amino acids

C-terminus and N-terminus pKa

2.34, 9.6

which AA is a good buffer at physiological pH

histidine, His, H (pKa =6)

glycine

Gly, G

R = H

- achiral

- flexible (small)

- hydrophobic technically

alanine

Ala, A

R = CH3

- hydrophobic, nonpolar

- not really reactive

valine

Val, V

R = isopropyl

- hydrophobic, nonpolar

- not really reactive

- branched side chain

leucine

Leu, L

R = isobutyl

- hydrophobic, nonpolar

- not really reactive

- branched side chain

isoleucine

Ile, I

R = sec-butyl

proline

Pro, P

R = 3 Cs forms "ring" w/ N terminus

- imino acid

- hydrophobic

- CONSTRAINED; causes kinks

serine

Ser, S

R = methoxy (-CH2-OH)

pKa = 13

- neutral at physio

- POLAR, hydrophilic

- H bonds

threonine

Thr, T

R = ethoxy (HO-C-CH3)

-OH bonded to first C !!!

pKa = 13

- neutral at physio

- POLAR, hydrophilic

- H bonds

asparagine

Asn, N

R = -CH2-amide

- neutral at physio

- POLAR, hydrophilic

glutamine

Gln, Q

R = ethyl amide (-CH2-CH2-amide)

- neutral at physio

- POLAR, hydrophilic

aspartate

Asp, D

R = -CH2-COOH

pKa = 3.7

- POLAR, hydrophilic

- H bond (only as acceptor at physio)

- NEG at physio

- acidic

glutamate

Glu, E

R = -CH2-CH2-COOH

pKa = 4.3

- POLAR, hydrophilic

- H bond (only as acceptor at physio)

- NEG at physio

- acidic

lysine

Lys, K

R = 4 CH2s, NH3+

pKa = 10.5

- BASIC

- PROTONATED & positive @ physio

- hydrophilic, polar

- H bond DONOR @ physio

Arginine

Arg, R

R = guanidinium group (3 CH2s, then complex w/ 3 Ns and 1 C)

pKa = 12.5

- BASIC

- positive & protonated at physio

- H bond donors @ physio

- guanidium is PLNAR; can stack

histidine

His, H

R = -CH2-IMIDAZOLE group; like right side, 5-mem-ring of purines, except NH is at "top"

pKa = 6

- IMPORTANT (i.e. for enzymes)

- GOOD BUFFER at physio pH

which AA is critical for enzymes

histidine; acts as a proton donor/acceptor for catalysis

phenylalanine

Phe, F

R = -CH2-benzene (methyl benzyl)

- hydrophobic

- AROMATIC, planar side chain can stack

tyrosine

Tyr, Y

R = phenol group (-CH2-benzene-OH)

pKa = 10.1

- -OH can hydrogen bond

- AROMATIC, planar side chain can stack

- absorb @ 280 nm

tryptophan

Trp, W

R = methyl indole group (weird looking 5 ring on benzene)

- NH can hydrogen bond

- AROMATIC, planar side chain can stack

- absorb @ 280 nm

methionine

Met, M

R = -CH2-CH2-S-CH3

- unreactive

- hydrophobic

cysteine

Cys, C

R = -CH2-SH

pKa = 8.2

- could lose H on S to have neg charge

- REACTIVE

- 2 cysteines can form disulfide bond --> important for quaternary structure

which AA can form disulfide bonds for quaternary structures (holding multiple polypeptide chains together)

cysteine (R = -CH2-SH)

5 non-essential AAs

DANES

D = aspartate (Asp)

A = alanine (Ala)

N = asparagine (Asn)

E = Glutamate (Glu)

S = Serine (Ser)

Essential AAs

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H = histidine (His)

I = isoleucine (Ile)

L = leucine (Leu)

K = lysine (Lys)

M = methionine (Met)

F = phenylalanine (Phe)

T = threonine (Thr)

W = tryptophan (Trp)

V = valine (Val)

essential AAs, many are:

Branched carbon chains: valine, leucine, isoleucine

Aromatic rings: phenylalanine, tryptophan

Sulfur-containing side chains (complex, not cysteine): methionine

Basic essential AAs: lysine, histidine

Other: threonine