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BCHS 3304 General Biochemistry (13830)

Monday/Wednesday 2:30-4:00pm, SW102
Course Homepage on Blackboard (Slides, Notes, Syllabus, etc.)

Steven J. Bark, Ph.D.
The Scripps Research Institute
Mass Spectrometry, Protein Chemistry, Biochemistry
Office: 4022 SERC
Office Hours: Monday/Tuesday 1-2pm or by appointment
Communications: Office 713-743-9638, Blackboard, sbark@uh.edu
Blackboard or email is the best way to reach me!

Sian Behrendt-McLeroy
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4 Exams and a Comprehensive Final (See Syllabus)
Good performance on the FINAL EXAM will replace poorer
performance on ONE earlier exam

Exams based on Lectures, Textbook, Study Guide, Problems

You MUST take ALL exams. NO exams are dropped. There are NO
makeups. There is NO extra credit.

This is not an Easy A Course!
You SHOULD attend every lecture! You SHOULD work through every
problem in the textbook and study guide!
You are responsible for all information!
Group homework and study sections is encouraged, but copying the
homework and not fully participating = disaster!
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I AM ON YOUR SIDE AND WILL DO WHAT I CAN TO
GUARANTEE YOUR SUCCESS IN THIS COURSE,
BUT I CANT DO IT FOR YOU!!!

BIOCHEMISTRY IS COMPLEX AND FAMILIARITY IS NOT
ENOUGH!

READ! STUDY! QUESTION! ORGANIZE! UNDERSTAND!

LEARNING IS AN ADVENTURE! HAVE FUN!


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Chapter 1: Intro to the Chemistry of Life

Biochemistry is the study of the chemistry of life.
Biochemistry is an interdisciplinary science overlapping with chemistry,
cell biology, genetics, immunology, microbiology, pharmacology, and
physiology.

Primary Questions in Biochemistry
1. Chemical and three-dimensional structures of biological molecules?
2. How do biological molecules interact with each other?
3. How does the cell synthesize and degrade biological molecules?
4. How is energy conserved and used by the cell?
5. What are the mechanisms for organizing biological molecules and
the coordinating of their activities?
6. How is genetic information stored, transmitted, and expressed?
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The physical laws of the universe apply to living organisms:

Laws of conservation of mass, energy
Laws of thermodynamics
Laws of chemical kinetics
Principles of chemical reactions

In practical terms, living organisms:

Assemble molecules with great complexity from simple subunits.
Combine these molecules to form organized supra molecular
components, organelles and finally assemble into a cell.
Replicate, store, and pass on information for the assembly of
future generations from simple non-living precursors
Convert energy to work
Employ catalytic chemical transformations


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Prebiotic World

~4.6-3.5 billion years ago
Earliest known fossil is ca. 3.5 billion
years old (filamentous bacterium).
Most organisms are ca. 70% water

Living matter consists of a small number
of elements

Elemental composition of the human
body (97%)
Trace: B, F, Al, Si, V, Cr, Mn, Fe, Co, Ni,
Cu, Zn, As, Se, Br, Mo, Cd, I

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Prebiotic World
No direct fossil record of prebiotic conditions!
Possible early atmosphere consisted of H
2
O, N
2
, CO
2
,
small amounts of CH
4
, NH
3

Sparking of a mixture of CH
4
, NH
3
, H
2
O, and H
2
for 1
week yielded (Stanley Miller and Harold Urey)

Acids (formic, glycolic, lactic, propionic, acetic,
succinic, aspartic, glutamic, etc.)
Amino acids (glycine, alanine, aspartic, glutamic)
Others (urea, sarcosine, N-methyl-alanine, N-methyl-
urea, etc.)
Some scientists propose that early biological
molecules were created in the dark underwater at
hydrothermal vents, thermophile bacteria
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IMPORTANT! charge state of some functional groups differ in different
environments/conditions (e.g., COOH and COO-; NH
3
and NH
4
+)
Key Organic Functional Groups
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Key Organic Functional Groups. cont
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Chemical Evolution
Many enzymes catalyze hydrolysis
and condensation reactions
Hydrolysis = water breaking
Condensation = assemble together
In particular, the condensation
reaction has been very useful
throughout evolution for increasing
biological complexity
Of course, the hydrolysis carries
out the reverse reaction, leading to
a loss in biological complexity
Complementarity enables replication
through templating (e.g., COO-NH
4
+)
Base complementarity in DNA
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Compartmentation = sequestering into a compartment (vesicle)
Vesicles (fluid-filled sacs) are thought to be the precursors to cells
These entities would have had the ability to shield self-replicating
chemical reactions and catalyzed reactions so that they were taking
place in a sheltered environment, higher concentration of nutrients
and ions, giving them a competitive advantage
Catalyst is a substance that promotes a chemical reaction.
This compartment then has the opportunity to further evolve in
order to enhance its advantage.
A typical animal cell contains as many as 100,000 different types of
molecules
A common bacterium, E. coli, contains millions of molecules,
representing 3000-6000 different compounds.
Cellular Architecture
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All modern organisms are based on the same morphological unit, the
cell

Prokaryotes lack a nucleus (e.g., bacteria, archaea): 1 to 10 M
Eukaryotes membrane enclosed nucleus encapsulating their DNA
(e.g., animals, plants, fungi): 10 to 100 M

Viruses are not cells and are not defined as living since they lack the
apparatus to reproduce outside of their host cells.

Eukaryote compartmentation extends to other cellular structures:
Endoplasmic Reticulum, Mitochondria, Golgi Apparatus, Lysosomes, etc.
Prokaryotes and Eukaryotes
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Taxonomy:
biological
classification
Phylogeny:
evolutionary
history
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Evolution

1. All organisms change over time to adapt to changes in their
environment.
This is an observation, not a theory.

2. On the Origin of Species (1859) by Charles Darwin articulated a
that evolutionary processes could occur by natural selection.
Natural selection is a theory, but has been subjected to
experimental observations and experiments.

3. Evolution occurs over short and enormously long time scales.
Adaptations occur within single members of a population (one
lifetime), but are continuous from the dawn of life (>3.5 billion
years ago) to the end of life (~2 billion years from now) on Earth.

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Principles of Evolution

1. Evolution is not directed toward a particular goal.
It proceeds via random changes called mutations. Organisms that
are better suited to reproduce in their environment flourish.

2. Evolution requires some built-in sloppiness.
This is the source of mutation. It allows for adjustment to
unforeseen changes in the environment.

3. Evolution is constrained by its past.
The new arises from the old.

4. Evolution is ongoing.
Not always toward increasing complexity.
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Size Matters! Length Scale for Life
Smaller Larger

Diffraction Methods (X-ray, EM, AFM, <0.2um) Light Microscope (>0.2um)

1 10 100 1000 10
4
10
5
10
6
10
7

10
-10
m 10
-9
m(1nm) 10
-8
m 10
-7
m 10
-6
m(1m) 10
-5
m 10
-4
m 10
-3
m


C-C bond (1.54)

Hemoglobin (65)

Ribosome (300)

Virus (100-1000)
Prokaryote Cell
(10k-100k, 1-10um))

Eukaryotic Cell
(100k-1000k, 10-100um)

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Time Matters! Life is Very Dynamic


10
-15
s 10
-12
s 10
-9
s 10
-8
s 10
-6
s 10
-3
s 10 s 10
3
s
femto pico nano micro milli sec

Reference Time Scales:
femto, fs excitation of chlorophyll
pico, ps charge separation in photosynthesis
nano, ns hinge protein action
10
-8
(10 ns) fluorescence lifetime
micro, s DNA unwind
milli, ms enzymatic reactions
10
3
s generation of bacteria
2.3 x 10
9
s average human life span

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Energy Matters! Life Uses Energy

Ultimate Energy Source = Stellar Fusion (Sun)
E = hv =57 kcal/mol of photons green light or 238.k kJ/mol

1 kcal = 4.184 kJoules
0.239 kcal = 1 kJ

ATP ADP + Pi = -7.3 kcal/mol or -30.5 kJ/mol
IR Energy (vibrational) = 0.6 kcal/mol or 2.5 kJ/mol

C - C bond = 83 kcal/mol or 348 kJ/mol
Ionic interactions ~86kJ/mol
van der Waals interactions < 20kJ/mol
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Thermodynamics First Law
Energy (U) is conserved it can be neither created
nor destroyed

The Enthalpy (H) of a process is defined as follows:
H = U + PV
Absolute measures of state functions can be very difficult to
obtain. Fortunately, most often interested in changes (A)
AH = AU + PAV (under constant pressure, the volume
will change like the expansion of a gas)
Under biological conditions, pressure is constant and the
volume changes are practically negligible:
AH AU
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Thermodynamics Second Law
Spontaneous processes are characterized by the
conversion of order to disorder, increased entropy (S).
A process is spontaneous if it can occur without the input of
additional energy from the outside of the system
Entropy (S) is the measure of the degree of disorder in a system, often
related to the number of states a system can adopt.

In the system to the right, the top
system is more ordered than the
bottom.
The entropy increases on going from
the top to the bottom system.
The change in entropy is measured
by: AS = AH/T (T=temperature)
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Gibbs Free Energy (G)
The Gibbs Free Energy (G) change of a
spontaneous process is negative, AG < 0
Free energy is defined as follows: G = H TS
Normally, we are interested in the change in free
energy so the following equation is more useful:
AG = AH TAS
If the AG is < 0, the process is called exergonic
If the AG is > 0, the process is called endergonic
If the AG is = 0, the process is called equilibrium
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Equilibrium Constants
Relationships between free energy of a system and
concentration of reactants and products at a particular state
AG
0
= free energy change in the equilibrium state




At equilibrium, AG=0 so AG
0
= -RT ln Keq
R (gas constant) = 8.3145 J/K-mol
RT G
b
eq
a
eq
d
eq
c
eq
eq
e
B A
D C
K
/
0
] [ ] [
] [ ] [
A
= =
|
|
.
|

\
|
+ A = A
b a
d c
B A
D C
RT G G
] [ ] [
] [ ] [
ln
0
dD cC bB aA + +
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Equilibrium Constants
Equilibrium constant varies with temperature. At
equilibrium:
AG
o
= AH
o
TAS
o


AG
o
= -RT ln(K
eq
)

Substitution and algebraic rearrangement:

ln(K
eq
) = - AH
o
1 + AS
o

R T R

Measurement of K
eq
at two different temperatures
enables calculation of AH
o
and AS
o
directly.
vant Hoff
Equation
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Biochemical processes operate in a forward
manner as long as the overall pathway is
exergonic! Have to consider all steps!

Coupling ATP hydrolysis (highly exergonic
reaction) to drive many otherwise endergonic
biological processes to completion!!
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Standard state conventions in
biochemistry
The activity of pure water is assigned a
value of 1 even though it concentration is
really 55.5 M (M = Molar). Therefore, the
terms for the concentration of water, [H
2
O],
in equilibrium expressions can be ignored.
The standard pH is 7.0 (10
-7
M)
Temperature is 25
o
C (298K)
Pressure is 1 atm (atmosphere)
Standard concentration is 1M
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For next time

Read Chapter 2, Section 1- We will cover most
of it next time in class.
Work as many problems in Chapter 1 Textbook
and Student Companion as you can.