Bentzen 5 - Transcription Flashcards
What are the two genetic processes that lead to ‘expression?’
Transcription and translation
What is the difference between gene expression processes in eukaryotic cell and prokaryotic cells in terms of mRNA?
A single strand of RNA can be transcribed and translated at the same time in prokaryotes. In eukaryotes it goes through RNA processing between transcription and translation.
What types of RNA do eukaryotes and prokaryotes share?
Messenger RNA (mRNA) Ribosomal RNA (rRNA) Transfer RNA (tRNA)
What types of RNA do eukaryotes have, and prokaryotes not have?
pre-messenger RNA (pre-mRNA) Small nuclear RNA (snRNA) Small nucleolar RNA (snoRNA) Small cytoplasmic RNA (scRNA) MicroRNA (miRNA) Small interfering RNA (siRNA)
What is transcription?
The SELECTIVE synthesis of RNA from DNA.
Is all DNA transcribed in a given cell?
no
What way is the template read in transcription?
3’ to 5’ direction
What group are ribonucleotides added to in transcription?
The 3’ OH group of the GROWING chain.
In what direction is RNA synthesized in in transcription?
The 5’ to 3’ direction
Can a DNA strand have multiple RNA molecules being synthesized from it at once?
Yes, think Christmas tree picture.
Is there a requirement for 3’ OH in RNA transcription?
NO
How many strands of DNA are involved in RNA transcription?
One strand, not both
How much of the genome is replicated in DNA replication?
The whole genome
How many time does DNA replicated? How many times does transcription occur?
DNA replicates once in the S stage of a cell’s life cycle. Transcription occurs many time.
Do DNA replication and transcription proceed in the same direction or a different direction? What direction do each go in?
Both go in the same direction, 5’ to 3’
What are three requirements for transcription?
- RNA nucleoside triphosphates (rNTPs)
- DNA template
- RNA polymerase and other proteins
What are the components of a ribonucleoside 5’ triphosphate (rNTP)
A triphosphate attached to the 5’ carbon of a ribose sugar. A base attached to the 1’ carbon on the ribose sugar ring.
What is a transcription unit?
A gene. A region of DNA that codes for a RNA molecule and the sequences necessary for transcription.
What are three critical regions of a transcription unit (gene)?
Promotor
RNA coding region
Termination site
Where is the promotor region of a transcription unit found?
Upstream of start site, adjacent to gene.
What does downstream (+) of gene mean?
Direction moving from start site +1 to the end of the transcription termination site +____
What does upstream (-) of gene mean?
Moving further away from promotor and not crossing through gene. Eg. Upstream - promotor - gene - terminator
Where is the RNA coding region?
Downstream of the start site
Where is the termination site
Downstream of start site
What is the ardor of a transcription unit (list all 5 sites and downstream/upstream)
Upstream (-) - promotor - transcription start site (+1) - RNA coding region - terminator - transcription termination site - downstream
What is the promotor of the transcription unit?
A DNA sequence that is recognized and bound by the transcription apparatus (RNA polymerase plus other proteins).
What indicates the direction of transcription?
The promotor
What are consensus sequences?
Short stretches of DNA in promotors that are conserved among promotor of different genes. Binding of transcription apparatuses to these sequences orients the RNA polymerase towards the start site
What is the most common consensus sequence?
The Pribnow box at -10 and -35 nucleotides upstream of the start site. -35 and -10 elements are not identical in all promotors
What does a slash (/) mean in base sequences?
That the bases involved have equal frequency
Each -35 and -10 sequence is a variation on a ____
consensus sequence
What does variation of sequence at -35 and -10 regions of promotors affect? What is the consequence of this effect?
Variation effects the strength of the promoter.
Strength = the frequency of transcription
- The more closely the sequence resembles the consensus sequence, the stronger promoter it is
What is an UP mutation of a promotor region at -35 and/or -10?
Making the sequence more closely resemble the consensus sequence. Strengthens it
What is a DOWN mutation of a promotor region at -35 and/or -10?
A down mutation makes the sequence less similar to the consensus sequence and therefore weakens the promoter
What unit does RNA polymerase use to synthesize RNA?
ribonucleoside 5’ triphosphates
What type of complex is RNA polymerase?
A multi protein complex
What does RNA polymerase catalyze
It catalyzes the formation of phosphodiester bonds
What does RNA polymerase do to DNA?
It unwinds the DNA duplex
How many RNA polymerases do prokayotes have? eukaryotes?
Prokaryotes have a single RNA polymerase
Eukaryotes have three or more seperate RNA polymerases
Many bacteria have multiple types of sigma factors, what are these?
Help in the recognition of multiple classes of promoters. Binds to the RNA protein-complex, allows for selective polymerization. Without it, the core enzyme initiates transcription randomly.
What is the holoenzyme RNA polymerase?
The complete enzyme complex composed of the core RNA polymerase and the sigma factor.
RNA transcription is initiated when core RNA polymerase binds to the promoter with the help of sigma
When does transcription of RNA end (what sequence).
Transcription ends AFTER a terminator sequence is transcribed
What are the two major types of terminators in bacteria?
Rho-dependent (requires Rho protein)
Rho-independent
What happens with transcription of Rho-independent terminators?
- There are inverted repeats of DNA
- polymerases pauses at U’s
- The RNA transcript being made forms a hairpin formation with the inverted sequence
- RNA transcript dissociates from RNA polymerase, DNA reanneals
Transcription terminates when inverted repeats from a hairpin followed by a string of uracils
Describe Rho-dependent termination
- Rho binds a stretch of RNA upstream of the terminator
- RNA polymerase pauses when it reaches the terminator seuqnce and Rho catches up
- Rho unwinds DNA-RNA hybrid using helicase activity
Which eukaryotic RNA polymerase transcribes pre-mRNA?
RNA polymerase II
What are the two components of a eukaryotic RNA polymerase II promoter?
Core promotor + regulatory promotor
What is the core promoter of RNA polymerase II in eukaryotes?
It is the minimal sequence required for accurate transcription initiation.
Where is the core promoter of RNA polymerase II found?
It extends upstream/downstream of transcription start site.
What are the components of the core promoter sequence in RNA polymerase II promoter?
Includes a number of consensus sequence (common elements include TFIIB, TATA, initiator and DCPE) for transcription factor binding
The initiator element of the core promoter is +1 and the TATA box is -25
What is the regulatory promoter of RNA polymerase II promoter? Where is it found?
Located upstream of the core promoter. It has consensus sequence that transcriptional activator proteins bind to and effect the rate of transcription.
What are the 3 components of the eukaryotic basal transcription apparatus? What is it?
RNA polymerase II
General transcription factors (TF)
Mediator protein
It’s necessary for transcription at minimal or basal levels.
Where does the basal transcription apparatus bind in eukaryotes?
Binds to core promoter near transcription start site.
How is the rate of transcription regulated at the level of teh basal transcription apparatus?
Additional regulatory proteins (eg. transcriptional activator proteins) bind to the regulatory promoter and enhancer sequences to affect the rate of transcription
Describe the assembly of the Basal transcription apparatus
- A TATA binding protein binds to the TATA box on the core promoter
- General transcription factors and mediators bind around RNA polymerase II and the core promoter
How is RNA polymerase II transcription terminated?
Transcription does not end at a specific sequence.
- There is cleavage of the mRNA at a specific site
- A 5’ to 3’ exonuclease degrades the remaining mRNA, terminating transcription
