Review for Chapters 7, 8, 9 and Microarrays (chapters 13 &14, partial) (part I)
Chapters 7 & 8
Terms:
1. restriction enzyme digestion
2. autoradiography
3. probe
4. Southern blotting
5. Northern blotting
6. gene cloning
7. polymerase chain reaction
8. Taq polymerase
9. reverse-transcription
10. DNA library
11. genomic library
12. cDNA library
13. colony lifting
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14. genetic mapping
15. physical mapping
16. chromosome walking
17. alkaline phosphatase
18. complementary DNA
19. partial digestion
20. melting temperature
21. denaturation
22. renaturation
23. heteroduplex
24. stringency
25. nick translation
26. in situ hybridization
27. radioactive isotope
28. fluorescent in situ hybridization (FISH)
29. nested PCR
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In chapters 7 and 8, students are expected to be able to
30. explain the ways to effectively clone a piece of foreign DNA into a plasmid vector
using PCR and restriction enzyme digestion.
31. explain the ways to identify the recombinant DNA clones using colony screening,
and Southern blotting.
32. explain the way to identifying the recombinant DNA clones using polymerase
chain reaction.
33. design oligonucleotide primers for performing polymerase chain reaction.
34. explain the important criteria in designing a set of oligonucleotide primers.
35. describe how to optimize a polymerase chain reaction.
36. compare and contrast the genomic and the cDNA libraries.
Quantitative RT-PCR (chapter 8 section 7)
Terms:
1.
2.
3.
4.
SYBR Green
conventional PCR
real-time PCR
CT value
In this chapter, students are expected to be able to
1. explain the major difference of conventional and real-time PCR.
2. explain how to use the real-time RTPCR to quantify two or more expressed
genes in a given tissue.
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Chapter 9. DNA sequencing
Terms
1. nucleotide
2. nucleoside
3. dideoxyribonucleotide
4. deoxynucleotide
5. primer
6. template strand
7. phosphodiester bond
8. DNA polymerase III
9. autoradiography
10. walking
11. universal primer
12. shotgun cloning and shot gun sequencing
13. contig assembly
In this section, students are expected to be able to
1. explain the mechanism for dideoxy chain termination sequencing.
2. explain how the dideoxy chain termination sequencing works.
3. explain the reason for extending the sequence
4. explain the similarities between manual and automatic sequencing methods.
5. explain the differences between manual and automatic sequencing methods.
6. explain what the “shotgun cloning” and “shotgun sequencing” are.
7. explain what the “contig assembly” is.
8. explain what the whole-genome shotgun sequencing is, and how it is was used.
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Microarray Technology (our textbook discusses this topic in 2 different chapters:
chapters 13 and 14)
Chapter 13. page 292; chapter 14.2 page 319.
Terms:
1.
2.
3.
4.
5.
6.
comparative genomic hybridization
DNA array
gene array (expression array)
oligonucleotide array
hybridization
post hybridization wash
In this section, students are expected to be able to
1. explain what the comparative genomic hybridization is.
2. explain how the array CGH works.
3. describe how to use a gene array to compare gene expression profiles in normal
vs. cancer tissues.
4. describe how to use the array CGH to detect and measure the sizes of
microdeletions in chromosomes.
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Other related review questions for the final exam:
1. The beta-globin gene family consists of 60 kb of DNA, yet only 5 percent of the
DNA encodes gene products. What are the functions of the remaining 95
percent of the DNA?
2. What, if any, features do bacterial genomes share with eukaryotic genome?
3. Describe the human genome in terms of genome size, the percentage of the
genome that codes for proteins, how much is composed of repetitive sequences,
and how many gene it contains. Describe 2 other features of the human
genome.
4. Based on a comparison of general features of eukaryotic and prokaryotic
genomes, why might we predict that the organization of eukaryotic genetic
material is more complex than that of bacteria?
5. Compare the organization of bacterial genes to that of eukaryotic genes. What
are the major differences?
6. What are gene microarrays? How are microarrays used to detect chromosome
deletions and translocation? How are microarrays used to measure gene
expression levels?