Amino acids

Describe the traits of aliphatic amino acids (4)

1. hydrocarbon chains of variable lengths and branching

2. non-polar, hydrophobic

3. cluster together in protein structures, away from water

4. methionine contains an S

Name the aliphatic amino acids (5)

alanine ala a

valine val v

leucine leu L

isoleucine ile i

methionine met m

describe the traits of aromatic amino acids (5)

•Stable ring of atoms with shared, delocalised electrons

•Larger and variable hydrophobicity

•Tyrosine has a hydroxyl (OH) group → hydrogen bonds

•Nitrogen in tryptophan indole ring → hydrogen bonds

•π-stacking – aromatic rings stack on top of each other

name the aromatic amino acids (3)

phenylalanine, phe, f

tyrosine, tyr, Y

tryptophan, trp, W

Describe the traits of polar amino acids (3)

•Hydrophillic – prefer to interact with water outside the protein, or with each other through hydrogen bonds

•Histidine can also be considered polar

•Cysteine can form disulfide bonds

name the polar amino acids (5)

cysteine, cys, c

serine, ser, s

threonine, thr, T
asparagine, asn, n

glutamine, glm, q

describe the traits of charged amino acids (4)

•Ionisable sidechains – become charged in the cellular environment

•Basic amino acids are positively charged

•Acidic amino acids are negatively charged

•Histidine is not always/fully charged

name the basic amino acids (3)

lysine, lys, k

arginine, arg, r

histidine, his, H

name the acidic amino acids (2)

aspartic acid, asp, d

glutamic acid, glu, E

Beer-Lambert Law

A = ε c l

A = absorbance

ε = extinction coefficient

c = concentration

l - path length

calculating the extinction coefficient

5690(#Tryptophans) + 1280(#Tyrosines)

zwitterionic form definition

molecule where net charge is 0, but atleast one functional group has positive charge, and atleast one functional group has negative charge.

isoelectric point (pI)

pH at which particular molecule carries no charge

pH below pKa, weak acid…

protonates

pKa below pH, weak acid…

dissociates

CORN rule spells CORN

L amino acid

CORN rule spells not corn

D amino acid

priority rule clockwise

R amino acid

priority group anticlockwise

S amino acid

the only natural amino acid that is R

L-cysteine