Long answer exam questions Flashcards
(14 cards)
DNA replication (prokaryotes)
semiconservative replication meaning each daughter molecule has one parental strand and one newly synthesised strand
single origin of replication (oriC) where DNAa binds causing unwinding of AT rich area
DNAb healicase unwinds DNA to create a replication fork which is stabilised by SSB
primase sysnthesises short RNA primers to initiate synthesis
DNA pol II adds nucleotides to 3’ end of RNA primer in the 5’ -> 3’ direction
leading strand is synthesised continuously
legging strand is synthesised discontinuously forming Okazaki fragments
DNA pol I removes RNA primers and replaces them with DNA
DNA ligase joins Okazaki fragments forming phosphodiester bonds
Eukaryotic DNA replication
semiconservative replication which means daughter molecules have a parent strand and a newly synthesised strand
has multiple origins of replication where the ORC binds
MCM acts as helicase and unwinds DNA
Topoisomerase I/II relives torsional strain by removing supercoil
RPA stabilises ssDNA
DNA polymerase epsilon synthesises leading strand continuously
DNA polymerase delta synthesises lagging strand discontinuously to form Okazaki fragments
DNA ligase I forms phosphodiester bonds completing DNA strand
at chromosome ends telomerase extends 3’ end with RNA template
Eukaryotic transcription initiation
TFIID binds to TATA Box via TBP
TFIIB recruited and binds to BPE which helps with orientation of synthesis
TFIIA binds to stabilise TBP
TFIIF chaperones RNA polymerase II to promoter
TFIIE binds and recruits TFIIH
Its helicase unwinds DNA and its kinase phosphorylates serine 5 to initiate transcription and release RNA polymerase II from promoter
Eukaryotic transcription elongation
DNA unwound around 3 base pairs before entering active site of RNAP
DNA held in place by RBP II
Mg 2+ required for formation of phosphodiester bonds
RNA pol II catalyses addition of nucleotides & proof reads
TFIIS recognises damage to DNA
Elongator complex helps transcribe chromatin template with acetyl transferase
5’ capping
fascilitates translation & stops degredation
occurs in elongation
phosphohydrolase removes phosphate from 5’ end
addition of guanine to N7 position
methylation occurs forming m7G cap
splicing
preRNA spliced by spliceosome containing snRNA
alternate splicing allows formation of mRNA isoforms
enzymes associate with serine 2
intronic and exonic enhancers and silencers control alternate splicing
removal of introns forms lariat structure
3’ AG and polypyrimidine tract
5’ GT
occurs in elongation
poly(A) tail
protects from degradation and transport
3’ end polyadenylated by polymerases
cleavage site recognised by CPSF and CstF so cleavage occurs and adenine bases are added forming poly(A)tail
Eukaryotic termination termination
there is no defined termination site for RNA pol II
it stops at various distances downstream from coding
eukaryotic translation
small ribosome 40S subunit binds to 5’ cap of mRNA
finds AUG start codon
initiator tRNA binds
large subunit 60S joins and forms 80S ribosome
tRNA brings amino acid and match with the correct codon
ribosomes catalyse the formation of a peptide bond and chain grows
when the ribosome reaches the stop codon no tRNA match
a release factor binds and frees the ribosome and the protein
energy for this is provided by hydrolysis of GTP
Prokaryotic transcription initiation
RNA polymerase core enzyme binds to sigma factors and form holoenzyme which can recognise the promoter region on the DNA
It binds tightly to the -35 and -10 region forming closed complex
The DNA then begins to unwind at the -10 and forms the open complex
abortive initiation occurs and short RNA fragments are transcribed
These are then released clearing the RNA polymerase for elongation
tProkaryotic translation elongation
RNA polymerase releases sigma factor
Core enzyme continues on its own and RNA polymerase adds nucleotides to 3’ end of RNA
transcription bubble moves along DNA
New RNA synthesised and DNA behind RNA polymerase re-anneals
This continues until termination signal reached.
Prokaryotic roh independent transcription termination
termination sequence transcribed of a GC rich inverted repeat
This then forms a hairpin loop as the inverted repeat is complementary so bind together with the nucleotides in between forming a loop
Then theres a long chain of As which pair with a long chain of Us transcribed by RNA polymerase
As the AU bond in very weak it causes RNA polymerase to detach from DNA and mRNA is released
Prokaryotic Rho dependent termination
Rho protein, a helicase, binds to a rut site on the RNA and moves along DNA using ATP
A pause site at the end of the gene causes RNA polymerase to stall
Rho catches up and when it reaches RNA polymerase it unwinds the RNA-DNA hybrid and RNA is released
Binding of amino acids to tRNA
Aminoactyl tRNA synthatase catalyses addition of amino acids to tRNA based on different binding energies
This converts ATP to AMP and PPi
PPi is then cleaved to Pi so each ‘activated’ amino acid costs 2 ATP
