L6 RNA structure, transcription

Question 1

What is the central dogma of molecular biology?

Answer 1

1. DNA is copied into RNA by a template-directed polymerisation reaction called transcription.
2. RNA transcripts can be decoded to generate cellular proteins in a process called translation.

Question 2

What is RNA made up of?

Answer 2

Linear polymer of nucleotides

Question 3

What are the four nucleotides that make up the RNA?

Answer 3

1. Uracil
2. adenine
3. Guanine
4. cytosine

Question 4

Explain the stem-loop structures in RNA?

Answer 4

1. They have a 5’phosphate group and 3’hydroxyl group.
2. Intramolecular base-pairing allows short helices.
3. The helices are irregular
4. Stem loops are secondary elements
5. The major grrove in narrow and many interactions involve the minor groove.

Question 5

What is the secondary structure of RNA?

Answer 5

It is the two dimensional map that is defined through localised intramolecular base pairing.

Question 6

What is the tertiary structure of RNA?

Answer 6

Tertiary structure interactions connect regions of RNA that are separated in the secondary structure. These can be canonical base-pair interactions.

Question 7

What is a minor motif?

Answer 7

A minor motif is RNA consisting of two ajacent A residues that interact with the edge of a G:C base pair.

Question 8

What is RNA transcription?

Answer 8

RNA transcription is the first step in gene expression, the process by which the information in a gene is used to create a functional product, such as a protein.

Question 9

What is RNA made up of?

Answer 9

RNA polymerases (RNAPs)

Question 10

How is transcription done?

Answer 10

1. The genetic sequence information in the coding (sense) strand is transcribed into RNA.
2. NTP’s are selected by base pairing with the template strand and are added into the 3’ extending RNA strand.

Question 11

What does the RNA active site contain?

Answer 11

RNA Heteroduplex

Question 12

What are the structural transcription units?

Answer 12

1. Regulatory sequence
2. Promoter region
3. Terminator region

Question 13

What happens in the promoter region?

Answer 13

RNA polymerase is targeted to promoter region of genes.

Question 14

What happens in the terminator region?

Answer 14

Transcription occurs until the polymerase reaches the terminator region, where it is released from the DNA.

Question 15

What is RNAP?

Answer 15

RNA polymerases (RNAPs).

Question 16

What is the core structure of the RNAP of E.coli?

Answer 16

The E. coli RNA polymerase core enzyme is a protein complex containing 5 subunits (a,a,b,b,w).

Question 17

What are the subunits of E.coli RNAP and give functions?

Answer 17

1. a,a (alpha) - Binds transcription factors
2. b,b (beta) - Catalytic
3. w (Symbol) - assemly and stability.

Question 18

What is the factor that target RNAP to genes?

Answer 18

Prokaryotic Sigma factors.

Question 19

What does prokaryotic sigma factors mean?

Answer 19

In prokaryotes, sigma (s) factors provide specificity to the RNAP for the gene promoter.

Question 20

How is target RNAP to genes done?

Answer 20

1. RNAP’s initiate transcription without an additional primase activity.
2. Sigma factor is released from RNAP as it moves away from the promoter.

Question 21

What are the three nuclear polymerases of eukaryotes?

Answer 21

1. mRNA - Messenger - RNAP 2
2. tRNA - Transporter - RNAP 3
3. rRNA - Ribosomal - RNAP 1

Question 22

How is eukaryotic transcription different from prokaryotic?

Answer 22

1. Eukaryotic cells do not express sigma factors.
2. Instead multiple general transcription factors (gTF) are needed to assemble RNAP 2 onto gene promoters.
3. Then gTFs are required for the recruitment of RNAP2 to all its promoters.
4. PIC preinitiation complex is assembled and it inititaed transcription upon activation by specific signals.