Ch. 4 - Protein StructureWorksheetSee all chapters
All Chapters
Ch. 1 - Introduction to Biochemistry
Ch. 2 - Water
Ch. 3 - Amino Acids
Ch. 4 - Protein Structure
Ch. 5 - Protein Techniques
Ch. 6 - Enzymes and Enzyme Kinetics
Ch. 7 - Enzyme Inhibition and Regulation
Ch. 8 - Protein Function
Ch. 9 - Carbohydrates
Ch. 10 - Lipids
Ch. 11 - Biological Membranes and Transport
Ch. 12 - Biosignaling
Clutch Review 1: Nucleic Acids, Lipids, & Membranes
Clutch Review 2: Biosignaling, Glycolysis, Gluconeogenesis, & PP-Pathway
Clutch Review 3: Pyruvate & Fatty Acid Oxidation, Citric Acid Cycle, & Glycogen Metabolism
Clutch Review 4: Amino Acid Oxidation, Oxidative Phosphorylation, & Photophosphorylation
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
Anfinsen Experiment
Protein Folding
Chaperone Proteins
Quaternary Structure
Simple Vs. Conjugated Proteins
Fibrous and Globular Proteins

Concept #1: How to Determine the Net Charge of a Peptide

Practice: What is the net charge if you drop the peptide above into bleach (pH 12)?

Practice: Answer the following questions (A, B & C) relating to the 4 tripeptides.

i) Tyr-Lys-Met                    ii) Asp-Trp-Tyr                    iii) Asp-His-Glu                  iv) Leu-Val-Phe

A. Which tripeptide is most negatively charged at pH = 7? _________

B. Which tripeptide contains the largest number of nonpolar R groups? __________

C. Which tripeptide contains sulfur? ____________

Practice: Estimate the net charge for a His-His-His-His peptide at pH 6 (His pK  R = 6).

Practice: Estimate the net charge for the following peptide at pH 7: ATLDAK.

Practice: A. Draw the predominant structure of the following peptide at pH 9: Asn-Arg-Cys. What is its net charge?

(Asn pKa1 = 8.8, Arg pKR = 12.48, Cys pKa2 = 1.96, Cys pKR = 8.18).

B. What is the net charge of the same peptide if the pH is lowered to pH = 2? Draw the newly ionized peptide.

C. Within what pH range would the net charge on the peptide above be approximately +1?

pH: ______________