Third Edition
Donald Voet • Judith G. Voet •
Charlotte W. Pratt
Chapter 1
Introduction to the Chemistry of Life
Copyright © 2008 by John Wiley & Sons, Inc.

• Biochemistry is more like – chemical biology
• Has aspects of many different disciplines
– Cell biology, genetics, immunology, microbiology, pharmacology, and physiology
• Study of how chemicals interact and influence biological systems

• What are the chemical and 3-D structures of biological molecules?
• How do biological molecules interact?
• Who do living organisms use biological molecules?
• How is energy made and used by living organisms?
• What are the mechanisms for organizing biological molecules and regulating their activities?
• How is genetic information stored, transmitted, and expressed?

• Only a few elements make up living organisms.
– Other elements may include
• B, F, Al, SI, V, Cr, Mn, Fe, Co, Ni, Cu,
Zn, As, Se, Br, Mo, Cd, I, and W
• Two theories of origins of life
– Miller & Urey, electric discharge to a “primordial” atmosphere
– Hydrothermal conditions in seawater
• Generation of functional groups

Interactions between functional groups replication

• Formation of cells
– From vesicles
• Compartmentation
– Protection from environment
– Higher concentration of reactants leads to more reactions
– Different composition from environment

• Problems
– Run out of precursor molecules
• Appearance of mechanisms to generate new ones
(catalysis)
– Need energy to make molecules
• Appearance of photosynthesis
– Survive in an oxygen rich environment
• Appearance of aerobic respiration
• Adaptation
– Diversification
– Differentiation of cells generated multicellular organisms

• Prokaryotes
– Lack a nucleus
– Various sizes
– Individual cells
– Suited to environment

• Eukaryotic
– Contain a nucleus
• Stores
DNA
– Much larger
– Contains organelles

• Natural Selection
– Mutation in genetic material arise by chemical damage or inherent errors
• Positive mutations are passed to future generations
• Negative mutations usually are eliminated
• Principles of Evolution
– Evolution is not directed toward a particular goal
– Individuals are varied
– The past determines the future
– Evolution is ongoing

• First Law of Thermodynamics – energy is conserved
• The study of energy (U)
– System, surroundings, heat (q) and work (w), enthalpy (H)
• ΔU = U final
– U initial
= q – w
• w = PΔV (for a system a constant pressure)
• H = U + PV
– ΔH = ΔU + PΔV = q
P
• ΔH = q
P
– w + PΔV
• In biological systems there is no volume change (PΔV = 0) and ΔH = ΔU
• Spontaneous Processes
– First Law of Thermodynamics cannot alone explain

• Second Law of Thermodynamics – a spontaneous process is defined as the conversion of order to disorder
• Disorder is defined as the number of energetically equivalent arrangement (W)
• Entropy (S) is a measure of randomness
• S = k
B ln W

• For a spontaneous process such as the exchange of gas, overall energy (U) and enthalpy (H) change is zero
• The change in entropy (S) must be greater than zero
– ΔS system
+ ΔS surroundings
= ΔS universe
> 0
• In biological systems, we cannot measure W
– ΔS ≥ (q/T)

• 2H
2
+ O
2
→ 2H
2
O
(with spark)
• At constant pressure
Spontaneous
S q
P


T T
H
H T S 0
• Gibbs free energy (G)
• G = H – TS
• ΔG = ΔH – TΔS
– Exergonic (spontaneous)
– Endergonic (not spontaneous)
– Equilibrium ( ΔG = 0)

• Entropy depends on volume, and therefore, concentration
• The free energy of substance A is:
– G
A
= G°
A
+ RT ln [A]
• For the general reaction:
– aA +bB ↔ cC + dD
G

G
 
RT ln K eq
K eq
G

RT ln


   
    d b



    eq d eq
    eq b eq

  e


G
RT

 van‘t Hoff ln K eq


R
H 1
  y
 mx
 b


S
R

• Convention: T = 25°C; P = 1 atm; activity = 1
• New definition of standard state
– Activity of water is 1 even though concentration is 55.5
M
– [H+] is 1 at pH = 7 NOT pH = 0
– Acid-base reactions are defined as the naturally occurring ion at pH = 7 NOT pH = 0.
• Therefore, define new ΔG
– Biochemists use ΔG°’ instead of ΔG° to distinguish between the different standard conditions

• Organisms obey thermodynamics
• Organisms are open systems and never reach equilibrium
• Organisms are at a steady state (the system does not change with time)
• Biological catalysts (enzymes) provide a better pathway for reactions to occur
– This allows for reasonable reaction rates
Practice – You should be able to complete all of the problems at the end of the chapter. Exam questions will require the understanding of all topics covered.