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Wikibooks

Up to date as of January 23, 2010

From Wikibooks, the open-content textbooks collection

Contents

What is Structural Biochemistry?

  1. Definition
  2. History
  3. Outside the Cell

Relations of Structural Biochemistry with other Sciences

  1. Physics
    1. Thermodynamics
      1. Zeroth Law
      2. First law
      3. Second law
      4. Third law
      5. Entropy
      6. Enthalpy
      7. Free energy
      8. Endergonic reaction
      9. Exergonic reaction
    2. Bioenergetics
    3. Energy coupling in chemical reactions
    4. Metabolism
      1. Anabolism
      2. Catabolism
  2. Chemistry
    1. Chemical Bonding
      1. Covalent Bonds
      2. Hydrogen bonds
      3. Hydrophobic Interaction
      4. Van der Waals Interaction
      5. Dipole Interaction
      6. Ionic Interaction
    2. Organic Chemistry
      1. Organic Functional Groups
        1. Hydroxyl
        2. Carbonyl
        3. Carboxyl
        4. Amino
        5. Sulfhydryl
        6. Phosphate
      2. Types of Macromolecules
        1. Carbohydrates
        2. Nucleic Acids
        3. Lipids
        4. Proteins
      3. Chemistry of Important Organic Molecules in Biochemistry
        1. Vitamins and Cofactors
      4. Important Organic Reactions in Biochemistry
        1. Peptide Bonding
      5. Techniques in Organic Chemistry
        1. Methods of Separation and Isolation
        2. Methods of Purification
        3. Methods of Identification
    3. Inorganic Chemistry
      1. Metals
        1. Alkali Metals
        2. Alkali Earth Metals
        3. Transition Metals
        4. Poor Metals
        5. Rare Earth Metals
        6. Biological Roles of Metal Ions
        7. Oxidation states
      2. Metalloids
      3. Nonmetals
        1. Halogens
        2. Noble Gases
  3. Biological Bases
    1. Evolutionary Bases
      1. RNA World Hypothesis
      2. Three Domains of Life
        1. Archaea
        2. Bacteria
        3. Eukarya
      3. The Endosymbiotic Theory
    2. Cellular Bases
      1. Cell Organelles and Structural Biochemistry
        1. Nucleus
        2. Nucleolus
        3. Ribosome
        4. Endoplasmic Reticulum
        5. Golgi Apparatus
        6. Mitochondria
        7. Centrioles
        8. Plant Cell
        9. Animal Cell
      2. Prokaryotes and Eukaryotes
      3. Stem Cells
    3. Genetic Bases
  4. Medicine & Drug Design
    1. Aspirin
    2. Phenelzine
    3. Pepcid
    4. Adalat
    5. Luvox
    6. Allegra

Water

  1. Unique Properties
  2. pH
  3. Buffer
  4. Osmosis
  5. Polarity
  6. Strong Intermolecular Forces

Proteins

  1. Amino Acids
  2. Proteins
    1. Structures
    2. Protein Folding
  3. Techniques to Study Proteins
    1. Synthesis
    2. Purification
      1. Differential Centrifugation
      2. Salting Out
      3. High pressure Liquid Chromatography (HPLC)
        1. Gel-filtration Chromatography
        2. Ion-Exchange Chromatography
        3. Affinity Chromatography
        4. Hydrophobic Interaction Chromatography (HIC)
        5. Column Chromatography
        6. Planar Chromatography
          1. Paper Chromatography
          2. Thin Layer Chromatography
        7. Gas Chromatography
        8. Liquid Chromatography
      4. Isoelectric Focusing
      5. Dialysis
    3. Analysis of Purification Results
      1. Quantifying Proteins
        1. Gel Electrophoresis
        2. SDS-Polyacrylamide Gel Electrophoresis
        3. Edman Sequencing
    4. Analytical Ultracentrifugation
    5. Crosslinking Technique
    6. Protein Sequence Determination Techniques
      1. Proteases
      2. Mass Spectroscopy
    7. Protein Structure Determination Methods
      1. NMR Spectroscopy
      2. X-ray Crystallography
      3. Cryo-Electron Microscopy
      4. Neutron Diffraction
    8. Measuring Enzymatic Activity Using Spectroscopy
    9. Protein Glycosylation
    10. Immunology: Another Approach Towards Protein Analysis
      1. Antibody and Antigen Interaction
        1. Agglunation Reactions
      2. Use of Antibodies in Protein Research
        1. Enzyme-Linked Immunoabsorbent Assay (ELISA)
        2. Western Blotting
        3. Fluorescent Marker
      3. Preparation of Monoclonal Antibodies
        1. Sources of Monoclonal Antibody Production
      4. Preparation of Polyclonal Antibodies
      5. Dynamic Light Scattering
    11. Quantum Dots
  4. Protein Translation
    1. Myristoylation
  5. Protein Modification
    1. Palmitoylation
    2. Prenylation
  6. Posttranslational Modification of Proteins
    1. Adenylation
    2. ADP-Ribosylation
    3. Acetylation
  7. Protein Phosphorylation by Protein Kinases
  8. Protein in Signal Transduction
  9. Protein O-GlcNAcylation by O-linked β-N-acetylglucosamine (O-GlcNAc)
  10. Protein Acetylation by Lipids
    1. Proteins are modified by fatty acids
  11. Protein Functions
    1. Structural
    2. Binding
      1. Myoglobin
      2. Hemoglobin
    3. Catalysis
      1. Enzyme Classification
    4. Switching
  12. Regulation
    1. Interferon
  13. Lysozyme

Carbohydrates

  1. Monosaccharides
    1. Stereochemistry of Monosaccharides
  2. Ketoses
  3. Aldoses
  4. Disaccharides
  5. Oligosaccharides
  6. Sequencing Oligosaccharides Using Glycosidases
  7. Polysaccharides
  8. Carbohydrate Derivatives
  9. Carbohydrates and Proteins
    1. Lectins
    2. Proteoglycans
    3. Blood Type
    4. Virus

Lipids

  1. Fatty Acids
  2. Cholesterol
  3. Biological Membranes
  4. Membrane Lipids
  5. Membrane Transport
  6. Membrane Fusion
  7. Micelles
  8. Lipid Bilayer
  9. Membrane Fluidity
  10. Fluid Mosaic Model
  11. Techniques to Study Membranes
    1. Electron Microscopy
    2. Preparation of Bilayers and Vesicles
    3. Scanning Calorimetry
    4. Fluorescence Photo Bleaching
  12. Waxes, Soaps, and Detergents
    1. Fatty Wax
    2. Soap
    3. Detergents
  13. Isoprenoids
  14. Lipid Rafts

Nucleic Acid

  1. Phosphate
  2. Sugars
    1. Deoxyribose
    2. Ribose
  3. Nitrogenous Bases
    1. Purines
      1. Adenine
      2. Guanine
      3. Purine
      4. Hypoxanthine
      5. Xanthine
      6. Theobromine
    2. Pyrimidines
      1. Cytosine
      2. Uracil
      3. Thymine
      4. Pyrimidine
  4. Connection Between Monomers
  5. DNA
    1. DNA structure
      1. Telomeres
      2. Unusual Structures
    2. Supercoiling and Nucleosomes
    3. DNA Denaturation
    4. Avery-MacLeod-McCarty Experiment
    5. Hershey-Chase Experiment
    6. Chargaff's Experiments
    7. Watson and Crick's Article
    8. Franklin's DNA X-ray Crystallography
    9. Replication Process
      1. DNA Polymerase
    10. Meselson-Stahl Experiment
    11. Knockout Mouse
    12. Transgenic Animals
  6. RNA
    1. Messenger RNA (mRNA)
    2. Transfer RNA (tRNA)
    3. Ribosomal RNA (rRNA)
    4. MicroRNA (miRNA)
    5. Other RNA
    6. RNA Polymerase
    7. Riboswitch
    8. Interference RNA (RNAi)
    9. Differences between DNA and RNA
    10. Transcription
      1. Nucleic Acid
      2. Transcription
      3. Reverse Transcription
    11. Translation
    12. RNA Modification
      1. Introns
      2. Exons
      3. RNA Splicing
      4. snRNP
    13. Telomere
    14. RNA Purification
  7. DNA Manipulation Techniques
    1. Restriction Endonucleases
    2. Southern Blot
    3. Northern Blot
    4. DNA Sequencing
    5. DNA Cataloging
    6. DNA Synthesis
    7. DNA Amplification
    8. Alcohol Precipitation
    9. Gene Regulation
    10. Bacterial Transformation Technique
  8. Genetic Code
  9. Gene Expression
  10. DNA Mutation
    1. Transposons
    2. Genetic Diseases
  11. Cloning Enzymes
    1. Enzymes Used for Cloning
      1. T4 DNA Ligase
      2. T4 RNA Ligase
      3. T4 Polynucleotide Kinase
      4. Calf Intestinal Alkaline Phosphatase
      5. RecA Protein
      6. AgarACE® Enzyme
    2. Cloning Tips
    3. Process of DNA Cloning and Vector Insertion
    4. Immune System
  12. Genome Analysis
    1. DNA Gel Electrophoresis
    2. DNA Microarrays
    3. Sequenced Genomes
    4. Single Nucleotide Polymorphisms (SNPs)
    5. The Impact of Genome Analysis on Medicine
  13. DNA Recombinant Techniques
    1. History and Study of Bacteriophage Lambda
    2. Plasmid
      1. Lytic Pathway
      2. Lysogenic Pathway
    3. Genomic Library
    4. Detecting Specific Genes
    5. Mutagenesis
    6. Designer Genes
    7. Human Genome Project
    8. Gene Therapy
    9. Artificial Chromosomes
      1. Bacterial Artificial Chromosomes (BAC)
      2. Yeast Artificial Chromosomes (YAC)
    10. Heredity and Related Experiments
    11. Directed Changes in DNA
    12. Eukaryotic Recombination
  14. Single Molecule DNA Sequencing
  15. Methods for Determining Recombinant DNA in the Environment
  16. Polyermase Chain Reaction
    1. How PCR is Performed
    2. Uses of PCR
  17. Biology of Cancer
    1. Defective Repair of DNA
    2. Mutagenesis
      1. Ames test

Bioinformatics

  1. Homology
  2. Sequences Alignments
  3. Structural Alignments
    1. Programs Used For Structural Alignment
      1. DALI
      2. Combinatorial Extension
      3. SSAP
      4. GANGSTA+
      5. MAMMOTH
      6. RAPIDO
      7. SABERTOOTH
      8. TOPOFIT
    2. RNA Structural Alignment
  4. Evolution Trees
  5. Combinatorial Chemistry
  6. Comparative Genomics
  7. Transgenic Animal
    1. Regulation

Protein Function

  1. Binding
  2. Ligand
  3. Binding Sites
  4. Lock and Key
  5. Induced Fit
  6. Cooperativity
  7. Myoglobin
    1. Heme Group
    2. Biological Roles of Metal Ions
    3. Myoglobin's Oxygen Binding Curve
    4. Additional Globins
  8. Hemoglobin
    1. Hemoglobin-Heme Group
    2. Sickle Cell Anemia
    3. Thalassemia
    4. AHSP
    5. Bohr Effect
    6. Affinity Constant
    7. Regulation
    8. Regulation by 2,3-Bisphosphoglycerate (2,3-BPG)
    9. Oxygen-Binding Curve
    10. Other Globins
  9. Antibodies
    1. Epitope
    2. Antigen
    3. Major Histocompatibility Complex (MHC)
      1. MHC Class I
      2. MHC Class II
  10. Myosin
  11. Actin
  12. Insulin
  13. Fluorescent Proteins
  14. Ferritin and transferrin
  15. Siderochromes

Catalysis

  1. Enzyme
    1. Binding Energy
    2. Desolvation
    3. States: Ground, Pre-steady,& Steady
    4. Coenzymes
    5. Cofactors
    6. Prosthetic Group
    7. Apoenzyme and Holoenzyme
    8. Active Site and Enzyme Specificity
    9. Catalytic Triad
    10. Evolution of Enzymes
  2. Zymogen
  3. Gibbs Free Energy Diagram
    1. Transition State
    2. Activation Energy
    3. Reaction Intermediates
  4. Rates and Constants
    1. Rate Constant
    2. Rate Equation
    3. Rate-limiting Step
    4. Equilibrium Constant
    5. Initial Rate
  5. Mechanisms
    1. Acid-Base Catalysis
    2. Covalent Catalysis
    3. Metal Ion Catalysis
    4. Catalysis By Approximation
  6. Michaelis-Menten Equation
    1. Michaelis Constant
    2. Kcat/K M
    3. Maximum Velocity
    4. Sequential Reactions
    5. Double Displacement Reactions
    6. Allosteric Enzymes
  7. Double-Reciprocal Plot
  8. Reversible Inhibitors
    1. Competitive Inhibitor
    2. Uncompetitive Inhibitor
    3. Noncompetitive Inhibitor
  9. Irreversible Inhibitor
    1. Group Specific Reagent
    2. Affinity Labels
    3. Suicide Inhibitors
  10. Time-dependent Inhibition
  11. Transition-State Analogs
  12. Penicillin
  13. Effects of pH on Enzyme Activity
  14. Site-Directed Mutagenesis
  15. Multi-substrate reactions

Specific Enzymes and Catalytic Mechanisms

  1. Proteases
    1. Hydrolysis
    2. Chymotrypsin
    3. Cysteine Proteases
    4. Aspartyl Proteases
    5. Serine Proteases
    6. Threonine Proteases
    7. Metalloproteases
    8. Catalytic Triad and S1 Pocket
  2. Dehydrogenases
  3. Carbonic Anhydrase
  4. Carboxypeptidase
  5. Restriction Enzyme
  6. Glutathione Reductase
  7. Nucleotide Monophosphate Kinase
  8. Phillips mechanism
  9. Isomerases
    1. Triose Phosphate Isomerase
  10. Pingpong Mechanism
  11. Summary

Enzyme Regulation

  1. Feedback Inhibition
  2. Isozymes
    1. Enzyme Regulation/Isoenzyme Analysis
  3. Reversible Covalent Modification
    1. Phosphorylation
    2. Ubiquitination
    3. Methylation
    4. Acetylation
    5. Adenylation
    6. Myristoylation
  4. Proteolytic Activation
  5. Enzyme Cascades
  6. Transcription Activation
  7. Allosteric Control

Membrane Proteins

  1. Active Transport
  2. Passive Transport
  3. Membrane Gradients and Thermodynamics
  4. P-type ATPases
  5. ATP-Binding Cassette Proteins
  6. Symporters
  7. Antiporters
  8. Uniporters
  9. Ion Channels
    1. Patch Clamp
  10. Ligand-gated Ion Channels
  11. Gap Junctions
  12. Water Channels
  13. /Membrane Proteins/Cotransporters
  14. /Membrane Proteins/Control Systems:Nervous System

Control Systems

  1. Nervous System
  2. Circulatory System
  3. Respiratory System
  4. Muscular System
  5. Endocrine System

Cell Signaling Pathways

  1. Juxtacrine Signaling
  2. Paracrine Signaling
  3. Endocrine Signaling
  4. G-Proteins and G-Protein Coupled Receptors
  5. Adenylate Cyclase and cAMP Signaling
  6. Phosphoinositol Signaling
  7. Calcium Signaling
  8. Protein Kinases Signaling Cascades
  9. Receptor Tyrosine Kinases
  10. Insulin Signaling
  11. Epidermal Growth Factor Signaling
  12. RAS
  13. Problems in Signaling that cause Cancer

Molecular Modeling

  1. Molecular Docking

Cells Transforming Energy

  1. Metabolism Coupled Reactions
  2. ATP

/Glycolysis and Gluconeogenesis/Glycolysis and Gluconeogenesis

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