Theme 2- Module 1 (Transcription) Flashcards
What does central dogma propose?
DNA Encodes RNA, RNA Encodes Protein. The central dogma of molecular biology describes the flow of genetic information in cells from DNA to messenger RNA (mRNA) to protein. It states that genes specify the sequence of mRNA molecules, which in turn specify the sequence of proteins
Is RNA double-stranded or single stranded? What about DNA?
RNA = single
DNA = double
Does RNA run parallel or antiparallel to DNA?
Antiparallel
What is the first step of transcription?
RNA Polymerase attaches to specific promoter regions of the DNA
Where are the promoter regions located with respect to the gene of interest?
Upstream of the gene (5’ relative)
Once transcription is initiated, which way will RNA Polymerase move along the DNA?
3’ to 5’ direction
What stops transcription of a particular gene?
Nucleotide sequence on template strand known as the terminator will stop transcription and release RNA transcript
Where is the terminator located?
At the end of a specific gene
True or false: Only one strand of DNA serves as a template for RNA. The other strand is never a template
False
Both strands can serve as templates, but only one at a time
What is the significance of TATAAT in prokaryotes?
It is a consensus nucleotide sequence that is positioned 10 base pairs upstream of the transcription site and serves as part of the promoter region
What is a consensus sequence?
A sequence of DNA having similar structure and function in different organisms.
What is another example of a consensus sequence in prokaryotes (besides the tata box)? Where is it located?
TTGCCA
Located 35 nucleotides upstream of the gene
If the DNA already has the TATAAT sequence, what is the purpose of additional sequences?
To enhance the rate of transcription
What are sigma factors?
Proteins that facilitate the binding of RNA polymerase to the promoter region of the DNA (IN PROKARYOTES)
What happens when RNA poly binds to a sigma factor on the DNA strand?
Creates a holoenzyme that unwinds the double stranded helix and allows transcription to occur
How do sigma factors assist with turning genes on and off?
There are various diff sigma factors that all bind to their respective promotor regions; this way you can transcribe diff types of genes
Where does the actual process of transcription occur?
RNA Polymerase Enzyme
What happens inside of the transcription bubble of the RNA Polymerase?
The template and complementary strand are revealed inside of the transcription bubble.
RNA Poly catalyzes the production of an antiparallel RNA strand complementary to the DNA (creates an RNA-DNA duplex)
The template strand is being “read” in which direction?
3’ to 5’
In which direction is the RNA being synthesized?
5’ to 3’
In which direction does RNA poly move from the promoter region?
a) Upstream
b) Downstream
B
Downstream
How is a cell able to produce RNA copies of a single gene in greater amounts?
Single genes are able to be transcribed by multiple RNA polymerase molecules at the same time
Describe the process in which ribonucleotides are added to the elongating RNA transcript
Incoming ribonucleotide triiphosphates pairs with the correct base pair on the template DNA
The 3’-OH end (on the growing strand) pairs with the phosphate bond on the incoming ribonucleotide –> this provides the energy to drive the reaction + creates a phosphodiester bond
Two phosphates from the incoming ribonucleotide are kicked out during the above reaction as pyrophosphates
Why is the polymerization reaction of the RNA transcript elongation irreversible?
The pyrophosphate (two phosphate) group is kicked out during the formation of the phosphodiester bond (can’t bring them back)
At what location on the DNA molecule does transcription stop?
At the nucleotide terminator sequences that lie near the end of the coding sequence of a gene
What are the two types of terminator sequences that prokaryotes have?
Rho-independent terminator sequences
Rho-dependent terminator sequences
What do rho-independent terminator sequences consist of?
Inverted nucleotide repeat sequences
= Sequences of nucleotides followed downstream by a specific reverse complement
Followed by a string of six adenine nucleotides
How do rho-independent terminator sequences stop transcription?
The inverted repeats being transcribed into RNA results in the RNA folding in on itself and forming a G-C rich hairpin loop.
This pauses the polymerase and leads to the release of the mRNA transcript
How do rho-dependent terminator sequences stop transcription?
Use a Rho factor (specific prokaryotic protein) that can bind to and use ATP energy to move along the transcript while unwinding it from the DNA template. Thus able to release the transcript from polymerase
“Transcription and translation coupled in prokaryotes”. What does this mean?
Ribosomes start to synthesize the proteins while the RNA is being transcribed
Why are prokaryotes able to couple transcription and translation?
–>Bc prok lack compartmentalization; they have no nuclear envelope that separates the two processes
–> Prok genes are organized differently compared to euk; their mRNA transcripts are diff
Prokaryotes have sigma factors; what do euk have?
General transcription factors
What are the diff types of RNA polymerase that eukaryotes posses? What do they do?
RNA Polymerase I, II, III
Poly I, III = transcribe structural, noncoding RNAs
- –> Poly I = genes for rRNA
- –> Poly III = genes for tRNA + small regulatory RNA
Poly II = mRNA
True or false: immediately after the mRNA is produced, it leaves the nucleus
False
Must be made into mature mRNA
What are the post-transcriptional modifications that occur at each end of the primary mRNA transcript?
- addition of 5’ cap
- addition of 3’ Poly A tail
Why are the 5’ cap and poly A tail important?
Ensure export of mRNA from nucleus
Help protect against ribonuclease enzymes that target phosphodiester bonds
Help with attachment of ribosome and initiation of translation once in the cytoplasm
Why is synthesized first, the 5’ cap or the 3’ tail?
5’ cap
How is the 5’ cap added to the mRNA?
Attaches a 7-methylguanosine to the mRNA thru a 5’ to 5’ triiphosphate linkage
Which enzyme removes the terminal 5’ phosphate from the original mRNA in order to attach the 5’ cap?
Phosphatase enzyme
Which enzyme catalyzes the attachment of the 5’ cap?
Guanosyl
Describe the process of polyadenylation
Polyadenylation signal sequence (AATAAA) is transcribed near the end of the gene sequence
One transcribe, the mRNA is cleaved and a poly A polymerase enzyme is able to add bw 150-200 adenine nucleotide bases to the 3’ end of the RNA transcript
Dose polyadenylation occur before or after termination of the transcript?
Neither
Occurs during
How are transcripts terminated in eukaryotes
Depends on the RNA polymerase
What is the termination system of RNA Polymerase II?
Poly A dependent mechanism of termination
= adding a poly A tail is coupled with termination of the transcript
What is the termination system of RNA Polymerase I?
Uses a specific eukaryotic termination factor
~ Similar to prok rho-dependent termination
What is the termination system of RNA Polymerase III?
Terminated after transcription of a terminations sequence
~ similar to prok rho-independent termination
What happens during RNA splicing?
Introns are removed
Exons are joined together
Why does RNA need to be spliced in eukaryotes?
The protein coding DNA sequence of the gene is interrupted by long, noncoding sequences of nucleotides that are not part of the message
They’re an important part of gene regulation, but they’re not needed for making the protein
What do spliceosomes do?
Catalyze RNA splicing
Describe the structure of spliceosomes
Composed of five, small nuclear ribonucleoproteins (snRNPs) that are made up of small nuclear RNAs and proteins
How do spliceosomes work?
RNA in the spliceosome recognize and form complementary base pairings with nucleotides at designated splice sites
Spliceosome then catalyzes a rxn that allows for a hydroxyl group on a nucleotide in the branch site to form a phosphodiester bond with a nucleotide at the donor site
Cut 5’ of the intron forms a lariat intermediate which forms a loop within the intron
3’ hydroxyl group on the 5’ exon at donor site forms a new phosphodiester bond between the 3’ end of the upstream exon and 5’ end of downstream exon
Release of intron and splicing of exons together
Excised intron lariat is broken down into individual nucleotides that are recycled
When does RNA processing occur?
Before exiting the nucleus
When a region of DNA that contains the genetic information for a protein is isolated from a bacterial cell and inserted into a eukaryotic cell in a proper position between a promoter and a terminator, the resulting cell usually produces the correct protein. But when the experiment is done in the reverse direction (eukaryotic DNA into a bacterial cell), the correct protein is often not produced. Can you suggest an explanation?
The eukaryotic DNA sequence contains introns, which the bacterial cell cannot splice out properly, and so the correct protein is not produced from the information in the bacterial RNA transcript.
