Questions and Answers
What does 16S rRNA do in the small ribosomal subunit?
It interacts with the RBS to position the AUG in the P-site.
What is the Shine-Dalgarno sequence?
It is a sequence element that acts as a ribosome binding site found just upstream of the start codon in many prokaryotic genes.
What binds to the Shine-Dalgarno sequence during translation?
The small ribosomal subunit recognizes the sequence, specifically a region of the 16S RNA.
Describe how the Shine-Dalgarno sequence can vary.
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What is the role of the 5′ cap during eukaryotic translation?
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What happens to mRNA molecules that are missing a cap?
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What are the steps by which aminoacyl tRNA synthetases charge tRNAs?
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How can some organisms have fewer than 20 synthetases and still charge tRNAs with all 20 amino acids?
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Explain how EF-Tu escorts charged tRNA to the A-site.
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How do eukaryotic cells recognize the stop codon during translation?
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How does recognition of the codon lead to the termination of protein synthesis?
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How does the degree of translation accuracy compare to DNA replication and transcription?
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What three key events must occur for the correct addition of an amino acid during translation elongation?
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Is translation elongation identical between prokaryotes and eukaryotes?
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To which of the three tRNA binding sites does the initiator tRNA bind?
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What are the four components of the translation machinery?
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What is meant by ORF?
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Explain the structure of tRNA.
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What type of 3D structure does tRNA have?
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What is the size of the ribosome for prokaryotes and eukaryotes?
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The large and small subunits undergo association and dissociation during each cycle of translation.
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What are the names of the different sites in the ribosome?
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What does it mean for tRNA to be charged?
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What is the function of each subunit in the ribosome?
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What is the error rate of translation?
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What type of catalysis occurs when forming a peptide bond?
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What catalyzes the peptidyl transferase reaction?
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What mechanisms ensure that the correct aminoacyl-tRNA is inserted?
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Study Notes
16S rRNA and Shine-Dalgarno Sequence
- 16S rRNA helps position the AUG start codon in the P-site of the ribosome by interacting with the ribosome binding site (RBS).
- The Shine-Dalgarno sequence (5′-GGAGG-3′) is crucial for translation initiation in prokaryotes, typically found 3 to 9 nucleotides upstream of the start codon.
- Recognition of the Shine-Dalgarno sequence by the small ribosomal subunit is facilitated by complementary sequences in 16S RNA.
Variability of the Shine-Dalgarno Sequence
- Variations in the Shine-Dalgarno sequence can affect translation efficiency.
- Sequences closely matching the ideal Shine-Dalgarno sequence display higher activity, while deviations generally reduce activity.
- Proper distance from the start codon also influences translation efficiency.
Eukaryotic Translation Initiation
- The 5′ cap on mRNA is recognized by eIFs, recruiting the small ribosomal subunit and assisting in scanning for the start codon.
- mRNA lacking a cap is vulnerable to degradation by exonucleases, underscoring the protective role of the cap.
Charging tRNA by Aminoacyl tRNA Synthetases
- Aminoacyl tRNA synthetases charge tRNAs in two steps: adenylation (binding amino acid to AMP) and tRNA charging (transferring the amino acid to tRNA).
- Some organisms have fewer than 20 synthetases yet can charge all amino acids by modifying others.
Role of EF-Tu in Translation
- Charged tRNA is bound to EF-Tu-GTP, which delivers it to the ribosome's A site.
- Upon correct codon-anticodon pairing, EF-Tu hydrolyzes GTP, releasing tRNA into the ribosome.
Stop Codon Recognition in Eukaryotes
- Stop codons are recognized by class I release factors RF1 and RF2 using a peptide anticodon that specifically binds to the codon.
- This recognition leads to the termination of protein synthesis by hydrolyzing the bond between the polypeptide and tRNA.
Termination of Translation
- Upon stop codon recognition, release factors facilitate polypeptide release and ribosome disassembly through a series of interactions, involving RF3 and RRF.
- EF-G helps displace deacylated tRNAs from the ribosome.
Translation Accuracy
- The error rate for translation (10^-3 to 10^-4) is higher than that for transcription (10^-4 to 10^-5) and DNA replication (as low as 10^-10).
- Higher error rates in translation are acceptable since they only affect individual proteins, unlike transcription which influences multiple proteins from a single mRNA.
Translation Elongation Events
- Key events for amino acid addition during elongation include the insertion of the correct aminoacyl-tRNA into the ribosome’s A site, peptidyl bond formation, and translocation of peptidyl-tRNA to the P site.
Differences in Translation between Prokaryotes and Eukaryotes
- While the processes are similar, distinct differences exist in translation elongation between prokaryotes and eukaryotes.
Ribosome Structure and Function
- Prokaryotic ribosome: 70S total (30S + 50S), Eukaryotic ribosome: 80S total (40S + 60S).
- The ribosome has three tRNA binding sites: A (aminoacyl), P (peptidyl), and E (exit).
Understanding tRNA
- Charged tRNA is one that has an amino acid attached, crucial for protein synthesis.
- tRNA structure features a 3' terminus with a CCA sequence and contains an anticodon that recognizes mRNA codons.
Peptidyl Transferase Reaction
- Catalyzed by the 23S rRNA of the large subunit, the reaction facilitates peptidyl bond formation.
Mechanisms Ensuring Accurate tRNA Insertion
- Hydrogen bonds between adenine residues in 16S rRNA and the anticodon-codon pair enhance specificity.
- Correct pairing allows for EF-Tu interaction with the ribosome, leading to subsequent peptide bond formation through tRNA accommodation.
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Test your knowledge on the roles of 16S rRNA and the Shine-Dalgarno sequence in translation. These flashcards cover key concepts important for understanding protein synthesis in prokaryotes. Ideal for biology students looking to reinforce their learning.