RNA molecules are a result of ________ of DNA
types of RNA
rRNA - function and structure
mRNA - informational role. Carries information from genome to the ribosome
tRNA - functional role, carries the amino acids for protein synthesis
-All three of these forms of RNA interact with the ribosome and are needed for protein synthesis.
4 main points about RNA
1) Has ribose rather than deoxyribose sugars 2) has uracil instead of thymine 3) usually occurs as single strands not double strands 4) It comes in at least three different forms that serve different functions (mRNA, tRNA, rRNA)
What is RNA polymerase?
the enzyme that copies DNA into RNA
5 subunits of RNA polymerase
alpha, beta, beta ', omega and sigma (there are two alpha subunits)
omega subunit needed for?
needed for enzyme assembly, but not for synthesis of RNA
alpha and betas are needed for what?
synthesis of RNA
sigma factor needed for?
recognition of the promoter region of the gene and initiates transcription
the subunits of RNA polymerase interact to form the active enzyme _________ , but the sigma factor is not as tightly bound as the others and easily dissociates, leading to the formation of the RNA polymerase _______ enzyme. What is the function of these separate units?
holoenzyme, but becomes core enzyme without sigma subunit.
core enzyme functions to make RNA, while subunit functions to recognize the appropriate site on the DNA for RNA synthesis to begin
To initiate RNA synthesis correctly, RNA polymerase must first recognize the initiation sites on the DNA called?
promoters, whic is a specific DNA sequence to which RNA polymerase binds
E. coli has how many different promoter sequences, and they are all recognized by the same sigma factor ________. If you compare the promoter sequences, you will see that they are not identical. However, two shorter sequences (shown in red) within the promoter region are highly conserved between promoters, and it is these that sigma recognizes.
six different promoter sequences
-sigma factor ^70 (70 kilodaltons)
Both of these shorter sequences precede the site where transcription starts at the _______ site. One of the red regions is _______ bases before the start of transcription, and is called the _______ region and the _______. Which bases occur most often at each position at this location?
transcription starts at the +1 site
-10 bases before the start of transciption, called the -10 region and is referred to as the pribnow box
The second region of conserved sequences in the promoter is about _______ bases from the start of transcription. What region is this? Also, what is the consensus seq?
about 35 bases before the start of transciption, -35 region.
consensus sequence is TTGACA
Note that although sigma recognizes the promoter seqs on the 5’ to 3’ (dark green) strand of DNA, the RNA pol core enzyme will actually transcribe the light green strand running ________because the core enzyme works only in the ________ direction .
5' to 3' direction
reads the DNA strand from 3' to 5' synthesizes from 5' to 3'
Once RNA polymerase (in green here) has bound to a promoter, transcription can proceed, this is called? What happens in this process?
In this process the DNA double helix at the promoter is opened up to form a transcription bubble.
As the polymerase moves, it unwinds the DNA in short segments. This transient unwinding exposes the ________ (aka the what strand?)
(aka the antisense or minus strand of DNA).
Like DNA, RNA is synthesized in the _____ direction.It starts to make an RNA polymer from ribonucleotides _________ ? RNA synthesis continues until RNA polymerase reaches a site on the DNA called the ____________.
5’ to 3’
(ATP,GTP,CTP and UTP)
It's important that only the genes needed are transcribed. So a specific protein factor, called what in E. coli? -- is needed to terminate the mRNA strand after it is transcribed. What is this entire process called?
Rho dependent termination, and the specific protein factor is known as Rho in E. coli
During Rho-dependent termination, the direct binding of this ______utilizing Rho protein to the RNA physically destabilizes RNA polymerases’ interaction with DNA, and RNA pol falls off the DNA, transcription stops.
termination of RNA synthesis is governed by?
specific base sequences on the DNA
In bacteria, a common termination signal on the DNA is a GC rich sequence containing an inverted repeat with a central nonrepeating segment. . When such a DNA seq is transcribed, the RNA forms a stem loop structure by intra-strand base pairing. Such stem loop structures followed by a run of adenosines (AAAA) in the DNA template and therefore a run of uridines (UUUUU) in the mRNA are effective transcription terminators.
This is due to the formation of a stretch of U:A base pairs that holds the RNA and DNA template together. This structure is very weak as U:A base pairs have only 2 hydrogen bonds each. The RNA pol pauses at the stem loop and the DNA and RNA come apart at the run of uridines., this terminates transcription without the addition of any extra factors are referred to as intrinsic terminators