Chapter 13 Test Questions

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Chapter 13 Test Questions
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  1. Why do we hesitate to call viruses living?
    They are not cells and because their life cycle. They are obligate parasites that produce only within a cell and must use the host’s genetic machinerery to replicate and express their genomes. Some possess genes coding for their own DNA polymerase and RNA polymerase enzymes, but may depend on the host enzymes for genome replication and transcription. All make use of the host’s ribosomes and translation apparatus for synthesis of the polypeptides that make up the protein coats of their progeny.
  2. Explain bacteriophages.
    They are constructed of protein and nucleic acid. They form a coat, or capsid, within which the nucleic acid genome is contained. 

    Three basic bacteriophage types are icosahedral, filamentous, and head-to-tail bacteriophages. 

    They can have DNA or RNA, which can be ss or ds. Some can have segmentnted genomes, meaninng that theyir genes are carried by a number of different RNA molecules. 

    Bacteriphage genomes can be small, containing relatively few genes, or they can be organized in a very complex manner. These overlapping genes share nucleotide sequences but code for different gene products because the transcripts are translated from different start positions and in different reading frames.
  3. What is the lytic life cycle?
    First, during the first 22 minutes, it is the latent period. There is no change in the nmber of infected cells during the first 22 minutes. After 22 minutes, the number of infected cells starts to increases, showing that lysis is occurring, and that new bacteriophages are infecting others.

    The initial event is attachment of the bacteriophage to a receptor protein on the outside of the bacterium. Then comes the latent period, a period of frenzied activity within the cell in which DNA, RNA, and protein stops and transcription of the bacteriophage genome begins. Within five minutes, the bacterial DNA molecule has been broken down and the resulting mucleotides are being utilized in replication of the T4 genome. After 12 minutes, new bacteriophage capsid proteins start to appear and the first complete bacteriophage particles are assembled. At the end of the latent period, the cell bursts and the new bacteriophages are released.
  4. How is the lytic infection cycle regulated?
    It is regulated by expression of early and late genes. Genome replication precedes synthesis of capsid proteins. Similary, synthesis of lysozyme is delayed until the end. With most other bacteriophages, there are distinct phases of gene expression. There is a cascade system, meaning that the appearance in the cell of the translation products from one set of genes switches on transcription of the next set of genes

    With T4, the very first genes to be expressed are transcribed by the E.coli RNA polymerase from a few standard E. coli promoter sequences present on the bacteriophage genome. The very early gene products include proteins that modify the sigma subunit of the host RNA polymerase so it no longer recognizes E. coli promoters, thereby switching off host gene expression. Instead, the RNA polymerase now specifically transcribes a second set of bacteriophage genes, one which specifies a new sigma subunit, the sigma-55 subunit, which replaces the host’s sigma-70 version, so the RNA polymerase transcribes a third set of bacteriophage genes.
  5. Brief summary of integration of a prophage.
    It integrates by a site-specific mechanism, meaning that it integrates at the same position.
  6. What happens if the prophage is induced?
    If it is induced, the bacteriophage genome is excised from the host DNA and converted into a circular molecule. The genome then replicates by the rolling-circle mechanism. This produces a series of concatamers (linear genomes linked end to end) that are cleaved by an endonuclease at a recognition sequence called the cos site. The linear genomes that result are packaged into the bacteriophage particles, and these new bacteriophages are released from the cell. The genomes recircularize immediately after injection into a new host.
  7. How is lysogeny maintained?
    The first step in the lytic infection cycle is expression of the early lambda genes. These are transcribed from two promoters, pL and pR, located on either side of a regulatory gene called cI. During lysogeny, pL and pR are switched off because the cI gene product, which is a repressor protein, is bound to operators adjacent to these promoters. As a result, the early genes are not expressed and the bacteriophage cannot enter the lytic cycle.Lysogeny is maintained for numerous cell divisions because the cI gene is continuousuly expressed, albeit at a low level, so that the amount of cI repressor present in the cell is always enough to keep pL and pR switched off. This continued expression of cI occurs because the cI repressor not only blocks transcription from pL and pR, but also stimulates transcription from pM, the promoter for the cI gene. The dual role of the cI repressor is therefore the key to lysogeny.
  8. How does the bacteriophage decide whether to follow the lytic or the lysogenic cycle?
    This depends on the outcome of a race between the cI and cro proteins. When a lambda DNA molecule enters an E. coli cell, the host’s RNA polymerase enzymes attach to the various promoters on the molecule and start transcribing the lambda genes. Once the cI gene is expressed the cI repressor blocks expression of the early genes, preventing entry into the lytic cycle and enabling lysogeny to be established.

    But lysogeny is not always the outcome. This is because a second gene, cro, also codes for a repressor, but in this case one that prevents transcription of cI. Both the cI and cro genes are expressed immediately after the lambda DNA molecules enters the cell. If the cI repressor is syntheized more quickly than the Cro repressor, then early gene expression is blocked and lysogeny follows. Howver, if the Cro repressor wins the race, it blocks expression of the cI gene before enough cI repressor has been synthesized to switch the early genes off. As a result, the bacteriophage enters the lytic infection cycle. The decision of whether to synthesize cI or cro the fastest is influenced by products of other lambda genes, which assess the physiological state of the host cell.
  9. How is lysogeny ended?
    This requires inactivation of the cI repressor. It is maintained as long as the cI repressor is bound to the operators adjacent to pL and pR. The prophage will therefore be induced if the levels of active cI repressor decline below a certain point. This can be spontaneous or via chemical/ physical stimuli, which leads to the SOS response. Part of this response is synthesis of the RecA protein, which inactivates the cI repressor by cutting it in half and switching on expression of the early genes, enabling the lytic cycle to be activation. It also means that transcription of the cI gene is no longer stimulated, avoiding the possibility of lysogeny being reestablished.
  10. Because eukaryotic viruses infect eukaryotes, what are differences between them and bacteriophages?
    Their genes have to be expressed within eukaryotic cells and so must resemble eukaryotic genes. They therefore need the complex upstream sequences required to activate transcription by RNA polymerase II, and they may contain introns. They may also have lipid membranes derived from the host when the new virus particle leaves the cell, and may subsequently be modified by insertion of virus-specific proteins.
  11. What can many eukaryotic viruses do?
    They can set up long-term infections without integrating into the host-cell DNA. A number of DNA and RNA viruses can also integrate into the host genome, such as viral retroelements, two of which are retroviruses and pararetroviruses.
  12. What is the general mechanism of entry for retroviral genomes?
    After entry into the cell the genome is copied into double-stranded DNA by a few molecules of reverse transcriptase that the virus carries in its capsid. The double-stranded version of the genome then integrates into the host DNA. Unlike lambda, the retroviral genome integrates randomly.
  13. Explain integration of the viral genome.
    It involves expression of three retrovirus genes—gag, pol, and env. Each codes for a protein that is cleaved after translation, into two or more functional gene products. These products include the virus coat proteins (from env) and the reverse transcriptase (from pol). The protein products combine with full-length RNA transcrips of the retroviral genome to produce new virus particles.
  14. What are the two distinct ways that retroviruses can cause cell transformation?
    With some, cell transformation is a natural consequence of infection, although it may be induced only after a long latent period during which the integrated form of the virus lies quiescent within the host genome.

    Others cause cell transformation because of abnormalities in their genome structures. These acute transforming viruses carry cellular genes that they have captured from previous cells that they have infected. The ability of an acute transforming virus to cause cell transformation lies in the nature of the cellular gene that has been captured. This captured gene is often a v-onc gene. The normal cellular version of such a gene is subject to strict regulation and expressed only in limited quantities when needed.
  15. What are RNA transposons?
    They are multiple copies of sequences that are able to move from place to place in the genome by a process that involves an RNA intermediate. Retrotransposition begins with synthesis of an RNA copy of the sequence by the normal process of transcription. The transcript is then copied into double-stranded DNA, which initially exists as an independent molecule outside the genome. Finally, the DNA copy of the transposon integrates into the genome, possibly back into the same chromosome occupied by the original unit, or possibly into a different chromosome.

    They can be classified into two types—those that have long terminal repeats (LTRs) and those that don’t.
  16. What is the difference between retrotransposition and replication of a viral retroelement?
    The one significant difference is that the RNA molecule that initiates retrotransposition is transcribed from an endogenous sequence, whereas the one that initiates replication of a viral retroelement comes from outside the cell.
  17. Explain Ty
    Ty1 is similar to the copia retrotransposon. Each Ty1/copia elements contains two genes, called TyA and TyB, which are similar to gag and pol genes. TyB codes for a polyprotein that includes the reverse transcriptase that plays a central role in transposition of the Ty1/copia element. Ty1/copia lacks an equivalent to env, however.=, meaning that it cannot form infectious virus particles and can’t escape from the host.
  18. What are the other molecules related to viruses?
    Satellite RNAs, also called virusoids, are RNA molecules that have a single or very small number of genes. They can’t construct their own capsids and move from cell to cell within the capsids of helper viruses. The distinction is that a satellite virus shares the capsid with the genome of the helper virus whereas a virusoid RNA molecule becomes encapsidated on its own.

    Viroids are RNA molecules that contain no genes. They never become encapsidated, spreading from cell to cell as naked RNA.

    Prions are infectious, disease-causing particles that contain no nucleic acid.

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