O GoConqr está de visual novo! Conte para nós o que você achou.

Registre-se grátis

Flashcards

Structural basis of biological function 3

Joanna Elliott Inglês 121 flashcards

Structural basis of biological function 3

Flashcards do conjunto (121)

  1. 1What is the native state of a proteinThe structure which shows biological activity
  2. 2What are the 2 processes identified for protein foldingNon-covalent (folding) & Covalent modification (eg glycosylation, phosphorylation etc) of the polypeptide chain
  3. 3Hierarchy of protein structures/foldingUnfolded -> Nucleation -> Secondary structure -> Supersecondary -> Domains -> Folded monomer -> Assembly -> Inactive oligomeric -> Active oligomeric
  4. 4What 3 conditions must be met for protein folding1. Uniqueness of the sequence. 2. Stability of the structure. 3. Kinetical accessibility.
  5. 5Amino acids favour the cis-state: True or FalseFalse they prefer Trans as it is more stable
  6. 6Proline isomerisation1. Incorperated in the protein chain as trans-isomers is the ribosome. 2. When cis-state occurs it can slow down protein folding.
  7. 7What catalyses cis-proline to trans-prolinePeptidyl propyl isomerases
  8. 8GlycosylationThe attachment of glycans to proteins during co-translational or post-translational modification
  9. 9N-linked glycosylation14 sugar precursor added to an asparagine in the polypeptide chain of the target protein.
  10. 10O-linked glycosylation1. Occurs in the Golgi apparatus to serine/threonine. 2. N-acetyl-galactosamine added to serine/threonine residues followed by other carbohydrates
  11. 11C-mannosylation & why is it unusual1. Mannose sugar added to the first tryptophan in the sequence. 2. Unusual because it is bound directly to a carbon, which is very unreactive
  12. 12GPI anchors (Glypiation)Form of glycosylation that attaches proteins to a hydrophobic lipid anchor via a glycan chain
  13. 13What can reverse phosphorylationPhosphatases
  14. 14Pro-sequences1. Required for proper protein folding before they are cleaved off in order to activate the protein. 2. Intermolecular chaperones
  15. 15Kinetic foldingNucleation & Cooperativity of an a-helix in bipolymers
  16. 16In the packing of alpha helices where are ridges and where are troughs1. Ridges are formed by side chains. 2. Troughs are between ridges
  17. 17What drives protein foldingFree energy (triangle)G.
  18. 18Name other interactions needed for protein foldingVan de Waal. Met coordination. Disulphide bonds. Electrostatic interactions between ions.
  19. 19Van der WaalsTemporary induction of a dipole between to atoms due to the uneven distribution of electrons
  20. 20What are molecular chaperonesProteins that fold/unfold/assemble/disassemble other proteins but are not permanent components of those proteins
  21. 21What conformation of proteins do chaperones interact withUnfolded or partially unfolded polypeptides, proteins or domains
  22. 22Chaperone proteins stabilise non-native conformation and facilitate correct folding: True or FalseTrue
  23. 23All chaperones are highly specific T or FFalse. Some are highly specific and some are always expressed an non-specific
  24. 24Chaperone proteins often couple ATP-hydrolysis to protein folding: True or FalseTrue
  25. 25Chaperone proteins main role is to degrade proteins which cannot be re-folded: True or FalseFalse. They do this, but their main function is to stabilise unfolded proteins and prevent inappropriate interactions
  26. 26What is a trigger factor & what are its 3 domainsA bacterial co-chaperone. 2. PPIase domain, C-terminal domain & N-terminal domain
  27. 27Which domain has chaperone activity, and how is it able to interact with the substrate1. C-terminal domain. 2. Hydrophyllic & Hydrophobic patches enable the trigger factor to interact with the substrate.
  28. 28What activity does the N-terminal have and what does it bind to1. Ribosome binding activity. 2. Binds to L23 of the ribosome
  29. 29The trigger factor is ATP dependent: True or falseFalse. ATP independent.
  30. 30As proteins emerge from the ribosome they interact with the trigger factor and what elseDNA/K chaperones
  31. 31What are proteins passed onto after they interact with the trigger factorGroEL chaperone system
  32. 32NAC1. Nascent polypeptide-associated complex. 2. Heterodimer. 3. Not related to trigger factor. 4. No PPIase domain. 5. Thought to be the initial factor that interacts with newly synthesised polypeptides and prevents them from aggregating.
  33. 33NEFNucleotide exchange factor
  34. 34HSP70Family of heat inducible unfolding chaperones eg DNAk
  35. 35What are the domains & subdomains of HSP70s1. Domains - N terminal ATP binding domain allosterically linked to the C-terminal substrate binding domain (which contains the lid domain). 2. There are 4 subdomains 1A 1B 2A 2B
  36. 36What type of residues does the C-terminal substrate binding domain preferHydrophobic eg leucine
  37. 37What are the 2 conformations of the lid domainATP bound, locked onto the ATPase domain (low substrate affinity). 2. ADP bound, lid domain is locked over the bound substrate (high substrate affinity).
  38. 38What does DNAk doBinds to proteins to prevent unfolding and aggregation
  39. 39What are DNAk's co-chaperonesGrpE & dnaJ
  40. 40What else is DNAJ known asHSP40
  41. 41The J domain on dnaJ is highly conserved: True or FalseTrue
  42. 42What is required for positioning the J-domain & ATPase domain of Hsp70Gly/Phe rich linker
  43. 43What domains does DnaJ containJ, G/F, ZN, C-terminal
  44. 44What does the G/F domain do1. It can interact with the substrate binding domain of DnaK. 2. It is flexible so allows substrate to be transferred from DnaJ -> DnaK.
  45. 45What catalyses the transfer of the substrate from DnaJ to DnaKATP hydrolysis
  46. 46What is the overall function of DnaJ1. Stimulates the ATPase activity of DnaK through its J-domain. 2. DnaJ also associates with unfolded polypeptide chains and prevents their aggregation.
  47. 47What do NEFs promote and what do they do1. Promote ADP release + substrate release. 2. They cause the opening of the ATPase site so that ADP affinity is reduced and the nucleotide can exchange with ATP
  48. 48Examples of NEFs & what they contact1. HspB1 contacts subdomain 2B. 2. Bag & GrpE contact subdomains 1B & 2B
  49. 49PrefoldinA heterohexameric chaperone. Nucleotide independent. Captures nascent polypeptides and transfers them to GroEL
  50. 50What is GroEL an example ofChaperonin (ATP dependent unfolders)
  51. 51What subunits does prefoldin havea + b
  52. 52What are the beta strands arranged as and what binds non-native proteinsA double beta barrel, with exposed hydrophobic residues in the distal end of the tentacles acting as binding sites for non-native proteins (which are then passed onto chaperonins)
  53. 53What is the basic function of GroEL/GroESGeneral proteins synthesis for proteins that can't fold spontaneously or that can't fold after interaction with Hsp70/40 chaperone systems
  54. 54What are the domains of GroELApical substrate binding domain. Hinge region. Equatorial ATPase domain.
  55. 55What does GroES create for unfolded proteinsA specific environment for them to fold in
  56. 56What domain on GroEL does GroES bind to and what does this cause1. Apical substrate binding domain. 2. Closes central cavity of the chaperone
  57. 57—Just so you know what it looks likeJust so you know what it looks like
  58. 58What does ATP cause when it binds to the chaperone system1. Rips away binding sites so they become inaccessible. 2. Allows GroEL to bind further. 3. Causes GroEL to release the substrate for folding
  59. 59The ATPase cycle of GroEL1. Automating action of binding and release. 2. Substrate binds to the apo ring of GroEL whilst the other rig contains ADP. 3 Biding of ATP + GroEL to the upper ring expels GroEL from the lower ring. 4. ATP hydrolysis occurs after a delay (which allows substrate to fold). 5. ATP + GroES bind to the lower ring, expelling GroEL + ADP from the top, along with the substrate.
  60. 60What is the difference in structure between GroES/GroEL and a Thermosome1. Thermosome has a conformation with both ends close. 2. Consists of 2 rings of 8 instead of 7.
  61. 61What does CCT have that GroEL doesn'tFlexible extensions built into the CCT chaperonin
  62. 62The Hsp100/Clp family1. Form large hexameric structures with unfoldase activity in the presence ATP
  63. 63What happens when you add a peptidase to the Clp complexIt degrades the substrate protein
  64. 64How is ClpB different to the other Clp complexesIt doesn't degrade proteins it disaggregates proteins and only has 1 ATPase domain (where the others have 2) (and is class 2 not class 1)
  65. 65—
  66. 66How does Clp degrade a misfolded protein1. The polypeptide chain is pulled through the central pore for refolding or degradation. 2. This process is driven by force generated by aromatic residues in loops situated at the central pore. 3. The residues bind & release the substrate in a nucleotide dependent manner
  67. 67What is the Hsp100/Clp complex associated with and what does this super complex do1. Peptidase. 2. Super complex is ClpP. 3. Acts to unravel the denatured protein and to degrade it.
  68. 68IF there is no ClpP then what is used insteadHsp70/40
  69. 69What do the ATPase domains on Clp doDrive conformational changes in loops that interact with the substrate
  70. 70Hsp901. ATPase dependent chaperones. 2. Interacts with folded but not completely mature/active proteins. 3. Binds, stabilises, regulates
  71. 71What are the Hsp90 domainsN-terminal ATP binding domain. Middle domain with a catalytic loop. C-terminal dimerisation domain.
  72. 72N-terminal dimerisation1. Binding of ATP induces ATP lid closure and N-terminal dimerisation. 2. N-terminal rotates and the middle domain aligns its dimerisation. 3. Beta strand exchange takes place. 4. Open when bound to ADP, Close when bound to ATP.
  73. 73What does the catalytic loop in the middle domain containArg380. Interacts with the gamma phosphate of ATP (allowing hydrolysis).
  74. 74What contains hydrophobic residues which help stabilise the catalytic loop in an open active stateClosed ATP lid
  75. 75Overall, what do conformation changes in H2p90 doThey conspire to form a catalytically active unit able to hydrolyse ATP
  76. 76What is required from kinase client-protein loadingPrevention of N-terminal dimerisation & ATPase activity, caused by the C-terminal domain of cdc binding as a dimer between the N-terminal domains of Hsp90
  77. 77What does the C-terminal of Sti1/HOP/p60 act as and howAn inhibitor. Couples Hsp90 and Hsp70 together.
  78. 78What does Aha1 act as and howA potent activator. Binds to the middle domain of Hsp90, modulating the catalytic loop & activating ATPase activity of Hsp90 by promoting the activate of the catalytic loop
  79. 79What does Sba1 act as and howA partial inhibitor of ATPase activity. Both inhibits and promotes the ATPase cycle, effectively slowing it down.
  80. 80Kinase activation1. Phosphorylated cdc37 interacts with immature kinases and transfers them to Hsp90. 2. PP5 can dephosphorylate cdc37 and cause the release of the activated kinase.
  81. 81How are Heat shock proteins regulatedphosphorylation
  82. 82What happens to Hsp27 during stress1. Develops chaperone activity. 2. Forms large oligomeric structures with high molecular weight. 3. These bind to unfolded proteins and store them for refolding/degradation.
  83. 83What happens during stress recoveryThe unfolded protein can be refolded spontaneously or using chaperones
  84. 84Immunoglobin domain1. Found in the chaperone domain of heat shock proteins. 2. Consists of b-sheets required for the stabilisation of dimers. 3. Exchange of the beta strands allows them to form dimers.
  85. 85In what order do pap proteins assemble to form the pili (from top to bottom)G, F, E, K, A, C, H, D (Go Fucking Eat Kebabs And Chilli Hot Dogs)
  86. 86What does Pap G containAdhesin in its tip, allowing it to attach to tissue
  87. 87What does pap C act asUsher (pore)
  88. 88PapD1. Periplasmic and acts as a chaperone. 2. Is the only Pap D protein with a C-terminal b-strand. 3. It donates its b-strand to the F-beta strand of PapK to complete its immunoglobin fold. 4. This prevents Pap proteins from making inappropriate interactions with other proteins.
  89. 89What else binds to PapKP2 - P3 conserved residues
  90. 90What pap protein doesn't have an N-terminal & why is the N-terminal importantPapG. Important for interacting with pap5.
  91. 91Describe the donor strand exchange1. Resiude P5 binds to the P5 site of a pap protein. 2. Residues P2-P4 then compete out the papD residue. 3. PapD comes out and is replace by the N-terminal
  92. 92In the E.coli secretion pathway, what regions does the sequence signal contain1. N-terminal basic residues. 2. Middle hydrophobic region (variable in length). 3. Peptidase cleavage recognition sight (at least 3 amino acid residues).
  93. 93What types of translocation are thereCo-translational & Post-translational.
  94. 94What is the driving force behind translocationThe ribosome & some proton motive force
  95. 95In translocation, what plays the part of the channelSecYEG
  96. 96In translocation what is the SRPSignal recognition protein
  97. 97In translocation what is FtsYGTPase which transfers peptide to the channel
  98. 98What happens when signal sequences are not hydrophobic enough so are not recognised by SRPSecB (which prevents folding) binds to these and docks with SecA (an ATPase motor), which provides the force for translocation (along with proton motive force)
  99. 99What happens to the polypeptide once is has been translocated across the membraneIt is cleaved by signal peptidase, releasing either a soluble protein or a membrane bound protein
  100. 100Is ER import a eukaryotic co-translational translocation or a post-translational translocationCo-translocational translocation
  101. 101What is Sec63 & where does it sit1. A j-domain containing protein that stimulates the ATPase activity of Bip and stimulates hydrolysis of ATP in Hsp70s. 2. It acts as a pore in the ER membrane.
  102. 102Eukaryotic co-translocational translocation is an SRP dependent pathway: True or FalseTrue. SRP docks onto SRa (an SRP receptor)
  103. 103What does Bip do in the ER lumenPrevents movement of polypeptide back out of the cell by acting like a ratchet
  104. 104What proteins are involved in Glycosylation in the ER lumenErp57 (protein disulphide isomerase) (catalyses formation & breakage of disulphide bonds while the protein is folding). Calnexin & Calrecticulin (structurally similar)
  105. 105Both Calnexin & Calrecticulin are membrane bound proteins: True or FalseFalse. Only Calrecticulin is membrane bound.
  106. 106What else does Erp57 bind to and why1. Calnexin & Calreticulin. 2. This allows it to interact with disulphides of the substrate and bring about correct disulphide bridge formation, and ultimately correct folding.
  107. 107What happens to proteins in the ER that are correctly and incorrectly folded1. Incorrect - Can be reglycosylated. 2. Correct - Glucose removed by Glucosidase and the protein exists in the ER
  108. 108What is ERAD quality controlRemoval of specific mannose residues by mannose 1 and EDEMs leads to proteins which exit the ER from proteasomal degradation.
  109. 109What is an amphipatic helixA helix charge on only one side
  110. 110Mitochondrial targeting sequenceBasic residues interspaced with hydrophobic residues, forming an ampiphatic helix
  111. 111TOM20Mitochondrial import receptor subunit.
  112. 112TOM22Acts as a receptor for the unfolded protein, and once its through the pore Tom22 rebinds the translocated polypeptide
  113. 113Mitochondrial import stimulation factor (MSF)Binds the nascent polypeptide, which then interacts wit the mitochondrial TOM70/20 import.
  114. 114Describe the 3 different routes to the GIP1. Pre sequence proteins enter via TOM70/20 22 & 5. 2. Post-translationally coupled via TOM70. 3. Carrier proteins enter via the dimeric TOM70.
  115. 115What determines which route a polypeptide will take into the GIPDepends on the state of the polypeptide
  116. 116What happens after the polypeptide has passed through the GIP into the inner mitochondrial spaceInner membrane translocase - Polypeptide is moved across the inner mitochondrial membrane and into the mitochondrial matrix
  117. 117What proteins form the poresTIM23 & TIM17
  118. 118Which part of TIM23 recognises the presequenceThe N-terminal domain
  119. 119What recruits the matrix Hsp70 to the TIM complexTIM44
  120. 120What acts as the NEF for this Hsp70 & what is the Hsp40Mge1 & Mdj1
  121. 121MPPMitochondrial processing peptidase. Heterodimeric.

Informações

Descrição
Chris P lectures
Criado por
Joanna Elliott
Visualizações
43
Avaliação

Fale Conosco

Sobre o que é sua mensagem?

O que você acha do novo visual?

Você gostou?