University of Houston

1
University of Houston BCHS 3304 General
Biochemistry I, Section 07553 Spring 2003
100-230 PM Mon./Wed. AH 101 Instructor
Glen B. Legge, Ph.D., Cambridge UK Phone
713-743-8380 Fax [phone] E-mail
glegge_at_uh.edu Office hours Mon. and Wed.
(230-400 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.
1
2
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

3
Thermodynamics and chemical equilibria

• Lecture 2 1/15/2003
• Chapter 1 Voet, Voet and Pratt

4
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!!!
5
Definitions System a defined part of the
universe a chemical reaction a bacteria a
reaction vessel a metabolic pathway Surrounding
s 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.
6
Units
7
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
8
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)
9
?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.)
10
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.
11
Enthalpy (H) At constant pressure w P?V
w1 w1 work from all means other than
pressure-volume work. PDV 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
12
Enthalpy (H) When considering only
pressure/volume work ?H qp - P?V P?V
qp DH 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)
13
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
14
Other examples Considering the random thermal
motion of molecules, why at any particular time
doesnt 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.
15

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.

16
But gas molecules are indistinguishable. Thus,
only N1 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 The
probability of occurrence of such a state
(Is its fraction of the total number of states)
17
N 4 particles, 2 orientations or 24 16
different arrangements of distinguishable
particles
1
4

N1 different states
6
4
1
The most probable state is the one with the
most arrangements
18
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 N10 the
probability that L lies within 20 of N/2 .66
N50 probability L lies within 20 of N/2
.88 N1023 , 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
19
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
for N 1023 This number is greater than
the number of atoms in the universe!!
Possible arrangements
20
Entropy (S) measure the degree of randomness
Each molecule has an inherent amount of energy
which drives it to the most probable state or
maximum disorder. kb or Boltzmans 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.
21
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 ?Sgt0 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!!
22
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?
23
It is difficult or (impossible) to count the
number of arrangements or the most probable
state! So how do we measure entropy? It
takes 80 kcal/mol of heat to change ice at zero
C to water at zero C 80,000 293 evs 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
24
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 DG is
negative, the process is spontaneous
25
?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-spontan
eous
26
STP Standard Temperature and Pressure and at 1M
concentration. We calculate DGs under these
conditions. aA bB cC dD We can
calculate a G for each component (1) (2) combin
ing (1) and (2) (3)
27
Now if we are at equilibrium or DG 0 Then
OR
So what does DGo really mean?
28
G
Go
Keq
If Keq 1 then DG 0 Go equates to how far Keq
varies from 1!!
29
Keq can vary from 106 to 10-6 or more!!!
DGo is a method to calculate two reactions whose
Keqs are different
However The initial products and reactants maybe
far from their equilibrium concentrations so
Must be used
30
Le Chateliers 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.
31
Fortunately, this does not happen in nature.
R gas constant for a 1M solution Plot lnKeq vs.
1/T ( remember T is in absolute degrees Kelvin)
Vant Hoff plot
Slope
lnKeq
Intercept
32
The Variation of Keq with DGo at 25 oC
Keq DGo
(kJmole-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
33
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.
34
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
35
Most times
However, species with either H2O or H requires
consideration. For A B C D nH2O
This is because water is at unity. Water is 55.5
M and for 1 mol of H2O formed
36
For A B C HD
H D-
K
Where a proton is in the equation
This is only valid for
37
Coupled Reactions
A B C D DG1 (1) D E F
G DG2 (2)
reaction 1 will not occur as written.
If
is sufficiently exergonic so
However, if
Then the combined reactions will be favorable
through the common intermediate D
A B E C F G DG3
38
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!!
39
Life obeys the Laws of Thermodynamics

• Living organisms are open systems
• Living things maintain a steady state
• Enzymes catalyze biological reactions

40
Water and elements in life processes

• Lecture 3 1/22/2003