Wikibooks

Structural Biochemistry


Structural biochemistry is a branch of the life sciences, specially biochemistry, that combines biology, physics, and chemistry to study living organisms and to summarize some mutual physicochemical underlying principles that all forms of life share. It is also referred to more generally as structural biology. Structural biochemists aim to describe, in atomic precision level, molecular terms of the structures, mechanisms, and chemical processes shared by all metabolism of all organisms, providing organizing principles that underlie life in all its diverse forms.

Depiction of interaction between cap analogue molecule and eIF4E protein.

A printable version of Structural Biochemistry is available. (edit it)

Relations of Structural Biochemistry with other Sciences

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Physics

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  1. Thermodynamics
    1. Zeroth Law
    2. First law
    3. Second law
      1. Thermodynamic Cycles
    4. Third law
    5. Internal Energy
    6. Entropy
    7. Enthalpy
    8. Heat capacity
    9. Free energy
    10. Material Equilibrium
    11. Phase Diagrams
    12. Phase Equilibria
    13. Endergonic reaction
    14. Exergonic reaction
    15. Molecular Thermodynamics
    16. Thermodynamic Equilibrium
    17. Ideal Gas
    18. Equation for Process Calculations for Ideal Gases
    19. Irreversible Process
    20. Application of the Virial Equations
  2. Bioenergetics
  3. Energy coupling in chemical reactions
  4. Metabolism
    1. Anabolism
    2. Catabolism
  5. Biophysics- Single Molecule techniques

Chemistry

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  1. Chemical Bonding
    1. Covalent Bonds
    2. Noncovalent Bonds
    3. Hydrogen bonds
    4. Hydrophobic Interaction
    5. Van der Waals Interaction
    6. Dipole Interaction
    7. Ionic Interaction
    8. Disulfide Bonds
      1. Multiple ways to make Disulfides
    9. Electronic Structure Theories
  2. Biochemical Natural Selection
    1. Electronic Structure Theories
  3. Organic Chemistry
    1. Organic Functional Groups
      1. Hydroxyl
      2. Carbonyl
      3. Carboxyl
      4. Amino
      5. Amide
      6. Sulfhydryl
      7. Phosphate
    2. Organic Synthesis
    3. Types of Macromolecules
      1. Carbohydrates
      2. Nucleic Acids
      3. Lipids
      4. Proteins
    4. Reagents
    5. Mechanisms of Organic Molecules
    6. Stereochemistry of Organic Molecules
    7. Chemistry of Important Organic Molecules in Biochemistry
      1. Vitamins and Cofactors
      2. Vitamin D
      3. Vitamin K
      4. Vitamin C
      5. Vitamin A
      6. Vitamin E
      7. Vitamin B
        1. Vitamin B12
        2. Vitamin B6
    8. Important Organic Reactions in Biochemistry
      1. Peptide Bonding
    9. Techniques in Organic Chemistry
      1. Methods of Separation and Isolation
      2. Methods of Purification
      3. Methods of Identification
      4. Method of Combustion Analysis
      5. Fischer Esterification
      6. Trans Esterification
    10. Organic Chemistry Terms
    11. Synthesis
    12. Organometallic Chemistry
      1. Bioorganometallic Chemistry
    13. Degree of Unsaturation
    14. Acid-Base Chemistry
  4. 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
      8. Copper Metallochaperones
      9. Bioremediation of Metals
    2. Metalloids/Semimetals
      1. Introduction of porous Silicon
      2. Carbon Nanomaterials
    3. Nonmetals
      1. Halogens
      2. Noble Gases
    4. Linear Combination of Atomic Orbitals
    5. Molecular Orbitals
    6. How to Construct Molecular Orbital Diagram
    7. Reduction Formula and Projection Operator
  5. Point Groups
  6. Character Table
  7. SALC
  8. Chemical Reactions
    1. Rate Laws
    2. Kinetic and Thermodynamic Control
    3. Reaction types
  9. Molecular Geometry
  10. Periodic trends
    1. Atomic Radius
    2. Electron Affinity
    3. Electronegativity
    4. Ionization Energy
    5. Metallic Behavior
    6. Melting Point
  11. Medicinal Chemistry
  12. Cystalline solid state
    1. Formulas and structures
  13. General Chemistry
    1. Significant Figures
    2. Matter

Biology

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  1. Properties of Living Organisms
  2. Retinoid

Evolution

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  1. History of the Earth
  2. RNA World Hypothesis
  3. Evolution in the Laboratory
  4. Evolution of Humans
  5. Evolution of Populations
  6. The Oparin-Haldane Hypothesis
  7. Molecular Evolution
  8. Three Domains of Life
    1. Archaea
      1. SAMPylation Protein in Archaea
    2. Bacteria
    3. Eukarya
      1. Community Ecology
  9. The Endosymbiotic Theory
  10. The Evolution of Membranes
  11. Natural Selection of Aluminum and Silicon
  12. Speciation
  13. Gene Flow
  14. Organismic and Evolutionary Biology
  15. Hardy-Weinberg Principle

The Cell

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  1. Cell Organelles and Structural Biochemistry
    1. Nucleus
    2. Nucleolus
    3. Ribosome
      1. Ribosome Synthesis
      2. Maturation
      3. RNP
    4. Chloroplast
    5. Proteins
    6. Endoplasmic Reticulum
      1. ER Stress & Type 2 Diabetes
    7. Golgi Apparatus
    8. Mitochondria
      1. Cardiolipin and the Mitochondria
    9. Centrioles
    10. Cytosol
    11. Lysosome
    12. Peroxisome
    13. Cytoskeleton
    14. Functional Categories of Eukaryotic Organelles
    15. Plant Cell
      1. Heat Stress Response
      2. Cellulosomes
    16. Animal Cell
      1. Membrane Contact Site
    17. Imaging cellular architecture with X-rays
    18. Fluorescence
    19. Cell Aging
    20. Cell Adhesion
  2. Prokaryotes and Eukaryotes
    1. CRISPR defense system (Prokaryotes)
    2. Control of Gene Expression in Prokaryotes
    3. Control of Gene Expression in Eukaryotes
    4. Eukaryotic Alternative Splicing
    5. Metal Levels in Eukaryotes
  3. Stem Cells
    1. Embryonic Stem Cells
    2. Adult Stem Cells
  4. Cells Transforming Energy
    1. Metabolism Coupled Reactions
    2. ATP
    3. Acetyl-CoA
    4. Glycolysis and Gluconeogenesis
      1. Anaerobic Respiration (Fermentation)
      2. Aerobic Respiration
      3. Pyruvate Dehydrogenase Complex
      4. Krebs Cycle (Citric Acid cycle)
      5. Oxidative Phosphorylation Cycle (Electron Transport Chain cycle)
      6. Gluconeogenesis
      7. Phosphofructokinase-1
        1. Micro-purification
    5. Light Reaction
    6. Calvin Cycle
    7. The Pentose Phosphate Pathway
  5. Control Systems
    1. Nervous System
      1. Parkinson's Disease
    2. Circulatory System
    3. Excretory System
    4. Respiratory System
      1. Asthma/Asthma symptoms
    5. Digestive System
      1. Lactose Intolerance
      2. Crohn's Disease
      3. Cirrhosis
    6. Muscular System
    7. Endocrine System
      1. Ovarian Cancer
      2. Graves Disease
      3. Addison's Disease
    8. Sensory System
      1. Biochemical Pathways of Vision
    9. Immune System
    10. Integumentary System
    11. Reproductive System
  6. 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. Kinases Inhibitors
      1. MPS1 protein kinase inhibitor development
    11. Insulin Signaling
    12. Epidermal Growth Factor Signaling
    13. RAS
    14. ROS
    15. Problems in Signaling that cause Cancer
    16. Transforming Growth Factor Beta
    17. Hormonal Signaling
    18. Apoptosis
    19. RAGE: Pattern Recognition Receptor
    20. Mobile Zinc and Nitric Oxide
    21. Nitric Oxide
    22. Heparan Sulfate
    23. Skeletal Muscle Remodeling
    24. Phagoptosis
    25. Necrosis
    26. Noise in Signaling
    27. Hippo Signaling
    28. JNK Signaling
    29. Immune Signaling
      1. RIG-I-like Receptors (RLR)
      2. NOD-like Receptors (NLR)
      3. IL23R
    30. Apoptosis-Inducing Factor
    31. Adipogenesis: From Stem Cell to Adipocyte
    32. Nitric Oxide and CGMP Response
  7. Secretins
  8. Microscopy
  9. Endocytosis
    1. Actin Assembly during Endocytosis
  10. Virus Entry by Endocytosis
  11. Mitotic Spindles
  12. Pili
    1. Type IV Pili
  13. Flagella
  14. Aging and Metabolic Control Analysis
  15. Short Linear Motifs and Viral Infection
  16. Phagocytosis
  17. Pinocytosis
  18. Cytokine Receptors
  19. Ras-ERK and PI3K-mTOR pathways

Genetics

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  1. The Genetics of Bacteria
  2. Properties of Mutant Alleles
  3. Foundation of Genetics
  4. Genetics terms
  5. Inheritance Patterns
  6. Chromosomes
  7. Epigenomics
    1. Epigenome reader
  8. Mitosis
  9. Meiosis
  10. Homeobox Genes
  11. How can you know if Genes are "on" or "off" in a cell?
  12. Genetic Variants
  13. Structural Variation

Biology of Cancer

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  1. Defective Repair of DNA
  2. Classifications of Cancer
    1. Carcinoma
    2. Sarcoma
    3. Lymphoma
    4. Leukemia
    5. Germ Cell Tumor
    6. Blastoma
  3. Mutagenesis
    1. Ames test
  4. Tumor suppressor genes
    1. PTEN
    2. p53
    3. p63
    4. p73
    5. sequestosome-1
    6. Retinoblastoma
    7. p62
    8. Brooke-Spiegler syndrome
  5. Glutamine Addiction in Cancer
  6. Ligand-Binding Site and Glutamate Receptor Trafficking
  7. Proto-oncogenes

Medicine & Drug Design

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  1. Drug Targeting
  2. Quantum Dot-Aptamer Conjugate
  3. Pharmaceutical Dosage Forms
    1. Solid Dosage Forms
    2. Liquid Dosage Forms
    3. Topical Dosage Forms
    4. Ophthalmic dosage forms
    5. Miscellaneous dosage forms
  4. Drug Platform
  5. Drug Classification
  6. Drug Development Challenges
  7. Development and Discovery of Zanamivir & Oseltamivir for Various Diseases
  8. Clinical Development of Drugs
  9. Controlled Substances Act
  10. Contribution of natural products
  11. How drugs cross the cell membrane
  12. MDR Pumps
  13. Response to Medicine
  14. Influenza Virus
  15. Alprazolam
  16. Amsacrine
  17. Aspirin
  18. Valsartan
  19. Dianabol
  20. Tylenol
  21. Prozac
  22. Anthrax
  23. Phenelzine
  24. Pepcid
  25. Adalat
  26. Bosulif
  27. Luvox
  28. Norethindrone
  29. Paclitaxel
  30. Allegra
  31. Adderall
  32. Ritalin
  33. Paxil
  34. Paxin
  35. Marijuana
  36. Benadryl
  37. Prednisone
  38. Tobacco and Nicotine
  39. Alcohol
  40. Acetaminophen
  41. Vicodin
  42. Folic acid
  43. Ayahuasca
  44. Viagra (Sildenafil Citrate)
  45. Vyvanse
  46. Retrovir/AZT
  47. Drug Antagonists
  48. Tyrosine Kinase Inhibitors
  49. Drug Resistance
  50. Antivirals
  51. Ketamine
  52. MDMA
  53. Cocaine
  54. Warfarin
  55. Ibuprofen
  56. Loratadine
  57. Nexium
  58. Methotrexate
  59. Vancomycin
  60. Thalidomide
  61. Simvastatin
  62. Drug Reward Path In The Brain
  63. Hurler Syndrome and Treatments
  64. RNA-Based Drugs
  65. Antibiotics
  66. Prodrugs
  67. Selective Serotonin Reuptake Inhibitors
  68. Stages of how a drug passes through the body
  69. Statin
  70. Caffeine
  71. Lysergic acid diethylamide
  72. Methamphetamine
  73. Minocycline
  74. Testosterone and the Anabolic-Androgenic Steroid (AASs)
  75. Oxycodone
  76. Contraceptives
  77. Morphine
  78. Diprivan
  79. Rituximab
  80. Plan B
  81. Routes of Drug Administration
    1. Topical
      1. Epicutaneous
      2. Eye Drop
      3. Inhalation
      4. Intranasal Route
    2. Enteral
      1. Oral
      2. Rectal
      3. Sublingual
    3. Parenteral
      1. Intravenous
      2. Intramuscular
      3. Subcutaneous
      4. Intraarterial
      5. Intradermal
      6. Transdermal
      7. Transmucosal
      8. Inhalation
  82. Pharmacokinetics
  83. PTP1B
  84. Amphetamine
  85. Juvenile Hormone
  86. Phylketonuria (PKU)
  87. Antibiotic
  88. Furosemide
  89. Vitamin C
  90. Lantipeptides
  91. ADME
  92. Pharmacology

Laboratory and Clinical Relationship

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  1. Translational Science
    1. Diabetes
    2. Alzheimers
  2. Personalized Medicine
  3. Model Organisms
  4. Bridging the gap between basic and clinical investigation

Histology

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  1. Types of Stains
    1. H and E

Immunohistochemistry

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Neuroscience

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  1. Neurons
    1. Action Potential
    2. Resting Potential
    3. Signaling Within Neurons
  2. Glial Cells
  3. Neurochemistry
    1. Neurotransmitters
  4. Axonal Transport and Disease
    1. Multiple Sclerosis
  5. Synapses
  6. Channelopathies
  7. Phases of Brain Development
    1. Neural Induction
    2. Proliferation
    3. Migration
    4. Differentiation
    5. Synaptogenesis
    6. Cell Death/Stabilization
    7. Synaptic Rearrangement
  8. Neurodegeneration
  9. Neuroglobin
  10. Motor Systems
    1. Basal Ganglia
    2. Cerebellum

Systems Biology

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  1. Analysis of Programmed Cell Death

Bioinformatics

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  1. Homology
  2. Sequences Alignments
  3. Structural Alignments
  4. Advances and pitfalls of protein structural alignment
    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
  5. Evolution Trees
  6. Bioimaging
  7. Combinatorial Chemistry
  8. Comparative Genomics
  9. Transgenic Animal
    1. Regulation
  10. Protein Fold Recognition
  11. SIRCh Link for Bioinformateics (Selected Internet Resources)
  12. Fold.it

Molecular Modeling

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  1. Molecular Docking
  2. Classical Molecular Dynamics
  3. Interactive 3D Model within a PDF

Mental Inertia

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  1. Incorrectly Established Results
  2. Incorrect Understanding of a Mechanism Action

Water

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  1. Unique Properties
  2. pH
  3. Buffer
  4. Osmosis
  5. Polarity
  6. Water Gas Reaction

Proteins

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  1. Amino Acids
    1. Total Chemical Synthesis of a D-Enzyme: The Enantiomers of HIV-1 Protease Show Demonstrations of Reciprocal Chiral Substrate Specificity
    2. Nitrogen Fixation
    3. Amino Acid Degradation
    4. Amino Acid Biosynthesis
    5. Proteins/Recent Progress in Understanding Alzheimer's β-Amyloid structures
  2. Proteins
    1. Structures
    2. Surface Layer Proteins
    3. Protein Folding
    4. Ramachandron Plot
    5. Protein Folding Problem
    6. Protein Folding on the Ribosome
    7. Assembly of bacterial inner membrane proteins
    8. Protein Folding to New Enzymes
    9. Fibrous Proteins
    10. Unfolded Protein Response
    11. Signaling Control of Splicing Proteins
    12. Analyzing and visualizing residue networks of protein structures
    13. Binding-sites Predictions assisting protein-protein Docking
  3. Developing Novel Classifications of Protein Structure
  4. Techniques to Study Proteins
    1. Counting proteins using fluorescence microscopy
  5. Proteostasis
    1. Synthesis
      1. Non Ribosomal Peptide Synthesis
      2. Bacterial Protein Synthesis
    2. Purification
      1. Differential Centrifugation
      2. Salting Out
      3. Capillary Electrophoresis
      4. 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
      5. Isoelectric Focusing
      6. Dialysis
      7. MicroPurification
    3. Analysis of Purification Results
      1. Identifying Proteins
        1. Cellulose Acetate Electrophoresis
      2. Quantifying Proteins
        1. Gel Electrophoresis
        2. SDS-Polyacrylamide Gel ElectrophoresisEdman Sequencing
        3. SDS-Polyacrylamide Gel ElectrophoresisEdman Sequencing
        4. Zonal Centrifugation
        5. Bradford Assay
      3. Quantum Dots
      4. Analysis of Membrane Proteins
        1. VDAC-1 and Analysis Using Solution NMR
    4. Analytical Ultracentrifugation
    5. Crosslinking Technique
    6. Protein Sequence Determination Techniques
      1. Proteolytic Analysis of Proteins
      2. Mass Spectroscopy
    7. Protein Structure Determination Methods
      1. NMR Spectroscopy
      2. Deuterium Exchange Mass Spectrometry
      3. X-ray Crystallography
      4. Cryo-Electron Microscopy
      5. Infrared Spectroscopy
      6. Neutron Diffraction
      7. Continuous Theory of Protein Structure
    8. Analyzing protein structure and function using ancestral gene reconstruction
    9. Measuring Enzymatic Activity Using Spectroscopy
    10. Protein Glycosylation
    11. Comparison of Vertebrate and Invertebrate Proteolytic Cascades
    12. Conformational changes in Adenylyl Cyclases control regulation of signal transduction
    13. Prion Protein Misfolding and Disease
    14. 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
        4. Enzyme-Linked ImmunoSpot Assay (ELISpot)
      3. Preparation of Monoclonal Antibodies
        1. Sources of Monoclonal Antibody Production
      4. Preparation of Polyclonal Antibodies
      5. Dynamic Light Scattering
    15. Site Prediction
    16. Protein Misfolding and Human Disease
  6. Protein Translation
    1. Myristoylation
    2. Internal Ribosome Entry Sites
  7. Protein Modification
    1. Palmitoylation
    2. Prenylation
  8. Posttranslational Modification of Proteins
    1. Adenylation
    2. ADP-Ribosylation
    3. Acetylation
    4. Histone Modifications
      1. Fast signals and slow marks: the dynamics of histone modifications
  9. Protein Phosphorylation by Protein Kinases
    1. NMP Kinase
    2. Phosphatase PHLPP
    3. Phosphatidylserine Binding Motif and PKC
    4. Pleckstrin Homology Domain Leucine-rich Repeat Protein Phosphatase
  10. Detection of Phosphorylation
  11. Protein in Signal Transduction
  12. Integrin Proteins
  13. Conformational changes in Adenylyl Cyclases control regulation of signal transduction
  14. Protein O-GlcNAcylation by O-linked β-N-acetylglucosamine (O-GlcNAc)
  15. Protein Acetylation by Lipids
    1. Proteins are modified by fatty acids
  16. Protein Functions
    1. Structural
    2. Binding
      1. Myoglobin
      2. Hemoglobin
      3. Hemocyanin
      4. Protein-Protein Interaction Network
    3. Catalysis
      1. Enzyme Classification
      2. Proteases
    4. Switching
  17. Regulation
    1. Interferon
    2. HIF
    3. HIF switch
    4. VHL
  18. Lysozyme
  19. Oct Proteins
  20. Lafora Disease
  21. Other Non-Common Amino Acids
  22. Inherently Disordered Proteins
  23. Stability, Mutation and Evolvability
  24. Protein Disorder
  25. Nonribosomal Peptide Synthestases (NRPSs)
  26. Overcoming Challenges of Protein Crystallography
  27. Protein Evolution
  28. Sirtuins
  29. Collagen
  30. Serpins
  31. Glycoproteins
    1. Ebola Virus
  32. Protein Design
  33. Protein Design & Drug Delivery
  34. Drug Delivery
  35. Beta-Propeller Proteins
  36. WD40 Domains
  37. Bub1 and BubR1
  38. APOBEC3G
  39. Glutaredoxins
  40. TAX1BP1
  41. TPD-43

Protein Function

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  1. Binding
    1. Conformational Selection
    2. Ligand
      1. Metal Binding Sites
    3. Binding Sites
    4. Lock and Key
    5. Induced Fit
    6. Transition-state Model
    7. Cooperativity
  2. Integral Membrane Protein
    1. Alpha Helical Membrane Protein
  3. Myoglobin
    1. Heme Group
      1. Bilirubin
    2. Biological Roles of Metal Ions
    3. Myoglobin's Oxygen Binding Curve
    4. Additional Globins
  4. Hemoglobin
    1. Hemoglobin-Heme Group
    2. Sickle Cell Anemia
    3. Thalassemia
    4. AHSP
    5. Bohr Effect
    6. Affinity Constant
    7. Dissociation Constant
    8. Regulation
    9. Regulation by 2,3-Bisphosphoglycerate (2,3-BPG)
    10. Oxygen-Binding Curve
    11. Other Globins
  5. Antibodies
    1. Epitope
    2. Antigen
    3. Major Histocompatibility Complex (MHC)
      1. MHC Class I
      2. MHC Class II
    4. Abzyme
  6. Myosin
  7. Actin
  8. Insulin
  9. DNA Binding
  10. Fluorescent Proteins
  11. G Proteins
  12. LPA Receptors
  13. G Protein Mechanism
  14. Ferritin
  15. Siderochromes
  16. The "fuzzy" interactome
  17. Protein Folding and Chaperones
    1. Protein Folding Rates
    2. Heat Shock Proteins
  18. CCN Proteins
  19. Prion Proteins
  20. Bacterial Proteins
  21. Ubiquitin
  22. Cdc48
  23. TGFβ and Integrins
  24. AB5 Toxins
  25. PHD Finger
  26. TATA-Binding Protein
  27. Chaperone Proteins
    1. HSP90
  28. Function Attribution
  29. Unfolded Protein Response
  30. TDP-43

Membrane Proteins

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  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
    2. Transient receptor potential channel
  10. Ligand-gated Ion Channels
  11. Gap Junctions
  12. Water Channels
  13. Nuclear Pore Compex
  14. Cotransporters
  15. Control Systems:Nervous System
  16. The Evolution of Membrane Proteins
  17. Organizational Scheme for Protein Function
  18. Methods for Studying Membrane Proteins
    1. Solution NMR Spectroscopy
    2. Electron crystallography of proteins in membranes
    3. Cryo-electron Tomography and 3D Image Averaging
  19. Assembly of Membrane Proteins into Complexes
  20. Topology
  21. G Protein Coupled Receptor
  22. Multidrug-Resistance Pumps
  23. Study of Protein structure in lipid bilayer: Electron crystallography
  24. Folding
  25. Membrane Curvature
  26. Hydrophobicity scales
  27. Membrane Protein stresses in fusion and fission
  28. Mucus Membrane System
  29. Secretin
  30. Binding of the Drug Amantadine to the Proton Channels of the M2 Protein in the Influenza Virus
  31. TA proteins (GET) pathway in young men

Carbohydrates

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  1. Monosaccharides
    1. Stereochemistry of Monosaccharides
  2. Carbohydrate Structure Elucidation through Periodic Acid Cleavage
  3. Ketoses
  4. Aldoses
  5. Disaccharides
  6. Oligosaccharides
  7. Sequencing Oligosaccharides Using Glycosidases
  8. Polysaccharides
  9. /Carbohydrates/Chitin
  10. Glycans
  11. Peptidoglycan Biosynthesis
  12. Glycoproteins
  13. Carbohydrate Derivatives
  14. Carbohydrates and Proteins
    1. Lectins
    2. Glycosaminoglycans
    3. Proteoglycans
    4. Blood Type
    5. Virus
      1. Mechanism behind HIV Infection
  15. Carbohydrate Metabolism
  16. Glycogen Breakdown

Lipids

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  1. Fatty Acids
    1. Triacylglycerols
  2. Cholesterol
    1. Biosynthesis of Cholestrol
    2. Lipoproteins
  3. Biological Membranes
  4. Membrane Lipids
  5. Membrane Transport
  6. Membrane Fusion
  7. Membrane Fission
  8. Micelles
  9. Lipid Bilayer
  10. Membrane Fluidity
  11. Fluid Mosaic Model
  12. Techniques to Study Membranes
    1. Electron Microscopy
    2. Preparation of Bilayers and Vesicles
    3. Scanning Calorimetry
    4. Fluorescence Photo Bleaching
  13. Waxes, Soaps, and Detergents
    1. Fatty Wax
    2. Soap
    3. Detergents
  14. Isoprenoids
  15. Lipid Rafts
  16. /Lipids/Sample Preparation for Mass Spectrometry-Based Lipidomics Studies
  17. Mass Spectrometry-Based Structure Determination of Novel Lipids
  18. Receptor-mediated Endocytosis
  19. Biosynthesis
    1. Triacylglycerols
  20. Lipid activation of protein kinases
  21. Degradation of Odd-Chain and Unsaturated Fatty Acids
  22. Liposomes
  23. Lipid Droplets and Cellular Lipid Metabolism

Nucleic Acids

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  1. Structure
    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
      3. Ribonucleotide Reductase
    4. Nucleotides
  2. Connection Between Monomers
  3. DNA
    1. DNA structure
      1. Telomeres
      2. Unusual Structures
    2. Supercoiling and Nucleosomes
    3. Palindromic Sequencing
    4. DNA Denaturation
    5. Avery-MacLeod-McCarty Experiment
    6. Hershey-Chase Experiment
    7. Chargaff's Experiments
    8. Watson and Crick's Article
    9. Franklin's DNA X-ray Crystallography
    10. Replication Process
      1. DNA Polymerase
      2. DNA Initiation
    11. Meselson-Stahl Experiment
    12. Knockout Mouse
    13. Transgenic Animals
    14. Transgenic Plants
    15. The Hypochromic Effect
    16. DNA Repair
      1. Mismatch Repair
      2. Polynucleotide kinase/phosphatase in DNA strand break repair
    17. DNA Packaging
    18. DNA as Nanomaterial
    19. Structural DNA Nanotechnology
    20. Holliday Junction
    21. Proliferative and Antiproliferative Genes
    22. Protein-DNA Recognition
    23. Transcription Regulation by Mediator
    24. Chromatin and Aging
    25. Chromatin regulation and genome maintenance by mammalian SIRT6
  4. RNA
    1. Messenger RNA (mRNA)
      1. Nonsense-Mediated mRNA Decay
    2. Transfer RNA (tRNA)
    3. Ribosomal RNA (rRNA)
    4. Small RNA
      1. MicroRNA (miRNA)
    5. Other RNA
    6. RNA Polymerase
      1. Single-molecule study of RNAP
    7. RNA-Dependent RNA Polymerase
    8. RNA Helicase
    9. Riboswitch
    10. RNA Folding
      1. Mechanical Unfolding of RNA
    11. Short RNAs
      1. Salt Effects on Mechanical Folding
    12. RNA Interference (RNAi)
      1. RISC (RNA-induced silencing complex)
    13. Differences between DNA and RNA
    14. Transcription
      1. Nucleic Acid
      2. Transcription
      3. Reverse Transcription
      4. RNA Polymerase II
    15. mRNA processing and transfer
    16. Translation
    17. RNA Modification
      1. Introns
      2. Exons
      3. RNA Splicing
      4. snRNP
    18. RNA Degradation
      1. RNaseT2 Functionality
      2. Ribonucleases
    19. Telomere
    20. RNA Purification
    21. RNA Extraction
    22. Short RNA (sRNA Sequencing)
    23. Nematode RNA
    24. RNA Secondary Structure
    25. Making RISC's
    26. Diverse Interctions of retroviral Gag proteins with RNAs
  1. DNA Manipulation Techniques
    1. /Maintaining Genome Integrity
    2. Restriction Endonucleases
    3. Southern Blot
    4. Northern Blot
    5. DNA Sequencing
    6. DNA Cataloging
    7. DNA Synthesis
    8. DNA Amplification
    9. Alcohol Precipitation
    10. Gene Regulation
      1. Synthetic Biology
      2. Zinc fingers
      3. Metabolites
      4. REM
    11. Bacterial Transformation Technique
  2. Genetic Code
  3. Gene Expression
    1. Gatekeepers of Chromatin: Small Metabolites Elicit Big Changes in Gene Expression
  4. DNA Mutation
    1. Transposons
    2. Copy Number Variants
    3. Genetic Diseases
      1. Tay-Sachs
    4. Mitochondrial Diseases
      1. Duchenne Muscular Dystrophy
  5. 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
  6. Genome Regulation
  7. 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
    6. Karyotyping
  8. 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. Bacterial Artificial Chromosomes (BAC)
    10. Electroporation
    11. 293T Cells
      1. Bacterial Gram Stain
    2. Heredity and Related Experiments
    3. Directed Changes in DNA
    4. Eukaryotic Recombination
  2. Single Molecule DNA Sequencing
  3. Methods for Determining Recombinant DNA in the Environment
  4. Polyermase Chain Reaction
    1. How PCR is Performed
    2. Uses of PCR
  5. DNA of the Future (The Many Faces of DNA)
  6. Mitochondrial DNA
  7. ATP
  8. Function Attribution of Gene & Gene Products
  9. 30nm chromatin fibers

Catalysis

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  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
    11. Transition-State Binding Principle
  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/KM
    3. Kinetic Perfection
    4. Maximum Velocity
    5. Sequential Reactions
    6. Double Displacement Reactions
    7. Ping-Pong Mechanism
    8. 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
  16. Catalytic antibodies
  17. Effects of Temperature on Enzyme Activity

Specific Enzymes and Catalytic Mechanisms

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  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
    9. AAA+ Proteases
    10. HIV-1 Proteases
  2. Dehydrogenases
  3. Enzyme Phenylalanine Hydrozylase (PAH)
  4. Carbonic Anhydrase
  5. Carboxypeptidase
  6. Kinase
    1. Cyclin-Dependent Kinase
    2. MPS1
  7. Biophysical Studies of Bacterial Ribosome Assembly
  8. Restriction Enzyme
    1. BamHI
    2. EcoRI
    3. HindIII
    4. XbaI
  9. Glutathione Reductase
  10. Nucleotide Monophosphate Kinase
  11. Phillips mechanism
  12. Isomerases
    1. Triose Phosphate Isomerase
  13. Ping-Pong Mechanism
  14. Acetyltransferase
  15. Deacetylase
  16. Radical-SAM Enzyme
    1. FeMo Cofactor and FeFe-Hydrogenase
  17. Summary
  18. Membrane Traffic
  19. Cold-Adapted enzymes
  20. Cholesterol 24-hydroxylase
  21. Cytochrome b6f Complex
  22. Cytochrome P450 Enzyme
  23. Deaminase
  24. Drug metabolism enzymes
  25. MAO B enzyme
  26. Cyclooxygenase enzyme
  27. PLC enzyme
  28. Polynucleotide Kinase/Phosphatase enzyme
  29. NLR Sensors
  30. GTPase
  31. Palmitoyl Transferase

Enzyme Regulation

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  1. Feedback Inhibition
  2. Isozymes
    1. Enzyme Regulation/Isoenzyme Analysis
    2. Enzyme Regulation/Enzyme and Metabolite Interactions and Gene Regulation based on RNA
  3. Reversible Covalent Modification
    1. Phosphorylation
    2. Ubiquitination
      1. Multitasking With Ubiquitin Through Multivalent Interactions
    3. Methylation
    4. Acetylation
    5. Adenylation
    6. Myristoylation
    7. Protein Lysine Acetylation in metabolism
  4. Proteolytic Activation
  5. Enzyme Cascades
  6. Transcription Activation
  7. Allosteric Control
  8. Irreversible Inhibition
  9. Amino Acid Sensing and Transporting

Hormones

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  1. Testosterone
  2. Estrogen
  3. Xenohormones
    1. Alkylphenols
  4. Human Chorionic Gonadotropins
  5. Pheromones
  6. Gastrin
  7. Epinephrine
  8. Human Placental Lactogen

Key Words

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  1. General Terms
  2. Protein Terms
  3. Contentious Terms
  4. Carbohydrate Terms
  5. Lipids and Cell Membrane Terms
  6. DNA and RNA Terms
  7. Evolution and Bioinformatics Terms
  8. Enzyme Terms
  9. Apoptosis

Influential Structural Biochemists

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  1. Dorothy Crowfoot Hodgkin
  2. Albert Claude
  3. Christian de Duve
  4. Venkatraman Ramakrishnan
  5. Roger D. Kornberg
  6. Elizabeth F. Neufeld
  7. Ivan Berkes
  8. James C. Wang
  9. Nobuhiko Katunuma
  10. Matthias W. Hentze
  11. Rosalind Franklin
  12. Shigeru Tsuiki
  13. Paul D. Boyer
  14. Maria Manasseina
  15. Frederick Sanger
  16. Edwin G. Krebs
  17. John C. Kendrew
  18. Selman A. Waksman
  19. William H. Stein
  20. Vaclaw L. Kretovich
  21. Linus Pauling

Helpful Mnemonics

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Natural Products

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  1. Carbon-Phosphorus Bond

Taxis

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  1. Chemotaxis

Biochemistry in Medicine

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  1. Carbon Monoxide: A Stealthy Killer
  2. Inherited Human Diseases Resulting from Abnormal Accumulations of Membrane Lipids
  3. Eat your Fruits and Veggies! How Vitamin C combats scurvy
  4. X-ray Crystallography
  5. Antibodies that target tumor cells

Biochemistry in Animals

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  1. Vibrio fischeri: Let there be light

Biochemical Role in Neuropsychiatric Disease

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  1. Schizophrenia
  2. Autism
  3. Bipolar
  4. Huntington's Disease

Structural Biochemistry Paper Topics

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  1. The RNA recognition motif, a plastic RNA-binding platform to regulate post-transcriptional gene expression
  2. The Molecular Regulation of Programmed Necrotic Cell Injury
  3. Ribosome Mediated Translation Initiation for Vesicular Stomatitus Virus
  4. The MPS1 Family of Protein Kinases

References

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  1. The Free Dictionary. Mosby's Medical Dictionary, 8th Edition. © 2009, Elsevier., 2009. Web. 28 Oct. 2012. http://medical-dictionary.thefreedictionary.com/compartment+model.
  2. Zhang, Liangfang. "Controlled Drug Delivery Systems." CENG 207 Lecture 9 “Pharmacokinetics of Drug Dispersion”. University of California, San Diego, La Jolla. 10 May 2012. Lecture.
  3. Dhillon, Soraya and Gill, Kiren. "Basic Pharmacokinetics." 28 Oct. 2012. http://www.pharmpress.com/files/docs/clinical_pharmacokinetics_samplechapter.pdf


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