Some topics to study for Test #1 (2007):

 Know how to work all the problems assigned, especially the handout problems.

You will be given a problem like the handout that involves determining the sequence of a peptide.

In chapter 2, know how to use data in Table 2-4;

-Know about Table 2-5, the relation of pH and pKa and their effect on solubility (ionic species are always more soluble; see problems 6,7,8 on p. 73);

In chapter 3, know amino acid groupings (Fig. 3-5).

- Know about the terms zwitterion, amphoteric, and pI;

- Know the interpretation of amino acid titration diagram (like Figs. 3-10 and 3-12; see problem #2, p, 112);

- Know the reactions involved in forming and hydrolyzing (using acid or base) peptide bonds;

- Know the 4 levels of protein structure (figure 3-16);

- As indicated above, be able to determine the amino acid sequence for a peptide (know specificity of trypsin, chymotrypsin, pepsin, and CNBr)

- Know the reactions used to modify cystine residues for analysis (Fig. 3-26);

- Know how Edman degradation works for sequencing purposes, including structures of phenylthiohydantoin derivative;

- Know the factors that can be utilized for purifying proteins; how ion-exchange, size-exclusion and affinity chromatography work and be able to apply them; how electrophoresis works, including PAGE and SDS-PAGE (Fig. 3-19 and 3-20), and be able to use the equation for electrophoretic mobility (p. 92).

In chapter 4, know what a Ramachandran plot is and how it is generated.

- Know the three main types of secondary structure and features of each including how certain amino acids help stabilize or destabilize the structures. (Be able to draw these structures given a backbone.)

-  Know examples of fibrous proteins (Table 4-1) and features of each including how certain amino acids help stabilize or destabilize the proteins.

- Know the role of disulfide bonds in fibrous proteins, including hair perms (Box 4-2).

- Know the repeating unit in collagen and its general structure.

- Know about the difference between motifs and domains

- Know about how sequence “determines” tertiary structure, for example with experiments on the denaturation of RNase (Fig. 4-27). Know these methods of denaturation, including what type of forces might be disrupted: heat, pH, organic solvents, urea, and detergents.

In chapter 5, know about myoglobin (Mb), its heme unit and elements of secondary structure.

- Know about hemoglobin (Hb), including key features (including structural features) of the heme unit and its ligands (don’t memorize the entire porphyrin ring structure).

- Given an O₂ binding curve, predict how it would shift under various conditions of pH, CO₂, and BPG.

- Know how BPG and CO₂ bind.

- Know how sickle-cell hemoglobin differs from normal Hb and how it causes sickling.

- Know about the oxygen binding curves (θ vs. pO₂) for Mb and Hb.

One color 3-D picture from the “Oxygen-Binding Proteins” exercise will be given in which questions based on the picture will be asked (you will have to draw on the picture)