Fundamentals of Biochemistry

Donald Voet Judith G. Voet Charlotte W.
Pratt
Fundamentals of Biochemistry
Second Edition
Chapter 1:
Introduction to the
Chemistry of Life
Copyright 2006 by John Wiley & Sons, Inc.

Biochemistry: the study of the chemistry of life
What are the chemical and 3D structures of biomolecules

How do bimolecules interact with each other
How does the cell synthesize and degrade biomolecules
How is energy conserved and used by the cell
What are the mechanisms for organizing biomolecules
and coordinating their activities
How is genetic information stored, transmitted, and expressed
Evolution
The origin of the universe and the chemical elements
from simple elements to biochemically important elements
The origin of the solar system and the earth
Chemical evolution: Abiotic synthesis of biomolecules

functional groups
condensation
complementary
Cellular evolution
compartmentation: the rise of protocells
primitive catalysts
energy
Organismal evolution
The earth, 4.6 billion yrs old
How old is life on earth?
Stromatolite, 3.5 billion yrs old

Chemical evolution
http://en.wikipedia.org/wiki/Abiogenesis
Origin of chemical evolution
simple compounds to biochemically significant molecules
1903s, Oparin & Haldane
1953, Miller & Urey
Life from the sea?
The Essential Role of Water
Water is the key to understanding the behavior of macromolecules

the solvent of life
all living transformations occur in an aqueous media
Water-insoluble compounds (lipid membranes)

derive their nature and function by their interactions with water
Common Functional Groups
Arise from simple organic compounds
Condensation reactions
Chemical Evolution, simple molecules condense to form
more complex forms (polymers)
Functional groups into larger molecules

and give rise to more complex molecules
complementary
Replication through complementarity
Self-perpetuation & natural selection
More complex molecules increases chemical versatility

Specific pairing of functional groups gives rise to complementarity
Complementarity makes it possible for macromolecules to replicate
Over time natural selection favored molecules that made accurate
copies of themselves
Double origin hypothesis: DNA & protein
RNA world hypothesis

Cellular evolution
Cell compartmentation: independent life
Required Biosynthesis & Energy
Fermentation as a source of energy
Development of photosynthesis
Evolution of aerobic metabolism
Replicate & propagate

differentiated & became multicellular
Physical Units of Space, Time, and Energy.
LENGTH You must know this and be comfortable using them.
Length is very important!!

C - C bond is 1.54 1 mm = 10-3 m
Hemoglobin 65 1 m = 10-6 m
Ribosomes 300 1 nm = 10-9 m
Viruses 100 - 1000
Cells 7 m or 7 x 104
1 = 10-10 m
Limit of a light microscope = 2000 or 0.2m
1 104
knowledge comes from X-ray crystallography, electron microscope or atomic
force microscope
Life is in constant flux
Enzyme catalyzed reactions- Substrates Products 10-3 sec - milli sec

Unwinding of DNA 10-6 sec - micro sec
10-15 s 10-12 s 10-9 s 10-8 s 10-6 s 10-3 s 10 s 103s

femto pico nano micro milli sec
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
103 sec generation of bacteria
2.3 x 109 sec average human life span
Organismal evolution
Symbiosis
Sexual reproduction
Evolution by mutations
Living organisms operate within the same
physical laws that apply to physics and
chemistry
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?

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.

The 1st Law of Thermodynamics: Energy is Conserved
Energy (U) is neither created or destroyed. U = Ufinal - Uinitial = q w

heat absorbed by the system from the surroundings
- work done by the system on the surroundings
change in internal energy
universe
q system w
U
surroundings (env)
Enthalpy (H) = U + PV
Enthalpy is the sum of the internal energy of matter and the product of its
volume and pressure.
Most biological processes take place at constant pressure (P=0)

H = H(products) H(reactants)
= U + PV
= qp - w + PV
= qp - PV + PV
= qp (heat at constant pressure)
therefore, H = U in biochemical reactions where volume changes

are insignificant
It is impossible to measure H, but possible to measure H
H = H(products) H (reactants) = q (+ or -; , )
Thermodynamics is useful for indicating the spontaneity of a process

However, H is not suitable for the purpose
Enthalpy shows heat change but not the direction

H < 0 exothermic (enthalpically favored)
H > 0 endothermic (enthalpically disfavored)
The 2nd law of thermodynamics
Systems tend to proceed from a state of low probability (ordered)

to a state of high probability (disordered)
Entropy (S): measure the degree of randomness

Entropy tends to increase: consider both system & env
S = k b LnW
kb : Boltzmans constant
W: all the equivalent arrangements of its components
It is difficult or (impossible)
to count the number of arrangements or the most probable state!
There is another expression for entropy at constant pressure conditions
q
S
T
Free energy
At constant pressure we have changes in qp (Enthalpy) and changes in order

A spontaneous process gives up energy and becomes more disordered
S > qp/T = H/T

H - TS < 0
G = H - TS
If G is negative, the process is spontaneous

G = H - T S < 0 exergonic
G = H - T S > 0 endergonic
G = H - T S = 0 equilibrium
Chemical equilibria & Standard state
Standard Temperature and Pressure and at 1M concentration.
We calculate Gs under these conditions.
aA + bB cC + dD
c d
[C] [D]
G = G o + RTln
[A] a [B] b
If we are at equilibrium (or G = 0)
c d
[C] [D]
G = 0 = G o + RTln
[A]a [B]b
c d
[C] [D]
G o = RTln
[A]a [B]b
OR G = RTlnK eq
o
What does Go really mean?

If Keq = 1, then Go = 0
Keq can vary from 106 to 10-6 or more!!!
c d G o
[C] [D]
Keq = =e
eq eq RT
a b
[A] [B]
eq eq
The Variation of Keq with Go at 25 oC Keq o

G
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
K depends on temperature
- H o 1 S
o
lnK eq = +
R T R
R = gas constant for a 1 M solution

Plot lnKeq vs. 1/T ( remember T is in absolute degrees Kelvin)
Vant Hoff plot

- H o
= Slope Measure H and S
lnKeq R
So
= Intercept
R
1
T
Standard State for Biochemistry
1 M, 1 atm, 25 oC
pH = 7.0 (not 0, as used in chemistry)
[H2O] is taken as 1
The prime indicates Biochemical standard state
Keq G o
G
Life obeys the Laws of Thermodynamics
Living organisms are open systems

Living things maintain a steady state not equilibrium
Enzymes catalyze biological reactions

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Donald Voet Judith G. Voet Charlotte W.

Copyright 2006 by John Wiley & Sons, Inc.

What are the chemical and 3D structures of biomolecules

Chemical evolution: Abiotic synthesis of biomolecules

Stromatolite, 3.5 billion yrs old

Water is the key to understanding the behavior of macromolecules

Water-insoluble compounds (lipid membranes)

Functional groups into larger molecules

Self-perpetuation & natural selection

More complex molecules increases chemical versatility

RNA world hypothesis

Replicate & propagate

LENGTH You must know this and be comfortable using them.

Length is very important!!

Limit of a light microscope = 2000 or 0.2m

Enzyme catalyzed reactions- Substrates Products 10-3 sec - milli sec

10-15 s 10-12 s 10-9 s 10-8 s 10-6 s 10-3 s 10 s 103s

femto fs excitation of chlorophyll

Will this reaction proceed in a forward direction as the reaction is written:

Will A react with B to form C or not?

System: a defined part of the universe

Surroundings: the rest of the universe

Open system: allows exchange of energy and matter

Closed system: no exchange of matter or energy.

Energy (U) is neither created or destroyed. U = Ufinal - Uinitial = q w

Most biological processes take place at constant pressure (P=0)

therefore, H = U in biochemical reactions where volume changes

Thermodynamics is useful for indicating the spontaneity of a process

Enthalpy shows heat change but not the direction

Systems tend to proceed from a state of low probability (ordered)

Entropy (S): measure the degree of randomness

There is another expression for entropy at constant pressure conditions

At constant pressure we have changes in qp (Enthalpy) and changes in order

S > qp/T = H/T

If G is negative, the process is spontaneous

We calculate Gs under these conditions.

What does Go really mean?

The Variation of Keq with Go at 25 oC Keq o

R = gas constant for a 1 M solution

Vant Hoff plot

The prime indicates Biochemical standard state

Living organisms are open systems

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