-pentene
11. What is wrong with each name?
a. 2-bromobenzene
b. 3,3-dichlorotoluene
c. 1,4-dimethylnitrobenzene
12. Following are line-angle formulas for three compounds. Draw the structure and give the name for each.
a.
b.
c.
13. Following are ball-and-stick molecular models for three compounds (blue balls represent H atoms; red balls are C atoms). Write
the condensed structural formula and give the name for each.
a.
b.
c.
Answers
1.
a. unsaturated
b. unsaturated
3.
a. C6H10
b. C4H8
5. Add bromine solution (reddish-brown) to each. Pentane will not react, and the reddish-brown color persists; 1-pentene will
react, leaving a colorless solution.
7. 2C6H6 + 15O2 → 12CO2 + 6H2O; 132 g
9. carcinogenic, flammable
11.
a. number not needed
b. can’t have two groups on one carbon atom on a benzene ring
c. can’t have a substituent on the same carbon atom as the nitro group
13.
a. CH3CH=CHCH2CH2CH3; 2-hexene
b.
c.
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CHAPTER OVERVIEW
2: Carbohydrates
2.2: Carbohydrates
2.7: Disaccharides
2: Carbohydrates is shared under a CC BY-NC-SA 4.0 license and was authored, remixed, and/or curated by LibreTexts.
1
In the United States, 17.9 million people have been diagnosed with diabetes, and experts estimate that at least another 5.7 million
people have the disease but have not been diagnosed. In 2006, diabetes was the seventh leading cause of death, listed on 72,507
death certificates. Moreover, it was a contributing factor in over 200,000 deaths in which the cause was listed as something else,
such as heart or kidney disease.
People with diabetes are impaired in their ability to metabolize glucose, a sugar needed by the body for energy; as a result,
excessive quantities of glucose accumulate in the blood and the urine. The characteristic symptoms of diabetes are weight loss,
constant hunger, extreme thirst, and frequent urination (the kidneys excrete large amounts of water in an attempt to remove the
excess sugar from the blood).
An important diagnostic test for diabetes is the oral glucose tolerance test, which measures the level of glucose in blood plasma. A
first measurement is made after a fast of at least 8 h, followed by another measurement 2 h after the person drinks a flavored
solution of 75 g of glucose dissolved in water. At the second measurement, the glucose plasma level should be no higher than 139
mg/dL. Individuals with a value between 140 and 199 mg/dL are diagnosed with prediabetes, while those with a value of 200
mg/dL or above are diagnosed with diabetes. Following a diagnosis of diabetes a person will need to monitor his or her blood
glucose levels daily (or more often) using a glucose meter.
Figure 2.1.1 : Using a Glucose Meter to Test Blood Glucose Level. Image used with permission (Public Domain; Centers for
Disease Control and Prevention).
2.1: Prelude to Carbohydrates is shared under a CC BY-NC-SA 4.0 license and was authored, remixed, and/or curated by LibreTexts.
2.2: Carbohydrates
Learning Objectives
To recognize carbohydrates and classify them as mono-, di-, or polysaccharides.
All carbohydrates consist of carbon, hydrogen, and oxygen atoms and are polyhydroxy aldehydes or ketones or are compounds that
can be broken down to form such compounds. Examples of carbohydrates include starch, fiber, the sweet-tasting compounds called
sugars, and structural materials such as cellulose. The term carbohydrate had its origin in a misinterpretation of the molecular
formulas of many of these substances. For example, because its formula is C6H12O6, glucose was once thought to be a “carbon
hydrate” with the structure C6·6H2O.
Example 2.2.1
Which compounds would be classified as carbohydrates?
a.
b.
c.
d.
SOLUTION
a. This is a carbohydrate because the molecule contains an aldehyde functional group with OH groups on the other two carbon
atoms.
b. This is not a carbohydrate because the molecule does not contain an aldehyde or a ketone functional group.
c. This is a carbohydrate because the molecule contains a ketone functional group with OH groups on the other two carbon
atoms.
d. This is not a carbohydrate; although it has a ketone functional group, one of the other carbons atoms does not have an OH
group attached.
Exercise 2.2.1
Which compounds would be classified as carbohydrates?
1.
2.
3.
4.
Green plants are capable of synthesizing glucose (C6H12O6) from carbon dioxide (CO2) and water (H2O) by using solar energy in
the process known as photosynthesis:
6 CO + 6 H O + 686 kcal → C H O +6 O (2.2.1)
2 2 6 12 6 2
(The 686 kcal come from solar energy.) Plants can use the glucose for energy or convert it to larger carbohydrates, such as starch or
cellulose. Starch provides energy for later use, perhaps as nourishment for a plant’s seeds, while cellulose is the structural material
of plants. We can gather and eat the parts of a plant that store energy—seeds, roots, tubers, and fruits—and use some of that energy
ourselves. Carbohydrates are also needed for the synthesis of nucleic acids and many proteins and lipids.
Animals, including humans, cannot synthesize carbohydrates from carbon dioxide and water and are therefore dependent on the
plant kingdom to provide these vital compounds. We use carbohydrates not only for food (about 60%–65% by mass of the average
diet) but also for clothing (cotton, linen, rayon), shelter (wood), fuel (wood), and paper (wood).
The simplest carbohydrates—those that cannot be hydrolyzed to produce even smaller carbohydrates—are called monosaccharides.
Two or more monosaccharides can link together to form chains that contain from two to several hundred or thousand
monosaccharide units. Prefixes are used to indicate the number of such units in the chains. Disaccharide molecules have two
monosaccharide units, trisaccharide molecules have three units, and so on. Chains with many monosaccharide units joined together
are called polysaccharides. All these so-called higher saccharides can be hydrolyzed back to their constituent monosaccharides.
Compounds that cannot be hydrolyzed will not react with water to form two or more
smaller compounds.
Summary
Carbohydrates are an important group of biological molecules that includes sugars and starches. Photosynthesis is the process by
which plants use energy from sunlight to synthesize carbohydrates. A monosaccharide is the simplest carbohydrate and cannot be
hydrolyzed to produce a smaller carbohydrate molecule. Disaccharides contain two monosaccharide units, and polysaccharides
contain many monosaccharide units.

1. Why is photosynthesis important?
2. Identify the differences among monosaccharides, disaccharides, and polysaccharides.
Answers
1. Photosynthesis is the process by which solar energy is used to reduce carbon dioxide to carbohydrates, which are needed for
energy by plants and other living organisms that eat plants.
2. A monosaccharide is the simplest carbohydrate and cannot be hydrolyzed to produce a smaller carbohydrate; a disaccharide is
composed of two monosaccharide units; and a polysaccharide contains many saccharide units.
Exercises
1. When an aqueous solution of trehalose is heated, two molecules of glucose are produced for each molecule of trehalose. Is
trehalose a monosaccharide, a disaccharide, or a polysaccharide?
2. When an aqueous solution of arabinose is heated, no other molecules are produced. Is arabinose a monosaccharide, a
disaccharide, or a polysaccharide?
Answer
1. Trehalose is a disaccharide because it is hydrolyzed into two molecules of glucose (a monosaccharide).
2.2: Carbohydrates is shared under a CC BY-NC-SA 4.0 license and was authored, remixed, and/or curated by LibreTexts.
Learning Objectives
Classify monosaccharides as aldoses or ketoses and as trioses, tetroses, pentoses, or hexoses.
Distinguish between a D sugar and an L sugar.
The naturally occurring monosaccharides contain three to seven carbon atoms per molecule. Monosaccharides of specific sizes may
be indicated by names composed of a stem denoting the number of carbon atoms and the suffix -ose. For example, the terms triose,
tetrose, pentose, and hexose signify monosaccharides with, respectively, three, four, five, and six carbon atoms. Monosaccharides
are also classified as aldoses or ketoses. Those monosaccharides that contain an aldehyde functional group are called aldoses; those
containing a ketone functional group on the second carbon atom are ketoses. Combining these classification systems gives general
names that indicate both the type of carbonyl group and the number of carbon atoms in a molecule. Thus, monosaccharides are
described as aldotetroses, aldopentoses, ketopentoses, ketoheptoses, and so forth. Glucose and fructose are specific examples of an
aldohexose and a ketohexose, respectively.
Example 2.3.1
Draw an example of each type of compound.
a. a ketopentose
b. an aldotetrose
SOLUTION
a. The structure must have five carbon atoms with the second carbon atom being a carbonyl group and the other four carbon
atoms each having an OH group attached. Several structures are possible, but one example is shown.
b. The structure must have four carbon atoms with the first carbon atom part of the aldehyde functional group. The other three
carbon atoms each have an OH group attached. Several structures are possible, but one example is shown.
Exercise 2.3.1
Draw an example of each type of compound.
a. an aldohexose
b. a ketotetrose
The simplest sugars are the trioses. The possible trioses are shown in part (a) of Figure 2.3.1; glyceraldehyde is an aldotriose, while
dihydroxyacetone is a ketotriose. Notice that two structures are shown for glyceraldehyde. These structures are stereoisomers, and
hence are isomers having the same structural formula but differing in the arrangement of atoms or groups of atoms in three-
dimensional space. If you make models of the two stereoisomers of glyceraldehyde, you will find that you cannot place one model
on top of the other and have each functional group point in the same direction. However, if you place one of the models in front of
a mirror, the image in the mirror will be identical to the second stereoisomer in part (b) of Figure 2.3.1. Molecules that are
nonsuperimposable (nonidentical) mirror images of each other are a type of stereoisomer called enantiomers (Greek enantios,
meaning “opposite”).
Note
These are another type of stereoisomers than the cis-trans (geometric) isomers previously discussed.
Figure 2.3.1 : Structures of the Trioses. (a) D- and L-glyceraldehyde are mirror images of each other and represent a pair of
enantiomers. (b) A ball-and-stick model of D-glyceraldehyde is reflected in a mirror. Note that the reflection has the same structure
as L-glyceraldehyde.
A key characteristic of enantiomers is that they have a carbon atom to which four different groups are attached. Note, for example,
the four different groups attached to the central carbon atom of glyceraldehyde (part (a) of Figure 2.3.1). A carbon atom that has
four different groups attached is a chiral carbon. If a molecule contains one or more chiral carbons, it is likely to exist as two or
more stereoisomers. Dihydroxyacetone does not contain a chiral carbon and thus does not exist as a pair of stereoisomers.
Glyceraldehyde, however, has a chiral carbon and exists as a pair of enantiomers. Except for the direction in which each
enantiomer rotates plane-polarized light, these two molecules have identical physical properties. One enantiomer has a specific
rotation of +8.7°, while the other has a specific rotation of −8.7°.
H. Emil Fischer, a German chemist, developed the convention commonly used for writing two-dimensional representations of the
monosaccharides, such as those in part (a) of Figure 2.3.1. In these structural formulas, the aldehyde group is written at the top, and
the hydrogen atoms and OH groups that are attached to each chiral carbon are written to the right or left. (If the monosaccharide is
a ketose, the ketone functional group is the second carbon atom.) Vertical lines represent bonds pointing away from you, while
horizontal lines represent bonds coming toward you. The formulas of chiral molecules represented in this manner are referred to as
Fischer projections.
The two enantiomers of glyceraldehyde are especially important because monosaccharides with more than three carbon atoms can
be considered as being derived from them. Thus, D- and L-glyceraldehyde provide reference points for designating and drawing all
other monosaccharides. Sugars whose Fischer projections terminate in the same configuration as D-glyceraldehyde are designated
as D sugars; those derived from L-glyceraldehyde are designated as L sugars.
By convention, the penultimate (next-to-last) carbon atom has been chosen as the carbon
atom that determines if a sugar is D or L. It is the chiral carbon farthest from the
aldehyde or ketone functional group.
Looking Closer: Polarized Light
A beam of ordinary light can be pictured as a bundle of waves; some move up and down, some sideways, and others at all other
conceivable angles. When a beam of light has been polarized, however, the waves in the bundle all vibrate in a single plane.
Light altered in this way is called plane-polarized light. Much of what chemists know about stereoisomers comes from studying
the effects they have on plane-polarized light. In this illustration, the light on the left is not polarized, while that on the right is
polarized.
Sunlight, in general, is not polarized; light from an ordinary light bulb or an ordinary flashlight is not polarized. One way to
polarize ordinary light is to pass it through Polaroid sheets, special plastic sheets containing carefully oriented organic
compounds that permit only light vibrating in a single plane to pass through. To the eye, polarized light doesn’t “look” any
different from nonpolarized light. We can detect polarized light, however, by using a second sheet of polarizing material, as
shown here.
In the photo on the left, two Polaroid sheets are aligned in the same direction; plane-polarized light from the first Polaroid sheet
can pass through the second sheet. In the photo on the right, the top Polaroid sheet has been rotated 90° and now blocks the
plane-polarized light that comes through the first Polaroid sheet.
Certain substances act on polarized light by rotating the plane of vibration. Such substances are said to be optically active. The
extent of optical activity is measured by a polarimeter, an instrument that contains two polarizing lenses separated by a sample
tube, as shown in the accompanying figure. With the sample tube empty, maximum light reaches the observer’s eye when the two
lenses are aligned so that both pass light vibrating in the same plane. When an optically active substance is placed in the sample
tube, that substance rotates the plane of polarization of the light passing through it, so that the polarized light emerging from the
sample tube is vibrating in a different direction than when it entered the tube. To see the maximum amount of light when the
sample is in place, the observer must rotate one lens to accommodate the change in the plane of polarization.
Figure 2.3.2 : Diagram of a Polarimeter
Some optically active substances rotate the plane of polarized light to the right (clockwise) from the observer’s point of view. These
compounds are said to be dextrorotatory; substances that rotate light to the left (counterclockwise) are levorotatory. To denote the
direction of rotation, a positive sign (+) is given to dextrorotatory substances, and a negative sign (−) is given to levorotatory
substances.
Summary
Monosaccharides can be classified by the number of carbon atoms in the structure and/or the type of carbonyl group they contain
(aldose or ketose). Most monosaccharides contain at least one chiral carbon and can form stereoisomers. Enantiomers are a specific
type of stereoisomers that are mirror images of each other.

1. What is a chiral carbon?
2. Describe how enantiomers differ.
Answers
1. A chiral carbon is a carbon atom with four different groups attached to it.
2. Enantiomers are mirror images of each other; they differ in the arrangements of atoms around a chiral carbon.
Exercises
1. Identify each sugar as an aldose or a ketose and then as a triose, tetrose, pentose, or hexose.
a. D-glucose
b. L-ribulose
c. D-glyceraldehyde
2. Identify each sugar as an aldose or a ketose and then as a triose, tetrose, pentose, or hexose.
a. dihydroxyacetone
b. D-ribose
c. D-galactose
3. Identify each sugar as an aldose or a ketose and then as a D sugar or an L sugar.
a.
b.
4. Identify each sugar as an aldose or a ketose and then as a D sugar or an L sugar.
a.
b.
Answers
1. a. aldose; hexose
b. ketose; pentose
c. aldose; triose
3. a. aldose; D sugar
b. ketose; L sugar
2.3: Classes of Monosaccharides is shared under a CC BY-NC-SA 4.0 license and was authored, remixed, and/or curated by LibreTexts.
Learning Objectives
To identify the structures of D-glucose, D-galactose, and D-fructose and describe how they differ from each other.
Although a variety of monosaccharides are found in living organisms, three hexoses are particularly abundant: D-glucose, D-
galactose, and D-fructose (Figure 2.4.1). Glucose and galactose are both aldohexoses, while fructose is a ketohexose.
Figure 2.4.1 : Structures of Three Important Hexoses. Each hexose is pictured with a food source in which it is commonly found.
Source: Photos © Thinkstock.
Glucose
D-Glucose, generally referred to as simply glucose, is the most abundant sugar found in nature; most of the carbohydrates we eat
are eventually converted to it in a series of biochemical reactions that produce energy for our cells. It is also known by three other
names: dextrose, from the fact that it rotates plane-polarized light in a clockwise (dextrorotatory) direction; corn sugar because in
the United States cornstarch is used in the commercial process that produces glucose from the hydrolysis of starch; and blood sugar
because it is the carbohydrate found in the circulatory system of animals. Normal blood sugar values range from 70 to 105 mg
glucose/dL plasma, and normal urine may contain anywhere from a trace to 20 mg glucose/dL urine.
Figure 2.4.2 : Fischer projection of D-glucose

The Fischer projection of D-glucose is given in Figure 2.4.2. Glucose is a D sugar because the OH group on the fifth carbon atom
(the chiral center farthest from the carbonyl group) is on the right. In fact, all the OH groups except the one on the third carbon
atom are to the right.
Galactose
D-Galactose does not occur in nature in the uncombined state. It is released when lactose, a disaccharide found in milk, is
hydrolyzed. The galactose needed by the human body for the synthesis of lactose is obtained by the metabolic conversion of D-
glucose to D-galactose. Galactose is also an important constituent of the glycolipids that occur in the brain and the myelin sheath of
nerve cells. For this reason it is also known as brain sugar. The structure of D-galactose is shown in Figure 2.4.1. Notice that the
configuration differs from that of glucose only at the fourth carbon atom.
Fructose
D-Fructose, also shown in Figure 2.4.1, is the most abundant ketohexose. Note that from the third through the sixth carbon atoms,
its structure is the same as that of glucose. It occurs, along with glucose and sucrose, in honey (which is 40% fructose) and sweet
fruits. Fructose (from the Latin fructus, meaning “fruit”) is also referred to as levulose because it has a specific rotation that is
strongly levorotatory (−92.4°). It is the sweetest sugar, being 1.7 times sweeter than sucrose, although many nonsugars are several
hundred or several thousand times as sweet (Table 2.4.1).
Table 2.4.1 : The Relative Sweetness of Some Compounds (Sucrose = 100)
Compound Relative Sweetness
lactose 16
maltose 32
glucose 74
sucrose 100
fructose 173
aspartame 18,000
acesulfame K 20,000
saccharin 30,000
sucralose 60,000
Looking Closer: Artificial Sweeteners

Although sweetness is commonly associated with mono- and disaccharides, it is not a property found only in sugars. Several
other kinds of organic compounds have been synthesized that are far superior as sweetening agents. These so-called high-
intensity or artificial sweeteners are useful for people with diabetes or other medical conditions that require them to control their
carbohydrate intake. The synthetic compounds are noncaloric or used in such small quantities that they do not add significantly
to the caloric value of food.
The first artificial sweetener—saccharin—was discovered by accident in 1879. It is 300 times sweeter than sucrose, but it passes
through the body unchanged and thus adds no calories to the diet. After its discovery, saccharin was used until it was banned in
the early 1900s. However, during the sugar-short years of World War I, the ban was lifted and was not reinstated at the war’s
end. One drawback to the use of saccharin is its bitter, metallic aftertaste. The initial solution to this problem was to combine
saccharin with cyclamate, a second artificial sweetener discovered in 1937.
In the 1960s and 1970s, several clinical tests with laboratory animals implicated both cyclamate and saccharin as carcinogenic
(cancer-causing) substances. The results from the cyclamate tests were completed first, and cyclamate was banned in the United
States in 1969. Then a major study was released in Canada in 1977 indicating that saccharin increased the incidence of bladder
cancer in rats. The US Food and Drug Administration (FDA) proposed a ban on saccharin that raised immediate public
opposition because saccharin was the only artificial sweetener still available. In response, Congress passed the Saccharin Study
and Labeling Act in 1977, permitting the use of saccharin as long as any product containing it was labeled with a consumer
warning regarding the possible elevation of the risk of bladder cancer. Today this warning is no longer required; moreover, the
FDA is currently reviewing the ban on cyclamate, as 75 additional studies and years of usage in other countries, such as Canada,
have failed to show that it has any carcinogenic effect.
A third artificial sweetener, aspartame, was discovered in 1965. This white crystalline compound is about 180 times sweeter
than sucrose and has no aftertaste. It was approved for use in 1981 and is used to sweeten a wide variety of foods because it
blends well with other food flavors. Aspartame is not used in baked goods, however, because it is not heat stable.
In the body (or when heated), aspartame is initially hydrolyzed to three molecules: the amino acids aspartic acid and
phenylalanine and an alcohol methanol. Repeated controversy regarding the safety of aspartame arises partly from the fact that
the body metabolizes the released methanol to formaldehyde. It should be noted, though, that a glass of tomato juice has six
times as much methanol as a similar amount of a diet soda containing aspartame. The only documented risk connected to
aspartame use is for individuals with the genetic disease phenylketonuria (PKU); these individuals lack the enzyme needed to
metabolize the phenylalanine released when aspartame is broken down by the body. Because of the danger to people with PKU,
all products containing aspartame must carry a warning label.
Acesulfame K, discovered just two years after aspartame (1967), was approved for use in the United States in 1988. It is 200
times sweeter than sugar and, unlike aspartame, is heat stable. It has no lingering aftertaste.
One of the newest artificial sweeteners to gain FDA approval (April 1998) for use in the United States is sucralose, a white
crystalline solid approximately 600 times sweeter than sucrose. Sucralose is synthesized from sucrose and has three chlorine
atoms substituted for three OH groups. It is noncaloric because it passes through the body unchanged. It can be used in baking
because it is heat stable.
All of the extensive clinical studies completed to date have indicated that these artificial sweeteners approved for use in the
United States are safe for consumption by healthy individuals in moderate amounts.
Summary
Three abundant hexoses in living organisms are the aldohexoses D-glucose and D-galactose and the ketohexose D-fructose.

1. Describe the similarities and differences in the structures of D-glucose and D-galactose.
2. Describe similarities and differences in the structures of D-glucose and D-fructose.
Answers
1. Both monosaccharides are aldohexoses. The two monosaccharides differ in the configuration around the fourth carbon atom.
2. Both monosaccharides are hexoses. D-glucose is an aldohexose, while D-fructose is a ketohexose.
Exercises
1. Identify each sugar by its common chemical name.
a. blood sugar
b. levulose
a. dextrose
b. brain sugar
3. Identify each sugar as an aldohexose or a ketohexose.
a. glucose
b. galactose
c. fructose
4. What hexose would you expect to be most abundant in each food?
a. honey
b. milk
c. cornstarch
Answers
1. a. D-glucose
b. D-fructose
3. a. aldohexose
b. aldohexose
c. ketohexose
2.4: Important Hexoses is shared under a CC BY-NC-SA 4.0 license and was authored, remixed, and/or curated by LibreTexts.
Learning Objectives
Define what is meant by anomers and describe how they are formed.
Explain what is meant by mutarotation.
So far we have represented monosaccharides as linear molecules, but many of them also adopt cyclic structures. This conversion
occurs because of the ability of aldehydes and ketones to react with alcohols:
You might wonder why the aldehyde reacts with the OH group on the fifth carbon atom rather than the OH group on the second
carbon atom next to it. Recall that cyclic alkanes containing five or six carbon atoms in the ring are the most stable. The same is
true for monosaccharides that form cyclic structures: rings consisting of five or six carbon atoms are the most stable.
Figure 2.5.1 : Cyclization of D-Glucose. D-Glucose can be represented with a Fischer projection (a) or three dimensionally (b). By
reacting the OH group on the fifth carbon atom with the aldehyde group, the cyclic monosaccharide (c) is produced.
When a straight-chain monosaccharide, such as any of the structures shown in Figure 2.5.1, forms a cyclic structure, the carbonyl
oxygen atom may be pushed either up or down, giving rise to two stereoisomers, as shown in Figure 2.5.2. The structure shown on
the left side of Figure 2.5.2, with the OH group on the first carbon atom projected downward, represent what is called the alpha (α)
form. The structures on the right side, with the OH group on the first carbon atom pointed upward, is the beta (β) form. These two
stereoisomers of a cyclic monosaccharide are known as anomers; they differ in structure around the anomeric carbon—that is, the
carbon atom that was the carbonyl carbon atom in the straight-chain form.
It is possible to obtain a sample of crystalline glucose in which all the molecules have the α structure or all have the β structure.
The α form melts at 146°C and has a specific rotation of +112°, while the β form melts at 150°C and has a specific rotation of
+18.7°. When the sample is dissolved in water, however, a mixture is soon produced containing both anomers as well as the
straight-chain form, in dynamic equilibrium (part (a) of Figure 2.5.2). You can start with a pure crystalline sample of glucose
consisting entirely of either anomer, but as soon as the molecules dissolve in water, they open to form the carbonyl group and then
reclose to form either the α or the β anomer. The opening and closing repeats continuously in an ongoing interconversion between
anomeric forms and is referred to as mutarotation (Latin mutare, meaning “to change”). At equilibrium, the mixture consists of
about 36% α-D-glucose, 64% β-D-glucose, and less than 0.02% of the open-chain aldehyde form. The observed rotation of this
solution is +52.7°.
Figure 2.5.2 : Monosaccharides. In an aqueous solution, monosaccharides exist as an equilibrium mixture of three forms. The
interconversion between the forms is known as mutarotation, which is shown for D-glucose (a) and D-fructose (b).
Even though only a small percentage of the molecules are in the open-chain aldehyde form at any time, the solution will
nevertheless exhibit the characteristic reactions of an aldehyde. As the small amount of free aldehyde is used up in a reaction, there
is a shift in the equilibrium to yield more aldehyde. Thus, all the molecules may eventually react, even though very little free
aldehyde is present at a time.
Commonly, (e.g., in Figures 2.5.1 and 2.5.2) the cyclic forms of sugars are depicted using a convention first suggested by Walter
N. Haworth, an English chemist. The molecules are drawn as planar hexagons with a darkened edge representing the side facing
toward the viewer. The structure is simplified to show only the functional groups attached to the carbon atoms. Any group written
to the right in a Fischer projection appears below the plane of the ring in a Haworth projection, and any group written to the left in
a Fischer projection appears above the plane in a Haworth projection.
The difference between the α and the β forms of sugars may seem trivial, but such structural differences are often crucial in
biochemical reactions. This explains why we can get energy from the starch in potatoes and other plants but not from cellulose,
even though both starch and cellulose are polysaccharides composed of glucose molecules linked together.
Summary
Monosaccharides that contain five or more carbons atoms form cyclic structures in aqueous solution. Two cyclic stereoisomers can
form from each straight-chain monosaccharide; these are known as anomers. In an aqueous solution, an equilibrium mixture forms
between the two anomers and the straight-chain structure of a monosaccharide in a process known as mutarotation.

1. Define each term.
a. mutarotation
b. anomer
c. anomeric carbon
2. How can you prove that a solution of α-D-glucose exhibits mutarotation?
Answers
1.
a. the ongoing interconversion between anomers of a particular carbohydrate to form an equilibrium mixture
b. a stereoisomer that differs in structure around what was the carbonyl carbon atom in the straight-chain form of a
monosaccharide
c. the carbon atom that was the carbonyl carbon atom in the straight-chain form of a monosaccharide
2. Place a sample of pure α-D-glucose in a polarimeter and measure its observed rotation. This value will change as mutarotation
occurs.
Exercises
1. Draw the cyclic structure for β-D-glucose. Identify the anomeric carbon.
2. Draw the cyclic structure for α-D-fructose. Identify the anomeric carbon.
3. Given that the aldohexose D-mannose differs from D-glucose only in the configuration at the second carbon atom, draw the
cyclic structure for α-D-mannose.
4. Given that the aldohexose D-allose differs from D-glucose only in the configuration at the third carbon atom, draw the cyclic
structure for β-D-allose.
Answers
1.
3.
2.5: Cyclic Structures of Monosaccharides is shared under a CC BY-NC-SA 4.0 license and was authored, remixed, and/or curated by LibreTexts.
Learning Objectives
To identify the physical and chemical properties of monosaccharides.
Monosaccharides such as glucose and fructose are crystalline solids at room temperature, but they are quite soluble in water, each
molecule having several OH groups that readily engage in hydrogen bonding. The chemical behavior of these monosaccharides is
likewise determined by their functional groups.
An important reaction of monosaccharides is the oxidation of the aldehyde group, one of the most easily oxidized organic
functional groups. Aldehyde oxidation can be accomplished with any mild oxidizing agent, such as Tollens’ reagent or Benedict’s
reagent. With the latter, complexed copper(II) ions are reduced to copper(I) ions that form a brick-red precipitate [copper(I) oxide;
Figure 2.6.1].
Any carbohydrate capable of reducing either Tollens’ or Benedict’s reagents without first undergoing hydrolysis is said to be a
reducing sugar. Because both the Tollens’ and Benedict’s reagents are basic solutions, ketoses (such as fructose) also give positive
tests due to an equilibrium that exists between ketoses and aldoses in a reaction known as tautomerism.
Figure 2.6.1 : Benedict’s Test. Benedict’s test was performed on three carbohydrates, depicted from left to right: fructose, glucose,
and sucrose. The solution containing sucrose remains blue because sucrose is a nonreducing sugar.
These reactions have been used as simple and rapid diagnostic tests for the presence of glucose in blood or urine. For example,
Clinitest tablets, which are used to test for sugar in the urine, contain copper(II) ions and are based on Benedict’s test. A green color
indicates very little sugar, whereas a brick-red color indicates sugar in excess of 2 g/100 mL of urine.
Summary
Monosaccharides are crystalline solids at room temperature and quite soluble in water. Monosaccharides are reducing sugars; they
reduce mild oxidizing agents, such as Tollens’ or Benedict’s reagents.

1. Why are monosaccharides soluble in water?
2. What is a reducing sugar?
Answers
1. Monosaccharides are quite soluble in water because of the numerous OH groups that readily engage in hydrogen bonding with
water.
2. any carbohydrate capable of reducing a mild oxidizing agent, such as Tollens’ or Benedict’s reagents, without first undergoing
hydrolysis
Exercises
1. Which gives a positive Benedict’s test—L-galactose, levulose, or D-glucose?
2. Which gives a positive Benedict’s test—D-glyceraldehyde, corn sugar, or L-fructose?
3. D-Galactose can be oxidized at the sixth carbon atom to yield D-galacturonic acid and at both the first and sixth carbon atoms
to yield D-galactaric acid. Draw the Fischer projection for each oxidation product.
4. D-Glucose can be oxidized at the first carbon atom to form D-gluconic acid, at the sixth carbon atom to yield D-glucuronic
acid, and at both the first and sixth carbon atoms to yield D-glucaric acid. Draw the Fischer projection for each oxidation
product.
Answers
1. All three will give a positive Benedict’s test because they are all monosaccharides.
3.
2.6: Properties of Monosaccharides is shared under a CC BY-NC-SA 4.0 license and was authored, remixed, and/or curated by LibreTexts.
2.7: Disaccharides
Learning Objectives
Identify the structures of sucrose, lactose, and maltose.
Identify the monosaccharides that are needed to form sucrose, lactose, and maltose
Previously, you learned that monosaccharides can form cyclic structures by the reaction of the carbonyl group with an OH group.
These cyclic molecules can in turn react with another alcohol. Disaccharides (C12H22O11) are sugars composed of two
monosaccharide units that are joined by a carbon–oxygen-carbon linkage known as a glycosidic linkage. This linkage is formed
from the reaction of the anomeric carbon of one cyclic monosaccharide with the OH group of a second monosaccharide.
The disaccharides differ from one another in their monosaccharide constituents and in the specific type of glycosidic linkage
connecting them. There are three common disaccharides: maltose, lactose, and sucrose. All three are white crystalline solids at
room temperature and are soluble in water. We’ll consider each sugar in more detail.
Maltose
Maltose occurs to a limited extent in sprouting grain. It is formed most often by the partial hydrolysis of starch and glycogen. In the
manufacture of beer, maltose is liberated by the action of malt (germinating barley) on starch; for this reason, it is often referred to
as malt sugar. Maltose is about 30% as sweet as sucrose. The human body is unable to metabolize maltose or any other
disaccharide directly from the diet because the molecules are too large to pass through the cell membranes of the intestinal wall.
Therefore, an ingested disaccharide must first be broken down by hydrolysis into its two constituent monosaccharide units.
In the body, such hydrolysis reactions are catalyzed by enzymes such as maltase. The same reactions can be carried out in the
laboratory with dilute acid as a catalyst, although in that case the rate is much slower, and high temperatures are required. Whether
it occurs in the body or a glass beaker, the hydrolysis of maltose produces two molecules of D-glucose.
+
H or maltase
maltose −−−−−−−−→ 2 D-glucose (16.6.2)
Maltose is a reducing sugar. Thus, its two glucose molecules must be linked in such a way as to leave one anomeric carbon that can
open to form an aldehyde group. The glucose units in maltose are joined in a head-to-tail fashion through an α-linkage from the
first carbon atom of one glucose molecule to the fourth carbon atom of the second glucose molecule (that is, an α-1,4-glycosidic
linkage; see Figure 2.7.1). The bond from the anomeric carbon of the first monosaccharide unit is directed downward, which is
why this is known as an α-glycosidic linkage. The OH group on the anomeric carbon of the second glucose can be in either the α or
the β position, as shown in Figure 2.7.1.
Figure 2.7.1 : An Equilibrium Mixture of Maltose Isomers
Lactose
Lactose is known as milk sugar because it occurs in the milk of humans, cows, and other mammals. In fact, the natural synthesis of
lactose occurs only in mammary tissue, whereas most other carbohydrates are plant products. Human milk contains about 7.5%
lactose, and cow’s milk contains about 4.5%. This sugar is one of the lowest ranking in terms of sweetness, being about one-sixth
as sweet as sucrose. Lactose is produced commercially from whey, a by-product in the manufacture of cheese. It is important as an
infant food and in the production of penicillin.
Lactose is a reducing sugar composed of one molecule of D-galactose and one molecule of D-glucose joined by a β-1,4-glycosidic
bond (the bond from the anomeric carbon of the first monosaccharide unit being directed upward). The two monosaccharides are
obtained from lactose by acid hydrolysis or the catalytic action of the enzyme lactase:
Many adults and some children suffer from a deficiency of lactase. These individuals are said to be lactose intolerant because they
cannot digest the lactose found in milk. A more serious problem is the genetic disease galactosemia, which results from the absence
of an enzyme needed to convert galactose to glucose. Certain bacteria can metabolize lactose, forming lactic acid as one of the
products. This reaction is responsible for the “souring” of milk.
Example 2.7.1
For this trisaccharide, indicate whether each glycosidic linkage is α or β.
SOLUTION
The glycosidic linkage between sugars 1 and 2 is β because the bond is directed up from the anomeric carbon. The glycosidic
linkage between sugars 2 and 3 is α because the bond is directed down from the anomeric carbon.
Exercise 2.7.1
For this trisaccharide, indicate whether each glycosidic linkage is α or β.
To Your Health: Lactose Intolerance and Galactosemia

Lactose makes up about 40% of an infant’s diet during the first year of life. Infants and small children have one form of the
enzyme lactase in their small intestines and can digest the sugar easily; however, adults usually have a less active form of the
enzyme, and about 70% of the world’s adult population has some deficiency in its production. As a result, many adults
experience a reduction in the ability to hydrolyze lactose to galactose and glucose in their small intestine. For some people the
inability to synthesize sufficient enzyme increases with age. Up to 20% of the US population suffers some degree of lactose
intolerance.
In people with lactose intolerance, some of the unhydrolyzed lactose passes into the colon, where it tends to draw water from the
interstitial fluid into the intestinal lumen by osmosis. At the same time, intestinal bacteria may act on the lactose to produce
organic acids and gases. The buildup of water and bacterial decay products leads to abdominal distention, cramps, and diarrhea,
which are symptoms of the condition.
The symptoms disappear if milk or other sources of lactose are excluded from the diet or consumed only sparingly.
Alternatively, many food stores now carry special brands of milk that have been pretreated with lactase to hydrolyze the lactose.
Cooking or fermenting milk causes at least partial hydrolysis of the lactose, so some people with lactose intolerance are still able
to enjoy cheese, yogurt, or cooked foods containing milk. The most common treatment for lactose intolerance, however, is the
use of lactase preparations (e.g., Lactaid), which are available in liquid and tablet form at drugstores and grocery stores. These
are taken orally with dairy foods—or may be added to them directly—to assist in their digestion.
Galactosemia is a condition in which one of the enzymes needed to convert galactose to glucose is missing. Consequently, the
blood galactose level is markedly elevated, and galactose is found in the urine. An infant with galactosemia experiences a lack
of appetite, weight loss, diarrhea, and jaundice. The disease may result in impaired liver function, cataracts, mental retardation,
and even death. If galactosemia is recognized in early infancy, its effects can be prevented by the exclusion of milk and all other
sources of galactose from the diet. As a child with galactosemia grows older, he or she usually develops an alternate pathway for
metabolizing galactose, so the need to restrict milk is not permanent. The incidence of galactosemia in the United States is 1 in
every 65,000 newborn babies.
Sucrose
Sucrose, probably the largest-selling pure organic compound in the world, is known as beet sugar, cane sugar, table sugar, or
simply sugar. Most of the sucrose sold commercially is obtained from sugar cane and sugar beets (whose juices are 14%–20%
sucrose) by evaporation of the water and recrystallization. The dark brown liquid that remains after the recrystallization of sugar is
sold as molasses.
The sucrose molecule is unique among the common disaccharides in having an α-1,β-2-glycosidic (head-to-head) linkage. Because
this glycosidic linkage is formed by the OH group on the anomeric carbon of α-D-glucose and the OH group on the anomeric
carbon of β-D-fructose, it ties up the anomeric carbons of both glucose and fructose.
This linkage gives sucrose certain properties that are quite different from those of maltose and lactose. As long as the sucrose
molecule remains intact, neither monosaccharide “uncyclizes” to form an open-chain structure. Thus, sucrose is incapable of
mutarotation and exists in only one form both in the solid state and in solution. In addition, sucrose does not undergo reactions that
are typical of aldehydes and ketones. Therefore, sucrose is a nonreducing sugar.
The hydrolysis of sucrose in dilute acid or through the action of the enzyme sucrase (also known as invertase) gives an equimolar
mixture of glucose and fructose. This 1:1 mixture is referred to as invert sugar because it rotates plane-polarized light in the
opposite direction than sucrose. The hydrolysis reaction has several practical applications. Sucrose readily recrystallizes from a
solution, but invert sugar has a much greater tendency to remain in solution. In the manufacture of jelly and candy and in the
canning of fruit, the recrystallization of sugar is undesirable. Therefore, conditions leading to the hydrolysis of sucrose are
employed in these processes. Moreover, because fructose is sweeter than sucrose, the hydrolysis adds to the sweetening effect. Bees
carry out this reaction when they make honey.
The average American consumes more than 100 lb of sucrose every year. About two-thirds of this amount is ingested in soft drinks,
presweetened cereals, and other highly processed foods. The widespread use of sucrose is a contributing factor to obesity and tooth
decay. Carbohydrates such as sucrose, are converted to fat when the caloric intake exceeds the body’s requirements, and sucrose
causes tooth decay by promoting the formation of plaque that sticks to teeth.
Summary
Maltose is composed of two molecules of glucose joined by an α-1,4-glycosidic linkage. It is a reducing sugar that is found in
sprouting grain. Lactose is composed of a molecule of galactose joined to a molecule of glucose by a β-1,4-glycosidic linkage. It is
a reducing sugar that is found in milk. Sucrose is composed of a molecule of glucose joined to a molecule of fructose by an
α-1,β-2-glycosidic linkage. It is a nonreducing sugar that is found in sugar cane and sugar beets.
Concept Review Exercise

1. What monosaccharides are obtained by the hydrolysis of each disaccharide?
a. sucrose
b. maltose
c. lactose
Answer
1.
a. D-glucose and D-fructose
b. two molecules of D-glucose
c. D-glucose and D-galactose
Exercises
a. milk sugar
b. table sugar
a. cane sugar
b. malt sugar
3. For each disaccharide, indicate whether the glycosidic linkage is α or β.
a.
b.
4. For each disaccharide, indicate whether the glycosidic linkage is α or β.
a.
b.
5. Identify each disaccharide in Exercise 3 as a reducing or nonreducing sugar. If it is a reducing sugar, draw its structure and
circle the anomeric carbon. State if the OH group at the anomeric carbon is in the α or the β position.
6. Identify each disaccharide in Exercise 4 as a reducing or nonreducing sugar. If it is a reducing sugar, draw its structure and
circle the anomeric carbon. State if the OH group at the anomeric carbon is in the α or β position.
7. Melibiose is a disaccharide that occurs in some plant juices. Its structure is as follows:
a. What monosaccharide units are incorporated into melibiose?

b. What type of linkage (α or β) joins the two monosaccharide units of melibiose?
c. Melibiose has a free anomeric carbon and is thus a reducing sugar. Circle the anomeric carbon and indicate whether the OH
group is α or β.
8. Cellobiose is a disaccharide composed of two glucose units joined by a β-1,4-glycosidic linkage.
a. Draw the structure of cellobiose.
b. Is cellobiose a reducing or nonreducing sugar? Justify your answer.
Answers
1.
a. lactose
b. sucrose
3.
a.
b.
5. 3a: nonreducing; 3b: reducing
7.
a. galactose and glucose
b. α-glycosidic linkage
c.
2.7: Disaccharides is shared under a CC BY-NC-SA 4.0 license and was authored, remixed, and/or curated by LibreTexts.
Learning Objectives
To compare and contrast the structures and uses of starch, glycogen, and cellulose.
The polysaccharides are the most abundant carbohydrates in nature and serve a variety of functions, such as energy storage or as
components of plant cell walls. Polysaccharides are very large polymers composed of tens to thousands of monosaccharides joined
together by glycosidic linkages. The three most abundant polysaccharides are starch, glycogen, and cellulose. These three are
referred to as homopolymers because each yields only one type of monosaccharide (glucose) after complete hydrolysis.
Heteropolymers may contain sugar acids, amino sugars, or noncarbohydrate substances in addition to monosaccharides.
Heteropolymers are common in nature (gums, pectins, and other substances) but will not be discussed further in this textbook. The
polysaccharides are nonreducing carbohydrates, are not sweet tasting, and do not undergo mutarotation.
Starch
Starch is the most important source of carbohydrates in the human diet and accounts for more than 50% of our carbohydrate intake.
It occurs in plants in the form of granules, and these are particularly abundant in seeds (especially the cereal grains) and tubers,
where they serve as a storage form of carbohydrates. The breakdown of starch to glucose nourishes the plant during periods of
reduced photosynthetic activity. We often think of potatoes as a “starchy” food, yet other plants contain a much greater percentage
of starch (potatoes 15%, wheat 55%, corn 65%, and rice 75%). Commercial starch is a white powder.
Starch is a mixture of two polymers: amylose and amylopectin. Natural starches consist of about 10%–30% amylose and 70%–90%
amylopectin. Amylose is a linear polysaccharide composed entirely of D-glucose units joined by the α-1,4-glycosidic linkages we
saw in maltose (part (a) of Figure 2.8.1). Experimental evidence indicates that amylose is not a straight chain of glucose units but
instead is coiled like a spring, with six glucose monomers per turn (part (b) of Figure 2.8.1). When coiled in this fashion, amylose
has just enough room in its core to accommodate an iodine molecule. The characteristic blue-violet color that appears when starch
is treated with iodine is due to the formation of the amylose-iodine complex. This color test is sensitive enough to detect even
minute amounts of starch in solution.
Figure 2.8.1 : Amylose. (a) Amylose is a linear chain of α-D-glucose units joined together by α-1,4-glycosidic bonds. (b) Because
of hydrogen bonding, amylose acquires a spiral structure that contains six glucose units per turn.
Amylopectin is a branched-chain polysaccharide composed of glucose units linked primarily by α-1,4-glycosidic bonds but with
occasional α-1,6-glycosidic bonds, which are responsible for the branching. A molecule of amylopectin may contain many
thousands of glucose units with branch points occurring about every 25–30 units (Figure 2.8.2). The helical structure of
amylopectin is disrupted by the branching of the chain, so instead of the deep blue-violet color amylose gives with iodine,
amylopectin produces a less intense reddish brown.
Figure 2.8.2 : Representation of the Branching in Amylopectin and Glycogen. Both amylopectin and glycogen contain branch
points that are linked through α-1,6-linkages. These branch points occur more often in glycogen.
Dextrins are glucose polysaccharides of intermediate size. The shine and stiffness imparted to clothing by starch are due to the
presence of dextrins formed when clothing is ironed. Because of their characteristic stickiness with wetting, dextrins are used as
adhesives on stamps, envelopes, and labels; as binders to hold pills and tablets together; and as pastes. Dextrins are more easily
digested than starch and are therefore used extensively in the commercial preparation of infant foods.
The complete hydrolysis of starch yields, in successive stages, glucose:
starch → dextrins → maltose → glucose
In the human body, several enzymes known collectively as amylases degrade starch sequentially into usable glucose units.
Glycogen
Glycogen is the energy reserve carbohydrate of animals. Practically all mammalian cells contain some stored carbohydrates in the
form of glycogen, but it is especially abundant in the liver (4%–8% by weight of tissue) and in skeletal muscle cells (0.5%–1.0%).
Like starch in plants, glycogen is found as granules in liver and muscle cells. When fasting, animals draw on these glycogen
reserves during the first day without food to obtain the glucose needed to maintain metabolic balance.
Glycogen is structurally quite similar to amylopectin, although glycogen is more highly branched (8–12 glucose units between
branches) and the branches are shorter. When treated with iodine, glycogen gives a reddish brown color. Glycogen can be broken
down into its D-glucose subunits by acid hydrolysis or by the same enzymes that catalyze the breakdown of starch. In animals, the
enzyme phosphorylase catalyzes the breakdown of glycogen to phosphate esters of glucose.
About 70% of the total glycogen in the body is stored in muscle cells. Although the
percentage of glycogen (by weight) is higher in the liver, the much greater mass of
skeletal muscle stores a greater total amount of glycogen.
Cellulose
Cellulose, a fibrous carbohydrate found in all plants, is the structural component of plant cell walls. Because the earth is covered
with vegetation, cellulose is the most abundant of all carbohydrates, accounting for over 50% of all the carbon found in the
vegetable kingdom. Cotton fibrils and filter paper are almost entirely cellulose (about 95%), wood is about 50% cellulose, and the
dry weight of leaves is about 10%–20% cellulose. The largest use of cellulose is in the manufacture of paper and paper products.
Although the use of noncellulose synthetic fibers is increasing, rayon (made from cellulose) and cotton still account for over 70%
of textile production.
Like amylose, cellulose is a linear polymer of glucose. It differs, however, in that the glucose units are joined by β-1,4-glycosidic
linkages, producing a more extended structure than amylose (part (a) of Figure 2.8.3). This extreme linearity allows a great deal of
hydrogen bonding between OH groups on adjacent chains, causing them to pack closely into fibers (part (b) of Figure 2.8.3). As a
result, cellulose exhibits little interaction with water or any other solvent. Cotton and wood, for example, are completely insoluble
in water and have considerable mechanical strength. Because cellulose does not have a helical structure, it does not bind to iodine
to form a colored product.
Figure 2.8.3 : Cellulose. (a) There is extensive hydrogen bonding in the structure of cellulose. (b) In this electron micrograph of the
cell wall of an alga, the wall consists of successive layers of cellulose fibers in parallel arrangement.
Cellulose yields D-glucose after complete acid hydrolysis, yet humans are unable to metabolize cellulose as a source of glucose.
Our digestive juices lack enzymes that can hydrolyze the β-glycosidic linkages found in cellulose, so although we can eat potatoes,
we cannot eat grass. However, certain microorganisms can digest cellulose because they make the enzyme cellulase, which
catalyzes the hydrolysis of cellulose. The presence of these microorganisms in the digestive tracts of herbivorous animals (such as
cows, horses, and sheep) allows these animals to degrade the cellulose from plant material into glucose for energy. Termites also
contain cellulase-secreting microorganisms and thus can subsist on a wood diet. This example once again demonstrates the extreme
stereospecificity of biochemical processes.
Career Focus: Certified Diabetes Educator
Certified diabetes educators come from a variety of health professions, such as nursing and dietetics, and specialize in the
education and treatment of patients with diabetes. A diabetes educator will work with patients to manage their diabetes. This
involves teaching the patient to monitor blood sugar levels, make good food choices, develop and maintain an exercise program,
and take medication, if required.
A certified diabetes educator at Naval Medical Center Portsmouth (left) and a registered dietician at the medical center
(center), provide nutritional information to a diabetes patient and her mother at the Diabetes Boot Camp.
Diabetes educators also work with hospital or nursing home staff to improve the care of diabetic patients. Educators must be
willing to spend time attending meetings and reading the current literature to maintain their knowledge of diabetes medications,
nutrition, and blood monitoring devices so that they can pass this information to their patients.
Summary
Starch is a storage form of energy in plants. It contains two polymers composed of glucose units: amylose (linear) and amylopectin
(branched). Glycogen is a storage form of energy in animals. It is a branched polymer composed of glucose units. It is more highly
branched than amylopectin. Cellulose is a structural polymer of glucose units found in plants. It is a linear polymer with the
glucose units linked through β-1,4-glycosidic bonds.

1. What purposes do starch and cellulose serve in plants?
2. What purpose does glycogen serve in animals?
Answers
1. Starch is the storage form of glucose (energy) in plants, while cellulose is a structural component of the plant cell wall.
2. Glycogen is the storage form of glucose (energy) in animals.
Exercises
1. What monosaccharide is obtained from the hydrolysis of each carbohydrate?
a. starch
b. cellulose
c. glycogen
2. For each carbohydrate listed in Exercise 1, indicate whether it is found in plants or mammals.
3. Describe the similarities and differences between amylose and cellulose.
4. Describe the similarities and differences between amylopectin and glycogen.
Answers
1. a. glucose
b. glucose
c. glucose
3. Amylose and cellulose are both linear polymers of glucose units, but the glycosidic linkages between the glucose units differ.
The linkages in amylose are α-1,4-glycosidic linkages, while the linkages in cellulose they are β-1,4-glycosidic linkages.
2.8: Polysaccharides is shared under a CC BY-NC-SA 4.0 license and was authored, remixed, and/or curated by LibreTexts.
Carbohydrates, a large group of biological compounds containing carbon, hydrogen, and oxygen atoms, include sugars, starch,
glycogen, and cellulose. All carbohydrates contain alcohol functional groups, and either an aldehyde or a ketone group (or a
functional group that can be converted to an aldehyde or ketone). The simplest carbohydrates are monosaccharides. Those with
two monosaccharide units are disaccharides, and those with many monosaccharide units are polysaccharides. Most sugars are
either monosaccharides or disaccharides. Cellulose, glycogen, and starch are polysaccharides.
Many carbohydrates exist as stereoisomers, in which the three-dimensional spatial arrangement of the atoms in space is the only
difference between the isomers. These particular stereoisomers contain at least one chiral carbon, a carbon atom that has four
different groups bonded to it. A molecule containing a chiral carbon is nonsuperimposable on its mirror image, and two molecules
that are nonsuperimposable mirror images of each other are a special type of stereoisomer called enantiomers. Enantiomers have
the same physical properties, such as melting point, but differ in the direction they rotate polarized light.
A sugar is designated as being a D sugar or an L sugar according to how, in a Fischer projection of the molecule, the hydrogen
atom and OH group are attached to the penultimate carbon atom, which is the carbon atom immediately before the terminal alcohol
carbon atom. If the structure at this carbon atom is the same as that of D-glyceraldehyde (OH to the right), the sugar is a D sugar; if
the configuration is the same as that of L-glyceraldehyde (OH to the left), the sugar is an L sugar.
Monosaccharides of five or more carbons atoms readily form cyclic structures when the carbonyl carbon atom reacts with an OH
group on a carbon atom three or four carbon atoms distant. Consequently, glucose in solution exists as an equilibrium mixture of
three forms, two of them cyclic (α- and β-) and one open chain. In Haworth projections, the alpha form is drawn with the OH
group on the “former” carbonyl carbon atom (anomeric carbon) pointing downward; the beta form, with the OH group pointing
upward; these two compounds are stereoisomers and are given the more specific term of anomers. Any solid sugar can be all alpha
or all beta. Once the sample is dissolved in water, however, the ring opens up into the open-chain structure and then closes to form
either the α- or the β-anomer. These interconversions occur back and forth until a dynamic equilibrium mixture is achieved in a
process called mutarotation.
The carbonyl group present in monosaccharides is easily oxidized by Tollens’ or Benedict’s reagents (as well as others). Any
mono- or disaccharide containing a free anomeric carbon is a reducing sugar. The disaccharide maltose contains two glucose units
joined in an α-1,4-glycosidic linkage. The disaccharide lactose contains a galactose unit and a glucose unit joined by a β-1,4-
glycosidic linkage. Both maltose and lactose contain a free anomeric carbon that can convert to an aldehyde functional group, so
they are reducing sugars; they also undergo mutarotation. Many adults, and some children, have a deficiency of the enzyme lactase
(which is needed to break down lactose) and are said to be lactose intolerant. A more serious problem is the genetic disease
galactosemia, which results from the absence of an enzyme needed to convert galactose to glucose.
The disaccharide sucrose (table sugar) consists of a glucose unit and a fructose unit joined by a glycosidic linkage. The linkage is
designated as an α-1,β-2-glycosidic linkage because it involves the OH group on the first carbon atom of glucose and the OH group
on the second carbon atom of fructose. Sucrose is not a reducing sugar because it has no anomeric carbon that can reform a
carbonyl group, and it cannot undergo mutarotation because of the restrictions imposed by this linkage.
Starch, the principal carbohydrate of plants, is composed of the polysaccharides amylose (10%–30%) and amylopectin (70%–
90%). When ingested by humans and other animals, starch is hydrolyzed to glucose and becomes the body’s energy source.
Glycogen is the polysaccharide animals use to store excess carbohydrates from their diets. Similar in structure to amylopectin,
glycogen is hydrolyzed to glucose whenever an animal needs energy for a metabolic process. The polysaccharide cellulose
provides structure for plant cells. It is a linear polymer of glucose units joined by β-1,4-glycosidic linkages. It is indigestible in the
human body but digestible by many microorganisms, including microorganisms found in the digestive tracts of many herbivores.
2.9: Carbohydrates (Summary) is shared under a CC BY-NC-SA 4.0 license and was authored, remixed, and/or curated by LibreTexts.
CHAPTER OVERVIEW
3: Lipids
3.2: Fatty Acids
3.3: Fats and Oils
3.5: Steroids
3.7: Exercises
3: Lipids is shared under a CC BY-NC-SA 4.0 license and was authored, remixed, and/or curated by LibreTexts.
1
On July 11, 2003, the Food and Drug Administration amended its food labeling regulations to require that manufacturers list the
amount of trans fatty acids on Nutrition Facts labels of foods and dietary supplements, effective January 1, 2006. This
amendment was a response to published studies demonstrating a link between the consumption of trans fatty acids and an
increased risk of heart disease. Trans fatty acids are produced in the conversion of liquid oils to solid fats, as in the creation of
many commercial margarines and shortenings. They have been shown to increase the levels of low-density lipoproteins (LDLs)
—complexes that are often referred to as bad cholesterol—in the blood. In this chapter, you will learn about fatty acids and what
is meant by a trans fatty acid, as well as the difference between fats and oils. You will also learn what cholesterol is and why it
is an important molecule in the human body.
Fats and oils, found in many of the foods we eat, belong to a class of biomolecules known as lipids. Gram for gram, they pack more
than twice the caloric content of carbohydrates: the oxidation of fats and oils supplies about 9 kcal of energy for every gram
oxidized, whereas the oxidation of carbohydrates supplies only 4 kcal/g. Although the high caloric content of fats may be bad news
for the dieter, it says something about the efficiency of nature’s designs. Our bodies use carbohydrates, primarily in the form of
glucose, for our immediate energy needs. Our capacity for storing carbohydrates for later use is limited to tucking away a bit of
glycogen in the liver or in muscle tissue. We store our reserve energy in lipid form, which requires far less space than the same
amount of energy stored in carbohydrate form. Lipids have other biological functions besides energy storage. They are a major
component of the membranes of the 10 trillion cells in our bodies. They serve as protective padding and insulation for vital organs.
Furthermore, without lipids in our diets, we would be deficient in the fat-soluble vitamins A, D, E, and K.
Lipids are not defined by the presence of specific functional groups, as carbohydrates are, but by a physical property—solubility.
Compounds isolated from body tissues are classified as lipids if they are more soluble in organic solvents, such as
dichloromethane, than in water. By this criterion, the lipid category includes not only fats and oils, which are esters of the
trihydroxy alcohol glycerol and fatty acids, but also compounds that incorporate functional groups derived from phosphoric acid,
carbohydrates, or amino alcohols, as well as steroid compounds such as cholesterol (Figure 3.1.1 presents one scheme for
classifying the various kinds of lipids). We will discuss the various kinds of lipids by considering one subclass at a time and
pointing out structural similarities and differences as we go.
Figure 3.1.1 : Lipid Organization Based on Structural Relationships
3.1: Prelude to Lipids is shared under a CC BY-NC-SA 4.0 license and was authored, remixed, and/or curated by LibreTexts.
3.2: Fatty Acids
Learning Objectives
To recognize the structures of common fatty acids and classify them as saturated, monounsaturated, or polyunsaturated.
Fatty acids are carboxylic acids that are structural components of fats, oils, and all other categories of lipids, except steroids. More
than 70 have been identified in nature. They usually contain an even number of carbon atoms (typically 12–20), are generally
unbranched, and can be classified by the presence and number of carbon-to-carbon double bonds. Thus, saturated fatty acids
contain no carbon-to-carbon double bonds, monounsaturated fatty acids contain one carbon-to-carbon double bond, and
polyunsaturated fatty acids contain two or more carbon-to-carbon double bonds.
Table 3.2.1 lists some common fatty acids and one important source for each. The atoms or groups around the double bonds in
unsaturated fatty acids can be arranged in either the cis or trans isomeric form. Naturally occurring fatty acids are generally in the
cis configuration.
Table 3.2.1 : Some Common Fatty Acids Found in Natural Fats
Abbreviated Structural Condensed Structural
Name Melting Point (°C) Source
Formula Formula
lauric acid C11H23COOH CH3(CH2)10COOH 44 palm kernel oil
myristic acid C13H27COOH CH3(CH2)12COOH 58 oil of nutmeg
palmitic acid C15H31COOH CH3(CH2)14COOH 63 palm oil
CH3(CH2)5CH=CH(CH2)7
palmitoleic acid C15H29COOH 0.5 macadamia oil
COOH
stearic acid C17H35COOH CH3(CH2)16COOH 70 cocoa butter
CH3(CH2)7CH=CH(CH2)7
oleic acid C17H33COOH 16 olive oil
COOH
CH3(CH2)3(CH2CH=CH)2
linoleic acid C17H31COOH −5 canola oil
(CH2)7COOH
CH3(CH2CH=CH)3(CH2)7
α-linolenic acid C17H29COOH −11 flaxseed
COOH
CH3(CH2)4(CH2CH=CH)4
arachidonic acid C19H31COOH −50 liver
(CH2)2COOH
Two polyunsaturated fatty acids—linoleic and α-linolenic acids—are termed essential fatty acids because humans must obtain them
from their diets. Both substances are required for normal growth and development, but the human body does not synthesize them.
The body uses linoleic acid to synthesize many of the other unsaturated fatty acids, such as arachidonic acid, a precursor for the
synthesis of prostaglandins. In addition, the essential fatty acids are necessary for the efficient transport and metabolism of
cholesterol. The average daily diet should contain about 4–6 g of the essential fatty acids.
To Your Health: Prostaglandins
Prostaglandins are chemical messengers synthesized in the cells in which their physiological activity is expressed. They are
unsaturated fatty acids containing 20 carbon atoms and are synthesized from arachidonic acid—a polyunsaturated fatty acid—
when needed by a particular cell. They are called prostaglandins because they were originally isolated from semen found in the
prostate gland. It is now known that they are synthesized in nearly all mammalian tissues and affect almost all organs in the
body. The five major classes of prostaglandins are designated as PGA, PGB, PGE, PGF, and PGI. Subscripts are attached at the
end of these abbreviations to denote the number of double bonds outside the five-carbon ring in a given prostaglandin.
The prostaglandins are among the most potent biological substances known. Slight structural differences give them highly
distinct biological effects; however, all prostaglandins exhibit some ability to induce smooth muscle contraction, lower blood
pressure, and contribute to the inflammatory response. Aspirin and other nonsteroidal anti-inflammatory agents, such as
ibuprofen, obstruct the synthesis of prostaglandins by inhibiting cyclooxygenase, the enzyme needed for the initial step in the
conversion of arachidonic acid to prostaglandins.
Their wide range of physiological activity has led to the synthesis of hundreds of prostaglandins and their analogs. Derivatives
of PGE2 are now used in the United States to induce labor. Other prostaglandins have been employed clinically to lower or
increase blood pressure, inhibit stomach secretions, relieve nasal congestion, relieve asthma, and prevent the formation of blood
clots, which are associated with heart attacks and strokes.
Although we often draw the carbon atoms in a straight line, they actually have more of a zigzag configuration (Figure 3.2.2a).
Viewed as a whole, however, the saturated fatty acid molecule is relatively straight (Figure 3.2.2b). Such molecules pack closely
together into a crystal lattice, maximizing the strength of dispersion forces and causing fatty acids and the fats derived from them to
have relatively high melting points. In contrast, each cis carbon-to-carbon double bond in an unsaturated fatty acid produces a
pronounced bend in the molecule, so that these molecules do not stack neatly. As a result, the intermolecular attractions of
unsaturated fatty acids (and unsaturated fats) are weaker, causing these substances to have lower melting points. Most are liquids at
room temperature.
Figure 3.2.2 : The Structure of Saturated Fatty Acids. (a) There is a zigzag pattern formed by the carbon-to-carbon single bonds in
the ball-and-stick model of a palmitic acid molecule. (b) A space-filling model of palmitic acid shows the overall straightness of a
saturated fatty acid molecule.
Waxes are esters formed from long-chain fatty acids and long-chain alcohols. Most natural waxes are mixtures of such esters. Plant
waxes on the surfaces of leaves, stems, flowers, and fruits protect the plant from dehydration and invasion by harmful
microorganisms. Carnauba wax, used extensively in floor waxes, automobile waxes, and furniture polish, is largely myricyl
cerotate, obtained from the leaves of certain Brazilian palm trees. Animals also produce waxes that serve as protective coatings,
keeping the surfaces of feathers, skin, and hair pliable and water repellent. In fact, if the waxy coating on the feathers of a water
bird is dissolved as a result of the bird swimming in an oil slick, the feathers become wet and heavy, and the bird, unable to
maintain its buoyancy, drowns.
Summary
Fatty acids are carboxylic acids that are the structural components of many lipids. They may be saturated or unsaturated. Most fatty
acids are unbranched and contain an even number of carbon atoms. Unsaturated fatty acids have lower melting points than
saturated fatty acids containing the same number of carbon atoms.

1. Give an example of each compound.
a. saturated fatty acid
b. polyunsaturated fatty acid
c. monounsaturated fatty acid
2. Why do unsaturated fatty acids have lower melting points than saturated fatty acids?
Answers
1. a. stearic acid (answers will vary)
b. linoleic acid (answers will vary)
c. palmitoleic acid (answers will vary)
2. Unsaturated fatty acids cannot pack as tightly together as saturated fatty acids due to the presence of the cis double bond that
puts a “kink” or bend in the hydrocarbon chain.
Exercises
1. Classify each fatty acid as saturated or unsaturated and indicate the number of carbon atoms in each molecule.
a. palmitoleic acid
b. myristic acid
c. linoleic acid
2. Classify each fatty acid as saturated or unsaturated and indicate the number of carbon atoms in each molecule.
a. stearic acid
b. oleic acid
c. palmitic acid
3. Write the condensed structural formula for each fatty acid.
a. lauric acid
b. palmitoleic acid
c. linoleic acid
4. Write the condensed structural formulas for each fatty acid.
a. oleic acid
b. α-linolenic acid
c. palmitic acid
5. Arrange these fatty acids (all contain 18 carbon atoms) in order of increasing melting point. Justify your arrangement.
a.
b.
c.
6. Arrange these fatty acids (all contain 16 carbon atoms) in order of increasing melting point. Justify your arrangement.
a. CH3(CH2)14COOH
b.
c.
Answers
1. a. unsaturated; 16 carbon atoms
b. saturated; 14 carbon atoms
c. unsaturated; 18 carbon atoms
3. a. CH3(CH2)10COOH
b. CH3(CH2)5CH=CH(CH2)7COOH
c. CH3(CH2)3(CH2CH=CH)2(CH2)7COOH
5. c < a < b; an increase in the number of double bonds will lower the melting point because it is more difficult to closely pack the
fatty acids together.
3.2: Fatty Acids is shared under a CC BY-NC-SA 4.0 license and was authored, remixed, and/or curated by LibreTexts.
3.3: Fats and Oils
Learning Objectives
Explain why fats and oils are referred to as triglycerides.
Explain how the fatty acid composition of the triglycerides determines whether a substance is a fat or oil.
Describe the importance of key reactions of triglycerides, such as hydrolysis, hydrogenation, and oxidation.
Fats and oils are the most abundant lipids in nature. They provide energy for living organisms, insulate body organs, and transport
fat-soluble vitamins through the blood.
Structures of Fats and Oils

Fats and oils are called triglycerides (or triacylcylgerols) because they are esters composed of three fatty acid units joined to
glycerol, a trihydroxy alcohol:
If all three OH groups on the glycerol molecule are esterified with the same fatty acid, the resulting ester is called a simple
triglyceride. Although simple triglycerides have been synthesized in the laboratory, they rarely occur in nature. Instead, a typical
triglyceride obtained from naturally occurring fats and oils contains two or three different fatty acid components and is thus termed
a mixed triglyceride.
A triglyceride is called a fat if it is a solid at 25°C; it is called an oil if it is a liquid at that temperature. These differences in melting
points reflect differences in the degree of unsaturation and number of carbon atoms in the constituent fatty acids. Triglycerides
obtained from animal sources are usually solids, while those of plant origin are generally oils. Therefore, we commonly speak of
animal fats and vegetable oils.
No single formula can be written to represent the naturally occurring fats and oils because they are highly complex mixtures of
triglycerides in which many different fatty acids are represented. Table 3.3.1 shows the fatty acid compositions of some common
fats and oils. The composition of any given fat or oil can vary depending on the plant or animal species it comes from as well as on
dietetic and climatic factors. To cite just one example, lard from corn-fed hogs is more highly saturated than lard from peanut-fed
hogs. Palmitic acid is the most abundant of the saturated fatty acids, while oleic acid is the most abundant unsaturated fatty acid.
Table 3.3.1 : Average Fatty Acid Composition of Some Common Fats and Oils (%)*
Lauric Myristic Palmitic Stearic Oleic Linoleic Linolenic
Fats
butter (cow) 3 11 27 12 29 2 1
tallow 3 24 19 43 3 1
lard 2 26 14 44 10
Oils
canola oil 4 2 62 22 10
coconut oil† 47 18 9 3 6 2
corn oil 11 2 28 58 1
olive oil 13 3 71 10 1
peanut oil 11 2 48 32
soybean oil 11 4 24 54 7
*Totals less than 100% indicate the presence of fatty acids with fewer than 12 carbon atoms or more than 18 carbon atoms.
†Coconut oil is highly saturated. It contains an unusually high percentage of the low-melting C8, C10, and C12 saturated fatty acids.
Terms such as saturated fat or unsaturated oil are often used to describe the fats or oils obtained from foods. Saturated fats contain
a high proportion of saturated fatty acids, while unsaturated oils contain a high proportion of unsaturated fatty acids. The high
consumption of saturated fats is a factor, along with the high consumption of cholesterol, in increased risks of heart disease.
Physical Properties of Fats and Oils

Contrary to what you might expect, pure fats and oils are colorless, odorless, and tasteless. The characteristic colors, odors, and
flavors that we associate with some of them are imparted by foreign substances that are lipid soluble and have been absorbed by
these lipids. For example, the yellow color of butter is due to the presence of the pigment carotene; the taste of butter comes from
two compounds—diacetyl and 3-hydroxy-2-butanone—produced by bacteria in the ripening cream from which the butter is made.
Fats and oils are lighter than water, having densities of about 0.8 g/cm3. They are poor conductors of heat and electricity and
therefore serve as excellent insulators for the body, slowing the loss of heat through the skin.
Chemical Reactions of Fats and Oils

Fats and oils can participate in a variety of chemical reactions—for example, because triglycerides are esters, they can be
hydrolyzed in the presence of an acid, a base, or specific enzymes known as lipases. The hydrolysis of fats and oils in the presence
of a base is used to make soap and is called saponification. Today most soaps are prepared through the hydrolysis of triglycerides
(often from tallow, coconut oil, or both) using water under high pressure and temperature [700 lb/in2 (∼50 atm or 5,000 kPa) and
200°C]. Sodium carbonate or sodium hydroxide is then used to convert the fatty acids to their sodium salts (soap molecules):
Looking Closer: Soaps
Ordinary soap is a mixture of the sodium salts of various fatty acids, produced in one of the oldest organic syntheses practiced
by humans (second only to the fermentation of sugars to produce ethyl alcohol). Both the Phoenicians (600 BCE) and the
Romans made soap from animal fat and wood ash. Even so, the widespread production of soap did not begin until the 1700s.
Soap was traditionally made by treating molten lard or tallow with a slight excess of alkali in large open vats. The mixture was
heated, and steam was bubbled through it. After saponification was completed, the soap was precipitated from the mixture by
the addition of sodium chloride (NaCl), removed by filtration, and washed several times with water. It was then dissolved in
water and reprecipitated by the addition of more NaCl. The glycerol produced in the reaction was also recovered from the
aqueous wash solutions.
Pumice or sand is added to produce scouring soap, while ingredients such as perfumes or dyes are added to produce fragrant,
colored soaps. Blowing air through molten soap produces a floating soap. Soft soaps, made with potassium salts, are more
expensive but produce a finer lather and are more soluble. They are used in liquid soaps, shampoos, and shaving creams.
Dirt and grime usually adhere to skin, clothing, and other surfaces by combining with body oils, cooking fats, lubricating
greases, and similar substances that act like glues. Because these substances are not miscible in water, washing with water alone
does little to remove them. Soap removes them, however, because soap molecules have a dual nature. One end, called the head,
carries an ionic charge (a carboxylate anion) and therefore dissolves in water; the other end, the tail, has a hydrocarbon structure
and dissolves in oils. The hydrocarbon tails dissolve in the soil; the ionic heads remain in the aqueous phase, and the soap
breaks the oil into tiny soap-enclosed droplets called micelles, which disperse throughout the solution. The droplets repel each
other because of their charged surfaces and do not coalesce. With the oil no longer “gluing” the dirt to the soiled surface (skin,
cloth, dish), the soap-enclosed dirt can easily be rinsed away.
The double bonds in fats and oils can undergo hydrogenation and also oxidation. The hydrogenation of vegetable oils to produce
semisolid fats is an important process in the food industry. Chemically, it is essentially identical to the catalytic hydrogenation
reaction described for alkenes.
In commercial processes, the number of double bonds that are hydrogenated is carefully controlled to produce fats with the desired
consistency (soft and pliable). Inexpensive and abundant vegetable oils (canola, corn, soybean) are thus transformed into margarine
and cooking fats. In the preparation of margarine, for example, partially hydrogenated oils are mixed with water, salt, and nonfat
dry milk, along with flavoring agents, coloring agents, and vitamins A and D, which are added to approximate the look, taste, and
nutrition of butter. (Preservatives and antioxidants are also added.) In most commercial peanut butter, the peanut oil has been
partially hydrogenated to prevent it from separating out. Consumers could decrease the amount of saturated fat in their diet by
using the original unprocessed oils on their foods, but most people would rather spread margarine on their toast than pour oil on it.
Many people have switched from butter to margarine or vegetable shortening because of concerns that saturated animal fats can
raise blood cholesterol levels and result in clogged arteries. However, during the hydrogenation of vegetable oils, an isomerization
reaction occurs that produces the trans fatty acids mentioned in the opening essay. However, studies have shown that trans fatty
acids also raise cholesterol levels and increase the incidence of heart disease. Trans fatty acids do not have the bend in their
structures, which occurs in cis fatty acids and thus pack closely together in the same way that the saturated fatty acids do.
Consumers are now being advised to use polyunsaturated oils and soft or liquid margarine and reduce their total fat consumption to
less than 30% of their total calorie intake each day.
Fats and oils that are in contact with moist air at room temperature eventually undergo oxidation and hydrolysis reactions that cause
them to turn rancid, acquiring a characteristic disagreeable odor. One cause of the odor is the release of volatile fatty acids by
hydrolysis of the ester bonds. Butter, for example, releases foul-smelling butyric, caprylic, and capric acids. Microorganisms
present in the air furnish lipases that catalyze this process. Hydrolytic rancidity can easily be prevented by covering the fat or oil
and keeping it in a refrigerator.
Another cause of volatile, odorous compounds is the oxidation of the unsaturated fatty acid components, particularly the readily
oxidized structural unit
in polyunsaturated fatty acids, such as linoleic and linolenic acids. One particularly offensive product, formed by the oxidative
cleavage of both double bonds in this unit, is a compound called malonaldehyde.
Rancidity is a major concern of the food industry, which is why food chemists are always seeking new and better antioxidants,
substances added in very small amounts (0.001%–0.01%) to prevent oxidation and thus suppress rancidity. Antioxidants are
compounds whose affinity for oxygen is greater than that of the lipids in the food; thus they function by preferentially depleting the
supply of oxygen absorbed into the product. Because vitamin E has antioxidant properties, it helps reduce damage to lipids in the
body, particularly to unsaturated fatty acids found in cell membrane lipids.
Summary
Fats and oils are composed of molecules known as triglycerides, which are esters composed of three fatty acid units linked to
glycerol. An increase in the percentage of shorter-chain fatty acids and/or unsaturated fatty acids lowers the melting point of a fat
or oil. The hydrolysis of fats and oils in the presence of a base makes soap and is known as saponification. Double bonds present in
unsaturated triglycerides can be hydrogenated to convert oils (liquid) into margarine (solid). The oxidation of fatty acids can form
compounds with disagreeable odors. This oxidation can be minimized by the addition of antioxidants.

1. What functions does fat serve in the body?
2. Which of these triglycerides would you expect to find in higher amounts in oils? In fats? Justify your choice.
Answers
1. Fats provide energy for living organisms. They also provide insulation for body organs and transport fat-soluble vitamins.
2. The triglyceride on the left is expected to be present in higher amounts in fats because it is composed of a greater number of
saturated fatty acids. The triglyceride on the right is expected to be present in higher amounts in oils because it is composed of a
greater number of unsaturated fatty acids.
Exercises
a. trimyristin
b. a triglyceride likely to be found in peanut oil
a. tripalmitin
b. a triglyceride likely to be found in butter
3. Draw structures to write the reaction for the complete hydrogenation of tripalmitolein (Table 3.3.1 for the condensed structure
of palmitoleic acid). Name the product formed.
4. Draw structures to write the reaction for the complete hydrogenation of trilinolein (Table 3.3.1 for the condensed structure of
linoleic acid). Name the product formed.
5. Draw structures to write the reaction for the hydrolysis of trilaurin in a basic solution (Table 3.3.1 for the condensed structure of
lauric acid).
6. Draw structures to write the reaction for the hydrolysis of tristearin in a basic solution (Table 3.3.1 for the condensed structure
of stearic acid).
7. a. What compounds with a disagreeable odor are formed when butter becomes rancid?
b. How are these compounds formed?
c. How can rancidity be prevented?
8. a. What compound with a disagreeable odor is formed when unsaturated fatty acids react with oxygen in the atmosphere?
b. How can this process be prevented?
Answers
1
3.
5.
7. a. smaller carboxylic acids, such as butyric, caprylic, and capric acids
b. These compounds are formed by the hydrolysis of the triglycerides found in butter.
c. Rancidity can be prevented by covering the butter (to keep out moisture) and storing it in a refrigerator. (Cold temperatures
slow down hydrolysis reactions.)
3.3: Fats and Oils is shared under a CC BY-NC-SA 4.0 license and was authored, remixed, and/or curated by LibreTexts.
Learning Objectives
Identify the distinguishing characteristics of membrane lipids.
Describe membrane components and how they are arranged.
All living cells are surrounded by a cell membrane. Plant cells (Figure 3.4.1A) and animal cells (Figure 3.4.1B) contain a cell
nucleus that is also surrounded by a membrane and holds the genetic information for the cell. Everything between the cell
membrane and the nuclear membrane—including intracellular fluids and various subcellular components such as the mitochondria
and ribosomes—is called the cytoplasm. The membranes of all cells have a fundamentally similar structure, but membrane function
varies tremendously from one organism to another and even from one cell to another within a single organism. This diversity arises
mainly from the presence of different proteins and lipids in the membrane.
Figure 3.4.1 : (A) An Idealized Plant Cell. Not all the structures shown here occur in every type of plant cell. (B) An Idealized
Animal Cell. The structures shown here will seldom all be found in a single animal cell.
The lipids in cell membranes are highly polar but have dual characteristics: part of the lipid is ionic and therefore dissolves in
water, whereas the rest has a hydrocarbon structure and therefore dissolves in nonpolar substances. Often, the ionic part is referred
to as hydrophilic, meaning “water loving,” and the nonpolar part as hydrophobic, meaning “water fearing” (repelled by water).
When allowed to float freely in water, polar lipids spontaneously cluster together in any one of three arrangements: micelles,
monolayers, and bilayers (Figure 3.4.2).
Figure 3.4.2 : Spontaneously Formed Polar Lipid Structures in Water: Monolayer, Micelle, and Bilayer
Micelles are aggregations in which the lipids’ hydrocarbon tails—being hydrophobic—are directed toward the center of the
assemblage and away from the surrounding water while the hydrophilic heads are directed outward, in contact with the water. Each
micelle may contain thousands of lipid molecules. Polar lipids may also form a monolayer, a layer one molecule thick on the
surface of the water. The polar heads face into water, and the nonpolar tails stick up into the air. Bilayers are double layers of lipids
arranged so that the hydrophobic tails are sandwiched between an inner surface and an outer surface consisting of hydrophilic
heads. The hydrophilic heads are in contact with water on either side of the bilayer, whereas the tails, sequestered inside the bilayer,
are prevented from having contact with the water. Bilayers like this make up every cell membrane (Figure 3.4.3).
Figure 3.4.3 : Schematic Diagram of a Cell Membrane. The membrane enclosing a typical animal cell is a phospholipid bilayer
with embedded cholesterol and protein molecules. Short oligosaccharide chains are attached to the outer surface.
In the bilayer interior, the hydrophobic tails (that is, the fatty acid portions of lipid molecules) interact by means of dispersion
forces. The interactions are weakened by the presence of unsaturated fatty acids. As a result, the membrane components are free to
mill about to some extent, and the membrane is described as fluid.
The lipids found in cell membranes can be categorized in various ways. Phospholipids are lipids containing phosphorus.
Glycolipids are sugar-containing lipids. The latter are found exclusively on the outer surface of the cell membrane, acting as
distinguishing surface markers for the cell and thus serving in cellular recognition and cell-to-cell communication. Sphingolipids
are phospholipids or glycolipids that contain the unsaturated amino alcohol sphingosine rather than glycerol. Diagrammatic
structures of representative membrane lipids are presented in Figure 3.4.4.
Figure 3.4.4 : Component Structures of Some Important Membrane Lipids
Phosphoglycerides (also known as glycerophospholipids) are the most abundant phospholipids in cell membranes. They consist of
a glycerol unit with fatty acids attached to the first two carbon atoms, while a phosphoric acid unit, esterified with an alcohol
molecule (usually an amino alcohol, as in part (a) of Figure 3.4.5) is attached to the third carbon atom of glycerol (part (b) of
Figure 3.4.5). Notice that the phosphoglyceride molecule is identical to a triglyceride up to the phosphoric acid unit (part (b) of
Figure 3.4.5).
Figure 3.4.5 : Phosphoglycerides. (a) Amino alcohols are commonly found in phosphoglycerides, which are evident in its structural
formula (b).
There are two common types of phosphoglycerides. Phosphoglycerides containing ethanolamine as the amino alcohol are called
phosphatidylethanolamines or cephalins. Cephalins are found in brain tissue and nerves and also have a role in blood clotting.
Phosphoglycerides containing choline as the amino alcohol unit are called phosphatidylcholines or lecithins. Lecithins occur in all
living organisms. Like cephalins, they are important constituents of nerve and brain tissue. Egg yolks are especially rich in
lecithins. Commercial-grade lecithins isolated from soybeans are widely used in foods as emulsifying agents. An emulsifying agent
is used to stabilize an emulsion—a dispersion of two liquids that do not normally mix, such as oil and water. Many foods are
emulsions. Milk is an emulsion of butterfat in water. The emulsifying agent in milk is a protein called casein. Mayonnaise is an
emulsion of salad oil in water, stabilized by lecithins present in egg yolk.
Sphingomyelins, the simplest sphingolipids, each contain a fatty acid, a phosphoric acid, sphingosine, and choline (Figure 3.4.6).
Because they contain phosphoric acid, they are also classified as phospholipids. Sphingomyelins are important constituents of the
myelin sheath surrounding the axon of a nerve cell. Multiple sclerosis is one of several diseases resulting from damage to the
myelin sheath.
Figure 3.4.6 : Sphingolipids. (a) Sphingosine, an amino alcohol, is found in all sphingolipids. (b) A sphingomyelin is also known as
a phospholipid, as evidenced by the phosphoric acid unit in its structure.
Most animal cells contain sphingolipids called cerebrosides (Figure 3.4.7). Cerebrosides are composed of sphingosine, a fatty acid,
and galactose or glucose. They therefore resemble sphingomyelins but have a sugar unit in place of the choline phosphate group.
Cerebrosides are important constituents of the membranes of nerve and brain cells.
Figure 3.4.7 : Cerebrosides. Cerebrosides are sphingolipids that contain a sugar unit.
The sphingolipids called gangliosides are more complex, usually containing a branched chain of three to eight monosaccharides
and/or substituted sugars. Because of considerable variation in their sugar components, about 130 varieties of gangliosides have
been identified. Most cell-to-cell recognition and communication processes (e.g., blood group antigens) depend on differences in
the sequences of sugars in these compounds. Gangliosides are most prevalent in the outer membranes of nerve cells, although they
also occur in smaller quantities in the outer membranes of most other cells. Because cerebrosides and gangliosides contain sugar
groups, they are also classified as glycolipids.
Membrane Proteins
If membranes were composed only of lipids, very few ions or polar molecules could pass through their hydrophobic “sandwich
filling” to enter or leave any cell. However, certain charged and polar species do cross the membrane, aided by proteins that move
about in the lipid bilayer. The two major classes of proteins in the cell membrane are integral proteins, which span the hydrophobic
interior of the bilayer, and peripheral proteins, which are more loosely associated with the surface of the lipid bilayer (Figure
3.4.3). Peripheral proteins may be attached to integral proteins, to the polar head groups of phospholipids, or to both by hydrogen
bonding and electrostatic forces.

Small ions and molecules soluble in water enter and leave the cell by way of channels through the integral proteins. Some proteins,
called carrier proteins, facilitate the passage of certain molecules, such as hormones and neurotransmitters, by specific interactions
between the protein and the molecule being transported.
Summary
Lipids are important components of biological membranes. These lipids have dual characteristics: part of the molecule is
hydrophilic, and part of the molecule is hydrophobic. Membrane lipids may be classified as phospholipids, glycolipids, and/or
sphingolipids. Proteins are another important component of biological membranes. Integral proteins span the lipid bilayer, while
peripheral proteins are more loosely associated with the surface of the membrane.

1. Name the structural unit that must be present for a molecule to be classified as a
a. phospholipid.
b. glycolipid.
c. sphingolipid.
2. Why is it important that membrane lipids have dual character—part of the molecule is hydrophilic and part of the molecule is
hydrophobic?
3. Why do you suppose lecithins (phosphatidylcholines) are often added to processed foods such as hot cocoa mix?
Answers
1. a. a phosphate group
b. a saccharide unit (monosaccharide or more complex)
c. sphingosine
2. The dual character is critical for the formation of the lipid bilayer. The hydrophilic portions of the molecule are in contact with
the aqueous environment of the cell, while the hydrophobic portion of the lipids is in the interior of the bilayer and provides a
barrier to the passive diffusion of most molecules.
3. Lecithin acts as an emulsifying agent that aids in the mixing of the hot cocoa mix with water and keeps the cocoa mix evenly
distributed after stirring.
Exercises
1. Classify each as a phospholipid, a glycolipid, and/or a sphingolipid. (Some lipids can be given more than one classification.)
a.
b.
2. Classify each as a phospholipid, a glycolipid, and/or a sphingolipid. (Some lipids can be given more than one classification.)
a.
b.
3. Draw the structure of the sphingomyelin that has lauric acid as its fatty acid and ethanolamine as its amino alcohol.
4. Draw the structure of the cerebroside that has myristic acid as its fatty acid and galactose as its sugar.
5. a. Distinguish between an integral protein and a peripheral protein.
b. What is one key function of integral proteins?
Answers
1. a. phospholipid
b. sphingolipid and glycolipid
3.
5. a. Integral proteins span the lipid bilayer, while peripheral proteins associate with the surfaces of the lipid bilayer.
b. aid in the movement of charged and polar species across the membrane
3.4: Membranes and Membrane Lipids is shared under a CC BY-NC-SA 4.0 license and was authored, remixed, and/or curated by LibreTexts.
3.5: Steroids
Learning Objectives
To identify the functions of steroids produced in mammals.
All the lipids discussed so far are saponifiable, reacting with aqueous alkali to yield simpler components, such as glycerol, fatty
acids, amino alcohols, and sugars. Lipid samples extracted from cellular material, however, also contain a small but important
fraction that does not react with alkali. The most important nonsaponifiable lipids are the steroids. These compounds include the
bile salts, cholesterol and related compounds, and certain hormones (such as cortisone and the sex hormones).
Figure 3.5.1 Steroids. (a) The four-fused-ring steroid skeleton uses letter designations for each ring and the numbering of the
carbon atoms. (b) The cholesterol molecule follows this pattern.
Steroids occur in plants, animals, yeasts, and molds but not in bacteria. They may exist in free form or combined with fatty acids or
carbohydrates. All steroids have a characteristic structural component consisting of four fused rings. Chemists identify the rings by
capital letters and number the carbon atoms as shown in Figure 3.5.1a. Slight variations in this structure or in the atoms or groups
attached to it produce profound differences in biological activity.
Cholesterol
Cholesterol (Figure 3.5.1b) does not occur in plants, but it is the most abundant steroid in the human body (240 g is a typical
amount). Excess cholesterol is believed to be a primary factor in the development of atherosclerosis and heart disease, which are
major health problems in the United States today. About half of the body’s cholesterol is interspersed in the lipid bilayer of cell
membranes. Much of the rest is converted to cholic acid, which is used in the formation of bile salts. Cholesterol is also a precursor
in the synthesis of sex hormones, adrenal hormones, and vitamin D.
Excess cholesterol not metabolized by the body is released from the liver and transported by the blood to the gallbladder. Normally,
it stays in solution there until being secreted into the intestine (as a component of bile) to be eliminated. Sometimes, however,
cholesterol in the gallbladder precipitates in the form of gallstones (Figure 3.5.2). Indeed, the name cholesterol is derived from the
Greek chole, meaning “bile,” and stereos, meaning “solid.”
Figure 3.5.2 : Numerous small gallstones made up largely of cholesterol, all removed in one patient. Grid scale 1 mm
To Your Health: Cholesterol and Heart Disease
Heart disease is the leading cause of death in the United States for both men and women. The Centers for Disease Control and
Prevention reported that heart disease claimed 631,636 lives in the United States (26% of all reported deaths) in 2006.
Scientists agree that elevated cholesterol levels in the blood, as well as high blood pressure, obesity, diabetes, and cigarette
smoking, are associated with an increased risk of heart disease. A long-term investigation by the National Institutes of Health
showed that among men ages 30 to 49, the incidence of heart disease was five times greater for those whose cholesterol levels
were above 260 mg/100 mL of serum than for those with cholesterol levels of 200 mg/100 mL or less. The cholesterol content
of blood varies considerably with age, diet, and sex. Young adults average about 170 mg of cholesterol per 100 mL of blood,
whereas males at age 55 may have cholesterol levels at 250 mg/100 mL or higher because the rate of cholesterol breakdown
decreases with age. Females tend to have lower blood cholesterol levels than males.
To understand the link between heart disease and cholesterol levels, it is important to understand how cholesterol and other
lipids are transported in the body. Lipids, such as cholesterol, are not soluble in water and therefore cannot be transported in the
blood (an aqueous medium) unless they are complexed with proteins that are soluble in water, forming assemblages called
lipoproteins. Lipoproteins are classified according to their density, which is dependent on the relative amounts of protein and
lipid they contain. Lipids are less dense than proteins, so lipoproteins containing a greater proportion of lipid are less dense than
those containing a greater proportion of protein.
Research on cholesterol and its role in heart disease has focused on serum levels of low-density lipoproteins (LDLs) and high-
density lipoproteins (HDLs). One of the most fascinating discoveries is that high levels of HDLs reduce a person’s risk of
developing heart disease, whereas high levels of LDLs increase that risk. Thus the serum LDL:HDL ratio is a better predictor of
heart disease risk than the overall level of serum cholesterol. Persons who, because of hereditary or dietary factors, have high
LDL:HDL ratios in their blood have a higher incidence of heart disease.
How do HDLs reduce the risk of developing heart disease? No one knows for sure, but one role of HDLs appears to be the
transport of excess cholesterol to the liver, where it can be metabolized. Therefore, HDLs aid in removing cholesterol from
blood and from the smooth muscle cells of the arterial wall.
Dietary modifications and increased physical activity can help lower total cholesterol and improve the LDL:HDL ratio. The
average American consumes about 600 mg of cholesterol from animal products each day and also synthesizes approximately 1 g
of cholesterol each day, mostly in the liver. The amount of cholesterol synthesized is controlled by the cholesterol level in the
blood; when the blood cholesterol level exceeds 150 mg/100 mL, the rate of cholesterol biosynthesis is halved. Hence, if
cholesterol is present in the diet, a feedback mechanism suppresses its synthesis in the liver. However, the ratio of suppression is
not a 1:1 ratio; the reduction in biosynthesis does not equal the amount of cholesterol ingested. Thus, dietary substitutions of
unsaturated fat for saturated fat, as well as a reduction in consumption of trans fatty acids, is recommended to help lower serum
cholesterol and the risk of heart disease.
Steroid Hormones
Hormones are chemical messengers that are released in one tissue and transported through the circulatory system to one or more
other tissues. One group of hormones is known as steroid hormones because these hormones are synthesized from cholesterol,
which is also a steroid. There are two main groups of steroid hormones: adrenocortical hormones and sex hormones.
The adrenocortical hormones, such as aldosterone and cortisol (Table 3.5.1), are produced by the adrenal gland, which is located
adjacent to each kidney. Aldosterone acts on most cells in the body, but it is particularly effective at enhancing the rate of
reabsorption of sodium ions in the kidney tubules and increasing the secretion of potassium ions and/or hydrogen ions by the
tubules. Because the concentration of sodium ions is the major factor influencing water retention in tissues, aldosterone promotes
water retention and reduces urine output. Cortisol regulates several key metabolic reactions (for example, increasing glucose
production and mobilizing fatty acids and amino acids). It also inhibits the inflammatory response of tissue to injury or stress.
Cortisol and its analogs are therefore used pharmacologically as immunosuppressants after transplant operations and in the
treatment of severe skin allergies and autoimmune diseases, such as rheumatoid arthritis.
Table 3.5.1 : Representative Steroid Hormones and Their Physiological Effects
Hormone Effect
regulates salt metabolism; stimulates kidneys to retain sodium and

excrete potassium
stimulates the conversion of proteins to carbohydrates
regulates the menstrual cycle; maintains pregnancy
stimulates female sex characteristics; regulates changes during the

menstrual cycle
stimulates and maintains male sex characteristics
The sex hormones are a class of steroid hormones secreted by the gonads (ovaries or testes), the placenta, and the adrenal glands.
Testosterone and androstenedione are the primary male sex hormones, or androgens, controlling the primary sexual characteristics
of males, or the development of the male genital organs and the continuous production of sperm. Androgens are also responsible
for the development of secondary male characteristics, such as facial hair, deep voice, and muscle strength. Two kinds of sex
hormones are of particular importance in females: progesterone, which prepares the uterus for pregnancy and prevents the further
release of eggs from the ovaries during pregnancy, and the estrogens, which are mainly responsible for the development of female
secondary sexual characteristics, such as breast development and increased deposition of fat tissue in the breasts, the buttocks, and
the thighs. Both males and females produce androgens and estrogens, differing in the amounts of secreted hormones rather than in
the presence or absence of one or the other.
Sex hormones, both natural and synthetic, are sometimes used therapeutically. For example, a woman who has had her ovaries
removed may be given female hormones to compensate. Some of the earliest chemical compounds employed in cancer
chemotherapy were sex hormones. For example, estrogens are one treatment option for prostate cancer because they block the
release and activity of testosterone. Testosterone enhances prostate cancer growth. Sex hormones are also administered in
preparation for sex-change operations, to promote the development of the proper secondary sexual characteristics. Oral
contraceptives are synthetic derivatives of the female sex hormones; they work by preventing ovulation.
Bile Salts
Bile is a yellowish green liquid (pH 7.8–8.6) produced in the liver. The most important constituents of bile are bile salts, which are
sodium salts of amidelike combinations of bile acids, such as cholic acid (part (a) of Figure 3.5.3) and an amine such as the amino
acid glycine (part (b) of Figure 3.5.3). They are synthesized from cholesterol in the liver, stored in the gallbladder, and then
secreted in bile into the small intestine. In the gallbladder, the composition of bile gradually changes as water is absorbed and the
other components become more concentrated.
Figure 3.5.3 Bile Acids. (a) Cholic acid is an example of a bile acid. (b) Sodium glycocholate is a bile salt synthesized from cholic
acid and glycine.
Because they contain both hydrophobic and hydrophilic groups, bile salts are highly effective detergents and emulsifying agents;
they break down large fat globules into smaller ones and keep those smaller globules suspended in the aqueous digestive
environment. Enzymes can then hydrolyze fat molecules more efficiently. Thus, the major function of bile salts is to aid in the
digestion of dietary lipids.
Surgical removal is often advised for a gallbladder that becomes infected, inflamed, or perforated. This surgery does not
seriously affect digestion because bile is still produced by the liver, but the liver’s bile is more dilute and its secretion into the
small intestine is not as closely tied to the arrival of food.
Summary
Steroids have a four-fused-ring structure and have a variety of functions. Cholesterol is a steroid found in mammals that is needed
for the formation of cell membranes, bile acids, and several hormones. Bile salts are secreted into the small intestine to aid in the
digestion of fats.

1. Distinguish between a saponifiable lipid and a nonsaponifiable lipid.
2. Identify a key function for each steroid.
a. bile salt
b. cholesterol
c. estradiol
Answers
1. A saponifiable lipid reacts with aqueous alkali to yield simpler components, while a nonsaponifiable lipid does not react with
alkali to yield simpler components.
2. a. acts as an emulsifying agent to break down large fat globules and keep these globules suspended in the aqueous digestive
environment
b. a key component of mammalian cell membranes (answers will vary)
c. stimulates female sex characteristics and regulates changes during the menstrual cycle
Exercises
1. Which of these compounds are steroids—tripalmitin, cephalin, or cholesterol?
2. Which of these compounds are steroids—vitamin D, cholic acid, or lecithin?
3. Draw the basic steroid skeleton and label each ring with the appropriate letter designation.
4. Identify each compound as an adrenocortical hormone, a female sex hormone, or a male sex hormone.
a. progesterone
b. aldosterone
c. testosterone
d. cortisol
Answers
1. cholesterol
3.
3.5: Steroids is shared under a CC BY-NC-SA 4.0 license and was authored, remixed, and/or curated by LibreTexts.
Lipids, found in the body tissues of all organisms, are compounds that are more soluble in organic solvents than in water. Many of
them contain fatty acids, which are carboxylic acids that generally contain an even number of 4–20 carbon atoms in an unbranched
chain. Saturated fatty acids have no carbon-to-carbon double bonds. Monounsaturated fatty acids have a single carbon-to-
carbon double bond, while polyunsaturated fatty acids have more than one carbon-to-carbon double bond. Linoleic and linolenic
acid are known as essential fatty acids because the human body cannot synthesize these polyunsaturated fatty acids. The lipids
known as fats and oils are triacylglycerols, more commonly called triglycerides—esters composed of three fatty acids joined to
the trihydroxy alcohol glycerol. Fats are triglycerides that are solid at room temperature, and oils are triglycerides that are liquid at
room temperature. Fats are found mainly in animals, and oils found mainly in plants. Saturated triglycerides are those containing a
higher proportion of saturated fatty acid chains (fewer carbon-to-carbon double bonds); unsaturated triglycerides contain a higher
proportion of unsaturated fatty acid chains.
Saponification is the hydrolysis of a triglyceride in a basic solution to form glycerol and three carboxylate anions or soap
molecules. Other important reactions are the hydrogenation and oxidation of double bonds in unsaturated fats and oils.
Phospholipids are lipids containing phosphorus. In phosphoglycerides, the phosphorus is joined to an amino alcohol unit. Some
phosphoglycerides, like lecithins, are used to stabilize an emulsion—a dispersion of two liquids that do not normally mix, such as
oil and water. Sphingolipids are lipids for which the precursor is the amino alcohol sphingosine, rather than glycerol. A glycolipid
has a sugar substituted at one of the OH groups of either glycerol or sphingosine. All are highly polar lipids found in cell
membranes.
Polar lipids have dual characteristics: one part of the molecule is ionic and dissolves in water; the rest has a hydrocarbon structure
and dissolves in nonpolar substances. Often, the ionic part is referred to as hydrophilic (literally, “water loving”) and the nonpolar
part as hydrophobic (“water fearing”). When placed in water, polar lipids disperse into any one of three arrangements: micelles,
monolayers, and bilayers. Micelles are aggregations of molecules in which the hydrocarbon tails of the lipids, being hydrophobic,
are directed inward (away from the surrounding water), and the hydrophilic heads that are directed outward into the water. Bilayers
are double layers arranged so that the hydrophobic tails are sandwiched between the two layers of hydrophilic heads, which remain
in contact with the water.
Every living cell is enclosed by a cell membrane composed of a lipid bilayer. In animal cells, the bilayer consists mainly of
phospholipids, glycolipids, and the steroid cholesterol. Embedded in the bilayer are integral proteins, and peripheral proteins are
loosely associated with the surface of the bilayer. Everything between the cell membrane and the membrane of the cell nucleus is
called the cytoplasm.
Most lipids can be saponified, but some, such as steroids, cannot be saponified. The steroid cholesterol is found in animal cells but
never in plant cells. It is a main component of all cell membranes and a precursor for hormones, vitamin D, and bile salts. Bile salts
are the most important constituents of bile, which is a yellowish-green liquid secreted by the gallbladder into the small intestine
and is needed for the proper digestion of lipids.
3.6: Lipids (Summary) is shared under a CC BY-NC-SA 4.0 license and was authored, remixed, and/or curated by LibreTexts.
3.7: Exercises
1. The melting point of elaidic acid is 52°C.
a. What trend is observed when comparing the melting points of elaidic acid, oleic acid, and stearic acid? Explain.
b. Would you expect the melting point of palmitelaidic acid to be lower or higher than that of elaidic acid? Explain.
2. Examine the labels on two brands of margarine and two brands of shortening and list the oils used in the various brands.
3. Draw a typical lecithin molecule that incorporates glycerol, palmitic acid, oleic acid, phosphoric acid, and choline. Circle all the
ester bonds.
4. In cerebrosides, is the linkage between the fatty acid and sphingosine an amide bond or an ester bond? Justify your answer.
5. Serine is an amino acid that has the following structure. Draw the structure for a phosphatidylserine that contains a palmitic acid
and a palmitoleic acid unit.
6. Explain whether each compound would be expected to diffuse through the lipid bilayer of a cell membrane.
a. potassium chloride
b. CH3CH2CH2CH2CH2CH3
c. fructose
7. Identify the role of each steroid hormone in the body.
a. progesterone
b. aldosterone
c. testosterone
d. cortisol
8. How does the structure of cholic acid differ from that of cholesterol? Which compound would you expect to be more polar?
Why?
9. a. What fatty acid is the precursor for the prostaglandins?
b. Identify three biological effects of prostaglandins.
10. Why is it important to determine the ratio of LDLs to HDLs, rather than just the concentration of serum cholesterol?
Answers
1. a. Stearic acid has the highest melting point, followed by elaidic acid, and then oleic acid with the lowest melting point. Elaidic
acid is a trans fatty acid, and the carbon chains can pack together almost as tightly as those of the saturated stearic acid.
Oleic acid is a cis fatty acid, and the bend in the hydrocarbon chain keeps these carbon chains from packing as closely
together; fewer interactions lead to a much lower melting point.
b. The melting point of palmitelaidic acid should be lower than that of elaidic acid because it has a shorter carbon chain (16, as
compared to 18 for elaidic acid). The shorter the carbon chain, the lower the melting point due to a decrease in
intermolecular interactions.
3.
5.
7. a. regulates the menstrual cycle and maintains pregnancy
b. regulates salt metabolism by stimulating the kidneys to retain sodium and excrete potassium
c. stimulates and maintains male sex characteristics
d. stimulates the conversion of proteins to carbohydrates
9. a. arachidonic acid
b. induce smooth muscle contraction, lower blood pressure, and contribute to the inflammatory response
3.7: Exercises is shared under a CC BY-NC-SA 4.0 license and was authored, remixed, and/or curated by LibreTexts.
CHAPTER OVERVIEW
4: Amino Acids, Proteins, and Enzymes

4.4: Peptides
4.5: Proteins
4.6: Enzymes
4.7: Enzyme Action
4: Amino Acids, Proteins, and Enzymes is shared under a CC BY-NC-SA 4.0 license and was authored, remixed, and/or curated by LibreTexts.
1
The 1923 Nobel Prize in Medicine or Physiology was awarded to Frederick Grant Banting and John James Richard Macleod for
their discovery of the protein insulin. In 1958, the Nobel Prize in Chemistry was awarded to Frederick Sanger for his discoveries
concerning the structure of proteins and, in particular, the structure of insulin. What is so important about insulin that two Nobel
Prizes have been awarded for work on this protein?
Insulin is a hormone that is synthesized in the pancreas. Insulin stimulates the transport of glucose into cells throughout the body
and the storage of glucose as glycogen. People with diabetes do not produce insulin or use it properly. The isolation of insulin in
1921 led to the first effective treatment for these individuals.
Figure 4.1.1 : Insulin pump, showing an infusion set loaded into spring-loaded insertion device. A reservoir is attached to the
infusion set (shown here removed from the pump). Image used with permission (Public Domain; User:David-i98 ).
4.1: Prelude to Amino Acids, Proteins, and Enzymes is shared under a CC BY-NC-SA 4.0 license and was authored, remixed, and/or curated by
LibreTexts.
Learning Objectives
To recognize amino acids and classify them based on the characteristics of their side chains.
The proteins in all living species, from bacteria to humans, are constructed from the same set of 20 amino acids, so called because
each contains an amino group attached to a carboxylic acid. The amino acids in proteins are α-amino acids, which means the amino
group is attached to the α-carbon of the carboxylic acid. Humans can synthesize only about half of the needed amino acids; the
remainder must be obtained from the diet and are known as essential amino acids. However, two additional amino acids have been
found in limited quantities in proteins: Selenocysteine was discovered in 1986, while pyrrolysine was discovered in 2002.
The amino acids are colorless, nonvolatile, crystalline solids, melting and decomposing at temperatures above 200°C. These
melting temperatures are more like those of inorganic salts than those of amines or organic acids and indicate that the structures of
the amino acids in the solid state and in neutral solution are best represented as having both a negatively charged group and a
positively charged group. Such a species is known as a zwitterion.
Classification
In addition to the amino and carboxyl groups, amino acids have a side chain or R group attached to the α-carbon. Each amino acid
has unique characteristics arising from the size, shape, solubility, and ionization properties of its R group. As a result, the side
chains of amino acids exert a profound effect on the structure and biological activity of proteins. Although amino acids can be
classified in various ways, one common approach is to classify them according to whether the functional group on the side chain at
neutral pH is nonpolar, polar but uncharged, negatively charged, or positively charged. The structures and names of the 20 amino
acids, their one- and three-letter abbreviations, and some of their distinctive features are given in Table 4.2.1.
Table 4.2.1 : Common Amino Acids Found in Proteins
Structural Formula (at pH
Common Name Abbreviation Molar Mass Distinctive Feature
6)
Amino acids with a nonpolar R group
the only amino acid

glycine gly (G) 75
lacking a chiral carbon
alanine ala (A) 89 —
a branched-chain amino
valine val (V) 117
acid
a branched-chain amino
leucine leu (L) 131
acid
6)
an essential amino acid

because most animals
isoleucine ile (I) 131 cannot synthesize
branched-chain amino
acids
also classified as an
phenylalanine phe (F) 165
aromatic amino acid
tryptophan trp (W) 204
aromatic amino acid
side chain functions as a

methionine met (M) 149
methyl group donor
contains a secondary amine

proline pro (P) 115 group; referred to as an α-
imino acid
Amino acids with a polar but neutral R group
found at the active site of

serine ser (S) 105
many enzymes
named for its similarity to

threonine thr (T) 119
the sugar threose
oxidation of two cysteine

cysteine cys (C) 121
molecules yields cystine
tyrosine tyr (Y) 181
aromatic amino acid
asparagine asn (N) 132 the amide of aspartic acid
glutamine gln (Q) 146 the amide of glutamic acid
Amino acids with a negatively charged R group

carboxyl groups are
ionized at physiological
aspartic acid asp (D) 132
pH; also known as
aspartate
6)
carboxyl groups are

ionized at physiological
glutamic acid glu (E) 146
pH; also known as
glutamate
Amino acids with a positively charged R group
the only amino acid whose

histidine his (H) 155 R group has a pKa (6.0)
near physiological pH
lysine lys (K) 147 —
almost as strong a base as

arginine arg (R) 175
sodium hydroxide
The first amino acid to be isolated was asparagine in 1806. It was obtained from protein found in asparagus juice (hence the name).
Glycine, the major amino acid found in gelatin, was named for its sweet taste (Greek glykys, meaning “sweet”). In some cases an
amino acid found in a protein is actually a derivative of one of the common 20 amino acids (one such derivative is hydroxyproline).
The modification occurs after the amino acid has been assembled into a protein.
Configuration
Notice in Table 4.2.1 that glycine is the only amino acid whose α-carbon is not chiral. Therefore, with the exception of glycine, the
amino acids could theoretically exist in either the D- or the L-enantiomeric form and rotate plane-polarized light. As with sugars,
chemists use glyceraldehyde as the reference compound for the assignment of configuration to amino acids. Its structure closely
resembles an amino acid structure except that in the latter, an amino group takes the place of the OH group on the chiral carbon of
the sugar.
We learned that all naturally occurring sugars belong to the D series. It is interesting, therefore, that nearly all known plant and
animal proteins are composed entirely of L-amino acids. However, certain bacteria contain D-amino acids in their cell walls, and
several antibiotics (e.g., actinomycin D and the gramicidins) contain varying amounts of D-leucine, D-phenylalanine, and D-valine.
Summary
Amino acids can be classified based on the characteristics of their distinctive side chains as nonpolar, polar but uncharged,
negatively charged, or positively charged. The amino acids found in proteins are L-amino acids.

1. What is the general structure of an α-amino acid?
2. Identify the amino acid that fits each description.
a. also known as aspartate
b. almost as strong a base as sodium hydroxide
c. does not have a chiral carbon
Answers
1.
2. a. aspartic acid
b. arginine
c. glycine
Exercises
1. Write the side chain of each amino acid.
a. serine
b. arginine
c. phenylalanine
a. aspartic acid
b. methionine
c. valine
3. Draw the structure for each amino acid.
a. alanine
b. cysteine
c. histidine
a. threonine
b. glutamic acid
c. leucine
5. Identify an amino acid whose side chain contains a(n)
a. amide functional group.
b. aromatic ring.
c. carboxyl group.
a. OH group
b. branched chain
c. amino group
Answers
1. a. CH2OH−
b.
c.
2.
3. a.
b.
c.
4.
5. a. asparagine or glutamine
b. phenylalanine, tyrosine, or tryptophan
c. aspartic acid or glutamic acid
4.2: Properties of Amino Acids is shared under a CC BY-NC-SA 4.0 license and was authored, remixed, and/or curated by LibreTexts.
Learning Objectives
To explain how an amino acid can act as both an acid and a base.
The structure of an amino acid allows it to act as both an acid and a base. An amino acid has this ability because at a certain pH value (different for each amino acid) nearly all the amino acid
molecules exist as zwitterions. If acid is added to a solution containing the zwitterion, the carboxylate group captures a hydrogen (H+) ion, and the amino acid becomes positively charged. If base is
added, ion removal of the H+ ion from the amino group of the zwitterion produces a negatively charged amino acid. In both circumstances, the amino acid acts to maintain the pH of the system—that
is, to remove the added acid (H+) or base (OH−) from solution.
Example 4.3.1
a. Draw the structure for the anion formed when glycine (at neutral pH) reacts with a base.
b. Draw the structure for the cation formed when glycine (at neutral pH) reacts with an acid.
SOLUTION
a. The base removes H+ from the protonated amine group.
b. The acid adds H+ to the carboxylate group.
Exercise 4.3.1
a. Draw the structure for the cation formed when valine (at neutral pH) reacts with an acid.
b. Draw the structure for the anion formed when valine (at neutral pH) reacts with a base.
The particular pH at which a given amino acid exists in solution as a zwitterion is called the isoelectric point (pI). At its pI, the positive and negative charges on the amino acid balance, and the
molecule as a whole is electrically neutral. The amino acids whose side chains are always neutral have isoelectric points ranging from 5.0 to 6.5. The basic amino acids (which have positively charged
side chains at neutral pH) have relatively high examples. Acidic amino acids (which have negatively charged side chains at neutral pH) have quite low examples (Table 4.3.1).
Table 4.3.1 : ExampIes of Some Representative Amino Acids
Amino Acid Classification
alanine nonpolar
valine nonpolar
serine polar, uncharged
threonine polar, uncharged
arginine positively charged (basic)
histidine positively charged (basic)
lysine positively charged (basic)
aspartic acid negatively charged (acidic)
glutamic acid negatively charged (acidic)
Amino acids undergo reactions characteristic of carboxylic acids and amines. The reactivity of these functional groups is particularly important in linking amino acids together to form peptides and
proteins, as you will see later in this chapter. Simple chemical tests that are used to detect amino acids take advantage of the reactivity of these functional groups. An example is the ninhydrin test in
which the amine functional group of α-amino acids reacts with ninhydrin to form purple-colored compounds. Ninhydrin is used to detect fingerprints because it reacts with amino acids from the
proteins in skin cells transferred to the surface by the individual leaving the fingerprint.
Summary
Amino acids can act as both an acid and a base due to the presence of the amino and carboxyl functional groups. The pH at which a given amino acid exists in solution as a zwitterion is called the
isoelectric point (pI).

a. zwitterion
b. isoelectric point
2. Draw the structure for the anion formed when alanine (at neutral pH) reacts with a base.
3. Draw the structure for the cation formed when alanine (at neutral pH) reacts with an acid.
Answers
1. a. an electrically neutral compound that contains both negatively and positively charged groups
b. the pH at which a given amino acid exists in solution as a zwitterion
2.
3.
Exercises
1. Draw the structure of leucine and determine the charge on the molecule in a(n)
a. acidic solution (pH = 1).
b. neutral solution (pH = 7).
c. a basic solution (pH = 11)
2. Draw the structure of isoleucine and determine the charge on the molecule in a(n)
c. basic solution (pH = 11).
Answer
1. a.
b.
c.
4.3: Reactions of Amino Acids is shared under a CC BY-NC-SA 4.0 license and was authored, remixed, and/or curated by LibreTexts.
4.4: Peptides
Learning Objectives
Explain how a peptide is formed from individual amino acids.
Explain why the sequence of amino acids in a protein is important.
Two or more amino acids can join together into chains called peptides. Previously, we discussed the reaction between ammonia and
a carboxylic acid to form an amide. In a similar reaction, the amino group on one amino acid molecule reacts with the carboxyl
group on another, releasing a molecule of water and forming an amide linkage:
An amide bond joining two amino acid units is called a peptide bond. Note that the product molecule still has a reactive amino
group on the left and a reactive carboxyl group on the right. These can react with additional amino acids to lengthen the peptide.
The process can continue until thousands of units have joined, resulting in large proteins.
A chain consisting of only two amino acid units is called a dipeptide; a chain consisting of three is a tripeptide. By convention,
peptide and protein structures are depicted with the amino acid whose amino group is free (the N-terminal end) on the left and the
amino acid with a free carboxyl group (the C-terminal end) to the right.
The general term peptide refers to an amino acid chain of unspecified length. However, chains of about 50 amino acids or more are
usually called proteins or polypeptides. In its physiologically active form, a protein may be composed of one or more polypeptide
chains.
Figure 4.4.1 : Space-filling model of bradykinin. Image used with permission (Public Domain; Fvasconcellos)
For peptides and proteins to be physiologically active, it is not enough that they incorporate certain amounts of specific amino
acids. The order, or sequence, in which the amino acids are connected is also of critical importance. Bradykinin is a nine-amino
acid peptide (Figure 4.4.1) produced in the blood that has the following amino acid sequence:
arg-pro-pro-gly-phe-ser-pro-phe-arg
This peptide lowers blood pressure, stimulates smooth muscle tissue, increases capillary permeability, and causes pain. When the
order of amino acids in bradykinin is reversed,
arg-phe-pro-ser-phe-gly-pro-pro-arg
the peptide resulting from this synthesis shows none of the activity of bradykinin.
Just as millions of different words are spelled with our 26-letter English alphabet, millions of different proteins are made with the
20 common amino acids. However, just as the English alphabet can be used to write gibberish, amino acids can be put together in
the wrong sequence to produce nonfunctional proteins. Although the correct sequence is ordinarily of utmost importance, it is not
always absolutely required. Just as you can sometimes make sense of incorrectly spelled English words, a protein with a small
percentage of “incorrect” amino acids may continue to function. However, it rarely functions as well as a protein having the correct
sequence. There are also instances in which seemingly minor errors of sequence have disastrous effects. For example, in some
people, every molecule of hemoglobin (a protein in the blood that transports oxygen) has a single incorrect amino acid unit out of
about 300 (a single valine replaces a glutamic acid). That “minor” error is responsible for sickle cell anemia, an inherited condition
that usually is fatal.
Summary
The amino group of one amino acid can react with the carboxyl group on another amino acid to form a peptide bond that links the
two amino acids together. Additional amino acids can be added on through the formation of addition peptide (amide) bonds. A
sequence of amino acids in a peptide or protein is written with the N-terminal amino acid first and the C-terminal amino acid at the
end (writing left to right).

1. Distinguish between the N-terminal amino acid and the C-terminal amino acid of a peptide or protein.
2. Describe the difference between an amino acid and a peptide.
3. Amino acid units in a protein are connected by peptide bonds. What is another name for the functional group linking the amino
acids?
Answers
1. The N-terminal end is the end of a peptide or protein whose amino group is free (not involved in the formation of a peptide
bond), while the C-terminal end has a free carboxyl group.
2. A peptide is composed of two or more amino acids. Amino acids are the building blocks of peptides.
3. amide bond
Exercises
1. Draw the structure for each peptide.
a. gly-val
b. val-gly
2. Draw the structure for cys-val-ala.
3. Identify the C- and N-terminal amino acids for the peptide lys-val-phe-gly-arg-cys.
4. Identify the C- and N-terminal amino acids for the peptide asp-arg-val-tyr-ile-his-pro-phe.
Answers
1. a.
b.
3. C-terminal amino acid: cys; N-terminal amino acid: lys
4.4: Peptides is shared under a CC BY-NC-SA 4.0 license and was authored, remixed, and/or curated by LibreTexts.
4.5: Proteins
Learning Objectives
Describe the four levels of protein structure.
Identify the types of attractive interactions that hold proteins in their most stable three-dimensional structure.
Explain what happens when proteins are denatured.
Identify how a protein can be denatured.
Each of the thousands of naturally occurring proteins has its own characteristic amino acid composition and sequence that result in
a unique three-dimensional shape. Since the 1950s, scientists have determined the amino acid sequences and three-dimensional
conformation of numerous proteins and thus obtained important clues on how each protein performs its specific function in the
body.
Proteins are compounds of high molar mass consisting largely or entirely of chains of amino acids. Because of their great
complexity, protein molecules cannot be classified on the basis of specific structural similarities, as carbohydrates and lipids are
categorized. The two major structural classifications of proteins are based on far more general qualities: whether the protein is (1)
fiberlike and insoluble or (2) globular and soluble. Some proteins, such as those that compose hair, skin, muscles, and connective
tissue, are fiberlike. These fibrous proteins are insoluble in water and usually serve structural, connective, and protective functions.
Examples of fibrous proteins are keratins, collagens, myosins, and elastins. Hair and the outer layer of skin are composed of
keratin. Connective tissues contain collagen. Myosins are muscle proteins and are capable of contraction and extension. Elastins are
found in ligaments and the elastic tissue of artery walls.
Globular proteins, the other major class, are soluble in aqueous media. In these proteins, the chains are folded so that the molecule
as a whole is roughly spherical. Familiar examples include egg albumin from egg whites and serum albumin in blood. Serum
albumin plays a major role in transporting fatty acids and maintaining a proper balance of osmotic pressures in the body.
Hemoglobin and myoglobin, which are important for binding oxygen, are also globular proteins.
Levels of Protein Structure

The structure of proteins is generally described as having four organizational levels. The first of these is the primary structure,
which is the number and sequence of amino acids in a protein’s polypeptide chain or chains, beginning with the free amino group
and maintained by the peptide bonds connecting each amino acid to the next. The primary structure of insulin, composed of 51
amino acids, is shown in Figure 4.5.1.
Figure 4.5.1 : Primary Structure of Human Insulin. Human insulin, whose amino acid sequence is shown here, is a hormone that is
required for the proper metabolism of glucose.
A protein molecule is not a random tangle of polypeptide chains. Instead, the chains are arranged in unique but specific
conformations. The term secondary structure refers to the fixed arrangement of the polypeptide backbone. On the basis of X ray
studies, Linus Pauling and Robert Corey postulated that certain proteins or portions of proteins twist into a spiral or a helix. This
helix is stabilized by intrachain hydrogen bonding between the carbonyl oxygen atom of one amino acid and the amide hydrogen
atom four amino acids up the chain (located on the next turn of the helix) and is known as a right-handed α-helix. X ray data
indicate that this helix makes one turn for every 3.6 amino acids, and the side chains of these amino acids project outward from the
coiled backbone (Figure 4.5.2). The α-keratins, found in hair and wool, are exclusively α-helical in conformation. Some proteins,
such as gamma globulin, chymotrypsin, and cytochrome c, have little or no helical structure. Others, such as hemoglobin and
myoglobin, are helical in certain regions but not in others.
Figure 4.5.2 A Ball-and-Stick Model of an α-Helix. This ball-and-stick model shows the intrachain hydrogen bonding between
carbonyl oxygen atoms and amide hydrogen atoms. Each turn of the helix spans 3.6 amino acids. Note that the side chains
(represented as green spheres) point out from the helix.
Another common type of secondary structure, called the β-pleated sheet conformation, is a sheetlike arrangement in which two or
more extended polypeptide chains (or separate regions on the same chain) are aligned side by side. The aligned segments can run
either parallel or antiparallel—that is, the N-terminals can face in the same direction on adjacent chains or in different directions—
and are connected by interchain hydrogen bonding (Figure 4.5.3). The β-pleated sheet is particularly important in structural
proteins, such as silk fibroin. It is also seen in portions of many enzymes, such as carboxypeptidase A and lysozyme.
Figure 4.5.3 : A Ball-and-Stick Model of the β-Pleated Sheet Structure in Proteins. The side chains extend above or below the sheet
and alternate along the chain. The protein chains are held together by interchain hydrogen bonding.
Tertiary structure refers to the unique three-dimensional shape of the protein as a whole, which results from the folding and
bending of the protein backbone. The tertiary structure is intimately tied to the proper biochemical functioning of the protein.
Figure 4.5.4 shows a depiction of the three-dimensional structure of insulin.
Figure 4.5.4 : A Ribbon Model of the Three-Dimensional Structure of Insulin. The spiral regions represent sections of the
polypeptide chain that have an α-helical structure, while the broad arrows represent β-pleated sheet structures.
Four major types of attractive interactions determine the shape and stability of the tertiary structure of proteins. You studied several
of them previously.
1. Ionic bonding. Ionic bonds result from electrostatic attractions between positively and negatively charged side chains of amino
acids. For example, the mutual attraction between an aspartic acid carboxylate ion and a lysine ammonium ion helps to maintain
a particular folded area of a protein (part (a) of Figure 4.5.5).
2. Hydrogen bonding. Hydrogen bonding forms between a highly electronegative oxygen atom or a nitrogen atom and a hydrogen
atom attached to another oxygen atom or a nitrogen atom, such as those found in polar amino acid side chains. Hydrogen
bonding (as well as ionic attractions) is extremely important in both the intra- and intermolecular interactions of proteins (part
(b) of Figure 4.5.5).
3. Disulfide linkages. Two cysteine amino acid units may be brought close together as the protein molecule folds. Subsequent
oxidation and linkage of the sulfur atoms in the highly reactive sulfhydryl (SH) groups leads to the formation of cystine (part (c)
of Figure 4.5.5). Intrachain disulfide linkages are found in many proteins, including insulin (yellow bars in Figure 4.5.1) and
have a strong stabilizing effect on the tertiary structure.
4. Dispersion forces. Dispersion forces arise when a normally nonpolar atom becomes momentarily polar due to an uneven
distribution of electrons, leading to an instantaneous dipole that induces a shift of electrons in a neighboring nonpolar atom.
Dispersion forces are weak but can be important when other types of interactions are either missing or minimal (part (d) of
Figure 4.5.5). This is the case with fibroin, the major protein in silk, in which a high proportion of amino acids in the protein
have nonpolar side chains. The term hydrophobic interaction is often misused as a synonym for dispersion forces. Hydrophobic
interactions arise because water molecules engage in hydrogen bonding with other water molecules (or groups in proteins
capable of hydrogen bonding). Because nonpolar groups cannot engage in hydrogen bonding, the protein folds in such a way
that these groups are buried in the interior part of the protein structure, minimizing their contact with water.
Figure 4.5.5 : Tertiary Protein Structure Interactions. Four interactions stabilize the tertiary structure of a protein: (a) ionic bonding,
(b) hydrogen bonding, (c) disulfide linkages, and (d) dispersion forces.
When a protein contains more than one polypeptide chain, each chain is called a subunit. The arrangement of multiple subunits
represents a fourth level of structure, the quaternary structure of a protein. Hemoglobin, with four polypeptide chains or subunits, is
the most frequently cited example of a protein having quaternary structure (Figure 4.5.6). The quaternary structure of a protein is
produced and stabilized by the same kinds of interactions that produce and maintain the tertiary structure. A schematic
representation of the four levels of protein structure is in Figure 4.5.7.
Figure 4.5.6 The Quaternary Structure of Hemoglobin. Hemoglobin is a protein that transports oxygen throughout the body.
Source: Image from the RCSB PDB (www.pdb.org) of PDB ID 1I3D (R.D. Kidd, H.M. Baker, A.J. Mathews, T. Brittain, E.N.
Baker (2001) Oligomerization and ligand binding in a homotetrameric hemoglobin: two high-resolution crystal structures of
hemoglobin Bart's (gamma(4)), a marker for alpha-thalassemia. Protein Sci. 1739–1749).
Figure 4.5.7 : Levels of Structure in Proteins
The primary structure consists of the specific amino acid sequence. The resulting peptide chain can twist into an α-helix, which is
one type of secondary structure. This helical segment is incorporated into the tertiary structure of the folded polypeptide chain.
The single polypeptide chain is a subunit that constitutes the quaternary structure of a protein, such as hemoglobin that has four
polypeptide chains.
Denaturation of Proteins
The highly organized structures of proteins are truly masterworks of chemical architecture. But highly organized structures tend to
have a certain delicacy, and this is true of proteins. Denaturation is the term used for any change in the three-dimensional structure
of a protein that renders it incapable of performing its assigned function. A denatured protein cannot do its job. (Sometimes
denaturation is equated with the precipitation or coagulation of a protein; our definition is a bit broader.) A wide variety of reagents
and conditions, such as heat, organic compounds, pH changes, and heavy metal ions can cause protein denaturation (Figure 4.5.1).
Figure 4.5.1 : Protein Denaturation Methods
Method Effect on Protein Structure
Heat or UV radiation supplies kinetic energy to protein molecules,

Heat above 50°C or ultraviolet (UV) radiation causing their atoms to vibrate more rapidly and disrupting relatively
weak hydrogen bonding and dispersion forces.
These compounds are capable of engaging in intermolecular hydrogen

Use of organic compounds, such as ethyl alcohol bonding with protein molecules, disrupting intramolecular hydrogen
bonding within the protein.
These ions form strong bonds with the carboxylate anions of the acidic
Salts of heavy metal ions, such as mercury, silver, and lead amino acids or SH groups of cysteine, disrupting ionic bonds and
disulfide linkages.
These reagents combine with positively charged amino groups in

Alkaloid reagents, such as tannic acid (used in tanning leather)
proteins to disrupt ionic bonds.
Anyone who has fried an egg has observed denaturation. The clear egg white turns opaque as the albumin denatures and
coagulates. No one has yet reversed that process. However, given the proper circumstances and enough time, a protein that has
unfolded under sufficiently gentle conditions can refold and may again exhibit biological activity (Figure 4.5.8). Such evidence
suggests that, at least for these proteins, the primary structure determines the secondary and tertiary structure. A given sequence of
amino acids seems to adopt its particular three-dimensional arrangement naturally if conditions are right.
Figure 4.5.8 : Denaturation and Renaturation of a Protein. The denaturation (unfolding) and renaturation (refolding) of a protein is
depicted. The red boxes represent stabilizing interactions, such as disulfide linkages, hydrogen bonding, and/or ionic bonds.
The primary structures of proteins are quite sturdy. In general, fairly vigorous conditions are needed to hydrolyze peptide bonds. At
the secondary through quaternary levels, however, proteins are quite vulnerable to attack, though they vary in their vulnerability to
denaturation. The delicately folded globular proteins are much easier to denature than are the tough, fibrous proteins of hair and
skin.
Summary
Proteins can be divided into two categories: fibrous, which tend to be insoluble in water, and globular, which are more soluble in
water. A protein may have up to four levels of structure. The primary structure consists of the specific amino acid sequence. The
resulting peptide chain can form an α-helix or β-pleated sheet (or local structures not as easily categorized), which is known as
secondary structure. These segments of secondary structure are incorporated into the tertiary structure of the folded polypeptide
chain. The quaternary structure describes the arrangements of subunits in a protein that contains more than one subunit. Four major
types of attractive interactions determine the shape and stability of the folded protein: ionic bonding, hydrogen bonding, disulfide
linkages, and dispersion forces. A wide variety of reagents and conditions can cause a protein to unfold or denature.

1. What is the predominant attractive force that stabilizes the formation of secondary structure in proteins?
2. Distinguish between the tertiary and quaternary levels of protein structure.
3. Briefly describe four ways in which a protein could be denatured.
Answers
1. hydrogen bonding
2. Tertiary structure refers to the unique three-dimensional shape of a single polypeptide chain, while quaternary structure
describes the interaction between multiple polypeptide chains for proteins that have more than one polypeptide chain.
3. (1) heat a protein above 50°C or expose it to UV radiation; (2) add organic solvents, such as ethyl alcohol, to a protein solution;
(3) add salts of heavy metal ions, such as mercury, silver, or lead; and (4) add alkaloid reagents such as tannic acid
Exercises
1. Classify each protein as fibrous or globular.
a. albumin
b. myosin
c. fibroin
a. hemoglobin
b. keratin
c. myoglobin
3. What name is given to the predominant secondary structure found in silk?
4. What name is given to the predominant secondary structure found in wool protein?
5. A protein has a tertiary structure formed by interactions between the side chains of the following pairs of amino acids. For each
pair, identify the strongest type of interaction between these amino acids.
a. aspartic acid and lysine
b. phenylalanine and alanine
c. serine and lysine
d. two cysteines
a. valine and isoleucine
b. asparagine and serine
c. glutamic acid and arginine
d. tryptophan and methionine
7. What level(s) of protein structure is(are) ordinarily disrupted in denaturation? What level(s) is(are) not?
8. Which class of proteins is more easily denatured—fibrous or globular?
Answers
1. a. globular
b. fibrous
c. fibrous
3. β-pleated sheet
5. a. ionic bonding
b. dispersion forces
c. dispersion forces
d. disulfide linkage
7. Protein denaturation disrupts the secondary, tertiary, and quaternary levels of structure. Only primary structure is unaffected by
denaturation.
4.5: Proteins is shared under a CC BY-NC-SA 4.0 license and was authored, remixed, and/or curated by LibreTexts.
4.6: Enzymes
Learning Objectives
Explain the functions of enzymes.
Explain how enzymes are classified and named.
A catalyst is any substance that increases the rate or speed of a chemical reaction without being changed or consumed in the
reaction. Enzymes are biological catalysts, and nearly all of them are proteins. The reaction rates attained by enzymes are truly
amazing. In their presence, reactions occur at rates that are a million (106) or more times faster than would be attainable in their
absence. What is even more amazing is that enzymes perform this function at body temperature (~37°C) and physiological pH (pH
~7), rather than at the conditions that are typically necessary to increase reaction rates (high temperature or pressure, the use of
strong oxidizing or reducing agents or strong acids or bases, or a combination of any of these). In addition, enzymes are highly
specific in their action; that is, each enzyme catalyzes only one type of reaction in only one compound or a group of structurally
related compounds. The compound or compounds on which an enzyme acts are known as its substrates.
Hundreds of enzymes have been purified and studied in an effort to understand how they work so effectively and with such
specificity. The resulting knowledge has been used to design drugs that inhibit or activate particular enzymes. An example is the
intensive research to improve the treatment of or find a cure for acquired immunodeficiency syndrome (AIDS). AIDS is caused by
the human immunodeficiency virus (HIV). Researchers are studying the enzymes produced by this virus and are developing drugs
intended to block the action of those enzymes without interfering with enzymes produced by the human body. Several of these
drugs have now been approved for use by AIDS patients.
Table 4.6.1 : Classes of Enzymes
Class Type of Reaction Catalyzed Examples
Dehydrogenases catalyze oxidation-reduction

reactions involving hydrogen and reductases
oxidoreductases oxidation-reduction reactions
catalyze reactions in which a substrate is
reduced.
Transaminases catalyze the transfer of amino
transfer reactions of groups, such as methyl,
transferases group, and kinases catalyze the transfer of a
amino, and acetyl
phosphate group.
Lipases catalyze the hydrolysis of lipids, and
hydrolases hydrolysis reactions
proteases catalyze the hydrolysis of proteins
reactions in which groups are removed without

Decarboxylases catalyze the removal of
lyases hydrolysis or addition of groups to a double
carboxyl groups.
bond
Isomerases may catalyze the conversion of an

aldose to a ketose, and mutases catalyze
reactions in which a compound is converted to
isomerases reactions in which a functional group is
its isomer
transferred from one atom in a substrate to
another.
reactions in which new bonds are formed Synthetases catalyze reactions in which two
ligases between carbon and another atom; energy is smaller molecules are linked to form a larger
required one.
The first enzymes to be discovered were named according to their source or method of discovery. The enzyme pepsin, which aids
in the hydrolysis of proteins, is found in the digestive juices of the stomach (Greek pepsis, meaning “digestion”). Papain, another
enzyme that hydrolyzes protein (in fact, it is used in meat tenderizers), is isolated from papayas. As more enzymes were
discovered, chemists recognized the need for a more systematic and chemically informative identification scheme. In the current
numbering and naming scheme, under the oversight of the Nomenclature Commission of the International Union of Biochemistry,
enzymes are arranged into six groups according to the general type of reaction they catalyze (Table 4.6.1), with subgroups and
secondary subgroups that specify the reaction more precisely.
Figure 4.6.1 : Structure of the alcohol dehydrogenase protein (E.C.1.1.1.1) (EE ISOZYME) complexed wtih nicotinamide adenini
dinulceotide (NAD) and zinc (PDB: 1CDO).
Each enzyme is assigned a four-digit number, preceded by the prefix EC—for enzyme classification—that indicates its group,
subgroup, and so forth. This is demonstrated in Table 4.6.2 for alcohol dehydrogenase. Each enzyme is also given a name
consisting of the root of the name of its substrate or substrates and the -ase suffix. Thus urease is the enzyme that catalyzes the
hydrolysis of urea.
Table 4.6.2 : Assignment of an Enzyme Classification Number
Alcohol Dehydrogenase: EC 1.1.1.1
The first digit indicates that this enzyme is an oxidoreductase; that is, an enzyme that catalyzes an oxidation-reduction reaction.
The second digit indicates that this oxidoreductase catalyzes a reaction involving a primary or secondary alcohol.
The third digit indicates that either the coenzyme NAD+ or NADP+ is required for this reaction.
The fourth digit indicates that this was the first enzyme isolated, characterized, and named using this system of nomenclature.
The systematic name for this enzyme is alcohol:NAD+ oxidoreductase, while the recommended or common name is alcohol dehydrogenase.
Reaction catalyzed:
Summary
An enzyme is a biological catalyst, a substance that increases the rate of a chemical reaction without being changed or consumed in
the reaction. A systematic process is used to name and classify enzymes.

In the small intestine, sucrose is hydrolyzed to form glucose and fructose in a reaction catalyzed by sucrase.
1. Identify the substrate in this reaction.
2. Name the enzyme.
Answers
1. sucrose
2. sucrase
Exercises
1. Identify the substrate catalyzed by each enzyme.
a. lactase
b. cellulase
c. peptidase
a. lipase
b. amylase
c. maltase
3. Identify each type of enzyme.
a. decarboxylase
b. protease
c. transaminase
a. dehydrogenase
b. isomerase
c. lipase
Answers
1. a. lactose
b. cellulose
c. peptides
3. a. lyase
b. hydrolase
c. transferase
4.6: Enzymes is shared under a CC BY-NC-SA 4.0 license and was authored, remixed, and/or curated by LibreTexts.
4.7: Enzyme Action
Learning Objectives
To describe the interaction between an enzyme and its substrate.
Enzyme-catalyzed reactions occur in at least two steps. In the first step, an enzyme molecule (E) and the substrate molecule or
molecules (S) collide and react to form an intermediate compound called the enzyme-substrate (E–S) complex. (This step is
reversible because the complex can break apart into the original substrate or substrates and the free enzyme.) Once the E–S
complex forms, the enzyme is able to catalyze the formation of product (P), which is then released from the enzyme surface:
S + E → E– S (4.7.1)
E– S → P + E (4.7.2)
Hydrogen bonding and other electrostatic interactions hold the enzyme and substrate together in the complex. The structural
features or functional groups on the enzyme that participate in these interactions are located in a cleft or pocket on the enzyme
surface. This pocket, where the enzyme combines with the substrate and transforms the substrate to product is called the active site
of the enzyme (Figure 4.7.1).
Figure 4.7.1 : Substrate Binding to the Active Site of an Enzyme. The enzyme dihydrofolate reductase is shown with one of its
substrates: NADP+ (a) unbound and (b) bound. The NADP+ (shown in red) binds to a pocket that is complementary to it in shape
and ionic properties.
The active site of an enzyme possesses a unique conformation (including correctly positioned bonding groups) that is
complementary to the structure of the substrate, so that the enzyme and substrate molecules fit together in much the same manner
as a key fits into a tumbler lock. In fact, an early model describing the formation of the enzyme-substrate complex was called the
lock-and-key model (Figure 4.7.2). This model portrayed the enzyme as conformationally rigid and able to bond only to substrates
that exactly fit the active site.
Figure 4.7.2 : The Lock-and-Key Model of Enzyme Action. (a) Because the substrate and the active site of the enzyme have
complementary structures and bonding groups, they fit together as a key fits a lock. (b) The catalytic reaction occurs while the two
are bonded together in the enzyme-substrate complex.
Working out the precise three-dimensional structures of numerous enzymes has enabled chemists to refine the original lock-and-
key model of enzyme actions. They discovered that the binding of a substrate often leads to a large conformational change in the
enzyme, as well as to changes in the structure of the substrate or substrates. The current theory, known as the induced-fit model,
says that enzymes can undergo a change in conformation when they bind substrate molecules, and the active site has a shape
complementary to that of the substrate only after the substrate is bound, as shown for hexokinase in Figure 4.7.3. After catalysis,
the enzyme resumes its original structure.
Figure 4.7.3 : The Induced-Fit Model of Enzyme Action. (a) The enzyme hexokinase without its substrate (glucose, shown in red)
is bound to the active site. (b) The enzyme conformation changes dramatically when the substrate binds to it, resulting in additional
interactions between hexokinase and glucose.
The structural changes that occur when an enzyme and a substrate join together bring specific parts of a substrate into alignment
with specific parts of the enzyme’s active site. Amino acid side chains in or near the binding site can then act as acid or base
catalysts, provide binding sites for the transfer of functional groups from one substrate to another or aid in the rearrangement of a
substrate. The participating amino acids, which are usually widely separated in the primary sequence of the protein, are brought
close together in the active site as a result of the folding and bending of the polypeptide chain or chains when the protein acquires
its tertiary and quaternary structure. Binding to enzymes brings reactants close to each other and aligns them properly, which has
the same effect as increasing the concentration of the reacting compounds.
Example 4.7.1
a. What type of interaction would occur between an OH group present on a substrate molecule and a functional group in the
active site of an enzyme?
b. Suggest an amino acid whose side chain might be in the active site of an enzyme and form the type of interaction you just
identified.
SOLUTION
a. An OH group would most likely engage in hydrogen bonding with an appropriate functional group present in the active site
of an enzyme.
b. Several amino acid side chains would be able to engage in hydrogen bonding with an OH group. One example would be
asparagine, which has an amide functional group.
Exercise 4.7.1
a. What type of interaction would occur between an COO− group present on a substrate molecule and a functional group in the
active site of an enzyme?
b. Suggest an amino acid whose side chain might be in the active site of an enzyme and form the type of interaction you just
identified.
One characteristic that distinguishes an enzyme from all other types of catalysts is its substrate specificity. An inorganic acid such
as sulfuric acid can be used to increase the reaction rates of many different reactions, such as the hydrolysis of disaccharides,
polysaccharides, lipids, and proteins, with complete impartiality. In contrast, enzymes are much more specific. Some enzymes act
on a single substrate, while other enzymes act on any of a group of related molecules containing a similar functional group or
chemical bond. Some enzymes even distinguish between D- and L-stereoisomers, binding one stereoisomer but not the other.
Urease, for example, is an enzyme that catalyzes the hydrolysis of a single substrate—urea—but not the closely related compounds
methyl urea, thiourea, or biuret. The enzyme carboxypeptidase, on the other hand, is far less specific. It catalyzes the removal of
nearly any amino acid from the carboxyl end of any peptide or protein.
Enzyme specificity results from the uniqueness of the active site in each different enzyme because of the identity, charge, and
spatial orientation of the functional groups located there. It regulates cell chemistry so that the proper reactions occur in the proper
place at the proper time. Clearly, it is crucial to the proper functioning of the living cell.
Summary
A substrate binds to a specific region on an enzyme known as the active site, where the substrate can be converted to product. The
substrate binds to the enzyme primarily through hydrogen bonding and other electrostatic interactions. The induced-fit model says
that an enzyme can undergo a conformational change when binding a substrate. Enzymes exhibit varying degrees of substrate
specificity.

1. Distinguish between the lock-and-key model and induced-fit model of enzyme action.
2. Which enzyme has greater specificity—urease or carboxypeptidase? Explain.
Answers
1. The lock-and-key model portrays an enzyme as conformationally rigid and able to bond only to substrates that exactly fit the
active site. The induced fit model portrays the enzyme structure as more flexible and is complementary to the substrate only
after the substrate is bound.
2. Urease has the greater specificity because it can bind only to a single substrate. Carboxypeptidase, on the other hand, can
catalyze the removal of nearly any amino acid from the carboxyl end of a peptide or protein.
Exercises
1. What type of interaction would occur between each group present on a substrate molecule and a functional group of the active
site in an enzyme?
a. COOH
b. NH3+
c. OH
d. CH(CH3)2
site in an enzyme?
a. SH
b. NH2
c. C6H5
d. COO−
3. For each functional group in Exercise 1, suggest an amino acid whose side chain might be in the active site of an enzyme and
form the type of interaction you identified.
Answers
1. a. hydrogen bonding
b. ionic bonding
c. hydrogen bonding
d. dispersion forces
3. a. The amino acid has a polar side chain capable of engaging in hydrogen bonding; serine (answers will vary).
b. The amino acid has a negatively charged side chain; aspartic acid (answers will vary).
c. The amino acid has a polar side chain capable of engaging in hydrogen bonding; asparagine (answers will vary).
d. The amino acid has a nonpolar side chain; isoleucine (answers will vary).
4.7: Enzyme Action is shared under a CC BY-NC-SA 4.0 license and was authored, remixed, and/or curated by LibreTexts.
Learning Objectives
To describe how pH, temperature, and the concentration of an enzyme and its substrate influence enzyme activity.
The single most important property of enzymes is the ability to increase the rates of reactions occurring in living organisms, a
property known as catalytic activity. Because most enzymes are proteins, their activity is affected by factors that disrupt protein
structure, as well as by factors that affect catalysts in general. Factors that disrupt protein structure include temperature and pH;
factors that affect catalysts in general include reactant or substrate concentration and catalyst or enzyme concentration. The activity
of an enzyme can be measured by monitoring either the rate at which a substrate disappears or the rate at which a product forms.
Concentration of Substrate
In the presence of a given amount of enzyme, the rate of an enzymatic reaction increases as the substrate concentration increases
until a limiting rate is reached, after which further increase in the substrate concentration produces no significant change in the
reaction rate (part (a) of Figure 4.8.1). At this point, so much substrate is present that essentially all of the enzyme active sites have
substrate bound to them. In other words, the enzyme molecules are saturated with substrate. The excess substrate molecules cannot
react until the substrate already bound to the enzymes has reacted and been released (or been released without reacting).
Figure 4.8.1 : Concentration versus Reaction Rate. (a) This graph shows the effect of substrate concentration on the rate of a
reaction that is catalyzed by a fixed amount of enzyme. (b) This graph shows the effect of enzyme concentration on the reaction
rate at a constant level of substrate.
Let’s consider an analogy. Ten taxis (enzyme molecules) are waiting at a taxi stand to take people (substrate) on a 10-minute trip to
a concert hall, one passenger at a time. If only 5 people are present at the stand, the rate of their arrival at the concert hall is 5
people in 10 minutes. If the number of people at the stand is increased to 10, the rate increases to 10 arrivals in 10 minutes. With 20
people at the stand, the rate would still be 10 arrivals in 10 minutes. The taxis have been “saturated.” If the taxis could carry 2 or 3
passengers each, the same principle would apply. The rate would simply be higher (20 or 30 people in 10 minutes) before it leveled
off.
Concentration of Enzyme
When the concentration of the enzyme is significantly lower than the concentration of the substrate (as when the number of taxis is
far lower than the number of waiting passengers), the rate of an enzyme-catalyzed reaction is directly dependent on the enzyme
concentration (part (b) of Figure 4.8.1). This is true for any catalyst; the reaction rate increases as the concentration of the catalyst
is increased.
Temperature
A general rule of thumb for most chemical reactions is that a temperature rise of 10°C approximately doubles the reaction rate. To
some extent, this rule holds for all enzymatic reactions. After a certain point, however, an increase in temperature causes a decrease
in the reaction rate, due to denaturation of the protein structure and disruption of the active site (part (a) of Figure 4.8.2). For many
proteins, denaturation occurs between 45°C and 55°C. Furthermore, even though an enzyme may appear to have a maximum
reaction rate between 40°C and 50°C, most biochemical reactions are carried out at lower temperatures because enzymes are not
stable at these higher temperatures and will denature after a few minutes.
Figure 4.8.2 : Temperature and pH versus Concentration. (a) This graph depicts the effect of temperature on the rate of a reaction
that is catalyzed by a fixed amount of enzyme. (b) This graph depicts the effect of pH on the rate of a reaction that is catalyzed by a
fixed amount of enzyme.
At 0°C and 100°C, the rate of enzyme-catalyzed reactions is nearly zero. This fact has several practical applications. We sterilize
objects by placing them in boiling water, which denatures the enzymes of any bacteria that may be in or on them. We preserve our
food by refrigerating or freezing it, which slows enzyme activity. When animals go into hibernation in winter, their body
temperature drops, decreasing the rates of their metabolic processes to levels that can be maintained by the amount of energy stored
in the fat reserves in the animals’ tissues.
Hydrogen Ion Concentration (pH)

Because most enzymes are proteins, they are sensitive to changes in the hydrogen ion concentration or pH. Enzymes may be
denatured by extreme levels of hydrogen ions (whether high or low); any change in pH, even a small one, alters the degree of
ionization of an enzyme’s acidic and basic side groups and the substrate components as well. Ionizable side groups located in the
active site must have a certain charge for the enzyme to bind its substrate. Neutralization of even one of these charges alters an
enzyme’s catalytic activity.
An enzyme exhibits maximum activity over the narrow pH range in which a molecule exists in its properly charged form. The
median value of this pH range is called the optimum pH of the enzyme (part (b) of Figure 4.8.2). With the notable exception of
gastric juice (the fluids secreted in the stomach), most body fluids have pH values between 6 and 8. Not surprisingly, most enzymes
exhibit optimal activity in this pH range. However, a few enzymes have optimum pH values outside this range. For example, the
optimum pH for pepsin, an enzyme that is active in the stomach, is 2.0.
Summary
Initially, an increase in substrate concentration leads to an increase in the rate of an enzyme-catalyzed reaction. As the enzyme
molecules become saturated with substrate, this increase in reaction rate levels off. The rate of an enzyme-catalyzed reaction
increases with an increase in the concentration of an enzyme. At low temperatures, an increase in temperature increases the rate of
an enzyme-catalyzed reaction. At higher temperatures, the protein is denatured, and the rate of the reaction dramatically decreases.
An enzyme has an optimum pH range in which it exhibits maximum activity.

1. The concentration of substrate X is low. What happens to the rate of the enzyme-catalyzed reaction if the concentration of X is
doubled?
2. What effect does an increase in the enzyme concentration have on the rate of an enzyme-catalyzed reaction?
Answers
1. If the concentration of the substrate is low, increasing its concentration will increase the rate of the reaction.
2. An increase in the amount of enzyme will increase the rate of the reaction (provided sufficient substrate is present).
Exercises
1. In non-enzyme-catalyzed reactions, the reaction rate increases as the concentration of reactant is increased. In an enzyme-
catalyzed reaction, the reaction rate initially increases as the substrate concentration is increased but then begins to level off, so
that the increase in reaction rate becomes less and less as the substrate concentration increases. Explain this difference.
2. Why do enzymes become inactive at very high temperatures?
3. An enzyme has an optimum pH of 7.4. What is most likely to happen to the activity of the enzyme if the pH drops to 6.3?
Explain.
4. An enzyme has an optimum pH of 7.2. What is most likely to happen to the activity of the enzyme if the pH increases to 8.5?
Explain.
Answers
1. In an enzyme-catalyzed reaction, the substrate binds to the enzyme to form an enzyme-substrate complex. If more substrate is
present than enzyme, all of the enzyme binding sites will have substrate bound, and further increases in substrate concentration
cannot increase the rate.
3. The activity will decrease; a pH of 6.3 is more acidic than 7.4, and one or more key groups in the active site may bind a
hydrogen ion, changing the charge on that group.
4.8: Enzyme Activity is shared under a CC BY-NC-SA 4.0 license and was authored, remixed, and/or curated by LibreTexts.
Learning Objectives
Explain what an enzyme inhibitor is.
Distinguish between reversible and irreversible inhibitors.
Distinguish between competitive and noncompetitive inhibitors.
Previously, we noted that enzymes are inactivated at high temperatures and by changes in pH. These are nonspecific factors that
would inactivate any enzyme. The activity of enzymes can also be regulated by more specific inhibitors. Many compounds are
poisons because they bind covalently to particular enzymes or kinds of enzymes and inactivate them (Table 4.9.1).
Table 4.9.1 : Poisons as Enzyme Inhibitors
Poison Formula Example of Enzyme Inhibited Action
glyceraldehyde 3-phosphate
arsenate AsO
3 −
substitutes for phosphate
4
dehydrogenase
iodoacetate ICH COO

2
−
triose phosphate dehydrogenase binds to cysteine SH group
diisopropylfluoro-phosphate
acetylcholinesterase binds to serine OH group
(DIFP; a nerve poison)
Irreversible Inhibition: Poisons

An irreversible inhibitor inactivates an enzyme by bonding covalently to a particular group at the active site. The inhibitor-enzyme
bond is so strong that the inhibition cannot be reversed by the addition of excess substrate. The nerve gases, especially Diisopropyl
fluorophosphate (DIFP), irreversibly inhibit biological systems by forming an enzyme-inhibitor complex with a specific OH group
of serine situated at the active sites of certain enzymes. The peptidases trypsin and chymotrypsin contain serine groups at the active
site and are inhibited by DIFP.
Reversible Inhibition
A reversible inhibitor inactivates an enzyme through noncovalent, more easily reversed, interactions. Unlike an irreversible
inhibitor, a reversible inhibitor can dissociate from the enzyme. Reversible inhibitors include competitive inhibitors and
noncompetitive inhibitors. (There are additional types of reversible inhibitors.) A competitive inhibitor is any compound that bears
a structural resemblance to a particular substrate and thus competes with that substrate for binding at the active site of an enzyme.
The inhibitor is not acted on by the enzyme but does prevent the substrate from approaching the active site.
The degree to which a competitive inhibitor interferes with an enzyme’s activity depends on the relative concentrations of the
substrate and the inhibitor. If the inhibitor is present in relatively large quantities, it will initially block most of the active sites. But
because the binding is reversible, some substrate molecules will eventually bind to the active site and be converted to product.
Increasing the substrate concentration promotes displacement of the inhibitor from the active site. Competitive inhibition can be
completely reversed by adding substrate so that it reaches a much higher concentration than that of the inhibitor.
Studies of competitive inhibition have provided helpful information about certain enzyme-substrate complexes and the interactions
of specific groups at the active sites. As a result, pharmaceutical companies have synthesized drugs that competitively inhibit
metabolic processes in bacteria and certain cancer cells. Many drugs are competitive inhibitors of specific enzymes.
A classic example of competitive inhibition is the effect of malonate on the enzyme activity of succinate dehydrogenase (Figure
4.9.1). Malonate and succinate are the anions of dicarboxylic acids and contain three and four carbon atoms, respectively. The
malonate molecule binds to the active site because the spacing of its carboxyl groups is not greatly different from that of succinate.
However, no catalytic reaction occurs because malonate does not have a CH2CH2 group to convert to CH=CH. This reaction will
also be discussed in connection with the Krebs cycle and energy production.
Figure 4.9.1 : Competitive Inhibition. (a) Succinate binds to the enzyme succinate dehydrogenase. A dehydrogenation reaction
occurs, and the product—fumarate—is released from the enzyme. (b) Malonate also binds to the active site of succinate
dehydrogenase. In this case, however, no subsequent reaction occurs while malonate remains bound to the enzyme.
To Your Health: Penicillin
Chemotherapy is the strategic use of chemicals (that is, drugs) to destroy infectious microorganisms or cancer cells without
causing excessive damage to the other, healthy cells of the host. From bacteria to humans, the metabolic pathways of all living
organisms are quite similar, so the search for safe and effective chemotherapeutic agents is a formidable task. Many well-
established chemotherapeutic drugs function by inhibiting a critical enzyme in the cells of the invading organism.
An antibiotic is a compound that kills bacteria; it may come from a natural source such as molds or be synthesized with a
structure analogous to a naturally occurring antibacterial compound. Antibiotics constitute no well-defined class of chemically
related substances, but many of them work by effectively inhibiting a variety of enzymes essential to bacterial growth.
Penicillin, one of the most widely used antibiotics in the world, was fortuitously discovered by Alexander Fleming in 1928,
when he noticed antibacterial properties in a mold growing on a bacterial culture plate. In 1938, Ernst Chain and Howard Florey
began an intensive effort to isolate penicillin from the mold and study its properties. The large quantities of penicillin needed for
this research became available through development of a corn-based nutrient medium that the mold loved and through the
discovery of a higher-yielding strain of mold at a United States Department of Agriculture research center near Peoria, Illinois.
Even so, it was not until 1944 that large quantities of penicillin were being produced and made available for the treatment of
bacterial infections.
Penicillin functions by interfering with the synthesis of cell walls of reproducing bacteria. It does so by inhibiting an enzyme—
transpeptidase—that catalyzes the last step in bacterial cell-wall biosynthesis. The defective walls cause bacterial cells to burst.
Human cells are not affected because they have cell membranes, not cell walls.
Several naturally occurring penicillins have been isolated. They are distinguished by different R groups connected to a common
structure: a four-member cyclic amide (called a lactam ring) fused to a five-member ring. The addition of appropriate organic
compounds to the culture medium leads to the production of the different kinds of penicillin.
The penicillins are effective against gram-positive bacteria (bacteria capable of being stained by Gram’s stain) and a few gram-
negative bacteria (including the intestinal bacterium Escherichia coli). They are effective in the treatment of diphtheria,
gonorrhea, pneumonia, syphilis, many pus infections, and certain types of boils. Penicillin G was the earliest penicillin to be
used on a wide scale. However, it cannot be administered orally because it is quite unstable; the acidic pH of the stomach
converts it to an inactive derivative. The major oral penicillins—penicillin V, ampicillin, and amoxicillin—on the other hand,
are acid stable.
Some strains of bacteria become resistant to penicillin through a mutation that allows them to synthesize an enzyme—
penicillinase—that breaks the antibiotic down (by cleavage of the amide linkage in the lactam ring). To combat these strains,
scientists have synthesized penicillin analogs (such as methicillin) that are not inactivated by penicillinase.
Some people (perhaps 5% of the population) are allergic to penicillin and therefore must be treated with other antibiotics. Their
allergic reaction can be so severe that a fatal coma may occur if penicillin is inadvertently administered to them. Fortunately,
several other antibiotics have been discovered. Most, including aureomycin and streptomycin, are the products of microbial
synthesis. Others, such as the semisynthetic penicillins and tetracyclines, are made by chemical modifications of antibiotics; and
some, like chloramphenicol, are manufactured entirely by chemical synthesis. They are as effective as penicillin in destroying
infectious microorganisms. Many of these antibiotics exert their effects by blocking protein synthesis in microorganisms.
Initially, antibiotics were considered miracle drugs, substantially reducing the number of deaths from blood poisoning,
pneumonia, and other infectious diseases. Some seven decades ago, a person with a major infection almost always died. Today,
such deaths are rare. Seven decades ago, pneumonia was a dreaded killer of people of all ages. Today, it kills only the very old
or those ill from other causes. Antibiotics have indeed worked miracles in our time, but even miracle drugs have limitations. Not
long after the drugs were first used, disease organisms began to develop strains resistant to them. In a race to stay ahead of
resistant bacterial strains, scientists continue to seek new antibiotics. The penicillins have now been partially displaced by
related compounds, such as the cephalosporins and vancomycin. Unfortunately, some strains of bacteria have already shown
resistance to these antibiotics.
Some reversible inhibitors are noncompetitive. A noncompetitive inhibitor can combine with either the free enzyme or the enzyme-
substrate complex because its binding site on the enzyme is distinct from the active site. Binding of this kind of inhibitor alters the
three-dimensional conformation of the enzyme, changing the configuration of the active site with one of two results. Either the
enzyme-substrate complex does not form at its normal rate, or, once formed, it does not yield products at the normal rate. Because
the inhibitor does not structurally resemble the substrate, the addition of excess substrate does not reverse the inhibitory effect.
Figure 4.9.2 : Feedback Inhibition of Threonine Deaminase by Isoleucine. Threonine deaminase is the first enzyme in the
conversion of threonine to isoleucine. Isoleucine inhibits threonine deaminase through feedback inhibition.
Feedback inhibition is a normal biochemical process that makes use of noncompetitive inhibitors to control some enzymatic
activity. In this process, the final product inhibits the enzyme that catalyzes the first step in a series of reactions. Feedback
inhibition is used to regulate the synthesis of many amino acids. For example, bacteria synthesize isoleucine from threonine in a
series of five enzyme-catalyzed steps. As the concentration of isoleucine increases, some of it binds as a noncompetitive inhibitor
to the first enzyme of the series (threonine deaminase), thus bringing about a decrease in the amount of isoleucine being formed
(Figure 4.9.2).
Summary
An irreversible inhibitor inactivates an enzyme by bonding covalently to a particular group at the active site. A reversible inhibitor
inactivates an enzyme through noncovalent, reversible interactions. A competitive inhibitor competes with the substrate for binding
at the active site of the enzyme. A noncompetitive inhibitor binds at a site distinct from the active site.

1. What are the characteristics of an irreversible inhibitor?
2. In what ways does a competitive inhibitor differ from a noncompetitive inhibitor?
Answers
1. It inactivates an enzyme by bonding covalently to a particular group at the active site.
2. A competitive inhibitor structurally resembles the substrate for a given enzyme and competes with the substrate for binding at
the active site of the enzyme. A noncompetitive inhibitor binds at a site distinct from the active site and can bind to either the
free enzyme or the enzyme-substrate complex.
Exercises
1. What amino acid is present in the active site of all enzymes that are irreversibly inhibited by nerve gases such as DIFP?
2. Oxaloacetate (OOCCH2COCOO) inhibits succinate dehydrogenase. Would you expect oxaloacetate to be a competitive or
noncompetitive inhibitor? Explain.
Answer
1. serine
4.9: Enzyme Inhibition is shared under a CC BY-NC-SA 4.0 license and was authored, remixed, and/or curated by LibreTexts.
Learning Objectives
To explain why vitamins are necessary in the diet.
Many enzymes are simple proteins consisting entirely of one or more amino acid chains. Other enzymes contain a nonprotein
component called a cofactor that is necessary for the enzyme’s proper functioning. There are two types of cofactors: inorganic ions
[e.g., zinc or Cu(I) ions] and organic molecules known as coenzymes. Most coenzymes are vitamins or are derived from vitamins.
Vitamins are organic compounds that are essential in very small (trace) amounts for the maintenance of normal metabolism. They
generally cannot be synthesized at adequate levels by the body and must be obtained from the diet. The absence or shortage of a
vitamin may result in a vitamin-deficiency disease. In the first half of the 20th century, a major focus of biochemistry was the
identification, isolation, and characterization of vitamins. Despite accumulating evidence that people needed more than just
carbohydrates, fats, and proteins in their diets for normal growth and health, it was not until the early 1900s that research
established the need for trace nutrients in the diet.
Table 4.10.1 : Fat-Soluble Vitamins and Physiological Functions
Vitamin Physiological Function Effect of Deficiency
formation of vision pigments; differentiation night blindness; continued deficiency leads to

vitamin A (retinol)
of epithelial cells total blindness
increases the body’s ability to absorb calcium osteomalacia (softening of the bones); known
vitamin D (cholecalciferol)
and phosphorus as rickets in children
vitamin E (tocopherol) fat-soluble antioxidant damage to cell membranes
formation of prothrombin, a key enzyme in the

vitamin K (phylloquinone) increases the time required for blood to clot
blood-clotting process
Because organisms differ in their synthetic abilities, a substance that is a vitamin for one species may not be so for another. Over
the past 100 years, scientists have identified and isolated 13 vitamins required in the human diet and have divided them into two
broad categories: the fat-soluble vitamins, which include vitamins A, D, E, and K, and the water-soluble vitamins, which are the B
complex vitamins and vitamin C. All fat-soluble vitamins contain a high proportion of hydrocarbon structural components. There
are one or two oxygen atoms present, but the compounds as a whole are nonpolar. In contrast, water-soluble vitamins contain large
numbers of electronegative oxygen and nitrogen atoms, which can engage in hydrogen bonding with water. Most water-soluble
vitamins act as coenzymes or are required for the synthesis of coenzymes. The fat-soluble vitamins are important for a variety of
physiological functions. The key vitamins and their functions are found in Tables 4.10.1 and 4.10.2.
Table 4.10.2 : Water-Soluble Vitamins and Physiological Functions
Vitamin Coenzyme Coenzyme Function Deficiency Disease
vitamin B1 (thiamine) thiamine pyrophosphate decarboxylation reactions beri-beri
flavin mononucleotide or flavin oxidation-reduction reactions

vitamin B2 (riboflavin) —
adenine dinucleotide involving two hydrogen atoms
nicotinamide adenine dinucleotide

oxidation-reduction reactions
vitamin B3 (niacin) or nicotinamide adenine pellagra
involving the hydride ion (H−)
dinucleotide phosphate
variety of reactions including the

vitamin B6 (pyridoxine) pyridoxal phosphate —
transfer of amino groups
methylcobalamin or intramolecular rearrangement

vitamin B12 (cyanocobalamin) pernicious anemia
deoxyadenoxylcobalamin reactions
biotin biotin carboxylation reactions —
carrier of one-carbon units such as

folic acid tetrahydrofolate anemia
the formyl group
pantothenic Acid coenzyme A carrier of acyl groups —
Vitamin Coenzyme Coenzyme Function Deficiency Disease
antioxidant; formation of
vitamin C (ascorbic acid) none collagen, a protein found in scurvy
tendons, ligaments, and bone
Vitamins C and E, as well as the provitamin β-carotene can act as antioxidants in the body. Antioxidants prevent damage from free
radicals, which are molecules that are highly reactive because they have unpaired electrons. Free radicals are formed not only
through metabolic reactions involving oxygen but also by such environmental factors as radiation and pollution.
β-carotene is known as a provitamin because it can be converted to vitamin A in the body.

Free radicals react most commonly react with lipoproteins and unsaturated fatty acids in cell membranes, removing an electron
from those molecules and thus generating a new free radical. The process becomes a chain reaction that finally leads to the
oxidative degradation of the affected compounds. Antioxidants react with free radicals to stop these chain reactions by forming a
more stable molecule or, in the case of vitamin E, a free radical that is much less reactive (vitamin E is converted back to its
original form through interaction with vitamin C).
Summary
Vitamins are organic compounds that are essential in very small amounts for the maintenance of normal metabolism. Vitamins are
divided into two broad categories: fat-soluble vitamins and water-soluble vitamins. Most water-soluble vitamins are needed for the
formation of coenzymes, which are organic molecules needed by some enzymes for catalytic activity.

1. What is the difference between a cofactor and a coenzyme?
2. How are vitamins related to coenzymes?
Answers
1. A coenzyme is one type of cofactor. Coenzymes are organic molecules required by some enzymes for activity. A cofactor can
be either a coenzyme or an inorganic ion.
2. Coenzymes are synthesized from vitamins.
Exercises
1. Identify each vitamin as water soluble or fat soluble.
a. vitamin D
b. vitamin C
c. vitamin B12
a. niacin
b. cholecalciferol
c. biotin
3. What vitamin is needed to form each coenzyme?
a. pyridoxal phosphate
b. flavin adenine dinucleotide
c. coenzyme A
d. nicotinamide adenine dinucleotide
4. What coenzyme is formed from each vitamin?
a. niacin
b. thiamine
c. cyanocobalamin
d. pantothenic acid
5. What is the function of each vitamin or coenzyme?
a. flavin adenine dinucleotide
b. vitamin A
c. biotin
a. vitamin K
b. pyridoxal phosphate
c. tetrahydrofolate
Answers
1. a. fat soluble
b. water soluble
c. water soluble
3. a. vitamin B6 or pyridoxine
b. vitamin B2 or riboflavin
c. pantothenic acid
d. vitamin B3 or niacin
5. a. needed by enzymes that catalyze oxidation-reduction reactions in which two hydrogen atoms are transferred
b. needed for the formation of vision pigments
c. needed by enzymes that catalyze carboxylation reactions
4.10: Enzyme Cofactors and Vitamins is shared under a CC BY-NC-SA 4.0 license and was authored, remixed, and/or curated by LibreTexts.
A protein is a large biological polymer synthesized from amino acids, which are carboxylic acids containing an α-amino group.
Proteins have a variety of important roles in living organisms, yet they are made from the same 20 L-amino acids. About half of
these amino acids, the essential amino acids, cannot be synthesized by the human body and must be obtained from the diet. In the
solid state and in neutral solutions, amino acids exist as zwitterions, species that are charged but electrically neutral. In this form,
they behave much like inorganic salts. Each amino acid belongs to one of four classes depending on the characteristics of its R
group or amino acid side chain: nonpolar, polar but neutral, positively charged, and negatively charged. Depending on the
conditions, amino acids can act as either acids or bases, which means that proteins act as buffers. The pH at which an amino acid
exists as the zwitterion is called the isoelectric point (pI).
The amino acids in a protein are linked together by peptide bonds. Protein chains containing 10 or fewer amino acids are usually
referred to as peptides, with a prefix such as di- or tri- indicating the number of amino acids. Chains containing more than 50
amino acid units are referred to as proteins or polypeptides. Proteins are classified globular or fibrous, depending on their structure
and resulting solubility in water. Globular proteins are nearly spherical and are soluble in water; fibrous proteins have elongated
or fibrous structures and are not soluble in water.
Protein molecules can have as many as four levels of structure. The primary structure is the sequence of amino acids in the chain.
The secondary structure is the arrangement of adjacent atoms in the peptide chain; the most common arrangements are α-helices
or β-pleated sheets. The tertiary structure is the overall three-dimensional shape of the molecule that results from the way the
chain bends and folds in on itself. Proteins that consist of more than one chain have quaternary structure, which is the way the
multiple chains are packed together.
Four types of intramolecular and intermolecular forces contribute to secondary, tertiary, and quaternary structure: (1) hydrogen
bonding between an oxygen or a nitrogen atom and a hydrogen atom bound to an oxygen atom or a nitrogen atom, either on the
same chain or on a neighboring chain; (2) ionic bonding between one positively charged side chain and one negatively charged
side chain; (3) disulfide linkages between cysteine units; and (4) dispersion forces between nonpolar side chains.
Because of their complexity, protein molecules are delicate and easy to disrupt. A denatured protein is one whose conformation has
been changed, in a process called denaturation, so that it can no longer do its physiological job. A variety of conditions, such as
heat, ultraviolet radiation, the addition of organic compounds, or changes in pH can denature a protein.
An enzyme is an organic catalyst produced by a living cell. Enzymes are such powerful catalysts that the reactions they promote
occur rapidly at body temperature. Without the help of enzymes, these reactions would require high temperatures and long reaction
times.
The molecule or molecules on which an enzyme acts are called its substrates. An enzyme has an active site where its substrate or
substrates bind to form an enzyme-substrate complex. The reaction occurs, and product is released:
E + S → E– S → E + P (4.11.1)
The original lock-and-key model of enzyme and substrate binding pictured a rigid enzyme of unchanging configuration binding to
the appropriate substrate. The newer induced-fit model describes the enzyme active site as changing its conformation after binding
to the substrate.
Most enzymes have maximal activity in a narrow pH range centered on an optimum pH. In this pH range, the enzyme is correctly
folded, and catalytic groups in the active site have the correct charge (positive, negative, or neutral). For most enzymes, the
optimum pH is between 6 and 8.
Substances that interfere with enzyme function are called inhibitors. An irreversible inhibitor inactivates enzymes by forming
covalent bonds to the enzyme, while a reversible inhibitor inactivates an enzyme by a weaker, noncovalent interaction that is
easier to disrupt. A competitive inhibitor is a reversible inhibitor that is structurally similar to the substrate and binds to the active
site. When the inhibitor is bound, the substrate is blocked from the active site and no reaction occurs. Because the binding of such
an inhibitor is reversible, a high substrate concentration will overcome the inhibition because it increases the likelihood of the
substrate binding. A noncompetitive inhibitor binds reversibly at a site distinct from the active site. Thus, it can bind to either the
enzyme or the enzyme-substrate complex. The inhibitor changes the conformation of the active site so that the enzyme cannot
function properly. Noncompetitive inhibitors are important in feedback inhibition, in which the amount of product produced by a
series of reactions is carefully controlled. The final product in a series of reactions acts as a noncompetitive inhibitor of the initial
enzyme.
Simple enzymes consist entirely of one or more amino acid chains. Complex enzymes are composed of one or more amino acid
chains joined to cofactors—inorganic ions or organic coenzymes. Vitamins are organic compounds that are essential in very small
amounts for the maintenance of normal metabolism and generally cannot be synthesized at adequate levels by the body. Vitamins
are divided into two broad categories: fat-soluble vitamins and water-soluble vitamins. Many of the water-soluble vitamins are
used for the synthesis of coenzymes.
4.11: Amino Acids, Proteins, and Enzymes (Summary) is shared under a CC BY-NC-SA 4.0 license and was authored, remixed, and/or curated by
LibreTexts.
1. What is the general structure of an α-amino acid?
2. Identify the amino acid that fits each description.
a. also known as aspartate
b. almost as strong a base as sodium hydroxide
c. does not have a chiral carbon
3.
4. a. aspartic acid
b. arginine
c. glycine
a. serine
b. arginine
c. phenylalanine
a. aspartic acid
b. methionine
c. valine
a. alanine
b. cysteine
c. histidine
a. threonine
b. glutamic acid
c. leucine
a. amide functional group.
b. aromatic ring.
c. carboxyl group.
a. OH group
b. branched chain
c. amino group
1. a. CH2OH−
b.
c.
2.
3. a.
b.
c.
4.
5. a. asparagine or glutamine
b. phenylalanine, tyrosine, or tryptophan
c. aspartic acid or glutamic acid

a. zwitterion
b. isoelectric point
2. Draw the structure for the anion formed when alanine (at neutral pH) reacts with a base.
3. Draw the structure for the cation formed when alanine (at neutral pH) reacts with an acid.
Answers
1. a. an electrically neutral compound that contains both negatively and positively charged groups
b. the pH at which a given amino acid exists in solution as a zwitterion
2.
3.
Exercises
1. Draw the structure of leucine and determine the charge on the molecule in a(n)
c. a basic solution (pH = 11)
2. Draw the structure of isoleucine and determine the charge on the molecule in a(n)
c. basic solution (pH = 11).
Answer
1. a.
b.
c.
18.3: Peptides
1. Distinguish between the N-terminal amino acid and the C-terminal amino acid of a peptide or protein.
2. Describe the difference between an amino acid and a peptide.
3. Amino acid units in a protein are connected by peptide bonds. What is another name for the functional group linking the amino
acids?
Answers
1. The N-terminal end is the end of a peptide or protein whose amino group is free (not involved in the formation of a peptide
bond), while the C-terminal end has a free carboxyl group.
2. A peptide is composed of two or more amino acids. Amino acids are the building blocks of peptides.
3. amide bond
Exercises
1. Draw the structure for each peptide.
a. gly-val
b. val-gly
2. Draw the structure for cys-val-ala.
3. Identify the C- and N-terminal amino acids for the peptide lys-val-phe-gly-arg-cys.
4. Identify the C- and N-terminal amino acids for the peptide asp-arg-val-tyr-ile-his-pro-phe.
Answers
1. a.
b.
3. C-terminal amino acid: cys; N-terminal amino acid: lys
18.4: Proteins

1. What is the predominant attractive force that stabilizes the formation of secondary structure in proteins?
2. Distinguish between the tertiary and quaternary levels of protein structure.
3. Briefly describe four ways in which a protein could be denatured.
Answers
1. hydrogen bonding
2. Tertiary structure refers to the unique three-dimensional shape of a single polypeptide chain, while quaternary structure
describes the interaction between multiple polypeptide chains for proteins that have more than one polypeptide chain.
3. (1) heat a protein above 50°C or expose it to UV radiation; (2) add organic solvents, such as ethyl alcohol, to a protein solution;
(3) add salts of heavy metal ions, such as mercury, silver, or lead; and (4) add alkaloid reagents such as tannic acid
Exercises
a. albumin
b. myosin
c. fibroin
a. hemoglobin
b. keratin
c. myoglobin
3. What name is given to the predominant secondary structure found in silk?
4. What name is given to the predominant secondary structure found in wool protein?
a. aspartic acid and lysine
b. phenylalanine and alanine
c. serine and lysine
d. two cysteines
a. valine and isoleucine
b. asparagine and serine
c. glutamic acid and arginine
d. tryptophan and methionine
7. What level(s) of protein structure is(are) ordinarily disrupted in denaturation? What level(s) is(are) not?
8. Which class of proteins is more easily denatured—fibrous or globular?
Answers
1. a. globular
b. fibrous
c. fibrous
3. β-pleated sheet
5. a. ionic bonding
b. dispersion forces
c. dispersion forces
d. disulfide linkage
7. Protein denaturation disrupts the secondary, tertiary, and quaternary levels of structure. Only primary structure is unaffected by
denaturation.
18.5: Enzymes
In the small intestine, sucrose is hydrolyzed to form glucose and fructose in a reaction catalyzed by sucrase.
1. Identify the substrate in this reaction.
2. Name the enzyme.
Answers
1. sucrose
2. sucrase
Exercises
a. lactase
b. cellulase
c. peptidase
a. lipase
b. amylase
c. maltase
a. decarboxylase
b. protease
c. transaminase
a. dehydrogenase
b. isomerase
c. lipase
Answers
1. a. lactose
b. cellulose
c. peptides
3. a. lyase
b. hydrolase
c. transferase
18.6: Enzyme Action

1. Distinguish between the lock-and-key model and induced-fit model of enzyme action.
2. Which enzyme has greater specificity—urease or carboxypeptidase? Explain.
Answers
1. The lock-and-key model portrays an enzyme as conformationally rigid and able to bond only to substrates that exactly fit the
active site. The induced fit model portrays the enzyme structure as more flexible and is complementary to the substrate only
after the substrate is bound.
2. Urease has the greater specificity because it can bind only to a single substrate. Carboxypeptidase, on the other hand, can
catalyze the removal of nearly any amino acid from the carboxyl end of a peptide or protein.
Exercises
site in an enzyme?
a. COOH
b. NH3+
c. OH
d. CH(CH3)2
site in an enzyme?
a. SH
b. NH2
c. C6H5
d. COO−
Answers
1. a. hydrogen bonding
b. ionic bonding
c. hydrogen bonding
d. dispersion forces
3. a. The amino acid has a polar side chain capable of engaging in hydrogen bonding; serine (answers will vary).
b. The amino acid has a negatively charged side chain; aspartic acid (answers will vary).
c. The amino acid has a polar side chain capable of engaging in hydrogen bonding; asparagine (answers will vary).
d. The amino acid has a nonpolar side chain; isoleucine (answers will vary).

1. The concentration of substrate X is low. What happens to the rate of the enzyme-catalyzed reaction if the concentration of X is
doubled?
2. What effect does an increase in the enzyme concentration have on the rate of an enzyme-catalyzed reaction?
Answers
1. If the concentration of the substrate is low, increasing its concentration will increase the rate of the reaction.
2. An increase in the amount of enzyme will increase the rate of the reaction (provided sufficient substrate is present).
Exercises
1. In non-enzyme-catalyzed reactions, the reaction rate increases as the concentration of reactant is increased. In an enzyme-
catalyzed reaction, the reaction rate initially increases as the substrate concentration is increased but then begins to level off, so
that the increase in reaction rate becomes less and less as the substrate concentration increases. Explain this difference.
2. Why do enzymes become inactive at very high temperatures?
3. An enzyme has an optimum pH of 7.4. What is most likely to happen to the activity of the enzyme if the pH drops to 6.3?
Explain.
4. An enzyme has an optimum pH of 7.2. What is most likely to happen to the activity of the enzyme if the pH increases to 8.5?
Explain.
Answers
1. In an enzyme-catalyzed reaction, the substrate binds to the enzyme to form an enzyme-substrate complex. If more substrate is
present than enzyme, all of the enzyme binding sites will have substrate bound, and further increases in substrate concentration
cannot increase the rate.
3. The activity will decrease; a pH of 6.3 is more acidic than 7.4, and one or more key groups in the active site may bind a
hydrogen ion, changing the charge on that group.

1. What is the difference between a cofactor and a coenzyme?
2. How are vitamins related to coenzymes?
Answers
1. A coenzyme is one type of cofactor. Coenzymes are organic molecules required by some enzymes for activity. A cofactor can
be either a coenzyme or an inorganic ion.
2. Coenzymes are synthesized from vitamins.
Exercises
a. vitamin D
b. vitamin C
c. vitamin B12
a. niacin
b. cholecalciferol
c. biotin
3. What vitamin is needed to form each coenzyme?
a. pyridoxal phosphate
b. flavin adenine dinucleotide
c. coenzyme A
d. nicotinamide adenine dinucleotide
4. What coenzyme is formed from each vitamin?
a. niacin
b. thiamine
c. cyanocobalamin
d. pantothenic acid
a. flavin adenine dinucleotide
b. vitamin A
c. biotin
a. vitamin K
b. pyridoxal phosphate
c. tetrahydrofolate
Answers
1. a. fat soluble
b. water soluble
c. water soluble
3. a. vitamin B6 or pyridoxine
b. vitamin B2 or riboflavin
c. pantothenic acid
d. vitamin B3 or niacin
5. a. needed by enzymes that catalyze oxidation-reduction reactions in which two hydrogen atoms are transferred
b. needed for the formation of vision pigments
c. needed by enzymes that catalyze carboxylation reactions

1. What are the characteristics of an irreversible inhibitor?
2. In what ways does a competitive inhibitor differ from a noncompetitive inhibitor?
Answers
1. It inactivates an enzyme by bonding covalently to a particular group at the active site.
2. A competitive inhibitor structurally resembles the substrate for a given enzyme and competes with the substrate for binding at
the active site of the enzyme. A noncompetitive inhibitor binds at a site distinct from the active site and can bind to either the
free enzyme or the enzyme-substrate complex.
Exercises
1. What amino acid is present in the active site of all enzymes that are irreversibly inhibited by nerve gases such as DIFP?
2. Oxaloacetate (OOCCH2COCOO) inhibits succinate dehydrogenase. Would you expect oxaloacetate to be a competitive or
noncompetitive inhibitor? Explain.
Answer
1. serine
1. Draw the structure of the amino acid γ-aminobutyric acid (GABA). Would you expect to find GABA in the amino acid
sequence of a protein? Explain.
2. Draw the structure of the amino acid homocysteine (R group = CH2CH2SH). Would you expect to find homocysteine in the
amino acid sequence of a protein? Justify your answer.
3. Write equations to show how leucine can act as a buffer (that is, how it can neutralize added acid or base).
4. Write equations to show how isoleucine can act as a buffer (that is, how it can neutralize added acid or base).
5. Glutathione (γ-glutamylcysteinylglycine) is a tripeptide found in all cells of higher animals. It contains glutamic acid joined in
an unusual peptide linkage involving the carboxyl group of the R group (known as γ-carboxyl group), rather than the usual
carboxyl group (the α-carboxyl group). Draw the structure of glutathione.
6. Draw the structure of the pentapeptide whose sequence is arg-his-gly-leu-asp. Identify which of the amino acids have R groups
that can donate or gain hydrogen ions.
7. Bradykinin is a peptide hormone composed of nine amino acids that lowers blood pressure. Its primary structure is arg-pro-pro-
gly-phe-ser-pro-phe-arg. Would you expect bradykinin to be positively charged, negatively charged, or neutral at a pH of 6.0?
Justify your answer.
8. One of the neurotransmitters involved in pain sensation is a peptide called substance P, which is composed of 11 amino acids
and is released by nerve-cell terminals in response to pain. Its primary structure is arg-pro-lys-pro-gln-gln-phe-phe-gly-leu-met.
Would you expect this peptide to be positively charged, negatively charged, or neutral at a pH of 6.0? Justify your answer.
9. Carbohydrates are incorporated into glycoproteins. Would you expect the incorporation of sugar units to increase or decrease
the solubility of a protein? Justify your answer.
10. Some proteins have phosphate groups attached through an ester linkage to the OH groups of serine, threonine, or tyrosine
residues to form phosphoproteins. Would you expect the incorporation of a phosphate group to increase or decrease the
solubility of a protein? Justify your answer.
11. Refer to Table 18.5 and determine how each enzyme would be classified.
a. the enzyme that catalyzes the conversion of ethanol to acetaldehyde
b. the enzyme that catalyzes the breakdown of glucose 6-phosphate to glucose and inorganic phosphate ion (water is also a
reactant in this reaction)
12. Refer to Table 18.5 and determine how each enzyme would be classified.
a. the enzyme that catalyzes the removal of a carboxyl group from pyruvate to form acetate
b. the enzyme that catalyzes the rearrangement of 3-phosphoglycerate to form 2-phosphoglycerate
13. The enzyme lysozyme has an aspartic acid residue in the active site. In acidic solution, the enzyme is inactive, but activity
increases as the pH rises to around 6. Explain why.
14. The enzyme lysozyme has a glutamic acid residue in the active site. At neutral pH (6–7), the enzyme is active, but activity
decreases as the pH rises. Explain why.
15. The activity of a purified enzyme is measured at a substrate concentration of 1.0 μM and found to convert 49 μmol of substrate
to product in 1 min. The activity is measured at 2.0 μM substrate and found to convert 98 μmol of substrate to product/minute.
a. When the substrate concentration is 100 μM, how much substrate would you predict is converted to product in 1 min? What
if the substrate concentration were increased to 1,000 μM (1.0 mM)?
b. The activities actually measured are 676 μmol product formed/minute at a substrate concentration of 100 μM and 698 μmol
product formed/minute at 1,000 μM (1.0 mM) substrate. Is there any discrepancy between these values and those you
predicted in Exercise 15a? Explain.
16. A patient has a fever of 39°C. Would you expect the activity of enzymes in the body to increase or decrease relative to their
activity at normal body temperature (37°C)?
17. Using your knowledge of factors that influence enzyme activity, describe what happens when milk is pasteurized.
Answers
1.
This amino acid would not be found in proteins because it is not an α-amino acid.
3.
5.
7. Bradykinin would be positively charged; all of the amino acids, except for arginine, have R groups that do not become either
positively or negatively charged. The two arginines are R groups that are positively charged at neutral pH, so the peptide would
have an overall positive charge.
9. Carbohydrates have many OH groups attached, which can engage in hydrogen bonding with water, which increases the
solubility of the proteins.
11.
a. oxidoreductase
b. hydrolase
13. The enzyme is active when the carboxyl group in the R group of aspartic acid does not have the hydrogen attached (forming
COO–); the hydrogen is removed when the pH of the solution is around pH 6 or higher.
15.
a. at 100 μM, you would predict that the rate would increase 100 times to 4,900 μmol of substrate to product in 1 min; at 1.0
mM, you would predict an increase to 49,000 μmol of substrate to product in 1 min.
b. There is a great discrepancy between the predicted rates and actual rates; this occurs because the enzyme becomes saturated
with substrate, preventing a further increase in the rate of the reaction (the reaction is no longer linear with respect to
substrate concentration because it is at very low concentrations).
17. When milk is pasteurized, it is heated to high temperatures. These high temperatures denature the proteins in bacteria, so they
cannot carry out needed functions to grow and multiply.
4.12: Amino Acids, Proteins, and Enzymes (Exercises) is shared under a CC BY-NC-SA 4.0 license and was authored, remixed, and/or curated by
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CHAPTER OVERVIEW
5: Nucleic Acids
5.2: Nucleotides
5.7: Viruses
5: Nucleic Acids is shared under a CC BY-NC-SA 4.0 license and was authored, remixed, and/or curated by LibreTexts.
1
Following the initial isolation of insulin in 1921, diabetic patients could be treated with insulin obtained from the pancreases of
cattle and pigs. Unfortunately, some patients developed an allergic reaction to this insulin because its amino acid sequence was not
identical to that of human insulin. In the 1970s, an intense research effort began that eventually led to the production of genetically
engineered human insulin—the first genetically engineered product to be approved for medical use. To accomplish this feat,
researchers first had to determine how insulin is made in the body and then find a way of causing the same process to occur in
nonhuman organisms, such as bacteria or yeast cells. Many aspects of these discoveries are presented in this chapter on nucleic
acids.
Figure 5.1.1 : A vial of insulin. It has been given a trade name, Actrapid, by the manufacturer. Image used with permission (Public
Domain; Mr Hyde).
5.1: Prelude to Nucleic Acids is shared under a CC BY-NC-SA 4.0 license and was authored, remixed, and/or curated by LibreTexts.
5.2: Nucleotides
Learning Objectives
To identify the different molecules that combine to form nucleotides.
The repeating, or monomer, units that are linked together to form nucleic acids are known as nucleotides. The deoxyribonucleic
acid (DNA) of a typical mammalian cell contains about 3 × 109 nucleotides. Nucleotides can be further broken down to phosphoric
acid (H3PO4), a pentose sugar (a sugar with five carbon atoms), and a nitrogenous base (a base containing nitrogen atoms).
can be broken can be broken
nucleic acids −−−−−−−−→ nucleotides −−−−−−−−→ H3 PO4 + nitrogen base + pentose sugar (5.2.1)
down into down into
If the pentose sugar is ribose, the nucleotide is more specifically referred to as a ribonucleotide, and the resulting nucleic acid is
ribonucleic acid (RNA). If the sugar is 2-deoxyribose, the nucleotide is a deoxyribonucleotide, and the nucleic acid is DNA.
The nitrogenous bases found in nucleotides are classified as pyrimidines or purines. Pyrimidines are heterocyclic amines with two
nitrogen atoms in a six-member ring and include uracil, thymine, and cytosine. Purines are heterocyclic amines consisting of a
pyrimidine ring fused to a five-member ring with two nitrogen atoms. Adenine and guanine are the major purines found in nucleic
acids (Figure 5.2.1).
Figure 5.2.1 The Nitrogenous Bases Found in DNA and RNA

The formation of a bond between C1′ of the pentose sugar and N1 of the pyrimidine base or N9 of the purine base joins the pentose
sugar to the nitrogenous base. In the formation of this bond, a molecule of water is removed. Table 5.2.1 summarizes the
similarities and differences in the composition of nucleotides in DNA and RNA.
The numbering convention is that primed numbers designate the atoms of the pentose ring, and unprimed numbers designate the
atoms of the purine or pyrimidine ring.
Table 5.2.1: Composition of Nucleotides in DNA and RNA
Composition DNA RNA
purine bases adenine and guanine adenine and guanine
pyrimidine bases cytosine and thymine cytosine and uracil
pentose sugar 2-deoxyribose ribose
inorganic acid phosphoric acid (H3PO4) H3PO4
The names and structures of the major ribonucleotides and one of the deoxyribonucleotides are given in Figure 5.2.2.
Figure 5.2.2 : The Pyrimidine and Purine Nucleotides

Apart from being the monomer units of DNA and RNA, the nucleotides and some of their derivatives have other functions as well.
Adenosine diphosphate (ADP) and adenosine triphosphate (ATP), shown in Figure 5.2.3, have a role in cell metabolism. Moreover,
a number of coenzymes, including flavin adenine dinucleotide (FAD), nicotinamide adenine dinucleotide (NAD+), and coenzyme
A, contain adenine nucleotides as structural components.
Figure 5.2.3 : Structures of Two Important Adenine-Containing Nucleotides
Summary
Nucleotides are composed of phosphoric acid, a pentose sugar (ribose or deoxyribose), and a nitrogen-containing base (adenine,
cytosine, guanine, thymine, or uracil). Ribonucleotides contain ribose, while deoxyribonucleotides contain deoxyribose.

1. Identify the three molecules needed to form the nucleotides in each nucleic acid.
a. DNA
b. RNA
2. Classify each compound as a pentose sugar, a purine, or a pyrimidine.
a. adenine
b. guanine
c. deoxyribose
d. thymine
e. ribose
f. cytosine
Answers
1. a. nitrogenous base (adenine, guanine, cytosine, and thymine), 2-deoxyribose, and H3PO4
b. nitrogenous base (adenine, guanine, cytosine, and uracil), ribose, and H3PO4
2. a. purine
b. purine
c. pentose sugar
d. pyrimidine
e. pentose sugar
f. pyrimidine
Exercises
1. What is the sugar unit in each nucleic acid?
a. RNA
b. DNA
2. Identify the major nitrogenous bases in each nucleic acid.
a. DNA
b. RNA
3. For each structure, circle the sugar unit and identify the nucleotide as a ribonucleotide or a deoxyribonucleotide.
a.
b.
a.
b.
5. For each structure, circle the nitrogenous base and identify it as a purine or pyrimidine.
a.
b.
a.
b.
Answers
1. a. ribose
b. deoxyribose
3. a.
b.
a.
b.
5.2: Nucleotides is shared under a CC BY-NC-SA 4.0 license and was authored, remixed, and/or curated by LibreTexts.
Learning Objectives
Identify the two types of nucleic acids and the function of each type.
Describe how nucleotides are linked together to form nucleic acids.
Describe the secondary structure of DNA and the importance of complementary base pairing.
Nucleic acids are large polymers formed by linking nucleotides together and are found in every cell. Deoxyribonucleic acid (DNA)
is the nucleic acid that stores genetic information. If all the DNA in a typical mammalian cell were stretched out end to end, it
would extend more than 2 m. Ribonucleic acid (RNA) is the nucleic acid responsible for using the genetic information encoded in
DNA to produce the thousands of proteins found in living organisms.
Primary Structure of Nucleic Acids

Nucleotides are joined together through the phosphate group of one nucleotide connecting in an ester linkage to the OH group on
the third carbon atom of the sugar unit of a second nucleotide. This unit joins to a third nucleotide, and the process is repeated to
produce a long nucleic acid chain (Figure 5.3.1). The backbone of the chain consists of alternating phosphate and sugar units (2-
deoxyribose in DNA and ribose in RNA). The purine and pyrimidine bases branch off this backbone.
Each phosphate group has one acidic hydrogen atom that is ionized at physiological pH.
This is why these compounds are known as nucleic acids.
Figure 5.3.1 Structure of a Segment of DNA. A similar segment of RNA would have OH groups on each C2′, and uracil would
replace thymine.
Like proteins, nucleic acids have a primary structure that is defined as the sequence of their nucleotides. Unlike proteins, which
have 20 different kinds of amino acids, there are only 4 different kinds of nucleotides in nucleic acids. For amino acid sequences in
proteins, the convention is to write the amino acids in order starting with the N-terminal amino acid. In writing nucleotide
sequences for nucleic acids, the convention is to write the nucleotides (usually using the one-letter abbreviations for the bases,
shown in Figure 5.3.1) starting with the nucleotide having a free phosphate group, which is known as the 5′ end, and indicate the
nucleotides in order. For DNA, a lowercase d is often written in front of the sequence to indicate that the monomers are
deoxyribonucleotides. The final nucleotide has a free OH group on the 3′ carbon atom and is called the 3′ end. The sequence of
nucleotides in the DNA segment shown in Figure 5.3.1 would be written 5′-dG-dT-dA-dC-3′, which is often further abbreviated to
dGTAC or just GTAC.
Secondary Structure of DNA

The three-dimensional structure of DNA was the subject of an intensive research effort in the late 1940s to early 1950s. Initial work
revealed that the polymer had a regular repeating structure. In 1950, Erwin Chargaff of Columbia University showed that the molar
amount of adenine (A) in DNA was always equal to that of thymine (T). Similarly, he showed that the molar amount of guanine
(G) was the same as that of cytosine (C). Chargaff drew no conclusions from his work, but others soon did.
At Cambridge University in 1953, James D. Watson and Francis Crick announced that they had a model for the secondary structure
of DNA. Using the information from Chargaff’s experiments (as well as other experiments) and data from the X ray studies of
Rosalind Franklin (which involved sophisticated chemistry, physics, and mathematics), Watson and Crick worked with models that
were not unlike a child’s construction set and finally concluded that DNA is composed of two nucleic acid chains running
antiparallel to one another—that is, side-by-side with the 5′ end of one chain next to the 3′ end of the other. Moreover, as their
model showed, the two chains are twisted to form a double helix—a structure that can be compared to a spiral staircase, with the
phosphate and sugar groups (the backbone of the nucleic acid polymer) representing the outside edges of the staircase. The purine
and pyrimidine bases face the inside of the helix, with guanine always opposite cytosine and adenine always opposite thymine.
These specific base pairs, referred to as complementary bases, are the steps, or treads, in our staircase analogy (Figure 5.3.2).
Figure 5.3.2 DNA Double Helix. (a) This represents a computer-generated model of the DNA double helix. (b) This represents a
schematic representation of the double helix, showing the complementary bases.
The structure proposed by Watson and Crick provided clues to the mechanisms by which cells are able to divide into two identical,
functioning daughter cells; how genetic data are passed to new generations; and even how proteins are built to required
specifications. All these abilities depend on the pairing of complementary bases. Figure 5.3.3 shows the two sets of base pairs and
illustrates two things. First, a pyrimidine is paired with a purine in each case, so that the long dimensions of both pairs are identical
(1.08 nm).
Figure 5.3.3 Complementary Base Pairing. Complementary bases engage in hydrogen bonding with one another: (a) thymine and
adenine; (b) cytosine and guanine.
If two pyrimidines were paired or two purines were paired, the two pyrimidines would take up less space than a purine and a
pyrimidine, and the two purines would take up more space, as illustrated in Figure 5.3.4. If these pairings were ever to occur, the
structure of DNA would be like a staircase made with stairs of different widths. For the two strands of the double helix to fit neatly,
a pyrimidine must always be paired with a purine. The second thing you should notice in Figure 5.3.3 is that the correct pairing
enables formation of three instances of hydrogen bonding between guanine and cytosine and two between adenine and thymine.
The additive contribution of this hydrogen bonding imparts great stability to the DNA double helix.
Figure 5.3.4 Difference in Widths of Possible Base Pairs
Summary
DNA is the nucleic acid that stores genetic information. RNA is the nucleic acid responsible for using the genetic information in
DNA to produce proteins.
Nucleotides are joined together to form nucleic acids through the phosphate group of one nucleotide connecting in an ester
linkage to the OH group on the third carbon atom of the sugar unit of a second nucleotide.
Nucleic acid sequences are written starting with the nucleotide having a free phosphate group (the 5′ end).
Two DNA strands link together in an antiparallel direction and are twisted to form a double helix. The nitrogenous bases face
the inside of the helix. Guanine is always opposite cytosine, and adenine is always opposite thymine.
1. a. Name the two kinds of nucleic acids.
b. Which type of nucleic acid stores genetic information in the cell?
2. What are complementary bases?
3. Why is it structurally important that a purine base always pair with a pyrimidine base in the DNA double helix?
Answers
1. a. deoxyribonucleic acid (DNA) and ribonucleic acid (RNA)
b. DNA
2. the specific base pairings in the DNA double helix in which guanine is paired with cytosine and adenine is paired with thymine
3. The width of the DNA double helix is kept at a constant width, rather than narrowing (if two pyrimidines were across from each
other) or widening (if two purines were across from each other).
Exercises
1. For this short RNA segment,
a. identify the 5′ end and the 3′ end of the molecule.
b. circle the atoms that comprise the backbone of the nucleic acid chain.
c. write the nucleotide sequence of this RNA segment.
2. For this short DNA segment,

c. write the nucleotide sequence of this DNA segment.
3. Which nitrogenous base in DNA pairs with each nitrogenous base?
a. cytosine
b. adenine
c. guanine
d. thymine
4. Which nitrogenous base in RNA pairs with each nitrogenous base?
a. cytosine
b. adenine
c. guanine
d. thymine
5. How many hydrogen bonds can form between the two strands in the short DNA segment shown below?
5′ ATGCGACTA 3′ 3′ TACGCTGAT 5′
5′ CGATGAGCC 3′ 3′ GCTACTCGG 5′
Answers
1.
c. ACU
3. a. guanine
b. thymine
c. cytosine
d. adenine
5. 22 (2 between each AT base pair and 3 between each GC base pair)
5.3: Nucleic Acid Structure is shared under a CC BY-NC-SA 4.0 license and was authored, remixed, and/or curated by LibreTexts.
Learning Objectives
Describe how a new copy of DNA is synthesized.
Describe how RNA is synthesized from DNA.
Identify the different types of RNA and the function of each type of RNA.
We previously stated that deoxyribonucleic acid (DNA) stores genetic information, while ribonucleic acid (RNA) is responsible for
transmitting or expressing genetic information by directing the synthesis of thousands of proteins found in living organisms. But
how do the nucleic acids perform these functions? Three processes are required: (1) replication, in which new copies of DNA are
made; (2) transcription, in which a segment of DNA is used to produce RNA; and (3) translation, in which the information in
RNA is translated into a protein sequence.
Replication
New cells are continuously forming in the body through the process of cell division. For this to happen, the DNA in a dividing cell
must be copied in a process known as replication. The complementary base pairing of the double helix provides a ready model for
how genetic replication occurs. If the two chains of the double helix are pulled apart, disrupting the hydrogen bonding between
base pairs, each chain can act as a template, or pattern, for the synthesis of a new complementary DNA chain.
The nucleus contains all the necessary enzymes, proteins, and nucleotides required for this synthesis. A short segment of DNA is
“unzipped,” so that the two strands in the segment are separated to serve as templates for new DNA. DNA polymerase, an enzyme,
recognizes each base in a template strand and matches it to the complementary base in a free nucleotide. The enzyme then catalyzes
the formation of an ester bond between the 5′ phosphate group of the nucleotide and the 3′ OH end of the new, growing DNA
chain. In this way, each strand of the original DNA molecule is used to produce a duplicate of its former partner (Figure 5.4.1).
Whatever information was encoded in the original DNA double helix is now contained in each replicate helix. When the cell
divides, each daughter cell gets one of these replicates and thus all of the information that was originally possessed by the parent
cell.
Figure 5.4.1 : A Schematic Diagram of DNA Replication. DNA replication occurs by the sequential unzipping of segments of the
double helix. Each new nucleotide is brought into position by DNA polymerase and is added to the growing strand by the
formation of a phosphate ester bond. Thus, two double helixes form from one, and each consists of one old strand and one new
strand, an outcome called semiconservative replications. (This representation is simplified; many more proteins are involved in
replication.)
Example 5.4.1
A segment of one strand from a DNA molecule has the sequence 5′‑TCCATGAGTTGA‑3′. What is the sequence of nucleotides
in the opposite, or complementary, DNA chain?
SOLUTION
Knowing that the two strands are antiparallel and that T base pairs with A, while C base pairs with G, the sequence of the
complementary strand will be 3′‑AGGTACTCAACT‑5′ (can also be written as TCAACTCATGGA).
Exercise 5.4.1
A segment of one strand from a DNA molecule has the sequence 5′‑CCAGTGAATTGCCTAT‑3′. What is the sequence of
nucleotides in the opposite, or complementary, DNA chain?
What do we mean when we say information is encoded in the DNA molecule? An organism’s DNA can be compared to a book
containing directions for assembling a model airplane or for knitting a sweater. Letters of the alphabet are arranged into words, and
these words direct the individual to perform certain operations with specific materials. If all the directions are followed correctly, a
model airplane or sweater is produced.
In DNA, the particular sequences of nucleotides along the chains encode the directions for building an organism. Just as saw means
one thing in English and was means another, the sequence of bases CGT means one thing, and TGC means something different.
Although there are only four letters—the four nucleotides—in the genetic code of DNA, their sequencing along the DNA strands
can vary so widely that information storage is essentially unlimited.
Transcription
For the hereditary information in DNA to be useful, it must be “expressed,” that is, used to direct the growth and functioning of an
organism. The first step in the processes that constitute DNA expression is the synthesis of RNA, by a template mechanism that is
in many ways analogous to DNA replication. Because the RNA that is synthesized is a complementary copy of information
contained in DNA, RNA synthesis is referred to as transcription. There are three key differences between replication and
transcription:
1. RNA molecules are much shorter than DNA molecules; only a portion of one DNA strand is copied or transcribed to make an
RNA molecule.
2. RNA is built from ribonucleotides rather than deoxyribonucleotides.
3. The newly synthesized RNA strand does not remain associated with the DNA sequence it was transcribed from.
The DNA sequence that is transcribed to make RNA is called the template strand, while the complementary sequence on the other
DNA strand is called the coding or informational strand. To initiate RNA synthesis, the two DNA strands unwind at specific sites
along the DNA molecule. Ribonucleotides are attracted to the uncoiling region of the DNA molecule, beginning at the 3′ end of the
template strand, according to the rules of base pairing. Thymine in DNA calls for adenine in RNA, cytosine specifies guanine,
guanine calls for cytosine, and adenine requires uracil. RNA polymerase—an enzyme—binds the complementary ribonucleotide
and catalyzes the formation of the ester linkage between ribonucleotides, a reaction very similar to that catalyzed by DNA
polymerase (Figure 5.4.2). Synthesis of the RNA strand takes place in the 5′ to 3′ direction, antiparallel to the template strand.
Only a short segment of the RNA molecule is hydrogen-bonded to the template strand at any time during transcription. When
transcription is completed, the RNA is released, and the DNA helix reforms. The nucleotide sequence of the RNA strand formed
during transcription is identical to that of the corresponding coding strand of the DNA, except that U replaces T.
Figure 5.4.2 : A Schematic Diagram of RNA Transcription from a DNA Template. The representation of RNA polymerase is
proportionately much smaller than the actual molecule, which encompasses about 50 nucleotides at a time.
Example 5.4.2
A portion of the template strand of a gene has the sequence 5′‑TCCATGAGTTGA‑3′. What is the sequence of nucleotides in the
RNA that is formed from this template?
SOLUTION
Four things must be remembered in answering this question: (1) the DNA strand and the RNA strand being synthesized are
antiparallel; (2) RNA is synthesized in a 5′ to 3′ direction, so transcription begins at the 3′ end of the template strand; (3)
ribonucleotides are used in place of deoxyribonucleotides; and (4) thymine (T) base pairs with adenine (A), A base pairs with
uracil (U; in RNA), and cytosine (C) base pairs with guanine (G). The sequence is determined to be 3′‑AGGUACUCAACU‑5′
(can also be written as 5′‑UCAACUCAUGGA‑3′).
Exercise 5.4.2
A portion of the template strand of a gene has the sequence 5′‑CCAGTGAATTGCCTAT‑3′. What is the sequence of nucleotides
in the RNA that is formed from this template?
Three types of RNA are formed during transcription: messenger RNA (mRNA), ribosomal RNA (rRNA), and transfer RNA (tRNA).
These three types of RNA differ in function, size, and percentage of the total cell RNA (Table 5.4.1). mRNA makes up only a
small percent of the total amount of RNA within the cell, primarily because each molecule of mRNA exists for a relatively short
time; it is continuously being degraded and resynthesized. The molecular dimensions of the mRNA molecule vary according to the
amount of genetic information a given molecule contains. After transcription, which takes place in the nucleus, the mRNA passes
into the cytoplasm, carrying the genetic message from DNA to the ribosomes, the sites of protein synthesis. Elsewhere, we shall see
how mRNA directly determines the sequence of amino acids during protein synthesis.
Table 5.4.1 : Properties of Cellular RNA in Escherichia coli
Approximate Number of
Type Function Percentage of Total Cell RNA
Nucleotides
mRNA codes for proteins 100–6,000 ~3
rRNA component of ribosomes 120–2900 83
adapter molecule that brings the

tRNA 75–90 14
amino acid to the ribosome
Ribosomes are cellular substructures where proteins are synthesized. They contain about 65% rRNA and 35% protein, held
together by numerous noncovalent interactions, such as hydrogen bonding, in an overall structure consisting of two globular
particles of unequal size.
Molecules of tRNA, which bring amino acids (one at a time) to the ribosomes for the construction of proteins, differ from one
another in the kinds of amino acid each is specifically designed to carry. A set of three nucleotides, known as a codon, on the
mRNA determines which kind of tRNA will add its amino acid to the growing chain. Each of the 20 amino acids found in proteins
has at least one corresponding kind of tRNA, and most amino acids have more than one.
Figure 5.4.3 : Transfer RNA. (a) In the two-dimensional structure of a yeast tRNA molecule for phenylalanine, the amino acid
binds to the acceptor stem located at the 3′ end of the tRNA primary sequence. (The nucleotides that are not specifically identified
here are slightly altered analogs of the four common ribonucleotides A, U, C, and G.) (b) In the three-dimensional structure of
yeast phenylalanine tRNA, note that the anticodon loop is at the bottom and the acceptor stem is at the top right. (c) This shows a
space-filling model of the tRNA.
The two-dimensional structure of a tRNA molecule has three distinctive loops, reminiscent of a cloverleaf (Figure 5.4.3). On one
loop is a sequence of three nucleotides that varies for each kind of tRNA. This triplet, called the anticodon, is complementary to
and pairs with the codon on the mRNA. At the opposite end of the molecule is the acceptor stem, where the amino acid is attached.
Summary
In DNA replication, each strand of the original DNA serves as a template for the synthesis of a complementary strand.
DNA polymerase is the primary enzyme needed for replication.
In transcription, a segment of DNA serves as a template for the synthesis of an RNA sequence.
RNA polymerase is the primary enzyme needed for transcription.
Three types of RNA are formed during transcription: mRNA, rRNA, and tRNA.

1. In DNA replication, a parent DNA molecule produces two daughter molecules. What is the fate of each strand of the parent
DNA double helix?
2. What is the role of DNA in transcription? What is produced in transcription?
3. Which type of RNA contains the codon? Which type of RNA contains the anticodon?
Answers
1. Each strand of the parent DNA double helix remains associated with the newly synthesized DNA strand.
2. DNA serves as a template for the synthesis of an RNA strand (the product of transcription).
3. codon: mRNA; anticodon: tRNA
Exercises
1. Describe how replication and transcription are similar.
2. Describe how replication and transcription differ.
3. A portion of the coding strand for a given gene has the sequence 5′‑ATGAGCGACTTTGCGGGATTA‑3′.
a. What is the sequence of complementary template strand?
b. What is the sequence of the mRNA that would be produced during transcription from this segment of DNA?
4. A portion of the coding strand for a given gene has the sequence 5′‑ATGGCAATCCTCAAACGCTGT‑3′.
Answers
1. Both processes require a template from which a complementary strand is synthesized.
3.
a. 3′‑TACTCGCTGAAACGCCCTAAT‑5′
b. 5′‑AUGAGCGACUUUGCGGGAUUA‑3′
5.4: Replication and Expression of Genetic Information is shared under a CC BY-NC-SA 4.0 license and was authored, remixed, and/or curated
by LibreTexts.
Learning Objectives
describe the characteristics of the genetic code.
describe how a protein is synthesized from mRNA.
One of the definitions of a gene is as follows: a segment of deoxyribonucleic acid (DNA) carrying the code for a specific
polypeptide. Each molecule of messenger RNA (mRNA) is a transcribed copy of a gene that is used by a cell for synthesizing a
polypeptide chain. If a protein contains two or more different polypeptide chains, each chain is coded by a different gene. We turn
now to the question of how the sequence of nucleotides in a molecule of ribonucleic acid (RNA) is translated into an amino acid
sequence.
How can a molecule containing just 4 different nucleotides specify the sequence of the 20 amino acids that occur in proteins? If
each nucleotide coded for 1 amino acid, then obviously the nucleic acids could code for only 4 amino acids. What if amino acids
were coded for by groups of 2 nucleotides? There are 42, or 16, different combinations of 2 nucleotides (AA, AU, AC, AG, UU,
and so on). Such a code is more extensive but still not adequate to code for 20 amino acids. However, if the nucleotides are
arranged in groups of 3, the number of different possible combinations is 43, or 64. Here we have a code that is extensive enough to
direct the synthesis of the primary structure of a protein molecule.
Translation
Video: NDSU Virtual Cell Animations project animation "Translation". For more information, see
http://vcell.ndsu.nodak.edu/animations
The genetic code can therefore be described as the identification of each group of three nucleotides and its particular amino acid.
The sequence of these triplet groups in the mRNA dictates the sequence of the amino acids in the protein. Each individual three-
nucleotide coding unit, as we have seen, is called a codon.
Protein synthesis is accomplished by orderly interactions between mRNA and the other ribonucleic acids (transfer RNA [tRNA]
and ribosomal RNA [rRNA]), the ribosome, and more than 100 enzymes. The mRNA formed in the nucleus during transcription is
transported across the nuclear membrane into the cytoplasm to the ribosomes—carrying with it the genetic instructions. The
process in which the information encoded in the mRNA is used to direct the sequencing of amino acids and thus ultimately to
synthesize a protein is referred to as translation.
Figure 5.5.1 : Binding of an Amino Acid to Its tRNA
Before an amino acid can be incorporated into a polypeptide chain, it must be attached to its unique tRNA. This crucial process
requires an enzyme known as aminoacyl-tRNA synthetase (Figure 5.5.1). There is a specific aminoacyl-tRNA synthetase for each
amino acid. This high degree of specificity is vital to the incorporation of the correct amino acid into a protein. After the amino
acid molecule has been bound to its tRNA carrier, protein synthesis can take place. Figure 5.5.2 depicts a schematic stepwise
representation of this all-important process.
Figure 5.5.2 : The Elongation Steps in Protein Synthesis

Early experimenters were faced with the task of determining which of the 64 possible codons stood for each of the 20 amino acids.
The cracking of the genetic code was the joint accomplishment of several well-known geneticists—notably Har Khorana, Marshall
Nirenberg, Philip Leder, and Severo Ochoa—from 1961 to 1964. The genetic dictionary they compiled, summarized in Figure
5.5.3, shows that 61 codons code for amino acids, and 3 codons serve as signals for the termination of polypeptide synthesis (much
like the period at the end of a sentence). Notice that only methionine (AUG) and tryptophan (UGG) have single codons. All other
amino acids have two or more codons.
Figure 5.5.3 : The Genetic Code
Example 5.5.1 : Using the Genetic Code
A portion of an mRNA molecule has the sequence 5′‑AUGCCACGAGUUGAC‑3′. What amino acid sequence does this code
for?
SOLUTION
Use Figure 5.5.3 to determine what amino acid each set of three nucleotides (codon) codes for. Remember that the sequence is
read starting from the 5′ end and that a protein is synthesized starting with the N-terminal amino acid. The sequence
5′‑AUGCCACGAGUUGAC‑3′ codes for met-pro-arg-val-asp.
Exercise 5.5.4
A portion of an RNA molecule has the sequence 5′‑AUGCUGAAUUGCGUAGGA‑3′. What amino acid sequence does this
code for?
Further experimentation threw much light on the nature of the genetic code, as follows:
1. The code is virtually universal; animal, plant, and bacterial cells use the same codons to specify each amino acid (with a few
exceptions).
2. The code is “degenerate”; in all but two cases (methionine and tryptophan), more than one triplet codes for a given amino acid.
3. The first two bases of each codon are most significant; the third base often varies. This suggests that a change in the third base
by a mutation may still permit the correct incorporation of a given amino acid into a protein. The third base is sometimes called
the “wobble” base.
4. The code is continuous and nonoverlapping; there are no nucleotides between codons, and adjacent codons do not overlap.
5. The three termination codons are read by special proteins called release factors, which signal the end of the translation process.
6. The codon AUG codes for methionine and is also the initiation codon. Thus methionine is the first amino acid in each newly
synthesized polypeptide. This first amino acid is usually removed enzymatically before the polypeptide chain is completed; the
vast majority of polypeptides do not begin with methionine.
Summary
In translation, the information in mRNA directs the order of amino acids in protein synthesis. A set of three nucleotides (codon)
codes for a specific amino acid.

1. What are the roles of mRNA and tRNA in protein synthesis?
2. What is the initiation codon?
3. What are the termination codons and how are they recognized?
Answers
1. mRNA provides the code that determines the order of amino acids in the protein; tRNA transports the amino acids to the
ribosome to incorporate into the growing protein chain.
2. AUG
3. UAA, UAG, and UGA; they are recognized by special proteins called release factors, which signal the end of the translation
process.
Exercises
1. Write the anticodon on tRNA that would pair with each mRNA codon.
a. 5′‑UUU‑3′
b. 5′‑CAU‑3′
c. 5′‑AGC‑3′
d. 5′‑CCG‑3′
2. Write the codon on mRNA that would pair with each tRNA anticodon.
a. 5′‑UUG‑3′
b. 5′‑GAA‑3′
c. 5′‑UCC‑3′
d. 5′‑CAC‑3′
3. The peptide hormone oxytocin contains 9 amino acid units. What is the minimum number of nucleotides needed to code for this
peptide?
4. Myoglobin, a protein that stores oxygen in muscle cells, has been purified from a number of organisms. The protein from a
sperm whale is composed of 153 amino acid units. What is the minimum number of nucleotides that must be present in the
mRNA that codes for this protein?
5. Use Figure 5.5.3 to identify the amino acids carried by each tRNA molecule in Exercise 1.
7. Use Figure 5.5.3 to determine the amino acid sequence produced from this mRNA sequence:
5′‑AUGAGCGACUUUGCGGGAUUA‑3′.
5′‑AUGGCAAUCCUCAAACGCUGU‑3′
Answers
1. a. 3′‑AAA‑5′
b. 3′‑GUA‑5′
c. 3′‑UCG‑5′
d. 3′‑GGC‑5′
3. 27 nucleotides (3 nucleotides/codon)
5. 1a: phenyalanine; 1b: histidine; 1c: serine; 1d: proline
7. met-ser-asp-phe-ala-gly-leu
5.5: Protein Synthesis and the Genetic Code is shared under a CC BY-NC-SA 4.0 license and was authored, remixed, and/or curated by
LibreTexts.
Learning Objectives
To describe the causes of genetic mutations and how they lead to genetic diseases.
We have seen that the sequence of nucleotides in a cell’s deoxyribonucleic acid (DNA) is what ultimately determines the sequence
of amino acids in proteins made by the cell and thus is critical for the proper functioning of the cell. On rare occasions, however,
the nucleotide sequence in DNA may be modified either spontaneously (by errors during replication, occurring approximately once
for every 10 billion nucleotides) or from exposure to heat, radiation, or certain chemicals. Any chemical or physical change that
alters the nucleotide sequence in DNA is called a mutation. When a mutation occurs in an egg or sperm cell that then produces a
living organism, it will be inherited by all the offspring of that organism.
Common types of mutations include substitution (a different nucleotide is substituted), insertion (the addition of a new nucleotide),
and deletion (the loss of a nucleotide). These changes within DNA are called point mutations because only one nucleotide is
substituted, added, or deleted (Figure 5.6.1). Because an insertion or deletion results in a frame-shift that changes the reading of
subsequent codons and, therefore, alters the entire amino acid sequence that follows the mutation, insertions and deletions are
usually more harmful than a substitution in which only a single amino acid is altered.
Figure 5.6.1 : Three Types of Point Mutations

The chemical or physical agents that cause mutations are called mutagens. Examples of physical mutagens are ultraviolet (UV) and
gamma radiation. Radiation exerts its mutagenic effect either directly or by creating free radicals that in turn have mutagenic
effects. Radiation and free radicals can lead to the formation of bonds between nitrogenous bases in DNA. For example, exposure
to UV light can result in the formation of a covalent bond between two adjacent thymines on a DNA strand, producing a thymine
dimer (Figure 5.6.2). If not repaired, the dimer prevents the formation of the double helix at the point where it occurs. The genetic
disease xeroderma pigmentosum is caused by a lack of the enzyme that cuts out the thymine dimers in damaged DNA. Individuals
affected by this condition are abnormally sensitive to light and are more prone to skin cancer than normal individuals.
Figure 5.6.2 : An Example of Radiation Damage to DNA. (a) The thymine dimer is formed by the action of UV light. (b) When a
defect in the double strand is produced by the thymine dimer, this defect temporarily stops DNA replication, but the dimer can be
removed, and the region can be repaired by an enzyme repair system.
Sometimes gene mutations are beneficial, but most of them are detrimental. For example, if a point mutation occurs at a crucial
position in a DNA sequence, the affected protein will lack biological activity, perhaps resulting in the death of a cell. In such cases
the altered DNA sequence is lost and will not be copied into daughter cells. Nonlethal mutations in an egg or sperm cell may lead
to metabolic abnormalities or hereditary diseases. Such diseases are called inborn errors of metabolism or genetic diseases. A
partial listing of genetic diseases is presented in Figure 5.6.1, and two specific diseases are discussed in the following sections. In
most cases, the defective gene results in a failure to synthesize a particular enzyme.
Figure 5.6.1 : Some Representative Genetic Diseases in Humans and the Protein or Enzyme Responsible
Disease Responsible Protein or Enzyme
alkaptonuria homogentisic acid oxidase
galactose 1-phosphate uridyl transferase, galactokinase, or UDP

galactosemia
galactose epimerase
Gaucher disease glucocerebrosidase
gout and Lesch-Nyhan syndrome hypoxanthine-guanine phosphoribosyl transferase
hemophilia antihemophilic factor (factor VIII) or Christmas factor (factor IX)
homocystinuria cystathionine synthetase
maple syrup urine disease branched chain α-keto acid dehydrogenase complex
McArdle syndrome muscle phosphorylase
Niemann-Pick disease sphingomyelinase
phenylketonuria (PKU) phenylalanine hydroxylase
sickle cell anemia hemoglobin
Tay-Sachs disease hexosaminidase A
tyrosinemia fumarylacetoacetate hydrolase or tyrosine aminotransferase
von Gierke disease glucose 6-phosphatase
Wilson disease Wilson disease protein
PKU results from the absence of the enzyme phenylalanine hydroxylase. Without this enzyme, a person cannot convert
phenylalanine to tyrosine, which is the precursor of the neurotransmitters dopamine and norepinephrine as well as the skin pigment
melanin.
When this reaction cannot occur, phenylalanine accumulates and is then converted to higher than normal quantities of
phenylpyruvate. The disease acquired its name from the high levels of phenylpyruvate (a phenyl ketone) in urine. Excessive
amounts of phenylpyruvate impair normal brain development, which causes severe mental retardation.
PKU may be diagnosed by assaying a sample of blood or urine for phenylalanine or one of its metabolites. Medical authorities
recommend testing every newborn’s blood for phenylalanine within 24 h to 3 weeks after birth. If the condition is detected, mental
retardation can be prevented by immediately placing the infant on a diet containing little or no phenylalanine. Because
phenylalanine is plentiful in naturally produced proteins, the low-phenylalanine diet depends on a synthetic protein substitute plus
very small measured amounts of naturally produced foods. Before dietary treatment was introduced in the early 1960s, severe
mental retardation was a common outcome for children with PKU. Prior to the 1960s, 85% of patients with PKU had an
intelligence quotient (IQ) less than 40, and 37% had IQ scores below 10. Since the introduction of dietary treatments, however,
over 95% of children with PKU have developed normal or near-normal intelligence. The incidence of PKU in newborns is about 1
in 12,000 in North America.
Every state in the United States has mandated that screening for PKU be provided to all
newborns.
Several genetic diseases are collectively categorized as lipid-storage diseases. Lipids are constantly being synthesized and broken
down in the body, so if the enzymes that catalyze lipid degradation are missing, the lipids tend to accumulate and cause a variety of
medical problems. When a genetic mutation occurs in the gene for the enzyme hexosaminidase A, for example, gangliosides cannot
be degraded but accumulate in brain tissue, causing the ganglion cells of the brain to become greatly enlarged and nonfunctional.
This genetic disease, known as Tay-Sachs disease, leads to a regression in development, dementia, paralysis, and blindness, with
death usually occurring before the age of three. There is currently no treatment, but Tay-Sachs disease can be diagnosed in a fetus
by assaying the amniotic fluid (amniocentesis) for hexosaminidase A. A blood test can identify Tay-Sachs carriers—people who
inherit a defective gene from only one rather than both parents—because they produce only half the normal amount of
hexosaminidase A, although they do not exhibit symptoms of the disease.
Looking Closer: Recombinant DNA Technology

More than 3,000 human diseases have been shown to have a genetic component, caused or in some way modulated by the person’s
genetic composition. Moreover, in the last decade or so, researchers have succeeded in identifying many of the genes and even
mutations that are responsible for specific genetic diseases. Now scientists have found ways of identifying and isolating genes that
have specific biological functions and placing those genes in another organism, such as a bacterium, which can be easily grown in
culture. With these techniques, known as recombinant DNA technology, the ability to cure many serious genetic diseases appears to
be within our grasp.
Isolating the specific gene or genes that cause a particular genetic disease is a monumental task. One reason for the difficulty is the
enormous amount of a cell’s DNA, only a minute portion of which contains the gene sequence. Thus, the first task is to obtain
smaller pieces of DNA that can be more easily handled. Fortunately, researchers are able to use restriction enzymes (also known as
restriction endonucleases), discovered in 1970, which are enzymes that cut DNA at specific, known nucleotide sequences, yielding
DNA fragments of shorter length. For example, the restriction enzyme EcoRI recognizes the nucleotide sequence shown here and
cuts both DNA strands as indicated:
Once a DNA strand has been fragmented, it must be cloned; that is, multiple identical copies of each DNA fragment are produced
to make sure there are sufficient amounts of each to detect and manipulate in the laboratory. Cloning is accomplished by inserting
the individual DNA fragments into phages (bacterial viruses) that can enter bacterial cells and be replicated. When a bacterial cell
infected by the modified phage is placed in an appropriate culture medium, it forms a colony of cells, all containing copies of the
original DNA fragment. This technique is used to produce many bacterial colonies, each containing a different DNA fragment. The
result is a DNA library, a collection of bacterial colonies that together contain the entire genome of a particular organism.
The next task is to screen the DNA library to determine which bacterial colony (or colonies) has incorporated the DNA fragment
containing the desired gene. A short piece of DNA, known as a hybridization probe, which has a nucleotide sequence
complementary to a known sequence in the gene, is synthesized, and a radioactive phosphate group is added to it as a “tag.” You
might be wondering how researchers are able to prepare such a probe if the gene has not yet been isolated. One way is to use a
segment of the desired gene isolated from another organism. An alternative method depends on knowing all or part of the amino
acid sequence of the protein produced by the gene of interest: the amino acid sequence is used to produce an approximate genetic
code for the gene, and this nucleotide sequence is then produced synthetically. (The amino acid sequence used is carefully chosen
to include, if possible, many amino acids such as methionine and tryptophan, which have only a single codon each.)
After a probe identifies a colony containing the desired gene, the DNA fragment is clipped out, again using restriction enzymes,
and spliced into another replicating entity, usually a plasmid. Plasmids are tiny mini-chromosomes found in many bacteria, such as
Escherichia coli (E. coli). A recombined plasmid would then be inserted into the host organism (usually the bacterium E. coli),
where it would go to work to produce the desired protein.
Proponents of recombinant DNA research are excited about its great potential benefits. An example is the production of human
growth hormone, which is used to treat children who fail to grow properly. Formerly, human growth hormone was available only in
tiny amounts obtained from cadavers. Now it is readily available through recombinant DNA technology. Another gene that has
been cloned is the gene for epidermal growth factor, which stimulates the growth of skin cells and can be used to speed the healing
of burns and other skin wounds. Recombinant techniques are also a powerful research tool, providing enormous aid to scientists as
they map and sequence genes and determine the functions of different segments of an organism’s DNA.
In addition to advancements in the ongoing treatment of genetic diseases, recombinant DNA technology may actually lead to cures.
When appropriate genes are successfully inserted into E. coli, the bacteria can become miniature pharmaceutical factories,
producing great quantities of insulin for people with diabetes, clotting factor for people with hemophilia, missing enzymes,
hormones, vitamins, antibodies, vaccines, and so on. Recent accomplishments include the production in E. coli of recombinant
DNA molecules containing synthetic genes for tissue plasminogen activator, a clot-dissolving enzyme that can rescue heart attack
victims, as well as the production of vaccines against hepatitis B (humans) and hoof-and-mouth disease (cattle).
Scientists have used other bacteria besides E. coli in gene-splicing experiments and also yeast and fungi. Plant molecular biologists
use a bacterial plasmid to introduce genes for several foreign proteins (including animal proteins) into plants. The bacterium is
Agrobacterium tumefaciens, which can cause tumors in many plants, but which can be treated so that its tumor-causing ability is
eliminated. One practical application of its plasmids would be to enhance a plant’s nutritional value by transferring into it the gene
necessary for the synthesis of an amino acid in which the plant is normally deficient (for example, transferring the gene for
methionine synthesis into pinto beans, which normally do not synthesize high levels of methionine).
Restriction enzymes have been isolated from a number of bacteria and are named after the bacterium of origin. EcoRI is a
restriction enzyme obtained from the R strain of E. coli. The roman numeral I indicates that it was the first restriction enzyme
obtained from this strain of bacteria.
Summary
The nucleotide sequence in DNA may be modified either spontaneously or from exposure to heat, radiation, or certain
chemicals and can lead to mutations.
Mutagens are the chemical or physical agents that cause mutations.
Genetic diseases are hereditary diseases that occur because of a mutation in a critical gene.

1. a. What effect can UV radiation have on DNA?
b. Is UV radiation an example of a physical mutagen or a chemical mutagen?
2. a. What causes PKU?
b. How is PKU detected and treated?
Answers
1. a. It can lead to the formation of a covalent bond between two adjacent thymines on a DNA strand, producing a thymine dimer.
b. physical mutagen
2. a. the absence of the enzyme phenylalanine hydroxylase
b. PKU is diagnosed by assaying a sample of blood or urine for phenylalanine or one of its metabolites; treatment calls for an
individual to be placed on a diet containing little or no phenylalanine.
Exercises
1. A portion of the coding strand of a gene was found to have the sequence 5′‑ATGAGCGACTTTCGCCCATTA‑3′. A mutation
occurred in the gene, making the sequence 5′‑ATGAGCGACCTTCGCCCATTA‑3′.
a. Identify the mutation as a substitution, an insertion, or a deletion.
b. What effect would the mutation have on the amino acid sequence of the protein obtained from this mutated gene (use Figure
19.14)?
2. A portion of the coding strand of a gene was found to have the sequence 5′‑ATGGCAATCCTCAAACGCTGT‑3′. A mutation
occurred in the gene, making the sequence 5′‑ATGGCAATCCTCAACGCTGT‑3′.
19.14)?
3. a. What is a mutagen?
b. Give two examples of mutagens.
4. For each genetic disease, indicate which enzyme is lacking or defective and the characteristic symptoms of the disease.
a. PKU
b. Tay-Sachs disease
Answers
1. a. substitution
b. Phenylalanine (UUU) would be replaced with leucine (CUU).
3. a. a chemical or physical agent that can cause a mutation
b. UV radiation and gamma radiation (answers will vary)
5.6: Mutations and Genetic Diseases is shared under a CC BY-NC-SA 4.0 license and was authored, remixed, and/or curated by LibreTexts.
5.7: Viruses
Learning Objectives
To explain how viruses reproduce in cells.
Viruses are visible only under an electron microscope. They come in a variety of shapes, ranging from spherical to rod shaped. The
fact that they contain either deoxyribonucleic acid (DNA) or ribonucleic acid (RNA)—but never both—allows them to be divided
into two major classes: DNA viruses and RNA viruses (Figure 5.7.1).
Figure 5.7.1 : Viruses. Viruses come in a variety of shapes that are determined by their protein coats.
Most RNA viruses use their nucleic acids in much the same way as the DNA viruses, penetrating a host cell and inducing it to
replicate the viral RNA and synthesize viral proteins. The new RNA strands and viral proteins are then assembled into new viruses.
Some RNA viruses, however, called retroviruses (Figure 5.7.2), synthesize DNA in the host cell, in a process that is the reverse of
the DNA-to-RNA transcription that normally occurs in cells. The synthesis of DNA from an RNA template is catalyzed by the
enzyme reverse transcriptase.
Figure 5.7.2 : Life Cycle of a Retrovirus

In 1987, azidothymidine (AZT, also known as zidovudine or the brand name Retrovir) became the first drug approved for the
treatment of AIDS. It works by binding to reverse transcriptase in place of deoxythymidine triphosphate, after which, because AZT
does not have a 3′OH group, further replication is blocked. In the past 10 years, several other drugs have been approved that also
act by inhibiting the viral reverse transcriptase.
Raltegravir (Isentress) is a newer anti-AIDS drug that was approved by the FDA in October 2007. This drug inhibits the integrase
enzyme that is needed to integrate the HIV DNA into cellular DNA, an essential step in the production of more HIV particles.
A major problem in treating HIV infections is that the virus can become resistant to any of these drugs. One way to combat the
problem has been to administer a “cocktail” of drugs, typically a combination of two reverse transcriptase inhibitors along with a
protease inhibitor. These treatments can significantly reduce the amount of HIV in an infected person.
Career Focus: Genetics Counselor
A genetics counselor works with individuals and families who have birth defects or genetic disorders or a family history of a
disease, such as cancer, with a genetic link. A genetics counselor may work in a variety of health-care settings (such as a
hospital) to obtain family medical and reproductive histories; explain how genetic conditions are inherited; explain the causes,
diagnosis, and care of these conditions; interpret the results of genetic tests; and aid the individual or family in making decisions
regarding genetic diseases or conditions. A certified genetics counselor must obtain a master’s degree from an accredited
program. Applicants to these graduate programs usually have an undergraduate degree in biology, psychology, or genetics.
Photo courtesy of the United States National Institutes for Health,

http://commons.wikimedia.org/wiki/File:Geneticcounseling.jpg.
Summary
Viruses are very small infectious agents that contain either DNA or RNA as their genetic material. The human immunodeficiency
virus (HIV) causes acquired immunodeficiency syndrome (AIDS).
Questions
1. Describe the general structure of a virus.
2. How does a DNA virus differ from an RNA virus?
3. Why is HIV known as a retrovirus?
4. Describe how a DNA virus invades and destroys a cell.
5. a. Describe how an RNA virus invades and destroys a cell.
b. How does this differ from a DNA virus?
6. What HIV enzyme does AZT inhibit?
7. What HIV enzyme does raltegravir inhibit?
Answers
1. A virus consists of a central core of nucleic acid enclosed in a protective shell of proteins. There may be lipid or carbohydrate
molecules on the surface.
2. A DNA virus has DNA as its genetic material, while an RNA virus has RNA as its genetic material.
3. In a cell, a retrovirus synthesizes a DNA copy of its RNA genetic material.
4. The DNA virus enters a host cell and induces the cell to replicate the viral DNA and produce viral proteins. These proteins and
DNA assemble into new viruses that are released by the host cell, which may die in the process.
5. -
6. reverse transcriptase
7. -
5.7: Viruses is shared under a CC BY-NC-SA 4.0 license and was authored, remixed, and/or curated by LibreTexts.
A cell’s hereditary information is encoded in chromosomes in the cell’s nucleus. Each chromosome is composed of proteins and
deoxyribonucleic acid (DNA). The chromosomes contain smaller hereditary units called genes, which are relatively short
segments of DNA. The hereditary information is expressed or used through the synthesis of ribonucleic acid (RNA). Both nucleic
acids—DNA and RNA—are polymers composed of monomers known as nucleotides, which in turn consist of phosphoric acid
(H3PO4), a nitrogenous base, and a pentose sugar.
The two types of nitrogenous bases most important in nucleic acids are purines—adenine (A) and guanine (G)—and pyrimidines
—cytosine (C), thymine (T), and uracil (U). DNA contains the nitrogenous bases adenine, cytosine, guanine, and thymine, while
the bases in RNA are adenine, cytosine, guanine, and uracil. The sugar in the nucleotides of RNA is ribose; the one in DNA is 2-
deoxyribose. The sequence of nucleotides in a nucleic acid defines the primary structure of the molecule.
RNA is a single-chain nucleic acid, whereas DNA possesses two nucleic-acid chains intertwined in a secondary structure called a
double helix. The sugar-phosphate backbone forms the outside the double helix, with the purine and pyrimidine bases tucked
inside. Hydrogen bonding between complementary bases holds the two strands of the double helix together; A always pairs with
T and C always pairs with G.
Cell growth requires replication, or reproduction of the cell’s DNA. The double helix unwinds, and hydrogen bonding between
complementary bases breaks so that there are two single strands of DNA, and each strand is a template for the synthesis of a new
strand. For protein synthesis, three types of RNA are needed: messenger RNA (mRNA), ribosomal RNA (rRNA), and transfer RNA
(tRNA). All are made from a DNA template by a process called transcription. The double helix uncoils, and ribonucleotides base-
pair to the deoxyribonucleotides on one DNA strand; however, RNA is produced using uracil rather than thymine. Once the RNA
is formed, it dissociates from the template and leaves the nucleus, and the DNA double helix reforms.
Translation is the process in which proteins are synthesized from the information in mRNA. It occurs at structures called
ribosomes, which are located outside the nucleus and are composed of rRNA and protein. The 64 possible three-nucleotide
combinations of the 4 nucleotides of DNA constitute the genetic code that dictates the sequence in which amino acids are joined to
make proteins. Each three-nucleotide sequence on mRNA is a codon. Each kind of tRNA molecule binds a specific amino acid and
has a site containing a three-nucleotide sequence called an anticodon.
The general term for any change in the genetic code in an organism’s DNA is mutation. A change in which a single base is
substituted, inserted, or deleted is a point mutation. The chemical and/or physical agents that cause mutations are called
mutagens. Diseases that occur due to mutations in critical DNA sequences are referred to as genetic diseases.
Viruses are infectious agents composed of a tightly packed central core of nucleic acids enclosed by a protective shell of proteins.
Viruses contain either DNA or RNA as their genetic material but not both. Some RNA viruses, called retroviruses, synthesize
DNA in the host cell from their RNA genome. The human immunodeficiency virus (HIV) causes acquired immunodeficiency
syndrome (AIDS).
5.8: Nucleic Acids (Summary) is shared under a CC BY-NC-SA 4.0 license and was authored, remixed, and/or curated by LibreTexts.
19.1: Nucleotides
1. Identify the three molecules needed to form the nucleotides in each nucleic acid.
a. DNA
b. RNA
2. Classify each compound as a pentose sugar, a purine, or a pyrimidine.
a. adenine
b. guanine
c. deoxyribose
d. thymine
e. ribose
f. cytosine
Answers
1. a. nitrogenous base (adenine, guanine, cytosine, and thymine), 2-deoxyribose, and H3PO4
b. nitrogenous base (adenine, guanine, cytosine, and uracil), ribose, and H3PO4
2. a. purine
b. purine
c. pentose sugar
d. pyrimidine
e. pentose sugar
f. pyrimidine
Exercises
1. What is the sugar unit in each nucleic acid?
a. RNA
b. DNA
2. Identify the major nitrogenous bases in each nucleic acid.
a. DNA
b. RNA
a.
b.
a.
b.
a.
b.
a.
b.
Answers
1. a. ribose
b. deoxyribose
3. a.
b.
a.
b.

1. a. Name the two kinds of nucleic acids.
b. Which type of nucleic acid stores genetic information in the cell?
2. What are complementary bases?
3. Why is it structurally important that a purine base always pair with a pyrimidine base in the DNA double helix?
Answers
1. a. deoxyribonucleic acid (DNA) and ribonucleic acid (RNA)
b. DNA
2. the specific base pairings in the DNA double helix in which guanine is paired with cytosine and adenine is paired with thymine
3. The width of the DNA double helix is kept at a constant width, rather than narrowing (if two pyrimidines were across from each
other) or widening (if two purines were across from each other).
Exercises
1. For this short RNA segment,
c. write the nucleotide sequence of this RNA segment.
2. For this short DNA segment,

c. write the nucleotide sequence of this DNA segment.
3. Which nitrogenous base in DNA pairs with each nitrogenous base?
a. cytosine
b. adenine
c. guanine
d. thymine
4. Which nitrogenous base in RNA pairs with each nitrogenous base?
a. cytosine
b. adenine
c. guanine
d. thymine
5′ ATGCGACTA 3′ 3′ TACGCTGAT 5′
5′ CGATGAGCC 3′ 3′ GCTACTCGG 5′
Answers
1.
c. ACU
3. a. guanine
b. thymine
c. cytosine
d. adenine
5. 22 (2 between each AT base pair and 3 between each GC base pair)

1. In DNA replication, a parent DNA molecule produces two daughter molecules. What is the fate of each strand of the parent
DNA double helix?
2. What is the role of DNA in transcription? What is produced in transcription?
3. Which type of RNA contains the codon? Which type of RNA contains the anticodon?
Answers
1. Each strand of the parent DNA double helix remains associated with the newly synthesized DNA strand.
2. DNA serves as a template for the synthesis of an RNA strand (the product of transcription).
3. codon: mRNA; anticodon: tRNA
Exercises
1. Describe how replication and transcription are similar.
2. Describe how replication and transcription differ.
3. A portion of the coding strand for a given gene has the sequence 5′‑ATGAGCGACTTTGCGGGATTA‑3′.
4. A portion of the coding strand for a given gene has the sequence 5′‑ATGGCAATCCTCAAACGCTGT‑3′.
Answers
1. Both processes require a template from which a complementary strand is synthesized.
3.
a. 3′‑TACTCGCTGAAACGCCCTAAT‑5′
b. 5′‑AUGAGCGACUUUGCGGGAUUA‑3′

1. What are the roles of mRNA and tRNA in protein synthesis?
2. What is the initiation codon?
3. What are the termination codons and how are they recognized?
Answers
1. mRNA provides the code that determines the order of amino acids in the protein; tRNA transports the amino acids to the
ribosome to incorporate into the growing protein chain.
2. AUG
3. UAA, UAG, and UGA; they are recognized by special proteins called release factors, which signal the end of the translation
process.
Exercises
1. Write the anticodon on tRNA that would pair with each mRNA codon.
a. 5′‑UUU‑3′
b. 5′‑CAU‑3′
c. 5′‑AGC‑3′
d. 5′‑CCG‑3′
2. Write the codon on mRNA that would pair with each tRNA anticodon.
a. 5′‑UUG‑3′
b. 5′‑GAA‑3′
c. 5′‑UCC‑3′
d. 5′‑CAC‑3′
3. The peptide hormone oxytocin contains 9 amino acid units. What is the minimum number of nucleotides needed to code for this
peptide?
4. Myoglobin, a protein that stores oxygen in muscle cells, has been purified from a number of organisms. The protein from a
sperm whale is composed of 153 amino acid units. What is the minimum number of nucleotides that must be present in the
mRNA that codes for this protein?
5′‑AUGAGCGACUUUGCGGGAUUA‑3′.
5′‑AUGGCAAUCCUCAAACGCUGU‑3′
Answers
1. a. 3′‑AAA‑5′
b. 3′‑GUA‑5′
c. 3′‑UCG‑5′
d. 3′‑GGC‑5′
3. 27 nucleotides (3 nucleotides/codon)
5. 1a: phenyalanine; 1b: histidine; 1c: serine; 1d: proline
7. met-ser-asp-phe-ala-gly-leu

1. a. What effect can UV radiation have on DNA?
b. Is UV radiation an example of a physical mutagen or a chemical mutagen?
2. a. What causes PKU?
b. How is PKU detected and treated?
Answers
1. a. It can lead to the formation of a covalent bond between two adjacent thymines on a DNA strand, producing a thymine dimer.
b. physical mutagen
2. a. the absence of the enzyme phenylalanine hydroxylase
b. PKU is diagnosed by assaying a sample of blood or urine for phenylalanine or one of its metabolites; treatment calls for an
individual to be placed on a diet containing little or no phenylalanine.
Exercises
1. A portion of the coding strand of a gene was found to have the sequence 5′‑ATGAGCGACTTTCGCCCATTA‑3′. A mutation
occurred in the gene, making the sequence 5′‑ATGAGCGACCTTCGCCCATTA‑3′.
19.14)?
2. A portion of the coding strand of a gene was found to have the sequence 5′‑ATGGCAATCCTCAAACGCTGT‑3′. A mutation
occurred in the gene, making the sequence 5′‑ATGGCAATCCTCAACGCTGT‑3′.
19.14)?
3. a. What is a mutagen?
b. Give two examples of mutagens.
4. For each genetic disease, indicate which enzyme is lacking or defective and the characteristic symptoms of the disease.
a. PKU
b. Tay-Sachs disease
Answers
1. a. substitution
b. Phenylalanine (UUU) would be replaced with leucine (CUU).
3. a. a chemical or physical agent that can cause a mutation
b. UV radiation and gamma radiation (answers will vary)
19.6: Viruses
Questions
1. Describe the general structure of a virus.
2. How does a DNA virus differ from an RNA virus?
3. Why is HIV known as a retrovirus?
4. Describe how a DNA virus invades and destroys a cell.
5. a. Describe how an RNA virus invades and destroys a cell.
b. How does this differ from a DNA virus?
6. What HIV enzyme does AZT inhibit?
7. What HIV enzyme does raltegravir inhibit?
Answers
1. A virus consists of a central core of nucleic acid enclosed in a protective shell of proteins. There may be lipid or carbohydrate
molecules on the surface.
2. A DNA virus has DNA as its genetic material, while an RNA virus has RNA as its genetic material.
3. In a cell, a retrovirus synthesizes a DNA copy of its RNA genetic material.
4. The DNA virus enters a host cell and induces the cell to replicate the viral DNA and produce viral proteins. These proteins and
DNA assemble into new viruses that are released by the host cell, which may die in the process.
5. -
6. reverse transcriptase
7. -
1. For this nucleic acid segment,
a. classify this segment as RNA or DNA and justify your choice.
b. determine the sequence of this segment, labeling the 5′ and 3′ ends.
2. For this nucleic acid segment,
a. classify this segment as RNA or DNA and justify your choice.

b. determine the sequence of this segment, labeling the 5′ and 3′ ends.
3. One of the key pieces of information that Watson and Crick used in determining the secondary structure of DNA came from
experiments done by E. Chargaff, in which he studied the nucleotide composition of DNA from many different species.
Chargaff noted that the molar quantity of A was always approximately equal to the molar quantity of T, and the molar quantity
of C was always approximately equal to the molar quantity of G. How were Chargaff’s results explained by the structural model
of DNA proposed by Watson and Crick?
4. Suppose Chargaff (see Exercise 3) had used RNA instead of DNA. Would his results have been the same; that is, would the
molar quantity of A approximately equal the molar quantity of T? Explain.
5. In the DNA segment
5′‑ATGAGGCATGAGACG‑3′ (coding strand) 3′‑TACTCCGTACTCTGC‑5′ (template strand)
a. What products would be formed from the segment’s replication?
b. Write the mRNA sequence that would be obtained from the segment’s transcription.
c. What is the amino acid sequence of the peptide produced from the mRNA in Exercise 5b?
6. In the DNA segment
5′‑ATGACGGTTTACTAAGCC‑3′ (coding strand) 3′‑TACTGCCAAATGATTCGG‑5′ (template strand)
a. What products would be formed from the segment’s replication?
b. Write the mRNA sequence that would be obtained from the segment’s transcription.
c. What is the amino acid sequence of the peptide produced from the mRNA in Exercise 6b?
7. A hypothetical protein has a molar mass of 23,300 Da. Assume that the average molar mass of an amino acid is 120.
a. How many amino acids are present in this hypothetical protein?
b. What is the minimum number of codons present in the mRNA that codes for this protein?
c. What is the minimum number of nucleotides needed to code for this protein?
8. Bradykinin is a potent peptide hormone composed of nine amino acids that lowers blood pressure.
a. The amino acid sequence for bradykinin is arg-pro-pro-gly-phe-ser-pro-phe-arg. Postulate a base sequence in the mRNA
that would direct the synthesis of this hormone. Include an initiation codon and a termination codon.
b. What is the nucleotide sequence of the DNA that codes for this mRNA?
9. A particular DNA coding segment is ACGTTAGCCCCAGCT.
a. Write the sequence of nucleotides in the corresponding mRNA.
b. Determine the amino acid sequence formed from the mRNA in Exercise 9a during translation.
c. What amino acid sequence results from each of the following mutations?
a. replacement of the underlined guanine by adenine
b. insertion of thymine immediately after the underlined guanine
c. deletion of the underlined guanine
10. A particular DNA coding segment is TACGACGTAACAAGC.
a. Write the sequence of nucleotides in the corresponding mRNA.
b. Determine the amino acid sequence formed from the mRNA in Exercise 10a during translation.
c. What amino acid sequence results from each of the following mutations?
a. replacement of the underlined guanine by adenine
b. replacement of the underlined adenine by thymine
11. Two possible point mutations are the substitution of lysine for leucine or the substitution of serine for threonine. Which is likely
to be more serious and why?
12. Two possible point mutations are the substitution of valine for leucine or the substitution of glutamic acid for histidine. Which
is likely to be more serious and why?
Answers
1.
a. RNA; the sugar is ribose, rather than deoxyribose
b. 5′‑GUA‑3′
3. In the DNA structure, because guanine (G) is always paired with cytosine (C) and adenine (A) is always paired with thymine
(T), you would expect to have equal amounts of each.
5.
a. Each strand would be replicated, resulting in two double-stranded segments.
b. 5′‑AUGAGGCAUGAGACG‑3′
c. met-arg-his-glu-thr
7.
a. 194
b. 194
c. 582
9.
a. 5′‑ACGUUAGCCCCAGCU‑3′
b. thr-leu-ala-pro-ala
c. a. thr-leu-thr-pro-ala
b. thr-leu-val-pro-ser
c. thr-leu-pro-gin
11. substitution of lysine for leucine because you are changing from an amino acid with a nonpolar side chain to one that has a
positively charged side chain; both serine and threonine, on the other hand, have polar side chains containing the OH group.
5.9: Nucleic Acids (Exercises) is shared under a CC BY-NC-SA 4.0 license and was authored, remixed, and/or curated by LibreTexts.
19.1: Nucleotides by Anonymous is licensed CC BY-NC-SA 4.0. Original source: https://2012books.lardbucket.org/books/introduction-to-
19.2: Nucleic Acid Structure by Anonymous is licensed CC BY-NC-SA 4.0. Original source:
19.3: Replication and Expression of Genetic Information by Anonymous is licensed CC BY-NC-SA 4.0. Original source:
19.4: Protein Synthesis and the Genetic Code by Anonymous is licensed CC BY-NC-SA 4.0. Original source:
19.5: Mutations and Genetic Diseases by Anonymous is licensed CC BY-NC-SA 4.0. Original source:
19.6: Viruses by Anonymous is licensed CC BY-NC-SA 4.0. Original source: https://2012books.lardbucket.org/books/introduction-to-
CHAPTER OVERVIEW
6: Energy Metabolism
Metabolism is the set of life-sustaining chemical transformations within the cells of living organisms. The three main purposes of
metabolism are the conversion of food/fuel to energy to run cellular processes, the conversion of food/fuel to building blocks for
proteins, lipids, nucleic acids, and some carbohydrates, and the elimination of nitrogenous wastes. These enzyme-catalyzed
reactions allow organisms to grow and reproduce, maintain their structures, and respond to their environments. Metabolism is
usually divided into two categories: catabolism, the breaking down of organic matter, for example, by cellular respiration, and
anabolism, the building up of components of cells such as proteins and nucleic acids. Usually, breaking down releases energy and
building up consumes energy.
6: Energy Metabolism is shared under a CC BY-NC-SA 4.0 license and was authored, remixed, and/or curated by LibreTexts.
1
The discovery of the link between insulin and diabetes led to a period of intense research aimed at understanding exactly how
insulin works in the body to regulate glucose levels. Hormones in general act by binding to some protein, known as the hormone’s
receptor, thus initiating a series of events that lead to a desired outcome. In the early 1970s, the insulin receptor was purified, and
researchers began to study what happens after insulin binds to its receptor and how those events are linked to the uptake and
metabolism of glucose in cells.
The insulin receptor is located in the cell membrane and consists of four polypeptide chains: two identical chains called α chains
and two identical chains called β chains. The α chains, positioned on the outer surface of the membrane, consist of 735 amino acids
each and contain the binding site for insulin. The β chains are integral membrane proteins, each composed of 620 amino acids. The
binding of insulin to its receptor stimulates the β chains to catalyze the addition of phosphate groups to the specific side chains of
tyrosine (referred to as phosphorylation) in the β chains and other cell proteins, leading to the activation of reactions that
metabolize glucose. In this chapter we will look at the pathway that breaks down glucose—in response to activation by insulin—for
the purpose of providing energy for the cell.
GLmol
Figure 6.1.1 : Model of the Structure of the Insulin Receptor (PDB code 4ZXB).
Life requires energy. Animals, for example, require heat energy to maintain body temperature, mechanical energy to move their
limbs, and chemical energy to synthesize the compounds needed by their cells. Living cells remain organized and functioning
properly only through a continual supply of energy. But only specific forms of energy can be used. Supplying a plant with energy
by holding it in a flame will not prolong its life. On the other hand, a green plant is able to absorb radiant energy from the sun, the
most abundant source of energy for life on the earth. Plants use this energy first to form glucose and then to make other
carbohydrates, as well as lipids and proteins. Unlike plants, animals cannot directly use the sun’s energy to synthesize new
compounds. They must eat plants or other animals to get carbohydrates, fats, and proteins and the chemical energy stored in them.
Once digested and transported to the cells, the nutrient molecules can be used in either of two ways: as building blocks for making
new cell parts or repairing old ones or “burned” for energy.
Figure 6.1.2 : Some Energy Transformations in Living Systems. Plants and animals exist in a cycle; each requires products of the
other.
The thousands of coordinated chemical reactions that keep cells alive are referred to collectively as metabolism. In general,
metabolic reactions are divided into two classes: the breaking down of molecules to obtain energy is catabolism, and the building
of new molecules needed by living systems is anabolism.
metabolite
Any chemical compound that participates in a metabolic reaction is a metabolite.
Most of the energy required by animals is generated from lipids and carbohydrates. These fuels must be oxidized, or “burned,” for
the energy to be released. The oxidation process ultimately converts the lipid or carbohydrate to carbon dioxide (CO2) and water
(H2O).
Carbohydrate:
C H O +6 O → 6 CO + 6 H O + 670 kcal (6.1.1)
6 12 6 2 2 2
Lipid:
C H O + 23 O → 16 CO + 16 H O + 2 , 385 kcal (6.1.2)
16 32 2 2 2 2
These two equations summarize the biological combustion of a carbohydrate and a lipid by the cell through respiration.
Respiration is the collective name for all metabolic processes in which gaseous oxygen is used to oxidize organic matter to carbon
dioxide, water, and energy.
Like the combustion of the common fuels we burn in our homes and cars (wood, coal, gasoline), respiration uses oxygen from the
air to break down complex organic substances to carbon dioxide and water. But the energy released in the burning of wood is
manifested entirely in the form of heat, and excess heat energy is not only useless but also injurious to the living cell. Living
organisms instead conserve much of the energy respiration releases by channeling it into a series of stepwise reactions that produce
adenosine triphosphate (ATP) or other compounds that ultimately lead to the synthesis of ATP. The remainder of the energy is
released as heat and manifested as body temperature.
6.1: Prelude to Energy Metabolism is shared under a CC BY-NC-SA 4.0 license and was authored, remixed, and/or curated by LibreTexts.
Learning Objectives
To describe the importance of ATP as a source of energy in living organisms.
Adenosine triphosphate (ATP), a nucleotide composed of adenine, ribose, and three phosphate groups, is perhaps the most
important of the so-called energy-rich compounds in a cell. Its concentration in the cell varies from 0.5 to 2.5 mg/mL of cell fluid.
Energy-rich compounds are substances having particular structural features that lead to a release of energy after hydrolysis. As a
result, these compounds are able to supply energy for biochemical processes that require energy. The structural feature important in
ATP is the phosphoric acid anhydride, or pyrophosphate, linkage:
The pyrophosphate bond, symbolized by a squiggle (~), is hydrolyzed when ATP is converted to adenosine diphosphate (ADP). In
this hydrolysis reaction, the products contain less energy than the reactants; there is a release of energy (> 7 kcal/mol). One reason
for the amount of energy released is that hydrolysis relieves the electron-electron repulsions experienced by the negatively charged
phosphate groups when they are bonded to each other (Figure 20.1.1).
Figure 6.2.1 : Hydrolysis of ATP to Form ADP

Energy is released because the products (ADP and phosphate ion) have less energy than the reactants [ATP and water (H2O)].
The general equation for ATP hydrolysis is as follows:
AT P + H2 O → ADP + Pi + 7.4 kcal/mol (6.2.1)
If the hydrolysis of ATP releases energy, its synthesis (from ADP) requires energy. In the cell, ATP is produced by those processes
that supply energy to the organism (absorption of radiant energy from the sun in green plants and breakdown of food in animals),
and it is hydrolyzed by those processes that require energy (the syntheses of carbohydrates, lipids, proteins; the transmission of
nerve impulses; muscle contractions). In fact, ATP is the principal medium of energy exchange in biological systems. Many
scientists call it the energy currency of cells.
Pi is the symbol for the inorganic phosphate anions H 2PO

−
4
and HP O 2−
4
.
ATP is not the only high-energy compound needed for metabolism. Several others are listed in Table 6.2.1. Notice, however, that
the energy released when ATP is hydrolyzed is approximately midway between those of the high-energy and the low-energy
phosphate compounds. This means that the hydrolysis of ATP can provide energy for the phosphorylation of the compounds below
it in the table. For example, the hydrolysis of ATP provides sufficient energy for the phosphorylation of glucose to form glucose 1-
phosphate. By the same token, the hydrolysis of compounds, such as creatine phosphate, that appear above ATP in the table can
provide the energy needed to resynthesize ATP from ADP.
Table 6.2.1 : Energy Released by Hydrolysis of Some Phosphate Compounds
Type Example Energy Released (kcal/mol)
acyl phosphate
1,3-bisphosphoglycerate (BPG) −11.8
acetyl phosphate −11.3
guanidine phosphates
creatine phosphate −10.3
arginine phosphate −9.1
pyrophosphates PPi* → 2Pi −7.8
ATP → AMP + PPi −7.7
ATP → ADP + Pi −7.5
ADP → AMP + Pi −7.5
glucose 1-phosphate −5.0

sugar phosphates
fructose 6-phosphate −3.8
AMP → adenosine + Pi −3.4
glucose 6-phosphate −3.3
glycerol 3-phosphate −2.2
*PPi is the pyrophosphate ion.
Summary
The hydrolysis of ATP releases energy that can be used for cellular processes that require energy.
1. Why is ATP referred to as the energy currency of the cell?
Answer
1. ATP is the principal molecule involved in energy exchange reactions in biological systems.
Exercises
1. How do ATP and ADP differ in structure?
2. Why does the hydrolysis of ATP to ADP involve the release of energy?
3. Identify whether each compound would be classified as a high-energy phosphate compound.
a. ATP
b. glucose 6-phosphate
c. creatine phosphate
a. ADP
b. AMP
c. glucose 1-phosphate
Answers
1. ATP has a triphosphate group attached, while ADP has only a diphosphate group attached.
3. a. yes
b. no
c. yes
6.2: ATP: the Universal Energy Currency is shared under a CC BY-NC-SA 4.0 license and was authored, remixed, and/or curated by LibreTexts.
Learning Objectives
To describe how carbohydrates, fats, and proteins are broken down during digestion.
We have said that animals obtain chemical energy from the food—carbohydrates, fats, and proteins—they eat through reactions
defined collectively as catabolism. We can think of catabolism as occurring in three stages (Figure 6.3.1). In stage I, carbohydrates,
fats, and proteins are broken down into their individual monomer units: carbohydrates into simple sugars, fats into fatty acids and
glycerol, and proteins into amino acids. One part of stage I of catabolism is the breakdown of food molecules by hydrolysis
reactions into the individual monomer units—which occurs in the mouth, stomach, and small intestine—and is referred to as
digestion.
In stage II, these monomer units (or building blocks) are further broken down through different reaction pathways, one of which
produces ATP, to form a common end product that can then be used in stage III to produce even more ATP. In this chapter, we will
look at each stage of catabolism—as an overview and in detail.
Figure 6.3.1 : Energy Conversions
The conversion of food into cellular energy (as ATP) occurs in three stages.
Digestion of Carbohydrates
Carbohydrate digestion begins in the mouth (Figure 6.3.2) where salivary α-amylase attacks the α-glycosidic linkages in starch, the
main carbohydrate ingested by humans. Cleavage of the glycosidic linkages produces a mixture of dextrins, maltose, and glucose.
The α-amylase mixed into the food remains active as the food passes through the esophagus, but it is rapidly inactivated in the
acidic environment of the stomach.
Figure 6.3.2 : The Principal Events and Sites of Carbohydrate Digestion

The primary site of carbohydrate digestion is the small intestine. The secretion of α-amylase in the small intestine converts any
remaining starch molecules, as well as the dextrins, to maltose. Maltose is then cleaved into two glucose molecules by maltase.
Disaccharides such as sucrose and lactose are not digested until they reach the small intestine, where they are acted on by sucrase
and lactase, respectively. The major products of the complete hydrolysis of disaccharides and polysaccharides are three
monosaccharide units: glucose, fructose, and galactose. These are absorbed through the wall of the small intestine into the
bloodstream.
Digestion of Proteins
Protein digestion begins in the stomach (Figure 6.3.3), where the action of gastric juice hydrolyzes about 10% of the peptide
bonds. Gastric juice is a mixture of water (more than 99%), inorganic ions, hydrochloric acid, and various enzymes and other
proteins.
The pain of a gastric ulcer is at least partially due to irritation of the ulcerated tissue by acidic gastric juice.
Figure 6.3.3 : The Principal Events and Sites of Protein Digestion
The hydrochloric acid (HCl) in gastric juice is secreted by glands in the stomach lining. The pH of freshly secreted gastric juice is
about 1.0, but the contents of the stomach may raise the pH to between 1.5 and 2.5. HCl helps to denature food proteins; that is, it
unfolds the protein molecules to expose their chains to more efficient enzyme action. The principal digestive component of gastric
juice is pepsinogen, an inactive enzyme produced in cells located in the stomach wall. When food enters the stomach after a period
of fasting, pepsinogen is converted to its active form—pepsin—in a series of steps initiated by the drop in pH. Pepsin catalyzes the
hydrolysis of peptide linkages within protein molecules. It has a fairly broad specificity but acts preferentially on linkages
involving the aromatic amino acids tryptophan, tyrosine, and phenylalanine, as well as methionine and leucine.
Protein digestion is completed in the small intestine. Pancreatic juice, carried from the pancreas via the pancreatic duct, contains
inactive enzymes such as trypsinogen and chymotrypsinogen. They are activated in the small intestine as follows (Figure 6.3.4):
The intestinal mucosal cells secrete the proteolytic enzyme enteropeptidase, which converts trypsinogen to trypsin; trypsin then
activates chymotrypsinogen to chymotrypsin (and also completes the activation of trypsinogen). Both of these active enzymes
catalyze the hydrolysis of peptide bonds in protein chains. Chymotrypsin preferentially attacks peptide bonds involving the
carboxyl groups of the aromatic amino acids (phenylalanine, tryptophan, and tyrosine). Trypsin attacks peptide bonds involving the
carboxyl groups of the basic amino acids (lysine and arginine). Pancreatic juice also contains procarboxypeptidase, which is
cleaved by trypsin to carboxypeptidase. The latter is an enzyme that catalyzes the hydrolysis of peptide linkages at the free
carboxyl end of the peptide chain, resulting in the stepwise liberation of free amino acids from the carboxyl end of the polypeptide.
Figure 6.3.4 : Activation of Some Pancreatic Enzymes in the Small Intestine
Aminopeptidases in the intestinal juice remove amino acids from the N-terminal end of peptides and proteins possessing a free
amino group. Figure 6.3.5 illustrates the specificity of these protein-digesting enzymes. The amino acids that are released by
protein digestion are absorbed across the intestinal wall into the circulatory system, where they can be used for protein synthesis.
Figure 6.3.5 : Hydrolysis of a Peptide by Several Peptidases

This diagram illustrates where in a peptide the different peptidases we have discussed would catalyze hydrolysis the peptide bonds.
Digestion of Lipids
Lipid digestion begins in the upper portion of the small intestine (Figure 6.3.6). A hormone secreted in this region stimulates the
gallbladder to discharge bile into the duodenum. The principal constituents of bile are the bile salts, which emulsify large, water-
insoluble lipid droplets, disrupting some of the hydrophobic interactions holding the lipid molecules together and suspending the
resulting smaller globules (micelles) in the aqueous digestive medium. These changes greatly increase the surface area of the lipid
particles, allowing for more intimate contact with the lipases and thus rapid digestion of the fats. Another hormone promotes the
secretion of pancreatic juice, which contains these enzymes.
Figure 6.3.6 : The Principal Events and Sites of Lipid (Primarily Triglyceride) Digestion
The lipases in pancreatic juice catalyze the digestion of triglycerides first to diglycerides and then to 2‑monoglycerides and fatty
acids:
The monoglycerides and fatty acids cross the intestinal lining into the bloodstream, where they are resynthesized into triglycerides
and transported as lipoprotein complexes known as chylomicrons. Phospholipids and cholesteryl esters undergo similar hydrolysis
in the small intestine, and their component molecules are also absorbed through the intestinal lining.
The further metabolism of monosaccharides, fatty acids, and amino acids released in stage I of catabolism occurs in stages II and
III of catabolism.
Summary
are broken down into monosaccharides, proteins are broken down into amino
During digestion, carbohydrates
acids, and triglycerides are broken down into glycerol and fatty acids. Most of the digestion reactions
occur in the small intestine.

1. Distinguish between each pair of compounds.
a. pepsin and pepsinogen
b. chymotrypsin and trypsin
c. aminopeptidase and carboxypeptidase
2. What are the primary end products of each form of digestion?
a. carbohydrate digestion
b. lipid digestion
c. protein digestion
3. In what section of the digestive tract does most of the carbohydrate, lipid, and protein digestion take place?
Answers
1. a. Pepsinogen is an inactive form of pepsin; pepsin is the active form of the enzyme.
b. Both enzymes catalyze the hydrolysis of peptide bonds. Chymotrypsin catalyzes the hydrolysis of peptide bonds following
aromatic amino acids, while trypsin catalyzes the hydrolysis of peptide bonds following lysine and arginine.
c. Aminopeptidase catalyzes the hydrolysis of amino acids from the N-terminal end of a protein, while carboxypeptidase
catalyzes the hydrolysis of amino acids from the C-terminal end of a protein.
2. a. glucose, fructose, and galactose
b. monoglycerides and fatty acids
c. amino acids
3. the small intestine
Exercises
1. What are the products of digestion (or stage I of catabolism)?
2. What is the general type of reaction used in digestion?
3. Give the site of action and the function of each enzyme.
a. chymotrypsin
b. lactase
c. pepsin
d. maltase
a. α-amylase
b. trypsin
c. sucrase
d. aminopeptidase
5. a. What is the meaning of the following statement? “Bile salts act to emulsify lipids in the small intestine.”
b. Why is emulsification important?
6. Using chemical equations, describe the chemical changes that triglycerides undergo during digestion.
7. What are the expected products from the enzymatic action of chymotrypsin on each amino acid segment?
a. gly-ala-phe-thr-leu
b. ala-ile-tyr-ser-arg
c. val-trp-arg-leu-cys
8. What are the expected products from the enzymatic action of trypsin on each amino acid segment?
a. leu-thr-glu-lys-ala
b. phe-arg-ala-leu-val
c. ala-arg-glu-trp-lys
Answers
1. proteins: amino acids; carbohydrates: monosaccharides; fats: fatty acids and glycerol
3. a. Chymotrypsin is found in the small intestine and catalyzes the hydrolysis of peptide bonds following aromatic amino acids.
b. Lactase is found in the small intestine and catalyzes the hydrolysis of lactose.
c. Pepsin is found in the stomach and catalyzes the hydrolysis of peptide bonds, primarily those that occur after aromatic
amino acids.
d. Maltase is found in the small intestine and catalyzes the hydrolysis of maltose.
5. a. Bile salts aid in digestion by dispersing lipids throughout the aqueous solution in the small intestine.
b. Emulsification is important because lipids are not soluble in water; it breaks lipids up into smaller particles that can be more
readily hydrolyzed by lipases.
7. a. gly-ala-phe and thr-leu
b. ala-ile-tyr and ser-arg
c. val-trp and arg-leu-cys
6.3: Stage I of Catabolism is shared under a CC BY-NC-SA 4.0 license and was authored, remixed, and/or curated by LibreTexts.
Learning Objectives
To describe the role of acetyl-CoA in metabolism.
A metabolic pathway is a series of biochemical reactions by which an organism converts a given reactant to a specific end product.
There are specific metabolic pathways—which are different for carbohydrates, triglycerides, and proteins—that break down the
products of stage I of catabolism (monosaccharides, fatty acids, and amino acids) to produce a common end product, acetyl-
coenzyme A (acetyl-CoA) in stage II of catabolism.
Figure 6.4.1 : The Structure of Acetyl-Coenzyme A (Acetyl-CoA)

Acetyl-CoA is shown in Figure 6.4.1. The acetyl unit, derived (as we will see) from the breakdown of carbohydrates, lipids, and
proteins, is attached to coenzyme A, making the acetyl unit more reactive. Acetyl-CoA is used in a myriad of biochemical
pathways. For example, it may be used as the starting material for the biosynthesis of lipids (such as triglycerides, phospholipids,
or cholesterol and other steroids). Most importantly for energy generation, it may enter the citric acid cycle and be oxidized to
produce energy, if energy is needed and oxygen is available. The various fates or uses of acetyl-CoA are summarized in Figure
6.4.1.
Figure 6.4.2 : Cell Chemistry. Acetyl-CoA plays a variety of roles in cell chemistry.
Glycolosis
Glycolysis is the catabolic process in which glucose is converted into pyruvate via ten enzymatic steps. There are three regulatory
steps, each of which is highly regulated that are separated into two phases:
1. the "priming phase" because it requires an input of energy in the form of 2 ATPs per glucose molecule and
2. the "pay off phase" because energy is released in the form of 4 ATPs, 2 per glyceraldehyde molecule.
The end result of Glycolysis is two new pyruvate molecules which can then be fed into the Citric Acid cycle (also known as the
Kreb's Cycle) if oxygen is present, or can be reduced to lactate or ethanol in the absence of of oxygen using a process known as
fermentation.
Glycolysis: An Overview
Video 6.4.1 : Glycolysis: An Overview. Glycolysis is a series of 10 reactions that converts sugars, like glucose, into 3-carbon
molecules called pyruvate. This animation provides an overview of the energy consumed and produced by the pathway. NDSU
VCell Production's animation; for more information please see http://vcell.ndsu.edu/animations.
Glycolysis occurs within almost all living cells and is the primary source of Acetyl-CoA, which is the molecule responsible for the
majority of energy output under aerobic conditions. The structures of Glycolysis intermediates can be found in Figure 6.4.3.
Figure 6.4.3 : Glycolysis pathway. Image used with permission from Wikipedia.
Phase 1: The "Priming Step"

The first phase of Glycolysis requires an input of energy in the form of ATP (adenosine triphosphate).
1. alpha-D-Glucose is phosphorolated at the 6 carbon by ATP via the enzyme Hexokinase (Class: Transferase) to yield alpha-D-
Glucose-6-phosphate (G-6-P). This is a regulatory step which is negatively regulated by the presence of glucose-6-phosphate.
2. alpha-D-Glucose-6-phosphate is then converted into D-Fructose-6-phosphate (F-6-P) by Phosphoglucoisomerase (Class:
Isomerase)
3. D-Fructose-6-phosphate is once again phosphorolated this time at the 1 carbon position by ATP via the enzyme
Phosphofructokinase (Class: Transferase) to yield D-Fructose-1,6-bisphosphate (FBP). This is the committed step of glycolysis
because of its large ΔG value.
4. D-Fructose-1,6-bisphosphate is then cleaved into two, three carbon molecules; Dihydroxyacetone phosphate (DHAP) and D-
Glyceraldehyde-3-phosphate (G-3-P) by the enzyme Fructose bisphosphate aldolase (Class: Lyase)
5. Because the next portion of Glycolysis requires the molecule D-Glyceraldehyde-3-phosphate to continue Dihydroxyacetone
phosphate is converted into D-Glyceraldehyde-3-phosphate by the enzyme Triose phosphate isomerase (Class: Isomerase)
Phase 2: The "Pay Off Step"

The second phase of Glycolysis where 4 molecules of ATP are produced per molecule of glucose. Enzymes appear in red:
1. D-Glyceraldehyde-3-phosphate is phosphorolated at the 1 carbon by the enzyme Glyceraldehyde-3-phosphate dehodrogenase to
yield the high energy molecule 1,3-Bisphosphoglycerate (BPG)
2. ADP is then phosphorolated at the expense of 1,3-Bisphosphoglycerate by the enzyme Phosphoglycerate kinase (Class:
Transferase) to yield ATP and 3-Phosphoglycerate (3-PG)
3. 3-Phosphoglycerate is then converted into 2-Phosphoglycerate by Phosphoglycerate mutase in preparation to yield another high
energy molecule
4. 2-Phosphoglycerate is then converted to phosphoenolpyruvate (PEP) by Enolase. H2O, potassium, and magnesium are all
released as a result.
5. ADP is once again phosphorolated, this time at the expense of PEP by the enzyme pyruvate kinase to yield another molecule of
ATP and and pyruvate. This step is regulated by the energy in the cell. The higher the energy of the cell the more inhibited
pyruvate kinase becomes. Indicators of high energy levels within the cell are high concentrations of ATP, Acetyl-CoA, Alanine,
and cAMP.
Because Glucose is split to yield two molecules of D-Glyceraldehyde-3-phosphate, each step in the "Pay Off" phase occurs twice
per molecule of glucose.
Beta-Oxidation
The best source of energy for eukaryotic organisms are fats. Glucose offers a ratio 6.3 moles of ATP per carbon while saturated
fatty acids offer 8.1 ATP per carbon. Also the complete oxidation of fats yields enormous amounts of water for those organisms
that do not have adequate access to drinkable water. Camels and killer whales are good example of this, they obtain their water
requirements from the complete oxidation of fats.
Beta oxidation | β-Oxidation
Video 6.4.2 : Fatty acid metabolism / beta oxidation / β-Oxidation

There are four distinct stages in the oxidation of fatty acids. Fatty acid degradation takes place within the mitochondria and requires
the help of several different enzymes. In order for fatty acids to enter the mitochondria the assistance of two carrier proteins is
required, Carnitine acyltransferase I and II. It is also interesting to note the similarities between the four steps of beta-oxidation and
the later four steps of the TCA cycle.
Entry into Beta-oxidation

Most fats stored in eukaryotic organisms are stored as triglycerides as seen below. In order to enter into beta-oxidation bonds must
be broken usually with the use of a Lipase. The end result of these broken bonds are a glycerol molecule and three fatty acids in the
case of triglycerides. Other lipids are capable of being degraded as well.
Figure 6.4.4 : Key molecules in beta-oxidation: (left) A triglyceride molecule, (middle) Glycerol, (right) Fatty Acids (unsaturated)
Activation Step
Once the triglycerides are broken down into glycerol and fatty acids they must be activated before they can enter into the
mitochondria and proceed on with beta-oxidation. This is done by Acyl-CoA synthetase to yield fatty acyl-CoA.
After the fatty acid has been acylated it is now ready to enter into the mitochondria.
There are two carrier proteins (Carnitine acyltransferase I and II), one located on the outer membrane and one on the inner
membrane of the mitochondria. Both are required for entry of the Acyl-CoA into the mitochondria.
Once inside the mitochondria the fatty acyl-CoA can enter into beta-oxidation.
Oxidation Step
A fatty acyl-CoA is oxidized by Acyl-CoA dehydrogenase to yield a trans alkene. This is done with the aid of an [FAD] prosthetic
group.
Hydration Step
The trans alkene is then hydrated with the help of Enoyl-CoA hydratase
Oxidation Step
The alcohol of the hydroxyacly-CoA is then oxidized by NAD+ to a carbonyl with the help of Hydroxyacyl-CoA dehydrogenase.
NAD+ is used to oxidize the alcohol rather then [FAD] because NAD+ is capable of the alcohol while [FAD] is not.
Cleavage
Finally acetyl-CoA is cleaved off with the help of Thiolase to yield an Acyl-CoA that is two carbons shorter than before. The
cleaved acetyl-CoA can then enter into the TCA and ETC because it is already within the mitochondria.
Summary
Acetyl-CoA is formed from the breakdown of carbohydrates, lipids, and proteins. It is used in many biochemical pathways.
References
1. Garrett, H., Reginald and Charles Grisham. Biochemistry. Boston: Twayne Publishers, 2008.
2. Raven, Peter. Biology. Boston: Twayne Publishers, 2005.

1. What is a metabolic pathway?
2. What vitamin is required to make coenzyme A?
3. What is the net yield of Glycolysis as far as ATP?
4. Name the enzymes that are key regulatory sites in Glycolysis.
5. Why are the enzymes in the previous question targets for regulation?
6. Why is the priming phase necessary?
7. Draw the entire pathway for glycolysis including enzymes, reactants and products for each step.
8. Where does beta-oxidation occur?
9. What is the average net yield of ATP per carbon?
10. Where exactly is water formed during the process of fatty acid degradation? (Hint: H2O is formed when when the one of the
products of beta-oxidation is passed through another of the metabolic pathways)
11. During the process of beta-oxidation, why is it that [FAD] is used to oxidize an alkane to an alkene while NAD+ is used to
oxidize an alchol to a carbonyl
12. Draw out the entire process of the degradation of a triglyceride, include enzymes and products and reactants for each step.
Answers
1. A metabolic pathway is a series of biochemical reactions by which an organism converts a given reactant to a specific end
product.
2. pantothenic acid
Contributors
Darik Benson, (University California Davis)
6.4: Overview of Stage II of Catabolism is shared under a CC BY-NC-SA 4.0 license and was authored, remixed, and/or curated by LibreTexts.
Learning Objectives
Describe the reactions of the citric acid cycle.
Describe the function of the citric acid cycle and identify the products produced.
Describe the role of the electron transport chain in energy metabolism.
Describe the role of oxidative phosphorylation in energy metabolism.
The acetyl group enters a cyclic sequence of reactions known collectively as the citric acid cycle (or Krebs cycle or tricarboxylic
acid [TCA] cycle). The cyclical design of this complex series of reactions, which bring about the oxidation of the acetyl group of
acetyl-CoA to carbon dioxide and water, was first proposed by Hans Krebs in 1937. (He was awarded the 1953 Nobel Prize in
Physiology or Medicine.) Acetyl-CoA’s entrance into the citric acid cycle is the beginning of stage III of catabolism. The citric acid
cycle produces adenosine triphosphate (ATP), reduced nicotinamide adenine dinucleotide (NADH), reduced flavin adenine
dinucleotide (FADH2), and metabolic intermediates for the synthesis of needed compounds.
Steps of the Citric Acid Cycle

At first glance, the citric acid cycle appears rather complex (Figure 6.5.1). All the reactions, however, are familiar types in organic
chemistry: hydration, oxidation, decarboxylation, and hydrolysis. Each reaction of the citric acid cycle is numbered, and in Figure
6.5.1, the two acetyl carbon atoms are highlighted in red. Each intermediate in the cycle is a carboxylic acid, existing as an anion at
physiological pH. All the reactions occur within the mitochondria, which are small organelles within the cells of plants and
animals.
Figure 6.5.1 : Reactions of the Citric Acid Cycle

1. In the first step, acetyl-CoA enters the citric acid cycle, and the acetyl group is transferred onto oxaloacetate, yielding citrate.
Note that this step releases coenzyme A. The reaction is catalyzed by citrate synthase.
2. In the next step, aconitase catalyzes the isomerization of citrate to isocitrate. In this reaction, a tertiary alcohol, which cannot be
oxidized, is converted to a secondary alcohol, which can be oxidized in the next step.
3. Isocitrate then undergoes a reaction known as oxidative decarboxylation because the alcohol is oxidized and the molecule is
shortened by one carbon atom with the release of carbon dioxide (decarboxylation). The reaction is catalyzed by isocitrate
dehydrogenase, and the product of the reaction is α-ketoglutarate. An important reaction linked to this is the reduction of the
coenzyme nicotinamide adenine dinucleotide (NAD+) to NADH. The NADH is ultimately reoxidized, and the energy released
is used in the synthesis of ATP, as we shall see.
4. The fourth step is another oxidative decarboxylation. This time α-ketoglutarate is converted to succinyl-CoA, and another
molecule of NAD+ is reduced to NADH. The α-ketoglutarate dehydrogenase complex catalyzes this reaction. This is the only
irreversible reaction in the citric acid cycle. As such, it prevents the cycle from operating in the reverse direction, in which
acetyl-CoA would be synthesized from carbon dioxide.
So far, in the first four steps, two carbon atoms have entered the cycle as an acetyl group, and two carbon atoms have been
released as molecules of carbon dioxide. The remaining reactions of the citric acid cycle use the four carbon atoms of the
succinyl group to resynthesize a molecule of oxaloacetate, which is the compound needed to combine with an incoming acetyl
group and begin another round of the cycle.
In the fifth reaction, the energy released by the hydrolysis of the high-energy thioester bond of succinyl-CoA is used to form
guanosine triphosphate (GTP) from guanosine diphosphate (GDP) and inorganic phosphate in a reaction catalyzed by succinyl-CoA
synthetase. This step is the only reaction in the citric acid cycle that directly forms a high-energy phosphate compound. GTP can
readily transfer its terminal phosphate group to adenosine diphosphate (ADP) to generate ATP in the presence of nucleoside
diphosphokinase.
Succinate dehydrogenase then catalyzes the removal of two hydrogen atoms from succinate, forming fumarate. This oxidation-
reduction reaction uses flavin adenine dinucleotide (FAD), rather than NAD+, as the oxidizing agent. Succinate dehydrogenase is
the only enzyme of the citric acid cycle located within the inner mitochondrial membrane. We will see soon the importance of this.
In the following step, a molecule of water is added to the double bond of fumarate to form L-malate in a reaction catalyzed by
fumarase.
One revolution of the cycle is completed with the oxidation of L-malate to oxaloacetate, brought about by malate dehydrogenase.
This is the third oxidation-reduction reaction that uses NAD+ as the oxidizing agent. Oxaloacetate can accept an acetyl group from
acetyl-CoA, allowing the cycle to begin again.
The Citric Acid Cycle: An Overview
Video: "The Citric Acid Cycle: An Overview". In the matrix of the mitochondrion, the Citric Acid Cycle uses Acetyl CoA molecules
to produce energy through eight chemical reactions. This animation provides an overview of the pathway and its products. NDSU
VCell Production's animation; for more information please see http://vcell.ndsu.edu/animations.
Cellular Respiration
Respiration can be defined as the process by which cells oxidize organic molecules in the presence of gaseous oxygen to produce
carbon dioxide, water, and energy in the form of ATP. We have seen that two carbon atoms enter the citric acid cycle from acetyl-
CoA (step 1), and two different carbon atoms exit the cycle as carbon dioxide (steps 3 and 4). Yet nowhere in our discussion of the
citric acid cycle have we indicated how oxygen is used. Recall, however, that in the four oxidation-reduction steps occurring in the
citric acid cycle, the coenzyme NAD+ or FAD is reduced to NADH or FADH2, respectively. Oxygen is needed to reoxidize these
coenzymes. Recall, too, that very little ATP is obtained directly from the citric acid cycle. Instead, oxygen participation and
significant ATP production occur subsequent to the citric acid cycle, in two pathways that are closely linked: electron transport and
oxidative phosphorylation.
All the enzymes and coenzymes for the citric acid cycle, the reoxidation of NADH and FADH2, and the production of ATP are
located in the mitochondria, which are small, oval organelles with double membranes, often referred to as the “power plants” of the
cell (Figure 6.5.2). A cell may contain 100–5,000 mitochondria, depending on its function, and the mitochondria can reproduce
themselves if the energy requirements of the cell increase.
Figure 6.5.2 : Respiration
Cellular respiration occurs in the mitochondria

Figure 6.5.2 shows the mitochondrion’s two membranes: outer and inner. The inner membrane is extensively folded into a series
of internal ridges called cristae. Thus there are two compartments in mitochondria: the intermembrane space, which lies between
the membranes, and the matrix, which lies inside the inner membrane. The outer membrane is permeable, whereas the inner
membrane is impermeable to most molecules and ions, although water, oxygen, and carbon dioxide can freely penetrate both
membranes. The matrix contains all the enzymes of the citric acid cycle with the exception of succinate dehydrogenase, which is
embedded in the inner membrane. The enzymes that are needed for the reoxidation of NADH and FADH2 and ATP production are
also located in the inner membrane. They are arranged in specific positions so that they function in a manner analogous to a bucket
brigade. This highly organized sequence of oxidation-reduction enzymes is known as the electron transport chain (or respiratory
chain).
Electron Transport
Figure 6.5.3 illustrates the organization of the electron transport chain. The components of the chain are organized into four
complexes designated I, II, III, and IV. Each complex contains several enzymes, other proteins, and metal ions. The metal ions can
be reduced and then oxidized repeatedly as electrons are passed from one component to the next. Recall that a compound is
reduced when it gains electrons or hydrogen atoms and is oxidized when it loses electrons or hydrogen atoms.
Figure 6.5.3 : The Mitochondrial Electron Transport Chain and ATP Synthase. The red line shows the path of electrons.
Electrons can enter the electron transport chain through either complex I or II. We will look first at electrons entering at complex I.
These electrons come from NADH, which is formed in three reactions of the citric acid cycle. Let’s use step 8 as an example, the
reaction in which L-malate is oxidized to oxaloacetate and NAD+ is reduced to NADH. This reaction can be divided into two half
reactions:
Oxidation half-reaction:
Reduction half-reaction:
In the oxidation half-reaction, two hydrogen (H+) ions and two electrons are removed from the substrate. In the reduction half-
reaction, the NAD+ molecule accepts both of those electrons and one of the H+ ions. The other H+ ion is transported from the
matrix, across the inner mitochondrial membrane, and into the intermembrane space. The NADH diffuses through the matrix and is
bound by complex I of the electron transport chain. In the complex, the coenzyme flavin mononucleotide (FMN) accepts both
electrons from NADH. By passing the electrons along, NADH is oxidized back to NAD+ and FMN is reduced to FMNH2 (reduced
form of flavin mononucleotide). Again, the reaction can be illustrated by dividing it into its respective half-reactions.
Complex I contains several proteins that have iron-sulfur (Fe·S) centers. The electrons that reduced FMN to FMNH2 are now
transferred to these proteins. The iron ions in the Fe·S centers are in the Fe(III) form at first, but by accepting an electron, each ion
is reduced to the Fe(II) form. Because each Fe·S center can transfer only one electron, two centers are needed to accept the two
electrons that will regenerate FMN.
+ −
F M N H2 → F M N + 2 H + 2e (6.5.1)
−
2F e(I I I ) ⋅ S + 2 e → 2F e(I I ) ⋅ S (6.5.2)
Electrons from FADH2, formed in step 6 of the citric acid cycle, enter the electron transport chain through complex II. Succinate
dehydrogenase, the enzyme in the citric acid cycle that catalyzes the formation of FADH2 from FAD is part of complex II. The
electrons from FADH2 are then transferred to an Fe·S protein.
+ −
F ADH2 → F AD + 2 H + 2e (6.5.3)
−
2F e(I I I ) ⋅ S + 2 e → 2F e(I I ) ⋅ S (6.5.4)
Electrons from complexes I and II are then transferred from the F e ⋅ S protein to coenzyme Q (CoQ), a mobile electron carrier that
acts as the electron shuttle between complexes I or II and complex III.
Coenzyme Q is also called ubiquinone because it is ubiquitous in living systems.

−
2F e(I I ) ⋅ S → 2F e(I I I ) ⋅ S + 2e (6.5.5)
Complexes III and IV include several iron-containing proteins known as cytochromes. The iron in these enzymes is located in
substructures known as iron porphyrins (Figure 6.5.4). Like the Fe·S centers, the characteristic feature of the cytochromes is the
ability of their iron atoms to exist as either Fe(II) or Fe(III). Thus, each cytochrome in its oxidized form—Fe(III)—can accept one
electron and be reduced to the Fe(II) form. This change in oxidation state is reversible, so the reduced form can donate its electron
to the next cytochrome, and so on. Complex III contains cytochromes b and c, as well as Fe·S proteins, with cytochrome c acting as
the electron shuttle between complex III and IV. Complex IV contains cytochromes a and a3 in an enzyme known as cytochrome
oxidase. This enzyme has the ability to transfer electrons to molecular oxygen, the last electron acceptor in the chain of electron
transport reactions. In this final step, water (H2O) is formed.
−
4C yt a3 – F e(I I ) → 4C yt a3 – F e(I I I ) + 4 e (6.5.6)
O2 + 4H+ + 4e− → 2H2O
Figure 6.5.4 : An Iron Porphyrin. Iron porphyrins are present in cytochromes as well as in myoglobin and hemoglobin.
Cellular Respiration (Electron Transport …
Video: Cellular Respiration (Electron Transport Chain). Cellular respiration occurs in the mitochondria and provides both animals
and plants with the energy needed to power other cellular processes. This section covers the electron transport chain.NDSU Virtual
Cell Animations Project animation; ror more information please see http://vcell.ndsu.edu/animations
Oxidative Phosphorylation
Each intermediate compound in the electron transport chain is reduced by the addition of one or two electrons in one reaction and
then subsequently restored to its original form by delivering the electron(s) to the next compound along the chain. The successive
electron transfers result in energy production. But how is this energy used for the synthesis of ATP? The process that links ATP
synthesis to the operation of the electron transport chain is referred to as oxidative phosphorylation.
Electron transport is tightly coupled to oxidative phosphorylation. The coenzymes NADH and FADH2 are oxidized by the
respiratory chain only if ADP is simultaneously phosphorylated to ATP. The currently accepted model explaining how these two
processes are linked is known as the chemiosmotic hypothesis, which was proposed by Peter Mitchell, resulting in Mitchell being
awarded the 1978 Nobel Prize in Chemistry.
Looking again at Figure 6.5.3, we see that as electrons are being transferred through the electron transport chain, hydrogen (H+)
ions are being transported across the inner mitochondrial membrane from the matrix to the intermembrane space. The concentration
of H+ is already higher in the intermembrane space than in the matrix, so energy is required to transport the additional H+ there.
This energy comes from the electron transfer reactions in the electron transport chain. But how does the extreme difference in H+
concentration then lead to ATP synthesis? The buildup of H+ ions in the intermembrane space results in an H+ ion gradient that is a
large energy source, like water behind a dam (because, given the opportunity, the protons will flow out of the intermembrane space
and into the less concentrated matrix). Current research indicates that the flow of H+ down this concentration gradient through a
fifth enzyme complex, known as ATP synthase, leads to a change in the structure of the synthase, causing the synthesis and release
of ATP.
In cells that are using energy, the turnover of ATP is very high, so these cells contain high levels of ADP. They must therefore
consume large quantities of oxygen continuously, so as to have the energy necessary to phosphorylate ADP to form ATP. Consider,
for example, that resting skeletal muscles use about 30% of a resting adult’s oxygen consumption, but when the same muscles are
working strenuously, they account for almost 90% of the total oxygen consumption of the organism.
Experiment has shown that 2.5–3 ATP molecules are formed for every molecule of NADH oxidized in the electron transport chain,
and 1.5–2 ATP molecules are formed for every molecule of FADH2 oxidized. Table 6.5.1 summarizes the theoretical maximum
yield of ATP produced by the complete oxidation of 1 mol of acetyl-CoA through the sequential action of the citric acid cycle, the
electron transport chain, and oxidative phosphorylation.
Table 6.5.1 : Maximum Yield of ATP from the Complete Oxidation of 1 Mol of Acetyl-CoA
Reaction Comments Yield of ATP (moles)
Isocitrate → α-ketoglutarate + CO2 produces 1 mol NADH
α-ketoglutarate → succinyl-CoA + CO2 produces 1 mol NADH
Succinyl-CoA → succinate produces 1 mol GTP +1
Succinate → fumarate produces 1 mol FADH2
Malate → oxaloacetate produces 1 mol NADH
1 FADH2 from the citric acid cycle yields 2 mol ATP +2
3 NADH from the citric acid cycle yields 3 mol ATP/NADH +9
Net yield of ATP: +12

1. What is the main function of the citric acid cycle?
2. Two carbon atoms are fed into the citric acid cycle as acetyl-CoA. In what form are two carbon atoms removed from the cycle?
3. What are mitochondria and what is their function in the cell?
Answers
1. the complete oxidation of carbon atoms to carbon dioxide and the formation of a high-energy phosphate compound, energy rich
reduced coenzymes (NADH and FADH2), and metabolic intermediates for the synthesis of other compounds
2. as carbon dioxide
3. Mitochondria are small organelles with a double membrane that contain the enzymes and other molecules needed for the
production of most of the ATP needed by the body.
Key Takeaways
The acetyl group of acetyl-CoA enters the citric acid cycle. For each acetyl-CoA that enters the citric acid cycle, 2 molecules of
carbon dioxide, 3 molecules of NADH, 1 molecule of ATP, and 1 molecule of FADH2 are produced.
The reduced coenzymes (NADH and FADH2) produced by the citric acid cycle are reoxidized by the reactions of the electron
transport chain. This series of reactions also produces a pH gradient across the inner mitochondrial membrane.
The pH gradient produced by the electron transport chain drives the synthesis of ATP from ADP. For each NADH reoxidized,
2.5–3 molecules of ATP are produced; for each FADH2 reoxidized, 1.5–2 molecules of ATP are produced.
Exercises
1. Replace each question mark with the correct compound.
aconitase
a. ?−−−−−→ isocitrate
citrate synthase
b. ?+?−−−−−−−−−→ citrate + coenzyme A

f umarase
c. f umarate −−−−−→?
?
d. isocitrate + NAD
+
→ α-ketoglurate + NADH + C O2

?
a. malate + NAD
+
→ oxaloacetate + NADH
nucleoside diphosphokinase
b. ?+?−−−−−−−−−−−−−−−→ GDP + ATP

succinyl-CoA synthetase
c. succinyl-CoA −−−−−−−−−−−−−→?+?
succinate dehydrogenase
d. succinate + FAD −−−−−−−−−−−−−→ ? + FADH2
3. From the reactions in Exercises 1 and 2, select the equation(s) by number and letter in which each type of reaction occurs.
a. isomerization
b. hydration
c. synthesis
a. oxidation
b. decarboxylation
c. phosphorylation
5. What similar role do coenzyme Q and cytochrome c serve in the electron transport chain?
6. What is the electron acceptor at the end of the electron transport chain? To what product is this compound reduced?
7. What is the function of the cytochromes in the electron transport chain?
8.
a. What is meant by this statement? “Electron transport is tightly coupled to oxidative phosphorylation.”
b. How are electron transport and oxidative phosphorylation coupled or linked?
Answers
1. a. citrate
b. oxaloacetate + acetyl-CoA
c. malate
d. α-ketoglutarate hydrogenase complex
3. a. reaction in 1a
b. reaction in 1c
c. reaction in 1b
5. Both molecules serve as electron shuttles between the complexes of the electron transport chain.
7. Cytochromes are proteins in the electron transport chain and serve as one-electron carriers.
6.5: Stage III of Catabolism is shared under a CC BY-NC-SA 4.0 license and was authored, remixed, and/or curated by LibreTexts.
Learning Objectives
Describe the function of glycolysis and identify its major products.
Describe how the presence or absence of oxygen determines what happens to the pyruvate and the NADH that are produced
in glycolysis.
Determine the amount of ATP produced by the oxidation of glucose in the presence and absence of oxygen.
In stage II of catabolism, the metabolic pathway known as glycolysis converts glucose into two molecules of pyruvate (a three-
carbon compound with three carbon atoms) with the corresponding production of adenosine triphosphate (ATP). The individual
reactions in glycolysis were determined during the first part of the 20th century. It was the first metabolic pathway to be elucidated,
in part because the participating enzymes are found in soluble form in the cell and are readily isolated and purified. The pathway is
structured so that the product of one enzyme-catalyzed reaction becomes the substrate of the next. The transfer of intermediates
from one enzyme to the next occurs by diffusion.
Steps in Glycolysis
The 10 reactions of glycolysis, summarized in Figures 6.6.1 and 6.6.2, can be divided into two phases. In the first 5 reactions—
phase I—glucose is broken down into two molecules of glyceraldehyde 3-phosphate. In the last five reactions—phase II—each
glyceraldehyde 3-phosphate is converted into pyruvate, and ATP is generated. Notice that all the intermediates in glycolysis are
phosphorylated and contain either six or three carbon atoms.
Figure 6.6.1 : Phase 1 of Glycolysis

When glucose enters a cell, it is immediately phosphorylated to form glucose 6-phosphate, in the first reaction of phase I. The
phosphate donor in this reaction is ATP, and the enzyme—which requires magnesium ions for its activity—is hexokinase. In
this reaction, ATP is being used rather than being synthesized. The presence of such a reaction in a catabolic pathway that is
supposed to generate energy may surprise you. However, in addition to activating the glucose molecule, this initial reaction is
essentially irreversible, an added benefit that keeps the overall process moving in the right direction. Furthermore, the addition
of the negatively charged phosphate group prevents the intermediates formed in glycolysis from diffusing through the cell
membrane, as neutral molecules such as glucose can do.
In the next reaction, phosphoglucose isomerase catalyzes the isomerization of glucose 6-phosphate to fructose 6-phosphate.
This reaction is important because it creates a primary alcohol, which can be readily phosphorylated.
The subsequent phosphorylation of fructose 6-phosphate to form fructose 1,6-bisphosphate is catalyzed by
phosphofructokinase, which requires magnesium ions for activity. ATP is again the phosphate donor.
When a molecule contains two phosphate groups on different carbon atoms, the convention is to use the prefix bis. When the
two phosphate groups are bonded to each other on the same carbon atom (for example, adenosine diphosphate [ADP]), the
prefix is di.
Fructose 1,6-bisphosphate is enzymatically cleaved by aldolase to form two triose phosphates: dihydroxyacetone phosphate and
glyceraldehyde 3-phosphate.
Isomerization of dihydroxyacetone phosphate into a second molecule of glyceraldehyde 3-phosphate is the final step in phase I.
The enzyme catalyzing this reaction is triose phosphate isomerase.
In steps 4 and 5, aldolase and triose phosphate isomerase effectively convert one molecule of fructose 1,6-bisphosphate into two
molecules of glyceraldehyde 3-phosphate. Thus, phase I of glycolysis requires energy in the form of two molecules of ATP and
releases none of the energy stored in glucose.
Figure 6.6.2 : Phase 2 of Glycolysis

In the initial step of phase II (Figure 6.6.2), glyceraldehyde 3-phosphate is both oxidized and phosphorylated in a reaction
catalyzed by glyceraldehyde-3-phosphate dehydrogenase, an enzyme that requires nicotinamide adenine dinucleotide (NAD+) as
the oxidizing agent and inorganic phosphate as the phosphate donor. In the reaction, NAD+ is reduced to reduced nicotinamide
adenine dinucleotide (NADH), and 1,3-bisphosphoglycerate (BPG) is formed.
BPG has a high-energy phosphate bond (Table 6.6.1) joining a phosphate group to C1. This phosphate group is now transferred
directly to a molecule of ADP, thus forming ATP and 3-phosphoglycerate. The enzyme that catalyzes the reaction is
phosphoglycerate kinase, which, like all other kinases, requires magnesium ions to function. This is the first reaction to produce
ATP in the pathway. Because the ATP is formed by a direct transfer of a phosphate group from a metabolite to ADP—that is,
from one substrate to another—the process is referred to as substrate-level phosphorylation, to distinguish it from the oxidative
phosphorylation discussed in Section 20.4.
In the next reaction, the phosphate group on 3-phosphoglycerate is transferred from the OH group of C3 to the OH group of C2,
forming 2-phosphoglycerate in a reaction catalyzed by phosphoglyceromutase.
A dehydration reaction, catalyzed by enolase, forms phosphoenolpyruvate (PEP), another compound possessing a high-energy
phosphate group.
The final step is irreversible and is the second reaction in which substrate-level phosphorylation occurs. The phosphate group of
PEP is transferred to ADP, with one molecule of ATP being produced per molecule of PEP. The reaction is catalyzed by
pyruvate kinase, which requires both magnesium and potassium ions to be active.
Table 6.6.1 : Maximum Yield of ATP from the Complete Oxidation of 1 Mol of Glucose
glucose → glucose 6-phosphate consumes 1 mol ATP −1
fructose 6-phosphate → fructose 1,6-

consumes 1 mol ATP −1
bisphosphate
glyceraldehyde 3-phosphate → BPG produces 2 mol of cytoplasmic NADH
BPG → 3-phosphoglycerate produces 2 mol ATP +2
phosphoenolpyruvate → pyruvate produces 2 mol ATP +2
pyruvate → acetyl-CoA + CO2 produces 2 mol NADH
isocitrate → α-ketoglutarate + CO2 produces 2 mol NADH
α-ketoglutarate → succinyl-CoA + CO2 produces 2 mol NADH
succinyl-CoA → succinate produces 2 mol GTP +2
succinate → fumarate produces 2 mol FADH2
malate → oxaloacetate produces 2 mol NADH
yields 2–3 mol ATP per NADH (depending on

2 cytoplasmic NADH from glycolysis +4 to +6
tissue)
2 NADH from the oxidation of pyruvate yields 3 mol ATP per NADH +6
2 FADH2 from the citric acid cycle yields 2 ATP per FADH2 +4
3 NADH from the citric acid cycle yields 3 ATP per NADH +18
Net yield of ATP: +36 to +38
In phase II, two molecules of glyceraldehyde 3-phosphate are converted to two molecules of pyruvate, along with the
production of four molecules of ATP and two molecules of NADH.
To Your Health: Diabetes

Although medical science has made significant progress against diabetes , it continues to be a major health threat. Some of the
serious complications of diabetes are as follows:
It is the leading cause of lower limb amputations in the United States.
It is the leading cause of blindness in adults over age 20.
It is the leading cause of kidney failure.
It increases the risk of having a heart attack or stroke by two to four times.
Because a person with diabetes is unable to use glucose properly, excessive quantities accumulate in the blood and the urine.
Other characteristic symptoms are constant hunger, weight loss, extreme thirst, and frequent urination because the kidneys
excrete large amounts of water in an attempt to remove excess sugar from the blood.
There are two types of diabetes. In immune-mediated diabetes, insufficient amounts of insulin are produced. This type of
diabetes develops early in life and is also known as Type 1 diabetes, as well as insulin-dependent or juvenile-onset diabetes.
Symptoms are rapidly reversed by the administration of insulin, and Type 1 diabetics can lead active lives provided they receive
insulin as needed. Because insulin is a protein that is readily digested in the small intestine, it cannot be taken orally and must be
injected at least once a day.
In Type 1 diabetes, insulin-producing cells of the pancreas are destroyed by the body’s immune system. Researchers are still
trying to find out why. Meanwhile, they have developed a simple blood test capable of predicting who will develop Type 1
diabetes several years before the disease becomes apparent. The blood test reveals the presence of antibodies that destroy the
body’s insulin-producing cells.
Type 2 diabetes, also known as noninsulin-dependent or adult-onset diabetes, is by far the more common, representing about
95% of diagnosed diabetic cases. (This translates to about 16 million Americans.) Type 2 diabetics usually produce sufficient
amounts of insulin, but either the insulin-producing cells in the pancreas do not release enough of it, or it is not used properly
because of defective insulin receptors or a lack of insulin receptors on the target cells. In many of these people, the disease can
be controlled with a combination of diet and exercise alone. For some people who are overweight, losing weight is sufficient to
bring their blood sugar level into the normal range, after which medication is not required if they exercise regularly and eat
wisely.
Those who require medication may use oral antidiabetic drugs that stimulate the islet cells to secrete insulin. First-generation
antidiabetic drugs stimulated the release of insulin. Newer second-generation drugs, such as glyburide, do as well, but they also
increase the sensitivity of cell receptors to insulin. Some individuals with Type 2 diabetes do not produce enough insulin and
thus do not respond to these oral medications; they must use insulin. In both Type 1 and Type 2 diabetes, the blood sugar level
must be carefully monitored and adjustments made in diet or medication to keep the level as normal as possible (70–120
mg/dL).
Metabolism of Pyruvate
The presence or absence of oxygen determines the fates of the pyruvate and the NADH produced in glycolysis. When plenty of
oxygen is available, pyruvate is completely oxidized to carbon dioxide, with the release of much greater amounts of ATP through
the combined actions of the citric acid cycle, the electron transport chain, and oxidative phosphorylation. However, in the absence
of oxygen (that is, under anaerobic conditions), the fate of pyruvate is different in different organisms. In vertebrates, pyruvate is
converted to lactate, while other organisms, such as yeast, convert pyruvate to ethanol and carbon dioxide. These possible fates of
pyruvate are summarized in Figure 6.6.2. The conversion to lactate or ethanol under anaerobic conditions allows for the
reoxidation of NADH to NAD+ in the absence of oxygen.
Figure 6.6.2 : Metabolic Fates of Pyruvate
ATP Yield from Glycolysis
The net energy yield from anaerobic glucose metabolism can readily be calculated in moles of ATP. In the initial phosphorylation
of glucose (step 1), 1 mol of ATP is expended, along with another in the phosphorylation of fructose 6-phosphate (step 3). In step 7,
2 mol of BPG (recall that 2 mol of 1,3-BPG are formed for each mole of glucose) are converted to 2 mol of 3-phosphoglycerate,
and 2 mol of ATP are produced. In step 10, 2 mol of pyruvate and 2 mol of ATP are formed per mole of glucose.
For every mole of glucose degraded, 2 mol of ATP are initially consumed and 4 mol of ATP are ultimately produced. The net
production of ATP is thus 2 mol for each mole of glucose converted to lactate or ethanol. If 7.4 kcal of energy is conserved per
mole of ATP produced, and the total amount of energy that can theoretically be obtained from the complete oxidation of 1 mol of
glucose is 670 kcal (as stated in the chapter introduction), the energy conserved in the anaerobic catabolism of glucose to two
molecules of lactate (or ethanol) is as follows:
2 × 7.4 kcal
× 100 = 2.2% (6.6.1)
670 kcal
Thus anaerobic cells extract only a very small fraction of the total energy of the glucose molecule.
Contrast this result with the amount of energy obtained when glucose is completely oxidized to carbon dioxide and water through
glycolysis, the citric acid cycle, the electron transport chain, and oxidative phosphorylation as summarized in Table 6.6.1. Note the
indication in the table that a variable amount of ATP is synthesized, depending on the tissue, from the NADH formed in the
cytoplasm during glycolysis. This is because NADH is not transported into the inner mitochondrial membrane where the enzymes
for the electron transport chain are located. Instead, brain and muscle cells use a transport mechanism that passes electrons from the
cytoplasmic NADH through the membrane to flavin adenine dinucleotide (FAD) molecules inside the mitochondria, forming
reduced flavin adenine dinucleotide (FADH2), which then feeds the electrons into the electron transport chain. This route lowers
the yield of ATP to 1.5–2 molecules of ATP, rather than the usual 2.5–3 molecules. A more efficient transport system is found in
liver, heart, and kidney cells where the formation of one cytoplasmic NADH molecule results in the formation of one mitochondrial
NADH molecule, which leads to the formation of 2.5–3 molecules of ATP.The total amount of energy conserved in the aerobic
catabolism of glucose in the liver is as follows:
38 × 7.4 kcal
× 100 = 42% (6.6.2)
670 kcal
Conservation of 42% of the total energy released compares favorably with the efficiency of any machine. In comparison,
automobiles are only about 20%–25% efficient in using the energy released by the combustion of gasoline.
As indicated earlier, the 58% of released energy that is not conserved enters the surroundings (that is, the cell) as heat that helps to
maintain body temperature. If we are exercising strenuously and our metabolism speeds up to provide the energy needed for muscle
contraction, more heat is produced. We begin to perspire to dissipate some of that heat. As the perspiration evaporates, the excess
heat is carried away from the body by the departing water vapor.
Summary
The monosaccharide glucose is broken down through a series of enzyme-catalyzed reactions known as glycolysis.
For each molecule of glucose that is broken down, two molecules of pyruvate, two molecules of ATP, and two molecules of
NADH are produced.
In the absence of oxygen, pyruvate is converted to lactate, and NADH is reoxidized to NAD+. In the presence of oxygen,
pyruvate is converted to acetyl-CoA and then enters the citric acid cycle.
More ATP can be formed from the breakdown of glucose when oxygen is present.

1. In glycolysis, how many molecules of pyruvate are produced from one molecule of glucose?
2. In vertebrates, what happens to pyruvate when
a. plenty of oxygen is available?
b. oxygen supplies are limited?
3. In anaerobic glycolysis, how many molecules of ATP are produced from one molecule of glucose?
Answers
1. two
2.
a. Pyruvate is completely oxidized to carbon dioxide.
b. Pyruvate is reduced to lactate, allowing for the reoxidation of NADH to NAD+.
3. There is a net production of two molecules of ATP.
Exercises
aldolase
a. f ructose 1, 6-bisphosphate −−−−→?+?

pyruvate kinase
b. ? + ADP −−−−−−−−−→ pyruvate + ATP

?
c. dihydroxyacetone phosphate → glyceraldehyde 3-phosphate

hexokinase
d. glucose + ATP −−−−−−→ ? + ADP

?
a. f ructose 6-phosphate + ATP → f ructose 1, 6-bisphosphate + ADP

phosphoglucose isomerase
b. ?−−−−−−−−−−−−−−→ f ructose 6-phosphate

?
c. glyceraldehyde 3-phosphate + NAD

+
+ Pi → 1, 3-bisphosphoglycerate + NADH
phosphoglyceromutase
d. 3-phosphoglycerate −−−−−−−−−−−−→?
a. hydrolysis of a high-energy phosphate compound
b. synthesis of ATP
a. isomerization
b. oxidation
5. What coenzyme is needed as an oxidizing agent in glycolysis?
6. Calculate
a. the total number of molecules of ATP produced for each molecule of glucose converted to pyruvate in glycolysis.
b. the number of molecules of ATP hydrolyzed in phase I of glycolysis.
c. the net ATP production from glycolysis alone.
7. How is the NADH produced in glycolysis reoxidized when oxygen supplies are limited in
a. muscle cells?
b. yeast?
8.
a. Calculate the number of moles of ATP produced by the aerobic oxidation of 1 mol of glucose in a liver cell.
b. Of the total calculated in Exercise 9a, determine the number of moles of ATP produced in each process.
a. glycolysis alone
b. the citric acid cycle
c. the electron transport chain and oxidative phosphorylation
Answers
1. a. glyceraldehyde 3-phosphate + dihydroxyacetone phosphate
b. phosphoenolpyruvate
c. triose phosphate isomerase
d. glucose 6-phosphate
3. a. reactions 1b, 1d, and 2a

b. reaction 1b
5. NAD+
7. a. Pyruvate is reduced to lactate, and NADH is reoxidized to NAD+.

b. Pyruvate is converted to ethanol and carbon dioxide, and NADH is reoxidized to NAD+.
6.6: Stage II of Carbohydrate Catabolism is shared under a CC BY-NC-SA 4.0 license and was authored, remixed, and/or curated by LibreTexts.
Learning Objectives
To describe the reactions needed to completely oxidize a fatty acid to carbon dioxide and water.
Like glucose, the fatty acids released in the digestion of triglycerides and other lipids are broken down in a series of sequential
reactions accompanied by the gradual release of usable energy. Some of these reactions are oxidative and require nicotinamide
adenine dinucleotide (NAD+) and flavin adenine dinucleotide (FAD). The enzymes that participate in fatty acid catabolism are
located in the mitochondria, along with the enzymes of the citric acid cycle, the electron transport chain, and oxidative
phosphorylation. This localization of enzymes in the mitochondria is of the utmost importance because it facilitates efficient
utilization of energy stored in fatty acids and other molecules.
Fatty acid oxidation is initiated on the outer mitochondrial membrane. There the fatty acids, which like carbohydrates are relatively
inert, must first be activated by conversion to an energy-rich fatty acid derivative of coenzyme A called fatty acyl-coenzyme A
(CoA). The activation is catalyzed by acyl-CoA synthetase. For each molecule of fatty acid activated, one molecule of coenzyme A
and one molecule of adenosine triphosphate (ATP) are used, equaling a net utilization of the two high-energy bonds in one ATP
molecule (which is therefore converted to adenosine monophosphate [AMP] rather than adenosine diphosphate [ADP]):
The fatty acyl-CoA diffuses to the inner mitochondrial membrane, where it combines with a carrier molecule known as carnitine in
a reaction catalyzed by carnitine acyltransferase. The acyl-carnitine derivative is transported into the mitochondrial matrix and
converted back to the fatty acyl-CoA.
Steps in the β-Oxidation of Fatty Acids

Further oxidation of the fatty acyl-CoA occurs in the mitochondrial matrix via a sequence of four reactions known collectively as
β-oxidation because the β-carbon undergoes successive oxidations in the progressive removal of two carbon atoms from the
carboxyl end of the fatty acyl-CoA (Figure 6.7.1).
Figure 6.7.1 : Fatty Acid Oxidation. The fatty acyl-CoA formed in the final step becomes the substrate for the first step in the next
round of β-oxidation. β-oxidation continues until two acetyl-CoA molecules are produced in the final step.
The first step in the catabolism of fatty acids is the formation of an alkene in an oxidation reaction catalyzed by acyl-CoA
dehydrogenase. In this reaction, the coenzyme FAD accepts two hydrogen atoms from the acyl-CoA, one from the α-carbon and
one from the β-carbon, forming reduced flavin adenine dinucleotide (FADH2).
The FADH2 is reoxidized back to FAD via the electron transport chain that supplies energy to form 1.5–2 molecules of ATP.
Next, the trans-alkene is hydrated to form a secondary alcohol in a reaction catalyzed by enoyl-CoA hydratase. The enzyme forms
only the L-isomer.
The secondary alcohol is then oxidized to a ketone by β-hydroxyacyl-CoA dehydrogenase, with NAD+ acting as the oxidizing
agent. The reoxidation of each molecule of NADH to NAD+ by the electron transport chain furnishes 2.5–3 molecules of ATP.
The final reaction is cleavage of the β-ketoacyl-CoA by a molecule of coenzyme A. The products are acetyl-CoA and a fatty acyl-
CoA that has been shortened by two carbon atoms. The reaction is catalyzed by thiolase.
The shortened fatty acyl-CoA is then degraded by repetitions of these four steps, each time releasing a molecule of acetyl-CoA.
The overall equation for the β-oxidation of palmitoyl-CoA (16 carbon atoms) is as follows:
Because each shortened fatty acyl-CoA cycles back to the beginning of the pathway, β-
oxidation is sometimes referred to as the fatty acid spiral.
The fate of the acetyl-CoA obtained from fatty acid oxidation depends on the needs of an organism. It may enter the citric acid
cycle and be oxidized to produce energy, it may be used for the formation of water-soluble derivatives known as ketone bodies, or
it may serve as the starting material for the synthesis of fatty acids. For more information about the citric acid cycle, see Section
20.4.
Looking Closer: Ketone Bodies
In the liver, most of the acetyl-CoA obtained from fatty acid oxidation is oxidized by the citric acid cycle. However, some of the
acetyl-CoA is used to synthesize a group of compounds known as ketone bodies: acetoacetate, β-hydroxybutyrate, and acetone.
Two acetyl-CoA molecules combine, in a reversal of the final step of β-oxidation, to produce acetoacetyl-CoA. The acetoacetyl-
CoA reacts with another molecule of acetyl-CoA and water to form β-hydroxy-β-methylglutaryl-CoA, which is then cleaved to
acetoacetate and acetyl-CoA. Most of the acetoacetate is reduced to β-hydroxybutyrate, while a small amount is decarboxylated
to carbon dioxide and acetone.
The acetoacetate and β-hydroxybutyrate synthesized by the liver are released into the blood for use as a metabolic fuel (to be
converted back to acetyl-CoA) by other tissues, particularly the kidney and the heart. Thus, during prolonged starvation, ketone
bodies provide about 70% of the energy requirements of the brain. Under normal conditions, the kidneys excrete about 20 mg of
ketone bodies each day, and the blood levels are maintained at about 1 mg of ketone bodies per 100 mL of blood.
In starvation, diabetes mellitus, and certain other physiological conditions in which cells do not receive sufficient amounts of
carbohydrate, the rate of fatty acid oxidation increases to provide energy. This leads to an increase in the concentration of acetyl-
CoA. The increased acetyl-CoA cannot be oxidized by the citric acid cycle because of a decrease in the concentration of
oxaloacetate, which is diverted to glucose synthesis. In response, the rate of ketone body formation in the liver increases further,
to a level much higher than can be used by other tissues. The excess ketone bodies accumulate in the blood and the urine, a
condition referred to as ketosis. When the acetone in the blood reaches the lungs, its volatility causes it to be expelled in the
breath. The sweet smell of acetone, a characteristic of ketosis, is frequently noticed on the breath of severely diabetic patients.
Because two of the three kinds of ketone bodies are weak acids, their presence in the blood in excessive amounts overwhelms
the blood buffers and causes a marked decrease in blood pH (to 6.9 from a normal value of 7.4). This decrease in pH leads to a
serious condition known as acidosis. One of the effects of acidosis is a decrease in the ability of hemoglobin to transport oxygen
in the blood. In moderate to severe acidosis, breathing becomes labored and very painful. The body also loses fluids and
becomes dehydrated as the kidneys attempt to get rid of the acids by eliminating large quantities of water. The lowered oxygen
supply and dehydration lead to depression; even mild acidosis leads to lethargy, loss of appetite, and a generally run-down
feeling. Untreated patients may go into a coma. At that point, prompt treatment is necessary if the person’s life is to be saved.
ATP Yield from Fatty Acid Oxidation

The amount of ATP obtained from fatty acid oxidation depends on the size of the fatty acid being oxidized. For our purposes here.
we’ll study palmitic acid, a saturated fatty acid with 16 carbon atoms, as a typical fatty acid in the human diet. Calculating its
energy yield provides a model for determining the ATP yield of all other fatty acids.
The breakdown by an organism of 1 mol of palmitic acid requires 1 mol of ATP (for activation) and forms 8 mol of acetyl-CoA.
Recall from Table 20.4.1 that each mole of acetyl-CoA metabolized by the citric acid cycle yields 10 mol of ATP. The complete
degradation of 1 mol of palmitic acid requires the β-oxidation reactions to be repeated seven times. Thus, 7 mol of NADH and 7
mol of FADH2 are produced. Reoxidation of these compounds through respiration yields 2.5–3 and 1.5–2 mol of ATP, respectively.
The energy calculations can be summarized as follows:
1 mol of ATP is split to AMP and 2Pi −2 ATP
8 mol of acetyl-CoA formed (8 × 12) 96 ATP
7 mol of FADH2 formed (7 × 2) 14 ATP
7 mol of NADH formed (7 × 3) 21 ATP
Total 129 ATP
The number of times β-oxidation is repeated for a fatty acid containing n carbon atoms is
n/2 – 1 because the final turn yields two acetyl-CoA molecules.
The combustion of 1 mol of palmitic acid releases a considerable amount of energy:
C16 H32 O2 + 23 O2 → 16C O2 + 16 H2 O + 2, 340 kcal (6.7.1)
The percentage of this energy that is conserved by the cell in the form of ATP is as follows:
energy conserved (129 ATP)(7.4 kcal/ATP)
× 100 = × 100 = 41% (6.7.2)
total energy available 2, 340 kcal
The efficiency of fatty acid metabolism is comparable to that of carbohydrate metabolism, which we calculated to be 42%. For
more information about the efficiency of fatty acid metabolism, see Section 20.5.
The oxidation of fatty acids produces large quantities of water. This water, which sustains
migratory birds and animals (such as the camel) for long periods of time.
Summary
Fatty acids, obtained from the breakdown of triglycerides and other lipids, are oxidized through a series of reactions known as
β-oxidation.
In each round of β-oxidation, 1 molecule of acetyl-CoA, 1 molecule of NADH, and 1 molecule of FADH2 are produced.
The acetyl-CoA, NADH, and FADH2 are used in the citric acid cycle, the electron transport chain, and oxidative
phosphorylation to produce ATP.

1. How are fatty acids activated prior to being transported into the mitochondria and oxidized?
2. Draw the structure of hexanoic (caproic) acid and identify the α-carbon and the β-carbon.
Answers
1. They react with CoA to form fatty acyl-CoA molecules.
2.
Exercises
1. For each reaction found in β-oxidation, identify the enzyme that catalyzes the reaction and classify the reaction as oxidation-
reduction, hydration, or cleavage.
a.
b.
c.
2. What are the products of β-oxidation?
3. How many rounds of β-oxidation are necessary to metabolize lauric acid (a saturated fatty acid with 12 carbon atoms)?
4. How many rounds of β-oxidation are necessary to metabolize arachidic acid (a saturated fatty acid with 20 carbon atoms)?
5. When myristic acid (a saturated fatty acid with 14 carbon atoms) is completely oxidized by β-oxidation, how many molecules
of each are formed?
a. acetyl-CoA
b. FADH2
c. NADH
6. When stearic acid (a saturated fatty acid with 18 carbon atoms) is completely oxidized by β-oxidation, how many molecules of
each are formed?
a. acetyl-CoA
b. FADH2
c. NADH
7. What is the net yield of ATP from the complete oxidation, in a liver cell, of one molecule of myristic acid?
8. What is the net yield of ATP from the complete oxidation, in a liver cell, of one molecule of stearic acid?
Answers
1.
a. enoyl-CoA hydratase; hydration
b. thiolase; cleavage
c. acyl-CoA dehydrogenase; oxidation-reduction
3. five rounds
5.
a. 7 molecules
b. 6 molecules
c. 6 molecules
7. 112 molecules
6.7: Stage II of Lipid Catabolism is shared under a CC BY-NC-SA 4.0 license and was authored, remixed, and/or curated by LibreTexts.
Learning Objectives
To describe how excess amino acids are degraded.
The liver is the principal site of amino acid metabolism, but other tissues, such as the kidney, the small intestine, muscles, and
adipose tissue, take part. Generally, the first step in the breakdown of amino acids is the separation of the amino group from the
carbon skeleton, usually by a transamination reaction. The carbon skeletons resulting from the deaminated amino acids are used to
form either glucose or fats, or they are converted to a metabolic intermediate that can be oxidized by the citric acid cycle. The latter
alternative, amino acid catabolism, is more likely to occur when glucose levels are low—for example, when a person is fasting or
starving.
Transamination
Transamination is an exchange of functional groups between any amino acid (except lysine, proline, and threonine) and an α-keto
acid. The amino group is usually transferred to the keto carbon atom of pyruvate, oxaloacetate, or α-ketoglutarate, converting the α-
keto acid to alanine, aspartate, or glutamate, respectively. Transamination reactions are catalyzed by specific transaminases (also
called aminotransferases), which require pyridoxal phosphate as a coenzyme.
Figure 6.8.1 ).
In an α-keto acid, the carbonyl or keto group is located on the carbon atom adjacent to
the carboxyl group of the acid.
Figure 6.8.1 : Two Transamination Reactions. In both reactions, the final acceptor of the amino group is α-ketoglutarate, and the
final product is glutamate.
Oxidative Deamination
In the breakdown of amino acids for energy, the final acceptor of the α-amino group is α-ketoglutarate, forming glutamate.
Glutamate can then undergooxidative deamination, in which it loses its amino group as an ammonium (NH4+) ion and is oxidized
back to α-ketoglutarate (ready to accept another amino group):
This reaction occurs primarily in liver mitochondria. Most of the NH4+ ion formed by oxidative deamination of glutamate is
converted to urea and excreted in the urine in a series of reactions known as the urea cycle.
The synthesis of glutamate occurs in animal cells by reversing the reaction catalyzed by glutamate dehydrogenase. For this reaction
nicotinamide adenine dinucleotide phosphate (NADPH) acts as the reducing agent. The synthesis of glutamate is significant
because it is one of the few reactions in animals that can incorporate inorganic nitrogen (NH4+) into an α-keto acid to form an
amino acid. The amino group can then be passed on through transamination reactions, to produce other amino acids from the
appropriate α-keto acids.
The Fate of the Carbon Skeleton

Any amino acid can be converted into an intermediate of the citric acid cycle. Once the amino group is removed, usually by
transamination, the α-keto acid that remains is catabolized by a pathway unique to that acid and consisting of one or more
reactions. For example, phenylalanine undergoes a series of six reactions before it splits into fumarate and acetoacetate. Fumarate
is an intermediate in the citric acid cycle, while acetoacetate must be converted to acetoacetyl-coenzyme A (CoA) and then to
acetyl-CoA before it enters the citric acid cycle.
Figure 6.8.2 : Fates of the Carbon Skeletons of Amino Acids

Those amino acids that can form any of the intermediates of carbohydrate metabolism can subsequently be converted to glucose via
a metabolic pathway known as gluconeogenesis. These amino acids are called glucogenic amino acids. Amino acids that are
converted to acetoacetyl-CoA or acetyl-CoA, which can be used for the synthesis of ketone bodies but not glucose, are called
ketogenic amino acids. Some amino acids fall into both categories. Leucine and lysine are the only amino acids that are exclusively
ketogenic. Figure 6.8.2 summarizes the ultimate fates of the carbon skeletons of the 20 amino acids.
Career Focus: Exercise Physiologist
An exercise physiologist works with individuals who have or wish to prevent developing a wide variety of chronic diseases,
such as diabetes, in which exercise has been shown to be beneficial. Each individual must be referred by a licensed physician.
An exercise physiologist works in a variety of settings, such as a hospital or in a wellness program at a commercial business, to
design and monitor individual exercise plans. A registered clinical exercise physiologist must have an undergraduate degree in
exercise physiology or a related degree. Some job opportunities require a master’s degree in exercise physiology or a related
degree.
Ergospirometry laboratory for the measurement of metabolic changes during a graded exercise test on a treadmill. Image used
with permission from Wikipedia.
Summary
Generally the first step in the breakdown of amino acids is the removal of the amino group, usually through a reaction known as
transamination. The carbon skeletons of the amino acids undergo further reactions to form compounds that can either be used for
the synthesis of glucose or the synthesis of ketone bodies.

1. a. Write the equation for the transamination reaction between alanine and oxaloacetate.
b. Name the two products that are formed.
2. What is the purpose of oxidative deamination?
Answers
1. a.
b. pyruvate and aspartate
2. Oxidative deamination provides a reaction in which the amino group [as the ammonium (NH4+) ion] is removed from a
molecule, not simply transferred from one molecule to another. Most of the NH4+ ion is converted to urea and excreted from the
body.
Exercises
1. Write the equation for the transamination reaction between valine and pyruvate.
2. Write the equation for the transamination reaction between phenylalanine and oxaloacetate.
3. What products are formed in the oxidative deamination of glutamate?
4. Determine if each amino acid is glucogenic, ketogenic, or both.
a. phenylalanine
b. leucine
c. serine
a. asparagine
b. tyrosine
c. valine
Answers
1.
3. α-ketoglutarate, NADH, and NH4+
5. a. glucogenic
b. both
c. glucogenic
6.8: Stage II of Protein Catabolism is shared under a CC BY-NC-SA 4.0 license and was authored, remixed, and/or curated by LibreTexts.
Metabolism is the general term for all chemical reactions in living organisms. The two types of metabolism are catabolism—those
reactions in which complex molecules (carbohydrates, lipids, and proteins) are broken down to simpler ones with the concomitant
release of energy—and anabolism—those reactions that consume energy to build complex molecules. Metabolism is studied by
looking at individual metabolic pathways, which are a series of biochemical reactions in which a given reactant is converted to a
desired end product.
The oxidation of fuel molecules (primarily carbohydrates and lipids), a process called respiration, is the source of energy used by
cells. Catabolic reactions release energy from food molecules and use some of that energy for the synthesis of adenosine
triphosphate (ATP); anabolic reactions use the energy in ATP to create new compounds. Catabolism can be divided into three
stages. In stage I, carbohydrates, lipids, and proteins are broken down into their individual monomer units—simple sugars, fatty
acids, and amino acids, respectively. In stage II, these monomer units are broken down by specific metabolic pathways to form a
common end product acetyl-coenzyme A (CoA). In stage III, acetyl-CoA is completely oxidized to form carbon dioxide and water,
and ATP is produced.
The digestion of carbohydrates begins in the mouth as α-amylase breaks glycosidic linkages in carbohydrate molecules. Essentially
no carbohydrate digestion occurs in the stomach, and food particles pass through to the small intestine, where α-amylase and
intestinal enzymes convert complex carbohydrate molecules (starches) to monosaccharides. The monosaccharides then pass
through the lining of the small intestine and into the bloodstream for transport to all body cells.
Protein digestion begins in the stomach as pepsinogen in gastric juice is converted to pepsin, the enzyme that hydrolyzes peptide
bonds. The partially digested protein then passes to the small intestine, where the remainder of protein digestion takes place
through the action of several enzymes. The resulting amino acids cross the intestinal wall into the blood and are carried to the liver.
Lipid digestion begins in the small intestine. Bile salts emulsify the lipid molecules, and then lipases hydrolyze them to fatty acids
and monoglycerides. The hydrolysis products pass through the intestine and are repackaged for transport in the bloodstream.
In cells that are operating aerobically, acetyl-CoA produced in stage II of catabolism is oxidized to carbon dioxide. The citric acid
cycle describes this oxidation, which takes place with the formation of the coenzymes reduced nicotinamide adenine dinucleotide
(NADH) and reduced flavin adenine dinucleotide (FADH2). The sequence of reactions needed to oxidize these coenzymes and
transfer the resulting electrons to oxygen is called the electron transport chain, or the respiratory chain. The compounds
responsible for this series of oxidation-reduction reactions include proteins known as cytochromes, Fe·S proteins, and other
molecules that ultimately result in the reduction of molecular oxygen to water. Every time a compound with two carbon atoms is
oxidized in the citric acid cycle, a respiratory chain compound accepts the electrons lost in the oxidation (and so is reduced) and
then passes them on to the next metabolite in the chain. The energy released by the electron transport chain is used to transport
hydrogen (H+) ions from the mitochondrial matrix to the intermembrane space. The flow of H+ back through ATP synthase leads to
the synthesis and release of ATP from adenosine diphosphate (ADP) and inorganic phosphate ions (Pi) in a process known as
oxidative phosphorylation. Electron transport and oxidative phosphorylation are tightly coupled to each other. The enzymes and
intermediates of the citric acid cycle, the electron transport chain, and oxidative phosphorylation are located in organelles called
mitochondria.
The oxidation of carbohydrates is the source of over 50% of the energy used by cells. Glucose is oxidized to two molecules of
pyruvate through a series of reactions known as glycolysis. Some of the energy released in these reactions is conserved by the
formation of ATP from ADP. Glycolysis can be divided into two phases: phase I consists of the first five reactions and requires
energy to “prime” the glucose molecule for phase II, the last five reactions in which ATP is produced through substrate-level
phosphorylation.
The pyruvate produced by glycolysis has several possible fates, depending on the organism and whether or not oxygen is present.
In animal cells, pyruvate can be further oxidized to acetyl-CoA and then to carbon dioxide (through the citric acid cycle) if oxygen
supplies are sufficient. When oxygen supplies are insufficient, pyruvate is reduced to lactate. In yeast and other microorganisms,
pyruvate is not converted to lactate in the absence of oxygen but instead is converted to ethanol and carbon dioxide.
The amount of ATP formed by the oxidation of glucose depends on whether or not oxygen is present. If oxygen is present, glucose
is oxidized to carbon dioxide, and 36–38 ATP molecules are produced for each glucose molecule oxidized, using the combined
pathways of glycolysis, the citric acid cycle, the electron transport chain, and oxidative phosphorylation. Thus, approximately 42%
of the energy released by the complete oxidation of glucose is conserved by the synthesis of ATP. In the absence of oxygen, only 2
molecules of ATP are formed for each molecule of glucose converted to lactate (2 molecules), and the amount of energy conserved
is much less (2%).
Fatty acids, released by the degradation of triglycerides and other lipids, are converted to fatty acyl-CoA, transported into the
mitochondria, and oxidized by repeated cycling through a sequence of four reactions known as β-oxidation. In each round of β-
oxidation, the fatty acyl-CoA is shortened by two carbon atoms as one molecule of acetyl-CoA is formed. The final round of β-
oxidation, once the chain has been shortened to four carbon atoms, forms two molecules of acetyl-CoA. β-oxidation also forms the
reduced coenzymes FADH2 and NADH, whose reoxidation through the electron transport chain and oxidative phosphorylation
leads to the synthesis of ATP. The efficiency of fatty acid oxidation in the human body is approximately 41%.
Amino acids from the breakdown of proteins can be catabolized to provide energy. Amino acids whose carbon skeletons are
converted to intermediates that can be converted to glucose through gluconeogenesis are known as glucogenic amino acids.
Amino acids whose carbon skeletons are broken down to compounds used to form ketone bodies are known as ketogenic amino
acids.
The first step in amino acid catabolism is separation of the amino group from the carbon skeleton. In a transamination, the amino
acid gives its NH2 to pyruvate, α-ketoglutarate, or oxaloacetate. The products of this reaction are a new amino acid and an α-keto
acid containing the carbon skeleton of the original amino acid. Pyruvate is transaminated to alanine, α-ketoglutarate to glutamate,
and oxaloacetate to aspartate. The amino groups used to form alanine and aspartate are ultimately transferred to α-ketoglutarate,
forming glutamate. The glutamate then undergoes oxidative deamination to yield α-ketoglutarate and ammonia.
Template:HideOrg
6.9: Energy Metabolism (Summary) is shared under a CC BY-NC-SA 4.0 license and was authored, remixed, and/or curated by LibreTexts.
20.1: ATP- the Universal Energy Currency
1. Why is ATP referred to as the energy currency of the cell?
Answer
1. ATP is the principal molecule involved in energy exchange reactions in biological systems.
Exercises
1. How do ATP and ADP differ in structure?
2. Why does the hydrolysis of ATP to ADP involve the release of energy?
a. ATP
b. glucose 6-phosphate
c. creatine phosphate
a. ADP
b. AMP
c. glucose 1-phosphate
Answers
1. ATP has a triphosphate group attached, while ADP has only a diphosphate group attached.
3. a. yes
b. no
c. yes

1. Distinguish between each pair of compounds.
a. pepsin and pepsinogen
b. chymotrypsin and trypsin
c. aminopeptidase and carboxypeptidase
2. What are the primary end products of each form of digestion?
a. carbohydrate digestion
b. lipid digestion
c. protein digestion
3. In what section of the digestive tract does most of the carbohydrate, lipid, and protein digestion take place?
Answers
1. a. Pepsinogen is an inactive form of pepsin; pepsin is the active form of the enzyme.
b. Both enzymes catalyze the hydrolysis of peptide bonds. Chymotrypsin catalyzes the hydrolysis of peptide bonds following
aromatic amino acids, while trypsin catalyzes the hydrolysis of peptide bonds following lysine and arginine.
c. Aminopeptidase catalyzes the hydrolysis of amino acids from the N-terminal end of a protein, while carboxypeptidase
catalyzes the hydrolysis of amino acids from the C-terminal end of a protein.
2. a. glucose, fructose, and galactose
b. monoglycerides and fatty acids
c. amino acids
3. the small intestine
Exercises
1. What are the products of digestion (or stage I of catabolism)?
2. What is the general type of reaction used in digestion?
a. chymotrypsin
b. lactase
c. pepsin
d. maltase
a. α-amylase
b. trypsin
c. sucrase
d. aminopeptidase
5. a. What is the meaning of the following statement? “Bile salts act to emulsify lipids in the small intestine.”
b. Why is emulsification important?
6. Using chemical equations, describe the chemical changes that triglycerides undergo during digestion.
7. What are the expected products from the enzymatic action of chymotrypsin on each amino acid segment?
a. gly-ala-phe-thr-leu
b. ala-ile-tyr-ser-arg
c. val-trp-arg-leu-cys
8. What are the expected products from the enzymatic action of trypsin on each amino acid segment?
a. leu-thr-glu-lys-ala
b. phe-arg-ala-leu-val
c. ala-arg-glu-trp-lys
Answers
1. proteins: amino acids; carbohydrates: monosaccharides; fats: fatty acids and glycerol
3. a. Chymotrypsin is found in the small intestine and catalyzes the hydrolysis of peptide bonds following aromatic amino acids.
b. Lactase is found in the small intestine and catalyzes the hydrolysis of lactose.
c. Pepsin is found in the stomach and catalyzes the hydrolysis of peptide bonds, primarily those that occur after aromatic
amino acids.
d. Maltase is found in the small intestine and catalyzes the hydrolysis of maltose.
5. a. Bile salts aid in digestion by dispersing lipids throughout the aqueous solution in the small intestine.
b. Emulsification is important because lipids are not soluble in water; it breaks lipids up into smaller particles that can be more
readily hydrolyzed by lipases.
7. a. gly-ala-phe and thr-leu
b. ala-ile-tyr and ser-arg
c. val-trp and arg-leu-cys
1. What is a metabolic pathway?
2. What vitamin is required to make coenzyme A?
3. What is the net yield of Glycolysis as far as ATP?
4. Name the enzymes that are key regulatory sites in Glycolysis.
5. Why are the enzymes in the previous question targets for regulation?
6. Why is the priming phase necessary?
7. Draw the entire pathway for glycolysis including enzymes, reactants and products for each step.
8. Where does beta-oxidation occur?
9. What is the average net yield of ATP per carbon?
10. Where exactly is water formed during the process of fatty acid degradation? (Hint: H2O is formed when when the one of the
products of beta-oxidation is passed through another of the metabolic pathways)
11. During the process of beta-oxidation, why is it that [FAD] is used to oxidize an alkane to an alkene while NAD+ is used to
oxidize an alchol to a carbonyl
12. Draw out the entire process of the degradation of a triglyceride, include enzymes and products and reactants for each step.
Answers
1. A metabolic pathway is a series of biochemical reactions by which an organism converts a given reactant to a specific end
product.
2. pantothenic acid

1. What is the main function of the citric acid cycle?
2. Two carbon atoms are fed into the citric acid cycle as acetyl-CoA. In what form are two carbon atoms removed from the cycle?
3. What are mitochondria and what is their function in the cell?
Answers
1. the complete oxidation of carbon atoms to carbon dioxide and the formation of a high-energy phosphate compound, energy rich
reduced coenzymes (NADH and FADH2), and metabolic intermediates for the synthesis of other compounds
2. as carbon dioxide
3. Mitochondria are small organelles with a double membrane that contain the enzymes and other molecules needed for the
production of most of the ATP needed by the body.
Exercises
aconitase
a. ?−−−−−→ isocitrate
citrate synthase
b. ?+?−−−−−−−−−→ citrate + coenzyme A

f umarase
c. f umarate −−−−−→?
?
d. isocitrate + NAD
+
→ α-ketoglurate + NADH + C O2

?
a. malate + NAD
+
→ oxaloacetate + NADH
nucleoside diphosphokinase
b. ?+?−−−−−−−−−−−−−−−→ GDP + ATP
succinyl-CoA synthetase
c. succinyl-CoA −−−−−−−−−−−−−→?+?
succinate dehydrogenase
d. succinate + FAD −−−−−−−−−−−−−→ ? + FADH2
a. isomerization
b. hydration
c. synthesis
a. oxidation
b. decarboxylation
c. phosphorylation
5. What similar role do coenzyme Q and cytochrome c serve in the electron transport chain?
6. What is the electron acceptor at the end of the electron transport chain? To what product is this compound reduced?
7. What is the function of the cytochromes in the electron transport chain?
8. a. What is meant by this statement? “Electron transport is tightly coupled to oxidative phosphorylation.”
b. How are electron transport and oxidative phosphorylation coupled or linked?
Answers
1. a. citrate
b. oxaloacetate + acetyl-CoA
c. malate
d. α-ketoglutarate hydrogenase complex
3. a. reaction in 1a
b. reaction in 1c
c. reaction in 1b
5. Both molecules serve as electron shuttles between the complexes of the electron transport chain.
7. Cytochromes are proteins in the electron transport chain and serve as one-electron carriers.

1. In glycolysis, how many molecules of pyruvate are produced from one molecule of glucose?
2. In vertebrates, what happens to pyruvate when
a. plenty of oxygen is available?
b. oxygen supplies are limited?
3. In anaerobic glycolysis, how many molecules of ATP are produced from one molecule of glucose?
Answers
1. two
2. a. Pyruvate is completely oxidized to carbon dioxide.
b. Pyruvate is reduced to lactate, allowing for the reoxidation of NADH to NAD+.
3. There is a net production of two molecules of ATP.
Exercises
aldolase
a. f ructose 1, 6-bisphosphate −−−−→?+?
pyruvate kinase
b. ? + ADP −−−−−−−−−→ pyruvate + ATP

?
c. dihydroxyacetone phosphate → glyceraldehyde 3-phosphate

hexokinase
d. glucose + ATP −−−−−−→ ? + ADP

?
a. f ructose 6-phosphate + ATP → f ructose 1, 6-bisphosphate + ADP

phosphoglucose isomerase
b. ?−−−−−−−−−−−−−−→ f ructose 6-phosphate

?
c. glyceraldehyde 3-phosphate + NAD

+
+ Pi → 1, 3-bisphosphoglycerate + NADH
phosphoglyceromutase
d. 3-phosphoglycerate −−−−−−−−−−−−→?
a. hydrolysis of a high-energy phosphate compound
b. synthesis of ATP
a. isomerization
b. oxidation
5. What coenzyme is needed as an oxidizing agent in glycolysis?
6. Calculate
a. the total number of molecules of ATP produced for each molecule of glucose converted to pyruvate in glycolysis.
b. the number of molecules of ATP hydrolyzed in phase I of glycolysis.
c. the net ATP production from glycolysis alone.
7. How is the NADH produced in glycolysis reoxidized when oxygen supplies are limited in
a. muscle cells?
b. yeast?
8. a. Calculate the number of moles of ATP produced by the aerobic oxidation of 1 mol of glucose in a liver cell.
b. Of the total calculated in Exercise 9a, determine the number of moles of ATP produced in each process.
a. glycolysis alone
b. the citric acid cycle
c. the electron transport chain and oxidative phosphorylation
Answers
1. a. glyceraldehyde 3-phosphate + dihydroxyacetone phosphate
b. phosphoenolpyruvate
c. triose phosphate isomerase
d. glucose 6-phosphate
3. a. reactions 1b, 1d, and 2a
b. reaction 1b
5. NAD+
7. a. Pyruvate is reduced to lactate, and NADH is reoxidized to NAD+.
b. Pyruvate is converted to ethanol and carbon dioxide, and NADH is reoxidized to NAD+.
1. How are fatty acids activated prior to being transported into the mitochondria and oxidized?
2. Draw the structure of hexanoic (caproic) acid and identify the α-carbon and the β-carbon.
Answers
1. They react with CoA to form fatty acyl-CoA molecules.
2.
Key Takeaways
Fatty acids, obtained from the breakdown of triglycerides and other lipids, are oxidized through a series of reactions known
as β-oxidation.
In each round of β-oxidation, 1 molecule of acetyl-CoA, 1 molecule of NADH, and 1 molecule of FADH2 are produced.
The acetyl-CoA, NADH, and FADH2 are used in the citric acid cycle, the electron transport chain, and oxidative
phosphorylation to produce ATP.
Exercises
1. For each reaction found in β-oxidation, identify the enzyme that catalyzes the reaction and classify the reaction as oxidation-
reduction, hydration, or cleavage.
a.
b.
c.
2. What are the products of β-oxidation?
3. How many rounds of β-oxidation are necessary to metabolize lauric acid (a saturated fatty acid with 12 carbon atoms)?
4. How many rounds of β-oxidation are necessary to metabolize arachidic acid (a saturated fatty acid with 20 carbon atoms)?
5. When myristic acid (a saturated fatty acid with 14 carbon atoms) is completely oxidized by β-oxidation, how many
molecules of each are formed?
a. acetyl-CoA
b. FADH2
c. NADH
6. When stearic acid (a saturated fatty acid with 18 carbon atoms) is completely oxidized by β-oxidation, how many molecules
of each are formed?
a. acetyl-CoA
b. FADH2
c. NADH
7. What is the net yield of ATP from the complete oxidation, in a liver cell, of one molecule of myristic acid?
8. What is the net yield of ATP from the complete oxidation, in a liver cell, of one molecule of stearic acid?
Answers
1. a. enoyl-CoA hydratase; hydration
b. thiolase; cleavage
c. acyl-CoA dehydrogenase; oxidation-reduction
3. five rounds
5. a. 7 molecules
b. 6 molecules
c. 6 molecules
7. 112 molecules

1. a. Write the equation for the transamination reaction between alanine and oxaloacetate.
b. Name the two products that are formed.
2. What is the purpose of oxidative deamination?
Answers
1. a.
b. pyruvate and aspartate
2. Oxidative deamination provides a reaction in which the amino group [as the ammonium (NH4+) ion] is removed from a
molecule, not simply transferred from one molecule to another. Most of the NH4+ ion is converted to urea and excreted from the
body.
Exercises
1. Write the equation for the transamination reaction between valine and pyruvate.
2. Write the equation for the transamination reaction between phenylalanine and oxaloacetate.
3. What products are formed in the oxidative deamination of glutamate?
a. phenylalanine
b. leucine
c. serine
a. asparagine
b. tyrosine
c. valine
Answers
1.
3. α-ketoglutarate, NADH, and NH4+
5. a. glucogenic
b. both
c. glucogenic
1. Hydrolysis of which compound—arginine phosphate or glucose 6-phosphate—would provide enough energy for the
phosphorylation of ATP? Why?
2. If a cracker, which is rich in starch, is chewed for a long time, it begins to develop a sweet, sugary taste. Why?
3. Indicate where each enzymes would cleave the short peptide ala-ser-met-val-phe-gly-cys-lys-asp-leu.
a. aminopeptidase
b. chymotrypsin
4. Indicate where each enzymes would cleave the short peptide ala-ser-met-val-phe-gly-cys-lys-asp-leu.
a. trypsin
b. carboxypeptidase
5. If the methyl carbon atom of acetyl-CoA is labeled, where does the label appear after the acetyl-CoA goes through one round of
the citric acid cycle?
6. If the carbonyl carbon atom of acetyl-CoA is labeled, where does the label appear after the acetyl-CoA goes through one round
of the citric acid cycle?
7. The average adult consumes about 65 g of fructose daily (either as the free sugar or from the breakdown of sucrose). In the
liver, fructose is first phosphorylated to fructose 1-phosphate, which is then split into dihydroxyacetone phosphate and
glyceraldehyde. Glyceraldehyde is then phosphorylated to glyceraldehyde 3-phosphate, with ATP as the phosphate group donor.
Write the equations (using structural formulas) for these three steps. Indicate the type of enzyme that catalyzes each step.
8. What critical role is played by both BPG and PEP in glycolysis?
9. How is the NADH produced in glycolysis reoxidized when oxygen supplies are abundant?
10. When a triglyceride is hydrolyzed to form three fatty acids and glycerol, the glycerol can be converted to glycerol 3-phosphate
and then oxidized to form dihydroxyacetone phosphate, an intermediate of glycolysis. (In this reaction, NAD+ is reduced to
NADH.) If you assume that there is sufficient oxygen to completely oxidize the pyruvate formed from dihydroxyacetone
phosphate, what is the maximum amount of ATP formed from the complete oxidation of 1 mol of glycerol?
11. How is the FADH2 from β-oxidation converted back to FAD?
12. If 1 mol of alanine is converted to pyruvate in a muscle cell (through transamination) and the pyruvate is then metabolized via
the citric acid cycle, the electron transport chain, and oxidative phosphorylation, how many moles of ATP are produced?
13. If the essential amino acid leucine (2-amino-4-methylpentanoic acid) is lacking in the diet, an α-keto acid can substitute for it.
Give the structure of the α-keto acid and the probable reaction used to form leucine from this α-keto acid.
Answers
1. The hydrolysis of arginine phosphate releases more energy than is needed for the synthesis of ATP, while hydrolysis of glucose
6-phosphate does not.
3.
a. The enzyme will cleave off amino acids one at a time beginning with alanine (the N-terminal end).
b. following phenylalanine
5. Half of the label will be on the second carbon atom of oxaloacetate, while the other half will be on the third carbon atom.
7.
9. When oxygen is abundant, NADH is reoxidized through the reactions of the electron transport chain.
11. FADH2 is reoxidized back to FAD via the electron transport chain.
13.
6.10: Energy Metabolism (Exercises) is shared under a CC BY-NC-SA 4.0 license and was authored, remixed, and/or curated by LibreTexts.
20.1: ATP- the Universal Energy Currency by Anonymous is licensed CC BY-NC-SA 4.0. Original source:
20.3: Overview of Stage II of Catabolism by Darik Benson is licensed CC BY-NC-SA 4.0. Original source:
20.4: Stage III of Catabolism by Anonymous is licensed CC BY-NC-SA 4.0. Original source:
20.6: Stage II of Lipid Catabolism by Anonymous is licensed CC BY-NC-SA 4.0. Original source:
20.7: Stage II of Protein Catabolism by Anonymous is licensed CC BY-NC-SA 4.0. Original source:
CHAPTER OVERVIEW
7: Chemical Messengers: Hormones, Neurotransmitters, and Drugs

An GOB Chemistry Textmap organized around the textbook
Fundamentals of General Organic & Biological

Chemistry
by John McMurry, Virginia Peterson, and Carl Hoegar
Topic hierarchy
Thumbnail: A ball-and-stick model of testosterone. Testosterone is the primary male sex hormone and an anabolic steroid. Image
used with perspective (Public Domain; Ben Mills).
7: Chemical Messengers: Hormones, Neurotransmitters, and Drugs is shared under a CC BY-NC-SA 4.0 license and was authored, remixed,
and/or curated by LibreTexts.
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Index
B F P
bile fats Poisons
3.5: Steroids 3.3: Fats and Oils 4.9: Enzyme Inhibition
fatty acids purine
C 3.2: Fatty Acids 5.2: Nucleotides
chirality pyrimidine
1.18: Chirality and Stereoisomers I 5.2: Nucleotides
cholesterol insulin
3.5: Steroids 4.1: Prelude to Amino Acids, Proteins, and Enzymes R
Renaturation
D M 4.5: Proteins
Denaturation membrane lipids
4.5: Proteins 3.4: Membranes and Membrane Lipids S
Diisopropyl fluorophosphate (DIFP) Membranes stereoisomers
4.9: Enzyme Inhibition 3.4: Membranes and Membrane Lipids 1.18: Chirality and Stereoisomers
Steroids
E N 3.5: Steroids
Energy Metabolism nucleotide
6: Energy Metabolism 5.2: Nucleotides T
Enzyme Classification Number Triglyceride
4.6: Enzymes O 3.3: Fats and Oils
Enzyme Inhibition oils
4.9: Enzyme Inhibition 3.3: Fats and Oils W
Enzymes Waxes
4.6: Enzymes 3.2: Fatty Acids
Glossary
Sample Word 1 | Sample Definition 1
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CHEM 121: CONCEPTS

1: Organic Chemistry Basics

7: Chemical Messengers: Hormones, Neurotransmitters, and Drugs

1: Organic Chemistry Basics

AgOC N + N H4 C l → AgC l + N H4 OC N (1.1.1)

low melting points −95°C high melting points 801°C

low boiling points 69°C high boiling points 1,413°C

low solubility in water; greater solubility in water;

flammable highly flammable nonflammable nonflammable

aqueous solutions do not aqueous solutions conduct conductive in aqueous

Figure 1.2.1 : The Three Simplest Alkanes

Figure 1.2.2 : The Tetrahedral Methane Molecule

methane CH4 CH4 —

ethane C2H6 CH3CH3 —

propane C3H8 CH3CH2CH3 —

butane C4H10 CH3CH2CH2CH3 2

pentane C5H12 CH3CH2CH2CH2CH3 3

hexane C6H14 CH3CH2CH2CH2CH2CH3 5

heptane C7H16 CH3CH2CH2CH2CH2CH2CH3 9

methane methyl CH3–

ethane ethyl CH3CH2–

propane propyl CH3CH2CH2–

butane butyl* CH3CH2CH2CH2–

methane CH4 –182 –164 0.668 g/L gas

ethane C2H6 –183 –89 1.265 g/L gas

propane C3H8 –190 –42 1.867 g/L gas

butane C4H10 –138 –1 2.493 g/L gas

pentane C5H12 –130 36 0.626 g/mL liquid

hexane C6H14 –95 69 0.659 g/mL liquid

octane C8H18 –57 125 0.703 g/mL liquid

decane C10H22 –30 174 0.730 g mL liquid

Looking Closer: Gas Densities and Fire Hazards

Looking Closer: An Alkane Basis for Properties of Other Compounds

Concept Review Exercises

Concept Review Exercises

3. What is the most important reaction of alkanes?

To Your Health: Cyclopropane as an Anesthetic

Concept Review Exercises

ethene C2H4 CH2=CH2 –169 –104

propene C3H6 CH2=CHCH3 –185 –47

1-butene C4H8 CH2=CHCH2CH3 –185 –6

1-pentene C5H10 CH2=CH(CH2)2CH3 –138 30

1-hexene C6H12 CH2=CH(CH2)3CH3 –140 63

1-heptene C7H14 CH2=CH(CH2)4CH3 –119 94

1-octene C8H16 CH2=CH(CH2)5CH3 –102 121

Concept Review Exercises

Concept Review Exercises

Looking Closer: Environmental Note

The bright red color of tomatoes is due to lycopene—a polyene.

Concept Review Exercises

Concept Review Exercises

Concept Review Exercises

starting material for the synthesis of dyes,

Figure 1.16.2: The Three Isomeric Dichlorobenzenes

Polycyclic Aromatic Hydrocarbons

To Your Health: Polycyclic Aromatic Hydrocarbons and Cancer

Biologically Important Compounds with Benzene Rings

Table 1.16.2 : Some Drugs That Contain a Benzene Ring

Concept Review Exercises