Module 2

Question 1

Name the 4 levels of protein structure and their (very) basic definition.

Answer 1

Primary - sequence of amino acids
Secondary - repeating interactions of amino acids
Tertiary - arrangement of atoms in a subunit
Quaternary - arrangement of subunits

Question 2

T or F: Fibrous proteins are more soluble than globular proteins.

Answer 2

False

Question 3

What are the two common secondary protein structures?

Answer 3

alpha-helix and beta-pleated sheets

Question 4

What bonds do the Φ and Ψ describe?

Answer 4

Φ - alpha-carbon and nitrogen bond
Ψ - alpha-carbon and carbon bond

Question 5

T or F: Trans configuration for chain of amino acids have more steric hindrance; therefore, it is less stable.

Answer 5

False. Less; more stable

Question 6

What are the two exceptions for the Ramachandran Plot?

Answer 6

Proline and Glycine

Question 7

Its permissible range of Φ and Ψ covers a large area of the Ramachandran diagram. Which amino acid is described?

Answer 7

Glycine

Question 8

It is the most conformationally restricted amino acid.

Answer 8

Proline

Question 9

Pitch of alpha-helix.

Answer 9

5.4 Å

Question 10

How many amino acids per turn in an alpha-helix structure.

Answer 10

3.6

Question 11

This amino acid creates a bend, disrupting alpha-helix structures.

Answer 11

Proline

Question 12

What are the three alpha-helix disruptions?

Answer 12

1. Presence of proline
2. Strong electrostatic repulsion - K and R
3. Crowding or steric repulsion

Question 13

In alpha-keratin, how much residue-units are repeated to form the structure?

Answer 13

Seven

Question 14

Collagen

Answer 14

• consists of three extended helical chains wrapped into a triple helix (superhelix)

Question 15

Amino acid derivatives found in collagen.

Answer 15

Hydroxyproline and hydroxylysine

Question 16

The smallest component of hair cortex, composed of four alpha-keratins twisted into a left-handed superhelix

Answer 16

Protofibril

Question 17

Component of hair cortex

Answer 17

Cortex -> Macrofibril -> Microfibril -> Protofibril

Question 18

Type of beta-sheet in which the hydrogen-bonded chains extend in the same direction

Answer 18

Parallel sheet

Question 19

Describe antiparallel sheet.

Answer 19

Neighboring hydrogen-bonded chains run in opposite directions

Question 20

T or F: Parallel beta-sheets are less stable than antiparallel beta-sheets

Answer 20

True

Question 21

Describe the parallelism of fibroin.

Answer 21

Anti-parallel

Question 22

Which interactions hold the tertiary structure of proteins?

Answer 22

• Hydrogen bonding:
  + between peptide groups
  + between side chains
• Metal ion coordination
• Disulfide bonds
• Hydrophobic interactions
• Ionic linkages

Question 23

Protein that is responsible for storing oxygen in muscles.

Answer 23

Myoglobin

Question 24

T or F: Hemoglobin is a quaternary tetrameric protein.

Answer 24

True

Question 25

What is the function of hemoglobin?

Answer 25

Transportation of oxygen

Question 26

Refers to the property of hemoglobin where if one heme group is bound with oxygen, it becomes easier for the next oxygen to bond.

Answer 26

Cooperative binding

Question 27

What are the compounds that lower the affinity of oxygen to hemoglobin?

Answer 27

H+ CO2 BPG (D-2,3-bisphosphoglycerate)

Question 28

What is the reagent used in Edman degradation?

Answer 28

PITC (phenyl isothiocynate)

Question 29

What is the Sanger's reagent's full name?

Answer 29

2,4-Dinitrofluorobenzene

Question 30

This analysis is done to identify amino acids.

Answer 30

Sanger Analysis

Question 31

It is an efficient way to identify the N-terminal amino acid

Answer 31

Edman degradation

Question 32

It cleaves internal peptide bonds

Answer 32

Endopeptidases

Question 33

It cleaves the scissile peptide bond flanked by the residues with specific side chain requirements

Answer 33

Protease

Question 34

It cleaves either N or C terminal

Answer 34

Exopeptidase

Question 35

Which amino acids do trypsin cleave?

Answer 35

R Arginine K Lysine

Question 36

This enzyme cleaves L F W and Y

Answer 36

Pepsin

Question 37

Which amino acids do chymotrypsin cleave?

Answer 37

F W Y

Question 38

T or F: Endopeptidase V8 cleaves Glutamate.

Answer 38

False. Glutamine.

Question 39

The amino acids valine, glycine, alanine, and serine are cleaved by _______________.

Answer 39

Elastase

Question 40

T or F: Cyanogen bromide cleaves the carboxyl side of every methionine residue

Answer 40

True