Biochemistry 153A
Lec 1: MTWF 9am: CS76
Lec 2: MTWF 10am: CS76
Instructor Heather L Tienson
Winter 2013
“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.”
-Coach John R. Wooden
Office Hours:
4077A Young Hall
• Tuesday: 1-2p
• Wednesday: 2-4p
• Friday: 12-1p
TA information
Sections
Office hours
Lecture 1:
Tim Chung
tsjchung@chem.ucla.edu
1F, 1G, 1H
Tues 2-4p MS 3114
Jeff McCormick
jeffmccormick@ucla.edu
1A, 1E, 1I
Fri 12-2p MS 3114
Theresa Nguyen
nguyenPT@chem.ucla.edu 1B, 1C, 1D
Thur 12-2p YH 6096
Joseph Warren
warren@chem.ucla.edu
2F, 2G, 2H
Fri 1-3p MS 3114
Izaak Miller
izaakm@ucla.edu
2A, 2B, 2I
Tues 11-1p Boyer
644 (Conf. Rm)
Zhe Wang
wangzhe0819@ucla.edu
2C, 2D, 2E
Wed 4-6p YH 1077
Lecture 2:
Textbooks
OR
Websites to know:
https://ccle.ucla.edu/course/view/13W-CHEM153A-1
https://ccle.ucla.edu/course/view/13W-CHEM153A-2
DISCUSSION FORUM
Syllabus, slides, study questions,
exam answer keys
www.bruincast.ucla.edu
Video and Audio casts of Lecture
Grading
2 Midterms (100pts each)
200
Monday, January 28th
Friday, February 22nd
1 Final Exam (200 pts)
200
Sunday, March 17, 11:30a-2:30p
3 of 4 Quizzes (20pts each)
60
Jan 11th, 18th, Feb 11th, 25th
2 Online Quizzes (10 pts each)
20
Due: Feb 1, Mar 4
Clicker Responses
Total:
20
500
Quiz #1: Amino acids
• Friday
• Identify an amino acid:
–
–
–
–
Full name
Three letter code
1 letter code
Net Charge
• List Categories and
which aa are in each one
Personal Response Card (Clicker)
OR
Store.turningtechnologies.com
Registering your Clicker: Your info
Registering your Clicker: My Info
Why are you taking this class?
A. It is a Degree requirement, I have to.
B. It is a requirement for graduate school,
I have to.
C. I want to learn about Biochemistry?
D. Biochemistry is Awesome!!
What is Biochemistry?
Bio = Life
Chemistry = Property of Molecules
Biochemistry
The Study of Life on the Molecular Level
Biochemistry
Chemistry of Life
Medicine asks the questions…
…Biochemistry answers them
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.
What Chemistry sequence did you take?
1. Only up to 30B
2. Through 30C
3. 14 series
4. Transfer student
What you should already know…
• General Chemistry:
– Weak acids/Titrations/Buffering (14A/20B)
– Thermodynamics (ΔG) (14B/20B)
• Organic Chemistry:
– Functional groups (14B/30A)
– Reactions (14B-D/30A-C)
What you might already know…
• Biology (high school)
– General protein structure (LS3)
– Cells/Organelles/Membranes (LS2)
– Carbohydrates/Lipids (14C/30C)
Composition, Structures, and Functions of
Biomolecules
Smaller Molecules
H2O
CO2
Macromolecules
O2
ATP
Coenzyme A
NAD+
153B
Principles of Enzyme Catalysis
Central
Metabolic
Pathways
of Energy
Transduction
Central
Metabolic
Pathways
of Energy
Transduction
Basis for Life:
Cells
Prokaryotes:
Eukaryotes:
Eukaryotes
(Differences with Prokaryotes)
• 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
Principle of Structural Simplicity:
with increasing diversity:
Polymerization
Precursors (few)
Polymerization
H2O
Macromolecules (many)
[Polymers]
Biological Macromolecules
Nucleic Acids
Proteins
Polysaccharides
(Lipids)
Biopolymers
Homopolymer
Linear
Branched
Heteropolymer
Nucleic Acids
(Nucleotides)
NH2
N
N
O
O
O P
O
O
P
O
O
O
P
NH2
N
O CH2
O
O
O
O P
O
OH OH
Ribonucleotides
O
O
P
O
O
O P
O
O
O
O
P
O
O
P
O
O CH2
N
O
OH
P
N
N
O CH2
O
O
O
P
N
O
OH
O
O
O
P
O
O
OH
O P O
O
O
O
O
O
N
O
N
N
N
O
OH
CH2
N
Nucleic
Acids
4 Nucleotides
O
OH
OH
Only linear structures
Dinucleotide
N1–N2–N3–…Nn
Number of structures = 4n
1,000,000 nucleotides per DNA molecule
41,000,000 molecules!!!
Proteins
(Amino Acids)
Only 20 naturally-occurring amino acids
Only linear structures
aa1–aa2–aa3–…aan
Number of structures = 20n
If only 100 amino acids per molecule
20100 molecules
Polysaccharides
(Sugars)
Only a few sugars (~8)
Linear and branched molecules
Homopolymers and Heteropolymers
Lipids
(Various Precursors)
Neutral Lipids
O
H2C OH
HC OH +
R1 COOH
+
R2
COOH
+
H2C OH
R3
Glycerol
Fatty Acids
COOH
3 H2O
H2C O C R1
O
HC O C R2
O
H2C O C R3
Triacylglycerol
(Neutral Lipid)
Lipids
(Various Precursors)
Phospholipids
At least 2 different backbones
At least 12 different fatty acids
Up to 7 different R3 substituents, or saccharides
Simple construction provides an
immense number of possible
structures fully capable of
providing the necessary diversity
required for life.
Thermodynamic Principles
A Review
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
Change in Gibbs Free Energy (∆G)
Indicator of Spontaneity
(of Biological Processes)
A ——> B
∆G = GB – GA
Exergonic: spontaneous
Endergonic: requires input of energy
Thermodynamics of the Reaction
A + B ——> P + Q
Transition State
CH3Br + OH–
H
OH- + H
H
H
C
H
Reactants
Br
HO
Br–
CH3OH +
C
Br
H
"Transition State"
H
HO
H + Br-
C
H
Products
Accelerating Chemical Reactions
(Heat)
Ea
Ea
Heat
#
molecules
Energy
(slow)
(fast)
Accelerating Chemical Reactions
(pH)
Accelerating Chemical Reactions
(Catalysis Reduces ∆G‡)
Chemical Equilibria
Time Course of Reaction
Equilibrium
A ——> B
B
A or B
t1/2 (half-life)
A
Time
Equilibrium Constant
aA + bB
cC + dD
[C]c[D]d
G = G° + RT ln
[A]a[B]b
G = G° + RT ln Keq
at equilibrium, G = 0, and
G° = –RT ln Keq
Standard Free Energy (ΔGo’)
(Biochemical Standard State Conventions)
25°C
1 Atmosphere
pH 7.0
At equilibrium
Direction of the reaction
Free energy changes:
Go’ = standard
G = in the cell
Concentrations:
Keq = standard
[P]/[R] = in the cell
G > 0
-Reverse (towards
reactants)
[P]/[R] > Keq
-Reverse (towards
reactants)
G < 0
-Forward (towards
products)
[P]/[R] < Keq
-Forward (towards
products)
G = 0
-Equilibrium (i.e. Death)
[P]/[R] = Keq
-Equilibrium (i.e. Death)