Lecture 2/3: Transcription and Translation Flashcards
(41 cards)
What is the +1 nucleotide
initiation point of RNA synthesis
upstream= promoter region
downstream= coding region
Where does sigma factor bind?
-10 and -35 regions in the promoter region, marks area so that it can be recognized by RNA polymerase
What direction does RNA polymerase work?
slides along template strand 3’-5’, forming nre RNA 5’-3’
What regions mark a termination sequence in prokaryotes?
G-Crich region followed by a long “A” string
- can create a hairpin loop
How does the termination sequence actually terminate transcription?
long A chain results in many A-U bonds, which are very unstable since they only have 2 H-bonds (rather than 3 H-bonds in G-C bonds)
- RNA polymerase backtracks to find a G-C to form a more stable bond, but they are all wrapped up in the hairpin loop and RNA polymerase cannot bind
- RNA polymerase keeps going back and forth and is eventually forced to stop transcription
What can regulate transcription in both prokaryotes and eukaryotes?
Gene regulatory protiens (transcription factors) bind specifically to regulatory regions of DNA
what is the most common DNA-binding motif? Example?
helix-turn-helix; allows binding to occur by fitting in major groove of DNA; found in tryptophan operon
Define negative regulation
competition between RNA polymerase and repressor protein for promoter binding
Define positive regulation
Activator protien recruits RNA polymerase to the promoter to activate transription
what is the NtrC protien
a transcriptional activator that directly interacts with RNA polymerase to activate transcription from a distance, occurs via DNA looping (kiss & go)
what is bacteriophage lambda
a virus that infects bacterial cells by attaching to host cell, injecting lambda DNA, and taking advantage of the cells own DNA replcation process to replicate
What replication pathway does bacteriophage lambda use under favorable conditions?
Prophage pathway. lambda DNA is integrated into host chromosome and replicates along with host chromosome; retained with cell division and passed on to daughter cells
what replication pathway does bacteriophage lambda use when the host cell becomes damaged
Lytic pathway. Hosts response to DNA damage is the “induction event”. This involves the release of repair proteins that the lambda DNA detect. Lambda DNA detaches from host DNA in a loop and synthesizes the viral proteins needed to form new viruses. Leads to rapid lambda DNA replication and it being packaged into complete viruses. Ends with cell lysis to release the large number of new viruses.
What two gene regulatory proteins are responsible for initiating the switch between prophage and lytic pathways
Lambda repressor protien (cI) and Cro protien repress each others synthesis to produce the two different states; they are both present in the VIRUS’S DNA
Prophage state, lambda repressor protien is ON and Cro protein is OFF
Lytic state, lambda repressor protein is OFF and Cro protein is ON
Describe repressor activity in the prophage state of bacteriophage lambda in bacteria
lambda repressor is on the operator
- blocks synthesis of Cro
- ACTIVATES its own synthesis by activating promoter site and attracting RNA polymerase (positive feedback loop)
- most bacteriophage DNA not transcribed
Describe repressor activity in the lytic state of bacteriophage lambda in bacteria
Cro protien is on the operator
- blocks synthesis of lambda repressor
- ALLOWS its own synthesis; not an activator
- most bacteriophage DNA is extensively transcribed
- DNA is replicated, packages, and the new bacteriophages are released via host cell lysis
What is prophage-lytic control in bacteriophage lambda an example of?
a transcriptional circuit
What is a Riboswitch
short RNA sequences that change conformation when bound by a small molecule; can be used for transcription attenuation and are found in prokaryotes, plants, and some fungi
Prokaryotic example of a riboswitch
- a prokaryotic riboswitch regulates purine biosynthesis (A, G)
- with low guanine levels, transcription of purine biosynthetic genes is ON
- with high guanine levels, transcription of purine biosynthetic genes is OFF
- guanine binds to the riboswitch and it under goes a conformational change that causes RNA polymerase ti terminate transcription
What is an operon
a prokaryotic feature that allows multiple genes to be transcribed into a single RNA molecule
Describe the trp operon
a region of the E. Coli chromosome where transcription of five genes that encode five different enzymes required for the biosynthesis of tryptophan are regulated by a single promoter
Describe the two potential protein-bound states of the trp operon
1) bound by RNA polymerase
- Trp gene expression on
2) bound by a trp repressor protein
- Trp gene expression repressed
Where does the trp repressor bind
the operator
Describe the tryptophan repressor
Negatively regulates tryptophan synthesis based upon the availability of free tryptophan
Must bind two molecules of tryptophan to bind to DNA (operator)
