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Biology 1001A Lecture Notes - Lecture 1: Reverse Transcriptase, Retrovirus, Antibody

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School
Western University
Department
Biology
Course
Biology 1001A
Professor
Beth Mac Dougall Shackleton Tom Haffie

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Document Summary

Characteristics of viruses and why they are not generally considered to be alive . Viruses lack many properties of life shared by all organisms: cannot reproduce on their own, lack a metabolic system to provide energy for their life cycles, depend on the host cells that they infect for these functions. Why viral infections are usually difficult to treat with drugs, and exceptions to this general principle. Viral infections are typically difficult to treat because viruses are, for much of the infection, Hidden inside host cells and use host cell machinery to replicate. Thus, there often are no obvious viral products to be targeted by drugs. Viral infections are unaffected by antibiotics and other treatment methods used for bacterial infections. As a result, many viral infections are allowed to run their course, with treatment limited to relieving the symptoms while the natural immune defences of the patient attack the virus.

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Related Questions


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. 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.

16. All of the following are true about ear infections EXCEPT:

Middle ear infections (otitis media) often produce a puslike exudate (referred to as otitis media with effusion) due to infection by genera of Streptococcus, Haemophilus, or various species of anaerobes.

External auditory canal (otitis externa) infections are typically caused by Staphylococcus aureus or Pseudomonas aeruginosa.

After successful treatment of middle ear infections with antibiotics, sometimes tubes are inserted to prevent fluid accumulation, repeated infections, and hearing loss.

Pseudomonad infections are common in swimmers because these organisms are able to produce a soluble greenish-blue pigment.

Repeated ear infections in children often decrease markedly because as the child ages and the Eustachian tube changes shape and develops an angle that prevents most organisms from reaching the middle ear.

17. Why are colds difficult to treat and prevent?

Different cold viruses predominate during different seasons.

Because there are so many different types of rhino- and coronaviruses, each with different antigens, development and administration of vaccines are currently prohibitive.

Although some human interferons have been shown to block or limit rhinovirus infections, delivery to infection sites is difficult, and unwanted side effects can occur.

All of the above.

Both a and c.

18. Which of the following is NOT true about parainfluenza viruses?

Most infants by the age of 6 months have been exposed to and develop antibodies against all 4 parainfluenza viruses.

They cause rhinitis characterized by nasal, pharyngeal, and bronchial inflammation, primarily in children.

Parainfluenza virus infection can be prevented by vaccination.

They can cause noisy respiration (stridor) and acute obstruction of the larynx called croup.

The viruses are spread by direct contact or by large droplets.

19. In whooping cough, patients experience violent coughing episodes during the _________ stage and can have bluing of the skin or _________ due to lack of oxygen from massive mucus and bacterial airway blockage.

Paroxysmal; cyanosis

Catarrhal; pigmentation

Convalescent; osmosis

Pneumotic; hydrolysis

Primary; emesis

20. Penicillins have no effect on Mycoplasma pneumoniae because:

Mycoplasmas are viruses

Mycoplasmas possess beta lactamases

Mycoplasmas are too small

Mycoplasmas are eukaryotes

Mycoplasmas lack cell walls

21. How many cases of tuberculosis are reported globally each year?

10

10,000

100,000

3 million

10 million

22. Mycobacteria are difficult to Gram stain, and are termed “acid-fast” due to their:

Ability to survive in acidic conditions

Resistance to drying

Thick, waxy cell walls

Resistance to sunlight

Lack of a peptidoglycan layer

23. Which of the following is true about pathogenic mycobacteria?

They have a long generation time of 12 to 18 hours.

They are obligate anaerobes sensitive to small amounts of oxygen.

They are highly resistant to drying and can remain viable in dried sputum 6 to 8 months later.

Both a and b.

Both a and c.

24. Clinical symptoms of tuberculosis are primarily due to:

Host inflammatory response

Mycotoxins

Endotoxin

Mucus production

Exotoxin

25. What characteristic of Coxiella burnetii, the causative agent of Q fever, allows it to survive for up to 2 years?

Metachromatic granule

Exotoxin

Endospore

Hemagglutinin

Cilia

26. The normal microflora of the heart includes species of:

Gram-positive bacteria

Gram-negative bacteria

Fungi

Viruses

None of these

27. Which of the following is commonly directly responsible for causing septic shock today?

Bacterial hemagglutinins

Bacterial endotoxins

Bacterial exotoxins

Fungal aflatoxins

Bacterial neurotoxins

28. All of the following are symptoms of septic shock EXCEPT

Shock

Lymphangitis

Chills

Fever

Collapsed blood vessels

29. What is the most likely explanation of how Streptococcus pyogenes causes rheumatic fever?

Strep throat infections migrate down to the heart.

Endotoxin production causes septicemia.

Vegetation followed by fibrin deposition.

Cross-reactivity of an antibody for a Streptococcus pyogenes antigen to a heart cell antigen.

It is an opportunistic infection triggered by coronary artery disease and atherosclerosis.

30. Bacterial endocarditis is an infection and inflammation of the lining and valves of the heart and occurs as a result of transient bacteria attaching to fibrin from exposed collagen fibers of damaged valvular surfaces. True or false?