BIOCHEMISTRY

JULIUS P. MARIO, RMT, MSci

ENERGY

• Capacity to do work
• unlike matter, it is known and recognized by
its effects
• cannot be seen, touched, smelled or weighed
• constant in the universe
TYPES OF ENERGY
Radiant = solar energy
Thermal = associated with random motion of atoms
and molecules
Chemical = stored within the structural units of
chemical substances
= can be released, stored or converted to
other energy forms
Potential = available by virtue of an object’s position
ENERGY CHANGES

• chemical reactions absorb or release energy,

generally in the form of heat

HEAT
• transfer of thermal energy between two bodies
that are at different temperatures
THERMOCHEMISTRY

• Study of heat change in chemical reactions

SYSTEM AND SURROUNDING

System = specific part of the universe that is of

interest to us
Surrounding = the rest of the universe outside the
system
TYPES OF SYSTEM

OPEN = can exchange mass and energy with its

surroundings
CLOSED = allows the transfer of energy but not
mass
ISOLATED = does not allow the transfer of
either mass or energy
EXOTHERMIC PROCESS

= any process that gives off heat

= transfers thermal energy to the surroundings
= total energy of products is less than the total
energy of the reactants
2H2 (g) + O2 (g) 2H2O() + energy
ENDOTHERMIC PROCESS

= any process that requires heat to be applied to

the system by the surroundings
= total energy of reactants is less than the total
energy of products
energy + 2HgO(s) 2Hg() + O2 (g)
THERMODYNAMICS

• scientific study of the interconversion of heat

and other kinds of energy
• study of the changes in the state of a system
• provide useful guidelines for understanding the
energetics and directions of processes
STATE OF THE SYSTEM

• the values of all relevant macroscopic

properties, for examples, composition, energy,
temperature, pressure and volume
STATE FUNCTIONS

= properties that are determined by the state of

the system, regardless of how that condition
was achieved
= magnitude of change depends only on initial
and final states of the system and not on how
the change is accomplished
SIGN CONVENTIONS FOR WORK & HEAT

PROCESS SIGN
work done by the system on the surroundings -
work done on the system by the surroundings +
heat absorbed by the system from the
surroundings (endothermic) +
heat absorbed by the surroundings from
the system (exothermic) -
LAWS OF THERMODYNAMICS
1ST LAW
= energy cannot be created nor destroyed but can be converted from
one form to another

2ND LAW
= the entropy of the universe increases in a spontaneous process and
remains unchanged in an equilibrium process

3RD LAW
= entropy of a perfect crystalline substance is zero at the absolute zero
temperature
Reaction Rates and Chemical Equilibrium

Chemical kinetics = study of reaction rates

Reaction rate = change in concentration of a
reactant or product per unit time
• molecular collisions - effective collisions
• activation energy - minimum energy necessary
for the reaction to happen
Depends on

1. Speed of colliding objects

2. Angle of approach = head-on is best
3. Must have proper orientation
energy collision of  activation energy - no
reaction
H2O() + HCl(g) H3O+(aq) + Cl-(aq)
Activation energy & Energy Diagrams
“Downhill” reactions - exothermic

Transition state

Activation E
energy

E of reactants E of products

E or rxn

Progress of reaction
Activation energy & Energy Diagrams
“Uphill” reactions - endothermic

Transisiton state

Activation E E of products
energy
E or rxn

E of reactants

Progress of reaction
Transition state - top of the energy hill
- one or more original bonds are
partially broken or
- one or more bonds (new) may
be in the process of formation
Activation energy - energy hill
- if low, faster reaction
- if high, slower reaction
Factors Affecting Rates of Reaction

A. Nature of reactants for solid = surface area

affects for gases, pressure- rate ions in
aqueous solution - instantaneous
B. Concentration
direct relationship between rate and
concentration
C. Temperature
= a 10oC rise in temp, reaction rate doubles
= has two reasons:
1. temp - more rapid movement of
molecules
- more probability of collision
2. Different distribution of speeds - more effective
collisions than total number of collisions
D. presence of catalyst - alternative pathway by
providing surface for molecules to meet
heterogeneous - separate phase from reactant
homogeneous - same phase as the reactant
Equilibrium Constants = value calculated from
the equilibrium expression for a given reaction
indicating in which direction the reaction goes

aA + bB cC + dD
 Once equilibrium is reached, the following equation is valid
K = [C]c[D]d the equilibrium expression
[A]a[B]b
CO(g) + H2O(g) CO2(g) + H2(g)
K = [CO2][H2] [x] = x in mol/L
[CO][H2O] x = liquid or gaseous

Ab equilibrium, the concentration of CO2 x concentration of

H2 & divided by the concentrations of H2O & CO is a
constant, K.
Universal custom is to write them with Products on top and
Reactants below.
Write the equilibrium expression for the reaction
SO3(g) + H2O() H2SO4(g)

O2(g) + 4Cl2(g) 2Cl2O5(g)

2NH3(g) N2(g) + 3H2(g)

I2(g) + H2(g) 2HI(g)

PCl3 + Cl2 PCl5

Le Chatelier’s Principle

When a reaction equilibrium, the forward and

reverse reactions take place at the same rate,
and the concentrations of all components do
not change as long as we don’t do anything to
the system.
If an external stress is applied to a system in equilibrium,
the system reacts in such a way as to partially relieve that
stress.
A. Addition of a Reaction Component
HCl - catalyst-doesn’t affect equi
CH3COOH + C2H5OH CH3COOC2H5 + H2O
acetic acid ethyl acetate
= results to equilibrium shift
B. Removal of a Reaction Component
reaction rate but not easy to do

NO MATTER WHAT HAPPENS TO THE

INDIVIDUAL CONCS, THE VALUES OF
THE EQUILIBRIUM CONSTANT (K)
REMAINS UNCHANGED.
C. Change in Temperature
The effect of a  T on a reaction that has reached equilibrium
depends on whether the rxn is exothermic (gives off heat) or
endothermic (required heat).
2H2(g) + O2(g) 2H2O() + 137,000 cal
temp  + heat
heat as product, its addition pushes
the equilibrium to the opposite
siteto the left
H2 & O2; & H2O
in T drives an exo rxn towards reactants (left)
in T drives an exo rxn towards product (right
for endo, opposite is true)
= changes both the position of equilibrium but also
the value of K, (equi contant)
D. Change in pressure
= influences the equilibrium only if one or more of
the components of the reaction is a gas
N2O4(g) 2NO2(g)
one mole of gas 2 moles of gas
(reactant) (product)
=  in P shifts the equi in the direction that will 
the moles in the gas phase and hence  the pressure.
With the above, the shift is to the left.
• An increase in pressure shifts the reaction toward the
side with fewer moles of gas (otherwise if there’s 
in P).
E. Effect of catalyst
=  the rates of both the forward and reverse
reactions to the same extent.
: addition of catalyst has no effect on the position
of equilibrium.
However, adding catalyst to a system not yet at equi
caused it to reach equi faster than it would without
the catalyst.
 ΔG and ΔGo
• G = Gibbs free energy
= energy available to do work

• ΔG = change in free energy

ΔG < 0 spontaneous in the forward reaction
ΔG > 0 nonspontaneous; spontaneous in the
opposite direction
ΔG = 0 at equilibrium; no net change
• ΔGo = standard free-energy of reaction
= free-energy change for a reaction when
it occurs under standard-state conditions,
when reactants in their standard states are
are converted to products in their standard
states.
GAS = 1 atm pressure
LIQUID = pure liquid
SOLID = pure solid
ELEMENTS => ΔGo f = 0
SOLUTION = 1 molar concentration
 Free energy is a useful thermodynamic function
for understanding enzymes
Some of the principles of thermodynamics:
To fully understand how enzymes operate, we need to consider
two thermodynamic properties of the reaction:
(1) the free-energy difference (G) between the products and
reactants and
(2) the energy required to initiate the conversion of reactants
to products.

The former determines whether the reaction will be spontaneous,

whereas the latter determines the rate of the reaction. Enzymes
affect only the latter.
The Free-Energy Change Provides Information
About the Spontaneity but Not the Rate of a
Reaction
The free-energy change of a reaction (G) tells us if the
reaction can occur spontaneously:
1. A reaction can occur spontaneously only if G is
negative. Such reactions are said to be exergonic.
2. A system is at equilibrium and no net change can take
place if G is zero.
3. A reaction cannot occur spontaneously if G is positive.
An input of free energy is required to drive such a
reaction. These reactions are termed endergonic.
 Two additional points need to be emphasized.

=the G of a reaction depends only on the free

energy of the products (the final state) minus the
free-energy of the reactants (the initial state)
= the G of a reaction is independent of the path
(or molecular mechanism) of the transformation.
The mechanism of a reaction has no effect on
G.
For example, the G for the oxidation of glucose
to CO2 and H2O is the same whether it occurs by
combustion in vitro or by a series of enzyme-
catalyzed steps in a cell.
 =the G provides no information about the rate of a
reaction

A negative G indicates that a reaction can occur

spontaneously, but it does not signify whether it will
proceed at a perceptible rate.

The rate of a reaction depends on the free energy of

activation (G‡), which is largely unrelated to the G of
the reaction.
 The Standard Free-Energy Change of a Reaction
Is Related to the Equilibrium Constant
As for any reaction, we need to be able to
determine G for an enzyme-catalyzed reaction
in order to know whether the reaction is
spontaneous or an input of energy is required.
To determine this important thermodynamic
parameter, we need to take into account the
nature of both the reactants and the products as
well as their concentrations.
Consider the reaction
A+B C+D
 The G of this reaction is given by
[C][D]
G = Go + RT ln [A][B]
where:
Go is the standard free-energy change
R is the gas constant
T is the absolute temperature,
and [A], [B], [C] and [D] are the molar concentrations (more precisely, the
activities) of the reactants

Go is the free-energy change for this reaction under

standard conditions, that is, when each of the reactants A,
B, C and D is present at a concentration of 1.0 M (for a
gas, the standard state is usually chosen to be 1
atmosphere).
 Relation between Go and K’eq
at 25oC
Go’
K’eq kcal mol-1 kJ/mol-1
10-5 6.82 28.53
10-4 5.46 22.84
10-3 4.09 17.11
10-2 2.73 11.42
10-1 1.36 5.69
1 0 0
10 -1.36 -5.69
102 -2.73 -11.42
103 -4.09 -17.11
104 -5.46 -22.84
105 -6.82 -28.53
The overall free-energy change for a chemically
coupled series of reactions is equal to the sum of the
free-energy changes of the individual steps.
A - B + C ΔGo ΄ = +5 kcal/mol
B - D ΔGo ΄ = -8 kcal/mol
______________________________________
A - C + D ΔGo ΄ = -3 kcal/mol

A thermodynamically unfavorable reaction can be

driven by a thermodynamically favorable reaction to
which it is coupled.
 Standard free energies of hydrolysis of
some phosphorylated compounds
• Phosphoenolpyruvate -14.8 kcal/mol
• 1,3-bisphosphoglycerate -11.8 kcal/mol
• Creatine phosphate -10.3 kcal/mol
• ATP to ADP -7.3 kcal/mol
• Glucose-1-phosphate -5.0 kcal/mol
• Pyrophosphate (PPi) -4.6 kcal/mol
• Glucose-6-phosphate -3.3 kcal/mol
• Glycerol-3-phosphate -2.2 kcal/mol