Transcript Document

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)
 Nutrien t storage (C,N sources)
 Structu re (tensile strength)
 Other (lu minescence, bonding...)
Protein structures
 Primary structure (linear polymer of amino acids)
 Secondary structure (standard 3-D patterns)
 Tertiary structure (detailed 3-D conformation)
 Quaterna ry structure (combined polymer chains)
The -carbon is chiral: L and D forms
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 a mino and carboxylate groups
Peptide bonds are planar and partially ionic
Note the
Directionality:
Side chains (R groups): group amino acids by
structure an d function
(Assignment: memorize amino acids by name, side
chain, abbreviations, cha racteristic)
Glycine and alanine have the smallest, simplest side chains.
Both have side chains that are non-polar and neutral.
Hydrophobicity (Go for transfer from butanol 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 gluta mate
(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, cha racteristics (hydro phobic,
polar, acidic, basic, etc.Ñ donÕ
t worry about values
of hydro phobicity)
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.