Translation

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Author:
mfawcett
ID:
153559
Filename:
Translation
Updated:
2012-05-12 14:10:49
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translation miska
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translation
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  1. polyU gives
    polyPhe
  2. polyA gives
    poly Lys
  3. What is the name for codons that specify the same amino acid?
    Synonym codons
  4. Sequence at 3' end of tRNA
    ...CCA, terminal 3'OH or 2'OH is aminoacylated
  5. tRNAs attached to amino acids by
    aminoacyl RNA synthetases
  6. 2 step mechanism for aminoacyl tRNA synthetases
    • amino acid: ATP in, pyrophosphate out
    • enzyme.aminoacyladenylate: tRNA in, AMP out
    • amino acid-tRNA
  7. aminoacyl tRNA synthetases recognise
    • 1 type of amino acid
    • all cognate tRNAs
  8. Accuracy depends on which step in activating tRNA? Example?
    The second step: IleRS can charge Val with AMP, but hydrolyses valul-aminoacyladenylate when tRNAile is added
  9. Inosine in the wobble position can pair with
    U, C or A
  10. Distribution of mass in ribosomes
    • 2/3 RNA
    • 1/3 protein
  11. Sizes of subunits in bacterial ribosomes
    • Complete: 70S
    • Large subunit (peptide transferase): 50S
    • Small subunit(mRNA): 30S
  12. Sizes of subunits in mammalian ribosomes
    • Complete: 80S
    • Large subunit (peptide transferase): 60S
    • Small subunit(mRNA): 40S
  13. Sedimentation coefficient dependent on? Units?
    • Mr
    • particle shape
    • Svedberg units
  14. How is protein synthesis initiated with regards to ribosome activation
    • Small subunit binds to mRNA
    • Large subunit joins it at the initiating AUG codon
  15. Maximum density of ribosomes
    1 ribosome/80nt
  16. What is at the beginning of bacterial mRNA strands and how does this relate to initiating protein synthesis?
    • Bacteria: start with formyl-methionine
    • Formyl rapidly removed, met may be removed more slowly
    • formyl-Met-X cut by deformylase then aminopeptidase
  17. What is at the beginning of eukaryotic mRNA strands and how does this relate to initiating protein synthesis?
    • Eukaryotes: start with methionine (AUG)
    • May be removed later depending on the next amino acid
    • Met-X, bond broken by aminopeptidase
  18. How do bacteria distinguish between initiating AUG codons and normal AUG codons?
    • Shine-Dalgarno sequence: 5'-GGAGG-3' nearer 5' end
    • Recognised by CCUCC at the end of the 16S RNA in the 30S subunit
    • Each cistron in polycistronic mRNA has its own AUG and Shine-Dalgarno sequence
  19. How do eukaryotes distinguish between initiating AUG codons and normal AUG codons?
    • 'Scanning ribosome model'
    • eIF4F (eukaryotic initiation factor) on 40S subunit binds to 5' cap
    • scans along RNA towards 3' end (using ATP)
    • Locks on at AUG, 60S subunit joins
    • sometimes, different start sites can be used to generate different proteins from one mRNA
  20. Viral method of initiation of translation
    • 'Internal initiation of translation'
    • first discovered in picornaviruses
    • IRES (internal ribosomal entry site) in the 5'UTR directs the binding of the ribosome to the mRNA
  21. How to define IRES sequences
    dicistronic assay: put IRES between two coding genes; if 2nd one is expressed, then the IRES works
  22. Major IRES drug target
    Hepatitis C
  23. 2 sites on ribosomes for binding charged tRNA
    • P site: for peptidyl-tRNA
    • A site: for aminoacyl-tRNA
  24. How does translation occur?
    • Charged aa-tRNA binds to A site, using EFTu (Elongation factor protein) (bac) or eEF-1 (euk)
    • GTP hydrolysis causes the dissociation of EFTu from the ribosome
    • A peptide bond forms from the peptide held by the tRNA already in the P site eg by peptidyl transferase
    • The bond between the P site peptide and the P site tRNA is broken
    • The ribosome moves 3 nucleotides along the mRNA (translocation) using EFG (bac) or eEF-2 (euk) and GTP
    • The peptidyl-tRNA (now with its peptide joined to the peptide next door) moves into the P site, while the deacylated peptide (that WAS in the P site) is kicked out, perhaps through the E site
  25. Two proteins that use GTP in translation (bacterial and eukaryotic for each)
    • EFTu (bac) and eEF-1 (euk) bind the aminoacyl-tRNA to the A site
    • EFG (bac) and eEF-2 (euk) cause translocation of the ribosome
  26. How is transcription terminated?
    If a stop codon (UAA, UAG, UGA) is in the A site, RF (release factor) binds, meaning peptidyl transferase binds to polypeptide to H2O - hydrolysis of the peptidyl-tRNA and therefore release
  27. 2 protein synthesis inhibitors
    • Diphtheria toxin: covalently modifies eEF2 - cell death
    • Ricin: ribsome inactiated by removal of a single adenosine base from the eukaryotic 28S rRNA via its glycosidase activity
  28. 5 antibiotics that affect protein synthesis
    • Streptomycin: binds to 30S unit, inhibits initiation, or causes misreading of mRNA at low concentrations
    • Tetracycline: inhibits binding of aminoacyl-tRNA to the 30S subunit
    • Oxazolidines: inihbit formation of initiation Meti-30S ribosomal subunit-mRNA complex
    • Chloramphenicol: inhibits peptidyltransferase activity of 50S subunit (for typhoid and bacterial meningitis)
    • Erythromycin: blocks progression of nascent peptide by binding to 50S subunit by the peptide exit tunnel
  29. Two types of control of translation
    • Global: eg interferon response
    • Specific: eg ferritin
  30. What is the interferon response?
    • eIF2 is an initiation factor that binds Met-tRNAi and GTP and delivers them to the 40S subunit
    • eIF2's activity is REDUCED by PHOSPHORYLATION
    • one eIF2 kinase is activated in response to dsRNA, which is usually a by-product of viral infection
    • replication is inhibited
  31. An example of specific translation control
    • Transferritin protects the cell from too much iron by binding it
    • When [Fe] is low, IRP (iron regulatory protein) binds to IRE (iron response element), which is in a hairpin in the 5'UTR of the ferritin gene
    • IRP binding to IRE means the 40S subunit cannot bind to the 5'cap
    • -> Initiation of ferritin synthesis does not happen when [Fe] is low
  32. What is RNAi?
    • When miRNAs:
    • Inhibit translation
    • Degrade mRNA
    • Degrade protein
  33. What are riboswitches? example?
    • RNA sequences in 5'UTR/introns that bind small molecules to regulate transcription
    • eg thiamine (B1) levels directly control thiamine synthesis
  34. Two ways to degrade proteins
    • Lysosomes
    • Proteasomes
  35. How do lysosomes work?
    • Non-selective in well-nourished cells: degrade longlived proteins and organelles all the time
    • Selective after prolonged fast
    • Import and degrade proteins with specific pentapeptide Lys-Phe-Glu-Arg-Gln (KFERQ) - selectively lost from tissues that atrophy in response to fasting eg liver, kidney, not brain, testes
    • Also macroautophagy
  36. How do proteasomes work?
    Mediate destruction of short lived and ubiquitinated proteins
  37. How is ubiquitin linked to proteins?
    • 1) E1 (ubiquitin activating enzyme) links C-terminal glycine in Ub to -SH in E1 forming a thioester bond (uses ATP)
    • 2) E2 (ubiquitin conjugating enzyme) ligates Ub to itself
    • 3) E3 (ubiquitin ligase) ligates Ub to the e-NH2 groups of lysines in the protein destined for destruction
    • This is related to Cyclin B?
  38. How are ubiquitins removed?
    Ubiquitin peptidases
  39. 4 stages of proteasomal destruction
    • 1) Recognition: Ubiquitinated proteins bind to proteins in cao
    • 2) Dissociation: ATP dependent process unravels the protein and spits out the Ubs
    • 3) Translocation: The protein is fed into the shaft - the inner two rings are responsible for proteolysis
    • 4) Destruction: protein is entirely degraded into 8 amino acid peptides which are released
  40. 3 other types of protein destruction sequences
    • N-end rule: 5 specific amino acids at N-terminus
    • PEST sequences: Pro, GLu, Ser, Thr - phosphorylated on S or T
    • D-box: seems to be a sequence required for cyclin ubiquitination

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