Chapter 3 & 4

Question 1

Nonpolar amino acids

Answer 1

Glycine, Alanine, Proline, Valine, Leucine, Isoleucine, Methionine

Question 2

Aromatic amino acids

Answer 2

Phenylalanine, Tyrosine, Tryptophan

Question 3

Polar amino acids

Answer 3

Serine, Threonine, Cysteine, Asparagine, Glutamine

Question 4

Basic amino acids

Answer 4

Lysine, Arginine, Histidine

Question 5

Acidic amino acids

Answer 5

Aspartate, Glutamate

Question 6

What is the equation for isoelectric point?

Answer 6

pI = (pka1 + pka2)/2

Question 7

What does the isoelectric point tell us?

Answer 7

What pH the molecule has no charge

Question 8

How to find the pI of acidic amino acids

Answer 8

Take the pI of the two smaller pKas

Question 9

How to find the pI of basic amino acids

Answer 9

Take the pI of the two larger pKas

Question 10

Label the phi, psi, and omega bonds of
         R      O
         I        II
N --- C ---- C -_- N
         I
        H

Answer 10

Phi: between first carbon and nitrogen
Psi: between two carbons
Omega: between second carbon and nitrogen (with O)

Question 11

Properties of alpha helix

Answer 11

• Lots of alanine (not glycine because it’s too small and flexible)
• Right handed helix most common (can be left handed)
• Like a battery with the positive charge on top, and negative charge on bottom
• No proline
• Stabilized by hydrogen bonds

Question 12

Properties of beta sheets

Answer 12

• Parallel or anti-parallel
• Rigid
• Beta turns
• Zig Zag like pattern
• Ring structure
• Stabilized by H bonds

Question 13

What are beta turns?

Answer 13

Connect antiparallel and parallel beta sheets when the carbonyl of the first amino acid forms an H-bond with the amino of the fourth amino acid

Question 14

How many types of beta turns exist?

Answer 14

2

Question 15

What is a type I beta turn?

Answer 15

The most common beta turn where proline is in the cis formation, in the second position

Question 16

What is a type II beta turn

Answer 16

The lesser common beta turn where glycine is in the third position

Question 17

What characteristics of glycine makes it a destabilizer or stabilizer of protein structure?

Answer 17

Small R group present that allows it to fold in on itself. Too many glycine present leads to increased flexibility of beta sheet and increased instability

Question 18

What characteristics of proline make it a stabilizer of protein structure?

Answer 18

R group is in cyclic formation which causes a rigid, stable structure

Question 19

Primary structure example and which bonds?

Answer 19

Single amino acids connected by covalent bonds

Question 20

Secondary structure example and which bonds?

Answer 20

Alpha helices and beta sheets with hydrogen bonding

Question 21

Tertiary structure example and which bonds?

Answer 21

Multiple alpha helices and beta sheets connected together with disulfide bonds, hydrogen bonds, and motifs.

Question 22

Quaternary structure example and which bonds?

Answer 22

Complexes of several proteins with hydrophobic and van der waals interactions

Question 23

Alpha-keratin characteristics

Answer 23

• Two parallel right handed helix
  
  • forms left handed super twist* that are connected with disulfide bonds and called pseudorepeats
• Pseudorepeats come together to make protofilaments, protofilaments come together to make protofibrils where the strands are kept together by H bonds
• Lots of alanine and glycine
• Tough
• Stabilized by cysteine disulfide bonds (15%)
• Present in hair and nails

Question 24

Beta-keratin characteristics

Answer 24

• Parallel beta sheets
• Lots of alanine and glycine repeats
• Soft, flexible
• Present in silk fibroin (spider’s web)

Question 25

Collagen characteristics

Answer 25

- Left handed alpha helix with three amino acids per turn * forms 3 alpha-chains - The three alpha chains super twist into a right handed helix - Tri repeat of Glycine - Proline - 4 hydroxyproline - Covalently linked - Insoluble - Present in tendons and carilage

Question 26

Fibrous protein characteristics

Answer 26

- Less common - Strands/sheets - One type of secondary structure - Simple tertiary structure - Strong, flexible support - Insoluble and phobic amino acid

Question 27

Globular protein characteristics

Answer 27

- More common - Folded, spherical shape - Many alpha helices and beta sheets - Large

Question 28

Describe a heat shock protein

Answer 28

Binds to regions of unfolded polypeptides that are rich in hydrophobic residues, thus protecting proteins subject to denaturation. Also protect other proteins from being folded if they need to be straight

Question 29

Describe a chaperone protein

Answer 29

Assist unfolded, partially folded, or improperly folded proteins in finding their shape -Require ATP

Question 30

Prosthetic group

Answer 30

Organometallic structure that is tightly bound to proteins

Question 31

Cofactor

Answer 31

Non-protein chemical compound that is required for protein's biological activity

Question 32

Coenzyme

Answer 32

Organic or organometallic structure that is loosely bound to proteins

Question 33

Motifs

Answer 33

A recognizable folding pattern involving two or more elements of secondary structure and the connections between them

Question 34

Parallel Beta Sheets

Answer 34

N --> C N --> C Consistent ring size (12) Bent H bonds

Question 35

Antiparallel beta sheets

Answer 35

N --> C C --> N Alternate ring size (10/14) Linear H bonds (stronger)

Question 36

Peptide bond common conformation

Answer 36

Cis

Question 37

Renaturation

Answer 37

Reformation of disulfide bonds that were broken during denaturation