RNA structure & transcription

Question 1

Describe RNA structure

Answer 1

• Like DNA → polynucleotide
• Nucleotide = 3 phosphates
• Linked together by phosphodiester links
• Sugar unit is ribose (OH on 2’ carbon instead of H)
• Uridine instead of thymine (G→C, A→U)
• Single stranded

Question 2

Describe RNA’s stem-loop structure

Answer 2

• Contains intramolecular base pairing interactions = irregular short helices with terminal loops (stem loops)
• Stem-loops = secondary structural elements
• The helical structures of stems have a major and minor groove

Question 3

Describe the base pairing in RNA

Answer 3

can be canonical or non-canonical e.g between G & U = strengthen RNA

Question 4

Which base binds to Adenine in RNA?

Answer 4

Uradine

Question 5

Which base binds to cytosine in RNA?

Answer 5

Guanine

Question 6

Describe the A-minor motif in RNA

Answer 6

Most common tertiary interaction in RNA
→ Adenine forms H bonds with the minor groove of the canonical base pair
(pulls structure together, strengthens)

Question 7

Describe the process of RNA transcription

Answer 7

• RNA is synthesised by DNA-dependent RNA polymerase (RNAPs)
• Genetic sequence info in the coding strand is transcribed into RNA
• Nucleotide triphosphate (NTPs) are selected by base-pairing with the template strand and added to the 3’ and of the extending RNA strand
• The RNAP active site contains short RNA/DNA heteroduplex

Question 8

What is the transcription bubble?

Answer 8

where DNA has been pulled apart, to expose the nucleotides

Question 9

Describe the structure of transcription units

Answer 9

• Transcription has ‘start’ and ‘stop’ sites
• RNA polymerase is targeted to promoter regions of genes (where enzymes bind)
• Transcription occurs until the polymerase reaches the terminator region → where it’s released from the DNA
• Adjacent genes can be transcribed in tandem, convergently or divergently

Question 10

What does RNAP stand for?

Answer 10

DNA-dependent RNA polymerase

Question 11

Describe the role of sigma factors

Answer 11

Sigma factor targets RNAP to gene promoters:
Binds to RNA polymerase as its moving along the DNA = enables recognition of promoter regions
No sigma factor = low levels of RNA transcription

Question 12

Describe the eukaryotic RNAPs

Answer 12

→ eukaryotes have 3, structurally similar to bacteria = highly conserved

A particular polymerase will transcribe a specific group of genes (they have specialised roles)
RNAPI → rRNA
RNAPII → mRNA, noncoding RNAs
RNAPIII → tRNA, 5S rRNA

Question 13

What does RNAPI transcribe?

Answer 13

rRNA

Question 14

What does RNAPII transcribe?

Answer 14

mRNA, noncoding RNAs

Question 15

What does RNAPII transcribe?

Answer 15

tRNA, 5S rRNA

Question 16

Describe the process of targeting RNA polymerase to promoter regions in eukaryotes

Answer 16

→ Requires the assembly of a large protein complex
- Driven by complexes (general transcription factors) at the region called the TATA box
- Finally, a preinitiation complex (PIC) is formed = RNAP is bound to promoter region