Transcription and Gene Expression Flashcards
RNA Pol polymerizes RNA in what direction? Are primers required?
RNA Pol moves in 5’-3’ direction
primers NOT required
but DNA strand serves as template (DNA-dependent RNA polymerase)
higher error rate than DNA polymerase, but this is OK because proteins are not inherited as genes are and mutated protein is less consequential than mutated gene
what kind of reaction does RNA pol catalyze? (organic chemistry)
nucleophilic attack to break alpha and beta phosphate on innermost phosphate group to create phosphodiester bond
what do RNA pol I, II, and III do in humans
RNA pol I —> rRNA synthesis
RNA pol II —> transcription (DNA —> mRNA)
RNA pol III —> tRNA synthesis
TATA box
DNA sequence present in promoters, which control initiation of RNA transcription
part of core (basal) promoter
cis-regulatory element
contrast cis-regulatory and trans-regulatory elements
cis-regulatory elements: present on same molecule of DNA that they regulate, make up core (basal) promoter clustered around the +1 base
trans-regulatory elements: proteins that regulate gene expression, freely diffuse within the cell
how is the RNA Pol II pre-initiation complex (PIC) assembled
General Transcription Factors (GTFs, aka basal transcription factors) bind to core promoter, recruit RNA Pol II
- TATA binding protein (TBP) recognizes TATA box
- PIC assembles
- RNA Pol II recruited by GTFs bound to core promoter
- RNA Pol II binding triggers more GTFs activity and helicase activity to unwind DNA (transcription bubble forms)
how does the C-terminal domain (CTD) of RNA pol II contribute to promoter escape in transcription?
CTD contains peptide repeats rich in Tyr, Ser, Thr -> contain hydroxyl groups that can be phosphorylated
kinase phosphorylate CTD tail, triggering promoter escape
different phosphorylation patterns of CTD serve as scaffolds for being in to different proteins that act on the newly transcribed mRNA
Which of these statements is true:
a. RNA polymerase molecules that are farther away from promoter region will have shorter RNA transcripts associated with the transcription bubble
b. promoters have directionality
TRUE: promoters have directionality
RNA pol farther away from promoter region will be associated with longer RNA transcripts (they’ve made more progress)
group these together:
template strand
positive strand
non-coding strand
sense strand
antisense strand
non-template strand
coding strand
negative strand
template strand = non-coding = negative strand = antisense strand
non-template strand = coding strand = positive strand = sense strand
transcribed mRNA will have the same sequence as the ____ strand but with uracil instead of thymine (give all 4 names)
coding strand / non-template strand / positive strand / sense strand
Your research team discovers a single-strand, positive sense RNA virus. If this virus were released into human cytoplasm, could it be directly translated by human ribosomes to produce viral proteins?
yes, the positive/coding/sense strand contains the code needed to produce the viral proteins, and because it is an RNA virus it already has the uracil needed for translation
Your clinical research team is hoping to develop a viral treatment against tumors. You deliver a single-stranded positive strand RNA genome into the cancer cells in order to produce viral RNA that will cause cell death, using human RNA polymerases. Why won’t this work?
eukaryotic polymerases need DNA template to make more RNA
viruses are packaged with their own RNA-dependent RNA polymerase
how does Molnupiravir cause viral mutagenesis in SARS-CoV-2?
substrate for RNA-dependent RNA polymerase
drug is incorporated into viral RNA and causes mutagenesis
Molnupiravir is a prodrug
which of these statements is true of prokaryotic transcription:
a. prokaryotic genes contain introns which are spliced from the pre-mRNA
b. transcription is performed by RNA Pol II
c. the ATG codon is the translation start site
the ATG codon is the translation start site in prokaryotic cells
prokaryotic genes do NOT have introns
a SINGLE RNA Pol performs all transcription in prokaryotes (do not confuse with multiple DNA Pol in prokaryotes)
instead of general transcription factors, promoter sequences in prokaryotes are recognized by…
sigma factors, which recruit RNA pol
during promoter escape, sigma factors remain bound to promoter with only RNA pol transitioning to elongation phase
different sigma factors recognize different promoter sequences
bacterial transcription termination comes in 2 flavors (hint: dependent vs not). Describe the differences
Rho-dependent: Rho acts as RNA-DNA helicase, hydrolyzes ATP to unwind
Rho-independent: termination sequence within DNA template facilitates stable hairpin loop and string of “U” residues (that will bond with A, weaker than G to C bond) to facilitate separation
