Structural Biochemistry

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Contents 1 What is Structural Biochemistry? 2 Relations of Structural Biochemistry with other Sciences 3 Water 4 Proteins 5 Carbohydrates 6 Lipids 7 Nucleic Acid 8 Bioinformatics 9 Protein Function 10 Catalysis 11 Enzyme Catalytic Mechanism 12 Enzyme Regulation 13 Catalytic Strategies 14 Polymerase Chain Reaction (PCR)

[edit] What is Structural Biochemistry?

1. Definition
2. History
3. Outside the Cell

[edit] 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 Group
         1. Hydroxyl
         2. Carbonyl
         3. Carboxyl
         4. Amino
         5. Sulfhydryl
         6. Phosphate
      2. Types of Macromolecules
         1. Carbohydrates
         2. Nucleic Acids (DNA)
         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
   3. Inorganic Chemistry
      1. Metals
         1. Alkali Metals
         2. Alkali Earth metals
         3. Transition Metals
         4. Poor Metals
         5. Rare Earth Metals
      2. Semimetals
      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 & 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. Genetic Bases

[edit] Water

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

[edit] 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. Isoelectric Focusing
      5. Dialysis
   3. Analysis of Purification Result
      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 toward Protein Investigation
       1. Antibody and Antigen Interaction
       2. Usage of Antibody in Protein Research
          1. Enzyme-Linked Immunoabsorbent Assay (ELISA)
          2. Western Blotting
          3. Fluorescent Marker
       3. Preparation of Monoclonal Antibody
          1. Sources of production of Monoclonal antibody
       4. Preparation of Polyclonal Antibody
       5. Dynamic Light Scattering
4. Protein Translation
5. Protein Modification
6. Posttranslational Modification of Proteins
7. Protein Phosphorylation by Protein Kinases
8. Protein O-GlcNAcylation by O-linked β-N-acetylglucosamine (O-GlcNAc)
9. Protein Acetylation by Lipids
10. Protein Functions
    1. Structural
    2. Binding
    3. Catalysis
    4. Switching

[edit] Carbohydrates

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

[edit] 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

[edit] Nucleic Acid

1. Phosphate
2. Sugars
   1. Deoxyribose Sugar
   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. Difference 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. DNA Mutation
   1. Transposons
10. Enzymes Used for Cloning
    1. The activities of the cloning enzymes
    2. 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
    3. Cloning Tips
    4. The Stepwise Process of How DNA is Cloned and Inserted into the Vector
    5. Immune System
11. Genome Analysis
    1. DNA Microarrays
    2. Sequenced Genomes
    3. Single Nucleotide Polymorphisms (SNPs)
    4. The Impact of Genome Analysis on Medicine
12. 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
13. Single Molecule DNA Sequencing
14. Methods for Determining Recombinant DNA in the Environment

[edit] Bioinformatics

1. Homology
2. Sequences Alignments
3. Structural Alignments
   1. Programs Used For Structural Alignment
      1. DALI
      2. Combinatorial Extension
      3. SSAP
4. Structural Alignments
5. Evolution Trees
6. Combinatorial Chemistry
7. Comparative Genomics
8. Transgenic Animal

[edit] Protein Function

1. Binding
2. Ligand
3. Binding sites
4. Induced Fit
5. Lock and Key
6. Association Constant
7. Dissociation Constant
8. Cooperativity
9. Allosterism
10. Allosteric Regulation
11. Hill Equation
12. Concerted Model
13. Sequential Model
14. Myoglobin
    1. Heme group
    2. Biological Roles of Metal Ions
15. Hemoglobin
    1. 1. Hemoglobin-Heme Group
       2. Sickle disease
       3. Thalassemia
       4. AHSP
       5. Bohr Effect
    2. Regulation
       1. Regulation by 2,3-bisphosphoglycerate
16. Oxygen-Binding Curve
17. Antibodies
    1. Epitope
    2. Antigen
    3. Major Histocompatibility Complex (MHC)
       1. MHC Class I
       2. MHC Class II
18. Myosin
19. Actin
20. Membrane Protein (1)
21. Membrane Protein (2)
22. Insulin
23. Additional Globins

[edit] Catalysis

1. Enzyme
   1. Cofactors
   2. Prosthetic Group
   3. Apoenzyme and Holoenzyme
   4. Substrate specificity
   5. Active Site
   6. Catalytic Triad
2. Zymogen
3. Enzyme Classification
   1. Oxidoreductases
   2. Transferases
   3. Hydrolases
   4. Lyases
   5. Isomerases
   6. Ligases
4. Characteristics of enzyme
   1. Binding energy
   2. Specificity
   3. Desolvation
   4. Ground state
   5. Pre-steady state
   6. Steady state
5. Gibbs free energy graph
   1. Transition state
   2. Activation energy
   3. Reaction intermediates
6. Rates and Constants
   1. Rate constant
   2. Rate equation
   3. Rate-limiting step
   4. Equilibrium constant
   5. Initial rate
7. Michaelis and Menten Equation
   1. Michaelis constant
   2. Kcat/Km
   3. Maximum velocity
   4. sequential reactions
   5. Double displacement reactions
8. Double-Reciprocal plot
9. Reversible Inhibitors
   1. Competitive Inhibitor
   2. Uncompetitive Inhibitor
   3. Noncompetitive Inhibitor
10. Irreversible Inhibitor
    1. Group Specific Reagent
    2. Affinity Labels
    3. Suicide Inhibitors
11. Time-dependent Inhibition
12. Transition-State Analogs
13. Penicillin
14. Effects of pH on enzyme activity

[edit] Enzyme Catalytic Mechanism

1. Proteases
   1. Chymotrypsin
   2. Cysteine Proteases
   3. Aspartyl Proteases
   4. Serine Proteases
   5. Threonine Proteases
   6. Metalloproteases
   7. Catalytic Triad and S1 Pocket
2. Dehydrogenases
3. Carbonic Anhydrase
4. Restriction Enzyme
5. Nucleotide Monophosphate Kinase

[edit] Enzyme Regulation

1. Feedback inhibition
2. Isozymes
3. Reversible covalent modification
   1. Phosphorylation
4. Proteolytic activation
5. Enzyme Cascades
6. Transcription activation
7. Allosteric Control

[edit] Catalytic Strategies

1. Covalent Catalysis
2. Metal Ion Catalysis
3. Catalysis by Approximation
4. Enzyme Classification

[edit] Polymerase Chain Reaction (PCR)

1. What is PCR?
2. How PCR is Performed
3. Uses of PCR