biochem amino acids

glycine code

gly

glycine letter

g

alanine code

ala

ala letter

a

valine code

val

valine letter

v

leucine code

leu

leucine letter

l

isoleucine code

ile

isoleucine letter

i

methionine code

met

methionine letter

m

phenylalanine code

phe

phenylalanine letter

f

tryptophan code

trp

tryptophan letter

w

proline code

pro

proline letter

p

cysteine code

cys

cysteine letter

c

tyrosine code

tyr

tyrosine letter

y

serine code

ser

serine letter

s

theronine code

thr

theronine letter

t

asparagine code

asn

asparagine letter

n

glutamine code

gln

glutamine letter

q

aspartic acid code

asp

aspartic acid letter

d

glutamic acid code

glu

glutamic acid letter

e

arginine code

arg

arginine letter

r

lysine code

lys

lysine letter

k

histidine code

his

histidine letter

h

what do all amino acids have?

carboxy group and amine group

how many carbons does glutmatic acid have?

3

how many carbons does aspartic acid have?

2

carbox pka is

2 to 3

amine pka is

8 to 9

at pH 7 carboxy group is

deprotonated

at pH 7 amine group is

protonated

what does pI represent

point at which amino acid net charge is zero

what factors affect pI

chain length, solvent, metal ions

how does chain length affect pI?

longer chain length puts more distance between fos so they can’t stabilize each other as well

how does solvent affect pI?

less polar solvents can’t stabilize charges as well

how do metal ions affect pI?

ions interact with the amino acids

first step in determining R or S

highest atomic number

second step in determining R or S

highest atomic mass

third step in determining R or S

use the next atom in the chain

fourth step in determining R or S

rotate mc so lowest priority is facing away from you

if priority goes clockwise, the mc is

R

if priority goes counter clockwise mc is

S

if the mc rotates light to the left it is

levorotary

if the mc rotates light to the right it is

dextorotary

what does L or D correlate to?

structural similarity to glyceraldehyde

before following CORN, do this

turn mc into a newman projection with H facing into the page

step one of CORN

carboxylate

step two of CORN

r group

step three of CORN

amine

with thumb pointing into the page, if you have to use right hand to follow priority

amino acid is D

with thumb pointing into the page, if you have to use left hand to follow priority

amino acid is L

what is a peptide bond

an amide linkage

how do we read amino acid sequences?

n terminus to c terminus

what is the n terminus

amine end

what is the c terminus

carboxylate end

nonpolar amino acids

galvip mfw

polar uncharged amino acids

cystnq

acidic amino acids

de

basic amino acids

hrk