Chapter 4. Amino acids

• The amino acids of proteins• Optical activity• “Nonstandard” amino acids

Structure of an α-Amino Acid

Zwitterion

3-D structure of amino acids

Non-polar amino acids

• Center of globular proteins• Transmembrane domains• Non-polar (hydrophobic) interactions

Uncharged polar amino acids

• Stabilizing protein structure• Protein-protein interactions• Enzyme substrate interactions

Participate in hydrogen bonding

Charged amino acids• Present on the surface of proteins• Ionic interactions

– other protein– membrane

• Histidine - pKR is 6.04– 10% is positively charged at pH 7.0– pKa can be affected by the local environment– Can donate or accept protons during

catalysis

Proline

Hydroxyl-containing amino acids

Condensation of two amino acids

Peptide bond

Dipeptide

Hydrolysis Condensation

“Peptides”

• Dipeptides, tripeptides, oligopeptides and polypeptides

• Polypeptide- Linear polymers • Potential diversity = 20n

• Proteins – One or more polypeptide chains• Estimation of molecular mass of proteins:

Average mass of amino acid (110D) x Number of amino acids

500 aa protein x 110 ≈ 55,000 Daltons or 55 kD

Disulfide-Bond Formation

Cystine

Ionization of amino acids

Isoelectric point (pI)The pH at which a molecule carries no net charge

pI = pK1 + pK2

2

• Amino acids with acidic side chains

pI = pK1 + pKR

2

• Amino acids with uncharged side chains

• Amino acids with basic side chains

pI = pK2 + pKR

2

Titration of alanine

Net charge = +1 Net charge = 0 Net charge = -1

pI = pK1 + pK2

2=

22.3 + 9.7

= 6.0

pI = pK1 + pKR

2=

22.0 + 3.9

= 3.0

Nomenclature

Nomenclature

(N-terminus) (C-terminus)

alanyltyrosylaspatylglycineAYDG

Amino terminus Carboxyl terminus

Enantiomers

Same Configurations

The Fischer Convention

“CORN crib” mnemonic of L-amino acids

Diastereomers

The Cahn-Ingold-Prelog System(The RS System)

All the L-amino acids from proteins are (S)-amino acids except L-cysteine

Prochiral center

Prochiral center

re face si face

21st and 22nd amino acids

(UGA codon) (UAG codon)

Modified amino acids in proteins

Biologically active amino acids

D-Amino acids

• Bacterial cell wall• Peptide antibiotics

Biologically important peptides