Chemical Biology 03BLOOD

Biomolecular Structure

III. Amino Acid to Protein

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Chemical Biology 03BLOOD

Biomolecular Structure

III. Amino Acids to Proteins

Lecture 5&6: 9/16/09

Organic Chemical Groups

PROTEINS

Biological Macromolecules: Proteins

• The general formula is

• H2N-CHR-COOH– amino ( H2N---- )

– acid ( ----COOH )

– ----CHR--- group varies, and gives its identity to one of 20 amino acids used in proteins

Proteins are made up of Amino Acids

• About half of the amino acids are "essential" meaning that they cannot be made by metabolic conversion from other molecules and thus need to be eaten

– For the ten essential amino acids:• Threonine, Tryptophan, Valine, Arginine, Histidine, Lysine, Phenylalanine,

Leucine, Isoleucine, Methionine

– Remember this phrase:• These Ten Valuable Amino Acids Have Long Preserved Life In Man

….20 amino acids that are used to make all Proteins

Post-translational Amino Acid Modification

• amino acids are used by the ribosome to make proteins

• these amino acids side groups in the protein may be further modified to have sugars, fats, other modifications elsewhere in the cell

Side Group Functionality

small

• Gly and Ala

nucleophillic

• Ser, Thr, Cys

Side Group Functionality

hydrophobic

• Val, Leu, Ile, Met, Pro

aromatic

• Tyr, Phe, Trp

Side Group Functionality

Acidic and Amide

• Asp, Glu, Asn, Gln

Basic

• Arg, Leu, His

Amino Acids join together using Peptide Bonds

• Peptide bonds link amino acids together through -NH2 on one amino acid and –COOH on another

Peptide Bond is Planar

* The peptide plane consists of six atoms, C 1, C, O, N, H, C

* H-N-C bond angle is 121o, not 109.5o.

Resonance in Peptide Bond

The peptide bond is rigid and planar due to the double bond resonance form, which shortens the C-N distance to 0.16 A shorter than a normal C-N bond.

..

Properties of Peptide Bond

• Barrier to Rotation about C-N bond is 20 kcal

• Peptide bond is planar with C groups typically trans to the peptide bond (better accommodate R groups)

• C and N are planar (2-D) and not able to rotate

• C groups are tetrahedral (3-D) and able to rotate though some angles are unfavorable due to steric repulsion with other atoms.

• C Naturally occurring amino acids are ALMOST exclusively the L stereoisomer.

Thinking Ahead: Why do we have twenty different amino acids and not just one or two or one hundred?