transcription and regulatory networks Flashcards
what is transcription
the generation of mRNA from a DNA template.
Where does transcription take place in an Escherichia coli cell?
in the cytoplasm
What is meant by translation?
The generation of polypeptide chain from an mRNA template
Where does translation take place in an Escherichia coli cell?
cytoplasm
What is meant by the “central dogma of molecular biology”?
The central dogma of molecular biology states that information cannot be transferred back from protein to either protein or nucleic acid
How does an RNA polymerase molecule floating in the cytoplasm of an Escherichia coli cell reach a gene on its DNA?
It binds to a promoter of a gene with the help of a sigma factor
In genetics what is a promoter?
A promoter is a region of DNA that helps to recruit RNA polymerase and thereby can initiate transcription of a particular gene
What are typical promoter sequence elements recognised by the housekeeping sigma factor sigma70?
-10 TATA box and -35 AT-rich region
What is the function of the -10 TATA box and the -35 AT-rich region?
They are AT-rich and therefore can be easily melted upon binding of RNA polymerase to facilitate transcription
What are typical promoter sequence elements recognised by the specialised sigma factor sigma54?
-12 TATA box and -24 AT-rich region
What is the approximate speed of transcription in Escherichia coli?
30-50 nt/s
How can a misincorporation event by RNA polymerase be repaired?
Misincorporations are repaired by additional factors such as GreA, which re-position the magnesium ions in the active centre and allow a short stretch of mRNA to be cut off
How is transcription terminated?
There either is a GC hairpin or a recognition sequence for the protein Rho. The hairpin or Rho interact with RNA polymerase and cause transcription to stop
Accuracy of transcription is much lower than accuracy of DNA replication. Why can transcription be less accurate than DNA replication?
DNA contains the entire genetic information and needs to be preserved. In contrast, the halflife of mRNA in E. coli is 7 min on average and many mRNA molecules are made, so one mRNA molecule with an error can be tolerated
How does the promoter sequence influence of transcription?
The stronger the promoter the more efficiently RNA polymerase is recruited and the higher are transcription levels
How can the sigma factor influence the level of transcription?
Different sigma factors recognise different promoter elements and therefore guide RNA polymerase to different sets of genes
How is a repressor protein influencing the level of transcription?
It shuts transcription off
How can a repressor protein downregulate transcription?
- It bends the DNA, thereby masking the promoter and preventing RNA polymerase from binding
- Steric hindrance; it binds in the promoter region of a gene and blocks access by RNA polymerase
How can a transcription activator such as CAP protein help to increase levels of transcription?
It binds at or near a promoter and actively recruits RNA polymerase, thereby increasing transcription from a gene
What function has β galactosidase, encoded by the lacZ gene?
It cleaves lactose in glucose and galactose
Where is the repressor gene for the lac operon, lacI, located in relation to the other genes of the lac operon?
Outside the lac operon under its own weak promoter
Which regulator elements are important to control transcription of the lac operon?
Promoter strength, binding sites for the CAP activator, binding sites for the Lac repressor
Escherichia coli cells are growing in medium with lactose and glucose. How strongly is the lac operon transcribed?
Not repressed but low, because cAMP, a starvation signal, is low and CAP protein does not bind to activate transcription
Escherichia coli cells are growing in medium with glucose but no lactose. How strongly is the lac operon transcribed?
Repressed because of the absence of lactose. In addition, the starvation signal cAMP is low, resulting in CAP protein not binding to the activator sequence
How can the bacterium Vibrio fisheri be beneficial to the squid Euprymna scolopes?
The bacterium resides in the light organ of the squid and can be used to mask the squid’s shadow when hunting at night
What is the main function of the lux operon in the bacterium Vibrio fisheri?
Generating proteins that allow chemiluminescence
What is meant by quorum sensing?
Quorum sensing enables bacteria to communicate with each other (or even other species) to synchronise certain activities such as expressing pathogenicity factors or chemiluminescence
