Prokaryotic Transcription Flashcards
What is the function of transcription?
Transcription copies DNA information to RNA
What happens during transcription?
- Proteins separate the double-stranded DNA
- One of the single-stranded DNA becomes the template
- RNA is synthesized according to the template, following base-pairing rules (catalyzed by RNA ploymerase)
What is a gene?
It is a segment of DNA, which controls a discrete hereditary trait, characteristic or phenotype
What is a gene at molecular level?
It is a segment of DNA that encodes information for a protein or functional RNA, as a linear sequence of nucleotides.
What are the two major components of a typical gene?
- information to make functional protein or RNA
- information to control when to make the protein / RNA it codes for
Do cells control genes? Why?
Yes, because cells do not want all genes to produce their products all the time without control.
How do cells control genes?
Turn genes on/off in response to cellular events and adjust the amount product each gene makes, which is commonly controlled by regulating the amount of transcription.
What are the components or parts of a prokaryotic gene? (Starting from upstream (5’) to downstream (3’))
Promoter, 5’ UTR, Protein Coding Sequence (CDS), and 3’ UTR
What is the function the promoter?
Promoter element regulates gene expression (when and how much a gene gets used).
What makes up the region downstream of promoter and what does it contain?
Region downstream of promoter includes the 5’ UTR, Protein Coding Sequence, and 3’ UTR and it contains the protein coding sequence – information to make the protein.
What happens when RNA polymerase binds to promoter of a prokaryotic gene?
It initiates transcription
Where does a prokaryotic gene get transcribed from?
From the +1 transcription start site (start of 5’ UTR)
Which part of a prokaryotic gene transcription gets terminated?
Downstream of protein CDS
What happens to the protein CDS on mRNA?
It gets translated to the protein
How do you determine the start of protein CDS on DNA and on mRNA?
By the start codon, ATG on DNA or AUG on mRNA
How do you determine the end of protein CDS on DNA and on mRNA?
By the stop codon, TAA on DNA and UAA on mRNA
What are the three stop codons a protein CDS can end with?
TAA, TAG, TGA in DNA and UAA, UAG, UGA in mRNA
True or false? A gene always codes for proteins. Explain why or why not.
False. A gene does not always code for proteins, it may code for a functional RNA, directly made from transcription.
What does a typical prokaryotic promoter contain?
The consensus UP element, -35 element and the -10 elements
What is a consensus sequence?
A sequence of a conserved genetic element representing the most frequently occurring nucleotide at each position.
What is the exact sequence of -35?
TTGACA
What is the exact sequence of -10?
TATAAT
In what element does transcription start?
+1
What elements does RNA Polymerase bind to? What does this cause?
-35 and -10; this causes DNA to separate
What does the relative position of -10 and -35 tell?
It tells RNA polymerase which way to go
Which strand is the template strand or the non-coding strand?
Bottom strand; it pairs with RNA
In what direction does RNA synthesize?
Always 5’ to 3’ direction
What is the coding strand or the non-template strand?
The upper strand; it has the same sequence as the newly synthesized RNA
Where does the ‘TTGACA’ of -35 and ‘TATAAT’ of -10 always occur?
On non-template or the coding strand
Which strand codes for protein sequence?
The coding or the non-template strand
How many letters away is -10 to +1?
9 letters away (there’s no 0, so -1 and then +1)
What happens as RNA polymerase moves?
RNA polymerase opens the dsDNA to synthesize more mRNA onto the template strand
True or false? Genes can be coded on both sides of double strand
True
What is the function of RNA polymerase?
It is responsible for transcription; it synthesizes RNA using DNA as a template
What results in the difference in the sugar between RNA and DNA?
The difference in the sugar makes RNA more unstable compared to DNA
What version of Uracil is Thymine?
Methylated version
What is the purpose of methylation?
It typically protects DNA from enzymes which break down DNA
True or false? Uracil cannot pair with other bases except for adenine.
False, uracil prefers to pair with adenine but can pair with other bases too
What does the additional methyl group cause?
Additional methyl group causes steric hindrance in the DNA double helix to make thymine only capable of pairing with adenine
What does RNA polymerase make?
A transcription bubble
What needs happen first before transcription?
RNA polymerase needs to recognize the promoter
What is an RNA polymerase core?
It is a 5-protein complex = alpha + alpha prime + beta + beta prime + omega subunit
True or False? RNA polymerase can not recognize all promoter elements by itself
True
What is the function of the alpha and alpha prime subunit
They recognize promoter UP elements
What is the function of the beta subunit?
It contains the polymerase activity
What is the function of the beta prime subunit?
It binds and holds onto DNA
What is the function of the omega subunit?
It enhances polymerase stability
What is an RNA polymerase holoenzyme?
RNA polymerase core plus the sigma factor
What is the function of the sigma factors?
They recognize and assist RNA polymerase core to bind to specific promoters
What does sigma factor 70 do?
It recognizes -35 and -10
What does sigma factor E do?
It regulates genes for sporulation
What does sigma factor N do?
It regulates genes for virulencece
What does sigma factor 32 do?
It regulates genes for heat shock response
What can bind to the ‘typical’ prokaryotic promoter with -35 and -10 promoter elements?
RNA polymerase Holoenzyme with sigma factor 70
Can RNA polymerase core still transcribe without sigma factors?
Yes, but at a much lower frequency and specificity
What are the three stages of transcription?
Initiation, Elongation and Termination
What happens during the initiation of transcription?
The binding of RNA polymerase to a promoter sequence
What happens during the elongation of transcription?
The sequential addition of NTPs using DNA as a template
What happens during the termination of transcription?
Dissociation of RNA polymerase and release of primary transcript from template
What part of the alpha subunit does the UP element binds to?
C-terminal domain
What do the protein-DNA interactions do?
They allow RNA polymerase holoenzyme to ‘load’ DNA onto it.
