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BIOCHEMISTRY 1 > Translation 02 > Flashcards

Translation 02 Flashcards

1
Q

What is Aminoacyl tRNA synthetase?

A

Enzyme that catalyzes the esterification of a specific amino acid to its compatible tRNA to form an aminoacyl-tRNA.

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2
Q

Where does the amino acid connect with the tRNA?

A

tRNA 3’ end -phosphate-ribose/adenine - AA attached to 2’ or 3’ position of the ribose.

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3
Q

What is synthetase proof-reading activity?

A

It can selectively edit the incorrect (non-cognate) amino acid at the enzyme proof reading site. It has an editing site and a synthesis site .

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4
Q

What must happen to amino acid before binding to tRNA?

A

It must be adenylated (aa-P-ribose-adenine)

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5
Q

What are the 2 levels of control to ensure that the proper amino acid is incorporate into protein?

A

1) Charging of proper tRNA: by tRNA synthetase

2) Matching the cognate tRNA to the mRNA: based on the correct base-pairing of tRNA anticodon and mRNA codon.

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6
Q

What are the two methionine tRNAs?

A
  1. Initiator methionine tRNA: ensures initiation of translation. Enters ribosomal P site with initiation factors.
  2. Elongator methionine tRNA: incorporates internal methionines. Carried by elongation factors to A site.

*Both aminoacylated by methyonyl-tRNA synthetase. Synthetase distinguishes the two.

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7
Q

What is the Shine-Dalgarno sequencw?

A

It is a ribosomal binding site in mRNA, 8 bases upstream of the start codon AUG. Exists in bacteria and archaea, and also present in some chloroplastic and mitochondial transcripts

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8
Q

What are the initiation factors?

A

IF-1: occludes A-site
IF-2: small GTP bp, binds initiator tRNA and helps it dock with 30S
IF-3: helps reposition complex to properly math codon to anticodon; binds 30S to free it from complex.

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9
Q

What are the elongation factors?

A
  • EF-Tu, EF-G: small GTP binding proteins
  • EF-Ts: guanine nucleotide exchange factor for EF-Tu catalyzing the release of GDP. This enables EF-Tu to bind to a new GTP molecule
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10
Q

What happens during elongation?

A
  1. EF-Tu-GTP delivers aminoacyl-tRNA to the A-site (EF-Tu recognizes all aminoacyl-tRNAs)
  2. Empty tRNA in E-site exits complex
  3. A ribosome domain functions as GAP for EF-Tu
  4. GTP is hydrolyzed & incorrectly base-paired tRNAs dissociate. EF-Tu dissociates.
  5. tRNA accommodation (conformation relaxes, & acceptor stem is repositioned for catalysis)
  6. Peptidyl transferase in 50S ribosome transfers growing polypeptide to newest tRNA in A-site
  7. Translocation
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11
Q

What does the 16S rRNA interact with?

A
  1. Shine-Dalgarno sequence

2. Minor groove of the first two bp of the double helical codon/anticodon complex

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12
Q

What is the proof-reading mechanism in translation?

A

16S interaction with minor groove of codon-anticodon complex stabilizes a particular ribosomal conformation. IF this conformation is not generated, there is release of the aminoacyl-tRNA prior to peptide formation.

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13
Q

What is the 23S rRNA?

A

It can be considered a ribozyme. Transpeptidation (peptide bond formation) involves acid/base catalysis by an adenosine in the 23S rRNA of the large ribosomal subunit.

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14
Q

Where is the protein exit tunnel?

A

It is located midway between A and P site.

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15
Q

What the factors in terminations?

A

Release factors:

  • RF1, RF2: recognize and bind the stop codons
  • RF-3-GTP: facilitates binding of RF-1 or RF-2 to ribosome
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16
Q

What happens during termination?

A
  1. Stop codon in A site: UAG, UAA, UGA
  2. No EF-Tu-aa-tRNA complex is bound
  3. A release factor binds ribosome and activates peptdyl transferease
  4. Peptidyl transferase catalyzes transfer of the peptifyl group to water releasing free peptide.
  5. Hydrolysis of GTP on RF-3 results in dissociation of release factors
  6. Disassembly
17
Q

What is required for disassembly?

A

-Ribosomal recycling factor (RRF), EF-G-GTP and IF-3 are required for release of uncharged tRNAs from the P-site, & dissociation of the 2 ribosome subunits from mRNA

18
Q

What are the overall steps of translation in prokaryotes?

A 
Initiation
1. binding of 30S with IFs
2. binding of mRNA and initiator tRNA
3. binding of ribosome 50S & release IFs
Elongation
1. binding of new aminoacyl-tRNA at A site
2. formation of new peptide bond
3. translocation
Termination
1. binding of RFs
2. hydrolysis of peptidyl-tRNA
Disassembly
1. binding of RRF
19
Q

What is the average mRNA half-life?

A

E.Coli: 4 min

Humans: 10 hrs

20
Q

What are the energy requirements for translation?

A

AA activation : 1ATP*
Assembly of 40S and 60S: 1GTP
Binding of aminoacyl-tRNA: 1GTP (EF-Tu)*
Translocation: 1GTP (EF-G)*
Termination: 1GTP (RF-3)
====> 1 ATP + 2GTP / cycle (4 high E-bonds)

21
Q

What is protein synthesis different in eukaryotes compared to prokaryotes?

A

1) In Eukaryotes, protein synthesis occurs in cytoplasm, & transcription/RNA processing in the nucleus.
2) In prokaryotes, it all occurs in the cytoplasm, and processes are coupled.
3) Eukaryotes have more elongation factors than prokaryotes, and only 1 termination factor
4) mRNA has a poly-A tail and 5’-cap
5) mRNA is circularized during the process
6) Regulation of eIF2 functions through reversible phosphorylation
7) 12 initiation factors

22
Q

What is special about eukaryotic mRNA?

A
  • Methyl guanosine cap at 5’ end (recognition feature for ribosome binding)
  • Coding and non-coding sequences
  • Poly-A tail at 3’ end
23
Q

What are nonsense, missense, and silent mutations?

A
  • Nonsense mutation: leads to a termination codon
  • Missense mutation: leads to a different aa
  • Silent mutation: leads to the same aa
24
Q

What happens in Huntington’s disease?

A
  • CAG tandem repeats in large numbers
  • mRNA is translated into huntingtin protein with abnormal glutamine repeats
  • Aggregated proteins cause damage
25
Q

What are 3 triplet expansion diseased?

A

Huntington disease (CAG) , Fragile X syndrome (CGG), Myotonic dystrophy (CUG)

26
Q

What does streptomycin do?

A

-Binds to 30S subunit and distorts its structure interfering with initiation of protein synthesis

27
Q

What does tetracyclin do?

A
  • Interacts with 30S blocking access of aminoacyl-tRNA to the A-site stopping elongation.
  • Broad spectrum antibiotic
28
Q

What does puromycin do?

A

Structural resemblance to aminoacyl-tRNA and becomes incorporated into the growing peptide chain. This causes inhibition of further elongation in eukaryotes and prokaryotes.

29
Q

What does chloramphenicol do?

A
  • Inhibits prokaryotic peptidyltransferase

- High levels may also inhibit mitochondrial protein synthesis

30
Q

What do Clindamycin and Erythromycin do?

A

Bind irreversibly to a site on the 50S inhibiting translocation in prokaryotes.

31
Q

What does diphteria toxin do?

A

It inactivates eukaryotic eEF-2 preventing translocation.

BIOCHEMISTRY 1 (7 decks)

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