RNA structure & transcription Flashcards
Describe RNA structure
- 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
Describe RNA’s stem-loop structure
- 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
Describe the base pairing in RNA
can be canonical or non-canonical e.g between G & U = strengthen RNA
Which base binds to Adenine in RNA?
Uradine
Which base binds to cytosine in RNA?
Guanine
Describe the A-minor motif in RNA
Most common tertiary interaction in RNA
→ Adenine forms H bonds with the minor groove of the canonical base pair
(pulls structure together, strengthens)
Describe the process of RNA transcription
- 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
What is the transcription bubble?
where DNA has been pulled apart, to expose the nucleotides
Describe the structure of transcription units
- 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
What does RNAP stand for?
DNA-dependent RNA polymerase
Describe the role of sigma factors
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
Describe the eukaryotic RNAPs
→ 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
What does RNAPI transcribe?
rRNA
What does RNAPII transcribe?
mRNA, noncoding RNAs
What does RNAPII transcribe?
tRNA, 5S rRNA
Describe the process of targeting RNA polymerase to promoter regions in eukaryotes
→ 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
