Protein Structure

Question 1

Two Types of Covalent Bonds Between AAs in Proteins

Answer 1

1. peptide bonds - link AAs together in polypeptide chains, formed between the carboxyl group of one AA and the alpha-amine of another AA (loss of water)
2. disulfide bridges - the thiol of one cysteine reacts with the thiol of another cysteine to produce a covalent sulfur-sulfur bond

Question 2

What is a residue?

Answer 2

An individual AA when it is part of a polypeptide chain
- amino terminus made first, carboxyl terminus later

Example
+NH3-Phe-Glu-Gly-Ser-Ala-COOH

Question 3

Proteolytic Cleavage (proteolysis)

Answer 3

Hydrolysis of a protein by another protein

• the protein that does the cutting is known as a protease or proteolytic enzyme
• i.e. chymotrypsin and trypsin

Question 4

Denaturation

Answer 4

the disruption of a protein’s shape without breaking peptide bonds

• proteins are denatured by urea, which disrupts hydrogen bonding interactions
• if improperly folded, the protein is non-functional

Question 5

Primary Structure

Answer 5

the order of AAs bonded to each other in the polypeptide chain
primary structure = sequence

Question 6

Secondary Structure

Answer 6

the initial folding of a polypeptide chain stabilized by H-bonds between NH and CO groups

• alpha helices (AAs close together)
• beta-pleated sheets (AAs distant from each other, or even on a separate polypeptide chain)
• urea unfolds alpha helices and beta sheets

Question 7

Tertiary Structure

Answer 7

folding of the secondary structure into the most stable 3D conformation

• van der Waals forces (non-polar side chains)
• hydrogen bonds (polar side chains)
• disulfide bonds (cysteine residues)
• electrostatic interactions (acidic and basic side chains)

Question 8

Hydrophobic Effect

Answer 8

Hydrophobic residues tend to fold into the interior of the protein - away from the solvent
Hydrophilic residues tend to be exposed to water on the surface of a protein

Question 9

Quaternary Structure

Answer 9

tertiary structure interactions between multiple polypeptide chains

• the arrangement of subunits (single polypeptide chain) into a multisubunit complex
• peptide bonds are not involved (these deal with a single polypeptide chain)

Question 10

Active Site

Answer 10

the region in an enzyme’s 3D structure that is directly involved in catalysis

• enzymes that act on hydrophobic substrates have hydrophobic AAs in their active sites
• enzymes that act on hydrophilic/polar substrates have hydrophilic/polar AAs in their active sites

Question 11

What shapes are enzymes?

Answer 11

Globular/Spherical

Question 12

What are there reactants in an enzyme-catalyzed reaction called?

Answer 12

substrates

Question 13

Active Site Model

Answer 13

states that the substrate and active site are perfectly complementary

Question 14

Induced Fit Model

Answer 14

asserts that the substrate and active site differ slightly in structure and that the binding of the substrate induces a conformational change in the enzyme
- greater acceptance than the active site model

Question 15

Enzymes accelerate a given reaction by …

Answer 15

stabilizing the transition state - they do not alter equilibria

Question 16

Cofactors

Answer 16

metal ions or small molecules that are required for enzymatic activity

Question 17

Conenzyme

Answer 17

when a cofactor is an organic molecule

- i.e. coenzyme A (CoA)

Question 18

Regulation of Enzyme Activity

Answer 18

1. Covalent modification - phosphorylation either activate or inactivates the enzyme
2. Proteolytic Cleavage - with a protease inactive enzymes can become active
3. Association with other polypeptides - some proteins require association with another chain to function
4. Allosteric Regulation

Question 19

Allosteric Regulation

Answer 19

the binding of small molecules to particular sites on an enzyme that are distinct from the active site
- the binding of the allosteric regulator to the allosteric site is generally noncovalent and reversible

Question 20

Feedback Inhibition

Answer 20

A -E1-> B -E2-> C -E3> D

When there is a lot of D it will shut off E1 so that excess B, C and D are not made - this would conserve A and conserve energy

• a.k.a negative feedback