RNA structure and transcription

Question 1

The central dogma of molecular biology

Answer 1

Concept that DNA is used to produce RNA and RNA used to produce protein
Transcription - template-directed polymerization reaction, DNA copied into RNA
Translation - RNA transcripts decoded, generate cellular proteins

Question 2

Structure of RNA

Answer 2

Is a linear polymer of nucleotides (polynucleotide)
Heterocyclen

Question 3

Stem-loop structures in DNA

Answer 3

Has 5’ monophosphate group and 3’ hydroxyl group
Contains intramolecular base-pairing interactions, caues irregular short helices, many have terminal (stem) loops
RNA can form double stranded helices
RNA normally has imperfect helical structures, that are kinked or bent or nucleotides are sticking out
S-L considered secondary structural elements in RNA
Helical structure of stems have major and minor grooves

Question 4

Base-pairing within RNA

Answer 4

B-P can be canonical (C-G and A-U) or non-canonical (GU called “wobble bp”)
Formed due to lack of regular helicals
Non-canonical bp can cause destabilisation because of … but also causes stabilisation because of hydrogen-bonds, so its neutral and is therefore allowed in RNA

Question 5

Long Range Tertiary structure interactions in RNA

Answer 5

BPairing can occur between bases faw away from each other, can form mini helicies within RNA
A-minor motif most common tertiary interaction in RNA
- Two consecutive A residues interact with adjacten bp in minor groove through sugar edge interation (and something else need to go back over the lecture)

Question 6

RNA transcription

Answer 6

Uses DNA-dependent RNA polymerases (RNAPs)
Genetic sequence in sense strand transcribed into RNA, so antisense strand used as template strand
Nucleotide triphosphates selected by BP with template strand, added 3’ end extended RNA strand
RNAP active site contains short RNA/DNA heteroduplex (a double stranded section of neucleotides)
Termination of transcription caused by destabilisation of heteroduplex

Question 7

Structure of transcription units

Answer 7

Transcription has start and stop positions that are definite
RNA polymerase target promoter region genes
Transcription occurs till polymerase reaches terminator region, then released from DNA
Adjacent genes can be transcribed in tandem (when polymerase move after each other), convergently (when polymerase come together) or divergently (when polymerase move away from each other)

Question 8

Structure of core RNAP in E coli

Answer 8

Number of enzymes synthesise RNA in absence DNA
In vitro transcription by DNAP enzyme demonstarted in 1960
E coli RNA polymerase core enzyme

Question 9

Sigma factor targets RNAP to gene promoters

Answer 9

Polymerase change cuases creation synthesis bubble that starts transcript
Need to relisten to this bit

Question 10

Eukaryotic cells have 3 nuclear RNA polymerases

Answer 10

All 3 are structurally similar (common and unique subunits) and are also related to bacterial polym (conserve the core structure)
All specialised to do different jobs
- RNA polymerase 1
- Very specific
- Only transcribes transcription unit
- Only generates rRNA
- RNA polymerase 2
- Generates protein coding transcripts
- Makes mRNA and noncoding RNAs
- RNA polymerase 3
- Transcripts many small, stably expressed something
- Makes tRNA and 5S rRNA

Question 11

gFTs assemble RNAP1II at eukaryotic gene promoters

Answer 11

TFIID - first complex to bind to promoter region of gene, identifies the TATA box (Promoter region)
Need to go back over this bit of the lecture