L15: Translation

• What is the characteristic of many bacterial mRNAs?

  Many bacterial mRNAs are polycistronic.
• What does it mean that bacterial mRNAs are polycistronic?

  It means that many ribosomes can traverse a single mRNA.
• What are the components of the bacterial large ribosomal subunit (50S)?

  It consists of 23S rRNA, 5S rRNA, and 31 proteins.
• What is the function of the bacterial ribosomes?

  They catalyze the formation of peptide bonds that join amino acids.
• What is the composition of the bacterial small ribosomal subunit (30S)?

  It consists of 16S rRNA and 21 proteins.
• What do Svedberg units measure?

  Svedberg units measure sedimentation coefficients based on size and shape.
• What role do ribosomal proteins play in the ribosome?

  They stabilize the ribosome.
• How does a ribosome find a messenger RNA?

  The Shine-Dalgarno sequence on the mRNA base pairs with a section of the 16S rRNA.
• What is the role of initiation factors in bacterial translation initiation?

  They coordinate ribosomal assembly and prevent premature binding.
• What happens after the L subunit is recruited to the 30S initiation complex?

  The initiation factors IF-1 and IF-2 are released, and the ribosome is ready for elongation.
• What is the role of EF-Tu during bacterial translational elongation?

  EF-Tu guides the next aminoacyl-tRNA into the A site.
• What occurs during the translocation step of bacterial translation elongation?

  The ribosome moves one codon towards the 3’ end of the mRNA.
• How does the ribosome build the nascent protein during translation?

  The ribosome adds new amino acids to the C terminus of the nascent protein.
• What is the role of release factors during bacterial translational termination?

  Release factors bind to the stop codon and cleave the peptidyl-tRNA bond.
• What is head polymerization in amino acid polymerization?

  It is the process where the energy from the bond is used for polymerization.
• What is required for the formation of peptide bonds between amino acids?

  A peptidyl transferase activity is required, which is provided by 23S rRNA.
• What are the components of eukaryotic ribosomes compared to bacterial ribosomes?

  Eukaryotic ribosomes are larger and more complex, with 80S ribosomes compared to 70S in bacteria.
• How are eukaryotic mRNAs modified compared to bacterial mRNAs?

  Eukaryotic mRNAs are capped and tailed by factors recruited by RNA polymerase.
• What is the significance of the pseudo-circularization of eukaryotic mRNAs?

  It facilitates the re-binding of ribosomes and protects the mRNA from degradation.
• What is the role of the helicase activity of eIF4A in eukaryotic translation initiation?

  It unwinds secondary structures in the mRNA to allow translation.
• What is the Kozak sequence's function in eukaryotic translation initiation?

  It provides a signal informing the ribosome that the next AUG is the initiator codon.
• Why is there no equivalent of the Shine-Dalgarno sequence in eukaryotic translation?

  Because the 5’ structures would be circumvented if it were present.
• What are the roles of translation initiation factors in bacteria and eukaryotes?

  They facilitate the binding of tRNAs and the assembly of ribosomal subunits.
• What are the key differences between bacterial and eukaryotic translation processes?

  • Bacterial mRNAs are polycistronic; eukaryotic mRNAs are monocistronic.
  • Bacterial ribosomes are 70S; eukaryotic ribosomes are 80S.
  • Bacterial translation initiation relies on the Shine-Dalgarno sequence; eukaryotic translation initiation relies on the Kozak sequence.
  • Eukaryotic mRNAs are capped and tailed, while bacterial mRNAs are not.
• What is the role of translation initiation factors in bacterial translation?

  They regulate the entry of the next ribosome.
• What are the roles of bacterial translation initiation factors IF-1, IF-2, and IF-3?

  • IF-1: Prevents premature binding of tRNAs to the A site.
  • IF-2: Guides fMet-tRNA to the 30S subunit.
  • IF-3: Prevents premature association of the 50S subunit.
• What are the roles of eukaryotic translation initiation factors eIF1, eIF2B, eIF3, eIF4A, eIF4B, eIF4E, eIF4G, eIF5, and eIF6?

  • eIF1: Guides Met-tRNA to the 40S subunit.
  • eIF2B, eIF3: First binders, facilitating later steps.
  • eIF4A: RNA helicase that unwinds secondary structures.
  • eIF4B: Binds mRNA and facilitates scanning.
  • eIF4E: Binds the 5’ cap of mRNA.
  • eIF4G: Binds eIF4E and pol(A) binding protein, circularizing the mRNA.
  • eIF5: Promotes dissociation of initiation factors.
  • eIF6: Promotes dissociation of 80S into 40S and 60S subunits.
• What are the principles of eukaryotic translational initiation?

  • Multiple eIFs (at least 9) coordinate the formation of the initiation complex.
  • They promote and facilitate scanning.
  • They circularize mRNAs.
  • They facilitate dissociation of inactive 80S into 40S and 60S subunits.
• What happens during eukaryotic translational elongation?

  An incoming aa-tRNA enters the A site and a peptide bond is formed.
• What is the role of eEF1α and eEF2 during eukaryotic translational elongation?

  eEF1α brings the aa-tRNA to the A site, and eEF2 translocates the ribosome by one codon.
• What is the role of the release factor eRF during eukaryotic translational termination?

  It recognizes all three STOP codons and cleaves the peptidyl-tRNA bond.
• How do ribosomes differ among Bacteria, Mitochondria/plastids, TACK Archaea, and Eukarya?

  • Ribosome size: Small in Bacteria, Mitochondria/plastids, and TACK Archaea; Large in Eukarya.
  • Primary RNA sequence: Bacterial-like in Mitochondria/plastids and TACK Archaea; Eukaryotic in Eukarya.
  • Ribosomal proteins: Similar in Bacteria and TACK Archaea; more ribosomal proteins in Eukarya.
  • Genetic code: Universal across all.
• What is the significance of TACK archaeal ribosomes compared to eukaryotic ribosomes?

  • TACK archaeal ribosomes are smaller than eukaryotic ribosomes.
  • They have a very similar RNA sequence.
  • Eukaryotic ribosomal proteins are more similar to archaeal ribosomal proteins than to bacterial.
• What are the key features of the evolution of the eukaryotic cell?

  • Eukaryotes have internal membranes and a TATA box promoter.
  • They process and transport mRNA differently than TACK Archaea.
  • Archaea have one RNA polymerase similar to eukaryotic RNA Pols.
  • Rickettsia prowazekii is a Gram-negative obligate intracellular bacterium.
• What is the best scientific approach to studying the origin of eukaryotes?

  Work in a naturalistic setting, use sequence information, and apply inductive reasoning.
• Who argued that plastids were derived from cyanobacteria?

  Konstantin Mereschkowski.
• What was Lynn Margulis's contribution to the endosymbiosis theory?

  She argued that eukaryotic cells originated as communities of interacting entities.
• What is the nearest relative of mitochondria thought to be?

  Rickettsia prowazekii.
• What evidence supports the bacterial origins of mitochondria?

  Sequence comparisons of ribosomal proteins and ATP synthase genes.
• How do the proteomes of Rickettsia prowazekii and mitochondria compare?

  • Rickettsia prowazekii: ~1000 proteins encoded by 834 genes.
  • Mitochondrial proteome: ~1000-1500 proteins, with only 13 encoded by mt genome.
  • Majority of mitochondrial proteins are encoded by the nucleus.