Biochemistry-Chapter 4: Amino Acids and the Peptide Bond

Chemistry of Amino Acids

~at pH =7, the carboxylic acid is deprotonated, and the amino group is protonated

~can polymerize to form peptides/proteins (result of having two different functional groups

~all amino acids have the S configuration at the alpha carbon with the exception of cysteine (R)

~L amino acids are the ones incorporated into living systems; few times D amino acids are used

zwitterion

A molecule that contains charges, but is neutral overall. Most often used to describe amino acids

Nonpolar hydrophobic side chains

glycine, alanine, valine, leucine, isoleucine, methionine, proline

Aromatic side chains

phenylalanine, tryptophan

Polar, uncharged

serine, threonine, cysteine, asparagine, glutamine, tyrosine

acid side chains (-) charged

aspartic acid, glutamic acid

basic amino acids (+) charged

lysine, arginine, histidine

Glycine

Gly, G

alanine

Ala, A

Valine

Val, V

Leucine

Leu, L

Isoleucine

Ile, I

Methionine

Met, M

Proline

Pro, P

Phenylalanine

Phe, F

Tryptophan

Trp, W

Serine

Ser, S

Threonine

Thr, T

Cysteine

Cys, C

Asparagine

Asn, N

Glutamine

Gln, Q

Tyrosine

Tyr, Y

Aspartic Acid

Asp, D

Glutamic Acid

Glu, E

Lysine

Lys, K

Arginine

Arg, R

Histidine

His, H

Acid-Base Chemistry

~weak acids and weak bases

~degree of dissociation of H+ depends on pH

~all have 2 ionizable groups, but some have more than 2 (2 pkas)

Stereochemistry

~all but glycine have stereocenter at alpha position

~natural amino acids are L configuration

~no correlation to R/S system or direction; plain polarized light is rotated

~based on comparison to D and L glyceraldehyde

~all but one amino acid of L configuration are S (cysteine is the exception since its R)

Protein structure

~unbranched, linear polymers of amino acids

~the repeat unit is amide nitrogen, alpha carbon with side chain, and carbonyl carbon

trans-configuration

~limits the rotation between amide nitrogen and carbonyl carbon

~all peptide bonds have resonance structures giving double bond character to amide

peptide

short polymer of up to 12 amino acids

dipeptide

two amino acids

tetrapeptide

four amino acids

oligopeptides

12-20 amino acids

polypeptides

greater than 20 amino acids