Organic Chemistry III

Professor Carl C. Wamser

Amino Acids and Proteins

Knowledge - Level 1

know the terminology:

amino acid, essential amino acid, amino acid residue
peptide, polypeptide, protein, enzyme
N-terminus, C-terminus, alpha-helix, beta-sheet
zwitterion, isoelectric point, electrophoresis

know the structures of the 20 common amino acids by name and 3-letter abbreviation

know the approximate pKa values for the amino acids

Concepts - Level 2

understand the relationship between the pKa values of amino acids and peptides and the different ionization states they may assume in solutions depending on the pH

understand the classification systems for proteins

based on composition (simple or conjugated)
based on shape and solubility (fibrous (insoluble) or globular (soluble))
based on function (enzymes, structural, etc.)

understand the classification system for protein structural features:

primary: amino acid sequence
secondary: chain conformations (alpha-helix, beta-sheet)
tertiary: 3-d structure of the entire protein
quaternary: interactions of multiple polypeptide chains

recognize the various reactions of amino acids and peptides:

peptide bonding
disulfide bonding
ninhydrin test
Edman degradation
BOC protecting group
cleavage by chymotrypsin and trypsin

Applications - Level 3 

identify the expected state of ionization of amino acids or peptides based on a given pH and their pKa values

name and give abbreviations for simple peptides

indicate the steps necessary for peptide sequencing

indicate the steps necessary for a peptide synthesis

Analytical Skills - Level 4

identify features that contribute to the various levels of protein structure

determine the amino acid sequence of a polypeptide based on partial hydrolysis and other results