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FunMed Week 3 > RNA translation & protein targeting > Flashcards

RNA translation & protein targeting Flashcards

1
Q

(basic) how are proteins made from RNA?

A
  • RNA acts as a template for the production of proteins in the cytoplasm
  • ribosomes synthesis proteins from the RNA
  • proteins are synthesised by the linking of a.a. to form peptide bonds
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2
Q

each 3 nucleotides on mRNA strand makes up what?

A

a codon: represents an amino acid.

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3
Q

what are rules for genetic code?

A
  1. genetic code is triplet code: three nucelotide codon = one a.a.
  2. codons are successive and non overlapping
  3. genetic code is almost universal
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4
Q

what are the DNA and RNA start and stop codons?

A

RNA: start - AUG. stop - UAA, UGA, UAG

DNA: start - ATG. stop - TAA, TGA, TAG

-

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5
Q

can a.a. be coded for more than one codon?

A

YES - e.g. glycine - (GGU / GGC / GGA / GGG)

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6
Q

how do you start reading DNA sequence?

A

- always read 5’ to 3’ (reading from N terminal to C terminal)

  • start from the start codon -> start from the A of the AUG / ATG.
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7
Q

what is codon bias?

A

there are 64 possible combinations, but only 20 amino acids -> some amino acids are represented by more than one a.a.

e.g. glycine -> can be encoded by 4 different codons, but GGC codes for 34% (more than the other 3 codons) = codon usage bias

(codon bias varies from species to species)

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8
Q
A
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9
Q

what needs to happen to mRNA before becomes final protein?

explain what rRNA, tRNA are and what they do. are they the final products of gene expression or not?

A

- mRNA has to be translated into protein for functional protein to be formed. function: mRNA caries genetic information from the DNA

  • rRNA gene makes the 60S and 40S ribosome. function: rRNA acts to catylse the process translation
  • tRNA gene encodes for the different transfer RNA genes. function: tRNA converts the mRNA to a.a.
  • both rRNA and tRNA are the final products of gene expression. functionally active as the RNA molecule
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10
Q

draw schematic diagram of ribosome

what are the three different sites on a ribosome?

A

three sites:

A site. (tRNA binding site)

P site - bind tRNA to ribsome

E site - tRNA goes before exiting

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11
Q

two most important sites on tRNA?

A

2 areas of note:

  1. one end is a of the molecule is attached to a amino acid group at one end. the a.a. is catalysed by aminoacyl tRNA synthase ( enzyme that attaches the appropriate amino acid onto its corresponding tRNA)
  2. anti-codon region -> sequence here is the anti-codon / complementary sequence to the mRNA
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12
Q

what is the function of tRNA?

A

translates between RNA and amino acid

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13
Q

what does aminoacyl RNA transfer synthase enzyme do?

A

(editing site on the tRNA)

(is an enzyme that attaches the appropriate amino acid onto its corresponding tRNA)

corrects its own errors, adds correct amino acids onto the tRNA, via hydrolysis reaction.

e.g. leucine and valine are very similar -> can correct for this

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14
Q

what is tRNA and wobble?

what is another way that can increase no. codons from tRNA

A
  • there are 64 possible codon comibations, but there are not 64 tRNAs
  • therefore get wobble at the 3rd position of codon, where can change the last bp on the anti-codon
  • allows a single tRNa to recognise more than one codon

ALSO

can use modified adenosine: Inosine. inosine can regcognise A, C or U

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15
Q

what are the different base pairs that can be coded for on tRNA?

A
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16
Q

how can untranslated regions of RNA structure can have effects on translational efficiency?

A
  • structure can prevent efficient ribosome loading. masks the translational start site
  • other proteins / temperature can effect RNA structure / decreased translation
17
Q

basic overview of translation?

A
  1. initiation
  2. elongation
  3. termination
18
Q

what is Methionine?

A

the start codon, AUG, which codes for the amino acid methionine.

19
Q

explain the mechanism of initiation of translation

A

(- recruitment of proteins to the 5’ cap binding region of mRNA occurs. this protein complex involves proteins called eukaryotic initiation factor (elF)4F. also includes the initiator methionine tRNA (first AUG in protein)

  • this complex is taken to the ribosome. the ribosome allows the recruitment of the initiator methionine and then the initiation of translation

- 40S scans mRNA in 5’ to 3’ direction until an appropriate start codon is found )

  • the small subunit of a ribosome binds to AUG start codon
  • a specific initiator transfter RNA (tRNAiMet) carrying methionine binds to the AUG start codon
  • the large 60S subunit of a ribosome binds to this complex such that the tRNA occupies the P site
20
Q

what is the IRES region?

A

internal ribosome entry site

not all translation starts from the CAP

21
Q

explain mechansim of elongation process of translation

A
  • tRNA with complementary anti-codon binds to the mRNA, occupying the A site in the ribosome
  • a peptide bond forms between two amino acids (the first a.a. and the a.a. bought in by tRNA)
  • the bond between the amino acid and the first tRNA is cleaved
  • the ribosome moves one codon further along the mRNA in 5’-3’ direction
  • the empty tRNA moves from the P to the E site
  • the A site is empty and ready for anther tRNA
  • the first, now uncharged tRNA is released from E site.
22
Q

explain the process of termination of translation

A
  • ribosome reaches a stop codon (UAG, UAA or UGA)
  • polypeptide released from the ribosome
  • tRNA is release from ribosome
  • ribosomal subunits dissociate from the mRNA
23
Q

where do proteins go if they are produced in RER or cytoplasm?

A
  • if proteins are synthesised in cytoplasm, destined for: cytoplasm, nucleus, mt or peroxisomes
  • if proteins are synthesised on RER, destined for export. go through golgi (carb can be added) and exit. OR can enter lysosome
24
Q

where do proteins know where to go?

A
  • proteins undergo protein targeting of short sequence of a.a. get tags that make a unique address

- can be on middle, N - or C- terminal of protein

  • BOTH where the tag is and what the tag is determines where protein is targeted to

(need specfic e.g?)

25
Q

how does protein targeting to ER occur?

A
  • polypeptide chain will have an endoplasmic reticulum (ER) signal sequence on it
  • the ER signal sequence interacts with signal recognition particle (SRP)
  • the SRP binds to receptor (on a translocation channel) within the membrane of ER

- the SRP leaves complex

  • the newly synthesised protein can translocate through the translocation channel.

- SRP is cleaved

  • leaves the new folded protein in correct place
26
Q
A
27
Q

what are differences in transcription and translation between pro and eukaryotes?

A

different RNA pol

different ribosome strucutre

CAN USE FOR TARGETS FOR ANTIBIOTICS

28
Q

how does chloramphenicol work as an antibiotic?

how does tetracycline work as an antibiotic?

A

chloramphenicol binds to 50S and inhibits the formation of peptide bond. bacteria dies

tetracycline interferes with attachment of tRNA to mRNA on 30S ribosome

29
Q
A
30
Q

there are very few antibiotics that target..?

name some of these antibiotics lol

A

bacterial polymerase

  • rifamycin series -> TB
  • streptolydigin - > TB
  • Fidaxomicin - > C. difficle
31
Q

what does mitchondria transcriptional / translational system replicate?

why is this important for therapy?

A

resembles that of alpha-proteobacteria.

THEREFORE WE NEED TO BE CAREFUL THAT WE DONT INTERFERE WTH OWN MT MACHINERY WHEN USING ANTIBIOTICS

32
Q

how does viral mRNA replicate regarding host machinery?

how can viral mRNA be intiated if not capped?

A

- viral mRNA are unable to replicate without taking over the host machinery

  • viral mRNA may not be capped, but can be initiated through IRES (cap independent translation)

SOMETIMES NOT ENOUGH AND REQUIRE A COMPLETE TAKE OVER .

33
Q
A
  • bind to eukaryotic initiation factor (elF4E) and viral protease cleave it

- viral proteases (2A and 3C) also cleave the Poly-A binding protein and transcription factors

  • aim is to stop host gene expression AND to hijack host translation intitiation factors and synthesis viral DNA.

FunMed Week 3 (10 decks)

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