Question 1

Which of the following questions is asked in functional genomics research?

Accepted Answer

A) What is the number of Drosophila genes? 
B) How does the GC content of human DNA vary across the genome? 
C) What is the pattern of gene expression during mouse development? 
D) How many introns exist in the human CFTR gene? 
E) How closely related are the visual pigment genes of mouse and human? 
A) What is the number of Drosophila genes? 
B) How does the GC content of human DNA vary across the genome? 
C) What is the pattern of gene expression during mouse development? 
D) How many introns exist in the human CFTR gene? 
E) How closely related are the visual pigment genes of mouse and human? C

Question 2

If alternative splicing did not occur,a prediction would be that

Accepted Answer

A) the human genome would contain many more genes. 
B) the yeast genome would contain many fewer genes. 
C) there would be little correlation between the complexity of organisms and genome size. 
D) there would be many fewer genes devoted to metabolism in Arabidopsis and yeast. 
E) there would be many fewer genes devoted to DNA replication and modification in humans. 
A) the human genome would contain many more genes. 
B) the yeast genome would contain many fewer genes. 
C) there would be little correlation between the complexity of organisms and genome size. 
D) there would be many fewer genes devoted to metabolism in Arabidopsis and yeast. 
E) there would be many fewer genes devoted to DNA replication and modification in humans. A

Question 3

Like DNA microarrays,Northern blots analyze the levels of mRNA.However,Northern blots are almost always prepared with a probe tagged with one label,whereas DNA microarrays almost always use two groups of probes,each one tagged with a different fluorescent label.What advantage is conferred by using two labels for the microarray probes?

Accepted Answer

A) The two labels increase the sensitivity of the microarray. 
B) The two labels allow the analysis of the expression of more genes. 
C) The two labels allow simultaneous assay of levels of DNA and RNA. 
D) The two labels allow comparison of gene expression between two samples. 
E) Probing the array with two labels is equivalent to doing two experiments at once. 
A) The two labels increase the sensitivity of the microarray. 
B) The two labels allow the analysis of the expression of more genes. 
C) The two labels allow simultaneous assay of levels of DNA and RNA. 
D) The two labels allow comparison of gene expression between two samples. 
E) Probing the array with two labels is equivalent to doing two experiments at once. D

Question 4

If practical applications arise from this or similar metagenomic studies,what might these be?

Accepted Answer

A) New genes with useful properties may be identified and ultimately put to use. 
B) New microbial species could be isolated from seawater. 
C) An increased knowledge of the diversity of marine ecosystems could lead to increased appreciation of diversity in all ecosystems. 
D) Species discovered in the Sargasso Sea may also be found to inhabit less-remote waters. 
A) New genes with useful properties may be identified and ultimately put to use. 
B) New microbial species could be isolated from seawater. 
C) An increased knowledge of the diversity of marine ecosystems could lead to increased appreciation of diversity in all ecosystems. 
D) Species discovered in the Sargasso Sea may also be found to inhabit less-remote waters.

Question 5

Figure 20.1  
-The figure above compares the proportion of genes devoted to various functions in a set of model organisms.Based on this figure,which one of the following statements is FALSE?

Accepted Answer

A) The function of roughly half of eukaryotic genes is unknown. 
B) Humans have the highest proportion of genes devoted to defense and immunity. 
C) The mustard plant and yeast have a small fraction of genes devoted to cell communication. 
D) A relatively small but similar proportion of genes are devoted to transcription and translation in all these organisms. 
E) Drosophila is unusual in having so few genes devoted to protein folding and degradation. 
A) The function of roughly half of eukaryotic genes is unknown. 
B) Humans have the highest proportion of genes devoted to defense and immunity. 
C) The mustard plant and yeast have a small fraction of genes devoted to cell communication. 
D) A relatively small but similar proportion of genes are devoted to transcription and translation in all these organisms. 
E) Drosophila is unusual in having so few genes devoted to protein folding and degradation.

Question 6

In comparing DNA sequences from two different eukaryotic organisms,which do you expect to vary the most?

Accepted Answer

A) sequences that code for exons 
B) sequences that code for introns 
C) sequences that code for a polypeptide 
D) sequences that regulate transcription 
E) sequences that code for micro-RNAs 
A) sequences that code for exons 
B) sequences that code for introns 
C) sequences that code for a polypeptide 
D) sequences that regulate transcription 
E) sequences that code for micro-RNAs

Question 7

Although transposable elements and simple tandem repeats (STRs)are both repetitive DNAs,they differ in that

Accepted Answer

A) STRs occur within exons;transposable elements occur within introns. 
B) STRs occur within introns;transposable elements occur within exons. 
C) the repeated unit in STRs is clustered one after another;transposable element repeats are scattered throughout the genome. 
D) the repeated unit in STRs is much larger than the repeated unit of transposable elements. 
E) variation in STR repeat number comes from STR movement in the genome;variation in transposable element repeat number comes from errors in DNA replication. 
A) STRs occur within exons;transposable elements occur within introns. 
B) STRs occur within introns;transposable elements occur within exons. 
C) the repeated unit in STRs is clustered one after another;transposable element repeats are scattered throughout the genome. 
D) the repeated unit in STRs is much larger than the repeated unit of transposable elements. 
E) variation in STR repeat number comes from STR movement in the genome;variation in transposable element repeat number comes from errors in DNA replication.

Question 8

One surprising discovery from the analysis of bacterial genomes is that

Accepted Answer

A) very few species contain plasmids. 
B) there is only one copy of each gene present within a bacterial genome. 
C) there are many genes of unknown function. 
D) bacterial genomes are always contained on a single circular chromosome. 
E) there is almost no difference between the genomes of diverse bacteria. 
A) very few species contain plasmids. 
B) there is only one copy of each gene present within a bacterial genome. 
C) there are many genes of unknown function. 
D) bacterial genomes are always contained on a single circular chromosome. 
E) there is almost no difference between the genomes of diverse bacteria.

Question 9

Sequencing eukaryotic genomes is more difficult than sequencing genomes of bacteria or archaea because of

Accepted Answer

A) the large size of eukaryotic genomes. 
B) the large amount of eukaryotic repetitive DNA. 
C) the high proportion of G-C base pairs in eukaryotic DNA. 
D) A and B only. 
E) all of the above. 
A) the large size of eukaryotic genomes. 
B) the large amount of eukaryotic repetitive DNA. 
C) the high proportion of G-C base pairs in eukaryotic DNA. 
D) A and B only. 
E) all of the above.

Question 10

As with many new endeavors,concerns have been raised by some that genomics will fundamentally change the way biological research is practiced.Examine the full reference for the Venter et al.paper and consider the way this work was done.Now think of some seminal works in the history of biology,for example,Darwin's On the Origin of Species and Watson and Crick's publication on DNA structure.What do you think the concern might be that has been voiced about genomics?

Accepted Answer

A) Genomics will offer deep insights too rapidly for the biological community to comprehend. 
B) Genomics is so based in technology that it cannot possibly reveal important knowledge of biology. 
C) Genomics makes biology a "big-team science" that will squeeze out innovative individuals or small groups of scientists who traditionally have provided our greatest insights. 
D) Genomics is really computer science,not biology,and therefore offers little for understanding life. 
A) Genomics will offer deep insights too rapidly for the biological community to comprehend. 
B) Genomics is so based in technology that it cannot possibly reveal important knowledge of biology. 
C) Genomics makes biology a "big-team science" that will squeeze out innovative individuals or small groups of scientists who traditionally have provided our greatest insights. 
D) Genomics is really computer science,not biology,and therefore offers little for understanding life.

Question 11

If one wished to test the hypothesis that humans and chimps differ due to differences in the expression of a large set of shared genes,the technique to use would be

Accepted Answer

A) Southern blotting. 
B) PCR. 
C) DNA sequencing. 
D) protein-protein interaction assays. 
E) DNA microarray analysis. 
A) Southern blotting. 
B) PCR. 
C) DNA sequencing. 
D) protein-protein interaction assays. 
E) DNA microarray analysis.

Question 12

When gene duplication occurs to its ultimate extent by doubling all genes in a genome,what has occurred?

Accepted Answer

A) pseudogene creation 
B) creation of a gene cluster 
C) creation of a polyploid 
D) creation of an aneuploid 
E) creation of a diploid 
A) pseudogene creation 
B) creation of a gene cluster 
C) creation of a polyploid 
D) creation of an aneuploid 
E) creation of a diploid

Question 13

The discipline that manages,analyzes,and interprets the vast amounts of sequence data generated from whole genome sequencing is

Accepted Answer

A) proteomics. 
B) functional genomics. 
C) evolutionary genomics. 
D) bioinformatics. 
A) proteomics. 
B) functional genomics. 
C) evolutionary genomics. 
D) bioinformatics.

Question 14

The goal of annotating a whole genome sequence is to

Accepted Answer

A) establish the nucleotide sequence. 
B) learn the number of nucleotides contained within the genome. 
C) identify genes and their positions within the genome. 
D) learn how gene products interact to produce phenotypes. 
A) establish the nucleotide sequence. 
B) learn the number of nucleotides contained within the genome. 
C) identify genes and their positions within the genome. 
D) learn how gene products interact to produce phenotypes.

Question 15

In establishing paternity by DNA fingerprinting,what proportion of microsatellite repeat alleles in a child come from the father?

Accepted Answer

A) none 
B) 1/4 
C) 1/2 
D) 3/4 
E) all 
A) none 
B) 1/4 
C) 1/2 
D) 3/4 
E) all

Question 16

What can proteomics reveal that genomics cannot?

Accepted Answer

A) The number of genes characteristic of a species. 
B) The patterns of alternative splicing. 
C) The set of proteins present within a cell or tissue type. 
D) The levels of mRNAs present in a particular cell type. 
E) The movement of transposable elements within the genome. 
A) The number of genes characteristic of a species. 
B) The patterns of alternative splicing. 
C) The set of proteins present within a cell or tissue type. 
D) The levels of mRNAs present in a particular cell type. 
E) The movement of transposable elements within the genome.

Question 17

Why are transposable elements considered to be selfish genes?

Accepted Answer

A) They produce products toxic to the host. 
B) They replicate outside of the chromosome. 
C) They replicate using the host's resources without direct benefit to the host. 
D) They spread rapidly throughout the genome. 
E) They produce products that prevent cooperation between cells. 
A) They produce products toxic to the host. 
B) They replicate outside of the chromosome. 
C) They replicate using the host's resources without direct benefit to the host. 
D) They spread rapidly throughout the genome. 
E) They produce products that prevent cooperation between cells.

Question 18

Table 20.1 The following table from the Venter et al. paper presents the numbers of different types of genes discovered in this study.
  
-How do you think putative genes were placed into the categories shown in the preceding table?

Accepted Answer

A) by searching for ORFs,especially those with translation start and stop sites 
B) by searching for matches,especially of the predicted gene products,with previously identified gene products of known function 
C) by expressing the cloned genes in E.coli and then running biochemical analyses of the products 
D) all of the above 
A) by searching for ORFs,especially those with translation start and stop sites 
B) by searching for matches,especially of the predicted gene products,with previously identified gene products of known function 
C) by expressing the cloned genes in E.coli and then running biochemical analyses of the products 
D) all of the above

Question 19

Imagine that your goal is to isolate mouse mutants that stabilize microsatellite repeat sequences (i.e.,lower the frequency at which their repeat number changes).Which of the following mutations would you predict to have this stabilizing effect?

Accepted Answer

A) a mutation that reduces the rate of transcription 
B) a mutation that reduces the rate of translation 
C) a mutation that increases the rate of DNA synthesis 
D) a mutation that reduces the occurrence of homologous recombination 
E) a mutation that inactivates reverse transcriptase and/or integrase 
A) a mutation that reduces the rate of transcription 
B) a mutation that reduces the rate of translation 
C) a mutation that increases the rate of DNA synthesis 
D) a mutation that reduces the occurrence of homologous recombination 
E) a mutation that inactivates reverse transcriptase and/or integrase

Question 20

Figure 20.2  
-In the microarray shown in the figure above,if you were searching for genes whose expression was inhibited by hormone treatment,you would search for sequences spotted on the array that showed ________ fluorescence.

Accepted Answer

A) no 
B) high levels of 
C) green 
D) red 
E) yellow 
A) no 
B) high levels of 
C) green 
D) red 
E) yellow

Exam 20: Genomics

Which of the following questions is asked in functional genomics research?

If alternative splicing did not occur,a prediction would be that

If practical applications arise from this or similar metagenomic studies,what might these be?

Figure 20.1 -The figure above compares the proportion of genes devoted to various functions in a set of model organisms.Based on this figure,which one of the following statements is FALSE?

In comparing DNA sequences from two different eukaryotic organisms,which do you expect to vary the most?

Although transposable elements and simple tandem repeats (STRs)are both repetitive DNAs,they differ in that

One surprising discovery from the analysis of bacterial genomes is that

Sequencing eukaryotic genomes is more difficult than sequencing genomes of bacteria or archaea because of

If one wished to test the hypothesis that humans and chimps differ due to differences in the expression of a large set of shared genes,the technique to use would be

When gene duplication occurs to its ultimate extent by doubling all genes in a genome,what has occurred?

The discipline that manages,analyzes,and interprets the vast amounts of sequence data generated from whole genome sequencing is

The goal of annotating a whole genome sequence is to

In establishing paternity by DNA fingerprinting,what proportion of microsatellite repeat alleles in a child come from the father?

What can proteomics reveal that genomics cannot?

Why are transposable elements considered to be selfish genes?

Table 20.1 The following table from the Venter et al. paper presents the numbers of different types of genes discovered in this study. -How do you think putative genes were placed into the categories shown in the preceding table?

Imagine that your goal is to isolate mouse mutants that stabilize microsatellite repeat sequences (i.e.,lower the frequency at which their repeat number changes).Which of the following mutations would you predict to have this stabilizing effect?

Figure 20.2 -In the microarray shown in the figure above,if you were searching for genes whose expression was inhibited by hormone treatment,you would search for sequences spotted on the array that showed ________ fluorescence.

Biology and the Tree of Life

Water and Carbon: the Chemical Basis of Life

Protein Structure and Function

Nucleic Acids and the Rna World

An Introduction to Carbohydrates

Lipids, membranes, and the First Cells

Inside the Cell

Cell-Cell Interactions

Cellular Respiration and Fermentation

Photosynthesis

The Cell Cycle

Meiosis

Mendel and the Gene

Dna and the Gene: Synthesis and Repair

How Genes Work

Transcription, RNA Processing, and Translation

Control of Gene Expression in Bacteria

Control of Gene Expression in Eukaryotes

Analyzing and Engineering Genes

Principles of Development

An Introduction to Animal Development

An Introduction to Plant Development

Evolution by Natural Selection

Evolutionary Processes

Speciation

Phylogenies and the History of Life

Bacteria and Archaea

Protists

Green Algae and Land Plants

Fungi

An Introduction to Animals

Protostome Animals

Deuterostome Animals

Viruses

Plant Form and Function

Water and Sugar Transport in Plants

Plant Nutrition

Plant Sensory Systems, signals, and Responses

Plant Reproduction

Animal Form and Function

Water and Electrolyte Balance in Animals

Animal Nutrition

Gas Exchange and Circulation

Electrical Signals in Animals

Animal Sensory Systems and Movement

Chemical Signals in Animals

Animal Reproduction

The Immune System in Animals

An Introduction to Ecology

Behavioural Ecology

Population Ecology

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Biodiversity and Conservation Biology

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