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Ahern. Biochemistry Free and Easy. V3.0. 2013.

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Chapter 1 Cells, Water, and Buffers
Introduction
Cells: The Bio of Biochemistry
Water, Water Everywhere
Buffers Keep the Cellular Environment Stable
Henderson-Hasselbalch
Chapter 2 Energy
Introduction
Oxidative Energy
Oxidation vs. Reduction
Energy Coupling
Entropy and Energy
Gibbs Free Energy
Cellular Phosphorylations
  Substrate Level Phosphorylation
  Oxidative Phosphorylation
  ATP Synthase
  Photophosphorylation
  Chloroplasts vs. Mitochondria
Energy Efficiency
Metabolic Controls
Molecular Battery Backups
Chapter 3 Structure & Function
Building Blocks
Proteins
  Primary Structure
  Secondary Structure
    Alpha helix
    Beta Strands
  Fibrous Proteins
  Ramachandran Plots
  Tertiary Structure
  Hydrophobic Effects
  Quaternary Structure
  Other Protein Structural Features
  Cooperativity
  Bohr Effect
  2,3 BPG
  Denaturation
  Forces Stabilizing Structure
  Refolding Denatured Proteins
  Irreversible Denaturation
  Prions and Misfolding
Nucleic Acids
  Superhelicity
  RNA Structures
  Denaturing Nucleic Acids
Carbohydrates
  Monosaccharides
  Stereoisomer Nomeclature
  Boat/Chair Conformations
  Oligosaccharides
  Polysaccharides
  Amylose/Amylopectin
  Glycogen
  Cellulose
  Glycosaminoglycans
Lipids and Membranes
  Fatty Acids
  Membrane Lipids
  Lipid Bilayers
  Membrane Proteins
  Membrane Transport
  Sodium-Potassium ATPase
  Bacteriorhodopsin
  Fat Soluble Vitamins
Chapter 4 Catalysis
Introduction
Activation Energy
General Mechanisms of Action
Substrate Binding
Enzyme Flexibility
Active Site
Chymotrypsin
Enzyme Parameters
  V MAX & K CAT
  K M
Perfect Enzymes
Lineweaver-Burk Plots
Enzyme Inhibition
  Competitive Inhibition
  No Effect On V MAX
  Increased K M
  Non-Competitive Inhibition
  Uncompetitive Inhibition
  Suicide Inhibition
Control of Enzymes
  Allosterism
  Covalent Control of Enzymes
  Other Controls of Enzymes
Ribozymes
Chapter 5 Flow of Genetic Information
DNA Replication
DNA Repair
Post-Replicative Mismatch Repair
Systems to Repair Damage to DNA
  Nucleotide Excision Repair
  Base Excision Repair
Transcription
Regulation of Transcription
RNA Processing
Translation
Chapter 6 Metabolism I
Definitions
Perspectives
Glycolysis
  Intermediates
  Reactions
  Enzymes/Control
  Pyruvate Metabolism
Gluconeogenesis
Citric Acid Cycle
Glyoxylate Pathway
Acetyl-CoA Metabolism
Cholesterol Metabolism
Ketone Body Metabolism
Prostaglandin Synthesis
Fatty Acid Oxidation
  Oxidation of Odd-Chain Fatty Acids
  Unsaturated Fatty Acid Oxidation
  Enzymes of Beta Oxidation
  Alpha Oxidation
Fatty Acid Synthesis
  Enzymes of Fatty Acid Synthesis
  Elongation of Fatty Acids
  Desaturation of Fatty Acids
Metabolism of Fat
Connections to Other Pathways
Chapter 7 Metabolism II
Carbohydrate Storage and Breakdown
  Glycogen Breakdown
    Regulation of Glycogen Metabolism
    GPa/GPb Allosteric Regulation
    GPa/GPb Covalent Conversion
    Turning Off Glycogen Breakdown
  Glycogen Synthesis
    Regulation of Glycogen Synthesis
    Maintaining Blood Glucose Levels
Pentose Phosphate Pathway
Calvin Cycle
C 4 Plants
Urea Cycle
Nitrogen Fixation
Amino Acid Metabolism
Amino Acid Catabolism
Nucleotide Metabolism
Pyrimidine de novo Biosynthesis
Purine de novo Biosynthesis
Deoxyribonucleotide de novo Biosynthesis
Chapter 8 Signaling
Cell Signaling
Ligand-gated Ion Channel Receptors
Nuclear Hormone Receptors
G-protein Coupled Receptors (GPCRs)
Receptor Tyrosine Kinases (RTKs)
Chapter 9 Techniques
Introduction
Cell Disruption
Fractionation
Ion Exchange Chromatography
Gel Exclusion Chromatography
Affinity Chromatography
HPLC
Histidiine Tagging
Electrophoresis
  Agarose
  SDS-PAGE
  Isoelectric Focusing
  2-D Gel Electrophoresis
Protein Cleavage
Microarrays
Blotting
Making Recombinant DNAs
PCR
Lac Z Blue-White Screening
Reverse Transcription
Chapter 10 Putting It All Together
Chapter 11 Outlines, Notes, Exams
Appendix - Class Materials
Appendix - Key Points