Protein Structure (Module 1 Lectures 3 & 4)

Question 1

What are Eight Functions of Proteins?

Answer 1

1. Catalyze chemical reactions (enzymes)
2. Provide mechanical strength (structural proteins)
3. Carry molecules in the blood and into the cell (transport proteins)
4. Generate movement of cells and tissues (motor proteins)
5. Bind small molecules (storage proteins)
6. Carry signals between cells (signal proteins)
7. Detect and respond to signals (receptor proteins)
8. Control differentiation (gene regulatory proteins)

Question 2

What Types of Diagrams do Biochemists Use to Depict Protein Structures?

Answer 2

1. Backbone
2. Ribbon
3. Wire Frame
4. Space Filling

Question 3

What is a Homodimer?

Answer 3

A quaternary protein structure with two identical subunits.

Question 4

What is a Heterodimer?

Answer 4

A quaternary protein structure with two DIFFERENT polypeptide chains, or non-identical subunits.

Question 5

What is a Tetramer?

Answer 5

A quaternary protein structure with four polypeptide chains (like hemoglobin).

Question 6

Describe the role and structure of collagen.

Answer 6

1. A structural protein in the extracellular matrix
2. Long, fibrous, insoluble protein that helps tissues fight stretching
3. A triple helix with three polypeptide chains coiled together (alpha helix)

Question 7

Describe the amino acid composition of collagen.

Answer 7

1. Every third residue in the helix is glycine.
2. Usually proline comes right after glycine and can be modified into hydroxyproline to increase hydrogen-bonding capacity and stabilize the triple helix structure.
3. Collagen structure can be called Gly-Pro-X motif because X can be any amino acid.

Question 8

How does Vitamin C deficiency affect collagen?

Answer 8

1. Ascorbic acid is necessary for the hydroxylation of proline into hydroxyproline.
2. Collagen without hydroxyproline cannot hydrogen bond as well and is therefore significantly less stable and easily broken down.
3. Scurvy (a vitamin C deficiency disease) therefore has characteristic symptoms of poor wound healing and capillary fragility.

Question 9

How are collagen fibers connected?

Answer 9

Fibrils are first formed by cross-linkage of collagen triple helices by Lysine residues which were modified to hydroxylysine.

Question 10

Compare and contrast elastin and collagen.

Answer 10

1. Both belong to the extra-cellular matrix.

2. Elastin can stretch and relax (not rigid like collagen).

Question 11

Describe antibodies, especially IgG’s.

Answer 11

1. Soluble proteins that bind to bacteria, viruses, fungi, etc.
2. IgG’s have four polypeptide chains (two heavy and two light) that are linked by disulfide bonds.
3. Each antibody has two different antigen-binding sites that recognizes a particular molecular motif (antigen).

Question 12

What are five things that can denature a protein?

Answer 12

1. Heat
2. High salt concentrations which can damage electrostatic bonds.
3. Urea and guanidinium chloride that disrupt non-covalent bonds.
4. Beta-mercaptoethanol and other reducing agents, which break disulfide bridges by reducing the sulfurs in disulfide bonds.
5. Organic solvents that disrupt hydrophobic interactions.

Question 13

Describe the specificity of antibody binding sites using immunoglobulins as an example.

Answer 13

1. IgGs all have common structures with multiple domains.
2. Variable domains are the parts of IgGs that bind to antigens and vary from one antibody to the next (for specificity).

Question 14

What is a prosthetic group and what are examples of proteins with prosthetic groups?

Answer 14

1. A prosthetic group is a no -amino acid component of a protein necessary for it’s specialized function.
2. Amino acid portion = apoprotein, and examples of prosthetic groups are the heme group in hemoglobin and myoglobin as well as various vitamin derivatives (like thiamin pyrophosphate and pyridoxal phosphate).

Question 15

Describe the function, location, and structure of myoglobin.

Answer 15

1. It is an oxygen-binding protein.
2. Found in muscle cells.
3. Polypeptide with mainly an alpha-helix structure, folded into a water-soluble globular protein.
4. It has one heme group which is a protoporphyrin molecule with an iron Fe3+ in the center.

Question 16

What is ribonuclease?

Answer 16

An enzyme that hydrolyzes (digests) RNA.

Question 17

Describe the denaturation of ribonuclease.

Answer 17

1. If treated with denaturing agents, like mercaptoethanol or urea, it will unfold and lose it’s catalytic ability.
2. If denatured agents are removed by dialysis ribonuclease will slowly regain its enzymatic activity, by reforming it’s disulfide bridges again and spontaneously refolding into it’s original structure.

Question 18

Explain why sometimes protein denaturation is irreversible.

Answer 18

1. Sometimes the molecules in a protein become tangled and refolding is no longer possible.
2. Also sometimes when disulfide linkages are broken (like in insulin) the different polypeptide chains become irreversibly separated.

Question 19

Explain the disulfide bondage in hair and the subsequent chemical curling or relaxing that is commonly practiced today.

Answer 19

1. Keratin is the major component in hair and is formed with alpha-helix fibers cross-linked by many disulfide bonds.
2. Thiol-containing solutions can either curl or straighten hair by gently breaking a few cross-links.
3. Hair can be curled or straightened mechanically and oxidizing agents ate added to re-build disulfide linkages and stabilize the desired shape.

Question 20

What are some examples of diseases caused by mis-folded proteins.

Answer 20

1. Mad Cow Disease (aka Jacobs-Kreuzfield syndrome) may be caused by mis-folded proteins (prions) that wind up propagating a chain of protein mis-folding.
2. Amyloid plaques associated with Alzheimer’s disease are mis-folded proteins.

Question 21

Explain the average protein sizes and how they can be separated bases on this physical property.

Answer 21

1. Average molecular weight of amino acid = ~100 Daltons, so proteins with 50 to 2k amino acid residues will weigh between 35.5 to 220 kiloDaltons.
2. Polyacrimide gel electrophoresis can separate proteins by their size after denaturing conditions are used to eliminate effects of shape or electrical charge on speed of protein movement across gel.

Question 22

What is the isoelectric point of a protein?

Answer 22

It is the pH at which the net charge on the protein is zero (same number of positive and negative charges).

Question 23

What is isoelectric focusing? Give one example of a protein used.

Answer 23

1. A process where proteins are moved along a pH gradient and stop in the region where it’s pH = it’s pI.
2. Example: serine albumin is an acidic protein with a pI of 4.8