Amino Acids & Proteins

Question 1

All AA residues in proteins are ….

Answer 1

L isomers

Question 2

Non polar, aliphatic AA sidechains

Answer 2

Gly, Ala, Val, Leu, Met, Ile

Question 3

Non polar, aromatic AA sidechains

Answer 3

Trp, Phe, Tyr

Question 4

Polar/uncharged AA sidechains

Answer 4

Thr, Ser, Cys, Asn, Gln, Pro

Question 5

Polar/positively charged (basic) AA sidechains

Answer 5

Lys, Arg, His
Lys and Arg are protonated at physiological pH; His has a pKa ~ 6.5, can be protonated or deprotonated depending on local conditions

Question 6

Polar/negatively charged (acidic) AA sidechains

Answer 6

Asp, Glu

Deprotonated at physiological pH

Question 7

Essential AAs

Answer 7

All Horny Lovers Kiss if Men Finally Touch Women’s Vaginas

Arg, His, Leu, Lys, Ile, Met, Phe, Thr, Trp, Val

Question 8

Scurvy

Answer 8

Lack of vitamin C required for the enzyme that synthesizes hydroxyproline, an essential AA in collagen

Question 9

Vitamin K Deficiency

Answer 9

Leads to disorders of blood clotting; Vitamin K is required by the enzyme that synthesizes carboxyglutamate, which is essential in proteins involved in blood-clotting

Question 10

Covalent modifications of AAs

Answer 10

Hydroxyproline 
Carboxyglutamate
Glycosylation - sugars added to AA residues, O-linked (Ser or Thr) or N-linked (Asn)
Acetylation (Lys)
Methylation (Lys, Arg) 
Phosphorylation (Ser, Thr, Tyr) 
Ubiquination

Question 11

Psi Angle

Answer 11

The angle around the alpha carbon and the carbonyl carbon in a peptide chain - this is the C-terminal angle

180 degrees in a fully extended polypeptide chain

Question 12

Phi angle

Answer 12

The angle between the alpha carbon and the amide Nitrogen - this is the N-terminal angle

180 degrees in a fully extended polypeptide chain

Question 13

Sickle Cell Anemia

Answer 13

Glu –> Val mutation; changes a hydrophilic residue to a hydrophobic residue, causing aggregation of mutated red blood cells

Question 14

Alpha Helix

Answer 14

H-bonds form between the carbonyl oxygen of the nth AA and the amide nitrogen of the n+4th AA within the same polypeptide chain, forming a right-handed screw
Ex: Leucine Zippers, Hemoglobin

Ala and Leu common
Pro and H do not occur

Question 15

B-sheets

Answer 15

Hydrogen bonds form between two polypeptide chains arranged parallel or anti-parallel
Ex: Immunoglobulin, antibodies

Question 16

Most common AAs in turns & loops

Answer 16

Gly and Pro

Question 17

Kd

Answer 17

Dissociation constant; Kd is the ligand concentration where 50% of the protein is bound. Smaller Kd implies stronger binding interaction.

Question 18

Function of Myoglobin

Answer 18

Stores oxygen; oxygen binds the Fe2+ atom in the Heme group, buried in the myoglobin protein; Kd is very low, so myoglobin stores oxygen but does not transport

Question 19

Carbon Monoxide Poisoning

Answer 19

Heme ring within myoglobin binds CO 250x tighter than it binds O2

Question 20

Function of Hemoglobin

Answer 20

Hemoglobin has 4 O2 binding sites that interact with allostery/cooperativity; O2 binding triggers a T to R conformational state change in which Hb has higher affinity for O2

Question 21

Bohr Effect

Answer 21

Hb binds O2 better under local conditions of higher pH (i.e. in the lungs) and releases O2 under local conditions of lower pH (i.e. in metabolically active tissues that produce CO2, which reacts with water to form carbonic acid)

Question 22

Hsp70 Proteins

Answer 22

Class of chaperone proteins that functions especially at high temp; binds to the hydrophobic region of unfolded proteins to prevent aggregation and facilitate re-folding

Question 23

GroEL/GroES

Answer 23

Part of chaperonin family of proteins; GroEL is two 7 unit subunits “capped” by GroES; facilitates ATP-dependent re-folding of proteins

Question 24

Protein disfulfide isomerase

Answer 24

Catalyzes the exchange between free Cysteine and disfulfide (Cystine) bonds

Question 25

Cyclosporin

Answer 25

An immunosuppressant drug that inhibits cyclophilin, a peptidyl prolyl isomerase that activates calcineurin, which is important for activation of T cells

Question 26

Cystic Fibrosis

Answer 26

Caused by misfolding of cystic fibrosis transmembrane conductance regular (CFTR) protein, a chloride channel

Question 27

Alzheimers - 2 primary genetic pathways

Answer 27

1. Missense mutations in APP presenilin 1 or 2 genes cause increased production of AB42
2. ApoE4 leads to decreased AB42 clearance

Question 28

Parkinson’s Disease

Answer 28

Due to accumulation of Synuclein protein deposits, called Lewy Bodies

Question 29

Phenylketonuria

Answer 29

Disorder caused by mutation in the gene for phenylalanine hydroxylase, an enzyme involved in the phenylalanine degradation pathway; presents as mental retardation and seizures

Question 30

Zymogen

Answer 30

An inactive enzyme precursor; ex: most digestive enzymes are initially synthesized as zymogens, which must be cleaved prior to activation

Question 31

Tetracycline, streptomycin, erythromycin

Answer 31

Antibiotic drugs that bind to the small subunit of the prokaryotic ribosome, preventing entry of aa-tRNAs into the A site and thus inhibiting bacterial protein synthesis