amino acids

GLY
Aliphatic, hydrophobic
R= H
Prefer an environment within a protein shielded from water

ALA
Aliphatic, hydrophobic
R= -CH3
Prefer an environment within a protein shielded from water

VAL
Aliphatic, hydrophobic

CH3
|
R= -CH3
|
CH3
Prefer an environment within a protein shielded from water

LEU
Aliphatic, hydrophobic

CH3
|
R= -CH2-CH3
|
CH3
Prefer an environment within a protein shielded from water

ILE
Aliphatic, hydrophobic

CH3
|
R= CH-CH2-CH2-CH3
Prefer an environment within a protein shielded from water

PRO
Aliphatic, hydrophobic

CH2
/ \
CH2 CH2
| |
R= +H3N --- C-COO-
|
H
Mainly aliphatic but difficult to fit into category, mainly hydrophobic
Prefer an environment within a protein shielded from water

SER
Hydroyl
R=CH2OH
Hard to ionize (very high Pka)
Relevant to enzyme mechanism

THR
Hydroyl
OH
|
R= -CHCH3

CYS
Sulfur R groups
R= CH2SH
Weakly polar, generally hydrophilic
Sulfhydryl group is ionizable

MET
Sulfur R groups
R= -CH2-CH2-S-CH3
Weakly polar, generally hydrophilic

PHE
Aromatic
R= benzene
Hydrophobic

TYR
Aromatic
R= benzene - OH
Some hydrophobic character but tempered by polar OH groups in side chain
Can be ionized at high pH

TRP
Aromatic
R= SEE NOTES

TRP, TYP & PHE conjugated rings exhibit strong UV abs.
A280 (TYR, TRP) + A260 (PHE)
(A280 responsible for most UV absorbance in proteins)

LYS
Basic
R= -CH2CH2CH2-NH3+
pKa2 ~9
Positively charged at physiological pH

ARG
Basic
R= -CH2CH2CH2-NH-C-NH2
||
NH2+
pKa2 ~9
Positively charged at physiological pH

HIS
Basic (less basic than LYS and ARG)
R= SEE NOTES
pKa imidazole = 6.5-7.4
pKa free a.a. ~6
pKa in proteins ~7
Side chain can exchange protons near physiological pH. Often it plays role in enzymatic mechanisms

strongly polar. Found on exterior surfaces of proteins. They are hydrated with surround aqueous environment

ASP
Acidic
O
||
R= -CH2C-O-
pKa2 ~4
Carry negative charge @pH 7
Only if pH < pKa, carboxyl groups neutralized, becomes aspartate
Tend toward protein surface + in contact with water

ASN
Acidic
O
||
R= -CH2-C-NH2
Unlike acidic analog, have uncharged side chains though decidedly polar
Like acidic analog tend toward protein surface + in contact with water

GLU
Acidic
O
||
R= -CH2-C-O-
pKa2 ~4
Carry negative charge @pH 7
Only if pH < pKa, carboxyl groups neutralized, becomes glutamate
Tend toward protein surface + in contact with water

GLN
O
||
R= -CH2-C-NH2
Unlike acidic analog, have uncharged side chains though decidedly polar
Like acidic analog tend toward protein surface + in contact with water