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22 Cards in this Set

  • Front
  • Back
Is the inside of the cell more positive or negative?
Is there more potassium inside of the cell or outside?
What happens after gp120 binds to CD4?
Changes shape so gp120 can recognize chemokine receptor on cell.
Why is activation energy good for gp41?
both native gp41 and gp41 in the presence of CD4 will spontaneously form hairpin, but activation energy prevents native gp41 from spontaneously changing into one
What does Fuzeon do?
Corresponds to a region from the carboxyl-terminus of Gp41; C-peptide creates an inhibited intermediate by binding to the amino terminal, (N-terminal) of the pre-hairpin intermediate, so that it is unavailable to bind to the authentic carboxy-terminal region (C-term) of the protein and form a hairpin
Are the cytosol and ER oxidizing environments or reducing environments?
Cytosol - oxidizing
ER - reducing
What are the envelope protein oligosaccharides of HIV?
gp120 and gp41
Are cells in equilibrium?
No - in a stead state, because require energy
What does the gag protein do?
Introduces the curvature necessary to bud new viral particles from the membrane.
What does DNA polymerase do?
Transcribes specific regions of DNA into complementary RNA
What does the Sigma factor subunit of RNA Pol do in bacteria?
recognizes the promoter sequence, (the beginning of the gene to be transcribed)
What do the fork loops do?
unwind the DNA double helix as it enters the front of the enzyme.
What do Conformational changes in an alpha helix, (the Bridge helix), do?
drive translocation of DNA/RNA through polymerase
Describe the function of the TATA box.
- TATA box – where transcription factors bind; The TATA box is typically located 25 nucleotides upstream from the transcription start site.
- The binding of this first transcription factor distorts the DNA helix of the TATA box, creating a physical
landmark for the location of an active promoter in the midst of a very large genome and allowing for subsequent protein assembly steps.
Describe the phosphorylation reaction.
The addition of phosphate groups to the CTD, (C-Terminal Domain), of RNA polymerase II changes the conformation such that it is able to complete transcription more efficiently.
catalyzed by a transcription factor which also happens to be a specialized enzyme known as a protein kinase.
What does pol do?
encodes a single large protein that is processed to yield three HIV enzymes: reverse transcriptase, which we touched on briefly that copies viral RNA into double stranded DNA; integrase, which integrates viral DNA into the human genome; protease which cleaves and processes specific viral proteins.
What does gag do?
encodes matrix proteins while env encodes the envelope proteins that we talked about before, gp41 and
What does TAT's function?
transactivating regulatory protein; enhances the rate of viral replication up to 1,000 fold
How does TAT work?
in the absence of Tat, RNA polymerase II is described as comparatively non-processive. In other words, it does not complete transcribing the entire proviral sequence and tends to fall off of the DNA. Nevertheless, a limited number of HIV RNA transcripts are made (after already used integrated using integrase?) and exported to the cytoplasm for use in protein expression. One of the viral proteins expressed using these RNAs is Tat, which is then imported into the nucleus where it can enhance HIV transcription
How does TAT physically work?
- Tat effectively attaches the CycT-Cdk9 complex to the RNA tail, and brings the Cdk9 enzyme in close proximity to RNA polymerase II. This enables Cdk9 to promote the addition of phosphate groups to the domain of RNA polymerase II. This addition alters effectivity and it the RNA polymerase becomes highly effective
Describe the 5' cap.
The capping reaction is performed by three enzymes acting in succession: one removes one phosphate from the 5’ end of the nascent RNA, another adds a GMP in a reverse linkage (5’ to 5’ instead of 5’ to 3’), and a third adds a methyl group to the guanosine. The cap therefore consists of an unusual 7-methyl guanosine.
Describe the 3' tail.
- Enzymes cleave the RNA’s sugar- phosphate backbone and then add approximately 200 A nucleotideto the 3’ end produced by the cleavage. This addition does not require a template; hence the poly-A tail of eukaryotic mRNAs is not directly encoded in the genome
- Poly-A-binding proteins remain bound to the poly-A tail as the mRNA makes its journey from the nucleus to the cytosol and they help to direct the synthesis of a protein on the ribosom