Lecture 1 - RNA Gene Regulation

Question 1

When can gene regulation occur?

Answer 1

at every stage of gene expression

Question 2

RNA can fold into structures that what?

Answer 2

…that perform diverse biological functions
* for ribosomes its a ribozyme
* gene regulation (trp leader)
etc

Question 3

What directionality does RNA have?

Answer 3

5’ to 3’ directionality (like DNA)

Question 4

On the ribose sugar, what is located on the 2’?

Answer 4

a 2’ hydroxyl

Question 5

What is RNA synthesized as?

Answer 5

a single-stranded polymer

Question 6

Does RNA stay single-stranded?

Answer 6

No, it forms structures… for example, like the transcription terminator hairpin

Question 7

What is the ribosome?

Answer 7

it is a ribozyme… ribosomal RNA catalyzes peptide bond formation

Question 8

What is tRNA?

Answer 8

the adapter for translating the genetic information into a polypeptide

Question 9

What are tRNA’s processed into?

Answer 9

they are processed into a mature form by a ribozyme called RNase P, which is present in all domains of life

Question 10

What does the spliceosome do?

Answer 10

it catalyzes RNA splicing… it is also a ribozyme

Question 11

What is a riboswitch?

Answer 11

they are cis-acting RNA chemical sensors

Question 12

What small molecules and ions can riboswitches sense?

Answer 12

small molecules: purines, amino acids, vitamins etc.
Ions: flourine, iron, manganese, magnesium

Question 13

What percentage of bacterial genes are thought to be regulated by riboswitches?

Answer 13

3-5%

Question 14

Riboswitches can control gene expression at several different levels… Name the levels:

Answer 14

transcription, translation, rna stability and rna splicing

Question 15

In transcription, what does the riboswitch control?

Answer 15

the riboswitch controls whether a terminator hairpin forms
* more rarely, some riboswitches control rho dependent transcription termination

Question 16

During translation, what does the riboswitch control?

Answer 16

it controls whether the ribosome can bind a Shine-Dalgarno sequence to initiate translation

Question 17

In RNA stability, what does the riboswitch control?

Answer 17

controls whether an RNA cleaves itself
*self cleavage causes RNA degradation

Question 18

During RNA splicing, what does the riboswitch control?

Answer 18

whether RNA splicing occurs

Question 19

What is the riboswitch aptamer?

Answer 19

a chemical sensor that can bind a ligand

Question 20

What does the expression platform control?

Answer 20

it controls the gene expression based on whether the aptamer bound to its ligand
* it tells the cell to turn gene expression on or off

Question 21

Without a ligand, what happens to the structure?

Answer 21

only one structure forms

Question 22

If the ligand is there what happens to the structure then?

Answer 22

both the structures form

Question 23

In the absence of a metabolite, the terminator hairpin does what and are the genes expressed or not?

Answer 23

• the terminator hairpin terminates transcription before the downstream genes are transcribed
• the genes are not expressed

Question 24

Give a real life example of of a riboswitch.

Answer 24

the ZTP riboswitch that controls purine biosynthesis

Question 25

What is an antisense RNA?

Answer 25

an antisense RNA is an RNA strand that is complementary to a segment of an mRNA sequence

Question 26

Are riboswitch RNA’s cis or trans acting?

Answer 26

cis-acting

Question 27

Are antisense RNA’s cis or trans acting?

Answer 27

trans-acting

Question 28

What can antisense RNA’s do?

Answer 28

they can inhibit or activate translation

Question 29

What is strategy 1 of gene regulation by antisense RNA’s?

Answer 29

the antisense RNA sequesters the ribosome binding site and/or start codon, which blocks translational initiation

Question 30

What is strategy 2 of gene regulation by antisense RNA’s?

Answer 30

the ribosome binding site and/or start codon is sequesteres by a structure in the mRNA, the antisense RNA opens this structure which permits translation initiation to occur.

Question 31

How are bacterial promoters recognized?

Answer 31

by sigma factors

Question 32

Cells need strategies to regulate what?

Answer 32

to regulate gene expression in response to changes in temperature

Question 33

What does bacteria use to cause a global change in transcription in response to heat shock?

Answer 33

a heat shock sigma factor

Question 34

What is the RNA thermometer used for?

Answer 34

to control translation of a heat shock sigma factor

Question 35

The RNA thermometer blocks translation at what temperature?

Answer 35

low temperature
* the AUG start codon is sequestered by RNA secondary structure

Question 36

The RNA thermometer allows translation at what temperature?

Answer 36

high temperature
* at high temps, the RNA secondary structure is less stable and the AUG codon becomes accessible, therefore allowing the ribosome to bind and initiate translation efficiently