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); The α-carbon is chiral: L and D forms
-amine (pKa ~ 9-10) All 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

Note the
Directionality:

Side chains (R groups): group amino acids by

structure and function

(Assignment: memorize amino acids by name, side

chain, abbreviations, characteristic)
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, and
alaphatic.

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.

(+ charge
below pH 7)

Hydrophobicities:
-3.9 -4.5 -3.2
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 probably
explain the toxicity of some deadly Chinese mushrooms:
2R-amino-4S-hydroxy-5-hexynoic acid;
2R-amino-5-hexynoic acid
gamma-guanidinobutyric acid.