THE PRIMARY STRUCTURES OF PROTEINS

AMINO ACIDS

Introduction to proteins: Protein functions • Enzymes (catalysts) • Transporters (membrane spanning) • Contraction, motion • Defense (antibodies, venoms) • Regulation (of catalysis, transport, motion) • Nutrient storage (C,N sources) • Structure (tensile strength) • Other (luminescence, bonding...)

Protein structures • Primary structure (linear polymer of amino acids) • Secondary structure (standard 3-D patterns) • Tertiary structure (detailed 3-D conformation) • Quaternary structure (combined polymer chains)

Amino acids (Proteins are linear polymers of amino acids)

Note: -carbon;

side chain; –carboxylic acid (pKa ~2-3); -amine (pKa ~ 9-10)

The α-carbon is chiral: L and D formsAll protein amino acids are L forms

Amino acids are: • Amphoteric, amphiprotic: act as acid or base • Ionic: electrolyte • Ampholyte: amphoteric electrolyte

(in a pH gradient under an electric field, moves to its isoelectric point)

Amino acids are: • Amphoteric, amphiprotic: act as acid or base • Ionic: electrolyte • Ampholyte: amphoteric electrolyte

(in a pH gradient under an electric field, moves to its isoelectric point)

+ _

Amino acids can connect with a peptide bond involving amino and carboxylate groups

Peptide bonds are planar and partially ionic

Side chains (R groups): group amino acids by structure and function (Assignment: memorize amino acids by name, side chain, abbreviations, characteristic)

Note theDirectionality:

Glycine and alanine have the smallest, simplest side chains.

Both have side chains that are non-polar and neutral.Hydrophobicity (related to ΔGo for transfer from vapor to water): -0.4 1.8

Valine, leucine, isoleucine, methionine, and proline are non-polar , neutral, andalaphatic.

Hydrophobicities: 4.2 3.8 4.5 1.9 -1.6

Phenylalanine and tryptophan are non-polar, neutral, and aromatic.

Hydrophobicities: 2.8 -0.9

Serine, threonine, and tyrosine are polar and neutral.

Hydrophobicities: -0.8 -0.7 -1.3

Cysteine, asparagine, and glutamine are neutral and… non-polar polar polar.

Hydrophobicities: 2.5 -3.5 -3.5

Lysine, arginine, and histidine are polar and positively charged.

Hydrophobicities: -3.9 -4.5 -3.2

(+ chargebelow pH 7)

Aspartate and glutamate are polar and negatively charged.

Hydrophobicities: -3.5 -3.5

Titration of glutamate

-

(Shoulders represent Transitions)

Titration of a small polypeptide: gly-lys-ala N C

Note: shoulders in titration curve only for C-term, N-term, and side chains

Assignment: memorize amino acids by name, side chain, abbreviations, characteristics (hydrophobic, polar, acidic, basic, etc.—don’t worry about values of hydrophobicity)

There are different, non-protein amino acids. Three amino acids probablyexplain the toxicity of some deadly Chinese mushrooms: 2R-amino-4S-hydroxy-5-hexynoic acid; 2R-amino-5-hexynoic acidgamma-guanidinobutyric acid.