Amino Acids

Description of amino acids and its structural classification.

1.amino acids


#300 amino acids found in nature
#20 commonly found in mammalian proteins
+these are coded for by DNA or genetic cell
#Proteins diverse molecules
+enzymes direct and regulate metabolism
+contractile proteins move muscle
+(in bone) protein collagen forms framework for deposition of Ca3(PO4)2 crystals
-like steel cables in reinforced concrete.
+(in bloodstream) hemoglobin, plasma albumin shuttle molecules
+immunoglobulins fight infectious bacteria and viruses.
#Linear polymers of amino acids.

2. Structure of Amino Acids

+amino acids has
-a carboxyl group
-a amino group
-R group (distinctive side chain) [bonded to alpha-carbon atom]
+carboxyl group is dissociated (negatively charged carboxylate ion)
+amino group is protonated (-NH3+)
+(in protein) carboxyl and amino groups are combined in peptide linkage
+generally they are not available for chemical reaction [except about H bond formation]
++ Nonpolar (even distribution of electrons )
++ Polar (uneven distribution of electrons)


Structural Classification of Amino Acids
->Amino Acids with nonpolar side chains
->Amino Acids with uncharged polar side chains
->Amino Acids with acidic side chain
->Amino Acids with basic side chain
->Optical properties of amino acids



Amino acids with nonpolar side chains

+has a nonpolar side chain
+that doesn''t bind or give off protons or participate in hydrogen or ionic bonds.
+these are "oily" or "lipid-like" promotes Hydrophobic interactions

1. Location of nonpolar amino acids in proteins
2. Proline

1. Location of nonpolar amino acids in proteins:

+protein has aqueous solutions
+cluster
+hydrophobicity of nonpolar R-groups
-like droplets of oil (aqueous environment)
-interior of the folded protein
+hydrophobic environment e.g. membrane
+nonpolar R-groups found on outside surface of protein
+that interacting with lipid environment
+hydrophobic interaction in stabilizing protein structure (importance)

2.Proline

+side chain of proline & alpha-amino group form a ring structure
+it contains an imino group
+unique geometry of proline (help forming of fibrous structure of collagen)
+that interrupts alpha-helix found in globular proteins.

Amino acids with uncharged polar side chains

+zero net charge at neutral pH
+cysteine and tyrosine can lose a poton at alkaline pH
+serine, threonine and tyrosine contain polar hydroxyl group
+that can participate in hydrogen bond formation
+asparagine , glutamine contain a carbonyl group and one amide group
+they can participate in hydrogen bond

1.Disulfide bond
2.Side chains as sites of attachment for other compounds

1. Disulfide Bond:

+side chain of cysteine contains 1 sulfhydryl group(-SH)
+that is component of active site of many enzymes
+(in proteins) -SH groups of 2 cysteines become oxidized
+and form a dimer
+cysteine contains a covalent cross-link [disulfide bond (-S-S-)]

2. Side chains as sites of attachment for other compounds

+serine, threonine, (rare) tyrosine contain a polar hydroxyl group
+that serve as a site of structure (e.g. phosphate group)
+serine side chain important for active site of enzymes
+asparagine has amide group
+that and hydroxyl group of serine or threonine serve as site of enzymes.


Amino acids with acidic side chains

+aspartic and glutamic acid are proton donor.
+at neutral pH, side chains are fully ionized.
+that contain negatively charged carboxylate group
+called aspartate or glutamate
+due to emphasize these amino acids are negatively charged at physiologic pH


Amino acids with basic side chains

+side chains of basic amino acids
+accepts proton
+at physiologic pH side chains of lysine and arginine are fully ionized
+positively charged
+histidine is weakly basic
+free amino acid is largely uncharged at physiologic pH.
+histidine incorporated to protein, it can be positively charged or neutral
+depend on ionic environment
+that is provided by polypeptide chains of protein.
+histidine functioning of proteins (e.g. hemoglobin)


Optical properties of amino acids

+chiral or optically active carbon atom.
+glycine is exception
+it has 2 hydrogen substituents
+optically inactive
+amino acids have asymmetric center at alpha-carbon
+2 forms D and L
+stereoisomers, optical isomers or enantiomers
+all amino acids is L-configuration in proteins
+D-amino acids found in antibiotics and in bacterial cell walls.