Bacterial gene regulation 2

Question 1

Where is the ribosome binding site?

Answer 1

8-10 base pairs upstream of the start codon

Question 2

How long is the ribosome binding site?

Answer 2

3-9bp long

Question 3

What is the ribosome binding site complementary to?

Answer 3

The 3’ end of 16S rRNA of ribosomes

Question 4

What is the ribosome binding site also called?

Answer 4

Shine-Dalgarno sequence

Question 5

What can the strength of the ribosome binding site affect?

Answer 5

The amount of protein that is produced

Question 6

Bacterial start codons?

Answer 6

AUG (main), GUG UUG

Question 7

What are leaderless mRNAs?

Answer 7

Genes that don’t have a shine dalgarno sequence

Question 8

WHen can regulation of gene expression occur?

Answer 8

Transcriptional, post-transcriptional, translational, post-translational

Question 9

What is global regulation?

Answer 9

Groups of individual genes/operons can be differentially expressed
I.e. a group of genes are all upregulated at a time in response to a stimulus

Question 10

What is a regulon?

Answer 10

A group of genes regulated by a particular factor (sigma or TF)

Question 11

What is a housekeeping sigma factor used for?

Answer 11

Controlling transcription of genes that are involved in general metabolism, cell division, RNA pol synthesis

Question 12

What can having multiple sigma factors do?

Answer 12

Give the RNA pol specificity–> can control a group of genes w/ one sigma factor

Question 13

How does a sigma factor control multiple genes?

Answer 13

The -10 or -35 genes are changed depending on the specific sigma factor that is regulating gene expression

Question 14

Differences between diff sigma factors?

Answer 14

They recognise diff promoter sequences in front of groups of genes
Groups that are transcribed together have the same promoter sequence

Question 15

WHy are sigma factors v important?

Answer 15

Production of small amounts of incorrect/alternative sigma factors can have big consequences 4 the bacteria

Question 16

What are sigma factors controlled by?

Answer 16

Transcriptionally, translationally, them being synthesised in an inactive state and needing to be activated, anti-sigma factors

Question 17

How does an anti sigma factor work?

Answer 17

Attaches to the sigma factor, and only lets it go when there is a specific condition that means the bacteria needs that sigma factor to be active

Question 18

Where do TFs bind DNA?

Answer 18

Close to the promoter

Question 19

What is -ve control by TFs?

Answer 19

Repressing transcription

Question 20

What is +ve control by TFs?

Answer 20

Activating transcription

Question 21

How can a TF +vely control using sigma factors?

Answer 21

It can bring the sigma factor to the -35 region

Question 22

Ways that repression can be done by TFs?

Answer 22

Steric hindrance, looping, modulation of an activator

Question 23

How does repression by steric hindrance work?

Answer 23

The TF sits in between the -10 and -35 region, stopping the sigma factor from getting into the promoter region

Question 24

How does repression by looping work?

Answer 24

Repressor protein binds to two sides of DNA and causes it to loop–> sigma factor cant get to the -10/-35 sequence(s)

Question 25

What is quorum sensing?

Answer 25

A molecular system to monitor population density

Question 26

How do bacteria do quorum sensing?

Answer 26

They produce autoinducer molecules

Question 27

What are autoinducer molecules?

Answer 27

Peptides or small molecules

Question 28

How does the production of autoinducer molecules help bacteria with quorum sensing?

Answer 28

The more bacteria present, the more molecules and the bacteria can react to the concentration of them by changing gene expression

Question 29

What in the bacteria makes autoinducers?

Answer 29

Luxi protein

Question 30

WHat happens when there is high concentrations of autoinducer molecule?

Answer 30

It interacts with a LuxR TF, which binds to the promoter regions of diff genes and turns them on/off

Question 31

Pseudmonas aeruginosa example of quorum sensing?

Answer 31

Low pop density--> harmless type (virulence genes off) high pop density--> harmful type (virulence genes on)

Question 32

What is metabolite repression?

Answer 32

Keeping genes used to metabolise a non-optimal carbon source inactivated when you're not using that source

Question 33

WHat is the glucose effect

Answer 33

In the presence of glucose, many carbon catabolite gene clusters are repressed

Question 34

WHat is the TF for the glucose effect?

Answer 34

Catabolite activator protein

Question 35

WHat is unique ab the catabolite activator protein?

Answer 35

It only binds DNA if cyclic adenosine monophosphate (cAMP) is bound to it

Question 36

When can RNA pol bind to catabolite repressed promoters?

Answer 36

When the CAP is bound to them first

Question 37

How is cAMP synthesised?

Answer 37

from ATP by adenylate cyclase

Question 38

What happes to cAMP synthesis in the presence of glucose?

Answer 38

It is inhibited

Question 39

Outcome of glucose's presence on cataboltite genes?

Answer 39

glucose causes cAMP to be repressed, meaning CAP won't bind to the repressed genes so they won't be transcribed