Exam 1 Stuff That Isn't Amino Acids

Question 0

1 strong force that stabilizes protein structure

Answer 0

Disulfide bonds

Question 1

4 weak forces that stabilize protein structure

Answer 1

1. Hydrogen bonds
2. Hydrophobic interactions
3. Electrostatic interactions
4. Van der Waals forces

Question 2

Primary structure of proteins

Answer 2

List of A.A. As they occur in the protein from N to C terminus

Example: N-CTRLASQNVLKT…-C

Question 3

Secondary structure of proteins

Answer 3

Localized areas within a protein that assume regular 3D conformations

Question 4

Types of secondary structures

Answer 4

1. Alpha helix
2. Beta sheet
3. Beta bend
4. Super secondary

Question 5

Alpha helix

Answer 5

Helical conformation

 - About 3.6 A.A. Per helical turn
 - All R groups outward of helix

Question 6

3 things that contribute to stabilizing alpha-helical structure

Answer 6

1. H-bonds between O of C=O and H of N-H
2. Carbonyl R groups (thermodynamically positive interactions
3. Charged A.A. Incorporated into the poles (satiate partial charges)

Question 7

Which A.A. Is never found in alpha helix?

Answer 7

Proline

Question 8

5 coenzymes to know

Answer 8

1. NADH/NAD+
2. FADH2/FADH
3. Coenzyme A
4. TPP
5. ATP

Question 9

Vitamin source and metabolic role of:

NADH/NAD+

Answer 9

Niacin (B3)

Redox reactions

Question 10

Vitamin source and metabolic role of:

FADH2/FADH

Answer 10

Riboflavin (B2)

Redox reactions

Question 11

Vitamin source and metabolic role of:

Coenzyme A

Answer 11

Pantothenate (B5)

Transfer of acyl groups
Breaking fatty acids down, etc.

Question 12

Vitamin source and metabolic role of:

TPP

Answer 12

Thiamine (B1)

Transfer of carbonyl groups

Question 13

Vitamin source and metabolic role of:

ATP

Answer 13

No vitamin source necessary

2 main roles:

1) energy transfer
2) phosphate source

Question 14

Induced Fit Mechanism

Answer 14

1) Substrate enters the active site and makes initial CATALYTIC CONTACTS
2) The initial catalytic contacts stimulates CONFORMATIONAL CHANGE in enzyme
3) This causes the active site to COLLAPSE down around the substrate, confining it in a SMALLER SPACE
4) This allows an INCREASED NUMBER OF CATALYTIC CONTACTS
5) The contacts PUSH/PULL/TUG at the electron densities of the substrate
6) This STABILIZES THE TRANSITION STATE, which LOWERS THE Ea OF THE REACTION, and results in PRODUCT FORMATION