Lecture 2: Regulation of Genome Expression

Question 1

what are most genomes made from?

Answer 1

DNA

Question 2

Why aren’t viruses considered living things?

Answer 2

because they don’t have cells

Question 3

What is transcriptome?

Answer 3

This is the repertoire of the RNA molecules present in a cell in a given time

Question 4

What is the first product of genome expression?

Answer 4

Transcriptome`

Question 5

Fill in the blank.
Transcriptome is maintained by ______.

Answer 5

The process of transcription

Question 6

What is the second product of transcription?

Answer 6

proteome

Question 7

proteome

Answer 7

all the proteins in the cell. this will define the biochemical functions in the cell

Question 8

What process gives a snapshot into the proteins in the cell

Answer 8

2D gel electrophoresis

Question 9

Fill in the blank.

Proteome is maintained by _____.

Answer 9

translation

Question 10

what is bio230’s version of the central dogma of molecular biology?

Answer 10

Genome (DNA)&raquo_space;> Transcriptome (RNA)»» Proteome (protein)

Question 11

How is it possible for us to produce different cell types if they all come from the same genome?

Answer 11

Because although the cells come from the same genome, the cells undergo different genome expression

Question 12

What is the regulation of gene expression important for?

Answer 12

1. defining cell types
2. responses to extracellular stimuli

Question 13

Briefly, what is transcription

Answer 13

it is DNA being transcribed into RNA by RNA polymerase

Question 14

What is the difference between pro and eukaryotic transcription?

Answer 14

in bacterial transcription RNA polymerase has a sigma factor

Question 15

Give a brief review of the steps of transcription for prokaryotes

Answer 15

1. sigma factor binds to the core RNA polymerase enzyme
2. the promoter (region of DNA) positions RNA polymerase and indicates transcription start site
3. holoenzyme is formed- sigma factor + promoter+RNA polymerase
4. polymerase begins unwinding DNA and transcription begins
5. once 10 nucleotides form, the sigma factor is released
6. Transcription elongation
7. Transcription Termination

Question 16

What is gene expression regulated by?

Answer 16

gene regulatory proteins known as transcription factors

Question 17

What do transcription factors bind to?

Answer 17

regulatory regions of DNA known as cis elements

Question 18

What can gene regulatory proteins do?

Answer 18

they can either turn gene expression on or off

Question 19

What are regulatory proteins that turn genes on called

Answer 19

positive regulators and more explicitly activators

Question 20

what are regulatory proteins that turn genes off called

Answer 20

negative regulators and more explicitly repressors

Question 21

What is an operon

Answer 21

the system that refers to multiple genes being transcribed into a single RNA molecule

Question 22

What is the tryptophan operon

Answer 22

it is 5 gene unit that encodes enzymes for the production of tryptophan

Question 23

in tryptophan operon how many promoters regulate its transcription?

Answer 23

a single promoter

Question 24

How many protein options does the TRP operon have to bind to? What are they?

Answer 24

TRP has to 2 protein bound states:
1. Bound by RNA polymerase (turns transcription on)
2. Bound by a tryptophan repressor protein (represses transcription)

Question 25

What does the tryptophan repressor bind to?

Answer 25

a specific DNA sequence of the promoter known as the operator

Question 26

How exactly does TRP repressor prevent transcription

Answer 26

1. It will first prevent RNA polymerase from binding to the promoter
2. This will negatively regulate TRP expression

Question 27

How is tryptophan repressor activity regulated?

Answer 27

In order for the repressor to bind to DNA it must first bind to two tryptophan molecules

Question 28

Structure of tryptophan repressor

Answer 28

It has a helix-turn-helix binding motif, meaning it will bind to the major groove of DNA, inducing a conformational change

Question 29

What is the lac operon

Answer 29

contains three genes that are required transport of lactose into cell and for its catabolism into glucose

Question 30

What is the activator protein called for Lac Expression

Answer 30

Catabolite Activator Protein (CAP)

Question 31

What conditions are required for CAP activation

Answer 31

Low glucose and high lactose because it works to catabolize lactose

Question 32

What is the repressor protein called for Lac repression

Answer 32

Lac Repressor Protein

Question 33

What conditions are required for Lac repressor protein

Answer 33

low lactose

Question 34

How is lac operon regulated

Answer 34

increase of lactose will cause the increase allolactose.

allolactose will bind to lac repressor and cause a conformation change decreasing the DNA-binding activity of repressor and and release the repressor from the operator

Question 35

how does the Lac promoter bind to the DNA

Answer 35

CAP will bind to cis-regulatory sequence because without CAP the lac promotor cannot bind sufficiently to RNA polymerase

Question 36

how is CAP DNA-binding activity activated?

Answer 36

it is activated by low glucose because the low levels increase levels of signalling molecule cyclic AMP (caMP)
after cAMP binds to CAP protein it will undergo conformation change, increasing DNA binding activity and therefore binds to CAP-binding site
Finally, CAP recruits RNA polymerase to the lac promoter `