biochem WEEK 2 lecture 3

amino acids intro, derivative/modifications, peptide bonds

12.5

arginine (R) side chain pKa

3.9

aspartic acid (D) side chain pKa

8.3

cysteine (C) side chain pKa

4.2

glutamic acid (E) side chain pKa

6.0

histidine (H) side chain pKa

10.0

lysine (K) side chain pKa

10.1

tyrosine (Y) side chain pKa

8

N terminus (-NH3+) pKa

4

C terminus (-COO-) pKa

+1

amino (N-term, lysine (K))charge when pH is below pKa

0

hydroxyl (serine(S), threonine(T), tyrosine(Y)) charge when pH is below pKa

0

SH (cysteine(C)) charge when pH is below pKa

0

carboxylate (C-term aspartic acid(D), glutamic acid(E)) charge when pH is below pKa

+1

imidazole (histidine(H)) charge when pH is below pKa

+1

Guanidinium (arginine(R)) charge when pH is below pKa

0

amino (N-term, lysine (K))charge when pH is above pKa

-1

hydroxyl (serine(S), threonine(T), tyrosine(Y)) charge when pH is above pKa

-1

SH (cysteine(C)) charge when pH is above pKa

-1

carboxylate (C-term aspartic acid(D), glutamic acid(E)) charge when pH is above pKa

0

imidazole (histidine(H)) charge when pH is above pKa

0

Guanidinium (arginine(R)) charge when pH is above pKa

Ala, Ile, Phe

three amino acids with non-polar side chains (from least to most hydrophobic)

gly, ala, pro, val, leu, ile, met

amino acids with aliphatic non-polar side chains, not many H bond donors or acceptors in R groups

glycine

AA has no side chain, alpha carbon is not a chiral center

proline

AAs side chain makes a ring by bonding with its main chain Nitrogen, rigidifies and provides structure

isoleucine

AA has aliphatic non polar side chain, is one of two amino acids with a chiral side chain (B carbon)

threonine

AA has uncharged polar side chain, is one of two amino acids with a chiral side chain (B carbon)

Ser, Thr, Cys, Asn, Gln

amino acids with uncharged polar side chains, have plenty of H bond donors and acceptors

cysteine

AA can form disulfide bridges, AA side chain has S which is a good nucleophile, is good in coordinating metals

Lys, Arg, His

amino acids with positively charged side chain

histidine

AA often involved in acid base catalysis, side chain s good in coordinating metals, has a pKa of around 6 so at a neutral pH it is in both its protonated and deprotonated state

Asp, Glu

amino acids with a negatively charged side chain, side chains are very hydrophilic, carboxylates can often coordinate metals (usually Mg2+ and Ca2+)

Phe, Tyr, Trp

amino acids with aromatic side chains that can absorb UV light

Tyr, Trp

two amino acids with aromatic side chains that can absorb much more light than Phenylalanine

-NH3+

amino group at a pH below pKa

-OH

hydroxyl group at a pH below pKa

-SH

SH group at a pH below pKa

-COOH

carboxylate group at a pH below pKa

-NH+

Imidazole group at a pH below pKa (leave out aromatic ring stuff)

-NH2+

guanidinium group at a pH below pKa (just part that changes)

-NH2

amino group at a pH above pKa

-O-

hydroxyl group at a pH above pKa

-S-

SH group at a pH above pKa

-COO-

carboxylate group at a pH above pKa

N

Imidazole group at a pH above pKa (leave out aromatic ring stuff)

NH

guanidinium group at a pH above pKa (just part that changes)

enantiomer

a pair of molecules that exist in two forms that are mirror images of one another but cannot be superimposed one upon the other

L

configuration AA enantiomer R group points away, bolded up or dashed down

D

configuration AA enantiomer R group points towards, dashed up or bolded down

L-configuration

configuration all AAs in proteins (except one) have

below

dotted bonds point (above/below) plane of projection for the L configuration

above

dotted bonds point (above/below) plane of projection for the D configuration

GABA, histamine, dopamine

biologically active amino acid derivatives act as as neurotransmitters and are not incorporated into polypeptide chains of proteins

thyroxine

biologically active amino acid derivative important for cell-to-cell communication, hormone used to regulate metabolism

GABA

biologically active amino acid derivative

histamine

biologically active amino acid derivative

dopamine

biologically active amino acid derivative

thyroxine

biologically active amino acid derivative

L-DOPA

deficiencies in dopamine production is associated with parkinson disease, what is the intermediate given to Parkinson patients?

cysteine

not genetically encoded, amino acid side chain modification in which thiol groups are oxidized forming a covalent bond “disulfide” bridge between this AAs residues

tyrosine

dopamine is derived from:

post translational modifications

done by specialized enzymes to make non standard amino acids in proteins

O-phosphoserine

amino acid side chain modification via phosphorylation, important for signal transduction

4-hydroxyproline

amino acid side chain modification via hydroxylation, major component of protein collagen for connective tissue

glutamate

amino acid that undergoes carboxylation to make a non standard AA

histidine

amino acid that undergoes methylation to make a non standard AA

lysine

amino acid that undergoes acetylation to make a non standard AA

Ser, Thr, Tyr

signal transduction: protein kinases phosphorylate these AAs side chains

protein kinases

attach phosphoryl groups (phosphorylate) to Ser, Thr, Tyr

protein phosphatases

remove phosphoryl groups (dephosphorylate) from Ser, Thr, Tyr

protein glycosylation

common type of modification of side chains on protein surface in which one or more sugars are attached to one or more specific residues

secreted and membrane associated

almost all of these proteins in eukaryotes are glycosylated

extracellular matrix (ECM)

formed by protein glycosylation, mixture of oligosaccharides and proteins between cells, key to cell positioning, crucial in complex precesses such as wound healing

O-glycosylation, N-glycosylation

two major types of glyosylation:

O

type of glycosylation, oligosaccharide is attached to side chain of Ser or Thr

N

type of glycosylation, oligosaccharide is attached to side chain of Asn

Ser, Thr

amino acids that undergo O-glycosylation (oligosaccharide attached to side chain O)

Asn

amino acid that undergoes N-glycosylation (oligosaccharide attached to side chain N)

O-glycosylation

What kind of amino acid modification occurred in this picture?

N-glycosylation

What kind of amino acid modification occurred in this picture?

pentasaccharide core

where all N linked glycans are added to during glycosylation forming a complex antenna

peptide bond

formed via condensation of two amino acids forming long polypeptide chains, process carried out by the ribosome

N term → C term

direction in which AAs are added forming polypeptide chains

aspartame

dipeptide used as an artificial sweetener, condensation of L-aspartic acid and methylated L-phenylalanine

L-aspartic acid, L-phenylalanine

condensation of these two amino acids results in the oligopeptide/dipeptide aspartame

L-phenylalanine

the condensation of two amino acids results in the dipeptide aspartame which is used as an artificial sweetener, which one is methylated?

reduced

most abundant form of the oligopeptide glutathione (GSH) which is highly reactive with free oxygen helping maintain reduced environment in cells

glutathione (GSH)

reduced form of this oligopeptide is highly reactive with free oxygen maintaining the reducing environment in cells

Glu, Cys, Gly

three AAs that make up glutathione (GSH) which is highly reactive with free oxygen helping maintain reduced environment in cells (order in proper linkage)

Glu, Cys

three AAs that make up glutathione (GSH) which is highly reactive with free oxygen helping maintain reduced environment in cells, these two are linked in a strange way via their side chains