CHAPTER 19—GENOMES AND PROTEOMES
MULTIPLE CHOICE
1. The study on mutations in germ-line cells indicates all of the following EXCEPT
a.
some mutations are inherited from our parents
b.
some mutations arise as new mutations in the germ-line
c.
the mutation rates are the same in all families
d.
more families need to be studied to draw any real conclusions
e.
this information can be used in medical research
2. The human genome has a size of approximately
a.
1 billion base pairs
b.
3 billion base pairs
c.
7 billion base pairs
d.
10 billion base pairs
e.
14 billion base pairs
3. All of the following are model organisms whose genomes were sequenced as part of the original
Human Genome Project except
a.
Mus musculus (mouse)
b.
Escherichia coli (bacteria)
c.
Drosophila melanogaster (fruit fly)
d.
Caenorrharbditis elegans (nematode)
e.
Danio rerio (zebrafish)
4. What is the difference between dideoxyribonucleotides (ddNTP) used in Sanger sequencing and the
deoxyribonucleotides (dNTP) normally found in DNA?
a.
ddNTPs have a 3′ H rather than OH
b.
dNTPs have a 3′ H rather than OH
c.
ddNTPs have a 5′ OH rather than H
d.
dNTPs have a 5′ OH rather than H
e.
ddNTPs have a 3′ OOH rather than OH
5. Why do normal nucleotides need to be included in the Sanger sequencing reaction mix?
a.
so the DNA polymerase has a substrate to work with
b.
to enhance the action of the dideoxynucleotides
c.
so a longer sequence (up to 300 additional base pairs) can be determined than without
(normally 200 bp).
d.
so multiple sequences of different lengths will be generated
e.
to prevent the DNA polymerase from making too many errors
6. What is an open reading frame?
a.
the protein coding sequence in a genome and the associated regulatory sequences
b.
the nucleotides between and including a start codon and an end codon in all chromosomes
c.
the nucleotides between and including a start codon and an end codon, minus the introns
d.
the nucleotides between and including a start codon and an end codon, minus the exons
e.
the nucleotides between a start codon and end codon in prokaryotes
7. What percentage of a typical eukaryotic genome is coding?
a.
10−20%
b.
1−2%
c.
20−30%
d.
25−50%
e.
50−75%
8. Now that the human genome has been sequenced, we know that there are fewer than expected protein
coding genes (approximately 20,000). Yet, the total number of proteins produced in humans
approaches 100,000. What accounts for this discrepancy in numbers?
a.
We have not yet identified all of the open reading frames in the human genome.
b.
We have not yet fully sequenced the human genome.
c.
The various mechanisms of mRNA processing lead to more proteins being produced than
the DNA directly encodes.
d.
Some proteins are converted into completely new proteins after translation.
e.
There has been a gross over-estimation of the number of proteins produced in humans.
9. Which of the following are added to a single-stranded DNA in order to perform a successful
sequencing reaction?
a.
a mixture of the four dideoxyribonucleotides, each with a different fluorescent label
b.
a DNA primer
c.
a mixture of the four deoxyribonucleotides
d.
a DNA polymerase
e.
all of these
10. I tried to sequence a DNA fragment and ended up with the trace pattern shown in the figure above.
What is the most likely cause of this result?
a.
I forgot to add the ddCTPs to the sequencing reaction.
b.
I forgot to add the normal dCTPs to the sequencing reaction.
c.
I forgot to add DNA polymerase to the sequencing reaction mix.
d.
The fluorescent tags for the ddGTPs are degraded.
e.
The polyacrylamide gel didn’t polymerize properly and is altering the migration patterns of
the DNA fragments.
11. In the whole-genome shotgun method, the genome is fragmented and individual fragments are
sequenced. How do we determine the order of the nucleotides in the intact chromosome?
a.
The fragmentation is done in a very systematic way such that the physical arrangement of
fragments is readily apparent.
b.
The sequence of the ends of the fragments overlap with the ends of other fragments.
c.
We supplement our information with data from a different technique to determine the final
chromosome arrangement.
d.
DNA hybridization assays are conducted to determine the physical arrangement of the
genes on the chromosome.
e.
After sequencing, the fragments are labeled and used as probes in a Southern blot.
12. During a sequencing reaction, the researcher adds all the required components to the reaction, but
accidentally adds only one of the four dideoxynucleotides, the ddC. What kinds of products will be
observed after this reaction is complete?
a.
All fragments will end in A.
b.
All fragments will end in C.
c.
All fragments will end in G.
d.
All fragments will end in T.
e.
No fragments will be made.
13. During annotation, which of the following are not identified?
a.
Protein coding genes.
b.
Noncoding RNA genes.
c.
Origins of replication.
d.
Pseudogenes.
e.
Protein interactions.
14. Which of the following organisms has the largest number of protein-coding genes?
a.
E. coli (bacteria)
b.
Saccharomyces cerevisiae (yeast)
c.
Homo sapiens (human)
d.
Oryza sativa (rice)
e.
Drosophila melanogaster (fruit fly)
15. How can microarrays help us understand cellular functions?
a.
Microarrays let us study different cells under different conditions.
b.
Microarrays let us directly measure protein expression in individual cells.
c.
Microarrays, by hybridizing cDNAs to DNA sequences already present on a chip, let us
identify which portions of a genome were being expressed in a cell at a particular time.
d.
Microarrays let us identify which DNA sequences are present in a particular cell type
under certain conditions.
e.
Microarrays, by hybridizing DNA to cDNA sequences already present on a chip, let us
identify which portions of a genome were being expressed in a cell at a particular time.
16. In the microarray shown in your book, the cDNAs were labeled with red and green fluorescent tags.
How then do you end up with spots on the microarray emitting yellow light?
a.
In light, red and green are two of the primary colors, and the combination of the two will
produce yellow light.
b.
The yellow light comes from the laser, and a yellow spot indicates that neither cDNA
hybridized to that spot on the microarray.
c.
The over expression of one cDNA relative to the other will skew the color pattern of the
spot on the microarray. This result in the yellow color.
d.
The color choice was an arbitrary decision by the artist and doesn’t reflect how the process
actually works.
e.
Yellow spots are those that contain no DNA probes on the chip.
17.
A portion of a microarray is shown above in which expression of genes on human chromosome 21
was examined in either brain cells from a normal individual (cDNAs labeled with a white fluor) or
brain cells from someone with a disorder (cDNAs labeled with a black fluor).
Which genes are over-expressed in the abnormal cells compared to the normal cells?
a.
A2, B1, B3, and C4
b.
B2 and C1
c.
A1, A3, A4, B4, C2, and C3
d.
A1, A2, B2, and C1
e.
A2, C2, and C4
18. All of the following are ways to determine the function of annotated genes except
a.
looking for similar gene sequences of known function
b.
examining the putative protein structure
c.
gene knockout experiments
d.
gene knockdown experiments
e.
finding a pseudogene for that gene
19. DNA microarrays are used when studying the
a.
genome
b.
transcriptome
c.
proteome
d.
interactome
e.
ribosome
20. During a microarray analysis, cDNAs made from normal cells are stained with a green fluor and
cDNAs from abnormal cells are stained with a red fluor. Which of the following statements is true
about the results of this experiment?
a.
Red spots indicate genes that are underexpressed in abnormal cells.
b.
Red spots indicate genes that are not expressed in abnormal cells.
c.
Red spots indicate genes that are overexpressed in abnormal cells.
d.
Red spots indicate genes that are overexpressed in normal cells.
e.
Red spots indicate pseudogenes.
21. Proteomics involves all of the following except
a.
determining protein structure.
b.
determining protein function.
c.
determining protein location.
d.
determining protein sequence.
e.
determining protein interactions.
22. New genes can evolve from all of the following except
a.
gene duplication from unequal crossing over.
b.
gene duplication from replicating transposable elements.
c.
gene duplication from crossing over.
d.
exon shuffling.
e.
combining parts of two or more genes.
23. Multigene families
a.
come from a single gene duplication event.
b.
come from repeated cycles of gene duplication followed by mutation.
c.
from single point mutations.
d.
come from exon shuffling.
e.
come from deletions of genes.
24. Which of the following is NOT an example of a CURRENT use of bioinformatics?
a.
locating individual genes in a genomic sequence
b.
aligning sequences in databases to determine similarities between organisms
c.
predicting the structure and function of gene products
d.
identifying possible evolutionary relationships between organisms
e.
determining the final protein structure of novel proteins based on just the nucleotide
sequence
25. Pharmacogenomics
a.
seeks to customize drugs to the cellular proteomes of a patient.
b.
might target specific disease mechanisms and thus minimize side effects.
c.
would account for an individual’s metabolism.
d.
would require a person’s genetic profile to be determined and subsequently stored in some
database.
e.
all of the above
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26. What does pharmacogenomics determine about a patient to help with dosage of drugs such as
warfarin?
a.
warfarin metabolism genes
b.
body size
c.
other diseases the patient may have
d.
medications the patient is taking
e.
patient age
MATCHING
Match each of the following terms with its correct definition.
a.
A protein that can be produced by a cell.
b.
All transcripts that are produced by a cell.
c.
The study of all of the proteins produced from an organism’s genome.
d.
Study of genome sequences for several organisms.
e.
The study of the whole genome of an organism.
f.
Using computer programs to extract biological information from sequence data.
g.
The study of all transcripts produced from an organism’s genome.
27. transcriptome
28. transcriptomics
29. genomics
30. proteome
31. comparative genomics
32. proteomics
33. bioinformatics
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Classification
Use the techniques listed below for the following question(s).
a.
Whole Genome Shotgun Sequencing
b.
Illumina/Solexa Sequencing
c.
Sanger sequencing
d.
DNA microarray analysis
e.
Gene knockout
f.
Gene knockdown
34. Used to replace a normal gene with a defective one to see the effect.
35. Used to determine the entire genome sequence of an organism by sequencing DNA fragments and then
assembling them using computer software.
36. Used to determine DNA sequence in an automated way.
37. Used to determine DNA sequence using dideoxynucleotides.
38. Used to compare the gene expression patterns of identical cells under different conditions.
39. Used to decrease a gene’s expression to see the effect.
Choice
For each of the following statements, choose the most appropriate macromolecule being studied or
manipulated from the list below.
a.
DNA
b.
mRNA/cDNA
c.
protein
40. Southern Blotting
41. PCR
42. Sequencing
43. Microarray
44. Genomics
45. Cellular proteomics
46. Shotgun library
47. Proteomics
48. Sanger method
SHORT ANSWER
49. What are the relationships among the following types of organisms with respect to genome size:
viruses, bacteria, archaea, and eukaryotes.
50. List at least three differences in how the E. coli and human genomes are arranged.
51. What is the difference between a gene knockout and a gene knockdown?
52. What is the main difference among the studies of genomics, transcriptomics, and proteomics?
53. How do gene duplication and exon shuffling lead to new genes?
ESSAY
54. Explain how proteomics is considered by some to be even more important than genome sequencing.
55. There are three types of sequencing described in the text: Sanger (dideoxy) sequencing, whole-genome
shotgun sequencing, and Illumin/Solexa sequencing. Which one(s) would be best to use for sequencing
a single gene versus an entire genome and why?
56. Comparative genomics is done to learn how genes and genomes have evolved. What are three different
concepts that we have learned from comparative genomics?