DNA Transcription. Flashcards
Define the antisense strand?
The template for RNA synthesis.
The RNA that is synthesised will be complimentary to which strand?
To the sense strand.
Define a holoenzyme?
An enzyme that is bound to its cofactor.
Define a primary RNA transcript?
A piece of RNA that has been produced by transcription and has not been processed.
Where does translation occur?
At the ribosomes.
Where does transcription occur?
In the nucleus.
Define the sense strand?
The strand of DNA that will be identical the transcribed piece of RNA.
Will the sense strand or antisense strand of DNA be copied?
The antisense strand is copied and the sense strand is complimentary.
Define transcription?
The process of making mRNA from DNA.
Define translation?
The process of making proteins from mRNA.
What is the 1st stage of gene expression?
Transcription.
What instructions does mRNA contain?
The exact instructions of how to make a protein.
What is the template for mRNA?
DNA.
What enzyme synthesises RNA from DNA?
RNA polymerase.
How many strands of DNA will RNA polymerase use as a template?
Only 1.
In what cells can transcription and translation occur at the same time?
In prokaryotic cells.
Why can transcription and translation occur at the same time in prokaryotes?
Because both processes occur in the cytoplasm.
Does transcription and translation occur at the same time in eukaryotes?
No.
Why can’t transcription and translation occur at the same time in eukaryotes?
As transcription occurs in the nucleus.
Translation occurs in the ribosomes.
What must happen to mRNA in eukaryotes before proteins can be synthesised?
The mRNA must be finished before translation can occur.
What is a fresh piece of mRNA called in eukaryotes?
A primary transcript.
When does a primary transcript become mRNA?
After it has been processed and modified to check for any mistakes
What and where is the promoter region of a prokaryotic gene located?
It is a region of DNA located upstream of the RNA coding sequence.
What is the job of the promoter region of a prokaryotic gene?
To make sure that transcription starts at the right location.
How does the promoter region ensure that transcription starts at the right location?
By ensuring that the transcription factors bind to the correct piece of DNA.
What is the RNA coding sequence?
The sequence of DNA that is going to be transcribed to RNA.
What is the terminator region of a prokaryotic gene located and where is it located?
It is downstream from the RNA coding sequence and it contains a stop codon which will signal the end of transcription.
What is the antisense strand of DNA?
The strand of DNA that is used to synthesise the RNA. (Template strand).
Is the antisense strand read by RNA polymerase?
Yes.
How does the newly synthesised RNA differ from the antisense strand?
It is complimentary.
Meaning that if there is a G on the antisense strand then it will form a C on the RNA strand.
Newly synthesised RNA will be identical to what strand of DNA?
The sense strand.
What is the sense strand also known as?
The coding strand or non-template strand.
What is the anti-sense strand also known as?
The non-coding strand or template strand.
If the antisense strand runs in the 5 to 3 direction, what directions will the sense stand and new RNA strand run in relative to the antisense strand?
They are both identical so will run in the 3 to 5 direction.
Can both DNA strands code for proteins in transcription?
Yes.
Although only 1 DNA strand is copied, both strands can code for genes that will produce proteins.
What are the 3 stages of transcription?
Initiation.
Elongation.
Termination.
Are the sense and antisense strand interchangeable?
Yes.
What direction will RNA polymerase read DNA in?
In 3 prime to 5 prime direction.
What determines which genes are read by RNA polymerase?
The proteins that are required by the cell will determine which genes are read on which strands.
Unless stated otherwise, you should always assume that polynucleotides run in what direction?
5 prime to 3 prime.
When does the initiation stage of transcription begin in prokaryotes?
When the DNA unwinds to free up a short region of genes.
What binds to the promoter region of the template strand
Transcription factors will bind to the promoter region.
How far away is the promoter region from the start of the site of transcription?
Around -35 base pairs away
How do transcription factors recognise the promoter region?
As the region will have a specific sequence of nucleotides.
What is the sequence of nucleotides that make up the promoter region at -35 nucleotides away from the start site?
5-TTGACA-3.
What is the sequence of nucleotides that is -35 and -10 base pairs away from the start sequence known as?
A consensus sequence.
What is the region of nucleotides that make up the sequence of nucleotides at -10 nucleotides away from the start site known as?
A pribnow box.
What is the sequence of nucleotides that make up the pribnow box at -10 nucleotides away from the start site?
5-TATAAT-3
What about the consensus sequence will affect the binding of the transcription factors and the rate of transcription?
Any variation in the sequences found at the consensus sequence (-35 and -10).
What happens in the elongation stage of transcription in prokaryotes?
The RNA polymerase will synthesise an RNA molecule.
The RNA molecule that is synthesised by RNA polymerase is synthesised in what direction?
In the 5 to 3 direction.
In what direction will RNA polymerase will read the template DNA strand?
In the 3 to 5 direction.
When is translation terminated?
When the genes have been copied.
What happens to the RNA polymerase once termination has occurred?
The RNA polymerase will fall off the DNA strand and no more transcription will occur.
Do eukaryotes use consensus sequences to mark the site of the beginning of transcription?
No.
What will eukaryotes use to mark the beginning of a transcription site?
A collection of conserved short sequence elements which are located near the transcription start site.
What are the short conserved sequences that are used to mark the start of transcription sites in eukaryotic DNA?
A TATA box which is made up of thymine and adenine and is located around -20 to -35 base pairs.
A CAAT box that is located around -80 base pairs away.
A GC box that is located between -70 and -200 base pairs away.
What is the most common conserved sequence in eukaryotes?
The TATA box.
What nucleotides make up the TATA box?
5-TATAAAA-3.
What are transcription factors in eukaryotes?
Proteins that help with the initiation of transcription in eukaryotes?
What are the transcription factors used to initiate transcription in eukaryotes?
A TATA box binding protein (TFIID)
Transcription factor IIB (TFIIB).
Transcription factor IIH (TFIIH).
Transcription factor IIE (TFIIE).
What is the TATA box binding protein a subunit of?
A subunit of transcription factor IID (TFIID).
Where will the TATA box binding protein bind to the TATA box?
At -25 nucleotides away from the start site.
What does the TATA box binding protein (TFIID) do the DNA strand once it binds to the TATA box?
It causes a distortion in the DNA double helix which allows other transcription factors to get involved.
What is TFIIB involved in during the initiation stage of eukaryotic transcription?
It binds to the promoter and will help RNA polymerase to bind to this region.
What happens when TFIIB has bound to the promoter region?
RNA polymerase II and the other transcription factors can bind to the promoter.
What is TFIIH involved in during the initiation stage of eukaryotic transcription?
TFIIH contains a helicase enzyme which helps to unwind DNA so that RNA polymerase II can read the base pairs on the template strand.
It will also phosphorylate RNA polymerase II which will activate it
What enzymatic domain does TFIIH have?
A kinase domain as it can phosphorylate RNA polymerase.
What is TFIIE involved in during the initiation stage of eukaryotic transcription?
It helps to position RNA polymerase II on the DNA strand.
What is the basal transcription machinery?
The RNA polymerase II combined with the eukaryotic transcription factors.
What kind of transcription can be performed by the basal transcription machinery?
Low level transcription.
When can the the basal transcription machinery be involved in high level transcription?
When an activator and mediator molecule are involved.
RNA polymerase will read what DNA strand?
The antisense strand.
How does RNA polymerase read the antisense strand in eukaryotes?
It separates the 2 strands to form a replication fork and will read either of the 2 strands to make an RNA molecule.
If RNA polymerase changes strands, will it be reading the sense strand?
The strand being read is always the antisense strand and it is always read in a 3 to 5 prime direction.
The RNA that is synthesised by RNA polymerase will always be complimentary to which strand?
The antisense or template strand.
RNA polymerase adds bases to what end of the RNA molecule?
To the 3 prime end meaning that it is synthesised in the 5 to 3 direction.
Does RNA polymerase require a primer molecule?
Unlike DNA polymerase, RNA polymerase does not need a primer.
Will RNA polymerase ever add thymine to RNA?
No, it uses uracil instead.
What does RNA polymerase use as its substrate?
Ribonuleoside triphosphate’s.
What does DNA polymerase use as its substrate?
Deoxyribonucleoside triphosphate’s.
How many RNA polymerases are used during transcription in bacteria?
Only a single RNA polymerase.
What are the 2 parts that make up the single RNA polymerase that is found in bacteria?
The core polymerase combined with sigma factor.
What is the core polymerase that makes up the RNA polymerase that is found in bacteria?
The core enzyme that reads the DNA strand and composes and RNA strand.
What is the sigma factor that makes up the RNA polymerase that is found in bacteria?
A cofactor that is used by the core polymerase.
How does RNA polymerase bind to bacterial DNA?
It binds loosely until it reaches the -35 and -10 sequences at the promoter region where it will bind tightly and start transcribing RNA.
What happens to the sigma factor when RNA polymerase starts transcribing bacterial DNA?
Once the polymerase has gone through about 10 bases, the cofactor will fall off.
When will RNA polymerase stop transcribing bacterial DNA?
When it reaches the termination sequence.
How will the bacterial RNA polymerase know that it has reached the termination sequence?
The termination sequence is made up of a series of complimentary nucleotides.
What happens when bacterial RNA polymerase reaches the termination sequence?
The complementary nucleotides will join together forming a short hairpin loop which signals the end of translation.
The polymerase will fall off and the double helix will be reformed.
What must RNA polymerase do when it is reading bacterial DNA?
It must unwind or relax the supercoiling.
How many base pairs per turn are there in a supercoil?
Around 10 base pairs per turn.
What happens to a bacterial DNA molecule when 1 turn is unwound?
If DNA is unwound by 1 turn, the double helix must rotate by 1 turn to form a supercoil at the other end to relieve tension.
How many bacterial supercoils are formed for every base pair that is unwound?
A new supercoil is formed for every 10 base pairs that are opened up.
What kind of supercoils will always form downstream or ahead of the RNA polymerase in bacteria?
Positive supercoils will always form ahead of RNA polymerase.
What kind of supercoils will always form upstream or behind of the RNA polymerase in bacteria?
Negative supercoils will always form behind RNA polymerase.
What enzyme will relax negative supercoils in bacterial DNA?
A topoisomerase enzyme.
What enzyme will form negative supercoils in bacterial DNA?
A DNA gyrase.
What is the bacterial termination sequence made up of?
Palindromic sequences that range from around 7-20 base pairs.
What is the structure of the loop that is found in the termination sequence of both eukaryotes and prokaryotes?
It includes a region that is rich in Gs and Cs and is then followed by a lot of U bases.
What is the point of the loop in the termination sequence of transcription?
It is an intrinsic method of stopping transcription that occurs in both eukaryotes and prokaryotes.
What extrinsic factors will help prokaryotes terminate transcription?
The RHO proteins.
How do RHO proteins help to terminate transcription?
They attach to the RNA molecule and will follow the polymerase.
When the polymerase stops at the loop, the RHO protein catches up and unwinds the DNA/RNA hybrid.
This pulls the RNA away from RNA polymerase so that they can be released separately.
Does RNA polymerase have proof reading ability?
No.
Is DNA replication or transcription a more accurate process?
Transcription?
Why does the prokaryotic cell tolerate the errors made during replication?
As so many copies of RNA come from each gene that most will be error free.
What is pre-mRNA?
Eukaryotic mRNA that has not been processed.
When does pre mRNA undergo RNA processing?
Before the RNA is released into the cytoplasm.
What ends of the primary transcript of eukaryotic mRNA are usually edited?
Both ends of the primary transcript are usually edited.
What internal parts of an mRNA molecule are removed from the pre-mRNA?
Introns.
What are the fragments of DNA called after the introns have been removed?
Exons.
What happens to exons after the introns have been removed?
They are spliced together.
What are the 5 and 3 prime ends of pre-mRNA made up of?
Of untranslated sequences.
What part of a eukaryotic mRNA strand will carry the protein coding region?
Only the middle.
What is the untranslated sequence of that makes up the 5 prime end of eukaryotic mRNA known as?
The 5 untranslated leader sequence (5,UTR).
What is the untranslated sequence of that makes up the 3 prime end of eukaryotic mRNA known as?
The 3 untranslated leader sequence (3,UTR).
Where is the beginning of the protein coding region of eukaryotic mRNA?
The end of the 5,UTR marks the beginning of the site of translation and the beginning of the protein coding region.
Where is the termination region of eukaryotic mRNA?
Where the protein coding region meets the 3,UTR is the site of termination of translation.
What are the 4 main types of RNA?
mRNA (messenger RNA).
tRNA (transfer RNA).
rRNA (ribosomal RNA).
snRNA (small nuclear RNA).
What is the job of mRNA?
To encodes for sequences of amino acids that are used in
to form a protein.
What is mRNA formed of?
Of copies of protein coding genes, meaning that it contains the instructions of how to build a protein.
What is the job of tRNA?
To bring different amino acids to the ribosome and adds them to the polypeptide while translation is occurring.
What tells the tRNA which amino acids to bring?
mRNA.
What is the job of rRNA?
To combine with ribosomal proteins and form the ribosome.
What is the job of snRNA?
It combines with specific proteins to form a spliceosome which is involved in mRNA processing in eukaryotes.
What are the 3 different forms of RNA polymerase?
RNA polymerase 1.
RNA polymerase 2.
RNA polymerase 3.
What is the job of RNA polymerase 1?
It helps to synthesise rRNA.
What is the job of RNA polymerase 2?
It helps to synthesise mRNA and some types of snRNA.
What is the job of RNA polymerase 3?
It helps to synthesise tRNA and some types of snRNA.
