Biochemistry 153A
Lec 1: MTWF 9am
Lec 2: MTWF 11am
CS24
Professor Heather L Tienson
Winter 2012
“Success is the peace of mind, which is a direct
result of the self-satisfaction in knowing you did
your best to do the best that you are capable of.”
-John R. Wooden
Office Hours:
Dr. Tienson Young 4077A Mon 2-4p; Tues 12-1p;
Fri 10-11a
Joseph Cao Boyer 5th Flr Fri 2-4p
Conf. room
John Isaak Miller Boyer 644 Wed 1-3p
Margaux Kreitman Young 1343 Wed 10-11a
Young 1336 Thurs 10-11a
David Leibly Young 1343 Wed 9-11a
Androulla Hadjikyriacou Young 1336 Thurs 9-11a
Michael Chambers Young 3114 Thurs 2-4p
Textbooks
OR
Websites to know:
http://voh.chem.ucla.edu/
Syllabus, slides, study questions,
exam answer keys
www.bruincast.ucla.edu
Video and Audio casts of Lecture
Grading
2 Midterms (100pts each) 200
Friday Feb 3
Friday Mar 2
1 Final Exam (200 pts) 200
Lec 1: Wed March 21, 2012 11:30a-2:30p
Lec 2: Thurs March 22, 2012 3-6p
4 of 5 Quizzes (20pts each) 80
Jan 17, 23; Feb 6, 21; Mar 6
Clicker Responses 20
Total: 500
Personal Response Card (Clicker)
OR
Biochemistry
The Study of Life on the Molecular Level
Bio = Life
Chemistry = Property of Molecules
Biochemistry
Chemistry of Life
What You Will Learn in 153A
• Composition, structures and functions of
biomolecules
• Principles of enzyme catalysis
• Central metabolic pathways of energy
transduction
• Beginning of an understanding of the integrated
picture of life and its basis in chemistry.
Composition, Structures, and Functions of
Biomolecules
Smaller Molecules Macromolecules
H2O CO2 O2
ATP
Coenzyme A
NAD+
Principles of Enzyme Catalysis
Central
Metabolic
Pathways
of Energy
Transduction
Basis for Life
Cells
Prokaryotes: lack nucleus
Eukaryotes: membrane-enclosed nucleus
Prokaryotes
(e.g. Escherichia coli)
Adapted to fluctuating
environments
Prokaryotic Cell
Eukaryotes
(e.g. Saccharomyces cerevisiae or human cells)
Adapted to stable environments
Eucaryotic Cell
Evolutionary Relationships
Eukaryotes
(Differences with Procaryotes)
• Increased complexity: >10,000 rxns vs.
~3,000 rxns
• Increased size: 103 – 106 x volume
• Smaller surface:volume ratio
• Membrane-enclosed organelles
– Increased solvent capacity
– Increased membrane surface
Compartmentation
Complexity of Biomolecules
Requirement for Structural
Diversity
Composition of a Typical Bacterial Cell
Component Avg. MW Variety (#) Complexity
Micromolecules
H2O 18 1 18
Inorganic Ions 40 12 480
Organic Compounds 200 500 1.0 x 105
Macromolecules
Proteins 40,000 3000 1.2 x 108
DNA 109 1 109
RNA 1 x 106 1000 109
Simply learning structures appears to be a
monumental task!
Principle of Structural Simplicity
Polymerization
Precursors (few) Macromolecules (many)
[Polymers]
H2O
Biopolymers
• Types
– Homopolymers
– Heteropolymers
• Length and Branching
– Linear
– Branched
Homopolymers
Linear Homopolymer
Branched Homopolymer
Heteropolymers
Linear Heteropolymer
Branched Heteropolymer
Biological Macromolecules
Proteins
(Amino Acids)
Only 21 naturally-occurring/genetically encoded
amino acids
Only linear structures
Polysaccharides
(Sugars)
Only a few sugars (~8)
Linear and branched molecules
Lipids (Various Precursors)
Neutral Lipids
O
H2C OH R1 COOH H2C O C R1
3 H2O
+ O
HC OH + R2 COOH HC O C R2
+ O
H2C OH R3 COOH H2C O C R3
Glycerol Fatty Acids Triacylglycerol
(Neutral Lipid)
Lipids (Various Precursors)
Phospholipids
Nucleic Acids
(Nucleotides)
NH2
N
N
NH2
N
O O O N N
N
O P O P O P O CH2
O
O O O O O O N
N
O P O P O P O CH2
O
O O O
OH OH
Nucleic
Ribonucleotides O
O
O
OH
Acids
N O P O N
O O O
O O O O O
N P O P N
O OH CH2
O P O P O P O CH2 O
O O O
O O O
OH OH
OH OH
Dinucleotide
Macromolecules are composed of
polymers of a few simple
precursor molecules
Structural Diversity
Proteins
aa1–aa2–aa3–…aan
Number of structures = 20n
~100 amino acids per molecule
20100 molecules
Nucleic Acids
N1–N2–N3–…Nn
Number of structures = 4n
1,000,000 nucleotides per DNA molecule
41,000,000 molecules!!!
Polysaccharides
Homopolymers and Heteropolymers
Many different sugar molecules
Linear and branched
Many different molecules!!!
Lipids
Many complex molecules!!!
Simple construction provides an
immense number of possible
structures fully capable of
providing the necessary diversity
required for life.
Thermodynamic Principles
A Review
Thermodynamics
Energy and Its Effects on
Matter
Thermodynamic Principles
• Thermodynamics determines whether
a physical process is possible (i.e.
spontaneous)
• Themodynamics provides no
information about the rate of a
physical process
Thermodynamic Systems
Closed: Physical Chemistry (Equilibrium)
A B
Open: Biochemistry (Steady-State)
A B
Inputs and Outputs
Thermodynamic Systems
Closed: Physical Chemistry (Equilibrium)
A B
Open: Biochemistry (Steady-State)
A B
Inputs and Outputs
First and Second Laws of
Thermodynamics
First Law of Thermodynamics
Energy is Conserved
Second Law of Thermodynamics
The Universe Tends Toward
Maximum Disorder
Consequences of Second Law of
Thermodynamics
• Spontaneous processes proceed in
directions that increase the overall
disorder of the universe
• Increased order in a system requires
decreased order of the surroundings
Free Energy
Indicator of Spontaneity
(of Biological Processes)
Gibbs Free Energy (G)
G = H – TS
H = Enthalpy (Heat Content)
S = Entropy (Disorder)
A ——> B
∆G = GB – GA
∆G = ∆H – T∆S
Change in Gibbs Free Energy (∆G)
Exergonic: spontaneous
Endergonic: requires input of energy
Change in Enthalpy (∆H)
[energy of bonds being broken]
minus
[energy of bonds being formed]
Exothermic: system releases heat
Endothermic: system gains heat
Change in Entropy (∆S)
[freedom of motion of products]
minus
[freedom of motion of reactants]
Change in Entropy (∆S)
Reaction Progress
and
Thermodynamics
Time Course of Reaction
Equilibrium
A ——> B
B
A or B
t1/2 (half-life)
A
Time
Transition State
CH3Br + OH– CH3OH + Br–
H H H H
OH- + H C Br HO C Br HO C H + Br-
H
H H
Reactants "Transition State" Products
Thermodynamics of the Transition State
A + B ——> P + Q
Accelerating Chemical Reactions
(Heat)
Ea Ea
# Heat
molecules
Energy
(slow) (fast)
Accelerating Chemical Reactions
(pH)
Accelerating Chemical Reactions
(Catalysis Reduces ∆G‡)
Chemical Equilibria
Equilibrium Constants
aA + bB cC + dD
[C]c[D]d
²G = ²G ° + RT ln
[A] a[B]b
²G = ²G ° + RT ln Keq
at equilibrium, ²G = 0, and
²G° = –RT ln Keq
Standard Free Energy Changes
(Standard State Conventions)
One Mole
25°C
1 Atmosphere