Open Question
Overlap, align & order the following peptide fragments to reveal the sequence of the original protein.
Fragments from cleavage method #1:
Fragments from cleavage method #2:
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Table of contents
- 1. Introduction to Biochemistry
- 2. Water
- 3. Amino Acids
- 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
- 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
- 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
- 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
- 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
- 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
- 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
- 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
- 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
- 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
- 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
- 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
- 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
- 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
5. Protein Techniques
Ordering Cleaved Fragments