Unit 1 - Amino Acids

Common features of amino acids

1. R group

2. Carboxylic acid (carboxylate at pH 7)

3. Amino group (

4. Alpha carbon (chiral except for glycine)

pH > pka

Deprotonated form

pH < pka

Protonated form

Which amino acid is achiral?

Glycine

What number is the α carbon

Carbon 2

What number is the β carbon

Carbon 3

What number is the γ carbon

Carbon 4

What number is the δ carbon

Carbon 5

What number is the ε carbon

Carbon 6

What amino acid does not contain a β carbon

Glycine

What amino acid is said to have conformational flexibility?

Glycine

Properties of Glycine (G)

• No beta carbon'

• achiral amino acid

• not really polar or nonpolar

• has conformational flexibility

Properties of Alanine (A)

• aliphatic

• non polar side chain

Properties of valine (V)

• non polar side chain

• aliphatic

• beta branched

Properties of leucine (L)

• non polar side chain

• aliphatic

• gamma branched

• has same number of atoms in the chain as I, M

Properties of isoleucine (I)

• non polar side chain

• aliphatic

• gamma branched

• contains a second stereogenic centre

• has same number of atoms in the chain as L, M

Properties of Methionine (M)

• non polar side chain

• “honorary” aliphatic

• has a thioether group (R-S-R’)

Properties of Proline (P)

• cyclic

• non polar side chain

• aliphatic (kinda)

• has conformational restrictions due to cyclic nature

• very small (same size as valine, but is functionally smaller and less hydrophobic)

Properties of Phenylalanine (F)

• non polar side chain

• aromatic

• hydrophobic

Properties of Tryptophan (W)

• non polar side chain

• heterocyclic (indole)

• aromatic

• can H bond as a donor but mostly hydrophobic

• typically found in membrane due too slightly amphipathic features

Properties of serine (S)

• uncharged polar side chain

• basically alanine + OH therefore can conservatively substitute for A unless S present for H bonding

• contains a hydroxyl

• can accept and donate in H bonds

Properties of Threonine (T)

• uncharged polar side chain

• presence of two chiral centres

• contains a hydroxyl

• can accept and donate in H bonds

Properties of Asparagine (N)

• uncharged polar side chain

• contains an amide

• contains delocalization in the side chain

• can accept and donate in H bonds

• one less carbon than Q

Properties of Glutamine (Q)

• uncharged polar side chain

• contains an amide

• contains delocalization in the side chain

• can accept and donate in H bonds

• one more carbon than N

Properties of Histidine (H)

• partially ionized polar side chain

• aromatic

• contains an imidazole with pkr ~ 6

• positive side chain partial charge

Properties of Tyrosine (Y)

• partially ionized polar side chain

• aromatic

• H bond donor and acceptor'

• weak acid

• hydrophilic/amphiphilic

• contains a phenol with pkr ~ 10.5

• negative side chain partial charge

Properties of Cysteine (C)

• partially ionized polar side chain

• contains a sulfhydryl with pkr ~ 8

• negative side chain partial charge

• cys + cys = cystine which becomes a non polar disulphide bridge

Properties of Lysine (K)

• completely ionized polar side chain

• basic amino acid

• positive side chain charge

• contains a ε-NH3+ with pkr ~ 10.5

Properties of Arginine (R)

• completely ionized polar side chain

• basic amino acid

• positive side chain charge

• contains guanidino group with pkr ~12.5

• Guanidino group is very stable, lots of resonance therefore very hard to deprotonate

Properties of Aspartate (D)

• completely ionized polar side chain

• acidic amino acid

• negative side chain charge

• contains β-COOH with pkr ~ 4

Properties of Glutamate (E)

• completely ionized polar side chain

• acidic amino acid

• negative side chain charge

• contains γ-COOH with pkr ~ 4

What units measure the mass of amino acids and proteins

Daltons (Da)

1 Da =

1g/mol, 1/12 the mass of ¹²C

Are there more daltons in a free amino acid or residue

free amino acid, 1 equivalent of water is lost in the formation of every peptide bond

How much does water weigh in Da

18 Da

Weighted average mass of amino acids

128 Da in free amino acids

110 Da in residues

**these incorporate both mass and frequency of incorporation

Do amides carry a formal charge

No!!