Translation 1 Flashcards

1
Q

What do ribosomes not know

A
  1. Ribosome doesn’t know which codon is located in which position- blind to translation procedure, just catalyses’ peptide bond formation
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2
Q

What is translation

A
  1. Translation is the process whereby genetic information, in the form of messenger
    RNA, is used to synthesize the corresponding sequence of amino acids found in
    proteins
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3
Q

What is the tRNA structure

A
  1. The “cloverleaf” model
  2. 2 major types of secondary structure, stem and loop domains.
  3. many modified bases, particularly in the loop domains.
  4. Tertiary structure involving non-standard base pairing and/or interactions involving three or more bases.
  5. tRNAs usually fold into an L-shaped tertiary structure.
  6. Extending out from the “acceptor stem”, the 3’ end of every tRNA has the sequence CCA.
  7. The anticodon loop is at the opposite end of the L shape.
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4
Q

Where does the amino acid attach

A
  1. The amino acid attaches to the ribose of the terminal A at the 3’ end of tRNA. - CCA Sequence
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5
Q

What catalyses translation

A
  1. The direct aminoacylation of tRNAs with amino acids is catalyzed by a family of enzymes collectively known as the aminoacyl-tRNA synthetases (AARSs)
  2. Ensures the attachment of the correct amino acid to a tRNA
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6
Q

Describe the mechanism of aminoacyl- synthetases

A
  1. Have binding site for specific amino acid- ATP binding site
  2. Amino acid is activated by covalent binding of ATP and pyrophosphate is released - forms an aminoacyl-adenylate
  3. The correct tRNA binds to the synthetase, the amino acid is covalently attached to the tRNA, AMP is released
  4. The charged tRNA is released
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7
Q

Describe Aminoacyl-tRNA synthetases structures

A
  1. There is a different Aminoacyl-tRNA Synthetase (aaRS) for each amino acid.
  2. Each aaRS recognizes its particular amino acid and the tRNAs coding for that amino acid.
  3. Accurate translation of the genetic code depends on attachment of each amino acid to an appropriate tRNA.
  4. Some have anticodon binding domains
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8
Q

What are aminoacyl-tRNAs

A

1.Aminoacyl-tRNAs are synthesized by the 3’ esterification of tRNAs with the appropriate amino acids.
2. For the majority of
aminoacyl-tRNAs this is accomplished by direct aminoacylation of a particular
tRNA with the corresponding amino acid in a two-step reaction

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9
Q

What is aminoacylation

A
  1. The mechanism of the AA addition reaction
  2. The mechanism by which the aaRS recognizes the correct tRNA
  3. The mechanism by which the aaRS recognizes the correct AA
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10
Q

What are the Two pathways of aminoacyl-tRNA formation

A
  1. Direct acylation of tRNAs by aminoacyl-tRNA synthetases
  2. Indirect acylation
    - transamidation of precursor amino acids
    - Asp–>Asn
    - Glu–>Gln (Catalysed by Glu-tRNAGln amido transferase)
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11
Q

Describe the direct acylation

A
  1. Direct acylation is a 2-step reaction:
  2. 1) amino acid + ATP –> aminoacyl-AMP + PPi
  3. 2) aminoacyl-AMP + tRNA –> aminoacyl-tRNA + AMP
  4. The 2-step reaction is spontaneous overall, because the concentration of PPi is kept low by its hydrolysis, catalyzed by Pyrophosphatase.
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12
Q

Describe the direct acylation step 1

A
  1. Nucleophilic attack by carboxyl oxygen
  2. an O atom of the amino acid alpha-carboxyl attacks the P atom of the initial phosphate of ATP.
  3. Release of a pyrophosphate (ppi) P2O7(4-)
  4. Amino acid + ATP <–> Aminoacyl-adenylate (AMP) + PPi
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13
Q

Describe the Direct acylation step 2

A
  1. the 2’ or 3’ OH of the terminal adenosine of tRNA attacks the amino acid carbonyl C atom.
  2. Forms aminoacyl-tRNA
  3. Aminoacyl-AMP + tRNA <–> aminoacyl-tRNA + AMP
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14
Q

What are the 2 classes of Aminoacyl-tRNA Synthetases

A
  1. Class I (aminoacylates 2prime hydroxyl of adenine) & Class II (aminoacylates 3prime hydroxyl of adenine)
  2. Two different ancestral proteins evolved into the 2 classes of aaRS enzymes, which differ in the architecture of their active site domains.
  3. Don’t bind at same time – don’t have binding on both sides
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15
Q

Where do the different classes bind but what does it always end up being

A
  1. They bind to opposite sides of the tRNA acceptor stem, resulting in aminoacylation of a different OH of the tRNA (2’ or 3’, respectively).
  2. Regardless of where the aminoacyl is initially attached to the nucleotide, the 2’-O-aminoacyl-tRNA will ultimately migrate to the 3’ position via transesterification. – always ends up being 3’.
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16
Q

Describe Class I of aminoacyl-tRNA synthetases

A
  1. Resemble glutaminyl-tRNA synthetase
  2. Enzyme always binds to the anticodon- in order to aminoacylate their cognate tRNAs
  3. Initially aminoacylate tRNA at the 2’ hydroxyl group. Transesterification results in transfer to the 3’ hydroxyl.
  4. Rossmann fold -Alpha-beta motif
  5. Characterized by HIGH and KMSKS motifs - components of a dinucleotide-binding fold (Rossmann fold)
  6. Mainly monomers
17
Q

Describe Class II of aminoacyl-tRNA synthetases

A
  1. Generally more complex (multiple subunits)
  2. Many do NOT bind to the anticodon – some do some don’t
  3. Happy to just bind to catalytic domain
  4. Aminoacylate tRNA at the 3’ hydroxyl group.
  5. Unrelated 7 stranded antiparallel beta-sheet arrangement- form core of catalytic domains
  6. Characterized by 3 degenerate sequence motifs
  7. Often homodimers
18
Q
  1. Describe aaRS tRNA recognition
A
  1. Domains of tRNA recognized by an aaRS are called identity elements.
  2. Most identity elements are in the acceptor stem & anticodon loop.
  3. Aminoacyl-tRNA Synthetases arose early in evolution.
  4. The earliest aaRSs probably recognized tRNAs only by their acceptor stems
19
Q

Describe the isoleucine ambiguity

A
  1. Isoleucine binding site valine can also bind
  2. Why editing domain has been evolved
  3. Important for hydrophobics
  4. Small amino acids can slip in and get attached even with specific anticodon binding domain and catalytic site so editing domain is needed to deal with this
  5. Editing domain recognises smaller amino acids but not isoleucine - they get clipped off
20
Q

What are the recognition steps required for accurate translation

A
  1. The choice of the correct amino acid for covalent attachment to a tRNA
  2. The selection of the amino acid-charged tRNA specified by mRNA
21
Q

What are the recognition steps required for accurate translation

A
  1. The choice of the correcwht amino acid for covalent attachment to a tRNA
  2. The selection of the amino acid-charged tRNA specified by mRNA
22
Q

What is the overall equation for the aminoacylation

A
  1. Amino acid + tRNA + ATP <–> Aminoacyl-tRNA + AMP + PPi