Biochemistry 153A

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Biochemistry 153A

• Professor Richard L. Weiss
• Fall 2009

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INTRODUCTION
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BiochemistryThe Study of Life on the Molecular
Level

• Bio Life
• Chemistry Property of Molecules

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What You Will Learn

• Composition , structures and functions of
  proteins, carbohydrates, and lipids
• 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.

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Principles of Enzyme Catalysis

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

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Central Metabolic Pathways of Energy Transduction

• Glycolysis
• Tricarboxylic Acid Cycle(TCA Cycle Krebs Cycle
  Citric Acid Cycle)
• Electron Transport Chain
• Oxidative Phosphorylation

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Properties of Life(Norman Horowitz)

• Replication
• Catalysis
• MutabilityOrganisms

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Cells(Basis for Life)

• Prokaryotes lack nucleus
• Eucaryotes membrane-enclosed nucleus

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Procaryotes(e.g. Escherichia coli)

• Adapted to fluctuating environments

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Procaryote Shapes
Figure 1-7
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Procaryote Structure
Figure 1-6
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Metabolic Energy Sources

• Autotrophs (self-feeding) synthesize all
  cellular constituents
• Chemolithotrophs oxidation of inorganic
  compounds
• Photoautotrophs photosynthesis
• Heterotrophs (other-feeding) dependent on
  autotrophs - oxidation of organic compounds
• Obligate aerobes
• Facultative anaerobes
• Obligate anaerobes

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Eucaryotes(e.g. Saccharomyces cerevisiae or
human cells)

• Adapted to stable environments

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Eucaryotes(Differences with Procaryotes)

• Increased complexity gt10,000 rxns vs. 3,000
  rxns
• Increased size 103 106 x volume
• Smaller surfacevolume ratio
• Membrane-enclosed organelles
• Increased solvent capacity
• Increased membrane surface
• Compartmentation

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Eucaryotic Cell Structure
Figure 1-8
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Evolutionary Relationships
Figure 1-9
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Fundamental Similarity of Biological Processes

• Procaryotes
• Eucaryotes

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Advantages of Studying Microorganisms

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

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Principles of Biochemistry

• Genetic Hypothesis
• Central Dogma (of Molecular Biology)
• Enzyme Hypothesis
• Energy Hypothesis
• Spontaneous Self-Assembly Hypothesis

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Genetic Hypothesis
DNA as the Genetic Material
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Central Dogma(of Molelcular Biology)
Figure 3-13
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Enzyme Hypothesis
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Energy Hypothesis(Biological Transformations)

• Catabolism exergonic oxidation
• Anabolism endergonic processes

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Anabolism and Catabolism(Heterotrophs)
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ATP
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Sources of ATP

• Phototrophs photosynthesis
• Chemotrophs oxidation of organic compounds
  (e.g. carbohydrates, lipids, and proteins)

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Figure 1-11
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Spontaneous Self-Assembly Hypothesis
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Characteristics of Biomolecules

• Self-Replication
• Self-Assembly
• Self-Regulation

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Self-Replication(Based on Templates)
Complementarity
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Complementarity within Molecules
Figure 1-5
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Self-Assembly

• Micromolecules gt Macromolecules
• Macromolecules gt Macromolecular Assemblies

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Self-Regulation
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Thermodynamics versus Kinetics
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Complexity of Biomolecules

• Requirement for Structural Diversity

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Composition of a Typical Bacterial Cell
Simply learning structures appears to be a
monumental task!
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Principle of Structural Simplicity
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Biopolymers

• Types
• Homopolymers
• Heteropolymers
• Length and Branching
• Linear homopolymers
• Branched homopolymers
• Linear heteropolymers
• Branched heteropolymers

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Homopolymers
Linear Homopolymer
Branched Homopolymer
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Heteropolymers
Linear Heteropolymer
Branched Heteropolymer
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Biological Macromolecules
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Proteins(Amino Acids)
Only 20 naturally-occurring amino acids Only
linear structures
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Polysaccharides(Sugars)
Only a few sugars (8) Linear and branched
molecules
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Lipids (Various Precursors)Neutral Lipids
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Lipids (Various Precursors)Phospholipids
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Nucleic Acids(Nucleotides)
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Combinations

• e.g.
• Glycoproteins
• Glycolipids

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Macromolecules are composed of polymers of a few
simple precursor molecules
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Structural Diversity
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Proteins

• aa1aa2aa3aan
• Number of structures 20n
• 100 amino acids per molecule
• 20100 molecules

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Nucleic Acids

• N1N2N3Nn
• Number of structures 4n
• 1,000,000 nucleotides per DNA molecule
• 41,000,000 molecules!!!

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Polysaccharides

• Homopolymers and Heteropolymers
• Many different sugar molecules
• Linear and branched
• Many different molecules!!!

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Lipids

• Many complex molecules!!!

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Simple construction provides an immense number of
possible structures fully capable of providing
the necessary diversity required for life.