# 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.

## Relations of Structural Biochemistry with other Sciences
### Physics

* Thermodynamics
** Zeroth Law
** First law
** Second law
*** Thermodynamic Cycles
** Third law
** Internal Energy
** Entropy
** Enthalpy
** Heat capacity
** Free energy
** Material Equilibrium
** Phase Diagrams
** Phase Equilibria
** Endergonic reaction
** Exergonic reaction
** Molecular Thermodynamics
** Thermodynamic Equilibrium
** Ideal Gas
** Equation for Process Calculations for Ideal Gases
** Irreversible Process
** Application of the Virial Equations
* Bioenergetics
* Energy coupling in chemical reactions
* Metabolism
** Anabolism
** Catabolism
* Biophysics- Single Molecule techniques

### Chemistry

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

### Biology

* Properties of Living Organisms
* Retinoid

#### Evolution

* History of the Earth
* RNA World Hypothesis
* Evolution in the Laboratory
* Evolution of Humans
* Evolution of Populations
* The Oparin-Haldane Hypothesis
* Molecular Evolution
* Three Domains of Life
** Archaea
*** SAMPylation Protein in Archaea
** Bacteria
** Eukarya
*** Community Ecology
* The Endosymbiotic Theory
* The Evolution of Membranes
* Natural Selection of Aluminum and Silicon
* Speciation
* Gene Flow
* Organismic and Evolutionary Biology
* Hardy-Weinberg Principle

#### The Cell

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

#### Genetics

* The Genetics of Bacteria
* Properties of Mutant Alleles
* Foundation of Genetics
* Genetics terms
* Inheritance Patterns
* Chromosomes
* Epigenomics
** Epigenome reader
* Mitosis
* Meiosis
* Homeobox Genes
* How can you know if Genes are "on" or "off" in a cell?
* Genetic Variants
* Structural Variation

#### Biology of Cancer

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

### Medicine & Drug Design

* Drug Targeting
* Quantum Dot-Aptamer Conjugate
* Pharmaceutical Dosage Forms
** Solid Dosage Forms
** Liquid Dosage Forms
** Topical Dosage Forms
** Ophthalmic dosage forms
** Miscellaneous dosage forms
* Drug Platform
* Drug Classification
* Drug Development Challenges
* Development and Discovery of Zanamivir & Oseltamivir for Various Diseases
* Clinical Development of Drugs
* Controlled Substances Act
* Contribution of natural products
* How drugs cross the cell membrane
* MDR Pumps
* Response to Medicine
* Influenza Virus
* Alprazolam
* Amsacrine
* Aspirin
* Valsartan
* Dianabol
* Tylenol
* Prozac
* Anthrax
* Phenelzine
* Pepcid
* Adalat
* Bosulif
* Luvox
* Norethindrone
* Paclitaxel
* Allegra
* Adderall
* Ritalin
* Paxil
* Paxin
* Marijuana
* Benadryl
* Prednisone
* Tobacco and Nicotine
* Alcohol
* Acetaminophen
* Vicodin
* Folic acid
* Ayahuasca
* Viagra (Sildenafil Citrate)
* Vyvanse
* Retrovir/AZT
* Drug Antagonists
* Tyrosine Kinase Inhibitors
* Drug Resistance
* Antivirals
* Ketamine
* MDMA
* Cocaine
* Warfarin
* Ibuprofen
* Loratadine
* Nexium
* Methotrexate
* Vancomycin
* Thalidomide
* Simvastatin
* Drug Reward Path In The Brain
* Hurler Syndrome and Treatments
* RNA-Based Drugs
* Antibiotics
* Prodrugs
* Selective Serotonin Reuptake Inhibitors
* Stages of how a drug passes through the body
* Statin
* Caffeine
* Lysergic acid diethylamide
* Methamphetamine
* Minocycline
* Testosterone and the Anabolic-Androgenic Steroid (AASs)
* Oxycodone
* Contraceptives
* Morphine
* Diprivan
* Rituximab
* Plan B
* Routes of Drug Administration
** Topical
*** Epicutaneous
*** Eye Drop
*** Inhalation
*** Intranasal Route
** Enteral
*** Oral
*** Rectal
*** Sublingual
** Parenteral
*** Intravenous
*** Intramuscular
*** Subcutaneous
*** Intraarterial
*** Intradermal
*** Transdermal
*** Transmucosal
*** Inhalation
* Pharmacokinetics
* PTP1B
* Amphetamine
* Juvenile Hormone
* Phylketonuria (PKU)
* Antibiotic
* Furosemide
* Vitamin C
* Lantipeptides
* ADME
* Pharmacology

### Laboratory and Clinical Relationship

* Translational Science
** Diabetes
** Alzheimers
* Personalized Medicine
* Model Organisms
* Bridging the gap between basic and clinical investigation

### Histology

* Types of Stains
** H and E

### Neuroscience

* Neurons
** Action Potential
** Resting Potential
** Signaling Within Neurons
* Glial Cells
* Neurochemistry
** Neurotransmitters
* Axonal Transport and Disease
** Multiple Sclerosis
* Synapses
* Channelopathies
* Phases of Brain Development
** Neural Induction
** Proliferation
** Migration
** Differentiation
** Synaptogenesis
** Cell Death/Stabilization
** Synaptic Rearrangement
* Neurodegeneration
* Neuroglobin
* Motor Systems
** Basal Ganglia
** Cerebellum

### Systems Biology

* Analysis of Programmed Cell Death

### Bioinformatics

* Homology
* Sequences Alignments
* Structural Alignments
* Advances and pitfalls of protein structural alignment
** Programs Used For Structural Alignment
*** DALI
*** Combinatorial Extension
*** SSAP
*** GANGSTA+
*** MAMMOTH
*** RAPIDO
*** SABERTOOTH
*** TOPOFIT
** RNA Structural Alignment
* Evolution Trees
* Bioimaging
* Combinatorial Chemistry
* Comparative Genomics
* Transgenic Animal
** Regulation
* Protein Fold Recognition
* SIRCh Link for Bioinformateics (Selected Internet Resources)
* Fold.it

### Molecular Modeling

* Molecular Docking
* Classical Molecular Dynamics
* Interactive 3D Model within a PDF

### Mental Inertia

* Incorrectly Established Results
* Incorrect Understanding of a Mechanism Action

## Water

* Unique Properties
* pH
* Buffer
* Osmosis
* Polarity
* Water Gas Reaction

## Proteins

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

### Protein Function

* Binding
** Conformational Selection
** Ligand
*** Metal Binding Sites
** Binding Sites
** Lock and Key
** Induced Fit
** Transition-state Model
** Cooperativity
* Integral Membrane Protein
** Alpha Helical Membrane Protein
* Myoglobin
** Heme Group
*** Bilirubin
** Biological Roles of Metal Ions
** Myoglobin's Oxygen Binding Curve
** Additional Globins
* Hemoglobin
** Hemoglobin-Heme Group
** Sickle Cell Anemia
** Thalassemia
** AHSP
** Bohr Effect
** Affinity Constant
** Dissociation Constant
** Regulation
** Regulation by 2,3-Bisphosphoglycerate (2,3-BPG)
** Oxygen-Binding Curve
** Other Globins
* Antibodies
** Epitope
** Antigen
** Major Histocompatibility Complex (MHC)
*** MHC Class I
*** MHC Class II
** Abzyme
* Myosin
* Actin
* Insulin
* DNA Binding
* Fluorescent Proteins
* G Proteins
* LPA Receptors
* G Protein Mechanism
* Ferritin
* Siderochromes
* The "fuzzy" interactome
* Protein Folding and Chaperones
** Protein Folding Rates
** Heat Shock Proteins
* CCN Proteins
* Prion Proteins
* Bacterial Proteins
* Ubiquitin
* Cdc48
* TGFβ and Integrins
* AB5 Toxins
* PHD Finger
* TATA-Binding Protein
* Chaperone Proteins
** HSP90
* Function Attribution
* Unfolded Protein Response
* TDP-43

### Membrane Proteins

* Active Transport
* Passive Transport
* Membrane Gradients and Thermodynamics
* P-type ATPases
* ATP-Binding Cassette Proteins
* Symporters
* Antiporters
* Uniporters
* Ion Channels
** Patch Clamp
** Transient receptor potential channel
* Ligand-gated Ion Channels
* Gap Junctions
* Water Channels
* Nuclear Pore Compex
* Cotransporters
* Control Systems:Nervous System
* The Evolution of Membrane Proteins
* Organizational Scheme for Protein Function
* Methods for Studying Membrane Proteins
** Solution NMR Spectroscopy
** Electron crystallography of proteins in membranes
** Cryo-electron Tomography and 3D Image Averaging
* Assembly of Membrane Proteins into Complexes
* Topology
* G Protein Coupled Receptor
* Multidrug-Resistance Pumps
* Study of Protein structure in lipid bilayer: Electron crystallography
* Folding
* Membrane Curvature
* Hydrophobicity scales
* Membrane Protein stresses in fusion and fission
* Mucus Membrane System
* Secretin
* Binding of the Drug Amantadine to the Proton Channels of the M2 Protein in the Influenza Virus
* TA proteins (GET) pathway in young men

## Carbohydrates

* Monosaccharides
** Stereochemistry of Monosaccharides
* Carbohydrate Structure Elucidation through Periodic Acid Cleavage
* Ketoses
* Aldoses
* Disaccharides
* Oligosaccharides
* Sequencing Oligosaccharides Using Glycosidases
* Polysaccharides
* /Carbohydrates/Chitin
* Glycans
* Peptidoglycan Biosynthesis
* Glycoproteins
* Carbohydrate Derivatives
* Carbohydrates and Proteins
** Lectins
** Glycosaminoglycans
** Proteoglycans
** Blood Type
** Virus
*** Mechanism behind HIV Infection
* Carbohydrate Metabolism
* Glycogen Breakdown

## Lipids

* Fatty Acids
** Triacylglycerols
* Cholesterol
** Biosynthesis of Cholestrol
** Lipoproteins
* Biological Membranes
* Membrane Lipids
* Membrane Transport
* Membrane Fusion
* Membrane Fission
* Micelles
* Lipid Bilayer
* Membrane Fluidity
* Fluid Mosaic Model
* Techniques to Study Membranes
** Electron Microscopy
** Preparation of Bilayers and Vesicles
** Scanning Calorimetry
** Fluorescence Photo Bleaching
* Waxes, Soaps, and Detergents
** Fatty Wax
** Soap
** Detergents
* Isoprenoids
* Lipid Rafts
* /Lipids/Sample Preparation for Mass Spectrometry-Based Lipidomics Studies
* Mass Spectrometry-Based Structure Determination of Novel Lipids
* Receptor-mediated Endocytosis
* Biosynthesis
** Triacylglycerols
* Lipid activation of protein kinases
* Degradation of Odd-Chain and Unsaturated Fatty Acids
* Liposomes
* Lipid Droplets and Cellular Lipid Metabolism

## Nucleic Acids

* Structure
** Phosphate
** Sugars
*** Deoxyribose
*** Ribose
** Nitrogenous Bases
*** Purines
**** Adenine
**** Guanine
**** Purine
**** Hypoxanthine
**** Xanthine
**** Theobromine
*** Pyrimidines
**** Cytosine
**** Uracil
**** Thymine
*** Ribonucleotide Reductase
** Nucleotides
* Connection Between Monomers
* DNA
** DNA structure
*** Telomeres
*** Unusual Structures
** Supercoiling and Nucleosomes
** Palindromic Sequencing
** DNA Denaturation
** Avery-MacLeod-McCarty Experiment
** Hershey-Chase Experiment
** Chargaff's Experiments
** Watson and Crick's Article
** Franklin's DNA X-ray Crystallography
** Replication Process
*** DNA Polymerase
*** DNA Initiation
** Meselson-Stahl Experiment
** Knockout Mouse
** Transgenic Animals
** Transgenic Plants
** The Hypochromic Effect
** DNA Repair
*** Mismatch Repair
*** Polynucleotide kinase/phosphatase in DNA strand break repair
** DNA Packaging
** DNA as Nanomaterial
** Structural DNA Nanotechnology
** Holliday Junction
** Proliferative and Antiproliferative Genes
** Protein-DNA Recognition
** Transcription Regulation by Mediator
** Chromatin and Aging
** Chromatin regulation and genome maintenance by mammalian SIRT6
* RNA
** Messenger RNA (mRNA)
*** Nonsense-Mediated mRNA Decay
** Transfer RNA (tRNA)
** Ribosomal RNA (rRNA)
** Small RNA
*** MicroRNA (miRNA)
** Other RNA
** RNA Polymerase
*** Single-molecule study of RNAP
** RNA-Dependent RNA Polymerase
** RNA Helicase
** Riboswitch
** RNA Folding
*** Mechanical Unfolding of RNA
** Short RNAs
*** Salt Effects on Mechanical Folding
** RNA Interference (RNAi)
*** RISC (RNA-induced silencing complex)
** Differences between DNA and RNA
** Transcription
*** Nucleic Acid
*** Transcription
*** Reverse Transcription
*** RNA Polymerase II
** mRNA processing and transfer
** Translation
** RNA Modification
*** Introns
*** Exons
*** RNA Splicing
*** snRNP
** RNA Degradation
*** RNaseT2 Functionality
*** Ribonucleases
** Telomere
** RNA Purification
** RNA Extraction
** Short RNA (sRNA Sequencing)
** Nematode RNA
** RNA Secondary Structure
** Making RISC's
** Diverse Interctions of retroviral Gag proteins with RNAs
* DNA Manipulation Techniques
** /Maintaining Genome Integrity
** Restriction Endonucleases
** Southern Blot
** Northern Blot
** DNA Sequencing
** DNA Cataloging
** DNA Synthesis
** DNA Amplification
** Alcohol Precipitation
** Gene Regulation
*** Synthetic Biology
*** Zinc fingers
*** Metabolites
*** REM
** Bacterial Transformation Technique
* Genetic Code
* Gene Expression
** Gatekeepers of Chromatin: Small Metabolites Elicit Big Changes in Gene Expression
* DNA Mutation
** Transposons
** Copy Number Variants
** Genetic Diseases
*** Tay-Sachs
** Mitochondrial Diseases
*** Duchenne Muscular Dystrophy
* Cloning Enzymes
** Enzymes Used for Cloning
*** T4 DNA Ligase
*** T4 RNA Ligase
*** T4 Polynucleotide Kinase
*** Calf Intestinal Alkaline Phosphatase
*** RecA Protein
*** AgarACE$^®$ Enzyme
** Cloning Tips
** Process of DNA Cloning and Vector Insertion
** Immune System
* Genome Regulation
* Genome Analysis
** DNA Gel Electrophoresis
** DNA Microarrays
** Sequenced Genomes
** Single Nucleotide Polymorphisms (SNPs)
** The Impact of Genome Analysis on Medicine
** Karyotyping
* DNA Recombinant Techniques
** History and Study of Bacteriophage Lambda
** Plasmid
*** Lytic Pathway
*** Lysogenic Pathway
** Genomic Library
** Detecting Specific Genes
** Mutagenesis
** Designer Genes
** Human Genome Project
** Gene Therapy
** Artificial Chromosomes
*** Bacterial Artificial Chromosomes (BAC)
*** Bacterial Artificial Chromosomes (BAC)
** Electroporation
** 293T Cells
*** Bacterial Gram Stain
** Heredity and Related Experiments
** Directed Changes in DNA
** Eukaryotic Recombination
* Single Molecule DNA Sequencing
* Methods for Determining Recombinant DNA in the Environment
* Polyermase Chain Reaction
** How PCR is Performed
** Uses of PCR
* DNA of the Future (The Many Faces of DNA)
* Mitochondrial DNA
* ATP
* Function Attribution of Gene & Gene Products
* 30nm chromatin fibers

## Catalysis

* Enzyme
** Binding Energy
** Desolvation
** States: Ground, Pre-steady,& Steady
** Coenzymes
** Cofactors
** Prosthetic Group
** Apoenzyme and Holoenzyme
** Active Site and Enzyme Specificity
** Catalytic Triad
** Evolution of Enzymes
** Transition-State Binding Principle
* Zymogen
* Gibbs Free Energy Diagram
** Transition State
** Activation Energy
** Reaction Intermediates
* Rates and Constants
** Rate Constant
** Rate Equation
** Rate-limiting Step
** Equilibrium Constant
** Initial Rate
* Mechanisms
** Acid-Base Catalysis
** Covalent Catalysis
** Metal Ion Catalysis
** Catalysis By Approximation
* Michaelis-Menten Equation
** Michaelis Constant
** K$_{cat}$/K$_M$
** Kinetic Perfection
** Maximum Velocity
** Sequential Reactions
** Double Displacement Reactions
** Ping-Pong Mechanism
** Allosteric Enzymes
* Double-Reciprocal Plot
* Reversible Inhibitors
** Competitive Inhibitor
** Uncompetitive Inhibitor
** Noncompetitive Inhibitor
* Irreversible Inhibitor
** Group Specific Reagent
** Affinity Labels
** Suicide Inhibitors
* Time-dependent Inhibition
* Transition-State Analogs
* Penicillin
* Effects of pH on Enzyme Activity
* Site-Directed Mutagenesis
* Multi-substrate reactions
* Catalytic antibodies
* Effects of Temperature on Enzyme Activity

### Specific Enzymes and Catalytic Mechanisms

* Proteases
** Hydrolysis
** Chymotrypsin
** Cysteine Proteases
** Aspartyl Proteases
** Serine Proteases
** Threonine Proteases
** Metalloproteases
** Catalytic Triad and S$_1$ Pocket
** AAA+ Proteases
** HIV-1 Proteases
* Dehydrogenases
* Enzyme Phenylalanine Hydrozylase (PAH)
* Carbonic Anhydrase
* Carboxypeptidase
* Kinase
** Cyclin-Dependent Kinase
** MPS1
* Biophysical Studies of Bacterial Ribosome Assembly
* Restriction Enzyme
** BamHI
** EcoRI
** HindIII
** XbaI
* Glutathione Reductase
* Nucleotide Monophosphate Kinase
* Phillips mechanism
* Isomerases
** Triose Phosphate Isomerase
* Ping-Pong Mechanism
* Acetyltransferase
* Deacetylase
* Radical-SAM Enzyme
** FeMo Cofactor and FeFe-Hydrogenase
* Summary
* Membrane Traffic
* Cold-Adapted enzymes
* Cholesterol 24-hydroxylase
* Cytochrome b6f Complex
* Cytochrome P450 Enzyme
* Deaminase
* Drug metabolism enzymes
* MAO B enzyme
* Cyclooxygenase enzyme
* PLC enzyme
* Polynucleotide Kinase/Phosphatase enzyme
* NLR Sensors
* GTPase
* Palmitoyl Transferase

### Enzyme Regulation

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

### Hormones

* Testosterone
* Estrogen
* Xenohormones
** Alkylphenols
* Human Chorionic Gonadotropins
* Pheromones
* Gastrin
* Epinephrine
* Human Placental Lactogen

## Key Words

* General Terms
* Protein Terms
* Contentious Terms
* Carbohydrate Terms
* Lipids and Cell Membrane Terms
* DNA and RNA Terms
* Evolution and Bioinformatics Terms
* Enzyme Terms
* Apoptosis

## Influential Structural Biochemists

* Dorothy Crowfoot Hodgkin
* Albert Claude
* Christian de Duve
* Venkatraman Ramakrishnan
* Roger D. Kornberg
* Elizabeth F. Neufeld
* Ivan Berkes
* James C. Wang
* Nobuhiko Katunuma
* Matthias W. Hentze
* Rosalind Franklin
* Shigeru Tsuiki
* Paul D. Boyer
* Maria Manasseina
* Frederick Sanger
* Edwin G. Krebs
* John C. Kendrew
* Selman A. Waksman
* William H. Stein
* Vaclaw L. Kretovich
* Linus Pauling

## Natural Products

* Carbon-Phosphorus Bond

## Taxis

* Chemotaxis

## Biochemistry in Medicine

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

## Biochemistry in Animals

* Vibrio fischeri: Let there be light

## Biochemical Role in Neuropsychiatric Disease

* Schizophrenia
* Autism
* Bipolar
* Huntington's Disease

## Structural Biochemistry Paper Topics

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

## References

* The Free Dictionary. Mosby's Medical Dictionary, 8th Edition. © 2009, Elsevier., 2009. Web. 28 Oct. 2012. http://medical-dictionary.thefreedictionary.com/compartment+model.
* 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.
* Dhillon, Soraya and Gill, Kiren. "Basic Pharmacokinetics." 28 Oct. 2012. http://www.pharmpress.com/files/docs/clinical_pharmacokinetics_samplechapter.pdf