KeyExam1versionABIos352Spring2020

Exam Overview

Course: Bios352/Chem352 Exam #1

• Date: Spring 2020

• Total Points: 100

• Pages: 6, including cover page

Page 1: Hemoglobin and Carbon Monoxide Toxicity

Question 1 (6 pts, 2 pts each) - Hemoglobin: Circle True or False

• True: O₂ binding triggers a conformational change in hemoglobin, which enhances its ability to bind additional O₂ molecules (a phenomenon known as positive cooperativity).

• True: Positive cooperativity occurs because the first binding event increases the affinity of available sites for subsequent binding. This mechanism is critical for efficient oxygen transport in the blood.

• True: Negative cooperativity may occur when binding of the first ligand reduces the binding affinity at remaining sites, which can be important in certain cellular contexts.

Question 2 (4 pts) - Carbon monoxide (CO) toxicity reason:

• Correct Answer: c. Carbon monoxide binds to the Fe atom in the heme group of hemoglobin, which prevents the binding of O₂, leading to hypoxia and potentially lethal consequences.

Page 2: Protein Structure and Acid-Base Chemistry

Question 3 (6 points, 1 pt each) - Circle TRUE or FALSE

• FALSE: The lock and key model does not account for the conformational change that occurs in the protein upon ligand binding; rather, it suggests a rigid configuration.

• FALSE: A beta-sheet is correctly characterized as an example of secondary structure, not quaternary structure.

• TRUE: Proteins can be denatured by extremes of pH, temperature, and other environmental factors which disrupt their native structure and function.

• TRUE: An independently stable part of a protein, known as a domain, can operate semi-independently and can often be found in multiple proteins.

• FALSE: O₂ does not dissolve easily in water, which underscores the necessity of hemoglobin for efficient oxygen transport.

• TRUE: Anfinsen's ribonuclease refolding experiment demonstrated that the primary amino acid sequence of the protein determines its native conformation, leading to significant insights into protein folding.

Question 4 (4 pts) - Amino acids Pro and Gly found in:

• Correct Answer: a. Beta turn, which is a common structural motif in proteins facilitating the reversal of direction in peptide chains.

Question 5 (6 pts) - Calculate the pH using the formula:

• Formula used: pH = pKa + log([A-]/[HA]); Given pKa = 4, substituting in values provides: pH = 4 + 2 = 6.

Page 3: Noncovalent Interactions and Titration Curves

Question 6 (6 pts, 1 pt each) - Match interaction to phrases:

• Electrostatic Interactions: Occur between charged groups, significant in stabilizing protein structure.

• Hydrophobic effect: Drives nonpolar side chains to the protein interior, minimizing exposure to water, stabilizing the folded structure.

• Hydrogen bonds: Lead to local regular structures such as α-helixes and β-sheets, contributing to overall protein stability.

• Van der Waals Interactions: Weak interactions present between all atoms that contribute to the overall stabilizing of the protein structure regardless of polarity.

Question 7 (10 pts, 2 pts each) - Matching titration curve:

• A. HCl (strong acid, sharp pH drop)

• B. Acetic acid (weak acid, gradual pH change, optimal buffering capacity between pH 3.8 to 5.8)

• C. Leucine (neutral pH behavior)

• D. Aspartate (pKa of the amino group = 9.5, significantly acidic)

Page 4: Protein Purification and Western Blot

Question 8 (6 pts, 2 pts each) - Protein purification methods:

1. EAESTSEE (confirmed through UV-Vis spectrophotometry at 280 nm; indicates the presence of aromatic amino acids).

2. AVLAVLAVLALVALVSLVLS (eluted first in gel filtration chromatography, indicating lower molecular weight).

3. AVLWYVVVV (exhibits strong binding to ion-exchange chromatography using positively charged beads, indicating a high net positive charge).

Question 9 (4 pts) - All are considered "weak" interactions except:

• d. Peptide bonds (these are strong covalent bonds that link amino acids together in proteins).

Question 10 (4 pts) - Western blot procedure:

• A: Refers to the product of an enzyme covalently bound to the secondary antibody, commonly used for detection.

• B: Represents an epitope on the antigen that is recognized by the primary antibody.

• C: Refers to the constant region of the primary antibody, which does not vary among antibodies of the same isotype.

• The purple color observed on the blot results from a reaction involving an enzyme substrate linked to the antibodies.

Page 5: Protein Characteristics and Structure

Question 11 (6 pts) - Gel results; pure protein found in lane:

• Lane 3 - Indicates the presence of a protein with a molecular weight of 21,500 Daltons, suggesting effective purification and isolation.

Question 12 (2 pts) - Planar bonds in polypeptide backbone:

• A: Cα-C bonds (these bonds allow for rotation, contributing to the flexibility of the protein backbone).

• B: C-N bonds (these bonds are generally rigid due to resonance).

• C: N-Cα bonds (also part of the backbone structure).

• D: Cα-Cα bonds (these bonds are not planar and allow for protein flexibility).

Question 13 (6 pts, 2 each) - Match protein structure to type:

• Keratin: A fibrous protein known for its properties of alpha-helices and the presence of disulfide bonds that contribute to its strength.

• Silk: Characterized by antiparallel beta-sheets that lend mechanical strength and flexibility.

• Myoglobin: A globular protein that binds oxygen in muscle tissue, featuring a single heme group for oxygen transport.

• Collagen: Provides structural integrity and strength in connective tissues, forming a triple helix structure.

Question 14 (8 pts) - Bicarbonate reaction:

• Is bicarbonate a stronger acid than acetic acid? No. (Bicarbonate pKa = 10.2, indicating it is a weak acid compared to acetic acid which has a pKa of 4.76, showing it can donate protons more readily).

Page 6: Peptide Structure and Modifications

Question 15 (18 pts) - Draw pentapeptide Tyr-Cys-Pro-Asp:

1. Begin with the peptide backbone featuring appropriate covalent bonds and designate R groups for each amino acid.

2. Add -SH group to cysteine, highlighting thiol nature and potential for disulfide bond formation.

3. Include phosphoryl group addition to hydroxyl-containing sidechains, indicating post-translational modifications.

4. Consider conversion of specific sidechains to gamma-carboxyglutamate, 4-hydroxyproline, or 5-hydroxylysine, demonstrating structural and functional diversity in proteins.

Amino Acid Codes and Their Weights:

• Arginine: 30

• Aspartic Acid: 150

• Cysteine: 185

• Glutamic Acid: 185

• Glutamine: 185.