BIOCHEM EXAM 1

amino acids, polarity/charge, structure, rough pKa, 3 letter and 1 letter codes

essential amino acids

HILKMFTWV

cannot be synth by body, come from diet

nonessential amino acids

ANDESCQGPY

can be synth by body

Asp pK

4

Glu pK

4

His pK

6

most common interaction and strongest between amino acids and small molecules (drugs)

hydrophobic

Lys pK

10.5

Arg pK

12.5

G/Gly/glycine

A/Ala/alanine

V/Val/valine

L/Leucine/leucine

I/Ile/isoleucine

M/Met/methionine

P/Pro/proline

F/Phe/phenylalanine

W/Trp/tryptophan

S/Ser/serine

T/Thr/threonine

A/Asn/asparagine

Q/Gln/glutamine

Y/Tyr/tyrosine

C/Cys/cysteine

K/Lys/lysine

R/Arg/arginine

H/His/histidine

D/Asp/aspartic acid (aspartate)

E/Glu/glutamic acid (glutamate)

AAs w/ nonpolar side chains

AFILMGVWP

(Aw Fuck I Left My Goddamn Violin With Patrice)

AAs w/ uncharged polar side chains

STNQYC

No, Stop! Quit That, You Clown

AAs w/ charged polar side chains

HKRDE

Happy Kids Run During Exercise

methylation

Lys, Arg, His

Cell marker

hydroxylation

Lys, Pro

stabilization of structures

phosphorylation

Ser, Thr, Tyr

Hydroxyl replaced by phosphate

pH < pK

protonated form dominates

pH > pK

deprotonated form dominates

amino pK

~9-10

thiol pK

~8-10

carboxyl pK

~2-4

hydroxyl pK

~16

amino @ neutral pH

protonated (NH3+)

carboxyl @ neutral pH

deprotonated (COO-)

hydroxyl @ neutral pH

protonated (OH/neutral)

thiol @ neutral pH

protonated (SH/neutral)

acidic groups (low pK) at neutral pH

negative

basic groups (high pK) at neutral pH

positive

weak acids/bases (thiol/hydroxyl) at neutral pH

mostly neutral

intermolecular interactions ranked strongest to weakest

ionic (salt bridge) > h-bonding > hydrophobic effect > VDW

acidic amino acids

Asp, Glu

basic amino acids

Lys, Arg, His

pI (isoelectric point)

pH where net charge = 0

primary structure

linear seq of amino acids (peptide bonds)

secondary structure

alpha helices, beta sheets (stabilized by H-bonds in backbone)

tertiary structure

3D fold (side chain interactions, hydrophobic effect, H-bonds, salt bridges, disulfides)

quarternary structure

multiple polypeptide

proline affects helices by:

breaking helices, introduces loops and bends due to no backbone N-H for H bonding

glycine affects helices by:

flexible, no steric hindrance

cysteine affects helices by:

forming disulfide bonds through oxidation, structural stability

Q 1 on RC diagram

left-handed alpha helix, not favorable

Q 2 on RC diagram

upper middle, beta sheet (more favorable)

triple helix (favorable)

Q 3 on RC diagram

upper middle top, alpha helix (favorable)

Q 4 on RC diagram

forbidden except for glycines

proline on RC diagram

very strict and rigid structure so least coverage on the RC diagram

phi angle for proline

-60

phi

x axis

psi

y axis