Transcription Flashcards
Transcription begins without a primer, this means RNA polymerases can start without ____
A 3’ OH group (reads the template similar to DNA polymerase)
What is the only thing that stops elongation?
Runs out of bases to read - bumps into a DNA section that has already been produced
- ____ strand is identical to mRNA except for T for U
2. ____ strand is complementary and antiparallel to the mRNA
- DNA coding strand (first strand)
- DNA template strand (second strand)
Then third and final strand is the mRNA
Prokaryotic RNA polymerase
- What is an RNA polymerase?
- ___ + ____ = holoenzyme
- Key features of both these components?
- An enzyme that synthesizes RNA from a DNA template (transcription)
- Core enzyme + sigma factor
- Core enzyme has RNA polymerase activity (holoenzyme is considered an RNA polymerase); Sigma factor is required for recognizing and binding promoter sequences
Sigma factor recruits the core enzyme to the DNA promoter; dissociates from core enzyme when transcription begins
All core enzymes are the same; is this true for sigma factors?
No, sigma factors are like a family; they all recognize different sequences in DNA that might need to be transcribed
Prokaryotic cont.
- What two promoter regions do the sigma factor recognize?
- Where is the location where transcription actually starts?
- Is TATA box located in prokaryotes or eukaryotes?
- Where is the location of the -35 sequence?
- TATA (pribnow) box and -35 sequence
- +1 position; this is the first nucelotide to get base paired (so negative numbers come first, then you get to +1)
- Both
- ~35 bases upstream (-35) (-70 in eukaryotes) from +1 transcriptional start site
Prokaryotic RNA synthesis (elongation)
- Supercoiling may occur- this is relieved by the action of?
- Net reaction?
- Pyrophosphate is further cleaved by pyrophosphatase; how many high energy bonds are cleaved?
- Topoisomerases
- Addition of a ribonucleotide to the growing RNA chain (to interact with the OH group), and release of pyrophosphate
- 2 high energy bonds are cleaved; irreversible coupled reaction
Two prokaryotic termination mechanisms of prokaryotic RNA synthesis and description?
- Rho dependent termination= requires a protein (rho) to dissociate the DNA template strand from RNA polymerase
- Rho independent termination= requires a GC rich stem loop followed by a poly-U stretch (causes RNA polymerase to fall off)
- What defines the AUG codon in PROKARYOTIC RNA synthesis?
- Prokaryotes are ___cistronic. Eukaryotes are ? What does this mean?
- How does this (2) relate to the Shine-delgarno sequence
- Shine-dalgarno sequence (establishes that the next AUG codon is the start site for translation)
- Pro= polycistronic; eu= monocystronic; this means in prokaryotes, one mRNA can code for several proteins
- Prokaryotes can have more than one gene product defined by shine delgarno (if there are 3 shine delgarno, there are 3 different proteins produced from this transcript and each gene is translated independently)
- What is rifampin (rifamycin)?
- What does it do in prokaryotic cells?
- What is it used to treat?
- An antibiotic
- It binds to RNA polymerase and changes its conformation, preventing transcription initiation/elongation. It does not work on eukaryotic cells*
- Tuberculosis
Whats the basic difference between tRNA and rRNA synthesis in prokaryotes vs eukaryotes?
In prokaryotes, the same RNA polymerase produces all types of RNA
Eukaryotic RNA synthesis
- Eukaryotic DNA is highly condensed (chromatin), in order for transcription, genes must be exposed why?
- What is a nucleosome?
- What does H1 do? How do you inhibit that effect?
- DNA in heterochromatin (condensed) is highly ____; which is important for what?
- To be more accessible to RNA polymerases (euchromatin=beads on a string)
- structural unit of eukaryotic chromosome consisting of DNA coiled around a core of histones
- Causes nucleosides to condense on each other (forms condensed DNA); acetylation of H1 inhibits it (gives beads on a string)
- Highly methylated, important for some of regulation of gene expression
Eukaryotic RNA polymerases:
- RNA poly. 1=
- RNA poly. 2=
- RNA poly. 3=
- Transcribes precursors to rRNA in the nucleolus
- Transcribes the precursor to mRNA (hnRNA) in nucleoplasm
- Transcribes tRNA precursors (tRNA gets processed very heavily)
Eukaryotic RNA synthesis
- RNA pol II recognizes two consensus sequences __ and __
~elongation is essentially the same as prokaryotes
- TATA box (Hogness box) (-25) and CAAT box (-70)
Rrna synthesis in eukaryotes?
RNA pol I transcribes 3 rRNAs as a single large precursor (transcript is generated to make pre rRNA
RNases cleave apart individual rRNAs
Eukaryotic tRNA synthesis
4 ways that tRNA is extensively modified
- Removal of intron loops by splicing
- Trimming of 5’ and 3’ ends
- Base modifications
- Addition of the 3’-CCA sequence (important for adding the amino acid)
- Location of eukaryotic transcription?
2. Location of eukaryotic translation?
- Nucleus
2. Cytoplasm
Eukaryotes dont have shine-delgarno, but what do they have thats similar?
5’ capping (addition of 7-methylguanosine to the 5’ end of mRNA) - the very first AUG defines the end of the 5’ translated region and beginning of the coding region
Serves as ribosome recognition signal and protects mRNA from nuclease degradation
Function of 3’ poly-A tail in eukaryotes?
Serves as a signal for transport out of the nucleus (and stabilizes mRNA from nuclease attack)
~3’ poly A terminus is not encoded in the gene (signal sequence is encoded but additional A’s are not)
- Introns =
Exons= - Which one must be removed for proper translation?
- What is splicing?
- ___ + ___ = spliceosome
- What is a Lariat?
- Introns = intervening sequences
Exons= expressed sequences - Introns
- The removal of introns and the joining of exons (exons are joined together to form mature mRNA)
- SnRNPs + primary transcript (this performs the splicing)
- The excised intron
What does alternative splicing permit?
The production of proteins with some common domains (but the overall function of the protein is different)
- Systemic Lupus Erythematosus onset and presentation?
2. What mushroom accounts for 95% of fatalities? What does it do?
- Late teen females; butterfly rash on the face
2. Genus Amanita - binds to RNA pol II to inhibit mRNA synthesis
Where is mature mRNA transported?
Cytoplasm
