BCHM-3050 Lecture Notes - Lecture 3: Rna Polymerase Ii, Lac Operon, Dna-Binding Domain

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20 Oct 2017

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Rho factor heli(cid:272)ase that is i(cid:374)a(cid:272)ti(cid:448)e so it does(cid:374)(cid:859)t (cid:271)(cid:396)eak any hydrogen bonds; follows dna polymerase then cuts. H-bonds between new formed dna and rna strand: eukaryotic rna polymerases, *note: eukaryotic rna polymerases cannot initiate transcription, initiation of eukaryotic transcription. Tfiif, tfiih, tfiij): transcription factors sequentially bind to tata region and polymerase. I(cid:374)di(cid:272)ates (cid:862)housekeepi(cid:374)g(cid:863) ge(cid:374)e. (adapted from garret & grisham) by the enzyme poly a polymerase: mrna. Thought to get rid of lactose-like molecules (transfers acetyl group from coa to c6 oh of thiogalactosides), but cells function ok w/o this gene/enzyme: cap binds camp (camp conc. Is high when cell has low glucose/low energy). Epigenetic regulation ( dna modification: addition of methyl groups to cytosines of dna, happens in cpg islands. If3 prevents premature binding: formation of the prokaryotic initiation complex. If-2 (with gtp) bind to 30s a site: (1) if-1 is displaced. (2) promotes fmet-trna* binding to p site: gtp is hydrolyzed.

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 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.

crimsonsalmon160

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.

greensea-lion551

1. Unlike Ebola virus, SARS virus
a. has large spikes that look like a âcrownâ.
b. is enveloped.
c. is helical.
d. is in the family Togaviridae.
e. is a ssRNA virus.

2. Which virus or virus family is described in the followingpassage?
Electron micrographs of the hemagglutinin subunits (in the presenceof SDS) showed
rods approximately 40 Ã wide and 140 Ã long. The neuraminidasesubunits had a quite
different appearance. In the presence of SDS, these were seen asoblong structures about 85 Ã long and 50 Ã wide with a centrallyattached fibre 100 Ã long possessing what appeared to be a diffusetail or small knob about 40 Ã in diameter at its end.1
a. Togaviridae
b. Epstein-Barr virus
c. Smallpox virus
d. Orthomyxoviridae
e. Filoviridae
f. Rabies virus

3-Following is a passage from the New England Journal ofMedicine:
______________________ is an exclusively human herpesvirus that ...becomes latent in
cranial-nerve and dorsal-root ganglia, and frequently reactivatesdecades later to produce shingles and postherpetic neuralgia. Inimmunocompetent elderly persons or
immunocompromised patients, ____________________ may producedisease of the central nervous system.
This passage refers to which virus?
a. West Nile virus
b. Smallpox virus
c. Epstein-Barr virus
d. Ebola virus
e. Varicella-zoster virus

4. Pneumoviruses can cause colds and pneumonia in humans. They aresingle-stranded,
negative-sense, nonsegmented RNA viruses. These enveloped virusesare surrounded by an envelope that is characterized by fusionglycoproteins and host-derived proteins. With this knowledge, it islikely that pneumoviruses
a. enter host cells via endocytosis.
b. leave host cells by budding.
c. enter host cells via membrane fusion.
d. A and B
e. B and C

5. Recall that poliovirus is a positive-sense (+) ssRNA virus. The5â Ã ? 3â strand of RNA,
once uncoating has taken place, can serve as an mRNA and encode forviral proteins.
However, in order for the virus to create more +ssRNA to package indaughter viruses, it must
a. generate a dsRNA molecule that can encode for the synthesis ofmore +RNA.
b. integrate into the host cell DNA.
c. utilize an RNA-dependent DNA polymerase to make aheteroduplex.
d. undergo reassortment
e. All of the above

6. Some influenza hosts, such as humans and pigs, cansimultaneously contract human,
avian and swine influenza viruses at the same time. What can occurduring the maturation phase of virus replication in such ahost?
a. Reassortment
b. RNA of all three sources: human, swine and avian, can bepackaged into a single
virion.
c. Genetic shift
d. All of the above

7. The HIV virion contains enzymes/proteins that do all of thefollowing EXCEPT
a. An enzyme that creates âDNA using +RNA as template.
b. A protein that serves as a chemokine receptor.
c. A DNA-dependent DNA polymerase.
d. An enzyme that allows +/- viral DNA to be spliced into the hostcellâs DNA.
e. A protein that mediates membrane fusion.

8. After a long series of biochemical tests, Kyle and Matt werefinally able to identify their Gram-negative unknowns asPseudomonas aeruginosa and Shigella dysenteriae,
respectively. As they compare notes, they realize that theirunknowns are in the
___________ Pseudomonadaceae and Enterobacteriaceae, respectively.However, they also note that both of their unknowns are in the______________ ? proteobacteria.
a. genera, species
b. phyla, family
c. families, class
d. order, phyla
e. classes, order

9-Hydrogenobaculum acidophilum is a resident of YellowstoneâsNorris Geyser basin. This thermoacidophilic microbe grows instringy, white mats and is a member of the phylum Aquificae.Hydrogenobaculum acidophilum
a. could be further researched in Volume 2 of Bergeyâs Manual ofSystematic
Bacteriology.
b. is in the domain Archaea.
c. is a deeply branching bacterium.
d. is a proteobacterium.
e. All of the above

10-After talking about the Group A Streptococci (GAS) and theircapability to sometimes cause a flesh-eating disease callednecrotizing fasciitis, Derek decides to research this group a bitmore. As he reads, he quickly learns that
a. they are microaerophilic Gram-negative rods.
b. they are in the phylum ?-proteobacteria.
c. they are found Volume 4 of Bergeyâs Manual of SystematicBacteriology.
d. they have less than 50 mol % GC content.
e. none of the above

BCHM-3050 Lecture Notes - Lecture 3: Rna Polymerase Ii, Lac Operon, Dna-Binding Domain

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