Chapter 11

What does fully virulent mean?

That the only reproductive option of the virus is to assemble progeny virions while destroying a host cell.

Which of the following viruses contains a DNA genome? Select one: a. Polio virus b. Influenza virus c. Human immunodeficiency virus d. Herpes simplex virus

d. Herpes simplex virus FEEDBACK: Herpes simplex virus is a DNA virus. All the other viruses listed contain different kinds of RNA genomes. For more information, see Section 11.4.

The HIV drug azidothymidine (AZT) has what mechanism of action? Select one: a. It blocks the CD4 receptor. b. It is an integrase inhibitor. c. It is a protease inhibitor. d. It is a reverse transcriptase inhibitor.

d. It is a reverse transcriptase inhibitor. FEEDBACK: AZT is a nucleotide analog that inhibits reverse transcriptase. For more information, see Section 11.4.

Herpes simplex virus (HSV) encodes a proofreading endonuclease that works during viral replication. From this, what can we reasonably predict? Select one: a. HSV is a single-strand DNA virus. b. The host cell it infects does not code for an endonuclease. c. HSV cannot have a latent phase. d. The viral mutation rate is relatively low.

d. The viral mutation rate is relatively low. FEEDBACK: Proofreading activity implies a low mutation rate. The presence of a viral enzyme implies nothing about whether the host cell can have its own endonuclease. HSV is a double-stranded DNA virus that has a latent phase. For more information, see Section 11.5.

Explain the location of fusion peptides before membrane contact

Before membrane contact, the fusion peptides are buried within the core of the hemagglutinin trimer. The HA C-terminal domains each bind a sialic acid receptor in the host membrane.

What is the key advantage of a segmented genome?

It facilitates recombination between two strains coinfecting the same cell. Coinfection can generate an instant new strain that evades a host immune system.

What is lysogeny?

The integration of the virus genome into that of their host cell. The integrated genome then replicates passively with the host.

Which HIV open reading frame codes for enzymes? Select one: a. env b. gag c. pol d. All of the above

c. pol FEEDBACK: The pol open reading frame codes for three enzymes; integrase, RT, and protease. The gag sequence encodes capsid and nucleocapsid proteins and env encodes envelope proteins. For more information, see Section 11.4.

One reason it is difficult to develop a vaccine for AIDS is because Select one: a. we do not know the causative agent of AIDS. b. vaccines can only be developed for bacterial diseases. c. HIV has a DNA genome similar to our own. d. HIV has a high mutation rate.

d. HIV has a high mutation rate. FEEDBACK: Due to the high error rate of reverse transcriptase, HIV envelope proteins change frequently. This makes vaccine development difficult. For more information, see Section 11.4.

The 5' internal ribosome entry site (IRES) is present in the genome of Select one: a. phage T4. b. HIV. c. varicella-zoster virus. d. Hepatitis C virus (HCV).

d. Hepatitis C virus (HCV). FEEDBACK: IRES segment is present in the genome of HCV. It contains numerous stem loop structures and initiates translation in the host cell. For more information, see Section 11.2.

What are the steps of the replicative cycle of influenza A?

1. Influenza virion undergoes endocytosis 2. Releases virion content into host cytoplasm 3. Viral (-) RNA segments with their prepackaged primers and polymerases are released. Each MP-coated RNA segment individually passes through the nuclear pores into the nucleus 4. The prepackaged RNA-dependent RNA polymerase uses each (-) strand RNA segment to synthesize mRNA (or steos 8,9) 5. The mRNA synthesis is primed by a 5-methylguanine "capped" RNA fragment. The influenza polymerase has obtained the cap fragments from the previous host by cleaving them from host nuclear pre-mRNA (cap snatching). The (+) strand mRNA molecules return to the cytoplasm 6. Segments encoding envelope proteins attach attach to the ER for ultimate transport to the host cell membrane 7. The nucleocapsid RNA-packaging proteins (NP), as well as newly synthesized RNA-dependent RNA polymerase components, subsequently return to the nucleus 8. Back in the nucleus, the original (-) strand RNA segments now serve as templates for RNA synthesis primed not by capsnatching, but instead by one of the subunits of the nucleocapsid protein NP 9. The NP-primed (+) strand RNA then becomes coated with the newly made NP subunits imported from the cytoplasm. The NP coated (+) strand serves as a template to synthesize (-) strand RNA 10. Coat newly synthesized (-) strand RNA with NP 11.

Influenza is...

A (-) stranded RNA virus with a segmented genome of 8 segments. (-) strand means that they are noncoding strands. Each of the 8 segments needs to be copied into a complimentary (+) strand by viral RNA polymerase before it can be used for translating proteins.

HIV gene expression/ replication pt. 1

A host cells tRNA, also packaged in the virus provides the 3' hydroxyl group needed to prime polymerization. Reverse transcriptase uses viral RNA genome as a template to create a DNA copy. While building the DNA strand, RT degrades the RNA. The ssDNA is used as a template to make a second DNA strand. dsDNA enters nucleus and enters into a random position on host chromosome (now called a provirus).

What is required for viral infection?

A molecular "fit" between a viral component and one or more molecules of the host cell surface

Influenza gene expression

Acidity of lysosome interior causes protons to enter virus through an ion channel, where it disrupts protein protein interactions, causing matrix proteins to detach from proteins covering viral RNA genome, the beginning of uncoating process. Acidity also induces structural change of HA, inserting itself into vesicle membrane, stimulating membrane fusion. RNA genome into cytoplasm, completion of uncoating process. The 8 RNA segments are covering in NP and attached to several other proteins that make up the viral RNA polymerase. Enter nucleus through nuclear pores. The RNA strands are (-) strands. Each of the 8 segments needs to be copied into a complimentary (+) strand by viral RNA polymerase before it can be used for translating proteins. To make a mRNA for translation boy host ribosomes, the virus needs to end 5' cap at beginning of RNA transcript (acquired via "cap snatching" in which the viral RNA polymerase cuts off the cap from one of the host cells own RNA molecules, and uses the cap to start transcription of viral RNA). The RNA gets a polyA tail that ends in RNA stability. The new viral mRNA leaves the nucleus for the cytoplasm, where the host cells ribosomes translate the mRNA.

How does influenza attach and enter into a host cell?

An influenza virion attaches to a cell when its hemagglutinin envelope protein binds to a host cell receptor protein that contains polysaccharide terminating with sialic acid.

Influenza replication

Back in the nucleus, the newly made NP prime and stabilize viral RNA as they're being synthesized into full length (+) strands, this time, lacking a 5' cap and polyA tail. Newly made RNA polymerase enters the nucleus and participate in production of additional full length (-) strands, that will serve as RNA genome segments of new viruses. 10 different types of proteins are synthesized by 8 RNA segments, and new (-) strand RNA segments are produced. The RNA genome segments, complexed with RNA polymerase, NP, Matrix protein, and packaging protein, are exported from nucleus. Envelope protein made on ER, move by transport vesicles to Golgi and to PM. RNA protein complexes are then packaged into progeny viruses, as they bud from cell membrane.

How is Phage T4 DNA synthesized?

By rolling-circle replication: First, the linear DNA duplex of phage T4 circularizes within its host cell by recombination between the terminally redundant ends. The circularized duplex then replicates by the rolling-circle method, generating a linear concatemer in which multiple genomes are joined end to end. The concatemer serves as as template to synthesize the complementary strand. Out of the linear T4 DNA concatemer, the individual genomes are packaged into head coats.

During infection of (-) stranded RNA virus:

Each (-) strand must be transcribed to a (+) strand mRNA for eukaryotic translation.

HIV mechanism of infection

HIV attaches to host cell, with primary receptor being a surface protein called CD4 that is found on a subset of T cell. Binding CD4 involves part of the viruses envelope protein called SU (surface protein). Binding of SU to CD4 induces a conformational change, allowing the binding of a secondary receptor called CCR. Binding triggers transmembrane component, TM, to unfold and push its tip (fusion peptide) into host membrane. Viral envelope fuses with plasma membrane, releases viral core into cytoplasm. In the core are twin RNA genomes and associated viral enzymes including two copies of reverse transcriptase.

HIV drugs can and cannot

HIV drugs can block cell-to-cell infection but cannot eradicate the HIV latent reservoir

What cell does HIV infect?

HIV infects a key cell type of the immune system, CD4+ lymphocytes

HIV is...

HIV is a retrovirus, an RNA virus possessing reverse transcriptase, it has two copies of a (+) strand genome (although it cannot be used as an mRNA), which is coated in nucleocapsid protein. Classified as a lentivirus, meaning slow virus, due to the fact that it can hide out in the host genome.

Influenza mechanism of infection

Influenza contains a shell of matrix proteins, and phospholipid envelope, with several embedded proteins, including hemagglutinin, which plays an essential role in viral cell entry. The influenza virus binds to host cell receptor proteins that contains polysaccharides terminating with siliac acid. Sialic acid that is attached to galactose provides a recognition site for the virus HA protein (can be connected at different positions on galactose). The HA complex consists of a trimer of subunits. Each subunit includes a domain that passes through the viral envelope and a domain that binds to the silica acid receptor on the host cell. For an influenza virus to become infective, HA must be cleaved (by an enzyme released from epithelial lining of human respiratory tract). The cleavage frees one end of the segment called the fusion peptide, which is hydrophobic. The host cell takes up the virus by endocytosis. The endocytic vesicle fuses with a lysosome, and as a result, its interior acidifies. The lowered pH induces a conformational change, shifting the receptor binding region back and triggering the fusion peptide forward to penetrate the vesicle membrane. A number of trimeric HA molecules in the same region mediate fusion between viral and host membranes, expelling viral contents into host cytoplasm, where its ready to begin its replication cycle.

HIV gene expression/replication pt. 2

Integration into host genome is required for HIV DNA to be replicated along with host genome, also required for the production of visions, which begins when RNApolII from host cell transcribes integrated viral DNA. Just like host cell mRNA, HIV RNA acquires a 5' cap and 3' polyA tail. A diversity of full length and spliced RNAs are produced. Some full length RNAs will become the RNA genome of new virion. The other RNAs will also leave the nucleus for the cytoplasm, where they will be used for the translation of viral proteins. The differentially spliced RNAs allow for the translation of multiple reading frames. Viral envelope proteins are made on ribosomes that dock on the endoplasmic reticulum, the new proteins thread through the protein into the lumen, transport vesicles bring the proteins to the Golgi for glycosylation and packaging, before export to cell membrane.

Early genes

Phage genes that are expressed early in the infectious cycle. Early gene products include proteins needed to cleave host DNA.

HIV, Influenza virus, and Polio virus are all...

RNA viruses

What does reverse transcriptase do?

Reverse transcriptase can synthesize DNA from a DNA or RNA template.

Coronavirus mechanism of infection

The initial attachment to the host cell is initiated by interactions between the S protein and its receptor, uses ACE2 as receptor. Following receptor binding, the virus must next gain access to the host cell cytosol: This is accomplished by acid-dependent proteolytic cleavage of the S protein by TMPTTS2, followed by fusion of the viral and cellular membranes (fusion generally occurs within acidified endosomes). Genomes is released into the host cytoplasm.

Coronavirus gene expression

The next step in the coronavirus lifecycle is the translation of the replicase genome from the virion genomic RNA. The replicase gene encodes two large ORFs. In order to express both poly proteins, the virus utilizes a slippery sequence and an RNA pseudo knot that cause ribosomal frame shifting from the rep1a reading frame into the rep1b ORF. The polyproteins contain nsp's (nonstructural proteins) 1-11 and -16. Coronaviruses encode either two or three proteases that cleave. the replicase polyproteins. Many of the nsps assemble into the replicase-transcriptase complex to create an environment suitable for RNA synthesis, and ultimately are responsible for RNA replication and transcription of the sub-genomic RNAs.

Late genes

Those that are induced to produce the capsid and tail proteins that assemble on the membrane to make a mature phage.

Coronavirus replication

Viral RNA synthesis follows the translation and assembly of the viral replicase complexes. Viral RNA synthesis produces both genomic and sub-genomic RNAs, subgenomic RNAs serve as mRNAs for the structural and accessory genes which reside down-stream of the replicase poly proteins.

What is a quasispecies?

Viral quasispecies is a population of viruses with a large number of variant genomes.

HIV gene expression/replication pt. 3

When ribosomes translate full length RNA, the predominant protein made is called gag, at end of gag encounter stop codon, terminating translation. frameshift causes the ribosome to being reading a different reading frame, bypassing the stop codon, and producing a larger protein called gag pol. gag and gag-pol proteins are known as polyproteins, because later, each will be cleaved to yield a number of distinct proteins. Gag consists of core structural proteins, needed for production of new visions. Gag-pol contains core structural proteins, as well as protease, reverse transcriptase, and integrase. The polyproteins, along with other viral proteins, twin RNA, and envelope proteins come together at the plasma membrane, where a viral particle begins to bud off. At this stage, protease cuts itself out of the polyprotein and cleaves polyprotein at other sites to release core proteins and enzymes. Protease activity is required to generate infective visions with conical core structure.

What happens when the virion is taken up by endocytosis?

When the virion is take up by endocytosis, the endocytic vesical fuses with a lysosome and its interior acidifies. The lowered pH induces a conformational change shifting the C terminal ends back and the N-terminal fusion peptides outward to face the vesicle membrane. The peptides extend into the membrane, where they mediate fusion between viral and host membranes. The fusion process expels the content of the virion into the host cytoplasm, where the RNA segments become uncoated.

Herpes Simplex Virus(HSV) is...

a double-stranded DNA virus that has a latent phase

The phage T4 virion consists of:

a head containing its DNA genome and accessory proteins; a tail composed of an internal tube with a sheath; and tail fibers.

What is a retrovirus?

a retrovirus is an RNA virus that codes for the enzyme revere transcriptase, which uses the RNA as a template for DNA synthesis

The RNA chromosome of influenza is loosely contained by:

a shell of matrix proteins that enclose the core or capsid, supplementing its connection to the membrane envelope (which derives from the phospholipid membrane of the host cell, which incorporates viral proteins such as hemagglutinin, HA, and neuraminidase,NA).

A hemagglutinin complex consists of:

a trimer of subunits, each of which has an N-terminal fusion peptide. A fusion peptide is a portion of an envelope protein that changes conformation so as to facilitate envelope fusion with the host cell membrane.

Which is true of influenza virus entry into a cell? Select one: a. HA in the viral envelope contacts sialic acid containing proteins in the host membrane. b. Sialic acid containing proteins in the viral envelope contact HA in the host cell membrane. c. The viral envelope fuses with the host cell plasma membrane to allow the viral genome into the cell. d. Neuraminidase in the viral envelope contacts sialic acid-containing proteins on the host cell membranes.

a. HA in the viral envelope contacts sialic acid containing proteins in the host membrane. FEEDBACK: Hemagglutinin in the viral envelope initially makes contact with sialic acid-containing glycoproteins on the host cell membrane. The virus then undergoes endocytosis and lysosomal fusion. For more information, see Section 11.3.

Compared to bacteriophages, animal viruses usually have an easier time entering cells because Select one: a. animal cells lack a cell wall. b. animal viruses do not need to latch on to specific cell membrane proteins. c. animal cells are kept at a constant high temperature and the more fluid membrane better allows virus entry. d. animal cells have a greater degree of internal membrane complexity.

a. animal cells lack a cell wall. FEEDBACK: The cell wall of bacteria poses problems for phage entry. Animal cells lack a cell wall and thus may ease viral entry. Animal viruses still contact specific membrane proteins to enter. For more information, see Section 11.1.

The phage T4 infects Select one: a. certain E. coli strains. b. human intestinal cells. c. phage lambda. d. plant meristem tissues.

a. certain E. coli strains. FEEDBACK: T4 infects E. coli containing the porin OmpC in their outer membrane. For more information, see Section 11.1.

Which HIV open reading frame encodes the SU and TM spike proteins? Select one: a. env b. gag c. pol d. vpu

a. env FEEDBACK: The SU (surface) and TM (transmembrane) proteins form spike proteins that peg the envelope. They are encoded by the env open reading frame. For more information, see Section 11.4.

Herpes simplex virus (HSV) causes latent infection in the region of the Select one: a. neurons of the ganglia. b. respiratory tract. c. liver. d. urinary tract.

a. neurons of the ganglia. FEEDBACK: The primary infection caused by HSV is epithelial in nature. However, it is followed by latent infection within the neurons of the ganglia and in particular the common site of infection is the trigeminal ganglion. For more information, see Section 11.5.

In HIV, the vpu ORF codes for

an accessory membrane protein (antagonizes tetherin and contributes to HIV-1 induced CD4 receptor dowregulation)

Coronavirus is...

an enveloped, nonsegmented, positive-sense RNA virus, characterized by club-like spikes that project from their surface, an unusually large RNA genome, and a unique replication strategy. Belongs to the Nidovirales order (Nido meaning nest) due to the expression of downstream genes by synthesis of 3' nested subgenomic mRNAs.

The T4 phage genome contains about how many genes? Select one: a. 17 b. 170 c. 1,700 d. 11,700

b. 170 FEEDBACK: The 166 kilobase T4 genome specifies 170 genes, many of which encode metabolic enzymes that replace host cell functions. For more information, see Section 11.1.

Which of the following is one of the two proteins of tight junction to which Hepatitis C virus (HCV) binds? Select one: a. LDLR b. Claudin-1 c. CD81 d. SR-B1

b. Claudin-1 FEEDBACK: Claudin-1 and occludinare the two proteins that form a part of the tight junction to which HCV binds and enters into the host cell. For more information, see Section 11.2.

Which enzyme transcribes the integrated HIV genome? Select one: a. Host DNA polymerase b. Host RNA polymerase c. Reverse transcriptase d. Virally encoded RNA polymerase

b. Host RNA polymerase FEEDBACK: Transcription involves making an RNA copy from a DNA template. RNA polymerase catalyzes this reaction. HIV does not have its own RNA polymerase; it relies on the host polymerase. For more information, see Section 11.4.

The causative agent of acquired immune deficiency syndrome is Select one: a. herpes simplex virus. b. Human immunodeficiency virus (HIV). c. influenza virus. d. M13.

b. Human immunodeficiency virus (HIV). FEEDBACK: Human immunodeficiency virus (HIV) is the causative agent of AIDS. For more information, see Section 11.4.

Which of the following is true? Select one: a. Human immunodeficiency virus (HIV) has a DNA genome. b. Lentiviruses are a type of retrovirus. c. Reverse transcriptase catalyzes the formation of RNA from DNA. d. HIV can be acquired by shaking hands with an HIV-positive individual.

b. Lentiviruses are a type of retrovirus. FEEDBACK: Lentiviruses (such as HIV) are a type of retrovirus, a virus with a single-stranded RNA genome that uses reverse transcriptase to form a double-stranded DNA.For more information, see Section 11.4.

What causes influenza virus hemagglutinin to undergo a structural change that mediates viral envelope fusion with host membranes and viral uncoating? Select one: a. Low pH inside the host cell nucleus b. Low pH inside lysosomes c. High pH inside the endoplasmic reticulum d. High pH inside the nucleus

b. Low pH inside lysosomes FEEDBACK: When hemagglutinin is exposed to the low pH inside the lysosome, it triggers conformational changes that allow a fusion peptide to penetrate the lysosomal membrane. This leads to viral uncoating and the release of the viral genome into the cytoplasm. For more information, see Section 11.3

Retroelements are Select one: a. ancient DNA sequences. b. decaying retroviral genomes in a host genome. c. periodic table elements discovered prior to 1950. d. retroviral-encoded mRNAs.

b. decaying retroviral genomes in a host genome. FEEDBACK: Retroelements are decaying retroviral genomes in a host genome. For more information, see Section 11.4.

Temperature-sensitive mutations Select one: a. display a mutant phenotype at all temperatures. b. display a mutant phenotype at one temperature but not another. c. are due to premature stop codons leading to truncated proteins. d. can only be obtained in eukaryotic organisms.

b. display a mutant phenotype at one temperature but not another. FEEDBACK: Temperature-sensitive mutations are conditional mutations, displaying the mutant phenotype under one environmental condition but not another. Premature stop codons will likely lead to defective proteins regardless of the temperature and temperature-sensitive mutations can be obtained in prokaryotes and viruses. For more information, see Section 11.1.

Which of the following is an enzymatic activity of reverse transcriptase? Select one: a. RNA synthesis from a DNA template b. RNA synthesis from an RNA template c. DNA synthesis from a DNA template d. RNA synthesis from a protein template

c. DNA synthesis from a DNA template FEEDBACK: RT can synthesize DNA from a DNA or an RNA template. For more information, see Section 11.4.

Which among the following viruses is the leading cause of mortality in outdoor cats in the United States? Select one: a. Hepatitis C virus (HCV) b. HIV c. Feline leukemia virus FEEDBACK: Feline leukemia virus is a major veterinary pathogen that is responsible for killing outdoor cats in the United States. Despite the availability of vaccine, it remains the number one killer. For more information, see Section 11.4. d. Herpes simplex virus

c. Feline leukemia virus FEEDBACK: Feline leukemia virus is a major veterinary pathogen that is responsible for killing outdoor cats in the United States. Despite the availability of vaccine, it remains the number one killer. For more information, see Section 11.4.

Which of the following statements correctly identifies some differences between H5N1 avian influenza and human influenza A? Select one: a. Only human influenza A recognizes sialic acid-modified galactose found on human respiratory cells. H5N1 does not recognize any human carbohydrates. b. Both human influenza A and H5N1 avian influenza recognize and bind to the same carbohydrates on human respiratory cells. c. Human influenza A recognizes carbohydrates found in the upper respiratory tract, whereas H5N1 avian influenza only binds carbohydrates deep in the lungs. d. Human influenza A relies on hemagglutinin for carbohydrate binding, whereas H5N1 avian influenza relies on a different viral envelope protein for host cell recognition.

c. Human influenza A recognizes carbohydrates found in the upper respiratory tract, whereas H5N1 avian influenza only binds carbohydrates deep in the lungs. FEEDBACK: Human influenza A and H5N1 avian influenza recognize different sialic acid-linked carbohydrates. The carbohydrates recognized by human influenza A are found in the upper respiratory tract, whereas those recognized by H5N1 avian influenza are found deep in the respiratory tract. For more information, see Section 11.3.

What would happen to an HIV virion that did not include reverse transcriptase due to a packaging error? Select one: a. It would probably be able to enter cells and complete its normal life cycle, eventually budding out to infect new cells b. It would be probably able to enter cells and replicate, but would not be able to bud out and infect new cells c. It would probably be able to enter cells, but would not replicate its genome. d. It would probably not be able to enter cells

c. It would probably be able to enter cells, but would not replicate its genome. FEEDBACK: Without reverse transcriptase (RT), the virus has no way to produce the double-stranded DNA needed for viral replication. If the HIV envelope glycoproteins are intact, it can enter new cells. RT is not needed for HIV fusion with host cells. For more information, see Section 11.4.

Hepatitis C virus (HCV) is primarily acquired through Select one: a. contaminated water. b. contaminated food. c. blood transfusion. d. a mosquito bite.

c. blood transfusion. FEEDBACK: HCV is known to cause liver cancer and cirrhosis and it is mainly transmitted by means of blood transfusions and injectable drug usage. For more information, see Section 11.2.

A segmented viral genome... a. fragments into nucleotides after infection. b. can only occur in viruses with DNA genomes. c. can facilitate rapid evolution of new viral strains. d. None of the above

c. can facilitate rapid evolution of new viral strains. FEEDBACK: Since segmented genomes are composed of multiple nucleic acids strands, coinfection with two viral strains can lead to swapping of segments, which may speed up evolution. For more information, see Section 11.3.

Viruses that are effective gene therapy vectors should Select one: a. promote an immune response in the patient. b. integrate the good copy of the gene near an oncogene. c. have virulence genes removed. d. transmit the transgene to the germ line.

c. have virulence genes removed. FEEDBACK: Viruses that are effective gene therapy vectors should have virulence genes removed to avoid patient illness. Promotion of an immune response, integration near an oncogene, and transmission to the germ line should all be avoided. For more information, see Section 11.6.

Phage T4 protects its genome from cleavage by host restriction endonucleases by Select one: a. methylating uracil nucleotides in its own genome. b. acetylating adenines in the host cell genome. c. modification of cytosines, via hydroxymethylation, in its own genome. d. pumping the restriction enzymes outside the host cell.

c. modification of cytosines, via hydroxymethylation, in its own genome. FEEDBACK: A viral enzyme replaces cytosines throughout the phage chromosome with the modified base 5-hydroxymethylcytosine. Restriction endonucleases will not recognize the modified cytosine bases. For more information, see Section 11.1.

In HIV the gag ORF codes for:

capsid and nucleocapsid proteins

Which of the following enzymes is a potential anti-HIV drug target? Select one: a. Integrase b. Protease c. Reverse transcriptase d. All of the above

d. All of the above FEEDBACK: All three HIV-encoded enzymes are attractive drug targets. For more information, see Section 11.4.

Which of the steps listed is the earliest in the replicative cycle of phage T4? Select one: a. Heads are assembled onto tails b. A phage-encoded lysozyme lyses the host cell c. Late genes are expressed to make head and tail components d. Phage DNA undergoes rolling-circle replication

d. Phage DNA undergoes rolling-circle replication FEEDBACK: Of the steps listed, phage replication comes first. After this, late genes are expressed to make head and tail components, genomes are packaged into heads, and heads are assembled onto tails. Lysis of the cell and release of new viral particles is the last step. For more information, see Section 11.1.

The following HIV encoded enzymes work in which temporal sequence during an HIV infection? Select one: a. Integrase, reverse transcriptase, protease b. Protease, reverse transcriptase, integrase c. Reverse transcriptase, protease, integrase d. Reverse transcriptase, integrase, protease

d. Reverse transcriptase, integrase, protease FEEDBACK: A DNA copy of the viral genome is first produced by reverse transcriptase, then integrase inserts the viral genome into the host cell DNA. Finally, viral proteins can be produced and cleaved by protease. For more information, see Section 11.4.

Which HIV envelope protein is necessary for host cell entry? Select one: a. CD4 b. CCR5 c. RT d. SU

d. SU FEEDBACK: SU is an envelope protein that initially makes contact with the host cell CD4 protein. For more information, see Section 11.4.

Which of the following statements is correct? Select one: a. The influenza envelope proteins are initially synthesized in the nucleus for eventual transport to the cell membrane. b. The influenza envelope proteins are initially synthesized in the endoplasmic reticulum for eventual transport to the nucleus. c. The influenza envelope proteins are initially synthesized in the cytoplasm for eventual transport to the endoplasmic reticulum. d. The influenza envelope proteins are initially synthesized in the endoplasmic reticulum for eventual transport to the cell membrane.

d. The influenza envelope proteins are initially synthesized in the endoplasmic reticulum for eventual transport to the cell membrane. FEEDBACK: The influenza envelope proteins ultimately need to be transported to the cell membrane. In eukaryotic cells, cell membrane-bound proteins pass through the endomembrane system consisting of the endoplasmic reticulum (ER) and Golgi. For more information, see Section 11.3.

The three-dimensional structure of the polyhedral T4 phage was determined in part by Select one: a. restriction enzyme analysis. b. polymerase chain reaction (PCR). c. two-dimensional protein gel electrophoresis. d. X-ray analysis.

d. X-ray analysis. FEEDBACK: X-ray crystallography can be used to determine structures. Restriction enzymes cut specific DNA sequences, PCR is used to amplify specific DNA sequences, and two-dimensional gel electrophoresis is used to separate proteins. For more information, see Section 11.1.

The envelope proteins E1 and E2 of Hepatitis C virus (HCV) form dimers, which are Select one: a. popcorn shaped. b. star shaped. c. spherical shaped. d. club shaped

d. club shaped. FEEDBACK: E1 and E2 are the main envelope proteins that make up the virion. They form a club-shaped dimer structure on the outer surface of the envelope. For more information, see Section 11.2.

The matrix shell of influenza contains:

eight RNA segments, which are noncoding (-) strands. The RNA segments are coated with nucleocapsid proteins, NP. Each NP coated RNA segment also possesses a bound RNA-dependent RNA polymerase complex.

Herpes simplex virus (HSV) infects which of the following cell types? Select one: a. Endothelial cells b. Epithelial cells c. Muscle cells d. Ganglial neural cells e. Both a and c f. Both b and d g. All of the above

f. Both b and d FEEDBACK: HSV can infect epithelial cells and also ganglial neural cells. For more information, see Section 11.5.

In HIV the pol ORF codes for:

integrase, RT, and protease

How does the assembly mechanism of influenza package exactly eight segments, one of each?

it doesn't: the segments are packaged at random, resulting in a vast majority of defective particles.

A segmented genome of a virus consists of:

multiple separate nucleic acids (like the multiple chromosomes of a eukaryotic cell).

Influenza is a:

segmented (-) strand RNA virus

In HIV the env ORF codes for:

the envelope proteins SU (Surface) and TM (transmembrane)

What is a provirus?

the genetic material of a virus as incorporated into, and able to replicate with, the genome of a host cell.