CHEM 4500: Material covered for Exam II

As a general rule, words in bold in the text are important. Know the meanings of these words.

Chapter 4

Section 4.1 Amino Acid Structure. Be able to draw the structure of an amino acid. Know the reaction of
peptide bond formation. Know the classifications of amino acids, which amino acids belong to which
class, and be able to draw the structure of one amino acid from each class. Be able to calculate a pI given
the pKa’s of an amino acid. Note naming convention on pg. 82.

Section 4.2 Stereochemistry. Be able to distinguish between an L- and a D-amino acid. Know which
enantiomer is used in making proteins.

Section 4.3 Amino Acid Derivatives. Be generally familiar with this section (types of modifications of
amino acids discussed in class, important features of glutathione).

Chapter 5

Section 5.1 Polypeptide Diversity. Know how many possible sequences can be made from a polypeptide
with N residues. Know what determines lower size limit and upper size limit of proteins.

Section 5.2 Protein Purification and Analysis. Know why protein purification is necessary. Note the
important factors listed on pp. 94-95. Know about the types of assays that were discussed in class. Know
what characteristics of proteins are exploited in purification. Know the techniques that were discussed in
class.

Section 5.3 Protein Sequencing. Know general strategy for sequencing a polypeptide chain. Know the
general scheme for Edman degradation (but don’t memorize structures, etc.).

Section 5.4 Protein Evolution. Know why sequence comparisons of proteins are useful. Know what a
phylogenetic tree is. Know why gene duplication is important for evolution. Understand the concept of
modules in protein evolution.

Chapter 6

Know definitions on pg. 126.

Section 6.1 Secondary Structure. Know key characteristics of peptide group as detailed in Section A
(e.g., resonance structures, preference for trans conformation, torsion angles, etc.). Know key features of
-helix and -sheet. Know general structural features of the proteins discussed in class.

Section 6.2 Tertiary Structure. Know what a motif is, and be able to give an example of one. Know
what a domain is, and note sentence in italics on pg. 151.

Section 6.3 Quaternary Structure and Symmetry. Know what quaternary structure is, and know
definitions of protomer and oligomer.

Section 6.4 Protein Stability. Know the relative contributions of the different forces that stabilize protein
structure (Section A). Know ways in which proteins can be denatured, and the implications of the Anfinsen
experiment.

Section 6.5 Protein Folding. Know general process whereby a protein folds. Know what PDI is and what
it does. Know what molecular chaperones are.

Section 6.6 Structural Bioinformatics. Do not cover this section.