amino acids

Question 1

acidic amino acids

Answer 1

Aspartic acid (D, Asp) - CH2 attached to COO-
Glutamic acid (E, Glu) - CH2 attached to CH2 attached to COO-

both contain carboxylic acid R groups

Question 2

basic amino acids

Answer 2

lysine (K, lys) - 4 CH2 attached to an amine
arginine (R, arg) - 3 CH2 attached to NH which attaches to a carbon that has two NH2 groups attached to it, one NH2 has a positive charge
histidine (H, his) - CH2 attached to 5 membered aromatic ring including NH and NH+

-histidine can sometimes act as an acid

Question 3

hydrophobic (non polar) amino acids

Answer 3

glycine (G, gly) - R group is hydrogen
alanine (A, ala) - methyl R group
valine (V, val) - R group is CH attached to two methyl groups
leucine (L, leu) - R group is CH2 attached to CH attached to two methyl groups
isoleucine (I, ile) - CH2 attched to a methyl and ethyl group
phenylalanine (F, phe) - methyl attached to phenyl group
tryptophan (W, Trp) - has a CH2 attached to two aromatic rings, one ring contains NH, one is just a 6 membered carbon ring
methionine (M, Met) - CH2 attached to CH2 attached to S attached to methyl
proline (P, Pro) - Nitrogen is part of side chain, three CH2 are part of R group with last one attaching to NH2+

F and W have aromatic side chains, the rest have alkyl side chains (CH)
methionine contains sulfur
proline’s amino group is covalently bound to its non polar side chain, disrupting backbone hydrogen bonding in secondary structure

Question 4

polar amino acids

Answer 4

serine (S, Ser) - CH2 attached to OH
threonine (T, Thr) - CH attached to methyl and OH
tyrosine (Y, Tyr) - methyl attached to phenyl which has a hydroxy group attached to it
asparagine (N, Asp) - CH2 attached to amide functional group
glutamine (Q, Gln) - CH2 attached to CH2 attached to amide functional group
cysteine (C, cys) - CH2 attached to SH

polar enough to form hydrogen bonds with water but don’t act as an acid or a base
cysteine contains sulfur

Question 5

what is the average molecular weight of an amino acid?

Answer 5

110 Da, (ex. 288 amino acids is about 32 kDa)

Question 6

isoelectric focusing

Answer 6

separates proteins based on their isoelectric point (the pH at which the net charge of the protein is 0)

Question 7

ion exchange chromatography -

Answer 7

separates proteins based on their net charge.

Question 8

affinity chromatography

Answer 8

separates proteins based on their interactions with specific ligands.

Question 9

SDS-PAGE

Answer 9

separates proteins based on their mass

Question 10

enzyme efficiency equation

Answer 10

Vmax / Km