Lectures 1+2: Protein Structure and Function

Question 1

Maple Syrup Urine Disease (MSUD)

Answer 1

Also known as branched chain amino acidemia; elevated urine keto acids and serum branched chain AAs. Caused by decreased ability to metabolize branched chain AAs like Val, Leu, Ile (essential AAs)

Question 2

Cystic fibrosis

Answer 2

Indicated by high Immunoreactive Trypsinogen (IRT). Mutation -> LOF in CFTR impairs chloride transport, leads to increased Na+ uptake and H2O uptake. Produces sticky mucus and dry airways. Sweat test shows high mEq/L.

Question 3

Essential amino acids

Answer 3

PVT TIM HALL: Phe, Val, Thr, Trp, Ile, Met, His, Arg, Lys, Leu

Question 4

Nonpolar amino acids

Answer 4

Gly, Ala, Val, Leu, Ile, Pro, Phe, Trp, Met

Question 5

Uncharged polar amino acids

Answer 5

Asn, Gln, Cys, Ser, Thr, Tyr

Question 6

Phosphorylation targeted amino acids

Answer 6

Ser, Thr, Tyr

Question 7

Oligosaccharide attachment site amino acids

Answer 7

Asn, Ser, Thr

Question 8

Role of -SH group in cysteine

Answer 8

Can be dimerized to form disulfide bridges within or between polypeptide chains (oxidation). -SH group also plays a role in coordinating certain metal ions.

Question 9

Acidic amino acids (negatively charged)

Answer 9

Asp, Glu

Question 10

Basic amino acids (positively charged)

Answer 10

Lys, Arg, His (weakly basic but can be uncharged)

Question 11

Mutation notation: Gly542X, 621+1G->T, F508Δ or F508del

Answer 11

Gly542X: change to stop codon
621+1G->T: splicing mutation
F508Δ or F508del: deletion

Question 12

Direction of protein synthesis and sequence reading

Answer 12

N- to C-terminus

Question 13

Alpha helix structural characteristics

Answer 13

3.6 AAs per turn, n - 4 h-bonds. Destabilized by Pro/Gly (sterics, flexibility), stabilized by charged AAs but too many can disrupt by repulsion. R groups stick out from helix, H-bond every 4 AAs.

Question 14

Motif

Answer 14

Common, classifiable 3D folding patterns in tertiary or quaternary structure, e.g. helix-turn-helix

Question 15

Domain

Answer 15

Region of a polypeptide chain that can fold stably and independently with respect to the entire protein; defined by functional role.

Question 16

Beta pleated sheet characteristics

Answer 16

2+ regions of 1 polypeptide chain OR 2+ polypeptide chains. Peptide bond h-bonding with R groups extending above/below plane of sheet. Strands can be parallel or antiparallel.

Question 17

Categories of proteins

Answer 17

1. Fibrous: polypeptides arr. in strands/sheets, e.g. collagen
2. Globular: highly diverse structure/function, e.g. hemoglobin

Question 18

Disordered proteins/regions

Answer 18

Proteins/regions without definable structure, allowing flexibility to interact w/ many other proteins, e.g. p53