CHEM351, Unit 1: amino acids, peptides, and proteins

L configuration

amino group is on the left

D configuration

amino group is on the right

highly polar amino acids

asparagine, glutamine, glycine, arginine, histidine, aspartic acid, and glutamic acid

which amino acids are highly nonpolar?

valine, leucine, isoleucine, methionine, and phenylalanine

nonpolar amino acids

are hydrophobic and have R groups that tend to cluster, stabilizing proteins through hydrophobic interactions

aromatic amino acids

absorb light, allowing you to follow signals

polar uncharged amino acids

hydrophilic

positively charged amino acids

basic

negatively charged amino acids

acidic

glycine

alanine

methionine

Met, M, contains a thioether

leucine

Leu, L

isoleucine

Ile, I

proline

Pro, P, can form ring structure leading to rigid conformation

valine

Val, V

phenylalanine

Phe, F

tyrosine

Tyr, Y

tryptophan

Trp, W

serine

Ser, S

thereonine

Thr, T

asparagine

Asn, N

glutamine

Gln, Q

cysteine

Cys, C, can form a disulfide bond when oxidized

arginine

Arg, R, guanidinium group

lysine

Lys, K, amino group at 4th carbon

histidine

His, H, has imidazole group, can act as a donor or acceptor due to pKa being near 7

aspartic acid

Asp, D, product of Asn when hydrolyzed

glutamic acid

Glu, E, produce of Gln when hydrolyzed

what contributes to the acid/base character of amino acids

all have at least two ionizable groups

pI

isoelectric point, indicates the pH where the zwitterion predominates

when pH is below pI...

charge is positive

when pH is at pI...

charge is neutral

when pH is above pI...

charge is negative

zwitterion

molecule that has equal positive and negative groups

where are peptide bonds formed?

at the amino group of one amino acid is joined to the carboxyl group of another to form an amide

three types of column chromatography

size exclusion, ion exchange, and affinity

size exclusion chromatography

large proteins exist first while small proteins are trapped by the beads in the column

ion exchange chromatography

proteins bind to bead based on charge, released by adding salt or changing pH gradient

affinity chromatography

beads are engineered to utilize a specific characteristic of a protein, like a ligand; released by adding additional ligands or something that mimics the protein