Study guide test 2

Strategies of nucleotide synthesis: precursors, when is ribose added, how is ribose activated and
added, what are first purines and pyrimidines made, how are the various forms of THF made
and/or interconverted, regulation of purine synthesis (where are committed steps), how is a
balance between AMP and GMP achieved, how do folic acid antagonists imapir purine synthesis.
Formation of nucleoside di- and triphosphates, adenylylate (AMP) kinase and ATP generation in
muscle.
Purine salvage pathways: the role of PRPP, and the two major phosphoribosyltransferases,
Lesch-Nyhan disease, gout and uric acid.
Nucleic acid degradation in intestine (fate of the base), and in cells; first common intermediate in
degradation of all purines, the two reactions of xanthine oxidase, the use of allopurinol.
SCID, adenosine deaminase deficiency, and resulting metabolic problems.
The function of the purine nucleoside cycle.
Pyrimidine synthesis: precursors, first pyrimidine made, first cytosine derivative made,
regulation, metabolic channeling
Deoxyribonucleotide synthesis and ribonucleotide reductase: source of reducing power,
thioredoxin, substrates, binding of substrates to catalytic site, the two regulatory sites.
Synthesis of dTMP: precursor, the THF derivatives (substrate and products), and the unusual
reaction of a THF derivative, why is this enzyme a target of inhibitors of DNA synthesis and how
do folic acid analogs block synthesis.
Tautomerizations: how do they affect base pairing, how do they cause mutations
What bonds in nucleotides and nucleic acids are unstable and under what conditions?
Know the difference between bases, nucleosides, nucleotides, and their names.
The glycosidic linkage and its stability.
Anti and syn configurations: what structure is not allowed and why?
The biological function of adenosine, effects of caffeine.
Conventions for writing polynucleotides sequences and structures.
Classes of nucleic acids and their properties. What are unique structures or components of each
type of RNA?
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Nucleic acid stability in acid and alkali.

Nucleic acid hydrolysis and nuclease specificity: where does cleavage occur?
The logic of nucleic acid sequencing by the Sanger method and 454 technology.
The structural differences between A-, B-, and Z-DNA. Do these occur inside cells?
Alternative hydrogen-bonded structures: how can cruciforms form; hoogsteen base pairs and
triplexes; what are the factors that favor quadruplexes and where are they found
Factors that affect denaturation and renaturation.
Nucleic acid hybridizations and DNA complexity.
DNA tertiary structure: supercoils, topoisomerases, and gyrases
Nucleosomes and higher order structures of DNA.
Structures of tRNA and rRNA: major features.
Features of DNA replication: semiconservative, bidirectional, role of helicases and
topoisomerases, semidiscontinuous synthesis, Okazaki fragments
Properties of DNA polymerases: the various activities, core and holoenzymes, the -complex and
its function, the clamp loader and the sliding clamp, the differences between DNP I and III and
their functions.
Telomere replication
What are the causes of errors during DNA replication?
How can you induce mutations?
DNA repair mechanisms.
Be able to distinguish adenine, guanine, hypoxanthine, uracil, cytosine, and thymine; adenosine,
guanosine, inosine, uridine, cytidine, thymidine, adenylic acid (AMP), GMP, IMP, UMP, CMP,
dAMP, dGMP, dIMP, dUMP, dGMP, dTMP
Underlined items are likely to be the subject of short essay question