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1. Introduction to Biochemistry(0)

What is Biochemistry?
(0)

Characteristics of Life
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Abiogenesis
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Nucleic Acids
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Proteins
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Carbohydrates
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Lipids
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Taxonomy
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Cell Organelles
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Endosymbiotic Theory
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Central Dogma
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Functional Groups
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Chemical Bonds
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Organic Chemistry
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Entropy
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Second Law of Thermodynamics
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Equilibrium Constant
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Gibbs Free Energy
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2. Water(0)

Properties of Water
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Osmosis
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Hydrophobic Effect
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Acids and Bases
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Autoionization of Water
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pH
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Acid Dissociation Constant
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Henderson Hasselbalch Equation
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Determining Predominate Species
(0)

Titration
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Buffer Solution
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3. Amino Acids(0)

Amino Acid Groups
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Amino Acid Three Letter Code
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Amino Acid One Letter Code
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Amino Acid Configuration
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Essential Amino Acids
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Nonpolar Amino Acids
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Aromatic Amino Acids
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Polar Amino Acids
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Charged Amino Acids
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How to Memorize Amino Acids
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Zwitterion
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Non-Ionizable Vs. Ionizable R-Groups
(0)

Isoelectric Point
(0)

Isoelectric Point of Amino Acids with Ionizable R-Groups
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Titrations of Amino Acids with Non-Ionizable R-Groups
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Titrations of Amino Acids with Ionizable R-Groups
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Amino Acids and Henderson-Hasselbalch
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4. Protein Structure(0)

Peptide Bond
(0)

Primary Structure of Protein
(0)

Altering Primary Protein Structure
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Drawing a Peptide
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Determining Net Charge of a Peptide
(0)

Isoelectric Point of a Peptide
(0)

Approximating Protein Mass
(0)

Peptide Group
(0)

Ramachandran Plot
(0)

Atypical Ramachandran Plots
(0)

Alpha Helix
(0)

Alpha Helix Pitch and Rise
(0)

Alpha Helix Hydrogen Bonding
(0)

Alpha Helix Disruption
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Beta Strand
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Beta Sheet
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Antiparallel and Parallel Beta Sheets
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Beta Turns
(0)

Tertiary Structure of Protein
(0)

Protein Motifs and Domains
(0)

Denaturation
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Anfinsen Experiment
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Protein Folding
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Chaperone Proteins
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Prions
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Quaternary Structure
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Simple Vs. Conjugated Proteins
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Fibrous and Globular Proteins
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5. Protein Techniques(0)

Protein Purification
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Protein Extraction
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Differential Centrifugation
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Salting Out
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Dialysis
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Column Chromatography
(0)

Ion-Exchange Chromatography
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Anion-Exchange Chromatography
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Size Exclusion Chromatography
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Affinity Chromatography
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Specific Activity
(0)

HPLC
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Spectrophotometry
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Native Gel Electrophoresis
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SDS-PAGE
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SDS-PAGE Strategies
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Isoelectric Focusing
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2D-Electrophoresis
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Diagonal Electrophoresis
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Mass Spectrometry
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Mass Spectrum
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Tandem Mass Spectrometry
(0)

Peptide Mass Fingerprinting
(0)

Overview of Direct Protein Sequencing
(0)

Amino Acid Hydrolysis
(0)

FDNB
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Chemical Cleavage of Bonds
(0)

Peptidases
(0)

Edman Degradation
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Edman Degradation Sequenator and Sequencing Data Analysis
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Edman Degradation Reaction Efficiency
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Ordering Cleaved Fragments
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Strategy for Ordering Cleaved Fragments
(0)

Indirect Protein Sequencing Via Geneomic Analyses
(0)

6. Enzymes and Enzyme Kinetics(0)

Enzymes
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Enzyme-Substrate Complex
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Lock and Key Vs. Induced Fit Models
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Optimal Enzyme Conditions
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Activation Energy
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Types of Enzymes
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Cofactor
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Catalysis
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Electrostatic and Metal Ion Catalysis
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Covalent Catalysis
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Reaction Rate
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Enzyme Kinetics
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Rate Constants and Rate Law
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Reaction Orders
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Rate Constant Units
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Initial Velocity
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Vmax Enzyme
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Km Enzyme
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Steady-State Conditions
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Michaelis-Menten Assumptions
(0)

Michaelis-Menten Equation
(0)

Lineweaver-Burk Plot
(0)

Michaelis-Menten vs. Lineweaver-Burk Plots
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Shifting Lineweaver-Burk Plots
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Calculating Vmax
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Calculating Km
(0)

Kcat
(0)

Specificity Constant
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7. Enzyme Inhibition and Regulation (0)

Enzyme Inhibition
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Irreversible Inhibition
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Reversible Inhibition
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Inhibition Constant
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Degree of Inhibition
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Apparent Km and Vmax
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Inhibition Effects on Reaction Rate
(0)

Competitive Inhibition
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Uncompetitive Inhibition
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Mixed Inhibition
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Noncompetitive Inhibition
(0)

Recap of Reversible Inhibition
(0)

Allosteric Regulation
(0)

Allosteric Kinetics
(0)

Allosteric Enzyme Conformations
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Allosteric Effectors
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Concerted (MWC) Model
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Sequential (KNF) Model
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Negative Feedback
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Positive Feedback
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Post Translational Modification
(0)

Ubiquitination
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Phosphorylation
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Zymogens
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8. Protein Function (0)

Introduction to Protein-Ligand Interactions
(0)

Protein-Ligand Equilibrium Constants
(0)

Protein-Ligand Fractional Saturation
(0)

Myoglobin vs. Hemoglobin
(0)

Heme Prosthetic Group
(0)

Hemoglobin Cooperativity
(0)

Hill Equation
(0)

Hill Plot
(0)

Hemoglobin Binding in Tissues & Lungs
(0)

Hemoglobin Carbonation & Protonation
(0)

Bohr Effect
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BPG Regulation of Hemoglobin
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Fetal Hemoglobin
(0)

Sickle Cell Anemia
(0)

Chymotrypsin
(0)

Chymotrypsin's Catalytic Mechanism
(0)

Glycogen Phosphorylase
(0)

Liver vs Muscle Glycogen Phosphorylase
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Antibody
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ELISA
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Motor Proteins
(0)

Skeletal Muscle Anatomy
(0)

Skeletal Muscle Contraction
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9. Carbohydrates(0)

Carbohydrates
(0)

Monosaccharides
(0)

Stereochemistry of Monosaccharides
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Monosaccharide Configurations
(0)

Cyclic Monosaccharides
(0)

Hemiacetal vs. Hemiketal
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Anomer
(0)

Mutarotation
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Pyranose Conformations
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Common Monosaccharides
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Derivatives of Monosaccharides
(0)

Reducing Sugars
(0)

Reducing Sugars Tests
(0)

Glycosidic Bond
(0)

Disaccharides
(0)

Glycoconjugates
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Polysaccharide
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Cellulose
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Chitin
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Peptidoglycan
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Starch
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Glycogen
(0)

Lectins
(0)

10. Lipids(0)

Lipids
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Fatty Acids
(0)

Fatty Acid Nomenclature
(0)

Omega-3 Fatty Acids
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Triacylglycerols
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Glycerophospholipids
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Sphingolipids
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Sphingophospholipids
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Sphingoglycolipids
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Sphingolipid Recap
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Waxes
(0)

Eicosanoids
(0)

Isoprenoids
(0)

Steroids
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Steroid Hormones
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Lipid Vitamins
(0)

Comprehensive Final Lipid Map
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Biological Membranes
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Physical Properties of Biological Membranes
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Types of Membrane Proteins
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Integral Membrane Proteins
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Peripheral Membrane Proteins
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Lipid-Linked Membrane Proteins
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11. Biological Membranes and Transport (0)

Biological Membrane Transport
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Passive vs. Active Transport
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Passive Membrane Transport
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Facilitated Diffusion
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Erythrocyte Facilitated Transporter Models
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Membrane Transport of Ions
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Primary Active Membrane Transport
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Sodium-Potassium Ion Pump
(0)

SERCA: Calcium Ion Pump
(0)

ABC Transporters
(0)

Secondary Active Membrane Transport
(0)

Glucose Active Symporter Model
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Endocytosis & Exocytosis
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Neurotransmitter Release
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Summary of Membrane Transport
(0)

Thermodynamics of Membrane Diffusion: Uncharged Molecule
(0)

Thermodynamics of Membrane Diffusion: Charged Ion
(0)

12. Biosignaling(0)

Introduction to Biosignaling
(0)

G protein-Coupled Receptors
(0)

Stimulatory Adenylate Cyclase GPCR Signaling
(0)

cAMP & PKA
(0)

Inhibitory Adenylate Cyclase GPCR Signaling
(0)

Drugs & Toxins Affecting GPCR Signaling
(0)

Recap of Adenylate Cyclase GPCR Signaling
(0)

Phosphoinositide GPCR Signaling
(0)

PSP Secondary Messengers & PKC
(0)

Recap of Phosphoinositide Signaling
(0)

Receptor Tyrosine Kinases
(0)

Insulin
(0)

Insulin Receptor
(0)

Insulin Signaling on Glucose Metabolism
(0)

Recap Of Insulin Signaling in Glucose Metabolism
(0)

Insulin Signaling as a Growth Factor
(0)

Recap of Insulin Signaling As A Growth Factor
(0)

Recap of Insulin Signaling
(0)

Jak-Stat Signaling
(0)

Lipid Hormone Signaling
(0)

Summary of Biosignaling
(0)

Signaling Defects & Cancer
(0)

Review 1: Nucleic Acids, Lipids, & Membranes(0)

Nucleic Acids 1
(0)

Nucleic Acids 2
(0)

Nucleic Acids 3
(0)

Nucleic Acids 4
(0)

DNA Sequencing 1
(0)

DNA Sequencing 2
(0)

Lipids 1
(0)

Lipids 2
(0)

Membrane Structure 1
(0)

Membrane Structure 2
(0)

Membrane Transport 1
(0)

Membrane Transport 2
(0)

Membrane Transport 3
(0)

Practice - Nucleic Acids 1
(0)

Practice - Nucleic Acids 2
(0)

Practice - Nucleic Acids 3
(0)

Lipids
(0)

Practice - Membrane Structure 1
(0)

Practice - Membrane Structure 2
(0)

Practice - Membrane Transport 1
(0)

Practice - Membrane Transport 2
(0)

Review 2: Biosignaling, Glycolysis, Gluconeogenesis, & PP-Pathway(0)

Biosignaling 1
(0)

Biosignaling 2
(0)

Biosignaling 3
(0)

Biosignaling 4
(0)

Glycolysis 1
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Glycolysis 2
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Glycolysis 3
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Glycolysis 4
(0)

Fermentation
(0)

Gluconeogenesis 1
(0)

Gluconeogenesis 2
(0)

Pentose Phosphate Pathway
(0)

Practice - Biosignaling
(0)

Practice - Bioenergetics 1
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Practice - Bioenergetics 2
(0)

Practice - Glycolysis 1
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Practice - Glycolysis 2
(0)

Practice - Gluconeogenesis
(0)

Practice - Pentose Phosphate Path
(0)

Review 3: Pyruvate & Fatty Acid Oxidation, Citric Acid Cycle, & Glycogen Metabolism(0)

Pyruvate Oxidation
(0)

Citric Acid Cycle 1
(0)

Citric Acid Cycle 2
(0)

Citric Acid Cycle 3
(0)

Citric Acid Cycle 4
(0)

Metabolic Regulation 1
(0)

Metabolic Regulation 2
(0)

Glycogen Metabolism 1
(0)

Glycogen Metabolism 2
(0)

Fatty Acid Oxidation 1
(0)

Fatty Acid Oxidation 2
(0)

Citric Acid Cycle Practice 1
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Citric Acid Cycle Practice 2
(0)

Citric Acid Cycle Practice 3
(0)

Glucose and Glycogen Regulation Practice 1
(0)

Glucose and Glycogen Regulation Practice 2
(0)

Fatty Acid Oxidation Practice 1
(0)

Fatty Acid Oxidation Practice 2
(0)

Review 4: Amino Acid Oxidation, Oxidative Phosphorylation, & Photophosphorylation(0)

Amino Acid Oxidation 1
(0)

Amino Acid Oxidation 2
(0)

Oxidative Phosphorylation 1
(0)

Oxidative Phosphorylation 2
(0)

Oxidative Phosphorylation 3
(0)

Oxidative Phosphorylation 4
(0)

Photophosphorylation 1
(0)

Photophosphorylation 2
(0)

Photophosphorylation 3
(0)

Practice: Amino Acid Oxidation 1
(0)

Practice: Amino Acid Oxidation 2
(0)

Practice: Oxidative Phosphorylation 1
(0)

Practice: Oxidative Phosphorylation 2
(0)

Practice: Oxidative Phosphorylation 3
(0)

Practice: Photophosphorylation 1
(0)

Practice: Photophosphorylation 2
(0)

4. Protein Structure

Determining Net Charge of a Peptide

4. Protein Structure

Determining Net Charge of a Peptide: Videos & Practice Problems

Video Lessons Practice Worksheet

Determining Net Charge of a Peptide Practice Problems

20 problems

Problem 1Multiple Choice

What is the net charge of a peptide when the pH is equal to the pKa of its ionizable group?

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Problem 2Multiple Choice

Why is it important to use the correct set of pKa values for amino acid residues instead of free amino acids when calculating the net charge of a peptide?

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Problem 3Multiple Choice

A peptide contains a lysine residue with a pKa of 10.5. If the microenvironment shifts the pKa to 9.5, what is the net charge of the lysine residue at pH 7.4?

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Problem 4Multiple Choice

Given a peptide with the following ionizable groups: N-terminus (pKa 8.0), C-terminus (pKa 3.1), and a glutamic acid side chain (pKa 4.1), what is the net charge at pH 7.4?

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Problem 5Multiple Choice

What predominates when the pH is lower than the pKa of an ionizable group?

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Problem 6Multiple Choice

How do the ionizable R groups of amino acids like arginine and aspartic acid affect the net charge of a peptide?

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Problem 7Multiple Choice

Calculate the net charge of a peptide at pH 7.4 with the following ionizable groups: N-terminus (pKa 9.0), lysine side chain (pKa 10.5), and C-terminus (pKa 3.0).

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Problem 8Multiple Choice

Why is it crucial to understand the ionizable nature of amino acids like arginine, histidine, and aspartic acid when determining peptide charge?

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Problem 9Multiple Choice

A peptide's serine residue has a pKa of 13.0 in a standard environment. If the microenvironment shifts the pKa to 12.0, how does this affect the charge at pH 7.4?

Problem 10Multiple Choice

Outline the steps to estimate the net charge of a peptide at pH 7.4 with the following ionizable groups: N-terminus (pKa 8.0), arginine side chain (pKa 12.5), and C-terminus (pKa 3.5).

Problem 11Multiple Choice

What happens to the charge of an ionizable group when the pH is higher than its pKa?

Problem 12Multiple Choice

What could be the consequence of using free amino acid pKa values instead of residue pKa values in peptide charge calculations?

Problem 13Multiple Choice

A peptide contains a histidine residue with a pKa of 6.0. If the microenvironment shifts the pKa to 7.0, what is the net charge of the histidine residue at pH 7.4?

Problem 14Multiple Choice

Given a peptide with the following ionizable groups: N-terminus (pKa 9.5), C-terminus (pKa 2.5), and a tyrosine side chain (pKa 10.1), what is the net charge at pH 7.4?

Problem 15Multiple Choice

What predominates when the pH is higher than the pKa of an ionizable group?

Problem 16Multiple Choice

How do the ionizable R groups of amino acids like lysine and glutamic acid affect the net charge of a peptide?

Problem 17Multiple Choice

Calculate the net charge of a peptide at pH 7.4 with the following ionizable groups: N-terminus (pKa 8.5), arginine side chain (pKa 12.5), and C-terminus (pKa 3.0).

Problem 18Multiple Choice

Why is it important to understand the ionizable nature of amino acids like lysine, histidine, and glutamic acid when determining peptide charge?

Problem 19Multiple Choice

A peptide's cysteine residue has a pKa of 8.3 in a standard environment. If the microenvironment shifts the pKa to 7.3, how does this affect the charge at pH 7.4?

Problem 20Multiple Choice

Outline the steps to estimate the net charge of a peptide at pH 7.4 with the following ionizable groups: N-terminus (pKa 9.0), lysine side chain (pKa 10.5), and C-terminus (pKa 3.0).

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Drawing a Peptide Practice Problems Isoelectric Point of a Peptide Practice Problems

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