Sept 6 Central Dogma of Molecular Biology Flashcards
what is the central dogma and the steps? (language analogy)
DNA synthesis –> replication
making a perfect copy
RNA synthesis –> transcription
rewriting in a different nucleotide font
Protein synthesis –> translation
rewriting in a different language (nucleotide to amino acid)
what are the 3 phosphates called on the rNTP
alpha, beta and gamma
what is the template in transcription?
exposed DNA strand
what enzyme is involved in transcription and what does it do?
RNA polymerase
catalyses the attack of the 3’ OH on the alpha phosphate of the rNTP
what happens to the other two phosphates of the rNTP?
they are “dropped”
to what end of the growing RNA strand are nucleotides added? and what is the direction relative to the DNA strand
the 3’ end
antiparallel
how do rNTPs come in contact with the growing RNA strand?
they diffuse randomly
to which strand of DNA is the new RNA strand identical with?
the non template strand
except for the substitution of T for U
where does transcription start? (where RNA polymerase starts its action)
at the promoter region
which enzymes unfolds the DNA molecule?
DNA helicase
what is formed when the RNA polymerase enzyme binds to a promoter and causes two DNA strands to detach?
the transcription bubble
moves along the DNA
unidirectionally!!
what happens as RNA polymerase advances along the strand?
the DNA duplex reforms behind the enzyme
“kicks out” the newly synthesised RNA strand, which exits through a channel in the polymerase
5’ end first
when does RNA polymerase stop?
certain DNA sequences destabilise the attachment of the enzyme to the DNA as it moves
RNA polymerase falls off DNA and releases RNA chain
what are the similarities between DNA transcription and DNA replication? (7)
- the template is the DNA
- DNA duplex locally unwound by helicase at initiation sites to expose templates
- chain growth at 3’ end, antiparallel to template
- monomers are dNTPs
- direct interaction (base pairing) between template DNA and incoming monomer
- attack of the 3’ OH on alpha phosphate of the incoming NTP
- beta and gamma phosphates dropped
what are the differences between DNA replication and transcription? (4 categories)
transcription:
monomers –> rNTPs
start and stop sites on template
newly synthesised strand (RNA) separates from template strand
only one of the original DNA strands is a template strand
start with one double strand DNA and end with that plus the RNA produced
replication:
monomers –> dNTPs
start sites (origins) but no stop sites
newly synthesised strand never separates from template
both of the original DNA strands independently serve as template strands
start with one molecule of DNA and end with two
what are the “words” for translation?
codons, made of three nucleotides
how many codons are there?
64
what does it mean when we say that the genetic code is degenerate?
several different codons code for the same amino acid
what are the three “stop” codons?
UAA, UAG, UGA
what is the “start” codon and what amino acid does it code for?
AUG
codes for methionine
what is the “adaptor” between the nucleotide and the amino acid sequence? and what does it also do
tRNA
energises the amino acid
what is the form of amino acids monomers used in translation?
high energy amino-acyl tRNA esters
what is present on the tRNA?
the anticodons: 3 nucleotide sequence that is complimentary to a codon
what are the different components of a ribosome?
ribosomes are ribonucleo-protein particles (RNA+protein)
consist of a large and small subunits
what is the template for protein synthesis?
mRNA
what does the large subunit act as?
acts as a catalyst
what reaction does the large subunit catalyse?
peptidyl transferase
(transferring the peptide)
what is the RNA world hypothesis?
hypothesis that RNA involved as an informational biopolymer before proteins, and even before DNA (maybe before cells)
suggested by the many key roles of RNA in protein synthesis
what do DNA polymerases require for the synthesis of a new DNA strand?
- a single stranded DNA template
- a DNA primer base paired with the template, and with a free OH group at the 3’ end to accept a new nucleotide
- a source of dNTPs precursors
what is a primer?
a short nucleotide sequence containing a free 3’ hydroxyl group that forms base pairs with complimentary template strand
acts and functions as the starting point for the addition of nucleotides to copy a template strand
where will the deoxyribonucleotides be added?
added to the free hydroxyl group at the 3’ end of the primer
which enzyme catalyses the release of the two phosphates as inorganic phosphates?
pyrophosphatase
what happens after the addition of a nucleotide?
a new primer 3’ end will be available to accept the next nucleotide
what is the site called where all the proteins come together to carry out the synthesis of a daughter strand?
the replication fork
which enzymes relieves torsional stress produced by the unwinding of DNA?
topoisomerase I
what is the major complication in the operation of a DNA replication fork?
DNA strands are antiparallel, and DNA polymerases can only add nucleotides in one direction
therefore there is a leading (continuously replicated) strand and a lagging strand
how is the lagging strand synthesised?
discontinuously, from multiple RNA primers that are formed periodically as each new region of the duplex is unwound
what does the elongation of the primers in the lagging strand produce?
okazaki fragments
the fragments are then tied together as each growing fragment approaches the previous primer
in what direction relative to the movement of the replication fork does the growth of the lagging strand occur?
in the opposite direction
which enzyme joins the okazaki fragments?
DNA ligase
what are the three stages of transcription?
initiation
elongation
termination
where does transcription happen?
in the cytoplasm
what is RNA splicing?
excise the introns and stitch together the coding exons
where does protein synthesis (translation) occur?
in the cytoplasm
what is the sequence of codons that runs from specific start to stop codon called?
the reading frame
how can the correct reading frame for a given mRNA sequence be identified?
it is the longest open reading frame that is not interrupted by stop codons
what is the base sequence at the 3’ end of a tRNA?
CCA
what are the two components of ribosomes?
ribosomes are made of 50% RNA and 50% protein approximately
both contribute to its enzymatic activity
what is a ribozyme?
an enzyme that also contains RNA (like ribosomes)
do stop codons code for amino acids?
no
