Exam 4: Viruses Part 2

Question 1

Bacteriophages

Answer 1

Viruses that infect bacteria, commonly called “phages”. Useful model organisms.

Question 2

T4 bacteriophage

Answer 2

can infect E.coli, have double stranded DNA virus, complex viral shape (polyhedral head, helical tail), and have lytic replication cycle.

Question 3

How does T4 bacteriophage attach to its host cell during its lytic cycle?

Answer 3

Phage tail fibers attach to host cell complementary receptors, viruses are non-motile so contact occurs via random collision.

Question 4

How does T4 bacteriophage enter its host cell? Does the entire virus enter? Explain.

Answer 4

Lysozyme released from the capsid weakens the peptidoglycan in the cell wall, entry is done by contracting the tail sheath and inserting a hollow tube through the cell wall and membrane. No, the entire virus does not enter the cell wall, only the viral genome. The capsid remains outside the cell.

Question 5

Describe the importance of the enzyme lysozyme in the lytic cycle of T4 bacteriophage. (It is important at two different points in this cycle.)

Answer 5

During entry it weakens the peptidoglycan in the cell wall for penetration. During release it weakens the cell wall for release.

Question 6

How long does the T4 lytic cycle take? What term is used to describe this?

Answer 6

Burst time= ~25 minutes

Question 7

How many virions are released after a lytic cycle of T4 bacteriophage. What term is used to describe this? How does this number compare to those of other bacteriophages such as Qβ?

Answer 7

Burst size for T4 bacteriophages ~100-200 virions. QB phages have burst size of ~10,000.

Question 8

What term is used to describe a bacteriophage that can initiate both lytic and lysogenic cycles?

Answer 8

“ temperate phage”, lambda is one example.

Question 9

List steps of T4 bacteriophage lytic cycle.

Answer 9

Attachment (absorption)
Entry (penetration)
Synthesis (replication)
Assembly
Release

Question 10

Describe the lytic cycle of T4 bacterophages.

Answer 10

Attachment (absorption)- phage tail fibers attach to host cell complementary receptors, viruses are non-motile so contact occurs via random collision.

Entry (penetration)- T4 releases lysozyme from the capsid, weakens peptidoglycan in the cell wall. Tail sheath contracts so the internal hollow tube penetrates the cell wall and membrane. Viral genome is injected through a “hypodermic needle”. Empty capsid remains outside the cell. Viral enzymes degrade host DNA.

Synthesis (replication)- Viral enzymes have degraded host DNA, energy and raw material available for viral replication. Viral genes are transcribed & translated.

Assembly- Capsomeres spontaneously assemble into capsids. DNA is likely pumped into the assembled capsid, Mature virions are formed.

Release- Viral lysosome weakens host cell wall, host cell lyses, releasing mature virions.

Question 11

What viral genes that are expressed during the synthesis (replication) part of the lytic cycle.

Answer 11

Nuclease that degrades host DNA.

Proteins sealing punctured cell walls.

Enzymes for viral DNA synthesis.

Capisd and other structural proteins.

Enzymes weakening cell wall for release.

Question 12

How do T4 Bacteriophage enter the host cell?

Answer 12

T4 releases lysozyme from the capsid, weakens peptidoglycan in the cell wall. Tail sheath contracts so the internal hollow tube penetrates the cell wall and membrane. Viral genome is injected through a “hypodermic needle”. Empty capsid remains outside the cell. Viral enzymes degrade host DNA.

Question 13

How is a lysogenic cycle similar to a lytic cycle? How is it different?

Answer 13

Attachment and entry are the same other than the lambda lagging tail fibers. The big difference is expression of prophage genes is largely suppressed by a virally encoded protein in the lysogenic cycle.Then replication occurs with each bacterial division. The lysogenic cycle is a “peaceful coexistence” with the host cell.

Question 14

What happens to the viral genome during the lysogenic cycle of bacteriophage lambda? What is this called?

Answer 14

The viral genome coexists with the bacterial DNA, “peaceful coexistence”.

Question 15

The steps of the bacteriophage lambda lysogenic cycle.

Answer 15

Attachment (absorption)
Entry (penetration)
Integration
Replication
“Questioning my decision”

Question 16

Describe the process of labda lysogenic cycle.

Answer 16

Attachment (absorption)- phage tail attaches to host complementary receptors. Lambda lacks tail fibers, contact occurs via random collison.

Entry (penetration)- releases lysozyme, tail sheath contracts, hollow tube penetration, viral genome injects, capsid remains outside cell.

Integration- lambda genome circularizes and integrates, single crossover between virus chromosomes. Integrated phage is called a prophage or provirus.

Expression of the viral genes is largely suppressed by a virtually encoded protein. Host genome is NOT degraded, capsid proteins are NOT produced, and the host cell is NOT killed. This suppression makes the bacterium resistant to superinfection by similar phages.

Replication- Pophage acts as part of the bacterial genome. Replicated with each bacterial division, vertical transmission of phage genes. Prophage may remain integrated for many generations, sometimes remaining integrated forever.

“Questioning my decision”- integration is reversible. Process termed “induction”. Environment no longer hospitable. Crossover occurs and lytic cycle initiated.

Question 17

Once a bacteriophage has initiated a lysogenic cycle, how does the virus reproduce?

Answer 17

Pophage acts as part of the bacterial genome. Replicated with each bacterial division, vertical transmission of phage genes. Prophage may remain integrated for many generations, sometimes remaining integrated forever.

Question 18

Does the lysogenic cycle benefit the host bacterium in any way? Explain.

Answer 18

The suppression of the viral encoded protein makes the bacterium resistant to superinfection by similar phages. If a new phage infects the host cell the few viral genes being expressed by the prophage will shut down the genes of that new infecting phage.

Question 19

Once a lysogenic cycle has been established, will this exist forever? Explain.

Answer 19

It can, but if the host environment is great it rarely happens ~1/10,000 bacterial divisions. If bacterial health is compromised it is more likely to happen. If SOS repair is initiated by the cell excision is virtually guaranteed.

Viral integration is reversible. Virus can excise from the bacterial chromosome , reverse of integration.

Question 20

What is lysogenic conversion?

Answer 20

When a prophage can alter the bacterial phenotype. New genes=new properties. Resistant to superinfection. May convert harmless form into a pathogen. Bacteriophage genes can encode virulence factors.

Question 21

How is a virus involved in the disease botulism?

Answer 21

Bacteriophage genes can encode
virulence factors. E.g.:
Clostridium botulinum + prophage 🡪 toxin 🡪 botulism

Question 22

What is the function of the restriction-modification system?

Answer 22

Protects bacteria from viral infections.

Question 23

What is a restriction enzyme and what does it do?

Answer 23

The restriction enzyme recognizes and cleaves specific DNA sequences. e.g., GAATTC, a “genetic palindrome” (read the complementary strand backwards). Problem is that palindromes exist in the bacterial genome as well. So the modification enzyme is needed to keep the restriction enzyme from also targeting the bacterial DNA.

The modification enzyme modifies DNA to prevent cleavage. Methylation of bases within target sequence, normally methylates A’s with occasional C’s. Restriction enzyme only recognizes non-methylated DNA.

Question 24

Why must the life cycles of animal viruses be more complex than those of bacteria?

Answer 24

Because of the multicellularity of animals, lack of cell wall in animals, eukaryotic nature of animal cells, and presence of viral envelopes.

Question 25

List and describe the three different means by which viruses can enter an animal cell. Which is used only by naked viruses? Which is used only by enveloped viruses? Which is used by both naked and enveloped viruses?

Answer 25

Direct penetration: Used by some naked viruses. e.g. poliovirus. Viral capsid sinks into the membrane, only viral genetic material enters the cytoplasm.

Membrane fusion: Only happens with enveloped viruses. Envelope fuses with cell membrane, nucleocapsid enters, “uncoating” releases genome from capsid (poor understanding of process. e.g. measles virus.

Endocytosis: Occurs with most enveloped viruses and some naked viruses. Viral binding to receptors stimulates endocytosis, membrane fusion releases nucleosides, and uncoating releases the genetic material from nucleocapsids. e.g. Herpesvirus (enveloped) and adenovirus (naked).

Question 26

Animal virus replication cycle

Answer 26

Attachment: Virus enters the animals body through respiratory system, ingestion, etc. Spike glycoproteins on viral surfaces bind to complementary receptor proteins on the cell surface. Spikes are on capsid of naked viruses and embedded within envelope within envelope of enveloped viruses.

Entry: entry via direct penetration, membrane fusion, or endocytosis.

Replication: mechanisms of replication vary widely, depending on the nature of the genetic material.

Assembly: most DNA viruses assemble in the nucleus and are released in the cytosol. Most RNA viruses developed solely in the cytoplasm. Replication takes longer than with bacteriophages e.g. almost 24 hours for herpesvirus.

Release: enveloped animal viruses often release by budding. Viral glycoproteins are inserted into the membrane before budding, a portion of the cell membrane becomes the envelope, budding does not lyse cells. Naked viruses are released in two ways, released en masse by lysis (similar to lytic phage release. Extruded from the cell by exocytosis, like budding but they do not acquire an envelope for the membrane.

Question 27

Replication of ssDNA viruses

Answer 27

viral genome enters nucleus, host enzymes prudence a DNA strand complementary to the original DNA strand. Complementary strand is copied to make virtual genomic DNA. Transcritpio n and translation uses cellular machinery, mRNA is transcribed complementary to the regional DNA. Assembly as the dsDNA virus.

Question 28

Describe the means by which viruses possessing a double-stranded DNA genome replicate this genome.

Answer 28

Viral genome enters the nucleus.
DNA synthesis, transcription, and translation occurs normally. Capsomeres enter the nucleus and virions spontaneously assemble in nucleus.

Question 29

How does the hepatitis B virus replicate its double-stranded DNA genome in a way different from most viruses with this type of genome?

Answer 29

Genomes enter the nucleus and are transcribed into RNA. RNA is used as a template to produce multiple copies of the DNA genome. RNA-> DNA is a catalyst by the enzyme reverse transcriptase.

Question 30

Describe the function of the enzyme reverse transcriptase. Does it accomplish transcription? Why is it named in this fashion?

Answer 30

It is the enzyme that catalyzes the transition from RNA to DNA. It is present within the virus, not the animal genome. It reverses transcription and builds DNA from RNA.

Question 31

How is the replication of single-stranded DNA genomes differ from the replication of double-stranded DNA genomes? In what ways are these processes the same?

Answer 31

For ssDNA viruses, viral genome enters the nucleus, the host enzyme produces a DNA strand complementary to the original DNA strand. Complementary strand is copied to make viral genomic DNA. Transcription and transplantation use cellular machinery. Assembly as with dsDNA viruses.

Question 32

Describe the means by which viruses possessing a ssDNA genome replicate this genome.

Answer 32

Viral genome enters nucleus, host enzymes prudence a DNA strand complementary to the original DNA strand. Complementary strand is copied to make virtual genomic DNA. Transcritpio n and translation uses cellular machinery, mRNA is transcribed complementary to the regional DNA. Assembly as the dsDNA virus.

Question 33

Describe the means by which viruses possessing a +ssRNA genome replicate this genome.

Answer 33

genome can function as mRNA, viral RNA polymerase synthesizes a complementary negative-strand RNA (-RNA). This -RNA serves as a template for the +ssRNA genomes.The virus?

Question 34

Describe the life cycle of a retrovirus, including the replication of its genome.

Answer 34

special case of +ssRNA virus. RNA enters nucleus, viral DNA polymerase, Synthesis dsDNA from viral RNA (“reverses transcriptase”.Viral enzyme is present within the viral capsid of the mature virion. dsDNA commonly integrates into the host genome. dsDNA serves as template for mRNA and genome synthesis.

Question 35

How is a -ssRNA genome replicated? Where do the enzymes catalyzing this replication originate (the host or the virus)? Compare it to the replication of +ssRNA viral genome.

Answer 35

-ssRNA, viral enzyme transcribes +RNA from viral genome. +RNA is tranlated as normal, +RNA also serves as a template for genome synthesis. Orginate in the viral genome. Unlike +ssRNA -ssRNA cannot function as mRNA.

Question 36

How do viruses with double-stranded RNA genomes replicate this genome? Where do the enzymes catalyzing this replication originate (the host or the virus)? Explain

Answer 36

+RNA strand is translated. Virally encoded RNA-dependent RNA polymerase transcribes RNA. Eac strand serves as a template for its complement, replacement of cellular DNA synthesis.

Question 37

How does the length of a typical animal virus life cycle compare to the life cycles of bacteriophages?

Answer 37

Animal viruses have a longer life cycle compared to that of bacteriophages.

Question 38

Animal viruses have a longer life cycle compared to that of bacteriophages.
Explain how enveloped viruses can be released by a host cell without killing the host cell.

Answer 38

Budding. Viral glycoproteins inserted into the membrane before budding. A portion of the cells membrane becomes the envelope

Question 39

Why is it important that the DNA of bacteria that produce restriction enzymes is modified? Exactly how is this DNA modified?

Answer 39

It has to be modified so that the restriction enzymes can tell the difference between the palindromes in the bacterial DNA vs the palindromes in the viral genome. This modification is done through methylation of the A’s and sometimes C’s of the bacterial DNA.

Question 40

Why is the treatment of viral diseases more difficult than the treatment of bacterial diseases?

Answer 40

Viruses are more difficult because viral replication cycles use cellular structures. This leaves fewer targets that discriminate between virus and host. Unlike bacterial diseases in which there are specific structures that differ between bacterial and eukaryotic cells.

Question 41

List and describe some valid types of target molecules for anti-viral therapies.

Answer 41

Viral DNA-polymerases such as reverse transcriptase or the polymerase of herpesviruses are valid targets.

Question 42

How are tumors produced?

Answer 42

Genetic control of cell division can be disrupted, cells begin to divide uncontrollably in a phenomenon termed neoplasia. Neoplastic cells create a cell mass termed a tumor.

Question 43

What is a protooncogene? What is their normal role in development?

Answer 43

Gene that can stimulate cell division. Very active in early development (embryo and fetus), normally shut down in adults in the majority of cells.

Question 44

What is a tumor suppressor gene?

Answer 44

Suppress cell division. These genes suppress protoncogenes.

Question 45

What is the difference between a benign tumor and a malignant tumor?

Answer 45

Benign tumors remain in one place and are generally not harmful. Their growth can press on other tissues and cause harm. Malignant (cancerous) tumors invade neighboring tissues.

Question 46

What is metastasis?

Answer 46

Malignant tumor cell movement throughout the body and the colonization of new areas where new tumors are formed.

Question 47

What is the relationship between protooncogenes and oncogenes?

Answer 47

Protooncogenes stimulate cell division but when they are activated uncontrollably they are called oncogenes.

Question 48

What two events are typically required for cancer to occur?

Answer 48

Most cancers are the result of multiple genetic events. Protooncogenes are activated resulting in oncogenes and tumor suppressor genes are inactivated as a result of loss-of-function mutations. There are two copies of tumor suppressor genes so both need to be inactivated. Sometimes due to genetics one set is already faulty, higher risk for cancer

Question 49

Carcinogens

Answer 49

Environmental factors that can causes genetic events resulting in cancer.

Question 50

List and describe the multiple ways in which viruses can lead to the development of cancer.

Answer 50

Viruses cause 20-25% of human cancers.

Activation of oncogenes: some viruses possess their own oncogenes or viral integration adjacent to a protooncogene can convert it into an oncogene. If the regulatory region of a virus inserts next to a host cell protooncogene it can convert it into an oncogene, this can occur even if the virus does not have its own oncogenes.

Inactivation of tumor suppressor genes: viral insertion into a tumor suppressor gene can inactivate the gene. Proviouses integrate next to a tumor suppressor gene, turning it off and making it dormant.

Question 51

Why might plant viruses be considered desirable?

Answer 51

Bad viruses can reduce yield. But sometimes it can increase color variation like in tulips.

Question 52

What three types of media are used to culture viruses?

Answer 52

Obligate intracellular parasites so cannot grow without host cells.

Mature organisms: bacteria, plants, mice, rabbits, rimates, etc.

Cell cultures: Diploid cell cultures derived from embryonic organisms. Continuous cell cultures derived from tumor cells.

Embryonated (fertilized) chicken eggs): inexpensive, axenic, and possessing large cells.

Question 53

What is a viral plaque and how is it formed?

Answer 53

Phages can be quantified via plaque assays. Phage added to bacteria in warm liquid media, mixture is spread across the surface of an agar plate. Uninfected bacteria will grow and form a “lawn” . Infected bacteria lyse, infect & lyse nearby cells. Each phage leads to the development of a single “plaque”, an area devoid of bacteria.

Question 54

How do plant viruses differ from animal viruses?

Answer 54

Enter via wounds, not via receptors. Sources of viruses include soil or vectors (insects, humans). e.g. Tobacco contains visible tobacco mosaic viruses which also infect tomatoes. Picking tomatoes after smoking can transfer this virus onto plant wounds. Virus resistant crops can be genetically engineered.