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1. List some of the proteins that are involved in homologous recombination

2. Some viruses have a lysogenic lifecycle. What are these viruses called in bacteria when they integrate into the bacterial chromosome? What are they called if the host cell is eukaryotic (you may have to look that one up)? What is an “attachment site”? If the virus enters the lytic cycle, which two enzymes are involved in the excision of the DNA from the host cell chromosome? Which of them was also involved in the insertion?

3. What are two examples of site-specific recombination

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Elin Hessel
Elin HesselLv2
28 Sep 2019

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Related questions

Some viruses have a lysogenic lifecycle. What are these viruses called in bacteria when they integrate into the bacterial chromosome? What are they called if the host cell is eukaryotic (you may have to look that one up)? What is an “attachment site”? If the virus enters the lytic cycle, which two enzymes are involved in the excision of the DNA from the host cell chromosome? Which of them was also involved in the insertion?


Class 6: Viruses (and Cells, continued)


Making connections: viruses and microbes Match the cell biology concept (on page 1) with an important application of that concept (on page 2). Then answer the follow-up questions at the bottom of page 2.


Cell Biology concepts
1. Bacteria that cannot construct new cell wall material become fragile and break down.
2. During influenza infection, the viral enzyme neuraminidase is required to release new viruses from the host cell in which they were made. Once released, the new viruses can infect many additional cells.
3. Thermus aquaticus is a bacterium found in hot springs and can live at temperatures up to ~80°C (175°F). It has adapted so that its enzymes are most functional at the elevated temperatures, compared with many organisms’ enzymes that function best ~37°C (98°F).
4. Until the isolation and investigation of retroviruses, scientists thought that RNA could be copied from DNA, but DNA could not be copied from RNA. Research on this class of viruses led to an update to this “Central Dogma” of biology.
5. Some bacteria have adapted, so that the enzymes involved in making cell wall materials have a slightly different shape and can no longer be bound by certain drugs.
6. Rhizobia are bacteria that colonize the roots of certain plants (legumes, including beans and peas). The host plant benefits from the prokaryotes’ ability to “fix” nitrogen, converting N2 from the atmosphere into a form that is usable by the plant.
7. Many species of bacteria contain the enzyme cellulase. More than 10 billion such bacteria and other symbiotic microbes may be found in a single milliliter of material from inside the digestive system of ruminant mammals.
8. Fungi, including those that cause athlete’s foot, use ergosterol to maintain healthy membranes. Animal cells do not make ergosterol, they use a similar lipid – cholesterol.
9. During retrovirus infection, a DNA copy is made of the virus’s RNA genome. A cut is made in the host cell’s DNA and the DNA copy of the viral genome is pasted into the host chromosome by a viral enzyme called integrase.
10. Prokaryotic cells contain smaller ribosomes (“70S” ribosomes) than eukaryotic cells (“80S” ribosomes). Both types of ribosomes synthesize proteins, but the macromolecules they use to do it are somewhat different.



2
Applications
_______ Oseltamivir, also called Tamiflu, binds and inhibits the viral protein neuraminidase.
_______ Clotrimazole is a drug that is used to treat certain infections. It interferes with synthesis of ergosterol, a lipid involved in phospholipid membranes.
_______ Penicillin is a drug that interferes with synthesis of peptidoglycans (these are biological molecules that are part protein and part carbohydrate) that are present in certain cell walls.
_______ HIV is often treated with several drugs that inhibit different parts of the viral replicative cycle. Raltegravir is an example of a drug that interferes with the integration of viral genes into the host cell’s chromosome.
_______ Cows, like other vertebrates, lack the ability to breakdown cellulose. Yet they are able to live on a diet of grass and other vegetation high in cellulose.
_______ Enzymes isolated from extremophiles have been very useful in laboratory research. For example, Taq polymerase facilitates PCR, a revolutionary technique for production of DNAs of particular sequences, which requires cycling reactions through high temperatures.
_______ Plants and animals require nitrogen to make biological macromolecules, however they’re unable to convert atmospheric nitrogen (N2) into a biologically useful form.
_______ Azithromycin is a drug that binds to 70S ribosomes and blocks synthesis of any new proteins.
_______ Methicillin-Resistant Staphylococcus aureus (MRSA) can cause life-threatening infections of the skin and bloodstream. One of the reasons MRSA infections are so serious is that they are resistant to treatment by many antibiotics, including methicillin and penicillin.
_______ The enzyme reverse transcriptase, isolated from retroviruses, is an important tool in molecular biology research. Scientists interested in learning what genes are turned on in particular cells use it to make DNA copies of RNAs they are studying (The DNA copies are useful because they are more stable).


When you have completed the matching activity, answer these follow-up questions:
• What types of infections can be treated with the following drugs?
o Penicillin
o Clotrimazole
o Azithromycin
o Tamiflu
o Raltegravir
• Why are these drugs (above) safe for you to take? That is, why don’t they kill your cells?
• Cancer cells are your own human cells that have become deregulated so that they divide and pile up in an uncontrolled way. Many chemotherapy drugs treat cancer by interfering with cell division and other cell processes.
o Why are there so many more side effects for individuals undergoing chemotherapy than for individuals taking antibiotics?

1. Select all of the true statements regarding phageconversion.

-The incorporation of viral genesinto the host cell's DNA is an example of phage conversion.
-The expression of the incorporatedgenes and the resulting alteration of the bacterial phenotype is anexample of phage conversion.
-Cholera toxin genes have a viralorigin.
-The cholera toxin is produced bythe virus.

-The cholera toxin itself is transferred to Vibriocholerae by a virus.

2. Viruses grown in media with radioactive sulfur haveradioactive capsids. Why?

Nucleotides contain sulfur
Cysteine amino acids containsulfur
Capsid peptidoglycans containsulfur

Phospholipids contain sulfur

3. Integrase inhibitors work by:

Agglutinating the reversetranscriptase inhibitors
Preventing the incorporation of theviral DNA into the genome
Blocking the final viralassembly

Degrading the viral envelope

4. Once a prophage is formed, the viral genes are reproducedevery time the bacterium multiplies. The genes that encode thelytic cycle are held in check by a repressor protein. Stressinduces the formation of proteases that degrade the repressor. Howwould this affect the prophage?

Apoptosis would be induced.
The virus enters the lyticcycle.
The bacterial genome isdenatured.

The bacterium rejects the viral genes.

5. Can a virus be killed?

No, viruses are non-living andcannot die.
No, viruses are capable ofself-assembly and cannot be permanently killed.
Yes, separating the genes from thecapsid kills it.

Yes, destroying its genome kills it.

6. Which class of drugs would be effective against HIV but notagainst most other pathogenic viruses?

Translation inhibitors that stopassembly of viral proteins.
Nucleotide analogs that haltreplication.
Non-nucleoside reversetranscriptase inhibitors that block reverse transcription.

Receptor antagonists that block viral entry.

7. An unscrupulous malcontent writes a computer program andembeds it in an e-mail that promises lucrative investmentopportunities. The e-mail is sent to thousands of anonymous users,when they open it the program copies itself into the computer'shard drive. The hard drive begins to fill up with copies of theprogram, once it is completely full the computer crashes. Match thecomponents of this story with the components of a viral lifecycle.

1. e-mail containing virus Virus
2. Innocent user Binding site onhostcell
3. User's hard drive andCPU Host cell'sribosomes
4. Program Uninfected host cell

8. Vaccines work by priming the immune system and inducing theformation of antibodies and memory cells. When the actual virusinfects the host the host's immune system recognizes it andresponds to it. Which feature of viruses helps them thwart thissystem?

The envelops prevents immune systemrecognition.
Autocatalytic proteins replicatewithout genetic material.
The high mutation rate of the viralgenome.
Integration of viral genescamouflages the virus.
Shedding the capsid inactivates theantibodies.

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