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What is the central dogma?
DNA (replication, repair, recombination) --> RNA (transcription)--> protein
WHow can genes be controoled?
- they can be expressed in different efficiencies
- - can control amount of proteins produced via the amount of RNA
can also affect timing of transcriptional, affecting development
RNA molecules can __ since they are __.
This is done through __.
RNA was probably what?
form 3D structures that are sequence determined
internal hydrogen bonding between complemnetary sequences; fold into distinct shapes
the first macromolecule that later got copied into DNA and became translated
What are the steps for transcription? Briefly.
- 1) Peel apart the DNA, exposing bases
- 2) Pick correct strand to ensure we get the right sequence
- 3) Transcribe RNA and separate it from teh template
- 4) Reform the Hydrogen bonds in DNA
DNA-dependent RNA polymerase: uses DNA template to create an RNA polmyer
Ribonucleoside triphosphate uptake channel
building blocks are channeled directly into this active site
True or False:
A three prime hydroxyl group is needed for RNA polymerase?
What else is contained in RNA polymerase?
divalent cation, usually, Mg
What drives the addition of ribonucleoside triphosphates
the energy stored int heir phosphate phosphate bonds provides the driving force
Bacterial RNA polymerase has __.
What is the domain structure?
double-psi barrel, which forms the core of the polymerases
- protien domain that forms core of RNA polymerases
- incldues dimerization of domain, insertion of large polypeptide "loops," the acquisition of two critical lysines and three aspartic acids
Explain upstream and downstream.
anything to the right of the promoter is downstream; anything to the left is upstream
In order for transcirption to start, what must happen?
- sequences must be recognized in the promoter sequence upstream of the transcription region:
- TATA box centered around -10 in prok. and -25 in euk.
- consensus sequence that is TTGACA, centered around -35 in pro and -75 in euk.
Aside from the TATA box and the consensus sequence, what are the other sequences?
enhancer sequences: located anywhere such as in introns; allows proteins to come and facilitate the start of the transcription
Why are there two sequences?
- sigma factor may hond on longer
- gives direction to transcription; lets it know to transcribe downstream
What is the transcription cycle of bacterial RNA polymerase?
- 1) The RNA polymerase holoenzyme assembles and then locates a promoter. The sigma factor binds to the two binding sites. It hydrogen bonds.
- 2) The polymerase unwinds the DNA (sigma factor helps melting of DNA) at the position at which transcription is to begin
- 3) Transcription begins. The initial RNA synthesis (abortive initiation) is relatively inefficient. However, once RNA polymersae manages to make 10 nucleotides of RNA, it breaks its interactions with the promoter DNA and weakens, and breaks, its interaction with the sigma factor.
- 4) The polymerase now shifts to the elongation mode of RNA synthesis, moving rightward along the DNA
- 5-6) During elongation, transcription is highly processive, with the polymerase leaving the DNA template and releasing the newly transcribed RNA when it encounters a termination signal.
- 7) The termination signal destabilizes the polymerase's hold on the RNA by forming a hairpin structure
RNA polymerase holoenzyme
polymerase core enzyme plus sigma factor
initial RNA synthesis that occurs before the elongation stage; inefficient
RNA polymerase is not fully committed to transcribing gene
at first 10 nucleotides due to confirmation
typically encoded in DNA; funciton by forming an RNA structure that destabilizes the polymeras's hold on the RNA
After abortive initiation, what occurs to allow elongation to proceed (in prokaryotes)?
Rutter goes up, prying transcript off template
sigma factor dislodges; full scale transcription mode
Why does formation of the hairpin structure allow dislodging?
There is less energy to overcome in the hydrogen bonds.
The hairpin forms when the transcript lops around to form a hairpin structure, opening the rudding and sloing transcription. There are several GC pairs.