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Cell & Molecular Biology > Lecture 12 - Translation > Flashcards

Lecture 12 - Translation Flashcards

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1
Q

Shine-Dalgarno Box:

A

a consensus sequence that pairs with the 16S RNA that is part of the small ribosomal unit in bacteria

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2
Q

what does the Shine-Dalgarno Box allow for?

A

the Shine-Dalgarno box is what allows for polycistronic genes in bacteria as it is a sequence that allows for the ribosome to bind throughout the transcript and to initiate transcription

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3
Q

AUG codon:

A

codon codes for the amino acid methionine, which is also the start or initiation codon

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4
Q

what is required only for the initiation of ribosome production in bacteria?

A

methionine with a formyl group (fMet) on a specialised tRNA that are required only for initiation

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5
Q

what does the specialisation of methionine allow for?

A

it allows specialised methionine to bind to the middle P-site of the ribosome from the start

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6
Q

once the tRNA is in place, how can the ribosome be created?

A

with the tRNA in place, the large ribosomal subunit is able to bind to the mRNA, tRNA and small ribosomal subunit, thus creating the ribosome

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7
Q

initiation factors:

A

proteins that are important to ensure that translation begins correctly

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8
Q

three initiation factors in prokaryotes and their roles:

A

–IF1 blocks tRNA from entering the ribosome subunit
–IF2 binds specifically to the initiator fMet tRNA to bring it to the start codon
–IF3 ensures that there is a match between codon and anticodon for the fMet

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9
Q

when do initiation factors dissociate in prokaryotes?

A

these all dissociate upon the joining of the large ribosomal subunit but are critical for ensuring a correct start to translation

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10
Q

Simultaneous Transcription and Translation in Bacteria:

A

both take place in the same space and they are seeking only the Shine-Dalgarno box for the ribosomes to bind, therefore can occur simultaneously

furthermore, multiple ribosomes or polyribosomes are able to bind at the same time to the same transcript

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11
Q

Shine-Dalgarno Box in eukaryotes?

A

no

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12
Q

how do eukaryotes initiate transcription given that they do not have a Shine-Dalgarno box?

A

instead, the small ribosomal subunit binds to the 5’ cap of the mRNA and then moves along the mRNA until it reads the AUG codon

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13
Q

what is recruited in eukaryotes before the assembly of the large ribosomal subunit?

A

in eukaryotes, a normal methionine amino acid on an initiator tRNA is recruited before the assembly of the large ribosomal subunit

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14
Q

Eukaryotic Initiator Factors:

A

much more numerous and have more substantive roles due to the less targeted nature for the binding of the small ribosomal unit

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15
Q

in eukaryotes, two initiation factors are required to ensure the mRNA transcript is complete:

A

–eIF4E – replaces the 5’ cap protein on the transcript
–eIF4G – binds to the poly(A) binding proteins and eIF4E

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16
Q

when can eukaryotic initiation factors dissociate?

A

Once the small ribosomal subunit as found the first AUG, these initiator factors can dissociate to allow the large ribosomal subunit to bind

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17
Q

what is separated in eukaryotes which is not separated in prokaryotes?

A

Translation is Separated from Transcription in Eukaryotes

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18
Q

additionally to location, what else is needed din eukaryotes to initiate translation?

A

Additionally to location, the 5’ cap and poly(A) tail modifications are needed to initiate translation

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19
Q

although transcription and translation can’t occur simultaneously in eukaryotes how can many copies of a protein be made at once?

A

polyribosomes can bind to the mRNA transcript and translate multiple copies of the protein

to enable this, mRNA tend to form a spiral shape as the initiation factors and the ribosomal subunits can leave and rejoin the transcript in close proximity

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20
Q

microRNA:

A

MicroRNA are small RNA transcripts that are normally negative regulators of gene expression

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21
Q

microRNA blocking transcription by two mechanisms:

A

–Binding to the mRNA transcript and blocking translation from initiating, elongation, of termination

–Degrading the mRNA transcript so no translation can occur

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22
Q

Summary of Initiation of Translation:

A

•The small ribosomal subunit binds first to the mRNA and recognises the start codon, allowing for the recruitment of the initiation tRNA

•This allows the large ribosomal subunit to bind with the initiation tRNA present in the P-site

•Between bacteria and eukaryotes, there are some minor differences in the initiation of translation related to initiation factors, the binding of the small ribosomal subunit, and the initiating methionine tRNA

23
Q

Inside the ribosome are three binding sites for the tRNA:

A

–A-site (aminoacyl)
–P-site (peptidyl)
–E-site (exit)

24
Q

where do tRNAs enter and exit the ribosome?

A

•tRNAs enter the ribosome through the A-site and exit through the E-site

•These sites exist on both the small and large ribosomal unit

25
Q

why is the tRNA in the P-site called the peptidyl-tRNA?

A

because it is the tRNA attached to the polypeptide chain

26
Q

where does anticodon binding occur?

A

the small ribosomal subunit

27
Q

We have our first amino acid and tRNA in the ribosome from initiation in the:

A

P-Site

28
Q

with the A-Site open an…

A

aminoacyl-tRNA is able to enter the ribosome and bind if the anticodon is correct

29
Q

what is the joining of the new amino acid to the polypeptide chain is mediated by?

A

peptidyl transferase, an RNA enzyme that is inside and part of large ribosomal subunit

30
Q

what does the enzyme peptidyl transferase (found within ribosomes) do?

A

the enzyme mediates a nucleophilic attack from the nitrogen terminal of the new amino acid onto the ester bond to the tRNA of the polypeptide chain

this breaks the ester bond between the polypeptide chain and the peptidyl-tRNA and creates a new peptide bond between the polypeptide chain and the amino acid on the aminoacyl-tRNA

the polypeptide chain from the peptidyl-tRNA in P-site is transferred to the amino acid on the aminoacyl-tRNA in the A-site

31
Q

peptides are formed in a _ to _ direction:

A

N → C

•For protein, we go N-terminal to C-terminal, which is related to the exposed group at the end of the polypeptide chain

•Polypeptide chains always involve amino acids being added to the C-terminal

32
Q

The Subunits Translocate:

A

peptide bond formed and polypeptide chain transferred the large ribosomal subunit translocates first, this moves the tRNA in the P-site & A-site to the E-site and P-site respectively

the small subunit then moves three nucleotides along consistent with codon size to pair up with the large subunit

this leaves the A-site now empty and ready to accept new tRNA with an amino acid and for E-Site to eject its empty tRNA

33
Q

what act act ‘elongation factors’ and what do they do?

A

there are a number of GTPases that act as elongation factors which help to enhance the cycle of tRNA within the ribosome

34
Q

elongation factors such at GTPases are not only there to help make translocation faster but also have a role in proof reading:

A

–EF-Tu/eEF-1a catalyzes the binding of aa-tRNA to the A site

–EF-G/eEF-2 catalyzes translocation of the peptidyl-tRNA from P/A to P site

35
Q

what is EF-Tu?

A

EF-Tu is a compound bound to aminoacyl-tRNA and helps to bring it to the A-site of the ribosome

36
Q

what happens to EF-Tu if there is correct codon to anticodon binding?

A

if there is correct codon to anticodon binding, the ribosome causes EF-Tu to hydrolyse GTP that is bound to it

37
Q

what does GTP hydrolysation into GDP cause?

A

GTP hydrolysation into GDP causes a conformational change to occur in EF-Tu, this in turn causes EF-Tu to dissociate from the tRNA-amino acid complex and to leave the ribosome

38
Q

what does the process of GTP hydrolysis act as within EF-Tu?

A

GTP hydrolysis acts as proof-reading to make sure the correct tRNA has associated as only with correct binding will it be placed correctly into the ribosome

39
Q

other from specific association with ribosomes, how does EF-Tu additionally act as a form of proof-reading?

A

additionally, there is a delay between the EF-Tu leaving the tRNA and the tRNA entering the A site fully, providing a second proof reading opportunity - if there is no match the tRNA will preferentially dissociate

40
Q

EF-G Helps with tRNA Move During Subunit Translocation 1:

A

• translocation in part occurs due to the tRNA molecules having a change in their affinities

• the old P-site tRNA prefers the E-site now that it does not have the polypeptide chain attached to it

• at the same time, the old A-site tRNA now prefers the P-site since it has the polypeptide chain

41
Q

what does the other main elongation factor EF-G help with?

A

EF-G helps with moving tRNAs from their old sites to their new site

EF-G enters ribosome via the A-site and binds to the hybrid state, stabilising it, placing it in the factor binding centre, leading to GTP hydrolysis

this again changes the confirmation of the protein which causes the tRNA in the A-/P-site hybrid location to be forced out of the A-site and only into the P-site, which in turn forces the oldest tRNA out

42
Q

tRNAs charged with amino acids enter the ribosome through:

A

the A-site and a peptide bond is formed between the amino acid and the polypeptide chain in the P-site

43
Q

the subunits translocate along:

A

with the tRNA along the mRNA transcript

44
Q

elongation factors help with both:

A

the loading of the tRNA into the ribosome, and the translocation of the subunits and tRNA following the peptide formation

45
Q

in general there are three stop codons:

A
  • UAA
  • UAG
  • UGA
46
Q

what is important to remember with stop codons?

A

it is important to remember that stop codons (translation) are not the same as termination sites (transcription)

47
Q

what are stop codons recognised / not recognised by?

A

stop codons are not reconciles by empty tRNA or any tRNA but instead by a release factor

48
Q

what do stop codons actually do?

A

stop codons end translation

49
Q

what are release factors?

A

release factors are a protein but are an example of molecular mimicry - the structure ands charge of this protein is very similar to that of charged tRNA which is how it is able to enter the ribosome

50
Q

why is it that release factor proteins can enter the ribosome?

A

release factors can easily enter the ribosome due to them having molecular mimicry that results in them having very similar charges to tRNA

51
Q

how specifically do release factors bind?

A

the release factor binds to the ribosome in the A-site, the release factor forces the peptidyl transferase to add a water molecule to the end of the peptide chain instead of an amino acid, this reaction then causes the release of the peptide from the tRNA in the P-site, and with additional proteins, the ribosome disassembles

52
Q

what is recruited to the ribosome when a stop codon is read?

A

when a stop codon is read a release factor is recruited to the ribosome

53
Q

how is the polypeptide chain released form the ribosome?

A

through forcing the addition of a water molecule to the end of the polypeptide chain it is released from the ribosome - for the ribosome to be broken down and components available for translation on other sites

Cell & Molecular Biology (24 decks)

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