RNA Error Correction Mechanisms

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Questions and Answers

What is the primary mechanism by which RNA polymerase reduces error rates during transcription?

Unwinding RNA structures to make them accessible to degradation

Recruiting RNA-binding proteins to proofread the RNA sequence

Cleaving RNA internally to initiate degradation

Backtracking and removing incorrect nucleotides from the growing RNA chain (correct)

Which of the following mechanisms is responsible for degrading aberrant RNA molecules in a 3' to 5' direction?

RNA helicases

RNA exosomes (correct)

Endoribonucleases

Nuclear RNA surveillance complex

What is the primary function of the nuclear RNA surveillance complex (NRSC)?

To correct mistakes during transcription

To initiate RNA degradation in a 3' to 5' direction

To monitor RNA processing and degradation (correct)

To unwind RNA structures for degradation

What type of RNA editing involves the use of guide RNA molecules to specify editing sites?

Guided editing Signup and view all the answers

What is the primary function of mismatch recognition proteins in mismatch repair?

To identify and bind to mismatched bases Signup and view all the answers

Which of the following mechanisms is responsible for correcting errors during transcription, but does not involve RNA polymerase?

Mismatch repair Signup and view all the answers

What is the basis of the mechanism by which RNA polymerase discriminates between correct and incorrect nucleotides?

Kinetic discrimination of nucleotides Signup and view all the answers

Which of the following is a function of certain amino acids in the RNA polymerase active center?

Enhancing selectivity between correct and incorrect nucleotides Signup and view all the answers

What is the role of the RNA polymerase active center in ensuring correct nucleotide incorporation?

It forms a molecular clamp that selects correct nucleotides Signup and view all the answers

How do certain amino acids in the RNA polymerase active center enhance selectivity between correct and incorrect nucleotides?

By forming hydrogen bonds between nucleotides Signup and view all the answers

What is similar between the mechanism of RNA polymerase and the mechanism of tRNA anticodon binding to mRNA codon?

Both involve a molecular clamp that enhances selectivity Signup and view all the answers

What is the outcome of incorrect nucleotide incorporation during transcription?

The RNA polymerase pauses and corrects the error Signup and view all the answers

What is the role of the factor of termination (RF1) in the recognition of a codon?

It forms a pair with the nucleotides of the codon through hydrogen bridges Signup and view all the answers

What happens when a nucleotide is introduced incorrectly during elongation?

The RNA polymerase stops and retrocedes, situating the incorrect nucleotide at the active center Signup and view all the answers

Why is the recognition of a codon by RF1 less precise?

Because it is not necessary to discriminate between different anticodons Signup and view all the answers

What is the role of TFIIS in the correction of errors during transcription?

It collaborates with the exonucleolytic activity to cut the RNA and release the incorrect nucleotide Signup and view all the answers

What happens to the RNA when it is backtracked during transcription?

The RNA polymerase cleaves the nascent RNA and resumes transcriptional elongation Signup and view all the answers

What is the purpose of the proofreading mechanism in E. coli RNA polymerase?

To correct errors during transcription Signup and view all the answers

What is the role of transcription factors GreA and GreB during transcription?

They stimulate transcript cleavage Signup and view all the answers

What is the purpose of the backtracking mechanism during transcription?

To correct errors during transcription Signup and view all the answers

What is the consequence of introducing a nucleotide incorrectly during transcription?

The RNA polymerase stops and retrocedes Signup and view all the answers

What is the significance of the error rate in translation compared to transcription and replication?

It is of inferior importance due to the smaller number of molecules involved and being the last molecule in the flow of information. Signup and view all the answers

During which stage of translation can errors occur due to incorrect recognition of codon by the anticodon?

During the elongation stage, specifically during the reading of codon-anticodon. Signup and view all the answers

What is the role of AaRS in the recognition of amino acids and tRNAs?

AaRS recognizes both amino acids and tRNAs, and forms an aminoacyl-tRNA. Signup and view all the answers

What is the mechanism by which AaRS discriminates between different amino acids and tRNAs?

Through a kinetic mechanism, where the reaction is slower for the correct amino acid and tRNA. Signup and view all the answers

What is the rate of error in the recognition of amino acids and tRNAs by AaRS?

10^-6 Signup and view all the answers

What is the role of the ribosome in the recognition of codon by the anticodon?

The ribosome provides a platform for the recognition of codon by the anticodon. Signup and view all the answers

What is the significance of the 16S RNA in the recognition of codon by the anticodon?

It is involved in the recognition of codon by the anticodon. Signup and view all the answers

What is the primary purpose of the initial tRNA recognition step by aminoacyl-tRNA synthetases?

To ensure accuracy in amino acid selection Signup and view all the answers

What is the role of AlkB and its homologues in the repair of nucleic acids?

They are involved in the repair of nucleic acids by oxidative demethylation. Signup and view all the answers

What is the significance of the slow reaction rate in the recognition process?

To ensure accurate recognition of tRNAs Signup and view all the answers

What is the role of the additional active site in aminoacyl-tRNA synthetases?

To proofread and correct errors Signup and view all the answers

What is the difference between the AaRS found in the cytoplasm and those found in the mitochondria?

The cytoplasmic AaRS are derived from nuclear genes, while the mitochondrial AaRS are derived from mitochondrial genes. Signup and view all the answers

What is the significance of the complex formation of up to 11 different AaRS in the cytoplasm?

It acts as a factory for the production of aminoacyl-tRNAs. Signup and view all the answers

How do aminoacyl-tRNA synthetases discriminate between similar amino acids?

Through differences in size and polarity Signup and view all the answers

What happens when an incorrect amino acid enters the active site of an aminoacyl-tRNA synthetase?

It undergoes a proofreading process Signup and view all the answers

What is the purpose of the error-correction mechanism in aminoacyl-tRNA synthetases?

To ensure the correct pairing of amino acids Signup and view all the answers

What is the consequence of a tRNA failing to bind to the synthetase?

The tRNA is released back into the cytoplasm Signup and view all the answers

What is the significance of the two-step recognition process in aminoacyl-tRNA synthetases?

To ensure the correct recognition of amino acids Signup and view all the answers

What is the primary function of the additional active site in the Ile-tRNA synthetase?

To correct errors in amino acid recognition Signup and view all the answers

Why is the error rate for aminoacyl-tRNA synthetases relatively low?

Due to the multiple steps of recognition and proofreading Signup and view all the answers

What is the role of the 16S rRNA in the translation process?

To recognize correct codon-anticodon pairing Signup and view all the answers

What is the consequence of incorrect amino acid loading during the formation of aminoacyl-tRNAs?

The incorrect amino acid is not discriminated during translation Signup and view all the answers

What is the purpose of the cellular mechanism of protein re-folding catalyzed by molecular chaperones?

To facilitate protein folding Signup and view all the answers

What happens to proteins that cannot be re-folded due to severe sequence errors or energy pitfalls?

They are degraded by the proteasome Signup and view all the answers

What is the result of errors in codon-anticodon pairing during the elongation stage of translation?

The incorrect amino acid is incorporated into the protein Signup and view all the answers

What is the primary function of the two independent stages of control during protein synthesis?

To verify the correct amino acid loading and codon-anticodon pairing Signup and view all the answers

What is the approximate frequency of error when discriminating between Ile and Val in the process of amino acid activation?

10^(-5) Signup and view all the answers

Why does the process of discrimination between Val and Thr in the AaRS of Val involve hidrofobicity?

Because Val is a hydrophobic amino acid that fits correctly in the center of recognition Signup and view all the answers

What is the function of EF-Tu in the process of translation?

To slow down the process of translation and increase fidelity Signup and view all the answers

What is the approximate error rate of the process of translation without EF-Tu?

1/100 Signup and view all the answers

Why does the process of kinectic discrimination involving EF-Tu reduce the error rate of translation?

Because it increases the time for incorrect tRNAs to leave the ribosome Signup and view all the answers

How many ATP molecules are consumed per error corrected in the process of amino acid activation?

2 Signup and view all the answers

What is the function of the center of correction in the process of amino acid activation?

To correct errors in the recognition of amino acids Signup and view all the answers

What is the distance between the two active centers of the AaRS?

34 A Signup and view all the answers

Why does the process of correction in the center of correction slow down the global process of amino acid activation?

Because it requires a movement of the tRNA from one site to another Signup and view all the answers

What is the approximate error rate of the process of translation with EF-Tu?

10^(-4) Signup and view all the answers

Study Notes

RNA Polymerase Error Checking

Proofreading

Occurs during transcription, allowing RNA polymerase to correct errors immediately
RNA polymerase can backtrack and remove incorrect nucleotides from the growing RNA chain
Error rates reduced by 10-100 fold due to proofreading

RNA Degradation

Degradation of aberrant or faulty RNA molecules
Mechanisms include:
- RNA exosomes: complexes that degrade RNA in a 3' to 5' direction
- RNA helicases: unwind RNA structures, making them accessible to degradation
- Endoribonucleases: cleave RNA internally, leading to degradation

RNA Quality Control

Surveillance mechanisms to detect and eliminate aberrant RNA molecules
Includes:
- Nuclear RNA surveillance complex (NRSC): monitors RNA processing and degradation
- Cytoplasmic RNA quality control: involves RNA-binding proteins and degradation machinery

Editing

Post-transcriptional modification of RNA to correct errors or change sequence
Types of editing:
- Insertion/deletion editing: adds or removes nucleotides from the RNA sequence
- Substitution editing: replaces incorrect nucleotides with correct ones
- Guided editing: uses guide RNA molecules to specify editing sites

Mismatch Repair

Corrects mismatches in RNA-DNA hybrids, resulting from errors during transcription
Involves:
- Mismatch recognition proteins: identify and bind to mismatched bases
- Helicases: unwind the RNA-DNA hybrid, allowing repair
- Repair enzymes: correct the mismatch, restoring the correct sequence

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Description

Learn about the various mechanisms that correct errors during RNA synthesis, including proofreading, RNA degradation, RNA quality control, editing, and mismatch repair. Understand how these processes ensure the accuracy of RNA sequences.