Cell Bio exam 2

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  1. 4 destinations in which proteins will be sent
    • organelles
    • organelle membrane
    • cytosol
    • plasma membrane
  2. signal peptides
    specific amino acid sequence that helps to indicate the destination of the protein
  3. organelle have receptors for signal sequences and translocators to move the proteins
  4. the rough ER is composed of a network of flattened sacs called
  5. is continuous with the outer mem of the nuclear envelope and has ribosomes on its cytosolic surface
    rough er
  6. the ribosomes attached to the ER are involved in the translation of mrna to protein
  7. protein synthesis starts in the cytosol and the presence of a 16-30 AA sequence in the nascent protein directs the ribosome to the ER
  8. protein synthesis starts in the cytosol and might go to the ER
  9. n-terminal signal sequence targets proteins to the rough ER
  10. cotranslation translocation
    when translocation and translation occur at the same time
  11. one or more positive AA next to a stretch of 6-12 hydrophobic AA
  12. is a cytoplasmic ribonucleoprotein particle
  13. functions of the signal recognition particle
    binds to the large ribosomal subunit and the er signal sequence and targets them to the er membrane where its receptor is located
  14. this receptor is located in the ER membrane
    srp receptor
  15. srp will stop translation until it binds to its receptor
  16. the interaction between srp and its receptor is strengthened by
    the addition of GTP to both proteins
  17. the translocon in animals is composed of three proteins known as the sec 61 complex
    sec61 alpha, beta, and gamma
  18. sec61 alpha is an integral protein with 10 alpha helicles
  19. energy from translocation comes from the elongation process
  20. location of the translocon
    in ER membrane
  21. post translational translocation has been found in yeast
  22. some secretory proteins enter the lumen after being translated
  23. all membrane proteins must be incorporated to the mem in the ER
  24. mem proteins will be sent to diff organelles
  25. topogenic sequences function
    direct the mem insertion and orientation of various classes of integral proteins
  26. refers to the # of times that a polypep chain spans the mem and the orientation of the segments in the mem
  27. 3 sequences a single pass protein can present
    • signal sequence
    • stop transfer anchor sequence
    • signal anchor sequence
  28. signal sequence has 1 or more + AA besides the stretch of 6-12 hydrophobic AA
  29. signal sequence is responsible for
    targeting protein to the ER (binds SRP)
  30. these kinds of proteins present a signal sequence and a stop transfer anchor sequence
    type 1 proteins
  31. these 2 types of proteins lack the N-terminal ER signal sequence
    type 2 & 3
  32. type 2 & 3 posses an internal hydrophobic signal anchor sequence that works as both an ER signal sequence and a mem anchor sequence
  33. the orientation of the type 1-3 proteins depends on the orientation of the signal anchor sequence in the translocon
  34. tail anchored proteins are known as
    c-terminal anchored proteins
  35. in tail anchored proteins when is the hydrophobic c-terminal available for insertion
    it is not available until the protein is completely finished
  36. tail anchored proteins are recognized by specialized complex of proteins including these 2
    • get 3
    • get 1/2
  37. Get 3 recognize tail anchored proteins when
    they are bound to ATP it recognizes the c-terminal sequence
  38. when get1/2 recognizes the tail anchored proteins and bind, they
    trigger the hydrolysis of ATP, this causes the release of the c-terminal which is then inserted into the mem
  39. get3 binds to ATP and leaves get1/2
  40. some proteins are attached to the mem by a covalently attached amphipathic molecule called
    glycosylphophatidylinositol (GPI)
  41. GPI are initially synthesized just like type 1 proteins
  42. a short sequence of AA in the luminal domain is recognized by a
  43. the function of the transamidase enyme
    cleaves the stop transfer anchor sequence and transfer the luminal portion of the protein to a GPI anchor
  44. how do hydrophobicity plots work
    they use the AA sequence to map the hydrophobicity of different protein segments. The AA gives a score of more positive and hydrophobic
  45. proteins encoded by mito/chloro DNA are synthesized by ribosomes w/in the organelles and directed to the correct subcompartment immediately after synthesis
  46. the majority of proteins located in mito and chloro are encoded by genes in the nucleus and are imported into organelles after their synthesis
  47. for proteins to go to the right organelle they need to have signal sequences that are recognized by receptors in the organelles
  48. additional sequences from the signal help to guide the protein to the right area of the organelles
  49. when proteins are imported into the mito they are kept unfolded in the cytosol by
    the binding of chaperons to the proteins
  50. the mito sequence binds to an import receptor in the outer mit mem. The diff import receptors recognize diff signals
  51. general import pore
    import channel in the outer mem
  52. the import receptor transfer the mito protein to an import channel in the outer mem known as the
    general import pore
  53. the driving force for unidirectional transport of the protein into the mito is due to the mito itself
  54. the general import pore of the mito is called
  55. translocation requires 3 diff energy inputs
    • ATP hydrolysis by HSc70 chaperon in cyto
    • "   " in matrix
    • PMF across the inner mem
  56. H+ electrochemical gradient aka
  57. if the electrochemical gradient has dissipated then the proteins will bind the outer mem but will fail to translocate
  58. mito proteins can be targeted to
    require a single/multiple signal
  59. single signaling in mito proteins occur in the
  60. multiple signals in mito proteins occurs in these 3 areas
    • intermem space
    • inner mem
    • outer mem
  61. proteins can be targeted to diff areas in the chloro such as these 4
    • outer mem
    • inner mem
    • stroma
    • thylakoids
  62. what kind of sequence is needed for the proteins to be targeted to the stroma of chloro
    n-terminal stromal import sequence
  63. in order for a protein to enter the thylakoids it must go through the stroma using its N-terminal stromal import sequence. Then another sequence guides the protein into the thylakoids
  64. the protein enters the thylakoid by what sequence
    intra protein thylakoid targeting sequence
  65. antibodies against supposed translocating proteins can be used to test whether they block translocation into the matrix
    targeted mutations to supposed signal sequences can be used to test their importance for proper translocation
  66. the movement of proteins and molecules in and out of the nucleus takes place
    through the nuclear pore
  67. proteins that are destined to be in the nucleus and are found in the nucleus have
    nuclear localization signals NLS
  68. proteins enter through the nuclear pore in a folded state
  69. NLS signal classical
    • SV40
    • pro-lys-lys-lys-arg-lys-val
  70. how do we confirm the NLS signal targets proteins to the nucleus
    chimeric proteins
  71. how do chimeric proteins confirm NLS signals targets proteins to nucleus
    chimeric proteins contain the sequence of a cytosolic protein and the NLS are targeted to the nucleus
  72. a detergent that removes everything in a cell except for the nucleus an the mem
  73. digitonin helps researchers to see what happenes to transport proteins when there are no cytosolic elements
  74. 2 additional cytosolic proteins required for nuclear protein translocation
    • ran
    • importin alpha/beta
  75. monomeric g-proteins that exist in either GTP or GDP bound conformation
  76. these 2 proteins are required for nuclear protein translocation
    importin alpha/beta
  77. importin alpha function
    bind to a basic NLS in proteins
  78. importin beta function
    interacts with proteins in the nuclear pore
  79. importin beta can also bind some NLS sequences and translocate proteins alone
  80. signal used for ran dependent nuclear export
    nuclear export signal
  81. 2 proteins involved for ran dependent nuclear export
    exporting 1/t
  82. export 1 is used for
  83. export t is used for
  84. Membrane and soluble proteins synthetised in theER undergo four main modifications:
    • glycosilation
    • form of disulfide bonds in ER
    • proper folding and multiunit assembly
    • proteolitic cleavages (ER, Golgi, secretory)
  85. this is the covalent addition and processing of carbohydrates in the ER and golgi
  86. only folded proteins are transported to the rough ER and golgi
    misfolded proteins stay in the ER
  87. carbohydrates chains may be added to the hydroxyl group in these 2 in protein glycosilation
    • serine and threonine
    • amide nitrogen of asparagine
  88. 2 carbo chains that may be added to the hydroxyl group in serine and threonine or asparagine
    • o-linked oligosaccharide
    • n-linked oligosaccharide
  89. n-linked oligosaccharides contains these 3
    • 3-glucose
    • 9-mannose
    • 2-n-acetylglucosamine
  90. these are preformed and are added to asparagine
    n-linked oligo
  91. what happens in protein glycosylation when the carbo chain n-linked oligo is attached to asparagine
    it will be modified in the ER and Golgi according to the protein
  92. n-linked oligo have 14 residues when added to asparagine, once added the 5 residue core always remains
  93. the synthesis of oligosaccharides takes place in the
    cytosolic portion of the ER
  94. proteins cant fold back into their native shape if they can it takes hours
  95. modifications of n-linked oligo are used to monitor folding and quality
  96. important protein folding catalyst in the ER lumen are
    peptidyl prolyl isomerases
  97. these are enzymes that accelerate the rotation about peptidyl-prolyl bonds at proline residues
    peptidyl prolyl isomerases
  98. improper folding of proteins are retained in the ER and are seen bound to the ER chaperones bip and calnexin
  99. the presence of unfolded proteins in the ER results in an increase in expression of ER chaperones and proteins, this is known as
    unfolded protein response
  100. proteins going from the ER to the golgi
    proteins going from the Golgi to the ER
    • anterograde
    • retrograde
  101. materials carried between compartments use
    coated vessicles
  102. 2 functions of protein coats
    • cause mem to curve and form vess
    • select what to be carried
  103. 3 kinds of coated vessicles
    • COPII
    • COPI
    • clathrin coated
  104. the function of COPII vess
    move materials from ER to the golgi
  105. function of COPI
    move materials from Golgi to ER, or trans Golgi to cis golgi
  106. function of clathrin
    move material from mem to endosome, lysosome, and plant vacuole
  107. if GTP hydrolysis is blocked, coated vesicles accumulate, this can only happen 2 ways
    • in vivo by mutations in GTPases
    • add of GTP-v-s
  108. addition of COPII proteins to a cell free sys induces protein coated buds from ER derived vesicles
  109. mechanism by which the vesicle coat selects proteins is by
    directly binding to specific sorting signals in the cytosolic portion of the mem cargo proteins
  110. this signal binds the luminal domains of certain cargo proteins
    luminal sorting sig
  111. soluble proteins are taken by vesicles that have luminal sorting sig
  112. mutations in the COPI proteins stops both retro and antero transport, ER s depleted of pro and mem necessary for sorting
  113. most soluble ER resident proteins carry these 4 amino acid sequences at their c-terminal KDEL
    • lys
    • asp
    • glu
    • leu
  114. KDEL signal sequence is the
    the ER soluble resident proteins carrying the amino acid sequence
  115. KDEL signal is sufficient and necessary for
    sorting proteins to the ER
  116. adding KDEL to a normally secreted protein causes
    KDEL to be sequestered to the ER
  117. when KDEL is removed from an ER destined protein
    it results in it being secreted
  118. KDEL receptor binding proteins are pH dependent
  119. KDEL receptor is located in vesicles between ER and golgi
  120. cystic fibrosis is caused by
    mutation in Cl channel encoded by the CFTR gene
  121. common mutation in CFTR gene  is
  122. function of mutated CFTR gene
    sorting of protein to its correct target
  123. 3 sub comparts of golgi
    • cis
    • medial
    • trans
  124. movement of proteins in the Golgi takes place by cisternal maturation
  125. uptake of cell surfaces receptors and bound extracellular ligands
  126. uptake of particular matter
  127. uptake of specific extracellular ligands following their binding to receptors
    receptor mediated eno
  128. substances that enter through RME become bound to
    coated pits on the plasma mam
  129. clathrin regions invagimate into the cyto then pinch free of the cyto
  130. clathrin contains 3 chains that form a triskelion
  131. coated vesicles contain adaptors between clathrin and mem
  132. this done by this is required for the final stages of vesicle budding during endo
    GTP hydrolysis by dynamin
  133. in the endocytic pathway vesicle bound materials are transported in vesicles and tubules called
  134. LDL cholesterol is bad for you
  135. low density lipoproteins
    are a complex of cholesterol and proteins
  136. LDL receptor are transported to the plasma mem and bound to a coated pit
  137. function of LDL
    are taken up by RME and taken to the lysosomes to release cholesterol for use by the cells
  138. transport cholesterol from tissue to the liver excretion
    high density lipoporteins
  139. LDL increase cholest while HDL lower
  140. deposition of LDL leads to plaque formation on the inner walls of blood vessels
  141. major glycoprotein of the blood
  142. function of transferrin
    transport Fe to all tissue cells from the liver and intestine
  143. Transferrin with Fe
    w/o Fe
    • apotransferrin
    • ferrotransferrin
  144. cells need to sense their environment and respond to it
  145. 4 things cells sense for
    • nutrients
    • foreign substances
    • tropic signals
    • hormones
  146. 4 things needed in order for cells to communicate
    • signaler
    • signal
    • medium for signal transmission
    • detector
  147. the signaler aka 
    signal aka
    detector aka
    • signaling cell
    • signal molecule
    • receptor proteins in target cell
  148. when signals in cell need to change physical state
    signal transduction
  149. distant sig from one cell to target cells by ligands secreted into the blood stream
    endocrine sig
  150. short range sig by a cell to adjacent ones
    paracrine sig
  151. special type of paracrine sig
    synaptic sig
  152. signaling by neuron to another neuron of an effecter cell
    synaptic sig
  153. sig by a cell to itself
  154. cells have fast and slow responses to sig
  155. sig molecules can bind a receptor in the cell mem or if lilophilic, one in the cyto
  156. steroid hormone cortisol acts by
    activating a transcription reg
  157. local sig molecule that can travel through the mem
  158. function of NO
    quickly convert to nitrates/ites
  159. enzymes that add phos groups
  160. 2 types of kinases that undergo switching by phos
    • serine/threonine
    • tyrosine
  161. enzymes that remove phos groups
  162. 3 cell surface receptor classes
    • ion channel coupled receptors
    • g protein coupled
    • enzyme coupled
  163. this receptor allows for the flow of ions
    ion channel coupled receptors
  164. ions going in/out of cells results in changes in the mem potential and can produce an electrical current
  165. first and second messengers in signaling from cell surface
    • ligands
    • certain metabolites
  166. function of 2nd messengers
    relay the signal from one ligand to other targets
  167. the binding of the ligand to its receptors alters the conc of the second messengers inside the cell
  168. advantages of second messengers
    • diffuse faster than proteins
    • amplify sign
  169. signals from cell surface reaches their targets through 2nd messengers
  170. 2 characteristics of the structure of g-protein coupled receptors
    • single polypep chain
    • cross the mem 7 times with serpentine receptors
  171. 4 terminations of g protein coupled receptors
    • desensitization
    • g-protein coupled receptor kinase
    • arrestins
    • regulators of g protein sig
  172. desensitization termination of the response of GPCR occurs
    by blocking active receptors from turning on additional g proteins
  173. G protein couple receptor kinase GRK termination of the response of GPCR function
    activates a GPCR via phos
  174. arrestins termination of the response of GPCR function
    compete with g proteins to bind GPCRs
  175. termination of the reponse of GPCR is accelerated by
    regulators of g protein signaling RGSs
  176. FRET study the interaction between 2 protein
  177. FRET
    fluorescence resonance energy transfer
  178. fret can be done to test to see how 2 known proteins interact and when in vitro and in vivo
  179. FRET function It relies on 2 fluorescent proteins of different absorption andemission spectra, with the special design characteristic thatthe emission wavelength of the first one matching theabsorption wavelength of the second one
  180. cAMP rises rapidly in response to an extracellular signal
  181. binding of serotonin to neurons results in
    increase in cAMP
  182. cholera
    is an infection of the smallintestine that is caused by thebacterium Vibrio cholerae.
  183. function of the cholera toxin enzyme
    catalyzes the transfer of ADP ribose from intracellular NAD+ to the alpha subunit of Gs
  184. alters the alpha subunit it so that it can no longer hydrolyze its bound GTP
    ADP ribosylation
  185. when ADP ribosylation can no longer hydrolyze its bound GTP it causes it to
    remain in an active state that stimulates adenylyl cyclase indefinitely
  186. the prolonged elevation in cAMP levels w/in intestinal epithelial cells causes a large efflux of Cl- and H2O into the gut (causes symptoms of cholera)
  187. is a protein-based toxinproduced by the bacterium Bordetella pertussis,which causes whooping cough.
    pertussis toxin
  188. pertussis toxin function
    catalyzes the ADP ribosylation of the alpha subunit of Gi
  189. pertussis toxin effect prevents the subunit from interacting withreceptors; as a result, this α subunit retains itsbound GDP and is unable to regulate its targetproteins.
  190. extracellular signals can induce long term responses
  191. receptors can be located in the mem or cyto
  192. 3 affects that extracellular signals do to cell function
    • division
    • differentiation
    • expression levels of the receptors
  193. 2 ways extracellular signals modulating gene transcription
    • alter chromatin structure
    • turn transcription factors on/off
  194. 2 functions of intracell domain
    • enzyme
    • forms a complex with another protein that acts as an enzyme
  195. enzyme coupled receptors are
    transmem proteins
  196. enzyme coupled receptors contain an extracell ligand binding domain
  197. Ras proteins is a family of small GTP biding proteins
  198. ras proteins structure
    bound by a lipid tail to the cytoplasmic tail of the plasma mem
  199. why are early response genes called this title
    they are induced well before the cell enters s phase
  200. 2 important early response genes
    • c-fos
    • c-jun
  201. function of the 2 most important response genes
    induce the activation of a many genes that are necessary for the cell to progress through the cell cycle
  202. receptors do not have enzymatic activity
  203. signal form unrelated receptors can ______ to activate a common effector
  204. identical signals can ______ to activate a variety of effectors
  205. signals can be passed back and fourth between pathways as a result of
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Cell Bio exam 2
cell bio exam 2
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