1) Viral envelopes can best be analyzed with which of the following techniques?
A) use of 15N to label specific nucleotides
B) antibodies against specific proteins not found in the host membranes
C) DNA staining and visualization with the light microscope
D) use of plaque assays for quantitative measurement of viral titer
E) immunofluorescent tagging of capsid proteins

b

2) The host range of a virus is determined by
A) the enzymes carried by the virus.
B) whether its nucleic acid is DNA or RNA.
C) the proteins in the host's cytoplasm.
D) the enzymes produced by the virus before it infects the cell.
E) the proteins on its surface and that of the host.

e

3) Which of the following accounts for someone who has had a herpesvirus-mediated cold sore
or genital sore getting flare-ups for the rest of his or her life?
A) re-infection by a closely related herpesvirus of a different strain
B) re-infection by the same herpesvirus strain
C) co-infection with an unrelated virus that causes the same symptoms
D) copies of the herpesvirus genome permanently maintained in host nuclei
E) copies of the herpesvirus genome permanently maintained in host cell cytoplasm

d

4) In many ways, the regulation of the genes of a particular group of viruses will be similar to the
regulation of the host genes. Therefore, which of the following would you expect of the genes of
the bacteriophage?
A) regulation via acetylation of histones
B) positive control mechanisms rather than negative
C) control of more than one gene in an operon
D) reliance on transcription activators
E) utilization of eukaryotic polymerases

c

5) Which of the following is characteristic of the lytic cycle?
A) Many bacterial cells containing viral DNA are produced.
B) Viral DNA is incorporated into the host genome.
C) The viral genome replicates without destroying the host.
D) A large number of phages are released at a time.
E) The virus-host relationship usually lasts for generations.

d

6) Which of the following statements describes the lysogenic cycle of lambda (λ) phage?
A) After infection, the viral genes immediately turn the host cell into a lambda-producing
factory, and the host cell then lyses.
B) Most of the prophage genes are activated by the product of a particular prophage gene.
C) The phage genome replicates along with the host genome.
D) Certain environmental triggers can cause the phage to exit the host genome, switching from
the lytic to the lysogenic.
E) The phage DNA is incorporated by crossing over into any nonspecific site on the host cell's
DNA.

c

7) Most molecular biologists think that viruses originated from fragments of cellular nucleic
acid. Which of the following observations supports this theory?
A) Viruses contain either DNA or RNA.
B) Viruses are enclosed in protein capsids rather than plasma membranes.
C) Viruses can reproduce only inside host cells.
D) Viruses can infect both prokaryotic and eukaryotic cells.
E) Viral genomes are usually similar to the genome of the host cell.

e

8) A researcher lyses a cell that contains nucleic acid molecules and capsomeres of tobacco
mosaic virus (TMV). The cell contents are left in a covered test tube overnight. The next day this
mixture is sprayed on tobacco plants. Which of the following would be expected to occur?
A) The plants would develop some but not all of the symptoms of the TMV infection.
B) The plants would develop symptoms typically produced by viroids.
C) The plants would develop the typical symptoms of TMV infection.
D) The plants would not show any disease symptoms.
E) The plants would become infected, but the sap from these plants would be unable to infect
other plants.

c

9) Which viruses have single-stranded RNA that acts as a template for DNA synthesis?
A) lytic phages
B) proviruses
C) viroids
D) bacteriophages
E) retroviruses

e

10) What is the function of reverse transcriptase in retroviruses?
A) It hydrolyzes the host cell's DNA.
B) It uses viral RNA as a template for DNA synthesis.
C) It converts host cell RNA into viral DNA.
D) It translates viral RNA into proteins.
E) It uses viral RNA as a template for making complementary RNA strands.

b

11) Why do RNA viruses appear to have higher rates of mutation?
A) RNA nucleotides are more unstable than DNA nucleotides.
B) Replication of their genomes does not involve proofreading.
C) RNA viruses replicate faster.
D) RNA viruses can incorporate a variety of nonstandard bases.
E) RNA viruses are more sensitive to mutagens.

b

12) Which of the following can be effective in preventing the onset of viral infection in humans?
A) taking vitamins
B) getting vaccinated
C) taking antibiotics
D) applying antiseptics
E) taking nucleoside analogs that inhibit transcription

b

13) Which of the following describes plant virus infections?
A) They can be controlled by the use of antibiotics.
B) They are spread via the plasmodesmata.
C) They have little effect on plant growth.
D) They are seldom spread by insects.
E) They can never be passed vertically.

b

14) The difference between vertical and horizontal transmission of plant viruses is that
A) vertical transmission is transmission of a virus from a parent plant to its progeny, and
horizontal transmission is one plant spreading the virus to another plant.
B) vertical transmission is the spread of viruses from the upper leaves to the lower leaves of the
plant, and horizontal transmission is the spread of a virus among leaves at the same general level.
C) vertical transmission is the spread of viruses from trees and tall plants to bushes and other
smaller plants, and horizontal transmission is the spread of viruses among plants of similar size.
D) vertical transmission is the transfer of DNA from one type of plant virus to another, and
horizontal transmission is the exchange of DNA between two plant viruses of the same type.
E) vertical transmission is the transfer of DNA from a plant of one species to a plant of a
different species, and horizontal transmission is the spread of viruses among plants of the same
species.

a

15) Which of the following is the best predictor of how much damage a virus causes?
A) ability of the infected cell to undergo normal cell division
B) ability of the infected cell to carry on translation
C) whether the infected cell produces viral protein
D) whether the viral mRNA can be transcribed
E) how much toxin the virus produces

a

16) Antiviral drugs that have become useful are usually associated with which of the following
properties?
A) ability to remove all viruses from the infected host
B) interference with viral replication
C) prevention of the host from becoming infected
D) removal of viral proteins
E) removal of viral mRNAs

b

17) Which of the following series best reflects what we know about how the flu virus moves
between species?
A) An avian flu virus undergoes several mutations and rearrangements such that it is able to be
transmitted to other birds and then to humans.
B) The flu virus in a pig is mutated and replicated in alternate arrangements so that humans who
eat the pig products can be infected.
C) A flu virus from a human epidemic or pandemic infects birds; the birds replicate the virus
differently and then pass it back to humans.
D) An influenza virus gains new sequences of DNA from another virus, such as a herpesvirus;
this enables it to be transmitted to a human host.
E) An animal such as a pig is infected with more than one virus, genetic recombination occurs,
the new virus mutates and is passed to a new species such as a bird, and the virus mutates and
can be transmitted to humans.

e

18) Which of the following is the most probable fate of a newly emerging virus that causes high
mortality in its host?
A) It is able to spread to a large number of new hosts quickly because the new hosts have no
immunological memory of them.
B) The new virus replicates quickly and undergoes rapid adaptation to a series of divergent hosts.
C) A change in environmental conditions such as weather patterns quickly forces the new virus
to invade new areas.
D) Sporadic outbreaks will be followed almost immediately by a widespread pandemic.
E) The newly emerging virus will die out rather quickly or will mutate to be far less lethal.

e

1) Which of the three types of viruses shown in Figure 17.1 would you expect to include
glycoproteins?
A) I only
B) II only
C) III only
D) I and II only
E) all three

d

2) Which of the three types of viruses shown in Figure 17.1 would you expect to include a
capsid(s)?
A) I only
B) II only
C) III only
D) I and II only
E) all three

e

3) In Figure 17.2, at the arrow marked II, what enzyme(s) are being utilized?
A) reverse transcriptase
B) viral DNA polymerase
C) host cell DNA polymerase
D) host cell RNA polymerase
E) host cell DNA and RNA polymerases

c

4) In Figure 17.2, when new viruses are being assembled (IV), what mediates the assembly?
A) host cell chaperones
B) assembly proteins coded for by the host nucleus
C) assembly proteins coded for by the viral genes
D) viral RNA intermediates
E) nothing; they self-assemble

e

5) Based on Table 17.1, which virus meets the Baltimore requirements for a retrovirus?
A) A
B) B
C) C
D) D
E) E

d

6) Based on Table 17.1, which virus meets the requirements for a bacteriophage?
A) A
B) B
C) C
D) D
E) E

a

Some viruses can be crystallized and their structures analyzed. One such virus is yellow mottle
virus, which infects beans. This virus has a single-stranded RNA genome containing about 6,300
nucleotides. Its capsid is 25-30 nm in diameter and contains 180 identical capsomeres.
1) If the yellow mottle virus capsid has 20 facets, how many proteins form each facet?
A) 1
B) 5
C) 9
D) 20
E) 180

c

You isolate an infectious substance that is capable of causing disease in plants, but you do not
know whether the infectious agent is a bacterium, virus, viroid, or prion. You have four methods
at your disposal that you can use to analyze the substance in order to determine the nature of the
infectious agent.
I. treating the substance with nucleases that destroy all nucleic acids
and then determining whether it is still infectious
II. filtering the substance to remove all elements smaller than what can
be easily seen under a light microscope
III. culturing the substance by itself on nutritive medium, away from
any plant cells
IV. treating the sample with proteases that digest all proteins and then
determining whether it is still infectious
2) If you already knew that the infectious agent was either bacterial or viral, which treatment
would allow you to distinguish between these two possibilities?
A) I
B) II
C) III
D) IV
E) either II or IV

c

3) If you already knew that the infectious agent was either a viroid or a prion, which treatment
would allow you to distinguish between these two possibilities?
A) I only
B) II only
C) III only
D) IV only
E) either I or IV

e

The herpesviruses are very important enveloped DNA viruses that cause disease in all vertebrate
species and in some invertebrates such as oysters. Some of the human ones are herpes simplex
virus (HSV) types I and II, causing facial and genital lesions, and the varicella zoster virus
(VSV), causing chicken pox and shingles. Each of these three actively infects nervous tissue.
Primary infections are fairly mild, but the virus is not then cleared from the host; rather, viral
genomes are maintained in cells in a latent phase. The virus can then reactivate, replicate again,
and be infectious to others.
4) If scientists are trying to use what they know about HSV to devise a means of protecting other
people from being infected, which of the following would have the best chance of lowering the
number of new cases of infection?
A) vaccination of all persons with preexisting cases
B) interference with new viral replication in preexisting cases
C) treatment of the HSV lesions to shorten the breakout
D) medication that destroys surface HSV before it gets to neurons
E) education about avoiding sources of infection

b

5) In electron micrographs of HSV infection, it can be seen that the intact virus initially reacts
with cell-surface proteoglycans, then with specific receptors. This is later followed by viral
capsids docking with nuclear pores. Afterward, the capsids go from being full to being "empty."
Which of the following best fits these observations?
A) Viral capsids are needed for the cell to become infected; only the capsids enter the nucleus.
B) The viral envelope is not required for infectivity, since the envelope does not enter the
nucleus.
C) Only the genetic material of the virus is involved in the cell's infectivity, and is injected like
the genome of a phage.
D) The viral envelope mediates entry into the cell, the capsid enters into the nuclear membrane,
and the genome is all that enters the nucleus.
E) The viral capsid mediates entry into the cell, and only the genomic DNA enters the nucleus,
where it may or may not replicate.

d

6) In order to be able to remain latent in an infected live cell, HSV must be able to shut down
what process?
A) DNA replication
B) transcription of viral genes
C) apoptosis of a virally infected cell
D) all immune responses
E) interaction with histones

c

1) Which of the following characteristics, structures, or processes is common to both bacteria
and viruses?
A) metabolism
B) ribosomes
C) genetic material composed of nucleic acid
D) cell division
E) independent existence

c

2) Emerging viruses arise by
A) mutation of existing viruses.
B) the spread of existing viruses to new host species.
C) the spread of existing viruses more widely within their host species.
D) all of the above
E) none of the above

d

3) A human pandemic is
A) a viral disease that infects all humans.
B) a flu that kills more than 1 million people.
C) an epidemic that extends around the world.
D) a viral disease that can infect multiple species.
E) a virus that increases in mortality rate as it spreads.

c

4) A bacterium is infected with an experimentally constructed bacteriophage composed of the T2
phage protein coat and T4 phage DNA. The new phages produced will have
A) T2 protein and T4 DNA.
B) T2 protein and T2 DNA.
C) a mixture of the DNA and proteins of both phages.
D) T4 protein and T4 DNA.
E) T4 protein and T2 DNA.

d

5) RNA viruses require their own supply of certain enzymes because
A) host cells rapidly destroy the viruses.
B) host cells lack enzymes that can replicate the viral genome.
C) these enzymes translate viral mRNA into proteins.
D) these enzymes penetrate host cell membranes.
E) these enzymes cannot be made in host cells.

b

1) What is metagenomics?
A) genomics as applied to a species that most typifies the average phenotype of its genus
B) the sequence of one or two representative genes from several species
C) the sequencing of only the most highly conserved genes in a lineage
D) sequencing DNA from a group of species from the same ecosystem
E) genomics as applied to an entire phylum

d

2) Which procedure is not required when the shotgun approach to sequencing is modified as
sequencing by synthesis, in which many small fragments are sequenced simultaneously?
A) use of restriction enzymes
B) sequencing each fragment
C) cloning each fragment into a plasmid
D) ordering the sequences
E) PCR amplification

c

3) What is proteomics?
A) the linkage of each gene to a particular protein
B) the study of the full protein set encoded by a genome
C) the totality of the functional possibilities of a single protein
D) the study of how amino acids are ordered in a protein
E) the study of how a single gene activates many proteins

b

4) What is bioinformatics?
A) a technique using 3-D images of genes to predict how and when they will be expressed
B) the application of computational methods to the storage and analysis of biological data
C) software programs available from NIH to design and synthesize genes
D) a series of search programs that allow a student to identify which labs around the world are
trying to sequence the genome of a given species
E) a procedure that uses software to order DNA sequences in a variety of comparable ways

b

5) A microarray known as a GeneChip, with most of the human protein-coding genetic
sequences, has been developed to aid in the study of human cancer by first comparing two to
three subsets of cancer subtypes. What kind of information might be gleaned from this GeneChip
to aid in cancer prevention?
A) information about whether or not a patient has this type of cancer prior to treatment
B) evidence that might suggest how best to treat a person's cancer with chemotherapy
C) data that could alert patients to what kind of cancer they were likely to acquire
D) information about which parent might have provided a patient with cancer-causing genes
E) information on cancer epidemiology in the United States or elsewhere

c

6) Which of the following most correctly describes the whole-genome shotgun technique for
sequencing a genome?
A) genetic mapping followed immediately by sequencing
B) physical mapping followed immediately by sequencing
C) cloning large genome fragments into very large vectors such as YACs, followed by
sequencing
D) cloning fragments from many copies of an entire chromosome, sequencing the fragments, and
then ordering the sequences
E) cloning the whole genome directly, from one end to the other

d

7) Which of the following is a representation of gene density?
A) Humans have 2,900 Mb per genome.
B) C. elegans has ~20,000 genes.
C) Humans have ~20,000 genes in 2,900 Mb.
D) Humans have 27,000 bp in introns.
E) Fritillaria has a genome 40 times the size of a human genome.

c

8) Why might the cricket genome have 11 times as many base pairs as that of Drosophila
melanogaster?
A) The two insect species evolved in very different geologic eras.
B) Crickets have higher gene density.
C) Drosophila are more complex organisms.
D) Crickets must have more noncoding DNA.
E) Crickets must make many more proteins.

d

9) The comparison between the number of human genes and those of other animal species has
led to many conclusions, including that
A) the density of the human genome is far higher than in most other animals.
B) the number of proteins expressed by the human genome is far more than the number of its
genes.
C) most human DNA consists of genes for protein, tRNA, rRNA, and miRNA.
D) the genomes of other organisms are significantly smaller than the human genome.

b

10) What characteristic of short tandem repeat DNA makes it useful for DNA fingerprinting?
A) The number of repeats varies widely from person to person or animal to animal.
B) The sequence of DNA that is repeated varies significantly from individual to individual.
C) The sequence variation is acted upon differently by natural selection in different
environments.
D) Every racial and ethnic group has inherited different short tandem repeats.

a

11) In humans, the embryonic and fetal forms of hemoglobin have a higher affinity for oxygen
than that of adults. This is due to
A) nonidentical genes that produce different versions of globins during development.
B) identical genes that generate many copies of the ribosomes needed for fetal globin production.
C) pseudogenes, which interfere with gene expression in adults.
D) the attachment of methyl groups to cytosine following birth, which changes the type of
hemoglobin produced.
E) histone proteins changing shape during embryonic development.

a

12) A multigene family is composed of
A) multiple genes whose products must be coordinately expressed.
B) genes whose sequences are very similar and that probably arose by duplication.
C) the many tandem repeats such as those found in centromeres and telomeres.
D) a gene whose exons can be spliced in a number of different ways.
E) a highly conserved gene found in a number of different species.

b

13) Which of the following can be duplicated in a genome?
A) DNA sequences above a minimum size only
B) DNA sequences below a minimum size only
C) entire chromosomes only
D) entire sets of chromosomes only
E) sequences, chromosomes, or sets of chromosomes

e

14) Unequal crossing over during prophase I can result in one sister chromosome with a deletion
and another with a duplication. A mutated form of hemoglobin, so-called hemoglobin Lepore,
exists in the human population. Hemoglobin Lepore has a deleted series of amino acids. If this
mutated form was caused by unequal crossing over, what would be an expected consequence?
A) If it is still maintained in the human population, hemoglobin Lepore must be selected for in
evolution.
B) There should also be persons whose hemoglobin contains two copies of the series of amino
acids that is deleted in hemoglobin Lepore.
C) Each of the genes in the hemoglobin gene family must show the same deletion.
D) The deleted gene must have undergone exon shuffling.
E) The deleted region must be located in a different area of the individual's genome.

b

15) Humans have 23 pairs of chromosomes. In contrast, chimpanzees have 24 pairs of
chromosomes and lack any pair resembling the long human chromosome 2 pair; instead,
chimpanzees have two pairs of medium-sized chromosomes. What is the most likely explanation
for these differences in the human and chimpanzee genomes?
A) The common ancestor of humans and chimpanzees had 24 pairs of chromosomes, and at
some point in the human lineage, two chromosomes fused end to end, providing some selective
advantage.
B) The common ancestor of humans and chimpanzees had 23 pairs of chromosomes, but when
chimpanzees evolved, one of the chromosomes broke in half.
C) At some point in evolution, human ancestors and chimpanzee ancestors were able to mate and
produce fertile offspring, making a new species.
D) Chromosome breakage resulted in additional centromeres being made, allowing meiosis to
proceed successfully.
E) Transposable elements transferred significantly large segments of the chromosomes to new
locations.

a

16) When does exon shuffling occur?
A) during splicing of DNA
B) during DNA replication
C) during meiotic recombination
D) during post-translational modification of proteins
E) during faulty DNA repair

c

17) In order to determine the probable function of a particular sequence of DNA in humans, what
might be the most reasonable approach?
A) Prepare a knockout mouse without a copy of this sequence and examine the mouse
phenotype.
B) Genetically engineer a mouse with a copy of this sequence and examine its phenotype.
C) Look for a reasonably identical sequence in another species, prepare a knockout of this
sequence in that species, and look for the consequences.
D) Prepare a genetically engineered bacterial culture with the sequence inserted and assess which
new protein is synthesized.
E) Mate two individuals heterozygous for the normal and mutated sequences.

c

18) Homeotic genes contain a homeobox sequence that is highly conserved among very diverse
species. The homeobox is the code for that domain of a protein that binds to DNA in a regulatory
developmental process. Which of the following would you then expect?
A) that homeotic genes are selectively expressed over developmental time
B) that a homeobox-containing gene has to be a developmental regulator
C) that homeoboxes cannot be expressed in nonhomeotic genes
D) that all organisms must have homeotic genes
E) that all organisms must have homeobox-containing genes

a

19) A recent study compared the H. sapiens genome with that of Neanderthals. The results of the
study indicated that there was a mixing of the two genomes at some period in evolutionary
history. The data that suggested this were
A) some Neanderthal sequences not found in humans.
B) a number of modern H. sapiens with Neanderthal sequences.
C) Neanderthal Y chromosomes preserved in the modern population of males.
D) mitochondrial sequences common to both groups.

b

20) Fragments of DNA have been extracted from the remnants of extinct woolly mammoths,
amplified, and sequenced. These can now be used to
A) introduce into relatives, such as elephants, certain mammoth traits.
B) clone live woolly mammoths.
C) study the relationships among woolly mammoths and other wool-producers.
D) understand the evolutionary relationships among members of related taxa.
E) appreciate the reasons why mammoths went extinct.

d

The pie chart in Figure 18.1 represents the relative frequencies of the following in the human
genome:
I. repetitive DNA unrelated to transposons
II. repetitive DNA that includes transposons
III. unique noncoding DNA
IV. introns and regulatory sequences
V. exons
1) Which region is occupied by exons only (V)?
A) A
B) B
C) C
D) D
E) E

a

2) Which region includes Alu elements and LI sequences?
A) A
B) B
C) C
D) D
E) E

e

3) The movement of these blocks suggests that
A) during evolutionary time, these sequences have separated and have returned to their original
positions.
B) DNA sequences within these blocks have become increasingly divergent.
C) sequences represented have duplicated at least three times.
D) chromosomal translocations have moved blocks of sequences to other chromosomes.
E) higher mammals have more convergence of gene sequences related in function.

d

4) Which of the following represents another example of the same phenomenon as that shown in
Figure 18.2?
A) the apparent centric fusion between two chromosome pairs of primates such as chimps to
form the ancestor of human chromosome 2
B) the difference in the numbers of chromosomes in five species of one genus of birds
C) the formation of several pseudogenes in the globin gene family subsequent to human
divergence from other primates
D) the high frequency of polyploidy in many species of angiosperms

a

Multigene families include two or more nearly identical genes or genes sharing nearly identical
sequences. A classical example is the set of genes for globin molecules, including genes on
human chromosomes 11 and 16.
1) How might identical and obviously duplicated gene sequences have gotten from one
chromosome to another?
A) by normal meiotic recombination
B) by normal mitotic recombination between sister chromatids
C) by transcription followed by recombination
D) by chromosomal translocation
E) by deletion followed by insertion

d

2) Several of the different globin genes are expressed in humans, but at different times in
development. What mechanism could allow for this?
A) exon shuffling
B) intron activation
C) pseudogene activation
D) differential translation of mRNAs
E) differential gene regulation over time

e

1) Bioinformatics includes all of the following except
A) using computer programs to align DNA sequences.
B) analyzing protein interactions in a species.
C) using molecular biology to combine DNA from two different sources in a test tube.
D) developing computer-based tools for genome analysis.
E) using mathematical tools to make sense of biological systems.

c

2) One of the characteristics of retrotransposons is that
A) they code for an enzyme that synthesizes DNA using an RNA template.
B) they are found only in animal cells.
C) they generally move by a cut-and-paste mechanism.
D) they contribute a significant portion of the genetic variability seen within a population of
gametes.
E) their amplification is dependent on a retrovirus.

a

3) Homeotic genes
A) encode transcription factors that control the expression of genes responsible for specific
anatomical structures.
B) are found only in Drosophila and other arthropods.
C) are the only genes that contain the homeobox domain.
D) encode proteins that form anatomical structures in the fly.
E) are responsible for differentiation in muscle cells.

a

4) Two eukaryotic proteins have one domain in common but are otherwise very different. Which
of the following processes is most likely to have contributed to this similarity?
A) gene duplication
B) alternative splicing
C) exon shuffling
D) histone modification
E) random point mutations

c

5) Two eukaryotic proteins are identical except for one domain in each protein, and these two
domains are completely different from each other. Which of the following processes is most
likely to have contributed to this difference?
A) gene duplication
B) alternative splicing
C) exon shuffling
D) histone modification
E) random point mutations

b