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aa Proteins > Translation 3- Initiation > Flashcards

Translation 3- Initiation Flashcards

1
Q

What are ribosomes

A
  1. Molecular machines that catalyze peptide bond formation directed by information in mRNA
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2
Q

What does polycistronic mean and give example

A
  1. Multiple genes encoded on a single messenger
  2. Bacterial mRNA
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3
Q

What is approx speed of translation, transcription and replication in bacteria and eukaryotes

A

1.Translation: add 15 amino acids per sec.
2. Transcription: add about 50 nucleotides per sec
3. Replication is much faster: 1000 nucleotides per sec
4. Euk- translation elongation is about 2 amino acids per sec

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4
Q

Describe the general composition of ribosomes

A
  1. Eukaryotes are bigger
  2. All have large and small subunit consisting of proteins and RNA
  3. Mostly made up of rRNA
  4. 60% RNA and 40% protein
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5
Q

Describe prokaryotic ribosome structure

A
  1. 70S = size of prokaryotic ribosome
  2. Large subunit = 50S
  3. Small subunit = 30S
  4. Doesn’t add up to 70S as surface area increases as you split them up
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6
Q

Describe composition of small ribosomal subunit in bacteria

A
  1. 16S rRNA (bacteria)
    2 .21 proteins (bacteria)
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7
Q

Describe composition of small ribosomal subunit in eukaryotes

A
  1. 18S rRNA (eukaryotes)
  2. 33 proteins (eukaryotes)
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8
Q

What is main role of small ribosomal subunit

A
  1. Initial binding of mRNA and initiator met-tRNA
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9
Q

Describe composition of large ribosomal subunit in bacteria

A
  1. 23S & 5S rRNA (bacteria)
  2. 31 proteins (bacteria)
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10
Q

Describe composition of large ribosomal subunit in eukaryotes

A
  1. 28S, 5.8S, & 5S rRNA (eukaryotes)
  2. 49 proteins (eukaryotes)
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11
Q

What are the 3 steps of translation cycle

A
  1. Initiation – small unit binding to initiator tRNA
  2. Elongation
  3. Termination and recycling
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12
Q

What direction does polypeptide synthesis occur

A
  1. From N-terminus to C-terminus
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13
Q

What direction do ribosomes read mRNA

A
  1. From 5’ to 3’ direction
  2. Accounts for observation that ribosomes initiate translation on nascent mRNAs
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14
Q

How does chain elongation occur

A
  1. By the linkage of the growing polypeptide to the incoming tRNA’s amino acid residue
  2. Amino acid residues are sequentially added to the C-terminus of the nascent, ribosomally bound polypeptide chain
  3. Nascent polypeptide must grow by being transferred from one peptidyl-tRNA to the incoming aminoacyl-tRNA to form a peptidyl-tRNA with one more residue
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15
Q

What are the three tRNA-binding site on the ribosome

A
  1. Peptidyl- p-site- binds the peptidyl-tRNA
  2. aminoacyl or A-site - binds the incoming aminoacyl-tRNA
  3. Exit site - binds outgoing deacylated tRNA
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16
Q

What is the initiator codon and how is its position mediated in E.coli

A
  1. AUG
  2. Mediated by base pairing between the ribosome-binding site in the 5’ untranslated region and the 3’ end of the 16s rRNA
  3. 16S Rrna determines where the AUG codon sits
17
Q

.What are the Factors and components needed for initiation

A
  1. Small ribosomal subunit
  2. mRNA
  3. Initiation factors – proteins that are not part of the ribosome- soluble proteins
  4. fmet-tRNAfMet – initiator tRNA
  5. GTP – hydrolysis, initiator factor 2 requires GTP
  6. Large subunit
18
Q

Describe structure of mRNA

A
  1. C rich region – 16S rRNA – positions messenger where it needs to be
  2. Base pairing to RBS – Ribosomal binding site- G rich - Shine-Dalgarno sequence
19
Q

What is fMET

A
  1. fMet is the N-terminal residue of prokaryotic polypeptides
  2. has been formylated- It has already an amide bond so can only be the N-terminal residue of polypeptide
  3. Resembles peptide bond- mimics
  4. An example of mimicry in translation
20
Q

How is the translational initiation site selected

A
  1. The masking of AUGs that are not initiation codons by mRNA secondary structure
  2. Interactions between the mRNA and the 16S rRNA that select the initiating AUG
21
Q

What are the initiation factors involved in initiation

A
  1. IF-1
  2. IF-2
  3. IF-3
22
Q

What are translation factors

A
  1. proteins used at only one step of the translation process
  2. Not permanent components of the ribosome, but cycle on and off
23
Q

What does IF-1 do

A
  1. Assists binding of IF-3 to the 30S ribosomal subunit.
  2. IF-1 also occludes the A site (blocks) of the small ribosomal subunit, helping ensure that the initiation aa-tRNA fMet-tRNAfMet can bind only in the P site & that no other aa-tRNA can bind in the A site during initiation.
24
Q

What does IF-2 do

A
  1. IF-2 is a small GTP-binding protein.
  2. IF-2-GTP binds the initiator fMet-tRNAfMet & helps it to dock with the small ribosome subunit.
25
Q

What does IF-3 do

A
  1. IF-3 binds to the 30S ribosomal subunit, freeing it from its complex with the 50S subunit.
  2. Breaks up small and large subunit
26
Q

Describe the first step of initiation

A
  1. On completing a cycle of polypeptide synthesis the 30S and 50S subunits are separated
  2. IF-3 then binds to the 30S subunit to prevent the reassociation of the 50S subunit
  3. IF-3 appears to bind to upper end- doesn’t function by physically blocking the binding of the 50S subunit
27
Q

Describe the second step of initiation

A
  1. mRNA and IF-2 in a ternary complex with GTP and fMet-tRNAfMet accompanied by IF-1 subsequently bind to the 30S subunit in either order
  2. Recognition not mediated by codon-anticodon interaction
  3. Interaction helps bind fMet-tRNAfMet to the ribosome
  4. IF-1 binds in the A site where it may function to prevent the inappropriate or premature binding of a tRNA
  5. IF-3 destabilises the binding of tRNAs that lack the 3 G-C pairs in the anticodon stem of RNAfMet and helps discriminate between matched and mismatched codon-anticodon interactions
28
Q

What is the 3rd step of initiation

A
  1. 50S subunit joins the 30S initiation complex in a manner that stimulates IF-2 to hydrolyse its bound GTP to GDP+P
  2. This irreversible reaction conformationally rearranges the 30S subunit and releases IF-2 for participation in further initiation reactions
29
Q

What does initiation result in

A
  1. In formation of an fMet-tRNAfMet -mRNA-Ribosome complex in which the fMet-tRNAfMet occupies the P-site while its A site is poised to accept an incoming aminoacyl-tRNA
30
Q

How is fMet-tRNAfMet formed

A
  1. In E.coli uncharged (deacylated) tRNAfMet is first aminoacylated with methionine by the same MetRS that charges the tRNAmMet
  2. Resulting Met-tRNAfMet is specifically N-formylated to yield fMet-tRNAfMet
31
Q

What is difference between tRNAfMet and tRNAmet

A
  1. Have same anticodon sequence- recognised by same synthetase
  2. Lack of base pair for fMet- important for formylation
  3. Base pair means tRNAmet is not recognised by transformylation

aa Proteins (5 decks)

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