L07 Chem 481 Lecture Notes - Lecture 5: Glyceraldehyde, Isoelectric Point, Selenocysteine

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9 September 2016
Lecture 5: Amino Acids
I. Amino Acids
A. Structures (See AA chart and memorize)
B. Properties
1. Side Chains
a. Hard to predict the 3° structure of proteins
b. AAs will fold into the lowest free energy state, most assume a stable 3° globular structure
Must look at side chains for such interactions
2. Ionic Forms of AAs (looking just at the carboxyl and amino groups)
a. The cationic form is the low pH form
b. Titration of the cationic species with base yields the zwitterion (neutral, found at
physiological pH) and eventually the anionic form as pH increases
3. AA Titrations and Determination of the pI (isoelectric point)
a. The pI is the pH where the molecule has a net charge of 0
b. pI = (pK0+ + pK0-)/2
Take the pKa values surrounding the inflection point of the neutrally charged spcies
Look at the C-terminus, N-terminus, and side chains to determine overall AA charge
4. Reactions of AAs
a. AAs are not terribly reactive under physiological conditions
They can be readily activated by a number of mechanisms
b. In cells, AA need energy dependent activation to form new covalent bonds (require
catalysis by enzymes or modifications to occur at appreciable rates)
Carboxy groups form amides and esters
Amino groups form Schiff bases and amides
Side chains show additional reactivity (few reactions are specific to a single kind of
side chain)
c. Cysteine residues can readily interact to form disulfides and can be easily alkylated
This is a reversible process and occurs easily if low redox potential environment
(usually around pH 7, if pH > 8.5, pKa cysteine)
5. Stereochemistry of AA
a. All but glycine are chiral (must have 4 different substituents around the -carbon to be
chiral)
b. L-amino acids are predominant in the biosphere
R-AA are not uncommon, but not what is synthesized and used by ribosomes
D,L-nomenclature is based on D and L-glyceraldehyde
Absolute configurations superior since it eliminates ambiguity for Ile and Thr, which
can have 2 chiral centers
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