26 expanded genetic code Flashcards
How many possible codons in the genetic code
64
Are there 61 types of tRNA (stop codons dont need)?
no
in most organisms, fewer than 45 types of tRNA are present
this is because of wobble base pairing
What is wobble base pairing
- pairing rules are relaxed at the third position of the codon (first position of the anticodon)
- First 2 need to follow the base pairing, but the 3rd position allows some flexibility
- Cell don’t need to waste resources to have 61, is redundant
- this way can reserve resources
How can tRNA also contain unusual modified nucleotides?
I = inosine, modified from A (looks similar)
reduce the number of tRNA needed to bring that glycine AA for translation
Does wobble base pairing exisit in both prokaryotes and eukaryotes?
yes
what are the advantages of wobble base pairing?
- less tRNA species are needed, save energy
- premits rapid dissociation of the tRNA from it codon during translation, strong pairing of 3 bases would limit the rate of translation
- 2 base is a bit loose, weaker bonding
Which stop codons correspond to which RF?
UAA - both
UAG - RF1
UGA - RF2
Are tRNA expressed equally?
no
What is codon bias?
the selective use of codons
biased codon usage is present in alsmot all sequenced genomes
what are 2 hypothesis of the existence of codon bias, why are they not expressed equally?
- mutation hypothesis - mutational pressures differs in different organisms
- selection hypothesis - codon bias provides a selective advantage by optimizing the level and accuracy of protein expression
What does biased codon usage affect?
protein expression level
what are the 2 types of codon?
Abundant and rare codon
for more abundant codons - need more tRNA to be efficient, dont want the tRNA to be the limiting factor
rare codon - very few of them
What does the optimized usage of codon increase?
increases the protein synthesis rate under most condition
What does non-optimal codon usage do?
improve bacterial fitness under certain conditions
What happens if more abundant codon is being used than normal?
ribosome works too fast = incorrectly folded protein or too much correctly folded protein
what are the benefits of having more rare than abundant codons?
allow normal speed of translation to correctly fold the protein, not too fast or too slow. If too fast, wont allow enough time for protein to fold properly
What are the 3 mechanisms of genetic code variation that generate genetic code diversity?
- codon bias
- codon reassignment
- ambiguous decoding
what does codon reassignment require?
evolution of a new tRNA to decode sense codons with a new AA or decode stop codons with an AA, or loss of the cognate tRNA
What is new tRNA
New tRNA refers to a type of transfer RNA that has evolved or been modified to recognize and bind to a specific codon
what are the changes that can occur in codon reassignment?
- stop to sense
- sense to stop
- sense to sense
Which stop codons uses which RF mechanism?
UAG - RF1
UGA - RF2
UAA - R1 and 2
How can codon reassignment be used by phage?
- use to interfere with the translation of the bacterial host
- Phage - infect host (bacteria) and conquer their cell machinary and produce as many virus protein to replicate themselves = survive
- phage reassign UAG stop codons to Gln = fewer UAG codons cant be targetted by host RF1 to inhibit phage genome
- phage expresses RF2 to suppress translation of UGA codons, which is found in host RF1
- Because RF1 of bacterial protein has some UGA codons in it, the phage’s RF2 can inhibit the translation of it so it becomes a stop codon and the host cant translate
- since phage has also reassigned UAG codons to Gln, they can use Gln-tRNA to drive expression
What is recoding?
tranditionally refers to partial codon reassignment that is context dependent
What is an example of recoding?
- UGA stop codons near a **SECIS **(sec insertion sequence element) are recoded to Sec in the presence of SelA and B while other UGA stop codons retain their abiity to signal translational termination
- SelA reprocress Ser (alr attached to tRNA) to Sec and SelB help incorporate it into the ribosome
- in the presence of SelA and B and SECIS, stop codon will not be stop codon and will add sec onto the protein and continue translation
What are the only known cases of natural genetic code expansion?
Sec and Pyl
what can UAG be reassigned to?
Pyl in the presence of EF-Tu
What can UGA and UAG be recoded to?
UGA - Sec with SelA B SECIS
UAG - Pyl with EF-Tu
what is ambiguous decoding
refer to simultaneous decoding of the same codon by 2 or more AA
single codon correspond to many AA
What are 3 ways ambiguous decoding can happen
- aminoacylation errors - tRNA is incorrectly charged with an AA - error in the aminoacetyl-tRNA synthetase enzyme
- ribosome errors - ribosome misread the codon and incorporate incorrect AA
- multiple aaRS recognise the same tRNA
What is an expanded genetic code?
an artificially modified genetic code in which on eo rmore specific codons have been re-allocated to encode an AA that is not among the 20 common naturally-encoded proteinogenic AA
what are the implications of a expanded genetic code?
if more than 20AA, maybe can generate some new beneficial protein
novel AA is possible cuz naturally there are modified AA i.e. Sec and Pyl, could be naturally incorporated into the protein
what are the 4 key prerequisites to expand the genetic code?
- the non-standard AA to encode
- an unused codon to adopt
- a tRNA that recognises this codon
- a tRNA synthetase that recognises only that tRNA an donly the non-standard AA
Did they find any evidence on expanded genetic code?
demonstrated synthetic X and Y as well as ACTG can be incorporated into the DNA
manage to incorporate it into bacterial cells in a confined enviornment
but dont know if it can be made into protein yet, after 3 years found they could
How were they able to get the unused codon prerequisites for expanded genetic code?
used codon reassignment
UAG, UAA and UGA are redundant - stop codons
scientist tried to remove all UAG codons and change them to UAA
Since UAG is gone, RF1 is no longer needed
still have UAA and UGA with RF2 to do the stop codon function
free up UAG codon for NSAA (new tRNA they generated) that recognise UAG (new repurposed codon to generate new AA)
worked
what are the concerns of expanded genetic code?
dk what these novel forms of life would do if released into the wild
What 2 processes allows us to balance accuracy, speed, and cost-effectiveness (and functional diversity) of translation?
recoding and expansion of genetic code
