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Biochemical bonds, Free energy and

biochemical reactions
Outline
different forms of chemical bonds
concept of free energy
chemical reactions involve changes in free energy
ATP is the main source of energy in cells
Reading assignments:
Molecular Biology of the Gene (Watson, 6th ed)
chapter 3, chapter 4

Types of chemical bonds


A chemical bond is an attraction between atoms
brought about by a sharing of electrons or a
complete transfer of electrons between atoms.
in aqueous solutions:
strong bonds --- covalent bond
weak bonds ---

ionic bond
hydrogen bond
Van der Waals interaction
hydrophobic interaction

Covalent bond
Strong bonds, short, hold atoms close together.
Involves the sharing of an electron pair (or
multiple pairs) between two atoms.
The valence of an atom determines the number of
covalent bonds it can form.
H-H,
O=O,
N N

Covalent bonds can have electrical


polarity
Polar:

Non-polar:

Differences in electronegativity between two atoms


bonded together results in an electrical dipole or
polar bond, which is the unequal sharing of
electrons in a covalent bond.

Single covalent bonds allow rotation of


atoms around the bond

Double and triple bonds do not allow for freedom of


rotation.

The numbers and types of bonds


determine the geometry of molecules
Bond angles are
determined by the
number of atoms
bonded together
and seek to
minimize the
proximity of
different atoms
electrons to each
other.

Non-covalent bonds
Ionic bond: formed by electrostatic attraction between charged
groups (ions) and are the strongest of the non-covalent
interactions.
Hydrogen bond: formed between an electronegative atom (e.g.
nitrogen or oxygen) and a hydrogen atom that is covalently
attached to another atom.
Hydrophobic interaction: occurs between hydrophobic molecules
because they are repelled by water.
Van der Waals attraction: occurs between all molecules as a result
of permanent and transient dipoles (unequal distribution of
electrons). This is a very weak force.

Ionic bonds can dissociate in solution

NaCl

Na+ +

Cl-

Ionization state (charge) of the


carboxyl group can depend on pH

Acidic and basic groups may be protonated or


deprotonated depending on the pH of the solution, which is
a measure of the concentration of free H+.

At its pKa, the concentration of the two forms will be equal


and there will be no net charge.

Hydrogen bonds stabilize biological


molecules

Remember: there is one hydrogen


atom in a hydrogen bond.

Water Forms a Hydrogen Bonding Lattice

Van der Waals forces act between all


molecules

A non-specific
attractive force.

Based on random and


induced charge
fluctuations give rise
to transient dipoles
(difference in charge).

Hydrophobic interactions occur


between non-polar molecules

Multiple weak bonds stabilize


associations between macromolecules

Complementary molecular surfaces


ensure specific interactions
antibody-antigen
interaction

the lock and key


model

Making and breaking chemical bonds


involve changes in the form of energy
free energy (G) is the amount of energy available to
do work (e.g.: thermal energy).
Energy can interconvert between forms such as
thermal energy (kinetic) and bond energy (potential).

G can be used to determine the


direction of a chemical reaction
For chemical reaction: A + B

AB

G = Gproducts - Greactants
G is related to Keq: G = -RT ln Keq
A decrease in free energy (G<0) always occurs in
spontaneous reaction --- 2nd law of thermodynamics.
If G < 0, reaction proceeds toward products
If G = 0, reaction is at equilibrium
If G > 0, reaction proceeds toward reactants

Activation energy is required for the


initiation of a reaction

Enzymes lower activation energy

Coupling of negative with positive G


in a multi-step reaction

ATP (adenosine triphosphate) is the


main cellular energy source

ATP hydrolysis

1) ATP + H2O

ADP + Pi + energy

2) ATP + H2O

AMP + PPi + energy


H2O
Pi + Pi + energy

Roles of ATP in Cells


Hydrolysis of the phosphoanhydride bonds of ATP
(particularly as pyrophosphate) provides much of the
free energy needed for many enzymatic reactions.
the major phosphate and adenylate donor in the cell.
a building block in RNA and is the precursor of dATP.
a major allosteric regulator of many proteins. May
involve binding of ATP only, or binding and hydrolysis
of ATP.

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