Humboldt State University ® Department of Chemistry

Richard A. Paselk

Chem432	Exam II Study Guide	Sp 2002
	© R. Paselk 2001

Final Version

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?

Translation: The genetic code: How many bases/aa? What do we mean when we say the code is conservative? Explain/ How universal is the "standard" code? t-RNA: What is its function? Describe the structure of t-RNA - include classification of this structure into 1°, 2°, and 3° levels ands major features of each. Aminoacyl t-RNA synthetase: What two reactions are catalyzed by this enzyme? Be able to write the chemical eqn for these reactions, including structures. Be able to explain, with examples, why the fidelity of these enzymes is so high. What kinds of catalysis seem to be used by the tyrosyl t-RNA synthetase? How are these enzymes related to each other? What does "wobble" refer too? How does it work? How many synthetase enzymes are required do to the occurrence of wobble? What is the relation of frequency of codons for a given aa and the number of isoaccepting t-RNAs? the number of synthetases? Mitochondrial genetic systems exhibit a number of violations of general rules - what are these violations and why do we think this is allowed to occur?

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 C_ot curves? How are they made? interpreted? Hyperchromic shift. What does C_ot data tell us about the eukaryotic chromosome? How is DNA classified according to C_ot 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:

• Determination of the Yeast RNA Polymerase II Structure at the Atomic Level
  • How was the structure of this molecule determined in these studies?
    • What kind of equipment was used in each case?
    • What kind of data were acquired in each case?
    • How was the data reduced to generate an image in each case?
  • How did the X-ray study build on the earlier work of Darst et.al. above?
  • How does the resolution of the techniques of Electron and X-ray Crystallography compare?
  • What are the advantages of each method?
• The Human Genome Project
  • Compare the methods and results of the two projects (public and private).
  • Is the "map" of the human genome complete? If not
    • What's missing?
    • What still needs to be done?
  • What are some of the implications of the knowledge now available? Consider:
    • Ethical implications.
    • Economic implications.
    • Medical implications.
    • Value to basic biological science.
• The Human Chromosome 20 Sequence
  • How does the complete sequence compare to the draft sequences of last year?
  • What is the meaning of "complete sequence" in this case?
  • What methods of analysis have the authors performed on their sequence?

  • What new approaches have the authors introduced and why?
  • How does the effort required to "finish" compare to creating the draft?

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

C432 Home

C432 Lecture Notes

Last modified 11 April 2002