Some topics to study for Test #2 -2007:

Know how to work the problems assigned.

Know how the experimental data (irreversible inhibition [DIFP] and affinity labeling) work and support the mechanism of chymotrypsin.

 Know how enzymes are controlled or regulated. Know how the few examples of regulation given in class work. Given a plot of V_o vs. [S] for a regulatory (allosteric) enzyme, predict how the curve would shift or change under different conditions.

Know what the following mean (including the composition and some features of each):  Blood sugar, dextrose, lactose, sucrose, cellulose, chitin, starch, amylose, amylopectin, glycogen.

Know the iodine test for starch.

Know the components of a proteoglycan and how its structure determines its function.

Know that oligosaccharides are O-linked or N-linked to peptide chains and know what aa are involved. Know what monosaccharides are responsible for “blood types A, B, AB, and O” and the importance of these.

Know about some functions of lectins including 1) the glycoprotein clearance mechanism that occurs in the blood and 2) their involvement in ulcer formation.

Know about glucosylated Hb.

With respect to DNA and RNA, know:

- the structure of the backbone, including ribose and 2-deoxyribose,

- what nucleotides are including what 5 bases (names (e.g. adenine) and abbreviations (e.g. A)) are used in making DNA or RNA, which bases are purines and which are pyrimidines,

- features of the double helix (B form)*, and related terms such as major and minor grooves, antiparallel, base-pairs and hydrogen bonding between (be able to draw these given the base structures)

- the features of DNA palindromes,

- use of base pairing rules,

- factors affecting the “melting” of DNA, hyperchromism,

- causes of “spontaneous” (e.g. deamination) and chemically-induced mutation using HONO, including changes in chemical structures involved.

- triple helix (triplex) DNA

- DNA sequencing

Know about how proteins interact with DNA, including:

- how to recognize sites on the base pairs that can interact by H-bonds to other bases or amino acid side chains

- how and what aa can H-bond with N-bases (be able to draw these given the base structures),

- the following binding motifs:

   helix-turn-helix*, including features of the recognition helix; zinc-fingers*, homeodomain

- leucine zippers*, helix-loop-helix

 *For these, given a 3-D picture of a structure be able to identify it, recognize features or write in missing pieces (in a general fashion).

 Topics you will not have questions on:

Know general features about enzymes: how do they cause such great catalysis (transition state) and bind with specificity. Know the Michaelis-Menten equation. By inspection of the data, determine K_M, V_max, k_cat, and estimation of catalytic efficiency (specificity constant) ( k_cat/K_M).

Know how the “catalytic triad” of chymotrypsin works.

Recognize the structure of a carbohydrate. (What is required for something to be a carbohydrate?)

Know and be able to use the following terms:  aldose, ketose, tetrose, pentose, hexose.  (& combinations of these terms, like “aldohexose”), anomers, epimers, enantiomers (D and L), diasteroisomers

Recognize the “ring” structures of:  glucose, galactose, mannose, and fructose

Know what reacts positively in the Benedict’s test and what the evidence for the test is.