Humboldt State University ® Department of Chemistry

Richard A. Paselk

 Chem 432

 Exam II Study Guide

Sp 2009

© R. Paselk 2008

Spring 2009 final Version

Amino Acid Biosynthesis and the One Carbon Pool: Be able to trace the biosynthesis of ala, asp, glu, ser, and gly from glucose (or any other glucogenic carbon source). What is the one carbon pool? What is it used for? What are the carriers? What are the major sources? Know the reaction for the activation of met. Know how S-adenosyl-methionine is used to make creatine or choline. What is H4Folate? Know the structure for the active portion of this molecule. What are the different oxidation states of carbon which may be carried by this cofactor? Know how to transfer carbon to folate from serine (and thus make glycine), and glycine (and make glycine by the reverse). How can folate be used in the regeneration of met? How can serine be used in the regeneration of met?

Nitrogen Metabolism: What is the reaction catalyzed by E. coli gluNH2 sythetase? How is it controlled? Know control mechanisms in some detail. What regulatory substances are involved? Why? Compare to mammalian enzyme. What is nitrogenase and what does it do? How is the majority of biological nitrogen "fixed"?

Purine and Pyrimidine Metabolism: What is a nucleotide? nucleoside? free base? Know (be able to draw) the basic purine and pyrimidine ring structures and in each case label and identify where the various atoms arise from. What strategies are employed in the biosynthesis of these two families of molecules? How do these strategies differ? What is the major intermediate for each pathway? How are these intermediates then modified to give the various final products? How are the various dNTP's formed? Know the first couple of reactions for each pathway. Know how each pathway is controlled in both bacteria and in mammals.

Know how the purines are degraded, including the AMP deaminase cycle. Be able to explain, using words and equations, how birds excrete N, starting with amino acids. How is this pathway important to mammals (or is it)?

Metabolic Integration: Glyoxalate cycle (plants). Where is this cycle important? What does it enable plants to do?

Be able to discuss adaptations and responses of fuel metabolism to starvation and overeating. Include basic hormonal control by insulin, glucagon and epinephrin. Keep in mind which fuels are used when, by which tissues and why. What are some causes of obesity? Pay attention to the pathways involved and the intermediates shared by these pathways!

Be able to discuss adaptations and responses of fuel metabolism to different types of exercise. What does this tell us about regulation of catabolism? What major hormonal controls did we discuss? What do these exercise studies tell us about fuel storage and use? Can we extrapolate this information to other situations such as injury, disease and/or stress? What other considerations might come into play?

DNA & RNA: What are the basic structures of these molecules? How do they differ from each other? How do these differences affect their chemical and biological behavior? Know base pairs for each, structures for A:T pair only. Discuss the forces involved in maintaining nuceic acid 3-D structures. How do they compare to the forces maintaining 3-D structures in proteins in aqueous environments?

Describe the structure of B-DNA in terms of 1° and 2° structure. How does DNA's structure "explain" its biological properties? correlation with genetics? Explain molecular basis of dominance and mozaicism. Semi-conservative. How does A-DNA differ from B-DNA? Why is each of these structures interesting? What is super-coiling? Why is it important in understanding replication, transcription, and DNA structure in the nucleus. Understand and be able to explain L=T+W and its terms. Understand how to use this relation to describe/understand supercoiling in DNA. How can supercoiled DNA be relaxed? What do topoisomerases do? What are the two types? DNA Gyrase?

What are the three main types of RNA? Characterize each in terms of structure (detail) and function (very basic). Compare/contrast the levels of structure in RNA folding to the analogous levels in protein folding

Transcription: Three types of RNA - name, characterize, and give the functions of each. Constitutive vs inducible proteins in prokaryotes. Know the operon model. RNA polymerase - what are its requirements? what reactions does it catalyze? Holoenzyme. Core-enzyme. What are the three stages of RNA transcription? Describe the process of initiation. What are the five eukaryotic RNA polymerases and what are their functions? Which transcribes rRNA? How is this RNA organized? How is its transcription controlled? Which transcribes protein mRNA? What is a TATA box? a Pribnow box? Be able to discuss, with examples, gene regulation in E. coli. Describe the process whereby eukaryotic RNA transcripts are made into mRNA molecules. Capping, poly(A) tails, exons and introns: what do these terms refer to and what are their functions? Spliceosome. Lariate structure. Compare prokaryotic to eukaryotic rRNA processing. How is tRNA processed?

DNA Replication and Repair: DNA replicates semi-conservatively at replication forks in the 5'Æ3' direction only. E. coli: What are the requirements, activities and purported functions of DNA Polymerase I (Pol I) in the process of DNA replication.? What are the requirements, activities and purported functions of DNA Polymerase III (Pol III) in the process of DNA replication? In what ways do these enzymes differ? Be specific. What additional activities does Pol III need to replicate DNA? Be able to diagram the replication fork in E. coli DNA as in figure 24-12 in Voet, Voet & Pratt. Describe the process of initiation of DNA replication in E. coli. Eukaryotes: What are the phases of the cell cycle and what happens in each? In which is DNA replicated? What are the eukaryotic Polymerases? Note that there seem to be two DNA replicases in eukaryotes. What is a replicon? How can eukaryotes replicate their DNA in a reasonable time when wukaryotic Pols are one twentieth as fast as Pol III and yet a chromosome is >60x larger than the DNA in E. coli?

Eukaryotic Chromosome Structure and Organization: Eukaryotic Genome organization C-value paradox - what is it? What is a C-value? What are Cot curves? How are they made? interpreted? Hyperchromic shift. What does Cot data tell us about the eukaryotic chromosome? How is DNA classified according to Cot curves? (unique, mod. repetitious, highly rep., inverted repeats) What can you say about the localizations, and function(s) of these different DNA categories? What is "selfish DNA"? Do you believe in it? Why or why not. What are tandem gene clusters? Where do they occur and what do they code for? What is the rationale for this restricted distribution? Why don't we see more? What is gene amplification? When is it seen? Where? What are clustered gene families? Describe the Hb families: 2 families, universality, exon/intron pattern. What are introns?

Class Discussions: Review the various Discussion topics, Case Studies and articles. Be able to briefly answer the questions we addressed in our discussions. For example:

You may bring a data/information sheet to the exam, however you must not exceed one side of a single sheet of 8.5" x 11" paper for this sheet - GOOD LUCK!

Pathway Diagrams

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Last modified 7 April 2009