Biological Chemistry

The universe is composed of energy and matter.

Life, the Universe, and Everything

At the beginning of the universe, energy was converted 2 into matter. Big Bang! Only in rare circumstances, like inside stars and atomic blasts, matter is converted back into energy.

m E=

Energy is often converted from one form into another:

(e.g., light energy into chemical energy; chemical enegy into kinetic energy; kinetic energy into heat energy; etc.)

but it is neither created nor destroyed. But matter, with rare exceptions, stays the same type of matter.

Matter is in the form of chemicals.

Chemicals are constructed from atoms. Different types of matter, i.e., different elements, have different atoms.

Atomic Structure
Neutrons and protons form the nucleus Atomic Mass (Atomic Weight) = number of protons and neutrons combined Electrons orbit around the nucleus
[p+] [n] [e-]

The Atom
A single unit of matter Composed of three types of subatomic particles
Neutrons (no): mass = 1 atomic mass unit no electrical charge (neutral) Protons (p+): mass = 1 atomic mass unit positive electrical charge (+1) Electrons (e): mass is trivial negative electrical charge (1)

Atomic Number
A chemical reaction is the interaction of electrons from different atoms. The number, distribution and activity of electrons around an atoms nucleus is determined by the number of protons in that nucleus. .. The chemical identity (type of element) for any atom is determined by the number of protons in its nucleus! # of p+ = the Atomic Number for that atom.

Partial Periodic Table

atomic number

E.g.: Any atom that has 6 p + in its nucleus (atomic number = 6) is defined as carbon, no matter how many e - or n it has!

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96% of body mass is composed of four different elements

Table 2.1

Isotopes

Oxygen (65%) Carbon (18%) Hydrogen (10%) Nitrogen (3%)

Atoms of the same element (i.e., same atomic number) but with differing numbers of neutrons, have the same chemical identity but different atomic weights. These variations of an element are called isotopes. Some isotopes are unstable and emit radioactive energy. Such isotopes are radioisotopes.

Remember: 65-75% of

total body weight is H20

Electron shell
Electrons have different levels of energy Each energy level is called an electron shell Outer shell called valence shell Only valence shell electrons participate in chemical reactions

Ions

If # p+ = # e: neutral atom If # p+ # e: charged atom = ion If the valence shell loses an electron = positive ion (cation). If the valence shell gains an electron = negative ion (anion).

Ions & Isotopes

Chemical reactions occur when bonds between atoms are formed or rearranged
+

2 H2

+ Reactants

O2 Reaction

2 H2O Products

Molecule: two or more atoms bonded together

Compound: molecule constructed of more than one kind of atom. E.g.: H2 and O2 and H2O are all molecules. But H2 and O2 are elemental molecules. And H2O is a compound molecule.

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Molecules can be represented in many ways

Name (molecular formula)
(a)

Living cells carry out millions of chemical reactions that rearrange matter in significant ways
Biological molecules have many atoms bound precisely in complex forms. How does the right rearrangement of the right bond at the right time happen?

Electronshell diagram
H H

Structural formula

Spacefilling model

Ball-and-stick model

Hybrid-orbital model (with ball-and-stick model superimposed)

Hydrogen (H 2 ).
Two hydrogen atoms can form a single bond.

(b)

Oxygen (O 2).

Two oxygen atoms share two pairs of electrons to form a double bond. (c)

Unbonded Electron pair

O

Water (H 2O).

Two hydrogen atoms and one oxygen atom are joined by covalent bonds to produce a molecule of water. (d)

O H

O H

O H H H

104.5

Methane (CH 4 ).
Four hydrogen atoms can satisfy the valence of one carbon atom, forming methane. H

H C H H

H C H H

H H C H H H

H C H H
Beta-carotene Vitamin A (2 molecules)

Tables 2.11 & 2.16

Covalent Bonds Types of Chemical Bonds

Covalent Bonds Ionic Bonds Hydrogen Bonds

Atoms share electrons to fill valence shell Electrons are shared in pairs Each pair forms one bond

Example: Water (H2O)

Oxygen: 6 valence e
Needs 2 e to fill shell Gets 1 e from each hydrogen atom

Two atoms can share more than one pair of electrons

Hydrogen: 1 valence e
Each needs 1 e to fill shell Each gets 1 e from oxygen

Double bonds: H O=O C=C H Triple bonds: NN

Covalent bonds

C
H

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Ionic Bonds
Based on electromagnetic attraction between ions of opposite charge Ions: charged atoms
Loss of e: positive charge on atom Gain of e: negative charge on atom

Ionic bond between Na+ and Cl form NaCl, table salt

Regular stacking of atoms cause salts to form crystals in absence of water

Salts: two ions of opposite charge bonded together

Ions separate in presence of water

Dissociation: breaking of ionic bond Dissolve: surrounding a molecule like NaCl with H2O Why? Because water is a polar molecule.

Water is a polar molecule

Nucleus of oxygen bigger than hydrogen Bigger nucleus attracts e better Distribution of electrons is uneven around molecule

Water is a versatile solvent Dissociated ions in water

Negative Oxygen regions of polar water molecules are attracted to sodium cations (Na+). Positive hydrogen regions of water molecules cling to chloride anions (Cl).

Na +

+ +

Cl

+ Cl

Na +

Salt ions dissolving in water

Glucose dissolved in water

Na+ surrounded by Cl surrounded by oxygen side of H2O hydrogen side of H2O

Solutes whose charges or polarity allow them to stick to water molecules dissolve in water
they form aqueous solutions

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Aqueous Solutions
Polar or ionic molecule dissolved in water forms a solution Solution: solutes dissolved by a solvent Solvent = water Solutes = dissolved substance
A protein solution = protein dissolved in water

Water: the universal solvent

Many substances dissolve in water Examples of water soluble substances:
Salts (ions, or electrolytes) Sugars and other nutrients Vitamins Hormones

Hydrogen bonds form between partial () charges

Both intermolecular and intramolecular
H of amino & alcohol side groups are + =O of carbonyl groups are Individual H-bond is very weak, but many combine to stabilize 3-D structure of biological macromolecules Important for protein shape, DNA, etc.

Many of waters unique properties relate to

hydrogen bonds formed among these small polar molecules

Solvent power (water to solute) Cohesion (water to solid)
Wetting & capillary attraction

Adhesion (water to water)

Surface tension & column tension High heat capacity & heat of vaporization Liquid density > solid density
Hydrogen bonds

Dissociation of Water
1 out of 500,000,000 water molecules ionizes:

Acids & Bases

So, in a neutral solution, [H+] = [OH]; pH = 7.00 An Acid is a compound that adds extra H+ to the solution. I.e., H+ donor Thus, an acidic solution has [H+] > [OH]

H2O Hydrogen+ OH H+ Hydroxide

ion ( = 1 p+ ) ion

= 6x1016 per liter of water = 107 moles per liter

Hence, neutral water contains:

107M H+ + 107M OH

pH < 7 (0.006.99) A Base is a compound that removes H+ from the

solution. I.e., H+ acceptor Thus, an basic (alkaline) solution has [H+] < [OH]

And [H+] = [OH] pH = log [H+] = log (107M ) = 7

pH > 7 (7.0114.00)

pH = acidity

&

pH = acidity

(Note: normal blood pH is 7.357.45 slightly basic!)

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Effects of pH on Bioactivity
Relative amount of H+ in solution (i.e., the pH) can alter the charge and polarity of other solutes. ionic or hydrogen bonds folding & 3-dimensional shape of large organic solutes (esp. proteins) 3-dimensional shape biological activity of those organic molecules.
even small pH can have major impacts on

Buffers
System of molecules and ions that act to prevent changes in [H+]. Stabilizes pH of a solution. Blood bicarbonate buffer system: H20 + C02 H2C03 H+ + HC03
bicarbonate ion

Reaction can proceed in either direction depending upon the concentration of molecules and ions. Thus if H+: HC03- + H + H2C03 H20 + C02 H+

But if H+: H20 + C02 H 2C03 H+ + HC03 H + Thereby maintaining normal blood pH range of 7.35 7.45 Acidosis: blood pH < 7.35 (Note: not acidic!) Alkalosis: blood pH > 7.45

biological activity.

Biological Molecules
Some molecules are special in biology H2O - small, slightly polar molecule universal solvent Organic molecules are based on carbon.

Carbon a unique element

H H C H lipid H methane

1. Each carbon atom forms four bonds. 2. Carbon atoms can bond to other carbons, thus constructing long and/or branched chains of carbon the carbon backbone of the molecule. 3. Carbon can form double bonds to modify the shape or flexibility of the chains. Thus only carbon can form the complex molecules needed for complex biological functions.

Organic Compounds
Have a carbon backbone a chain of more than one carbon.

Functional Groups of Organic Molecules

(R groups = reactive side groups)
Ketone: C=O on C within chain Aldehyde: C=O on terminal C of chain

Organic originally meant made by organisms.

(Most still are. But some are synthetically derived from those that are.)

Alcohol Carboxylic acid

C.f., Fig. 4.10

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Organic Macromolecules
Forms & Features
Large macromolecules are constructed from smaller subunits. Forms Carbohydrates Proteins Sugars and starch Amino acids and Proteins Features Energy source; Structural units Enzymes; Structural units; Energy source Genetic instructions; Cellular energy units Hydrophobic; Energy source

Dehydration synthesis (condensation reaction)

Nucleic Acids Lipids

Nucleotides, RNA, DNA Fats, oils, and steroids

Dehydration (removing water) synthesis: Forming polymers produces water as a byproduct.

Hydrolysis (digestion reaction)

Organic Macromolecules
Monomers & Polymers
Large macromolecules are constructed from smaller subunits. Subunit Carbohydrates Proteins Nucleic Acids Lipids Monosaccharide Amino acid Nucleotides Macromolecule Polysaccharides Polypeptide RNA, DNA

Fatty acids Triglyceride, wax, + glycerol phospholipid or other carbon backbone

Hydrolysis (water breaking) is opposite of dehydration synthesis. Breakdown of a polymer requires water

1. Carbohydrates
Used for: Energy, structure

Monosaccharides
single sugar
Molecular formula: n(CH2O) n = 37 C3 sugar: triose C5 sugar: pentose C6 sugar: hexose

Simple sugar structures

Monomer: Mono-saccharide one sugar Polymer: Poly-saccharide many sugars

hexose sugars

Bees with honey a mix of 2 monosaccharides

Glucose [a type of hexose] is main circulating energy source for animal cells Occurs in alternate linear or circular forms

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Disaccharides
double sugar
Cells link 2 single sugars to make 1 disaccharide

Polysaccharides

Glycogen is the main polysaccharide in animals, but plants make many varieties (dietary fiber). Glycogen, starch, and cellulose are all poly-glucose. But very different bioactivity (and digestibility) varies because of different chain branching.

2. Proteins, Essential to Life

proteios: primary
Important for the operation and regulation of all life processes!

2. Proteins, Essential to Life

Structural Transport
E.g., collagen & keratin E.g., hemoglobin E.g., muscle filaments & cytoskeletal elements E.g., insulin & growth hormone E.g., hormone and neural receptors E.g., membrane gates & pumps E.g., antibodies E.g., RNA-polymerase Regulate all biochemical reactions

Proteins run everything!

Movement

Communication messengers Communication receivers

Selective cellular permeability Defense

Enzymes

Bacterial flagellum

Proteomics and Emergent Systems

Proteomics: deducing the structure of all proteins from an organism. Emergent Systems Analysis: mapping all interactions Fig. 1.10 within the holistic living complex.
CELL

2. Proteins, Essential to Life

Monomer: Amino Acid
20 different amino acids used to make proteins

Polymer: Polypeptide
The precise sequence of amino acids in the polypeptide determines the function of the protein
Nucleus

Cytoplasm Outer membrane and cell surface

A systems map of known interactions among 3500 proteins in a fly cell

Hair made of keratin, a structural protein

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Proteins are made from Amino Acids

Amino acid structure

amino acid R-groups may be

small/simple
glycine

or

large/complex
tyrosine

Different R-groups define different amino acids

arginine alanine

All amino acids have an amino group, a carboxyl group, and an R group R groups define a specific amino acid

tryptophan

amino acid R-groups may be

polar
or

amino acid R-groups may be

cationic
arginine aspartate

nonpolar

or

anionic

tyrosine

phenylalanine

lysine asparagine leucine glutamate

histidine

serine

valine

Charge is dependent upon pH

Stereo Isomers (Enantiomers)

20 amino acids used in protein synthesis
Group I: nonpolar Group II: polar Group III: charged
Isomer (same unit): two molecules with the same molecular formula, but arranged differently. CO 2H CO 2H Enantiomers: Non-superimposable mirror image molecules. Right-handed [Dextro-] & Left-handed [Levo-] versions of the molecule.
C
CH 3

Alanine (A) Isoleucine (I) Leucine (U) Methionine (M) Phenylalanine (F) Proline (P) Tryptophan (W) Valine (V)

Asparagine (N) Cysteine (C) Glutamine (Q) Glycine (G) Serine (S) Threonine (T) Tyrosine (Y)

Arginine (R) Aspartic Acid (D) Glutamic Acid (E) Histidine (H) Lysine (K)

NH 2 NH 2

C
CH 3

L isomer

D isomer

L-Dopa

D-Dopa

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Stereo Isomers (Enantiomers)

One of the great mysteries of the origin of living cells All non-biological synthesis reactions of organic molecules produce both D- and L- isomers in equal yield. And all non-biological reactions using organic molecules as reactants react with both D- and L- isomers equally. Yet, living cells are constructed only of D-sugars and their derivatives, and only L-amino acids and their derivatives!

Peptide Bonds Link Amino Acids

Peptide bond formation

L-Dopa

D-Dopa

Amino acids linked by dehydration synthesis peptide bond Polymer of amino acids = polypeptide Different polypeptides have different amino acid sequences

(biologically active)

(biologically inactive)

Protein Shape Determines Function

Specific 3-D shape Shape is critical to function

3. Nucleic Acids Information & Energy Carrying Molecules

Used for:
Information (DNA, RNA) Cellular Energy (ATP)

Monomer:
Nucleotide

Polymer: Denaturation = loss of shape and function

Nucleic acid Ribbon model of lysozyme protein Human chromosomes

Nucleotides
5 possible types of Nitrogenous Base

1, 2, or 3 phosphates off #5 carbon of sugar

Nucleic Acids are linear polymers of Nucleotide monomers

2 possible types of C5 Sugar

Nucleotides to make RNA = Ribose sugar + A, G, C, or U base Nucleotides to make DNA = Deoxyribose sugar + A, G, C, or T base

Condensation reaction between phosphate on #5 carbon of the sugar in one nucleotide, and the hydroxyl on #3 carbon of the sugar in the other nucleotide Polymer forms sugar-phosphate-sugar-phosphate-sugar-phosphate- linear chain with nitrogenous bases to the side

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Nucleic Acids linear polymers

DNA is doublestranded
Two polymers held together by hydrogen-bonding between bases Condensation of sugars and phosphates form polymer backbone

complementary base pairing

Complementary base pairing in DNA

Bases form side groups not involved in formation of polymer

C pairs only with G A pairs only with T

complementary base pairing

H N N H O CH 3 N Sugar N O Adenine (A) N N Sugar Thymine (T) H N O H N

dsDNA Structure
\ the sequence of
bases in the two strands are complimentary to each other (not identical).

Each pair = 1 purine + 1 pyrimidine

A=T (2 H-bonds) GC (3 H-bonds)

N Sugar N

N N

N Figure 16.8 H Guanine (G)

Sugar

Cytosine (C)

DNAs complementary base sequence

4. Lipids Include Fats and Cholesterol

Used for:
Energy storage, insulation, steroids, vitamins

Fatty Acids
Long C 816 hydrocarbon tail = non-polar = hydrophobic = fatty Carboxyl head = acid

Fatty Acid

Subunit:
fatty acids Saturated: all C-C single bonds
Two hydrogens on each carbon

Macromolecule:
(not a polymer subunits attached to a different carbon backbone) triglycerides & phospholipids sphyngolipids waxes

Unsaturated: chain contains double bonds

Causes rigid kinks in chain

Cholesterol, a modified fatty acid

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Triglycerides
Tri = three; glyceride = on glycerol
Formed by dehydration synthesis of fatty acid side-chains linked onto glycerol
One fatty acid on the glycerol = monoglyceride = acyl-glycerol Two fatty acids on the glycerol = diglyceride = diacyl-glycerol [DAG] Three fatty acids on the glycerol = triglyceride = triacyl-glycerol [TAG]

Saturated fat forms solids at room temp

(animal fat)

Storage form of lipids

Animal fat is a mixture of triglycerides with >50% of fatty acids saturated.

Unsaturated fats are liquid at room temp

(vegetable oil)

Phospholipids
Used to make cell membranes
Plasma membrane Cell membranes

Phosphate:
Hydrophilic head

2 Fatty acid chains:

Hydrophobic tail

Plant oil is a mixture of triglycerides with <15% of fatty acids saturated.

Hydrophilic heads

Isolated activity compartments

Phospholipid Bilayer
Hydrophobic tails

Hydrophilic heads associate together

Form outer layer of cell membrane

Hydrophobic tailsassociate together

Form inner layer of cell membrane Keep water soluble molecules from crossing membrane

Form double layer of cell membranes

Cell membrane Organelle membranes

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