Biochemistry 153A

Professor Richard L. Weiss Fall 2012

INTRODUCTION

The Study of Life on the Molecular Level

Biochemistry

Chemistry of Life
What are the chemical and three-dimensional structures of biological molecules? How do biological molecules interact with each other? How does the cell synthesize and degrade biological molecules? How is energy conserved and used in the cell? What are the mechanisms for organizing biological molecules and coordinating their activities? How is genetic information stored, transmitted, and expressed?

Biochemistry

Bio = Life Chemistry = Property of Molecules

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

Micromolecules Macromolecules
Proteins Carbohydrates Lipids Nucleic Acids

Principles of Enzyme Catalysis The role of proteins as enzymes Enzyme kinetics Catalytic mechanisms Regulation of enzyme catalysis

Central Metabolic Pathways of Energy Transduction Glycolysis Tricarboxylic Acid Cycle Electron Transport Oxidative Phosphorylation
(TCA Cycle; Krebs Cycle; Citric Acid Cycle)

Integration of Biological Processes

What happens How it happens When it happens Why it happens Coordination | Regulation | Signaling Intracellular Signaling Intercellular Signaling

Properties of Life
(Norman Horowitz) Replication Catalysis Mutability

Organisms

Distinguishing Features of Living Organisms

Chemical Complexity and Microscopic Organization Systems for Extracting, Transforming, and Using Energy from the Environment Defined Functions for each Component and Regulated Interactions Among Them Mechanisms for Sensing and Responding to Alterations in Surroundings Capacity for Precise Self-Replication and Assembly Capacity to Change over Time by Gradual Evolution

Basis for Life Cells

Prokaryotes: lack nucleus Eukaryotes: membrane-enclosed nucleus

Prokaryotic Cell
(e.g. Escherichia coli)

Prokaryotes

Adapted to fluctuating environments

Eucaryotic Cell
(e.g. Saccharomyces cerevisiae or human cells)

Eukaryotes

Adapted to stable environments

(Differences with Procaryotes)

Eukaryotes

Evolutionary Relationships

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

Advantages of Studying Microorganisms Fundamental Similarity of Biological Processes

Prokaryotes Eukaryotes Ethics Availability of large numbers of identical individuals Ease of manipulation Genetics Molecular Biology Inexpensive

Principles of Biochemistry
(1) Genetic Theory (2) Central Dogma (of Molecular Biology) (3) Enzyme Theory (4) Energy Theory (5) Spontaneous Self-Assembly Theory

Genetic Theory

DNA as the Genetic Material

(of Molelcular Biology)

Central Dogma

Enzyme Theory

Reactants

Enzymes

Products

Figure 3-13

(Biological Transformations)

Energy Theory

Energy Flow in the Biosphere

Biological processes require the acquisition and utilization of energy

Energy Currency ATP

NH2 N N Adenine N O
O

Metabolic Energy Sources

Autotrophs ( self-feeding ): synthesize all cellular constituents
Chemolithotrophs: oxidation of inorganic compounds Photoautotrophs: photosynthesis

O O P O O

O P O O CH2 O Ribose

P O

Heterotrophs ( other-feeding ): dependent on autotrophs - oxidation of organic compounds

Obligate aerobes Facultative anaerobes Obligate anaerobes

Triphosphate OH OH

Photosynthesis
Light Energy 6 CO2 + 6 H2O C6H12O6 + 6 O2

Breakdown of Carbohydrates

C6H12O6 + O2

6 CO2 + 6 H2O + energy (ATP)

(light-driven reduction of CO2) Light Energy ADP + Pi ATP (light-driven production of ATP)

(energy-yielding oxidation of glucose)

Anabolism and Catabolism

(Heterotrophs)
Proteins Fats Carbohydrates (Nutrients) ADP Catabolism (Oxidation) ATP NADP+ NADPH Intermediates Anabolism (Biosynthesis)

Spontaneous Self-Assembly Theory

micromolecules > macromolecules macromolecules > macromolecular assemblies macromolecular assemblies > organelles organelles > cells cells > tissues and organs tissues and organs > organisms

Waste (CO2/Urea/etc.)

Self-Replication

Characteristics of Biomolecules
Template

(Based on Templates)

Complement

(1) Self-Replication (2) Self-Assembly (3) Self-Regulation Complementarity

Complement Template

Complementarity within Molecules

Self-Assembly

Micromolecules > Macromolecules Macromolecules > Macromolecular Assemblies

Physical Complementarity Chemical Complementarity

Self-Regulation
B Input A C Output Output Output

Complexity of Biomolecules
Requirement for Structural Diversity

Dynamic Steady-State Catalysts > Control > Self-Regulation

Composition of a Typical Bacterial Cell

Component Avg. MW 18 4 0 200 40,000 109 1 x 106 V a r i ety (#) 1 1 2 500 3000 1 1 000 C o m p lexity 1 8 4 8 0 1 .0 x 105 1 .2 x 108 1 09 1 09

Principle of Structural Simplicity

Micromolecules H2O
Inorganic Ions Organic Compounds

Precursors (few)

Polymerization H2O

Macromolecules
Proteins DNA RNA

Macromolecules (many) [Polymers]

Simply learning structures appears to be a monumental task!

Biopolymers
Types
Homopolymers Heteropolymers

Homopolymers

Length and Branching

Linear homopolymers Branched homopolymers Linear heteropolymers Branched heteropolymers

Linear Homopolymer

Branched Homopolymer

Heteropolymers

Biological Macromolecules
Linear Heteropolymer

Branched Heteropolymer

(Amino Acids)
CH2OH

Proteins

Polysaccharides
(Sugars)
H2O OH O HO OH OH OH HO OH OH OH OH CH2OH O OH CH2OH O CH2OH O OH O

R1 O H2N C H Amino Acid C OH H

H N

R2 C H COOH

H2O
H2N

R1 O C H C N H Protein

R2 C H COOH
HO OH

Amino Acid

Glucose

Glucose

Cellobiose Disaccharide

(Monosaccharide)

Only 20 naturally-occurring amino acids Only linear structures

Only a few sugars (~8) Linear and branched molecules

Lipids

(Various Precursors) Neutral Lipids

O
O H2C O C O HC O C O H2C O C

Lipids

(Various Precursors) Phospholipids

O

H2C OH HC OH + H2C OH Glycerol

R1 COOH + R2 R3 COOH + COOH

3 H2O

H2C O C R1 O HC O C R2 O H2C O C R3 Triacylglycerol (Neutral Lipid)

R1

H2C

C O

R1

Fatty Acids

R2

Glycerol

HC

C O

R2 Alcohol

R3

H2C

P O-

R3

Fatty Acids

Neutral Lipid

Phosphate Phospholipid

Nucleic Acids
(Nucleotides)
NH2 N N NH2 N O CH2 N O O O P O O O P O O O P O N N

O O P O O

O P O O

O P O

Combinations
O
N

N O CH2

N O

OH OH

Ribonucleotides
N O O P O O O P O O O P O

OH

Nucleic Acids

O P O O

O O CH2 O

O
O P O OH

O O CH2 O N

P O

e.g. Glycoproteins Glycolipids

OH

OH

OH

OH

Dinucleotide

Macromolecules are composed of polymers of a few simple precursor molecules

Structural Diversity

Proteins
aa1aa2aa3aan Number of structures = 20n ~100 amino acids per molecule 20100 molecules

Nucleic Acids
N1N2N3Nn 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

Thermodynamic Principles Thermodynamics

Energy and Its Effects on Matter Thermodynamics determines whether a physical process is possible (i.e. spontaneous) Themodynamics provides no information about the rate of a physical process

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Thermodynamic Systems
Closed: Physical Chemistry (Equilibrium)

First and Second Laws of Thermodynamics

First Law of Thermodynamics Energy is Conserved Second Law of Thermodynamics The Universe Tends Toward Maximum Disorder

Open: Biochemistry (Steady-State)

Inputs and Outputs

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 TS Exergonic: spontaneous Endergonic: requires input of energy

Change in Gibbs Free Energy (G)

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Change in Enthalpy (H)

[energy of bonds being broken] minus [energy of bonds being formed]

Change in Entropy (S)

[freedom of motion of products] minus [freedom of motion of reactants]

Exothermic: system releases heat Endothermic: system gains heat

Change in Entropy (S) Reaction Progress and Thermodynamics

Time Course of Reaction

Equilibrium

Transition State
CH3Br + OH
H H C H Br HO C H "Transition State" H Br HO C H

CH3OH +

Br
H H + Br-

A > B
B A or B
OH- + H

t1/2 (half-life)
A Time

Reactants

Products

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Thermodynamics of the Transition State

A + B > P + Q

Accelerating Chemical Reactions

(Heat)

Ea

Ea

# molecules

Heat

Energy (slow)

(fast)

Accelerating Chemical Reactions (Catalysis Reduces G) Chemical Equilibria

Equilibrium Constants
aA + bB cC + dD

Standard Free Energy Changes

(Standard State Conventions)

!G = !G + RT ln

[C]c[D]d [A]a[B]b

!G = !G + RT ln Keq at equilibrium, !G = 0, and !G = RT ln Keq

One Molar 25C 1 Atmosphere

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Standard State Conventions in Biochemistry

[H2O] = 1
(actual value = 55.5 M incorporated into Keq)

Coupled Reactions
Additivity of Free Energy Changes

[H+] = 107 M (pH = 7)

Coupled Reactions
!G (kJ/mol) Fructose-6-P + Pi > Fructose-1,6-bisP + H2O ATP + H2O > ADP + Pi Fructose-6-P + ATP > Fructose-1,6-bisP + ADP 13.3 -30.5 -17.2
o

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