Fundamentals of Biochemistry 3/e

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Fundamentals of
Biochemistry
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.
What is Biochemistry?
• 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
Central Questions
• 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?
Section 1 - Origins of life
• 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
Section 2 – Cellular Architecture
• 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
Types of Cells
• Prokaryotes
–
–
–
–
Lack a nucleus
Various sizes
Individual cells
Suited to
environment
• Eukaryotic
– Contain a
nucleus
• Stores
DNA
– Much
larger
– Contains
organelles
Relationship of Organisms
Evolution
• 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
Section 3 - Thermodynamics
• First Law of Thermodynamics – energy is conserved
• The study of energy (U)
– System, surroundings, heat (q) and work (w), enthalpy (H)
• ΔU = Ufinal – Uinitial = q – w
• w = PΔV (for a system a constant pressure)
• H = U + PV
– ΔH = ΔU + PΔV = qP – w + PΔV
• ΔH = qP
• 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 = kB 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
– ΔSsystem + ΔSsurroundings = ΔSuniverse > 0
• In biological systems, we cannot measure W
– ΔS ≥ (q/T)
• 2H2 + O2 → 2H2O
• At constant pressure
(with spark)
Spontaneous
qP H
S 

H  T S  0
T
T
• 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:
 C c  D d
G  G  RT ln 
  Aa  B b

G   RT ln K eq
– GA = G°A + RT ln [A]
• For the general
reaction:
 C   D    G
eq
eq
RT


K eq 

e
a
b
  Aeq  B eq 


c
– aA +bB ↔ cC + dD
van‘t Hoff
d
H  1  S
ln Keq 
 
R T  R
y  mx  b




• 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.
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