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Table of contents
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1. Introduction to Biochemistry
Worksheet
What is Biochemistry?
Characteristics of Life
Abiogenesis
Nucleic Acids
Proteins
Carbohydrates
Lipids
Taxonomy
Cell Organelles
Endosymbiotic Theory
Central Dogma
Functional Groups
Chemical Bonds
Organic Chemistry
Entropy
Second Law of Thermodynamics
Equilibrium Constant
Gibbs Free Energy
2. Water
Worksheet
Properties of Water
Osmosis
Hydrophobic Effect
Acids and Bases
Autoionization of Water
pH
Acid Dissociation Constant
Henderson Hasselbalch Equation
Determining Predominate Species
Titration
Buffer Solution
3. Amino Acids
Worksheet
Amino Acid Groups
Amino Acid Three Letter Code
Amino Acid One Letter Code
Amino Acid Configuration
Essential Amino Acids
Nonpolar Amino Acids
Aromatic Amino Acids
Polar Amino Acids
Charged Amino Acids
How to Memorize Amino Acids
Zwitterion
Non-Ionizable Vs. Ionizable R-Groups
Isoelectric Point
Isoelectric Point of Amino Acids with Ionizable R-Groups
Titrations of Amino Acids with Non-Ionizable R-Groups
Titrations of Amino Acids with Ionizable R-Groups
Amino Acids and Henderson-Hasselbalch
4. Protein Structure
Worksheet
Peptide Bond
Primary Structure of Protein
Altering Primary Protein Structure
Drawing a Peptide
Determining Net Charge of a Peptide
Isoelectric Point of a Peptide
Approximating Protein Mass
Peptide Group
Ramachandran Plot
Atypical Ramachandran Plots
Alpha Helix
Alpha Helix Pitch and Rise
Alpha Helix Hydrogen Bonding
Alpha Helix Disruption
Beta Strand
Beta Sheet
Antiparallel and Parallel Beta Sheets
Beta Turns
Tertiary Structure of Protein
Protein Motifs and Domains
Denaturation
Anfinsen Experiment
Protein Folding
Chaperone Proteins
Prions
Quaternary Structure
Simple Vs. Conjugated Proteins
Fibrous and Globular Proteins
5. Protein Techniques
Worksheet
Protein Purification
Protein Extraction
Differential Centrifugation
Salting Out
Dialysis
Column Chromatography
Ion-Exchange Chromatography
Anion-Exchange Chromatography
Size Exclusion Chromatography
Affinity Chromatography
Specific Activity
HPLC
Spectrophotometry
Native Gel Electrophoresis
SDS-PAGE
SDS-PAGE Strategies
Isoelectric Focusing
2D-Electrophoresis
Diagonal Electrophoresis
Mass Spectrometry
Mass Spectrum
Tandem Mass Spectrometry
Peptide Mass Fingerprinting
Overview of Direct Protein Sequencing
Amino Acid Hydrolysis
FDNB
Chemical Cleavage of Bonds
Peptidases
Edman Degradation
Edman Degradation Sequenator and Sequencing Data Analysis
Edman Degradation Reaction Efficiency
Ordering Cleaved Fragments
Strategy for Ordering Cleaved Fragments
Indirect Protein Sequencing Via Geneomic Analyses
6. Enzymes and Enzyme Kinetics
Worksheet
Enzymes
Enzyme-Substrate Complex
Lock and Key Vs. Induced Fit Models
Optimal Enzyme Conditions
Activation Energy
Types of Enzymes
Cofactor
Catalysis
Electrostatic and Metal Ion Catalysis
Covalent Catalysis
Reaction Rate
Enzyme Kinetics
Rate Constants and Rate Law
Reaction Orders
Rate Constant Units
Initial Velocity
Vmax Enzyme
Km Enzyme
Steady-State Conditions
Michaelis-Menten Assumptions
Michaelis-Menten Equation
Lineweaver-Burk Plot
Michaelis-Menten vs. Lineweaver-Burk Plots
Shifting Lineweaver-Burk Plots
Calculating Vmax
Calculating Km
Kcat
Specificity Constant
7. Enzyme Inhibition and Regulation
Worksheet
Enzyme Inhibition
Irreversible Inhibition
Reversible Inhibition
Inhibition Constant
Degree of Inhibition
Apparent Km and Vmax
Inhibition Effects on Reaction Rate
Competitive Inhibition
Uncompetitive Inhibition
Mixed Inhibition
Noncompetitive Inhibition
Recap of Reversible Inhibition
Allosteric Regulation
Allosteric Kinetics
Allosteric Enzyme Conformations
Allosteric Effectors
Concerted (MWC) Model
Sequential (KNF) Model
Negative Feedback
Positive Feedback
Post Translational Modification
Ubiquitination
Phosphorylation
Zymogens
8. Protein Function
Worksheet
Introduction to Protein-Ligand Interactions
Protein-Ligand Equilibrium Constants
Protein-Ligand Fractional Saturation
Myoglobin vs. Hemoglobin
Heme Prosthetic Group
Hemoglobin Cooperativity
Hill Equation
Hill Plot
Hemoglobin Binding in Tissues & Lungs
Hemoglobin Carbonation & Protonation
Bohr Effect
BPG Regulation of Hemoglobin
Fetal Hemoglobin
Sickle Cell Anemia
Chymotrypsin
Chymotrypsin's Catalytic Mechanism
Glycogen Phosphorylase
Liver vs Muscle Glycogen Phosphorylase
Antibody
ELISA
Motor Proteins
Skeletal Muscle Anatomy
Skeletal Muscle Contraction
9. Carbohydrates
Worksheet
Carbohydrates
Monosaccharides
Stereochemistry of Monosaccharides
Monosaccharide Configurations
Cyclic Monosaccharides
Hemiacetal vs. Hemiketal
Anomer
Mutarotation
Pyranose Conformations
Common Monosaccharides
Derivatives of Monosaccharides
Reducing Sugars
Reducing Sugars Tests
Glycosidic Bond
Disaccharides
Glycoconjugates
Polysaccharide
Cellulose
Chitin
Peptidoglycan
Starch
Glycogen
Lectins
10. Lipids
Worksheet
Lipids
Fatty Acids
Fatty Acid Nomenclature
Omega-3 Fatty Acids
Triacylglycerols
Glycerophospholipids
Sphingolipids
Sphingophospholipids
Sphingoglycolipids
Sphingolipid Recap
Waxes
Eicosanoids
Isoprenoids
Steroids
Steroid Hormones
Lipid Vitamins
Comprehensive Final Lipid Map
Biological Membranes
Physical Properties of Biological Membranes
Types of Membrane Proteins
Integral Membrane Proteins
Peripheral Membrane Proteins
Lipid-Linked Membrane Proteins
11. Biological Membranes and Transport
Worksheet
Biological Membrane Transport
Passive vs. Active Transport
Passive Membrane Transport
Facilitated Diffusion
Erythrocyte Facilitated Transporter Models
Membrane Transport of Ions
Primary Active Membrane Transport
Sodium-Potassium Ion Pump
SERCA: Calcium Ion Pump
ABC Transporters
Secondary Active Membrane Transport
Glucose Active Symporter Model
Endocytosis & Exocytosis
Neurotransmitter Release
Summary of Membrane Transport
Thermodynamics of Membrane Diffusion: Uncharged Molecule
Thermodynamics of Membrane Diffusion: Charged Ion
12. Biosignaling
Worksheet
Introduction to Biosignaling
G protein-Coupled Receptors
Stimulatory Adenylate Cyclase GPCR Signaling
cAMP & PKA
Inhibitory Adenylate Cyclase GPCR Signaling
Drugs & Toxins Affecting GPCR Signaling
Recap of Adenylate Cyclase GPCR Signaling
Phosphoinositide GPCR Signaling
PSP Secondary Messengers & PKC
Recap of Phosphoinositide Signaling
Receptor Tyrosine Kinases
Insulin
Insulin Receptor
Insulin Signaling on Glucose Metabolism
Recap Of Insulin Signaling in Glucose Metabolism
Insulin Signaling as a Growth Factor
Recap of Insulin Signaling As A Growth Factor
Recap of Insulin Signaling
Jak-Stat Signaling
Lipid Hormone Signaling
Summary of Biosignaling
Signaling Defects & Cancer
Review 1: Nucleic Acids, Lipids, & Membranes
Worksheet
Nucleic Acids 1
Nucleic Acids 2
Nucleic Acids 3
Nucleic Acids 4
DNA Sequencing 1
DNA Sequencing 2
Lipids 1
Lipids 2
Membrane Structure 1
Membrane Structure 2
Membrane Transport 1
Membrane Transport 2
Membrane Transport 3
Practice - Nucleic Acids 1
Practice - Nucleic Acids 2
Practice - Nucleic Acids 3
Lipids
Practice - Membrane Structure 1
Practice - Membrane Structure 2
Practice - Membrane Transport 1
Practice - Membrane Transport 2
Review 2: Biosignaling, Glycolysis, Gluconeogenesis, & PP-Pathway
Worksheet
Biosignaling 1
Biosignaling 2
Biosignaling 3
Biosignaling 4
Glycolysis 1
Glycolysis 2
Glycolysis 3
Glycolysis 4
Fermentation
Gluconeogenesis 1
Gluconeogenesis 2
Pentose Phosphate Pathway
Practice - Biosignaling
Practice - Bioenergetics 1
Practice - Bioenergetics 2
Practice - Glycolysis 1
Practice - Glycolysis 2
Practice - Gluconeogenesis
Practice - Pentose Phosphate Path
Review 3: Pyruvate & Fatty Acid Oxidation, Citric Acid Cycle, & Glycogen Metabolism
Worksheet
Pyruvate Oxidation
Citric Acid Cycle 1
Citric Acid Cycle 2
Citric Acid Cycle 3
Citric Acid Cycle 4
Metabolic Regulation 1
Metabolic Regulation 2
Glycogen Metabolism 1
Glycogen Metabolism 2
Fatty Acid Oxidation 1
Fatty Acid Oxidation 2
Citric Acid Cycle Practice 1
Citric Acid Cycle Practice 2
Citric Acid Cycle Practice 3
Glucose and Glycogen Regulation Practice 1
Glucose and Glycogen Regulation Practice 2
Fatty Acid Oxidation Practice 1
Fatty Acid Oxidation Practice 2
Review 4: Amino Acid Oxidation, Oxidative Phosphorylation, & Photophosphorylation
Worksheet
Amino Acid Oxidation 1
Amino Acid Oxidation 2
Oxidative Phosphorylation 1
Oxidative Phosphorylation 2
Oxidative Phosphorylation 3
Oxidative Phosphorylation 4
Photophosphorylation 1
Photophosphorylation 2
Photophosphorylation 3
Practice: Amino Acid Oxidation 1
Practice: Amino Acid Oxidation 2
Practice: Oxidative Phosphorylation 1
Practice: Oxidative Phosphorylation 2
Practice: Oxidative Phosphorylation 3
Practice: Photophosphorylation 1
Practice: Photophosphorylation 2
Review 1: Nucleic Acids, Lipids, & Membranes
Nucleic Acids 1
Review 1: Nucleic Acids, Lipids, & Membranes
Nucleic Acids 1
Next Topic: Nucleic Acids 2
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Nucleic Acids 1
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