Lecture 10 - Transcriptional Regulation 2

Question 1

Promoter

Answer 1

Sequence of DNA near the 5’ end of the coding region of a gene where RNA polymerase binds and initiates transcription

Question 2

Two important sequences in a promoter

Answer 2

1. Recognition sequence

2. TATA box

Question 3

Recognition sequence

Answer 3

The sequence recognized by RNA polymerase

Question 4

TATA box

Answer 4

Called this because it is rich in AT base pairs. Sequence closer to the transcription initiation site where DNA begins to denature so that the template strand can be exposed

Question 5

Transcription cannot start until what happens

Answer 5

Until transcription factors have assembled on the chromosome

Question 6

Explain what happens before RNA polymerase II can bind

Answer 6

1. Transcription factor TFIID binds to the promoter at the TATA box changing its own shape and that of the DNA
2. Other transcription factors join it to form a transcription complex
3. RNA polymerase II binds only after several transcription factors are already bound to DNA

Question 7

Enhancers

Answer 7

Positive regulators which bind activator proteins

Question 8

Silencers

Answer 8

Negative regulators which bind repressor proteins

Question 9

What determines the rate of transcription?

Answer 9

Efficiency of binding of GTFs to the core promoter DNA sequences determines levels of transcription (promoter strength)

Question 10

Remodelling of chromatin

Answer 10

Increases the accessibility for trancription

Question 11

Transcriptional regulation

Answer 11

Controlling when and how often a given gene is trancribed

Question 12

RNA Processing control

Answer 12

Controlling the splicing and processing of RNA transcripts

Question 13

RNA transport and localisation control

Answer 13

Selecting which completed mRNAs are exported from the nucleus to the cytosol and determining where in the cytosol they are localized

Question 14

Translational control

Answer 14

Selecting which mRNAs in the cytoplasms are translated by ribosomes

Question 15

Post-translational modification

Answer 15

Control of protein like phosphorylation, acetylation, ubiquitination of them

Question 16

Protein activity control

Answer 16

Selectively activating, inactivating, degrading, or localizing specific protein molecules after that have been made

Question 17

Core promoter binding sites for TFIIB

Answer 17

TFIIB can bind the BRE elements

Question 18

Core promoter binding sites for TFIID

Answer 18

TBP subunit of TFIID can bind the TATA box

Question 19

mRNA degradation control

Answer 19

Selectively destabilizing certain mRNA molecules in the cytoplasm

Question 20

Transcription regulators

Answer 20

Recognize specific sequences of DNA that are often called cis-regulatory sequences. This binding ultimately specifies which genes are to be transcribed and at what rate

Question 21

cis-regulatory sequences

Answer 21

They must be on the same chromosome (in cis) to the genes they control

Question 22

What do transcriptional activators or repressors do?

Answer 22

They bind to DNA regulatory elements (promoter proximal or distal sequences) and either enhance or repress transcription levels directed by the basal transcription factors and RNA polymerase at the core promoter

Question 23

What type of transcription factors are activators and repressor proteins?

Answer 23

Sequence-specific transcription factors

Question 24

What can DNA bending do?

Answer 24

It can bring the activator protein, that was bound to an enhancer element far from the promoter, into contact with the transcription complex

Question 25

Where is the minor groove of DNA?

Answer 25

Occurs where the back bones are close together

Question 26

Where is the major groove of DNA?

Answer 26

Occurs where the backbones are far apart

Question 27

Structural motifs

Answer 27

Different combinations of structural elements (protein confirmations) and may include special components such as zinc

Question 28

Four common structural motifs in DNA binding domains

Answer 28

1. Helix-turn-helix
2. Leucine zipper
3. Zinc finger
4. Helix-loop-helix

Question 29

Criteria for the structure of a protein motif that will recognize an intact DNA double helix

Answer 29

1. Fits into the major or minor groove
2. Has amino acids that can project into the interior of the double helix
3. Has amino acids that can form hydrogen bonds with the interior bases

Question 30

Helix-turn-helix motif

Answer 30

• Two a-helices are connected via a non-helical turn
• Interior-facing ‘recognition’ helix is the one whose amino acids interact with the bases inside the DNA
• The exterior-facing helix sits on the sugar-phosphate backbone, ensuring that the interior helix is presented to the bases in the correct configuration

Question 31

What type of proteins have the helix-turn-helix in their structure?

Answer 31

Repressor proteins

Question 32

What do proteins with helix-turn-helix motifs in their structure do?

Answer 32

They regulate genes involved in development

Question 33

Transcription factors reach into which groove?

Answer 33

Major groove

Question 34

What do the proteins with leucine zipper motifs do?

Answer 34

These proteins regulate cell division genes.

Mutation in these give rise to cancer

Question 35

What do the proteins with zinc finger motif motifs do?

Answer 35

These proteins are steorid hormone receptors

Question 36

What do the proteins with helix-loop-helix motifs do?

Answer 36

These proteins regulate immune system genes.

Sets cells on the path to become muscle tissue

Question 37

3 functional domains

Answer 37

1. DNA binding domains
2. Dimerization doman
3. Activation/repression domain

Question 38

Dimerization domain

Answer 38

Homodimers or heterodimers are formed with other regulatory proteins

Question 39

Cooperative binding

Answer 39

The arrangement of transcription factor binding sites, such that two different transcription factors can interact, stabilizing each other’s binding to the DNA

Question 40

How can genes be coordinately regulated by transcription factors?

Answer 40

The expression of genes can be coordinated if they share regulatory sequences that bind the same transcription factors.

Question 41

Epigenetics

Answer 41

Changes in the expression of a gene or set of genes that occur without changing the DNA sequence