amino acids

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amino acid (general functions and characteristics)
- - the building block molecules: structural units of proteins
- -protein's struc and func are determined by the struc + properties of its AA's
- - contains a carboxylic acid w/ an amino grp
- - 20 commonly found in proteins (standard/ common/ alpha AA's)
- -almost all have an asymetric alpha-c except lysine
- - all diff substituents connected to that C
- - have acid/base properties
what does "alpha- AA's" mean?
- -carbonyl + amino grp are bonded to alpha-carbon
alpha C is a chiral center because:
- 1. optically active: rotates plane of plane polarized light right or left
- 2. 2 possible configurations exist:
- -spatial (3D) arrangement of grps about chiral centers, forming stereoisomers (L/D)
- - also known as enantionmers: non-super imposable mirror images
AA's with non-polar, hydrophobic, aliphatic (non- benzene- like) R grps
- - R grps cluster together in interior of protein
- - shielded from H20
- - hydrophobic interactions
- list:
- glycine
- L-alanine
- L-proline
- L-valine
- L-leucine
- L-isoleucine
- L-methionine
Glycine (Gly)
- - branched H grp
- - little hydrophobic character
- - b/c of 2 H's: no asymetric carbon, not chiral
L-Alanine (Ala)
- -branched methyl grp
- -diphatic hydrocarbon
L-proline (Pro)
- L-Proline
- hydroxyproline
- - only AA with N linked to C
- - whenever it appears there is a bend in the 3-D structure of protein
- - found in lrg amnts in collagen (primary protein in connective tissues)
- - need to be converted by switching one of H2 grps to hydroxy grp
- - restricts geometry of polypep
- - abrupt change in direction of polypep chain
L-valine (Val)

-branched aliphatic grp: CHCH3CH3
L-Leucine (Leu)

-branched aliphatic after an attachment of CH2: CHCH3CH3
L-Isoleucine (Ile)
- -branched aliphatic:CH3CHCH2CH3
- - 2 chiral centers
L-methionine (Met)

-branched methyl thio ether that is non polar
AA's with aromatic R grps
- - relatively nonpolar + hydrophobic
- - can participate in hydrophobic interactions
- list:
- L-Phenylalanine
- L-Tyrosine
- L-Trytophan
L-Phenylalanine (Phe)

-branched benzyl grp
L-Tyrosine (Tyr)

-branched polar grp
L-Tryptophan (Trp)
- -branched polar grp - indole grp
- - aromatic heterocyclic
- - NH- polar grp
AA's w/ polar uncharged R grps
- more soluble in H2O than nonpolar AA's
- list:
- L-Serine
- L-Threonine
- L-Cysteine
- L-Asparagine
- L- Glutamine
L-Serine (Ser)

- branched Beta-hydroxyl grp
L-Threonine (Thr)
- -branched hydroxyl grp
- - 2 chiral centers
L-Cysteine (Cys)
- - SH: can form weak H-bonds
- sulfhydryl grp (thiol grp)
What is cystine?
- (Cys-Cys)
- - the sulfhydryl bonds to one another to form S-S bridge between 2 cysteine = disulfide bond
- - has special role in struc. of some proteins
- 1. Intrachain of disulfide bond
- links different regions of polypep covalently
- stabilizes the struc.
- 2. Interchain of disulfide bond
- links different polypep to ea. other
L-Asparagine (Asn)
- - branched amide grp
- - NH2- not charge b/c protons not avail. to share w/ H
L-Glutamine (Gln)

- branched amide grp
AA's w/ positively charged R grps
contain nitrogenous base that's protnated at pH 7.0
- list:
- L-Lysine
- L-Arginine
- L- Histidine
L-Lysine (Lys)
- -branched (CH2)4NH3
- -NH3: epsilon- amino grp
L-Arginine (Arg)

-branched guanidino grp: NHC(NH2)2
L-Histidine (His)
- -this mol represents 91% in soln. at pH 7.0 (net chrg = 0)
- - the other 9% is the other struc, which is protonated (net chrg = +1)
AA's w/ negatively charged R grps
- list:
- L-Aspartate
- L-Glutamate
L-Aspartate (Asp)
- -branched: CH2COO-
- - COO- : Beta carboxyl grp
- -L-aspartic acid
L- Glutamate (Glu)
- - branched: CH2CH2COO-
- - COO- : alpha carboxyl grp
- - L-glutamic acid