University of Houston 1

BCHS 3304: General Biochemistry I, Section 07553

Spring 2003 1:00-2:30 PM Mon./Wed. AH 101

Instructor:
Glen B. Legge, Ph.D., Cambridge UK
Phone: 713-743-8380
Fax: 713-743-2636
E-mail: glegge@uh.edu

Office hours:
Mon. and Wed. (2:30-4:00 PM) or by appointment
353 SR2 (Science and Research Building 2)

Research Interests:
Molecular mechanisms of cell adhesion, using primarily multi-
dimensional nuclear magnetic resonance (NMR) spectroscopy.
 Lecture 1 Summary
• Life arose from simple organic molecules
• Compartmentalization gave rise to cells
• All cells are either prokaryotic or eukaryotic
• Eukaryotic cells contain membrane-bound
oragnelles
• Three domains based on phylogeny
– Archea, bacteria, and eukarya
• Natural selection directs evolution
 Thermodynamics and chemical
equilibria

• Lecture 2 1/15/2003
• Chapter 1 Voet, Voet and Pratt
 Thermodynamics:
Allows a prediction as to the spontaneous nature of
a chemical reaction:

Will this reaction proceed in a forward direction as the

reaction is written:

A + B C

Will A react with B to form C or not?

Is this reaction going from higher to lower energy?

ENERGY not necessarily just heat!!!

Definitions:
System: a defined part of the universe
a chemical reaction
a bacteria
a reaction vessel
a metabolic pathway

Surroundings: the rest of the universe

Open system: allows exchange of energy and matter

Closed system: no exchange of matter or energy.

i.e. A perfect insulated box.
Units
Direction of heat flow by definition is most important.

q = heat absorbed by the system from surroundings

If q is positive reaction is endothermic

system absorbs heat from surroundings

If q is negative exothermic
system gives off heat.

A negative W is work done by the system on the

surroundings i.e expansion of a gas
First Law of Thermodynamics: Energy is Conserved

Energy is neither created or destroyed.

In a chemical reaction, all the energy must be accounted for.

Equivalence of work w and energy (heat) q

Work (w) is defined as w = F x D (organized motion)

Heat (q) is a reflection of random molecular motions (heat)

 U = Ufinal - Uinitial = q - w
Exothermic system releases heat = -q
Endothermic system gains heat = +q
U = a state function dependent on the current properties only.

U is path independent while q and w are not state functions

because they can be converted from one form of energy to the
other. (excluding other forms of energy, e.g. electrical, light
and nuclear energy, from this discussion.)
Path: is a process by which energy changes in a system

I have $100 in my bank account, I

withdrew $50, now I have $50. I could

have added $100 and withdrew $150.

U (money in the account) is same but the

path is different.
 Enthalpy (H)
At constant pressure w = PV + w1

w1 = work from all means other than pressure-volume work.

PV is also a state function.

By removing* this type of energy from U, we get enthalpy or

‘to warm in’
*remember the signs and direction

H = U + PV
H = U + PV = qp -w + PV = qp - w1
 Enthalpy (H)
When considering only pressure/volume work

H = qp - PV + PV = qp

H = qp when other work is 0

qp is heat transferred at constant pressure.

In biological systems the differences between

U and H are negligible (e.g. volume changes)

The change in enthalpy in any hypothetical reaction
pathway can be determined from the enthalpy
change in any other reaction pathway between the
same products and reactants.

This is a calorie (joule) “bean counting”

Hot Cold

Which way does heat travel? This directionality, is

not mentioned in First Law
 Other examples

Considering the random thermal motion of molecules, why at

any particular time doesn’t all the atoms in the air in this room
end up into the upper right corner of the room?

or

When a driver jumps into the water, energy from that person is
dissipated to the water molecules. Have you ever seen the
water molecules act in unison and retransfer this energy back
to the driver and push him out of the water?

In all cases Energy is conserved.

Gas on its own will expand to the available volume.

• Disorder increases

• Can we put a numerical

value on disorder? Yes, most
definitely!!

• N identical molecules in a
bulb, open the stop cock you
get 2N equally probable
ways that N molecules can
be distributed in the bulb.
 But gas molecules are indistinguishable.

Thus, only N+1 different states exist in the bulb or 0, 1, 2,

3, 4,…., (N-1) molecules in left bulb

WL = number of probable ways of placing L of the N

molecules in the left bulb is

N!
WL 
L! (N - 1)!
WL
The probability of occurrence of such a state  N
(Is its fraction of the total number of states) 2
N = 4 particles, 2 orientations or 24 = 16 different
arrangements of distinguishable particles

1{

4{

6* {

4{
} N+1
different
states

1{

* The most probable state is the one with the most arrangements
 The state that is the most probable is one with the highest
value of WL= N/2 in one bulb and N/2 in the other.

The probability that L is equal to N/2 increases when N is

large

For N=10 the probability that L lies within 20% of N/2 = .66
N=50 probability L lies within 20% of N/2 = .88
N=1023 , L = 1

For a mole of gas in the two bulbs 6.0221 x 1023

The probability of a ratio of 1 in 1010 (one in ten billion) difference or

10,000,000,000 vs. 10,000,000,001 on one side to the other is

10-434 = 0
The reason that direction occurs is not by the laws of
motion, but the aggregate probability of all other states is
So low!! or insignificant that only the most probable state
will occur.
Entropy

WN  10 NLn2

for N = 1023 W5x10 2 2  10 7 x102 2

Possible arrangements

This number is greater than the number of atoms in the

universe!!
 Entropy (S)
measure the degree of randomness

S  k b LnW
Each molecule has an inherent amount of energy which
drives it to the most probable state or maximum disorder.

kb or Boltzman’s constant equates the arrangement

probability to calories (joules) per mole.

Entropy is a state function and as such its value depends

only on parameters that describe a state of matter.
The process of diffusion of a gas from the left bulb initially W2 = 1 and
S = 0 to Right (N/2) + Left (N/2) at equilibrium gives a :

S that is (+) with a constant energy process such that U = 0

while S>0

This means if no energy flows into the bulbs from the outside
expansion will cool the gas! Conservation of Energy says that
the increase in Entropy is the same as the decrease in thermal
(kinetic) energy of the molecules!!
 Entropy is the arrow of time

The entropy of the universe is always increasing.

What does this mean in a closed system?

What does this mean in an open system?

What if the universe starts to collapse, does time go

backwards?
 It is difficult or (impossible) to count the number of
arrangements or the most probable state!

So how do we measure entropy?

final
dq
S  
inital
T
It takes 80 kcal/mol of heat to change ice at zero °C to water at zero °C

80,000 = 293 ev’s or entropy units

273
A Reversible process means at equilibrium during the change. This is
impossible but makes the calculations easier but for irreversible process
q
S 
T
 At constant pressure we have changes in qp (Enthalpy) and
changes in order - disorder (Entropy)

A spontaneous process gives up energy and becomes more

disordered.

G = H - TS
Describes the total usable energy of a system

A change from one state to another produces:

G = H - TS = qp - TS

If G is negative, the process is spontaneous

S H
+ - All favorable
at all temperature
spontaneous

- - Enthalpy favored.
Spontaneous at
temperature below
T = H
S

+ + Entropy driven,
enthalpy opposed.
Spontaneous at
Temperatures above
T = H
S
- + Non-spontaneous
 STP
Standard Temperature and Pressure and at 1M concentration.

We calculate G’s under these conditions.

aA + bB cC + dD

We can calculate a G for each component

__ __ __ __
(1) G  c G c  d G d - a G a - b G b
o
(2) G a - G  RTln[A]
a

combining (1) and (2)

c d
[C] [D]
(3)
G  G  RTln
o

[A]a [B] b
 Now if we are at equilibrium or G = 0
Then

c d
[C] [D]
G  0  G  RTln
o
a b
[A] [B]
c d
[C] [D]
G   RTln
o

[A]a [B] b
OR

G  RTlnK eq
o

So what does Go really mean?

 c d
[C] [D]
G  G o  RTln
[A]a [B] b

Go

Keq
If Keq = 1 then G = 0

Go equates to how far Keq varies from 1!!

 Keq can vary from 106 to 10-6 or more!!!

Go is a method to calculate two reactions whose Keq’s are different

However
The initial products and reactants maybe far from their equilibrium
concentrations

c d
so
[C] [D] Must be used
a b
[A] [B]
 c d  G o
[C] [D]
Keq  e
eq eq RT
a b
[A] [B]
eq eq

Le Chatelier’s principle
Any deviation from equilibrium stimulates a process which restores
equilibrium. All closed systems must therefore reach equilibrium
What does this mean?
Keq varies with 1/T
If Keq varied with temperature things would be very unstable.
Exothermic reactions would heat up causing an increase in Keq
generating more heat etc….
 Fortunately, this does not happen in nature.

- H  1  S
o o
lnK eq   
R T R
R = gas constant for a 1M solution
Plot lnKeq vs. 1/T ( remember T is in absolute degrees Kelvin)
Van’t Hoff plot

- H o
lnKeq = Slope
R
So = Intercept
R
1
T
The Variation of Keq with Go at 25 oC
Keq o
G
(kJ·mole-1

106 -34.3
104 -22.8
102 -11.4
101 -5.7
100 0.0
10-1 5.7
10-2 11.4
10-4 22.8
10-6 34.3
G   G (products) -  G (reactants )
o o
f
o
f

The f = for formation.

By convention, the free energy of the elements is taken
as zero at 25 oC

The free energies of any compound can be measured as

a sum of components from the free energies of
formation.
 Standard State for Biochemistry

Unit Activity
25 oC
pH = 7.0 (not 0, as used in chemistry)
[H2O] is taken as 1, however, if water is in the Keq equation
then [H2O] = 55.5

The prime indicates Biochemical standard state

K eq G o
G
 Most times G  G o o

However, species with either H2O or H+ requires consideration.

For A + B C + D + nH2O
n
[C][D][H O] [C][D]
G o  - RTln 2
G  - RTln Keq  - RTln
o
[A][B] [A][B]
This is because water is at unity. Water is 55.5 M
and for 1 mol of H2O formed:

G  G  nRTln[H 2O]

o o

Go  G o  9.96 kJ  mol -1

 For: A+B C + HD
K

H+ + D -  -
[H ][D ]
Where a proton is in the equation K
[HD]

Go  G o - RT ln

1 - [H ]  
 RT ln[ H
o 
]o
K

This is only valid for [H ]o  10 M -7
 Coupled Reactions

A+B C + D G1 (1)

D+E F +G G2 (2)
If G1  0 reaction 1 will not occur as written.

However, if G 2 is sufficiently exergonic so G1  G2  0

Then the combined reactions will be favorable through
the common intermediate D

A+B+E C+F+G G3 G 3  G1  G 2  0

As long as the overall pathway is exergonic,
it will operate in a forward manner.

Thus, the free energy of ATP hydrolysis, a

highly exergonic reaction, is harnessed to
drive many otherwise endergonic biological
processes to completion!!
Life obeys the Laws of Thermodynamics

• Living organisms are open systems

• Living things maintain a steady state
• Enzymes catalyze biological reactions
 Water and elements in life processes

• Lecture 3 1/22/2003