transcription and regulatory networks

Question 1

what is transcription

Answer 1

the generation of mRNA from a DNA template.

Question 2

Where does transcription take place in an Escherichia coli cell?

Answer 2

in the cytoplasm

Question 3

What is meant by translation?

Answer 3

The generation of polypeptide chain from an mRNA template

Question 4

Where does translation take place in an Escherichia coli cell?

Answer 4

cytoplasm

Question 5

What is meant by the “central dogma of molecular biology”?

Answer 5

The central dogma of molecular biology states that information cannot be transferred back from protein to either protein or nucleic acid

Question 6

How does an RNA polymerase molecule floating in the cytoplasm of an Escherichia coli cell reach a gene on its DNA?

Answer 6

It binds to a promoter of a gene with the help of a sigma factor

Question 7

In genetics what is a promoter?

Answer 7

A promoter is a region of DNA that helps to recruit RNA polymerase and thereby can initiate transcription of a particular gene

Question 8

What are typical promoter sequence elements recognised by the housekeeping sigma factor sigma70?

Answer 8

-10 TATA box and -35 AT-rich region

Question 9

What is the function of the -10 TATA box and the -35 AT-rich region?

Answer 9

They are AT-rich and therefore can be easily melted upon binding of RNA polymerase to facilitate transcription

Question 10

What are typical promoter sequence elements recognised by the specialised sigma factor sigma54?

Answer 10

-12 TATA box and -24 AT-rich region

Question 11

What is the approximate speed of transcription in Escherichia coli?

Answer 11

30-50 nt/s

Question 12

How can a misincorporation event by RNA polymerase be repaired?

Answer 12

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

Question 13

How is transcription terminated?

Answer 13

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

Question 14

Accuracy of transcription is much lower than accuracy of DNA replication. Why can transcription be less accurate than DNA replication?

Answer 14

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

Question 15

How does the promoter sequence influence of transcription?

Answer 15

The stronger the promoter the more efficiently RNA polymerase is recruited and the higher are transcription levels

Question 16

How can the sigma factor influence the level of transcription?

Answer 16

Different sigma factors recognise different promoter elements and therefore guide RNA polymerase to different sets of genes

Question 17

How is a repressor protein influencing the level of transcription?

Answer 17

It shuts transcription off

Question 18

How can a repressor protein downregulate transcription?

Answer 18

• 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

Question 19

How can a transcription activator such as CAP protein help to increase levels of transcription?

Answer 19

It binds at or near a promoter and actively recruits RNA polymerase, thereby increasing transcription from a gene

Question 20

What function has β galactosidase, encoded by the lacZ gene?

Answer 20

It cleaves lactose in glucose and galactose

Question 21

Where is the repressor gene for the lac operon, lacI, located in relation to the other genes of the lac operon?

Answer 21

Outside the lac operon under its own weak promoter

Question 22

Which regulator elements are important to control transcription of the lac operon?

Answer 22

Promoter strength, binding sites for the CAP activator, binding sites for the Lac repressor

Question 23

Escherichia coli cells are growing in medium with lactose and glucose. How strongly is the lac operon transcribed?

Answer 23

Not repressed but low, because cAMP, a starvation signal, is low and CAP protein does not bind to activate transcription

Question 24

Escherichia coli cells are growing in medium with glucose but no lactose. How strongly is the lac operon transcribed?

Answer 24

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

Question 25

How can the bacterium Vibrio fisheri be beneficial to the squid Euprymna scolopes?

Answer 25

The bacterium resides in the light organ of the squid and can be used to mask the squid’s shadow when hunting at night

Question 26

What is the main function of the lux operon in the bacterium Vibrio fisheri?

Answer 26

Generating proteins that allow chemiluminescence

Question 27

What is meant by quorum sensing?

Answer 27

Quorum sensing enables bacteria to communicate with each other (or even other species) to synchronise certain activities such as expressing pathogenicity factors or chemiluminescence