AMINO ACIDS
I. Function of amino acids
A. Building blocks of polypeptides
1. polymerized to form polypeptides(a) linked by a peptide bond
(b) synthesized during translation of messenger RNA
2. primary structure of a protein is the sequence of amino acids
3. both peptides and polypeptides can be functional
Structure –OOC–CH2–CH2–NH3+ GABA
Structure +H3N–CH2–CH2–SO3–TAURINE
B. Amino acids may be functional
1. neurotransmitters- glutamate and aspartate (excitory)- glycine, taurine, and aminobutyric acid (GABA) (inhibitory)
C. Precursors to other molecules
1. metabolic intermediates citrulline and ornithine in urea cycle can be metabolized to form glucose or acetyl CoA2. neurotransmitters – serotonin, dopamine, epinephrine, etc.
3. tyrosine (thyroid hormone)
4. porphyrins
5. creatine (energy storage)
6.histamine (mediator of immune response)
7. nucleotide synthesis – S-adenosylmethionine
II. Structure of amino acids
A. 20 standard alpha-amino acids1. Structure.
- alpha-carbon
- alpha-amino group
- alpha-carboxyl group
- side chain (R group)
2. “Standard” amino acids are encoded by messenger RNA
3. Amino acids are abbreviated by a 3-letter and 1-letter code
B. Some amino acids are not incorporated into proteins during translation
1. Modified amino acids
(a) Hydroxyproline and hydroxylysine
(i) hydroxylated enzymatically after translation
(ii) important in collagen structure (Structures of phosphoserine, 4-OH-
proline, 5-OH-lysine)
(b) phosphoamino acids
(i) Tyr, Ser, Thr hydroxyl groups can be phosphorylated
(ii) important in activation and inhibition of enzymatic or signalling activity
2. Other important amino acids
(a) Urea cycle intermediates – ornithine, citrulline, arginosuccinate
(b) Thyroid hormone (tyrosine Æ thyroxine)
III. Chemical Properties of Amino Acids
A. Physical characteristics
1. Charge(a) Amino acids are dipolar ions (zwitterions) at neutral pH
(i) zwitterion is a dipolar molecule with pos. and neg. charges spatially separated
(ii) definition of zwitterion in book is incorrect
(b) Ionic states of amino acids depend on pH
(i) amino acids have two or three dissociable protons
(ii) pKa of the dissociable proton and the pH determine its degree of dissociation
H–H equation: pH = pKa + log{[A–]/[HA]}
2. Titration curve of an amino acid
(a) calculated using the H-H equation
(b) Isoelectric point (pI) – pH at which the molecule has a net charge = 0 (average of
the two appropriate pKa values)
3. Polarity
(a) nine nonpolar amino acids
(i) tend to orient to the inside of proteins
(ii) Gly, Ala, Val, Leu, Ile, Met, Pro, Phe, Trp
(b) eleven polar amino acids
(i) tend to orient to the outside of proteins
(ii) Ser, Thr, Tyr, Asp, Glu, Asn, Gln, Cys, Arg, Lys, His
4. Hydropathicity – index of solubility characteristics in H2O
(a) combines hydrophobic and hydrophilic tendencies
(b) can be used to predict protein structure
Hydrophobic Ile>Val>Leu>Phe>Met (listed from most hydrophobic)
Less Hydrophobic Ala>Gly>Cys>Trp>Tyr>Pro>Thr>Ser
Hydrophilic His>Glu>Asn>Gln>Asp>Lys>Arg (arg is most hydrophilic)
5. UV absorbance
(a) aromatic a.a.s (Trp, Tyr, Phe) absorb UV light
(b) absorbs UV light between 260-280 nm
B. Stereochemistry
1. Most amino acids have optical activity(a) chiral centers are asymmetric centers (usually carbons)
(b) a-carbon of amino acids is chiral
(c) chirality yields stereospecificity
(d) Gly is not chiral (has no a-carbon)
2. L and D enantiomers (stereoisomers)
(a) enantiomers are nonsuperimposable mirror images of the same molecule
(i) L is levorotatory, D is dextrarotatory
(b) L and D nomenclature from L and D-glyceraldehyde (Fisher convention)
(i) not equivalent to R and S
(ii) most natural a.a.s are L
(iii) some a.a.s are R, some are S
(c) L and D forms are chemically and physically distinguishable
(i) different activity, melting points, and spectra
C. Cysteine can form disulfide bonds
1. cysteine is the reduced form (sulfhydryl)2. cystine is the oxidized form (disulfide)
3. disulfide bridges formed between cysteines are important in protein structure
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