Week 5 Readings Flashcards
two chemical differences between DNA and RNA
- the nucleotides in RNA are ribonucleotides (contain a ribose sugar) rather than deoxyribonucleotides
- RNA contains uracil (U) instead of the thymine (T) found in DNA - this can base-pair by hydrogen bonding with A
two structural differences between DNA and RNA
- DNA always occurs as a double-stranded helix; RNA is largely single stranded
- this allows it to fold into a variety of shapes; DNA is very still and cannot fold in this fashion
describe the main functional difference between DNA and RNA
whereas DNA functions solely as an information store, RNA can have structural, regulatory, or catalytic roles
how does transcription differ from DNA replication in terms of the binding between the DNA and the strand being formed?
RNA strand does not remain hydrogen-bonded to the DNA template strand. Instead, just behind the region where the ribonucleotides are being added, the RNA chain is displaced and the DNA helix reforms.
describe the work of RNA polymerase
- moves along DNA, unwinding the helix
- growing RNA chain elongated in the 5’ to 3’ direction
- incoming ribonucleoside triphosphate (ATP, CTP, UTP, and GTP) provide the energy needed to drive the reaction forward, like DNA synthesis
- RNA polymerases catalyse the formation of the phosphodiester bonds that link the nucleotides together and form the sugar-phosphate backbone of the RNA chain
two main differences between RNA and DNA polymerase
- RNAP turns ribonucleoside triphosphates as substrates not deoxyribocleoside triphosphates
- RNAP can start RNA chain without a primer and do not accurately proofread their work
how does transcription start and stop in bacteria?
- bacterial RNA contains a subunit called a sigma factor that recognises the promoter of a gene
- once transcription has begun, the sigma factor is released and the polymerase moves forward and continues synthesising the RNA
- elongation continues until the polymerase encounters a terminator sequence
- after transcribing this sequence into RNA the enzyme halts
are both the promoter and terminator sequences transcribed?
no; only the terminator
how do we name bacterial promoter sequences?
- numbers indicate positions of nucleotides counting from the first nucleotide transcribed, which is designated + 1
- all bacterial promoters contain DNA sequences at positions -10 and -35
why is the asymmetry of the promoter important?
it orients the polymerase and determines which DNA strand is transcribed
how does the sigma factor see the promoter within the double helix?
each base presents unique features to the outside of the double helix, allowing the sigma factor to initially identify the promoter sequence without having to separate the entwined DNA strands
how does the RNAP know which DNA strand to transcribe?
- every promoter has a certain polarity: it contains two different nucleotide sequences, laid out in a specific 5’ to 3’ order.
- these asymmetric sequences position the RNA polymerase such that it binds to the promoter in only one orientation
- because the polymerase can synthesise RNA only in the 5’ to 3’ direction, once the enzyme is positioned on DNA it can only use the DNA strand that is oriented in the 3’to 5’ direction as its template
four differences between eukaryotic and prokaryotic initiation of transcription
- eukaryotic uses more than one RNAP; RNAP I and II transcribe genes encoding tRNA, rRNA, and other RNAs that play structural and catalytic roles . RNAP II transcribes the rest (inc proteins)
- bacterial RNAP relies on a single accessory protein - sigma factor - to initiate transcription. Eukaryotic RNA polymerase requires many general transcription factors
- in eukaryotes, single genes are controlled by a large variety of regulatory DNA sequences; more complex forms of transcriptional regulation than bacteria
- eukaryotic transcription initiation must deal with the packing of DNA into nucleosomes and higher-order forms of chromatin structure
describe the initiation of transcription in eukaryotes
- most eukaryotic promoters contain a TATA box (segment of DNA composed primarily of T and A nucleotides)
- TATA is recognised by TBP, a subunit of TFIID.
- The binding of TFIID distorts the DNA and enables adjacent binding of TFIIB
- rest of the general transcription factors, as well as the RNAP assemble at the promoter, forming a transcription initiation complex
- using energy provided by ATP hydrolysis, TFIIH opens the double helix at the transcription point and phosphorylates RNAP II’s tail, releasing its attachment to the general transcription factors and allowing it to begin transcription
- once RNAP II moves away from the promoter, it is loaded with elongation factors and most of the general transcription factors are released from the DNA except for TFIID
- at the end of the gene, RNAP is dephosphorylated by protein phosphatases
how are mRNA processing steps different in bacteria compared to eukaryotes?
in bacteria, the 5’ end of an mRNA molecule is simply the first nucleotide of the transcript and the 3’ end is simply the end of the chain synthesised by RNAP
how do RNA processing proteins know where to assemble?
phosphorylation of the tail of RNA polymerase II allows the proteins to assemble there
what are ribozymes
RNA molecules that have the ability to catalyze specific biochemical reactions, including RNA splicing in gene expression
how is the nucleus functionally organised?
RNAs are synthesised and processed within biomolecular condensates that serve to condensate these components:
- large nucleoli: subcompartments in which rRNAs are synthesised and ribosomes assembled
- Cajal bodies: maturation of snRNPs and snRNAs takes place
- interchromatin granule clusters: stockpiles of snRNPs and other RNA-processing components used in the production of mRNA
how are biomolecular condensates held together>
by the weak noncovalent interactions that continually form and break between their constituent macromolecules
how does the cell ensure that only mature eukaryotic mRNAs are exported from the nucleus?
- transport of mRNA from the nucleus to the cytosol is highly selective
- 5’ cap and poly-A tail of a mature mRNA molecule are marked by proteins that recognise these modifications
- successful splices are marked by exon junction complexes
- once an mRNA is deemed export ready a nuclear transport receptor associates with the mRNA and guides it through the nuclear pore and into the cytosol
why is the lifespan of an mRNA important?
- it helps the cell control how much protein will be produced
- this is usually controlled by the 3’ UTR
- each mRNA molecule is eventually degraded into nucleotides by ribonucleases (RNases) in the cytosol
