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

• Phosphate group
• Ribose sugar
• A nitrogenous base

They have a 5’ phosphate group and 3’ hydroxyl group

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

Intramolecular Base Pairing: - Imagine the single-stranded RNA molecule folding back on itself. If complementary base pairs (A-U and G-C) are present within the sequence, they can form hydrogen bonds.

• Stem: The region where these complementary base pairs form a double-stranded helix, resembling the stem of a plant.
• Loop: The unpaired nucleotides at the end of the stem form a single-stranded loop, like the top of a hairpin.

Question 5

Describe the major and minor grooves within the RNA

Answer 5

The major groove of RNA is narrow and many interactions with RNA involve the minor groove.

Question 6

What is the secondary structure of RNA?

Answer 6

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

Stem- loops are elements of the secondary structure of an RNA

Question 7

What is the tertiary structure of RNA?

Answer 7

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

They are able to fold u

Question 8

What is A minor motif?

Answer 8

Involves two adjacent adenosine nucleotides inserted into the minor groove of an RNA stem that interact along the edge of G:C base-pairs within that stem structure

Most common tertiary interaction within RNA

Question 9

What is RNA transcription?

Answer 9

RNA transcription is the first step in gene expression, where the information stored in DNA is transferred to RNA

Question 10

What is RNA made by?

Answer 10

RNA polymerases (RNAPs)

Question 11

Describe the process of transcription

Answer 11

1. The RNA transcript has the same sequence as the coding strand in the DNA
2. RNA is synthesised in a 5’ to 3’ direction. A short stretch of DNA in the catalytic centre of the RNA polymerase is pulled apart to form a transcription bubble
3. NTP’s are selected for addition to the 3’ end of the RNA by base- pairing with the template strand.
4. Destabilisation of the short RNA/DNA heteroduplex in the catalytic centre ( due to inherent base-pair instability) causes release of the RNA polymerase from the DNA and transcription termination

Question 12

What does the RNA active site contain?

Answer 12

It contains a short RNA/DNA Heteroduplex

Question 13

What are the structural transcription units?

Answer 13

1. Coding sequence
2. Promoter
3. Terminator

Question 14

What happens in the promoter region?

Answer 14

RNA polymerase is targeted to promoter region of genes.

Question 15

What happens in the terminator region?

Answer 15

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

Question 16

What is RNAP?

Answer 16

RNA polymerases (RNAPs).

Question 17

What does the E.coli RNA polymerase core enzyme contain?

Answer 17

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

2 Alpha, 1 beta, 1 beta prime, 1 omega

Question 18

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

Answer 18

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

Question 19

What is the factor that target RNAP to genes?

Answer 19

Prokaryotic Sigma factors.

Question 20

What do prokaryotic sigma factors do?

Answer 20

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

Question 21

How is target RNAP to genes done?

Answer 21

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

Question 22

What are the three nuclear polymerases of eukaryotes?

Answer 22

1) RNA polymerase I - rRNA
2) RNA polymerase II - mRNA and noncoding RNAs
3) RNA polymerase III - tRNA, 5S rRNA

Question 23

Are gTFs needed for RNAPII?

Answer 23

Yes.
Multiple general transcription factors (gTF) are needed to assemble RNAP 2 onto gene promoters. These are called TFIIA, TFIIB etc

gTFs are required for the recruitment of RNAP2 to all its promoters. Assembly of the PIC involves a multi-step pathway

The assembled PIC initiates transcription upon activation through specific signals

Eukaryotic cells do not express sigma factors.

Question 24

What are gTFs?

Answer 24

General transcription factor

Question 25

What are the similarities and differences of transcription in prokaryotic and eukaryotic systems?

Answer 25

• Both transcriptions aim to synthesise RNA molecules from a DNA template
• Both utilise RNA polymerase enzymes to catalyse the synthesis of RNA
• Pro - Single type of RNA polymerase
• Euk - Multiple types of RNA polymerase (e.g., RNA polymerase I, II, III)

Question 26

What is meant by the secondary and tertiary structure of RNA?

Answer 26

Secondary: Refers to the local folding patterns of the RNA molecule, primarily driven by base pairing between complementary

Tertiary: The overall three-dimensional shape of the RNA molecule, resulting from interactions between secondary structural elements and other parts of the molecule