Download Study Guide Chapters 8-9 Nucleic Acids, and Molecular Engineering

Study Guide Chapters 8-9 Nucleic Acids, and Molecular
Engineering (DNA Technology)
1. How do the ribose sugars in DNA and RNA differ?
2. Please you should be able to draw the nucleotides of DNA and RNA. And
given a series of bases draw a DNA or RNA.
3. Describe the backbone structure of DNA. What is the charge of a
polynuceotide?
4. How are the bases geometrically arranged in relationship to the ribose sugar
in a polyncleotide?
5. Explain Chargoff’s rule, and relate it to the structure of DNA. How is this
the same as Watson-Crick Base pairing?
6. Describe the ‘puckering’ of the ribose sugar. Explain syn and anti structures
based on rotation.
7. Describe the three forms of the DNA molecule. (There similarities and
differences structurally.) Is RNA helical?
8. Why is there a major and minor groove formed in the double helix of DNA?
9. Explain secondary structure in DNA and RNA. What are palindromes?
Hairpins and cruciforms?
10. What is the Tm of DNA due too, which base pairs is it dependent upon, and
why?
From ‘melting’ of DNA what enzyme did we realize had to exist? What
‘chaperone’ like protein needed also to exist? What makes RNA polymerase
unique in this regard?
11. What are hybrid heteroduplexes? What can you do with this phenomena?
12. Explain mutations? How does that help in our understanding the role of
specific amino acids in a protein?
13. How do we sequence DNA?
14. There are posted on WORDPRESS papers about miRNA and iRNA. What
are there functions? Structure?
15. How are miRNA and siRNA produced in a cell?
16. Explain the structure of the following co-enzymes (co-substrates), CoA,
FAD, NAD, and FMN.
17. Explain T-T dimerization? Could this cause a disease? (hint what body parts
are exposed to UV radiation??? OH! Goldberg asked one of those Medicine
questions again! Drat!)
Chapter 9.
19. From the WORPRESS articles on miRNA and siRNA, how might you employ
these experimentally?
20. Explain what is a Restriction Endonuclease. How might these enzymes work
in eukaryotic cells?
21. How do we employ this unique sequence driven enzyme of bacteria?
22. What exactly is reveres transcriptase? (hint this is a nickname)?
23. Do explain the functions of the following enzymes as technological tools in
clone, transforming and expressing genes; DNA ligase, Alkaline Phosphotase,
Terminal transferase, polynucleotide kinase, reverse transcriptase, Exonuclease
and Restriction Endonucleases.
24. What is a plasmind? How was a plasmid constructed? What was used before
plasmids? What is a Transposable Element?
25. Why are Selectable Marker necessary? Antibiotic resistance genes? Βglactosidase?
26. What is the origin of replication (ori)?
27. Compare two well-established plasmid; pBR322 and YAC. How are they
similar? Different? Why does Goldberg use TOPO pCR2.1 or pCR4.0 instead of
overnight PCR? (from lecture) Why remove the fragment from TOPO and clone
it into pQE32?
28. Looking at your answer to question 12, explain site-directed mutagenesis.
29. How do we engineer the expression of a protein to aid in affinity
purification of that protein?
30. Describe how PCR works. RTPCR and qPCR work.
31. What is an otholog, a paralog?
32. Explain Synteny.
33. Explain Introns and Exons.
34. What is a SNP? SSRs? CONTIG?
35. From our lecture explain the concept of Alignment (nucleotides and amino
acids)? What can we learn about a genes/protein from alignments?
36. Where does the information needed for an alignment about a particular
gene come from? (this came from lecture).
37. What is a BLAST of a particular gene? Why is the e value important? (also
from lecture).