Proteins

Proteins are made up of a chain of amino acids.

Each amino acid is joined by a peptide bond. This is a covalent bond.

Condensation occurs when they are joined. NH2 (amino group) provides a H, COOH (carboxyl group) from the C' provides a OH.

Each amino acid that made up the polypeptide chain is a residue.

N (amino) terminal is the start (NH2), C (carboxyl COOH) terminal is the end

The peptide bond is rigid and planar

Peptide bonds: Formation and cleavage at Khan Academy.

Amino Acids

There are 20 naturally occurring amino acids.

Letter 3 letter Amino Acid Side-chain Properties
M Met Methionine CH2-CH2-S-CH3 Contains S.
I Ile Isoleucine CH(CH3)CH2CH3 hydrophobic
L Leu Leucine CH2CH(CH3)2 hydrophobic
F Phe Phenylalanine CH2C6H5 hydrophobic, phenyl group
V Val Valine CH(CH3)2 hydrophobic
A Ala Alanine CH3 hydrophobic
P Pro Proline pyrrole group including Calpha joining back to N in the amino part. In peptide chain, N is not bound to H, so can't act has a hydrogen bond donor. steric constraints.
D Asp Aspartic Acid CH2-COOH negative charge, acidic
E Glu Glutamic Acid CH2-CH2-COOH negative charge, acidic
K Lys Lysine CH2CH2CH2CH2NH3 positive charge, basic
R Arg Arginine CH2CH2CH2NH-CNH2NH2
H His Histidine CH2-5 ring (C=C-N=C-N-) Imidazole.
Y Tyr Tyrosine CH2(C6H4OH) 6 ring with OH, phenol group
S Ser Serine CH2OH polar
T Thr Threonine CH(OH)-CH3 polar
C Cys Cysteine CH2SH Contains S. Residues form disulphide bridges support the tertiary structure
N Asn Asparagine CH2-CONH2
Q Gln Glutamine CH2-CH2-CONH2
W Try Tryptophan CH2-(CCCNC)-(CCCCCC) Indole. 5 ring pyrrole with N, then 6 ring phenyl (benzene).
G Gly Glycine H very flexible. non chiral.

In nature these are found in L form. See the CORN law. To test we view the C alpha and its immediate bonds. It always has a H, R (sidechain), CO (OH) and NH. For glycine, R is H (hydrogen), so glycine is indistinguishable between L and D-forms, so it is achiral or non-chiral. This test still works for other amino acids. View the C alpha with the H closest to you, then you can see the other 3 bonds. Reading clockwise you should see CO, R, N.