Amino Acids and Proteins

Question 1

what is unique about methionine

Answer 1

always the N-terminal amino acid (can be removed post translationally) Sulfur group can be oxidized to impair protein function

Question 2

what does having a moderate pI allow certain amino acids to serve as

Answer 2

buffers - important in preserving internal pH

Question 3

which amino acid does not exhibit chirality

Answer 3

glycine (contains two hydrogen groups)

Question 4

General characteristics of a peptide linkage

Answer 4

covalent bond formed via condensation reaction - rigid planar structure due to the double bond resonance exhibited - generally trans configuration to minimize steric hindrance

Question 5

describe the folding cascade of a protein

Answer 5

a protein may fold in both “correct” and “incorrect” ways - “correct” folds however will tend to facilitate progressively more “correct” folds that result in a polypeptide reaching its native form

Question 6

describe the stages of protein folding

Answer 6

primary -> secondary -> tertiary (independently stable domain formed) multiple domains or “subunits” can come together to form a quaternary structure

Question 7

describe a right handed alpha helix

Answer 7

3.6 residues per turn - stabilized by hydrogen bonds between the carbonyl of an amino acid and the amide proton of the amino acid located 4 positions away side chains project outward, amphipathic (hydrophobic inner face, hydrophilic outer face)

Question 8

Describe a B-pleated sheet

Answer 8

Stabilized by hydrogen bonds - R groups alternative between projecting above and below the sheet Can be parallel or anti-parallel or a mix of both A beta sheet formed using one polypeptide requires a turn, often involving proline due to its rigid structure

Question 9

What does a ramachandran plot show

Answer 9

The most likely forms of secondary structures given the limitations of phi and psi bond rotation

Question 10

Why are secondary structures useful

Answer 10

Take polar aspects of amino acids and occupy them with hydrogen bonds so that they can be placed in the hydrophobic interiors of proteins

Question 11

Define metamorphic proteins

Answer 11

Proteins that can form different native structures of similar thermodynamic stability The function of each variation can be significantly different

Question 12

Describe α-keratin

Answer 12

Supersecondary structure consisting of two right-handed alpha helices forming a left-handed super-coil Structure stabilized by hydrophobic interactions, salt bridges, hydrogen bonds, and disulfide bonds (from cysteine interactions)

Question 13

Describe collagen

Answer 13

Supersecondary structure consisting of three left-handed alpha helices forming a right-handed super coil

Question 14

How do collagen chains adhere to each other

Answer 14

Large amount of side chains exposed on the surface, allows for large degree of sidechain-sidechain interaction

Question 15

How do the symptoms of scurvy arise?

Answer 15

Polypeptide sequence of collagen is typically Gly-Pro-(hydroxyproline or hydroxylysine) Hydroxyproline and hydroxylysine require the cofactors, ascorbate (vitamin C) - vitamin C deficiency leads to defective collagen bleeding gums, coiled hair, muscle pain, etc

Question 16

Describe the process of collagen formation

Answer 16

Triple helix is synthesized in the cell (procollagen) -> exported -> N and C terminals are cleaved to form the mature triple helix (tropocollagen) -> tropocollagen lines up to form fibrils -> fibrils cross-link to form mature collagen

Question 17

Describe elastin

Answer 17

Rubber-like connective tissue - formed from small nonpolar amino acids (glycine, alanine, valine, etc) and proline and lysine Highly interlinked chain networked formed by reactive lysyl (lysine terminated) side chains which crosslink with other lysyl side chains

Question 18

Describe α-AT (antitrypsin) deficiency

Answer 18

α-AT is used to inhibit various proteases including elastase (which degrades elastin)’ α-AT deficiency is caused by a mutation that prevents α-AT from being exported from the cell - Glu342Lys Excess elastase activity leads to degradation of epithelial tissues, often leading to emphysema

Question 19

Describe smoking facilitated α-AT deficiency

Answer 19

Cigarette smoke can oxidize a Met residue on α-AT which is critical to binding target enzymes. α-AT is thus inhibited, which can lead to emphysema

Question 20

which configuration are mammalian amino acids found in

Answer 20

L configuration

Question 21

isoelectric point

Answer 21

pH at which an amino acid will have a net charge of 0

Question 22

what is unique about cysteine

Answer 22

2 thiol groups can spontaneously form a disulfide linkage

Question 23

which peptide bonds are observed in the cis configuration

Answer 23

those involving proline - ring structure makes cis configuration just as likely as trans

Question 24

what is the main driving force behind the process of folding a polypeptide into its final native shape

Answer 24

hydrophobic forces that fold a polypeptide into its most thermodynamically stable conformation

Question 25

What roles do proline and glycine serve in collagen triple helix formation

Answer 25

Proline gives the structure rigidity, glycine is found at every third position so that the three chains have enough space to fit together

Question 26

Henderson-Hasselbach Equation

Answer 26