Chapter 6: Part II

Which viral genome is likely to require an RNA-dependent RNA polymerase for transcription upon viral entry?

(-) sense single-stranded RNA

CRISPR is ________.

-A set of short DNA sequences that allow the bacterium to "remember" past infections. -CRISPR stands for Clustered Repeated Interspaced Short Palindromic Repeats, which are found in the bacterial genome. These are homologues to phage DNA and are transcribed and used in conjunction with a Cascade protein to cleave phage DNA on infection.

Identify an infectious agent that is comprised of only a nucleic acid particle.

-A viroid.

Tropism can be defined as the ________.

-Ability to infect a particular type of cell (tissue) within the host.

Viruses express tissue tropism and host specificity. In particular, the avian influenza strain H5N1 has rare incidences in humans due to the reduced distribution of alpha-2,3 silica acids in the lower respiratory tract. As a consequence, when the H5N1 strain does infect a human, the disease is very severe due to the risk of pneumonia. In contrast, human influenza strains (H1N1, among others) attach to alpha-2,6 silica acids, which are readily expressed in the upper and lower respiratory tract. Which would be true if a mutation were to allow the H5N1 strain to attach to the alpha-2,6 silica acids?

-An epidemic would likely ensue due to the lack of immunity to the new avian influenza strain. -The avian influenza strain could be transmitted directly from birds to humans. -The avian influenza strain could be transmitted easily from human to human.

HPV is a dsDNA virus that enters the cytoplasm before undergoing uncoating. Although the virus us replicated by the host DNA polymerase in the nuclear, viral replication is closely ties to epithelial cell differentiation. In particular, viral DNA replication is inhibited until _______ are differentiated into ______, which are ready to be shed from the epithelial layer, increasing the likelihood that HPV will be transmitted to a new host.

-Basal cells; Keratinocytes -Basal cells differentiate into keratinocytes and HPV DNA replication is tied to the maturation of the epithelial cells to ensure that the host cell is ready to slough off from the surface. HPV virions are released when keratinocytes are shed from the epithelial surface.

A temperate phage is one that _________.

-Can undergo lysogeny. -Temperate phages may embark on a pathway called lysogeny, where the phage genome integrate into the host cell genome. The viral genome is replicated along with the host cell genome. If the host cell becomes stressed, the phage may switch to a lytic life cycle.

The innate immune system recognizes double-stranded RNA (dsRNA), an indicator or viral replication in the host call, and signals the immune response with ________.

-Interferons -Interferons are signaled as a consequence of protein recognition of dsRNA in an infected cell. Interferons play a critical role in the early innate immune response to viruses, increasing antiviral proteins and facilitating immune cell activation for viral clearance.

Temperate bacteriophages can undergo two routes of infection. During _______ the phage DNA is inserted into the bacterial genome and replicated each time the bacterial cell divides.

-Lysogeny.

The temperate phage lambda can undergo two life cycles depending on the environmental cues. During which cycle does phage lambda form a prophage?

-Lysogeny.

HIV, which only infects humans, is considered to have a __________ host range, whereas rabies virus, which can infect a number of animals and humans, is considered to have a _______ host range.

-Narrow; Broad.

All strains of human papillomavirus (HPV) are capable of integrating their dsDNA viral genome into host basal cells while waiting for keratinocyte differentiation before initiating viral replication for virion shedding. As a consequence of the integrated genome, HPV strains that more readily transform host cells are more likely to cause an increased expression of viral _______.

-Oncogenes. -Cells transformed by viral infection often result in a "gain-of-function" mutation that causes excess proliferation in host cells. In the case of HPV, genes E6 and E7 are viral oncogenes involved in cervical carcinogenesis that destabilize two cellular tumor suppressors, p53 and pRB, respectively.

Match the virus with the mechanism of uncoating the viral genome.

-Plasma Membrane: picornavirus. -Cytosol: retrovirus, papillomavirus. -Endosome: influenza virus.

RNAi ________________.

-Recognizes viral mRNA and prevents further viral gene expression. -RNAi is a eukaryotic host defense that recognizes viral mRNA and silences it.

Bacteria and bacteriophages are undergoing an evolutionary battle. In particular, phages that infect salmonella enterica can use outer membrane proteins, such as OmpF or TolC, for drug efflux or to attach to the bacterial surface. What would be the impact of a significant mutation of these phage proteins?

-The phage may not be able to bind to salmonella's surface, blocking viral infection. -As little as a single amino acid substitution can alter a protein's shape significantly enough for a phage to lose specificity for the host cell protein. Similar to how viruses rapidly mutate, requiring humans to create vaccines to maintain immunity, bacteria can mutate and thereby prevent viral entry.

RNA retroviruses use _________.

-Viral reverse transcriptase (RT) to make a DNA copy that is integrated into the host genome and then the host RNA polymerase transcribes it.

Under what condition would a temperate bacteriophage infecting Staphylococcus aureus (an aerobic bacteria commonly found on the human body) be shifted by environmental cues from lysogeny to lytic cycle?

-When phage-infected cells are incubated at 50 degC. -S. aureus is a mesophile that grows best in the range of 20-40 degC and especially well at human body temperature (37 degC). When the temperature increases to 50 degC, S. aureus undergoes heat street, which causes the phage to shift from lysogeny to a lytic cycle.

A prophage is a _________.

A phage genome integrated into a host genome.

A gene for a ________ is likely to be encoded in the viral genome.

Capsid protein.

Viral genomes may comprise __________.

Double or single-stranded DNA or double or single-stranded RNA.

Picornaviruses can avoid detection by synthesizing virally induced vesicles, or replication complexes, formed from the ________.

Endoplasmic Reticulum.

Oder the terms to list the steps from HIV retroviral genome to protein synthesis.

I. (+) ssRNA genome. II. Reverse transcriptase. III. dsDNA genome. IV. Integration into host genome. V. RNA pol II transcription. VI. Translation of viral proteins by host ribosomes.

Phage lambda can undergo a lytic cycle or a lysogenic cycle. Range the steps of the lytic cycle from initial onset of bacteriophage invasion until lysis.

I. Phage attacks to host cell and inserts genome. II. Linear dsDNA cyclizes to circular DNA. III. Capsid proteins are synthesized. IV. Phage DNA is replicated and packaged into capsids. V. Phage lyses host cell and progeny are released.

Lit the steps in order from beginning to end of the slow-release bacteriophage replication cycle.

I. Phage inserts ssDNA. II. Phage DNA forms a double-stranded circle. III. Cell replicates circular single-stranded DNA. IV. Phages assemble and exit without lysis. V. How cell slows reproduction while the phage progeny replicate.

Identify the steps in order of the retrovirus life cycle.

I. Virion binding to host cell receptor. II. Uncoating of envelope. III. Uncoating of capsid and genome. IV. (+) RNA revers transcribed to dsDNA. V. dsDNA integration into host genome. VI. RNA polymerase transcribing viral RNA. VII. Translation of viral proteins.

A ________ virus cycle leads to cell lysis, and a ________ virus cycle involves phage genome integration into the host genome.

Lytic; Lysogenic.

Viroids lack _______.

Proteins.

The enzyme reverse transcriptase (RT) is found in __________.

Some DNA (pararetrovirus) and some RNA (retrovirus) viruses.