Study Unit 8: Molecules of Life

Dr. Rebamang Mosa

Department of Biochemistry, Genetics and Microbiology
Agricultural Science Building, Office Number: 3-5
1
E-mail: [email protected]
 Lecture 1: Learning Outcomes (LO)

1. Understand that the common atoms/elements found in living systems only

support life when they are held together by chemical bonds.
2. Distinguish between polar and non-polar covalent bonds.
3. Distinguish between hydrophilic (polar) and hydrophobic (nonpolar)
substances. Explain how these substances interact with water.

2
 Chemical elements
H

Figure 2.3 Periodic table of the elements.

3
LO 1
Chemical scaffolding

Macromolecules
(Functional
biomolecules)

Atoms Molecules 4
LO 1
Atoms are held together in molecules or compounds by
chemical bonds

**
Note: Covalent bonds can exist as single, double or triple bonds

5
LO 1
Nature of chemical bonds: Covalent bond

• Forms when 2 atoms share one or more pairs of valence electrons

(e-)- results in no net charge, satisfies octet rule, no unpaired
electrons (e-)

6
LO 2
Polar and non-polar covalent bonds

• Depending on e- affinity (electronegativity) of atoms, sharing of

valence e- in a covalent bond can either be equal or unequal
• For covalent bonds formed between:
– atoms of equal electronegativity- e- are shared equally
– atoms of far different electronegativity- e- are not equally
shared (are closer to the atom with greater electronegativity)

Electronegativity increases

7
LO 2
Polar and non-polar covalent bonds
The unequal distribution of the e- results in:
▪ regions of partial –ve charge (δ-) near the more electronegative atom
▪ regions of partial +ve charge (δ+) near the less electronegative atom

Covalent bond formed between

− atoms that differ greatly in electronegativity is polar
− identical atoms or atoms of equal electronegativity is non-polar
Non-polar covalent bond

Polar covalent bond

LO 2
Polar covalent bonds

Different electronegativities between atoms cause polarity.

• In a molecule of water,
− the electrons will be closer to the
oxygen most of the time because
the electronegativity of oxygen is
greater than that of hydrogen.
− oxygen has a slight negative
charge (δ-) while the two
hydrogen atoms have a slight
positive charge (δ+) because of
the electronegativity of oxygen.
LO 1
Nature of chemical bonds: Ionic bond

Ionic bond results from the transfer of electrons from a less

electronegative atom to a highly electronegative atom.

• The electron transfer produces oppositely charged atoms (ions).

• The interaction between the two atoms occurs because opposite
charges attract one another.

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LO 1&3
Why do salts dissolve in water?

• Ionic bonds form crystals

In water, the partial positive charge on the hydrogen ions associates with the
negative charge on the chloride ions (Cl-), and the partial negative charge on the
oxygen ions associates with the positive charge on the sodium ions (Na+).
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LO 2&3
Interaction of water with other molecules: polarity

Water molecule (H2O)

• Has two single polar covalent bonds between H and O atoms
• Carries 2 partial –ve charges (δ-) near O and 2 partial +ve
charges (δ+) on each H atom – Polar molecule

Polar molecules tend to easily interact

with other polar molecules, whereas
nonpolar molecules tend not to interact
with polar molecules.
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LO 3
Hydrophilic and hydrophobic compounds

Depending on their interaction with water, compounds can be

classified as hydrophilic and hydrophobic.

• Hydrophilic compounds are polar:

− are “water loving”, thus readily dissolve in water

• Hydrophobic compounds are nonpolar:

− are “water fearing”, thus do not interact well with water
− they arrange themselves in such a way as to minimize
their contact with water. eg oil in water

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 Practice questions
Indicate the correct answers with TRUE or FALSE; if false explain why.
a) A covalent bond is likely polar when:
i. Oxygen is one of the two atoms sharing electrons.
ii. The two atoms sharing electrons are equally electron negative.
iii. One of the atoms sharing electrons is much more electron negative
than the other atom.
iv. The electrons are shared between two different atoms.

a) Noncovalent molecular interactions are important to life because:

i. They are weak in a cellular environment, so they can be made, broken,
and reformed easily
ii. They are strong in a cellular environment that holds atoms together
tightly.
iii. They can only occur in cells.

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 Lecture 2: Learning Outcomes

4. Explain the relevance of water’s unusual properties for living systems and
illustrate how hydrogen bonding affects the properties of water.
5. Distinguish, based on chemical properties, between acids and bases.
6. Calculate the pH of a solution given its hydrogen ion concentration.
Convert the hydrogen ion concentration (M) of a solution to a pH value,
and vice versa

15
LO 4
Polarity and Hydrogen bonding

The structure and polarity of H2O molecule allows H2O molecules to

be attracted to one another (intermolecular attractions) by weak
attractions- hydrogen bonds

16
LO 4
Nature of chemical bonds: H-bond

Hydrogen bond (H-bond):

• weak attraction between one
electronegative atom, usually O or
N, and a H atom that is covalently
bonded to another
electronegative atom.

• Most important non-covalent,

weak bond in the chemistry of life

17
LO 4
H-bonds give water many unusual properties

Liquid water and ice. H-bonds create (a) a dense structure in

water and (b) a highly ordered, less dense, crystalline
structure in ice.

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LO 4
Unusual Properties of water

Property Chemical explanation Benefit to life

Excellent solvent Polar H2O molecules interact well Medium for biochemical
with ions and polar compounds reactions
Molecules are cohesive H2O molecules are held together Allows H2O to move from the
by H-bonds roots to the leaves
High specific heat It requires energy (heat) to break H2O minimizes large temp.
capacity H-bonds in H2O, and heat is changes in organisms and the
released when the bonds break environment
High heat of vaporization Many H-bonds must be broken for H2O evaporation cools body
H2O to evaporate surfaces
Less dense at solid state H2O expands on freezing- H-bonds Allows aquatic organisms to
(low density of ice) hold molecules relatively far from survive in freezing temp.
each other in the ice crystal (winter)

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Temp. - temperature
LO 4&5
Ionization of Water

• Water is not inert in its service as a solvent for biochemical

reactions
• Water is a weak electrolyte that spontaneously dissociates
(only slightly) to form hydrogen (H+) and hydroxide (OH-)
ions- Ionization

H2O OH- + H+
water Hydroxide Hydrogen
ion ion (proton)
H2O
H2O OH- + H+ OH- + H3O+ 20

Hydronium ion
NOTE: H+ is used to represent H3O+
LO 5 Acids and Bases

Dissociation of H2O produces equal amounts of H+ and OH-

• [H+] and [OH-] in a solution is described by terms acidity and

basicity, respectively
• Pure water with [H+] = [OH-] = 1 X 10-7 M- neutral

• An acid- substance that donates a proton (H+) and thus

increases the [H+] of a solution

• A base is a substance that accepts a proton (or donates

a hydroxide ion, OH-) and therefore reduces the [H+] of
a solution

General: Acid + water Proton + Base

HA + H2O H+ + A- (Source: Reece et al. 9th Ed) 21

LO 5&6
Acids and Bases: pH

✓ pH measures the acidity or

basicity of a solution
- a measure of [H+] in a
solution

✓ pH scale is logarithmic, ranges

from 0 to 14
- a difference of 1 unit on the
scale = 10-fold change in [H+],

e.g Difference between:

pH 4 and 5 = 101
pH 4 and 6 = 102
pH 4 and 1 = 103
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LO 5&6
Acids and Base: pH

• pH is expressed as a negative logarithm (log) of [H+] in a solution

pH = -log [H+] pH = -log [H+]

Similarly, [OH-] can be expressed as pOH;

pOH = -log [OH-]

Since
H2O → H+ + OH-,

Kw= [H+][OH-]
= (1 X 10-7)(1 X 10-7) pH + pOH = 14
= 1 x 10-14, Kw- ionic product of H2O
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LO 6
Calculations of [H+] and pH: Examples

In pure water; [H+] = [OH-] = 1 X 10-7 M

pH = -log [H+]
= -log (1 X 10-7) = 7 (neutral pH)
a) Assume the [H+] of a solution is 1 x 10-5 M. Calculate the
pH of the solution
pH = -log [H+]
= -log [H+]
= -log (1 x 10-5) = 5

b) Calculate [H+] in a solution of pH 5;

pH = -log [H+]
[H+] = 10-pH or (antilog of -pH)
= 10-5 = 1 x 10-5 M
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 Practice questions
Answer the following statements with TRUE or FALSE; if false explain why.
a) H-bonding between H2O molecules affects the specific heat capacity and
heat of vaporization of water in such a way that:
i. The specific heat capacity and heat of vaporization of water are low.
ii. The specific heat capacity and heat of vaporization of water are high.
iii. The specific heat capacity of water is high but its heat of vaporization is
low.
iv. The heat of vaporization of water is high but its specific heat capacity is
low.

b) If solution X has a pH of 4, and solution Y has a pH of 7, it can be concluded

that:
i. Solution Y has no free hydrogen ions (H+)
ii. The [H+] in solution Y is 1,000 times greater than the [H+] in solution X.
iii. The [H+] in solution X is 3 times greater than the [H+] in solution Y.
iv. The [H+] in solution X is 1,000 times greater than the [H+] in solution Y.
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 Lecture 3: Learning Outcomes

7. Describe the features of carbon that allow it to form diverse structures-

organic vs inorganic compounds.
8. Describe and identify structural isomers.
9. Describe the biological functions of the four essential macromolecules
(polysaccharides, nucleic acids, proteins, and lipids).
10.Understand how macromolecules are formed through the condensation of
monomers into polymers (dehydration reaction), and broken down
through hydrolysis of polymers into monomers (hydrolysis reaction).
11.Identify the major functional groups found in biomolecules and describe
their properties.

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LO 7
Carbon: Life’s Chemical Backbone

• The four major elements that

make up the human body are:
• carbon
• oxygen
• hydrogen
• nitrogen
• Molecules containing carbon
and hydrogen are called
organic molecules.

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LO 7
Carbon: organic vs inorganic compounds

• Since C has 4 valence electrons, it can form 4

covalent bonds with a variety of atoms.
- C is found in various kinds of compounds e.g.
organic compounds

• Organic compounds contain C and

H (C-H) and many also contain O,
N, S or P – (CHON)

R- can be C (-C-C-), H, O, N, S, P

• Inorganic substances- any other compounds that do not contain

C-H 28
LO 8
Isomers
Isomers are molecules that have the same molecular formula but
different structures.

Isomers

**
Structural isomers Stereoisomers

Positional/Functional

vs
LO 8
Isomers: Structural

The isomers isoleucine and leucine.

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LO 9&10
Organic macromolecules (Biomolecules)

• Chemical processes in the cell depend on just a few classes of

carbon-based molecules- biomolecules

Macromolecule General structure Building block Main function(s)

Carbohydrate Polysaccharide Monosaccharide • Provides structural support
• Source of energy

Nucleic acid Polynucleotide Nucleotide • Encode and transmit genetic

information

Protein Polypeptide Amino acid • Provide structural support

• Act as catalysts

Lipid Diverse structures Diverse • Store energy

molecules • Make up cell membranes
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Note: Polymers are synthesized by dehydration reaction and broken down by hydrolysis reaction
LO 11

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 Practice questions
Indicate the correct answer with TRUE or FALSE; if false explain why.
a) The five most abundant elements found in living organisms are:
i. Carbon, hydrogen, oxygen, nitrogen, iron
ii. Sodium, carbon, oxygen, nitrogen, phosphorus
iii. Magnesium, carbon, hydrogen, oxygen, nitrogen
iv. Carbon, hydrogen, oxygen, nitrogen, phosphorus

b) Which of the following is a polymer?

i. Starch
ii. Triacylglycerol
iii. Protein
iv. Ribonucleic acid
v. Cholesterol

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 Lecture 4: Learning Outcomes

12. Describe the basic structure of amino acids

13. Recognize that each amino acid has at least two ionizable chemical
groups.
14. Classify the 20 amino acids of proteins as hydrophobic (non-polar) and
hydrophilic (polar).
15. Understand how proteins are formed through the condensation of
monomers into polymers (dehydration reaction), and broken down
through hydrolysis of polymers into monomers (hydrolysis reaction).
16. Understand how amino acid monomers are linked by peptide bonds, to
form a polypeptide (Protein)

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LO 12
Proteins- polymers of amino acid subunits

General structure of an amino acid: A central carbon atom (α carbon)

is covalently linked to four groups:
− Carboxyl (-COOH)

− Amino (-NH2)

− Hydrogen (-H)

− R group (side chain)

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The R group distinguishes one amino acid from another
LO 13
Ionization of amino acids: acid-base behavior

• Each amino acid has at least two

ionizable chemical groups- that of
α-COOH and α-NH2 groups.
• R-group can also carry a charge if
the amino acid is basic (has R–
NH2) or acidic (has R–COOH).

At pH 7 amino acids are

predominantly dipolar ions 36
 LO 12-14

37
There are 20 naturally occurring amino acids in proteins.
LO 14 Hydrophobic Amino Acids

Hydrophobic R groups of amino acids tend to aggregate in the center

of proteins away from the aqueous environment found inside and
outside of cells.
LO 14 Hydrophilic Amino Acids

• Acidic and basic amino acids are strongly polar and hydrophilic.
• Polar R groups can interact with each other and with water
molecules via hydrogen bonding.
• Hydrophilic amino acids are typically found on the “outer” surface
of proteins.
 Special Amino Acids

• Glycine is a small and nonpolar amino

acid that provides flexibility to a
protein.
• Proline’s cyclic R group restricts protein
folding and often results in sharp bends
in the protein structure.
• Cysteine can form disulfide bridges
within the same protein or between
two proteins.
LO 15&16
Reaction of amino acids: Peptide bond formation

• Two amino acids are linked by a covalent bond called a peptide

bond

• A peptide bond forms when the carboxyl end of one amino reacts
41
with the amino end of another amino acid (dehydration reaction).
LO 15&16
Reaction of amino acids: Peptide bond formation
• When amino acids are linked in a chain, they form a protein
(polypeptide).

42
 Practice questions
Indicate the correct answer with TRUE or FALSE; if false explain why.
a) Based on the chemical properties of amino acid side chains (R-groups), it is
concluded that:
i. R-groups of serine, aspartate and histidine are basic.
ii. R-groups of serine, aspartate and histidine are ionizable at pH 7.0.
iii. R-groups of serine, aspartate and histidine are hydrophilic.

b) How many water molecules would be required for a complete hydrolysis of

a pentapeptide into its monomers?
i. 1
ii. 2
iii. 3
iv. 4
v. 5

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 Lecture 5: Learning Outcomes

17.Distinguish between the 4 levels of protein structure. Distinguish by the

different shapes and chemical bonds that stabilize each structural level.
18.Explain the phenomenon of protein denaturation, and state why it causes a
loss of normal function of a protein.

44
LO 17 The 4 Levels of Protein Structure

The sequence of amino acids and the interactions among the R groups
govern protein folding and ultimately the shape of the final protein
45
product.
LO 17
Primary structure of a protein
Primary structure: sequence of amino acids in a peptide chain
• The sequence of amino acids determines a protein’s 3-D structure

Ala–Met–Leu–Glu

Protein = polypeptide containing 50 or more amino acid residues

✓ Peptides: contain less than 50 amino acid residues 46
LO 17 Secondary structure of a protein

Secondary structure: the folding of the

polypeptide chain into a repeating
pattern
• Includes the -helix and the -
pleated sheets
• It is stabilized by H-bonding between
-NH & -C=O of nearby peptide bonds

47
LO 17 Tertiary structure of a protein

• The final folded shape of the protein (3-dimensional structure).

• The tertiary structure results in the functional form of the protein
• The final folded form (native form) is stabilized by various forces
of attraction (van der Waals, ionic, H-bond etc.) between R-
groups of amino acid residues- note the formation of S-S
between 2 Cys residues (Stabilizes the 3-D structure)
48
LO 17 Protein structure: tertiary

• A protein’s structure determines its

function.
• The primary structure governs the
secondary and tertiary structure of a
protein.
• The shape of the functional protein
results in pockets that may be active
sites for enzymes, and R groups on the
exterior may affect how a protein
interacts with other molecules or
proteins in or out of the cell.

49
LO 17 Quaternary structure of a protein

The subunits of the quaternary structure can be identical or different.

• Results from the association of two or more polypeptide chains
(subunits)
• Subunits held together by non-covalent interactions
• The combination of subunits influences the function of the protein.
50
LO 18 Protein Denaturation

• Change or loss of the 3-D structure of a protein molecule without

hydrolysis of peptide bond - denaturation

• Denaturation can be caused by:

− pH
− Temperature
− organic solvents
• A denatured protein loses biological
function (inactive)

Note: denaturing agents only affect the

secondary, tertiary and/or quaternary structures
of a protein
51
 Practice questions
Answer the following statements with TRUE or FALSE; if false explain why.
a) A mutation that alters a single amino acid within a protein can alter:
i. The primary level of protein structure
ii. The secondary level of protein structure
iii. The tertiary level of protein structure
iv. Only the secondary and tertiary levels of protein structure
v. Only the tertiary and quaternary levels of protein structure

b) Considering the different protein structures you can conclude that:

i. A disulfide bond formation in a protein requires that the two
participating cysteine residues are adjacent to each other in the
primary sequence of the protein.
ii. The information required for the correct protein folding is contained in
the specific sequence of amino acids along the polypeptide chain.
iii. The denaturation of proteins leads to irreversible loss of primary,
secondary and tertiary structure.
52
 Lecture 6: Learning Outcomes

19. Describe the basic structures of nucleotides and monosaccharides

20. Understand how nucleic acids and polysaccharides are formed through
the condensation of monomers into polymers (dehydration reaction),
and broken down through hydrolysis of polymers into monomers
(hydrolysis reaction).
21. Understand how nucleotide monomers are linked by phosphodiester
bonds, to form a polynucleotide (Nucleic acid).
22. Distinguish between aldoses and ketoses.
23. Understand how monosaccharide monomers are linked by glycosidic
bonds, to form a polysaccharide (Carbohydrate).
24. Know the different types of carbohydrates.

53
LO 19 Nucleic Acids- polymers of nucleotide subunits
Nucleic acids- informational macromolecules carrying genetic
information that directs all cellular functions
✓ classified into deoxyribonucleic acid (DNA) and ribonucleic acid
(RNA)

A five-carbon
sugar
Phosphate
group A base
containing
nitrogen

54
Structure of a nucleotide.
LO 19 Nucleotide Bases
This base is only This base is only
found in DNA. found in RNA.

Pyrimidine bases and purine bases. (a) Pyrimidines have a single-ring

structure and (b) purines have a double-ring structure 55
LO 19-21 Bonds Between Nucleotides

• The phosphodiester bond joins two

nucleotides together.
• The bond is formed between the
phosphate group of each nucleotide
and the 3′-OH of the last nucleotide.

56
LO 19-21 Bonds Between Nucleotides

The bases are complementary: A is always paired with T, and

G is always paired with C. Base pairing is stabilized by H-bonds
57
LO 19 Carbohydrates
• Carbohydrates- organic compounds containing C, H, and O in
the molar ratio 1:2:1
- have empirical formula: (CH2O)n , n = no. of C atoms
- important energy storage molecules

• Monosaccharides are the simplest of the carbohydrates

- contain as few as 3C atoms, but important for energy storage
are 6C atom containing, eg. glucose

• They can be linear but are more

commonly cyclic

58
LO 22 Carbohydrates: aldose and ketose
• Monosaccharides are classified into aldoses and ketoses
• Sugars containing an aldehyde group are aldose sugars, and those
containing a ketone group are ketose sugars.

(-C=O at C1)

(-C=O not at C1)

59
LO 23&24 Types of Carbohydrates

Monosaccharide

Disaccharide

Polysaccharide

60
LO 23&24 Other monosaccharides and disaccharides

61
LO 23&24 Complex carbohydrates: energy storage molecules
 Practice questions
Answer the following statements with TRUE or FALSE; if false explain why.
a) Cleavage of two unknown disaccharides is shown by infrared spectroscopy
to result in 4 individual monosaccharide molecules, 2 with ketone
functionality, and 2 with aldehyde functionality. Based on this data, it can
be concluded that the two unknown disaccharides are:

i. Lactose and maltose

ii. Lactose and sucrose
iii. Sucrose and sucrose
iv. Maltose and maltose

b) An aldose form of fructose is:

i. Sucrose
ii. Galactose
iii. Maltose
iv. Ribose
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v. Glucose
 Lecture 7: Learning Outcomes

25. Distinguish among the three types of lipids: triacylglycerols, steroids and
phospholipids
26. Describe the composition, characteristics, and biological functions of
each of the three types of lipids.
27. Understand that lipids are defined by property and NOT chemical
structure- a chemically diverse group
28. Describe the basic structure of fatty acids
29. Differentiate between saturated and unsaturated fatty acids. Explain how
these characteristics influence the liquid-solid state of lipids

64
LO 25-27 Lipids: chemically diverse group of organic
compounds
• Lipids are grouped together because they share the same
physical property—they are all hydrophobic.

• Some of the important functions of lipids:

1.major source of energy in living things
2.components of membranes (structural)

• Some biologically important lipids:

– Triacylglycerols (Triglycerides)
– Phospholipids
– Steroids

65
 LO 25-27 Triacylglycerol
Triacylglycerols are the most abundant lipids in nature (> 95% of
dietary fats)
− esters of glycerol with fatty acids (dehydration reaction)
• are uncharged (neutral)
Fatty acid chain

Glycerol

• Serve as main energy storage (have largest no. of C-H) 66

LO 28 Fatty acids: mono-carboxylic acids

• Fatty acid- hydrocarbon chain with a carboxyl group

• Most fatty acids

– have straight chains (14-20 C long)
– hydrocarbon chain could be saturated (C-H with no double
bond) or unsaturated (C=H with 1 or more double bonds)

Animal fats consist of more saturated fatty acids than unsaturated

Vegetable oils consist of more unsaturated fatty acids than saturated
67
LO 28&29 Fatty acids: saturated vs unsaturated

(Saturated)

68
LO 28-29 Fatty acids: Van der Waals Forces

• The hydrocarbon chains in fatty

acids have non-polar covalent
bonds.
• Electrons are still moving around
the atoms in the fatty acids, creating
short-lived regions with slight
negative charges. These are
attracted to slight positive regions in
another atom.
• The longer the hydrocarbon tail, the
greater the strength of van der
Waals forces.

69
LO 28-29 Fatty acids: Saturated vs unsaturated

Animal fats are saturated.

Without double bonds causing kinks
in the structure, animal fats can stack
closely together and are stabilized by
more van der Waals interactions
than unsaturated fats.
This also contributes to the quality of
animal fats, where they are solid at
room temperature.

70
LO 28-29 Some properties of fatty acids: summary

• Soluble in organic solvents but have poor solubility in water

• Melting point is determined by structure:

High melting point Low melting point

Saturated chain Unsaturated chain
Straight chain Branched chain
Long chain Short chain

71
LO 25-27 Steroids: cholesterol
Steroids are lipids characterized by a carbon skeleton consisting
of 4 fused rings- e.g. cholesterol

Cholesterol is the principal steroid in animals:

− has both polar and nonpolar regions
− maintaining membrane fluidity and permeability
− precursor for steroid hormones, e.g. estrogen, testosterone 72
LO 25-27 Steroids: phospholipids
Phospholipids (phosphoglycerides)- main lipids in the cell
membrane and nervous system.

• Usually contain fatty acids at C1

and C2, the OH on C3 is
esterified with phosphoric acid.
• Have both hydrophobic,
nonpolar regions and
hydrophilic, polar regions

73
 Practice questions
Answer these statements with TRUE or FALSE; if false explain why.
a) The membranes of two bacterial species have been compared. Species X
is found naturally in a much hotter environment than species Y. You
would expect that the membrane lipids of species X contain:

i. More saturated fatty acids than lipids from Y

ii. More unsaturated fatty acids than lipids from Y
iii. Longer fatty acids than lipids from Y
iv. Fatty acids very similar to those found in Y

b) The spontaneous formation of a lipid bilayer in aqueous environment

occurs because:
i. The polar head groups of the phospholipids can interact with water
ii. The long fatty acid tails of the phospholipids can interact with water
iii. The fatty acid tails of the phospholipids are hydrophobic

74