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BIO 202 > Translation > Flashcards

Translation Flashcards

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1
Q

Translation

A

mRNA directed polypeptide synthesis

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2
Q

Ribosome

A

Structure made of proteins (~50) and rRNA (3-5) which catalyzes peptide bond formation

–> The actual place/machine where translation occurs

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3
Q

tRNA

A

Transfer RNA –> The “translator”

–> “Adapter” molecules which LINK info in mRNA codons with specific amino acids

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4
Q

tRNA Synthetases

A

20 of them

–> Enzymes that recognize specific tRNAs and amino acids and causes the attachment of AAs to tRNAs

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5
Q

Molecular components needed for translation: (4)

A

1) Ribosome
2) tRNA
3) tRNA synthetases
4) At least 9 soluble accessory proteins

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6
Q

What is the role of accessory proteins in translation?

A

Have functions in regulating steps of translation (initiation, elongation, and termination)

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7
Q

Translation uses…

But cells are willing to do it because…

A

1) more energy than any other biosynthetic pathway

2) It is so fundamental to life

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8
Q

tRNA structure

A

CLOVERLEAF Structure

–> This is a 3D structure that is highly structured

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9
Q

How long are tRNAs roughly?

A

typically ~80 nucleotides long

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10
Q

How does intra-molecular base pairing impact tRNA structure?

A

Causes the molecule to fold in on itself producing its characteristic loops and stems

–> Creates a 3D structure

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10
Q

What causes the specific structure of tRNA?

A

INTRA-molecular base pairing (the RNA base pairs with ITSELF)

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11
Q

“free”/exposed sections of the tRNA molecule:

A

1) Amino acid attachment site (3’ End of the tRNA)

2) Anti-codon region

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12
Q

What does “free” or “exposed”-regions mean in terms of tRNA?

A

Sections of tRNA not involved in intra-molecular base pairing therefore leaving the nucleotides “free” and exposed (able to interact with other things)

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13
Q

Protruding 3’ End of tRNA sequence =

A

CCA (5’ –> 3’)

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14
Q

What is the amino acid attachment site?

A

Where an amino acid is covalently attached to a tRNA

–> This site is located on the free 3’ end of a tRNA molecule

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15
Q

Anti-Codon

A

A particular nucleotide triplet on a tRNA that base pairs to a specific mRNA codon

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16
Q

Anticodons are written…

Because…

A

3’ to 5’

–> To more easily show the anti-parallel pairing of codon and anti-codon

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17
Q

Functions of tRNA structure (3)

A

1) “fit” in the ribosome
2) Interaction with correct codon
3) Correct amino acid attachment

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18
Q

tRNAs are NOT _____________

–> They differ in:

A

NOT identical

Differ in:

1) Each has a specific covalently attached amino acid
2) Each has a unique anticodon

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19
Q

Each tRNA is continuously….

A

recycled

–> a tRNA gained a designated amino acid in the cytosol where it then deposits the amino acid at the ribosome

–> Once deposited, it returns to the cytosol to pick up another amino acid (recycling itself)

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20
Q

TWO recognition events must occur for proper translation (as a whole):

A

1) tRNA anticodon must pair to correct mRNA codon

2) tRNA must carry the correct amino acid

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21
Q

Pairing of tRNA and amino acid is mediated by:

A

An enzyme –> Aminoacyl-tRNA synthetase

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22
Q

Aminoacyl-tRNA synthetase

A

A family of enzymes which catalyze the attachment of an amino acid to the 3’ end of the tRNA

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23
Q

Active site of aminoacyl-tRNA synthetase

A

Active site of these enzymes fit only a specific combo of AA and tRNA

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24
Q

recognition of specific tRNA by tRNA-synthetase

A

Occurs through recognition of specific residues in the anti-codon and amino-acid accepting arm/site

– >Allows correct tRNA to be recognized by the enzyme

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25
Q

If the wrong amino acid is connected to a tRNA…

A

Translation WILL NOT STOP

–> Translation will continue on and just produce an incorrect protein

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26
Q

Why is correct recognition of tRNA by tRNA synthetases especially important?

A

Because there is NO proofreading mechanisms for attaching AAs to tRNAs

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27
Q

Raney Nickel Experiment proved…

A

tRNA is the adapter molecule between protein and mRNA

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28
Q

Raney Nickel Experiment: Methodology

A

1) Purified a tRNA with cysteine anti-codon and cysteine AA attached (tRNA-cys)

2) Incubated tRNA-cys with RANEY NICKEL

3) Raney nickel converted the AA on tRNA-cys to ALANINE

–> Produced tRNA with cysteine anti-codon BUT ALANINE AA (anticodon and AA didn’t match): “ala-tRNA-cys”

4) Inserted this ala-tRNA-cys into an in-vitro hemoglobin synthesis system

5) Analyzed hemoglobin product

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29
Q

Raney Nickel Experiment: Results

A

Hemoglobin protein produced had ALANINE at every position normally occupied by cysteine

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30
Q

Raney Nickel Experiment: Conclusion

A

The amino acid attached to the tRNA is passively brought to the mRNA and becomes part of the polypeptide dictated by
CODON-ANTICODON INTERACTIONS

–> The actual amino acid on the tRNA has no effect on the recognition event between the codon and anti-codon

31
Q

Ribosome Structure

A

Has 2 subunits: One large and one small

32
Q

Ribosome subunits come together to form ____________ ONLY when…

A

to form a functional ribosome complex

ONLY WHEN attached to an mRNA molecule

33
Q

Ribosomes of prokaryotes and eukaryotes are largely ___________ but have slight _____________

A

1) Largely similar

BUT

2) Have SLIGHT differences

34
Q

Implications of ribosomal differences between prokaryotes and eukaryotes

A

Major medical implications –> Specifically with antibiotics

35
Q

Role of ribosomes and ribosomal differences in antibiotics

A

Antibiotics must have SELECTIVE KILLING of bacteria
–> Must be able to kill bacteria but not us

–> Many antibiotics inhibit bacterial protein synthesis by targeting ribosomal components that differ from eukaryotes

36
Q

rRNA is a…

A

ribozyme

37
Q

What component of the ribosome catalyzes peptide bond formation?

A

rRNA

(NOT protein)

38
Q

Translation Process Steps

A

1) Initiation
2) Elongation
3) Termination

39
Q

Translation requires energy input from…

A

GTP hydrolysis

40
Q

Initiation

A

Phase that brings together:

1) an mRNA
2) tRNA bearing first AA of polypeptide (initiator)
3) both ribosomal units

…to create the translation initiation complex (essentially the set up for protein synthesis to begin)

41
Q

Initiation Process (steps)

A

1) Small ribosomal unit binds to the mRNA (different processes for prokaryotes and eukaryotes)

2) first tRNA (initiator) –> tRNA-met –> base pairs with the AUG start codon on mRNA

3) Large subunit binds to complete the complex
–> Binds so that the initiator tRNA is within the p-site of the ribosome

42
Q

Small Ribosomal Subunit Binding in PROKARYOTES

A

Small ribosomal subunit rRNA binds to the:

SHINE-DALGARNO SEQUENCE on the mRNA

43
Q

Shine-Dalgarno Sequence

A

A sequence upstream the AUG start codon on the mRNA

that small ribosomal rRNA binds to to properly position ribosome for translation

(ONLY IN PROKARYOTES)

44
Q

Where is the Shine-Dalgarno Sequence located?

A

In the 5’ UTR region before the first start codon

45
Q

Small Ribosomal Subunit Binding in EUKARYOTES

A

1) Small subunit interacts with the 5’ mG cap on mRNA molecule

2) Small subunit moves along mRNA “scanning” for start codon

3) Reaches start codon and initiator binds to the codon

(Not fully understood yet: just a hypothesis)

46
Q

Small subunit binding position sets the…

A

Reading frame for translation

47
Q

Once the translation initiation complex is assembled:

A

Elongation is ready to begin

48
Q

Ribosomal “cavities”

A

Binding sites for tRNA: 3 of them

1) E site
2) A site
3) P site

49
Q

E Site

A

Exit Site (LEFT)

–> Where “spent” tRNAs leave the ribosome to go get “recharged” in the cytosol

50
Q

A Site

A

Aminoacyl Site (RIGHT )

–> Holds tRNA with next AA to be added to the peptide chain (where new charged tRNA comes in and base pairs with mRNA codon)

51
Q

P SIte

A

Peptidyl Site (MIDDLE)

–> Holds tRNA with the growing polypeptide attached to it

–> Exit tunnel above it

52
Q

Exit Tunnel

A

Channel in ribosome through which elongated polypeptide chain passes through the ribosome as elongation continues

53
Q

Elongation Steps

A

1) Codon Recognition
2) Peptide Bond Formation
3) Translocation
4) Next Round

54
Q

Codon Recognition Step: Elongation Phase

A

The anticodon of an incoming charged tRNA base pairs with the complementary mRNA codon at the ribosomal A-SITE

55
Q

Peptide Bond Formation Step: Elongation Phase

A

rRNA catalyzes formation of a peptide bond between polypeptide from P-SITE with AA attached to the tRNA in the A-SITE

–> Peptide bond between chain and P-Site tRNA is broken –> chain then goes and attaches to the new AA in the A-Site tRNA

56
Q

Translocation Step: Elongation Phase

A

Ribosome MOVES along the mRNA to the next codon

1) New codon at A-SITE and the site is vacant (awaiting new tRNA)

2) A-SITE tRNA with the polypeptide chain attached to it is now in the P-SITE

3) Previous P-SITE tRNA is now exiting the ribosome through the E-SITE

57
Q

“Next Round” Step: Elongation Phase

A

Process of first 3 steps is ready to begin all over again: ribosome ready for next charged tRNA to come along

58
Q

Termination begins when…

A

a STOP codon in the mRNA reaches the A-SITE

59
Q

Termination Steps

A

1) STOP codon recognition

1.1) Release factor binding

2) Peptide Release

3) Ribosome recycling + Disassembly

60
Q

STOP Codon Recognition + Release Factor Binding: Termination Phase

A

Ribosome A-SITE comes into position with a STOP codon in the mRNA

–> Release factor enters A-SITE and base pairs to the STOP codon

61
Q

What does the release factor carry/cause?

A

Has a water molecule with it

–> Attaches the H2O to the peptide causing hydrolysis of the peptide bond from the tRNA holding it = release of protein

62
Q

Peptide Release: Termination Phase

A

Release factor adds water to the peptide causing hydrolysis of the bond between polypeptide and tRNA molecule

–> Protein is released through the EXIT TUNNEL in the ribosome

63
Q

Ribosome Recycling: Termination Phase

A

Everything falls apart

–> All components break apart but go on to be recycled for another round of translation

64
Q

Why are release factors needed?

A

No naturally occurring tRNA has an anti-codon that base pairs with a STOP codon in the mRNA

65
Q

Release Factor

A

A protein shaped like a charged tRNA that base pairs with a STOP codon in the mRNA in the A-SITE of the ribosome

–> Catalyzes the release of the polypeptide, bringing about the end of translation

66
Q

Polarity of RNA vs Proteins

A

mRNA is made: **5’ —> 3’ **
–> Nucleotides added to free 3’ end

proteins are made: N terminus –> C Terminus
–> Free C terminus of the growing protein chain bonds to the free N-terminus of the NEW, INCOMING AA

67
Q

N and C Terminals of proteins correspond to what ends of RNA

A

N-Terminus = 5’ end of mRNA

C-Terminus = 3’ end of mRNA

68
Q

Codon is read________________

Anticodon is read _____________

A

Codon: Read 5’ to 3’

Anticodon: Read 3’ to 5’

69
Q

Polyribosome

A

Many ribosomes translating the SAME mRNA sequentially and AT THE SAME TIME

70
Q

What does a polyribosome allow for?

A

Allows for the production of many polypeptides from just one mRNA very quickly

–> Important for meeting cellular protein demands

71
Q

Coordination of Transcription and Translation in Prokaryotes vs Eukaryotes

A

Prokaryotes = Coupled transcription and translation
(NO compartmentalization so transcription and translation can occur at the same time)

Eukaryotes = Uncoupled transcription and translation
(Temporally separated due to compartmentalization)

72
Q

Monocistronic mRNA

A

In EUKARYOTES

–> 1 mRNA for 1 gene = production of ONE protein per mRNA

73
Q

Polycistronic mRNA

A

In PROKARYOTES

–> 1 mRNA may contain info from multiple genes = production of multiple proteins per mRNA

74
Q

What does the polycistronic nature of prokaryotic mRNA allow for?

A

Allows for regulation of transcription and translation of genes that are related to one another (Ex: In the same pathway)

75
Q

Codons are found in ____________ NOT in ___________

A

Codons are in mRNA!!!

NOT IN THE DNA

BIO 202 (33 decks)

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