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Biology 1002B Lecture Notes - Lecture 2: Mobile Genetic Elements, Central Dogma Of Molecular Biology, Thymine

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School
Western University
Department
Biology
Course
Biology 1002B
Professor
Tom Haffie

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Document Summary

Do not metabolize, cannot reproduce by themselves, etc. It has been thought that a free living organism lost ability to metabolize and broke off and gave rise to virus. )mobile genetic elements gained ability to enter/exit cells. Viruses are obligate integrate parasites and do not have their metabolism; it uses host cell to do everything making it harder to attack by modern medicine. Hiv is retro virus so it needs reverse transcription ( which has no proofreading allowing lots of mutation) Hiv goes rna -> dna -> protein disobeying central dogma, we can target this step and attack hiv at this stage. Azt is almost same shape as thymine molecule, therefore fooling reverse transcriptase during the process. Once azt is added reverse transcriptase stalls reverse transcription. Azt eventually stopped working after 6 months, the dosage needed rapidly increased and eventually in a year it is useless. This is due to mutations happening and vulnerable ones die while resistant ones survive.

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Related Questions

1. A mutation in the gene encoding the integrase enzyme rendersthe protein non-functional. How would the affect the HIV infectioncycle?

Formation of the provirus would bestopped.
Reverse transcription would nolonger be possible.
The gp120 glycoprotein would nolonger be able to bind to the CCR5 receptor.

Cutting and assembling the capsid would be halted.

2. If the viral gene is AUGCCCAGG and the mRNA used to make theviral protein is UACGGGUCC, then the virus is a :

Negative strand RNA virus
Double stranded DNA virus
Retrovirus

Positive strand RNA virus

3. Would treating prions with enzymes that digest nucleotides bean effective neutralization method?

No, prions lack amino acids.
Yes, prion nucleic acids would besusceptible to enzymatic digestion.
No, prions lack phosphodiesterbonds and would not be subject to digestion by these types ofenzymes.

Yes, the bonds between the amino acids would be hydrolyzed.

4. Most Americans born before 1970 have a permanent scar ontheir shoulders from the smallpox vaccine. Why don't youngerAmericans have one?

Smallpox has been eradicated by aworldwide vaccination program.
Smallpox is no longer lethal.
A safer less damaging vaccine wasdeveloped in the early 1970's.

The vaccine is no longer effective due to antigenic shift.

5. What kind of pathogen would retain its ability to causeinfections after being treated with powerful proteolytic chemicalsthat would destroy all proteinaceous material?

A virus
A bacterium
A prion
A fungus

A viroid

6. Select all of the false statements concerning AIDS.

AIDS kills the patient.
Patients die as a result ofopportunistic infections.
AIDS shuts down the immunesystem.
HIV therapy (HAART) can clear thevirus from the bloodstream.

HIV therapy (HAART) can clear the virus from the patient'sbody.

7. Why do viruses only infect specific types of cells?

Viruses only attack epithelialcells, such as the cells lining the lungs.
If a host cell is weakened, viruseshave an easier time infecting it.
The initial choice is random butonce a cell type is chosen it becomes the preferred host.
The host cells have the correctsurface receptor that the virus can fit into.

Viruses infect the first cells they encounter.

8. Nucleotide analogs are a class of drugs that are highlyeffective against many types of viruses. They work by halting thereplication of viral genes. They are equally effective at stoppingthe spread of prion diseases.

True

False

9. An experimental chemical has been shown to selectively cleavephosphodiester bonds. How would the affect a virus?

Dissociate the envelope
Fragment the genome
Hydrolyze the protein coating
Alter the host binding site

Digest the capsid

10. HIV uses cell surface receptors to enter host cells. Whydoes switching from a CCR5 co-receptor to a CXCR4 co-receptoreventually shut down the immune system?

Macrophages have CCR5co-receptors.
T-helper cells have CXCR4co-receptors.
T-helper cells are not involved incoordinating immune responses.
Only macrophages are killed byHIV.

1. A mutation in the gene encoding the integrase enzyme rendersthe protein non-functional. How would the affect the HIV infectioncycle?

Formation of the provirus would be stopped.
Reverse transcription would no longer be possible.
The gp120 glycoprotein would no longer be able to bind to the CCR5receptor.
Cutting and assembling the capsid would be halted.

2. If the viral gene is AUGCCCAGG and the mRNA used to make theviral protein is UACGGGUCC, then the virus is a :

Negative strand RNA virus
Double stranded DNA virus
Retrovirus
Positive strand RNA virus

3. Would treating prions with enzymes that digest nucleotides bean effective neutralization method?

No, prions lack amino acids.
Yes, prion nucleic acids would be susceptible to enzymaticdigestion.
No, prions lack phosphodiester bonds and would not be subject todigestion by these types of enzymes.
Yes, the bonds between the amino acids would be hydrolyzed.

4. Most Americans born before 1970 have a permanent scar ontheir shoulders from the smallpox vaccine. Why don't youngerAmericans have one?

Smallpox has been eradicated by a worldwide vaccinationprogram.
Smallpox is no longer lethal.
A safer less damaging vaccine was developed in the early1970's.
The vaccine is no longer effective due to antigenic shift.

5. What kind of pathogen would retain its ability to causeinfections after being treated with powerful proteolytic chemicalsthat would destroy all proteinaceous material?

A virus
A bacterium
A prion
A fungus
A viroid

6. Select all of the false statements concerning AIDS.

AIDS kills the patient.
Patients die as a result of opportunisticinfections.
AIDS shuts down the immune system.
HIV therapy (HAART) can clear the virus from thebloodstream.

HIV therapy (HAART) can clear the virus from the patient'sbody.

7. Why do viruses only infect specific types of cells?

Viruses only attack epithelial cells, such as the cells liningthe lungs.
If a host cell is weakened, viruses have an easier time infectingit.
The initial choice is random but once a cell type is chosen itbecomes the preferred host.
The host cells have the correct surface receptor that the virus canfit into.
Viruses infect the first cells they encounter.

8. Nucleotide analogs are a class of drugs that are highlyeffective against many types of viruses. They work by halting thereplication of viral genes. They are equally effective at stoppingthe spread of prion diseases.

True
False

9. An experimental chemical has been shown to selectively cleavephosphodiester bonds. How would the affect a virus?

Dissociate the envelope
Fragment the genome
Hydrolyze the protein coating
Alter the host binding site
Digest the capsid

10. HIV uses cell surface receptors to enter host cells. Whydoes switching from a CCR5 co-receptor to a CXCR4 co-receptoreventually shut down the immune system?

Macrophages have CCR5 co-receptors.
T-helper cells have CXCR4 co-receptors.
T-helper cells are not involved in coordinating immuneresponses.
Only macrophages are killed by HIV.


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?