Overview of Eukaryotic Gene Expression

Question 1

What is the primary purpose of gene control in multicellular organisms?

Answer 1

Ensure precise developmental programs so that the proper genes are expressed in the proper cells at the proper times.

Question 1

Name the two scenarios where gene control takes place.

Answer 1

Embryologic development and cellular differentiation.

Question 2

Transcription in eukaryotes takes place on DNA that is wrapped in ________.

Answer 2

Chromatin.

Question 3

Chromatin needs to be open for two reasons. Name them.

Answer 3

For the gene to be activated and for transcription to proceed.

Question 4

What is epigenetic regulation?

Answer 4

Chromatin-mediated regulation (entirely new mechanism compared to prokaryotes).

Question 5

Describe heterochromatin.

Answer 5

• Regions of chromosome that are more intensely stained.
• DNA is more tightly packed.
• It is rich in repetitive DNA (transposons), centromeres, and telomeres.
• It is not accessible to transcriptional machinery.
• Inactive genes are found here.

Question 6

Describe euchromatin.

Answer 6

• ‘Eu’ = True
• Lightly stained chromosome regions
• Active genes are found here

Question 7

Describe euchromatin.

Answer 7

• ‘Eu’ = True.
• Lightly stained chromosome regions.
• Active genes are found here.

Question 8

Where are inactive genes found?

Answer 8

Heterochromatin.

Question 9

Where are active genes found?

Answer 9

Euchromatin.

Question 10

What kind of RNA is transcribed by RNA polymerase I?

Answer 10

Pre-rRNA (28S, 18S, 5.8S rRNAs)

Question 11

What is the function of Pre-rRNA?

Answer 11

Ribosome components and protein synthesis.

Question 12

What are the four kinds of RNAs transcribed by RNA Polymerase II?

Answer 12

• mRNA
• snRNAs
• siRNAs
• miRNAs

Question 13

What is the function of mRNA?

Answer 13

Encode proteins.

Question 14

What is the function of snRNAs?

Answer 14

RNA splicing.

Question 15

What is the function of siRNAs?

Answer 15

Chromatin-mediated repression and translation control.

Question 16

What is the function of miRNAs?

Answer 16

Translation control.

Question 17

What are the five kinds of RNA polymerase transcribed by RNA polymerase III?

Answer 17

• tRNAs
• 5S rRNA
• snRNA U6
• 7S RNA
• Other small stable RNAs

Question 18

What is the function of tRNAs?

Answer 18

Protein synthesis.

Question 19

What is the function of 5S rRNA?

Answer 19

Ribosome component and protein synthesis.

Question 20

What is the function of snRNA U6?

Answer 20

RNA splicing.

Question 21

What is the function of 7S RNA?

Answer 21

Signal recognition particle for insertion of polypeptides into the endoplasmic reticulum.

Question 22

What is the function of ‘other small stable RNAs’?

Answer 22

Various functions, unknown for many.

Question 23

How many polypeptides are found in RNA pol II?

Answer 23

12 (RPB1-RPB12)

Question 24

True or false? Eukaryotic RNA polymerase share a very high level of homology with the yeast RNA pol II?

Answer 24

True.

Question 25

The clamp domain in the polymerase ________ accommodates DNA and then is closed by _______.

Answer 25

RPB1, a bridge.

Question 26

Where does the synthesized RNA exit through?

Answer 26

A "channel".

Question 27

What is unique about the RPB1 subunit of RNA polymerase II?

Answer 27

It contains a carboxy-terminal domain (CTD). This is not found in any other polymerase, prokaryotic or eukaryotic. Key role in initiation, release, elongation, and processing of the synthesized RNA.

Question 28

What is the role of the CTD (carboxy-terminal domain) found in RNA polymerase II of the RPB1 subunit?

Answer 28

Involved in many regulatory interactions and plays a key role in the initiation, release, elongation and processing of the synthesized mRNAs.

Question 29

What is the amino acid sequence of the CTD? How many repeats exist regularly? In mammals?

Answer 29

Tyr-Ser-Pro-Thr-Ser-Pro-Ser. 26 repeats. In mammals it is 52 repeats. (The Sad Player Tried Some Pro Soccer). TSPTSPS

Question 30

What is the fate of the Ser residues in the CTD upon transition from initiation to elongation.

Answer 30

The Ser residues are phosphorylated.

Question 31

True or False? The CTD is structured and can be analyzed by crystallography?

Answer 31

False.

Question 32

List the four ways that RNA polymerase II transcribed genes are regulated?

Answer 32

1. CONSERVED BASAL ELEMENTS (CORE PROMOTER SEQUENCES) 2. Promoter proximal binding sites for transcriptional activators. 3. Distal enhances or repressors. 4. Chromatin structure.

Question 33

Name the position of the Core Promoter Element 'BRE'

Answer 33

-37 to -32

Question 34

Name the position of the Core Promoter Element 'TATA Box'

Answer 34

-31 to -26

Question 35

Name the position of the Core Promoter Element 'Inr' (Initiator)

Answer 35

-2 to +4

Question 36

Name the position of the Core Promoter Element 'DPE' (Downstream promoter element)

Answer 36

+28 to +32

Question 37

At promoters regulated by TATA box and initiator transcription starts at a defined point. Which TGCA does it usually bind to?

Answer 37

A

Question 38

Where is the TATA box prevalent in?

Answer 38

Highly transcribed genes.

Question 39

Some genes contain an initiator but no TATA box. Are these initiators highly or poorly conserved?

Answer 39

Poorly

Question 40

'BRE' is know as the TFII__ (A-H) Recognition Element

Answer 40

TFIIB

Question 41

RNA polymerases must recognize the promoter and correctly INITIATE transcription at a very specific point, however, it cannot do this alone. What does it require the help from?

Answer 41

General POLII Transcription Factors (GTFs).

Question 42

What do the GTFs assemble?

Answer 42

The preinitation complex over the core promoter sequences.

Question 43

True or False? Protein kinases release the polymerase?

Answer 43

True

Question 44

List the 2 types of RNA Pol I TFIs?

Answer 44

TFIA and TFIB (A,B)

Question 45

List the 5 types of RNA Pol 2 TFIIs?

Answer 45

TFIIA, TFIIB, TFIID, TFIIE, TFIIH (A,B,D,E,H)

Question 46

List the 2 types of RNA Pol 3 TFIIIs?

Answer 46

TFIIIB, TFIIIS (B,S)