Bio135 Final Exam Lecture Notes.txt

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Bio135 Final Exam Lecture Notes.txt
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Bio135 Final Exam Lecture Notes
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Bio135 Final Exam Lecture Notes
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  1. What makes up the cell membrane?
    • Phospolipid bilayer
    • Proteins
    • Cholesterol (animals)
  2. What kinds of proteins make up the cell membrane?
    • Peripheral
    • Integral (Transmembrane)
  3. What part of a protein is glycosylated?
    The portion facing the extracellular matrix
  4. What are the functions of the membrane?
    • Selective barrier
    • In eukaryotes, formation of organelles/compartments
    • Localization of enzymatic reactions
    • Cell-cell communication
    • Transmission/reception of signals
    • Shape
    • Receive stimuli
    • Site of ECM attachment
  5. Where does glycoslyation occur, and what is the destination?
    • Golgi
    • Cell membrane (i.e. not organelles)
  6. What does flippase do?
    It "evens out" enzymes since most are on cytosol side
  7. What is a lipid raft?
    A "microdomain" of the plasma membrane which aggregates proteins and phospholpids for transportation.
  8. How does a lipid raft travel?
    Via vesicle
  9. Do proteins for organelles get glycosylated? Why or why not?
    • No.
    • Glycosylation is for cell-cell recognition
  10. What is an advantage of a compartment/organelle?
    • Useful for specialized enzymatic reactions.
    • Greater rate of collisions for reactions to occur.
  11. What is the minimum length of a transmembrane protein?
    20 a.a.'s
  12. What are some functions of transmembrane proteins on the cytoplasmic side?
    • Intrinsic or associated enzymatic activity
    • Provide cell with shape
  13. What are functions of transmembrane proteins on the outside?
    • Receptors for soluble ligands
    • Channel/gate
    • ECM attachment (e.g. integrins)
    • Cell-cell attachment (e.g. cadherins)
  14. How are gates/channels activated?
    Hormones or action potentials
  15. What are types of secondary structures for transmembrane proteins?
    • Alpha helices
    • Beta barrels
  16. For alpha helices in a gate, where is the hydrophobic side?
    Facing the outside surface of the gate
  17. What transports water thru the membrane?
    Aquaporin
  18. What is the function of membrane cholesterol?
    Provides membrane fluidity
  19. What types of molecular movement are there in the membrane?
    • Rotation on axis
    • Lateral (sideways)
    • Flip-flopping (from one side to the other)
  20. Describe flip-flopping movement in a membrane.
    • Requires energy and is thus uncommon
    • Requires the flippase enzyme
    • Proteins are too large for this movement
  21. What can cross a membrane by simple diffusion?
    CO2 and O2
  22. What happens if a cell membrane has no fluidity?
    The cell dies
  23. What are some ways to alter membrane fluidity?
    • Change length of hydrocarbon tails
    • Change saturation
    • Change cholesterol content
    • Change temperature
  24. What does an increase in cholesterol do?
    Increases fluidity
  25. What does an increase in temp do?
    Increases fluidity
  26. What does an increase in saturation do?
    Decreases fluidity
  27. What does an increase in hydrocarbon tail length do?
    Decreases fluidity
  28. What is a ligand?
    A signal that is received by the cell usually resulting in a response.
  29. What is a receptor?
    A feature on the cell which receives a ligand
  30. How does a receptor respond?
    • Intrinsically as an enzyme.
    • Associated with an enzyme.
    • With the cytoskeleton directly.
  31. What are some responses to a ligand being received?
    • Gene expression
    • Metabolism
    • Movement
  32. What are effector proteins?
    They are proteins activated by intracellular signalling proteins
  33. What are three types of effector proteins?
    • Metabolic enzyme
    • Gene regulatory protein
    • Cytoskeletal protein (altered cell shape or movement)
  34. What types of interactions are there between effectors and cells?
    • Direct contact between transmembrane molecules of two neighboring cells
    • Paracrine system (local)
    • Synaptic (neurotransmitters)
    • Cytonemes (thin cytoplasmic extensions releasing hormones)
    • Endocrine (via bloodstream)
  35. Which type of signalling requires the most signal molecules?
    Endocrine
  36. Which type of signalling is not soluble?
    • Contact dependent
    • Maybe Cytonemes?
  37. What are three types of signalling responses?
    • Quick; < 1 hour; protein de/activation; synaptic
    • Slow; 18-24 hours; transcription/translation; endocrine
    • Single cell or group in development; autocrine
  38. What are four end-results of a cell in response to a signal?
    • Survive
    • Grow + Divide
    • Differentiate
    • Die
  39. Describe how acetylcholine can cause two different reponses.
    • Heart muscle - decreased rate and force of contraction
    • Skeletal muscle - contraction
  40. What are two types of signals wrt to water?
    • Soluble - interact with transmembrane receptors
    • Insoluble - interact with cytoplasmic receptors
  41. Non-soluble signals affect ___.
    transcription
  42. What are examples of non-soluble signals?
    Vitamin D, estrogen, testosterone, cortisol, estradiol, retinoic acid, and thhroxine
  43. Non-soluble signals have a ___ effect due to ___.
    • longer-lasting
    • their duration in the blood
  44. Non-soluble signals enter the cytoplasm by ___.
    diffusion
  45. Non-soluble receptor responses include ___.
    • Early - first 30 min
    • Delyated
    • Depends on type of protein and timing of synthesis
  46. Gene expression regulation falls into two general categories:
    • Activation
    • Repression
  47. All nuclear receptors bind as either ___ or ___.
    Homodimers, heterodimers
  48. An inactive receptor protein is bound to ___ proteins.
    Inhibitory
  49. Proteins in the primary response can ____.
    Activate other proteins for a delayed/secondary response.
  50. Describe responses to testosterone.
    • Early - male characteristics in development
    • Delayed - muscle growth
  51. Describe responses to estrogen.
    • Early - female characteristics
    • Delayed - retention of bone mass
  52. What are three classes of cell-surface receptors?
    • Ion-channel-coupled (open channel)
    • G-protein-coupled (G activates enzyme)
    • Enzyme-coupled (intrinsic and associated enzymatic)
  53. What are three types of "players" that affect the cell?
    • First messengers - ligands such as hormones
    • Intracellular signaling proteins
    • Second messengers - not unique to one pathway
  54. What are examples of second messengers?
    cAMP, cGMP, 1,2-diacylglycerol (DAG), IP3, Ca+2
  55. What second messengers require ATP?
    cAMP, cGMP
  56. What second messengers are derived from phospholipids
    DAG, IP3
  57. Name various proteins/molecules in signalling pathways/cascades.
    Anchoring, amplifier, integrator, modular, relay, scaffold, transducer
  58. Describe an anchoring protein.
    Anchors proteins to a structure at a precise location where needed.
  59. Describe amplifier proteins.
    Greatly increases signal they receive.
  60. Describe Integrator proteins.
    Combine signals from two or more pathways before forwarding.
  61. Describe modular proteins.
    Modify the activity of signaling proteins to regulate signal strength.
  62. Describe relay proteins.
    Pass messages to the next signaling component in the pathway.
  63. Describe scaffold proteins.
    Bind to multiple signaling proteins together in a functional complex for quicker and more efficient interaction.
  64. Describe transducer proteins.
    Convert singal to a different form.
  65. Describe the structure of a G Protein-linked receptor (or G protein-coupled).
    • Seven transmembrane spanning domains.
    • Large cytoplasmic region that associates/activates with trimeric G proteins
  66. Does the GPCR have intrinsic enzymatic activity?
    No.
  67. What are 4 classic downstream targets of G Proteins that regulate different effectors?
    • Adenylyl cyclases
    • Phospholipases
    • Ion channels
    • Protein kinases
  68. What are the basic subunits of a G protein?
    alpha, beta, gamma
  69. What about G proteins might explain highly specific responses?
    Different isoforms
  70. What part of the G protein binds with GDP?
    The alpha subunit
  71. When activated, the beta/gamma complex can ___.
    move and activate other targets.
  72. What else provides specific signaling specifity?
    • Cell-specific receptors, G isoforms, and effectors
    • Amount of receptors, G isoforms, and effectors
    • Organization of signaling cascades
    • Accessory proteins
  73. How do accessory proteins regulate G protein action?
    They regulate the strength, efficiency, and specificity of the transmitted signal.
  74. What are some examples of accessory proteins?
    • GAP-43 - promotes GDP dissociation
    • AGS3 - stabilizes G-alpha-GDP interaction
    • Tubulin - directly transfers GTP to G-alpha
  75. What are three types of accessory proteins?
    • Activators of G protein signaling (AGS)
    • Regulator of G protein signaling (RGS)
    • Inhibitors of GDP dissociation
  76. Describe activators of G protein signaling.
    Can activate G proteins without the use of a receptor
  77. Describe regulators of G protein signaling.
    • Accelerate the GTPase activity of specific G-alpha subunits.
    • Quick inactivation - hydrolysis
  78. What is the typical end of a pathway?
    Cell division
  79. What are other roles associated with G proteins?
    • Golgi stability (alternative binding partners)
    • Cell polarity in the fruit fly and nematode
    • Neurite outgrowth and path-finding
  80. What do G protein-linked receptors activate?
    • Adenylyl cyclase
    • Phospholipase C-beta
  81. What effect does the activation of adenylyl cyclase typically have?
    • Increase of cyclic AMP concentration in the cytosol.
    • This rise activates PKA.
    • PKA enters the nucleus and phosphorylates CREB.
    • CREB recruits CBP, and both stimulate gene transcription.
  82. What is produced from the hydrolysis of PIP2?
    • inositol 1,4,5-trisphosphate (IP3) - releases Ca2+ from the ER
    • diacylglycerol (DAG) - helps to activate PKC
  83. Describe how GPCRs increase cytosolic Ca2+ and activate PKC.
    • PLC-beta is activated by G protein (via alpha, beta/gamma, or both).
    • Two messenger molecules, P3 and DAG, produced from hydrolysis of PIP2.
    • IP3 releases Ca2+ from ER
    • Ca2+ and DAG activate PKC
  84. What other purpose does the release of Ca2+ serve?
    Prevents polyspermy by creating fertilization envelope
  85. In the notch pathway, ___ and Jagged are ___.
    Delta, ligands
  86. Notch is composed of ___.
    • NECD - Notch extracellular domain
    • transmembrane domain
    • NID - Notch intracellular domain
  87. ___ cleaves the NECD from the ___.
    ADAM TM-NICD
  88. What is ADAM?
    A desintegrin and metalloprotease
  89. The NICD makes its way to the ___ and generally results in ___.
    • nucleus
    • transcription, cell division, differentiation
  90. Hh are ___, a ___.
    • ligands
    • family of secreted proteins
  91. Hh generally functions in ___.
    development
  92. In adult cells Hh can lead to ___.
    cancer
  93. Hh homologues in vertebrates include ___.
    sonic, desert, Indian Hh
  94. What is the receptor for Hh?
    Patch
  95. What are the receptors for Hh in mammals?
    • Hip1
    • Patched1
    • Patched2
  96. Besides Patch and Hip, what else is needed for Hh pathway activation?
    Smo
  97. The ultimate target of Hh in the fruitfly is ___, a ___.
    • cubitus interruptus (Ci)
    • transcription factor
  98. What vertebrate homologue most closely resembles Drosophila Hh?
    Desert
  99. How do Shh, Dhh, and Ihh differ?
    Typically by potency - Shh>Ihh>Dhh
  100. What role in develoment does Hh play?
    cellular proliferation, growth, and axon path finding
  101. What are examples of human developmental disorders from Hh?
    • Holoprosencephaly
    • Greig cephalopolysyndactyly syndrome
    • Pallister-Hall Syndrome
    • Gorlin's syndrome
  102. What are some cancers triggered by malfunctioning Hh?
    • Basal cell carcinoma
    • Rhabomyosarcoma
    • Medulloblastoma
    • Small cell lung cncer
    • Pancreatic cancer
  103. What are some components of the Hh pathway?
    • Patch(Ptc) - membrane receptor
    • Smoothened (Smo) - intermembrane protein
    • Intracellular Hh Signaling complex (HSC)
  104. Describe Patch.
    • Membrane receptor which activates Smo when bound to Hh.
    • After binding, Ptc levels decrease as a result of endocytosis
  105. In vertebrates, Ptc does not have ___, so it needs ___.
    • Dimer
    • Hip
  106. Describe Smoothened.
    Intermembrane protein that when activated relays signals to HSC
  107. In vertebrates, Smo is always ___.
    at the cell membrane
  108. Describe HSC.
    • Coastal 2 (Co2) - kinesin-related protein
    • Fused (Fu) - Ser/Threo kinase
    • Supressor of fused (Su/Fu)
    • Cubitus Interruptus (Ci)
  109. What are three Ci homologs as activators in mammals?
    Gli1, Gli2, Gli3
  110. Since Gli is acts only as an activator, it does not get ___.
    truncated
  111. What happens to Ci when there is no Hh?
    HSC truncates Ci which becomes a repressor
  112. What happens when Hh binds to Ptc?
    Production of Ci which becomes an activator
  113. In the Drosophila wing imaginal disc, Ci is truncated where?
    In all but cell fate 1 nearest the posterior
  114. In the Drosophila wing imaginal disc, Hh concentration results in activation where?
    In all but cell fate 5 (nearest the Anterior) which results in repressor.
  115. In the Drosophila wing imaginal disc, how does Hh concentration affect expression?
    [Hh] is proportional to activation
  116. What is involved in Hh processing?
    • Autocleavage
    • Binding of cholesterol to C end
    • Addition of palmitate to amino terminus
  117. Describe the binding of Hh to cholesterol.
    • Critical for target cell intake
    • Critical for signal transduction after Hh binds to Ptc
    • If binding is inhibited, Hh doesn't work
  118. In the absence of Hh, Ptc ___.
    blocks the phosphorylation and stability of Smo.
  119. What type of receptor does Smoothened have?
    G protein coupled receptor
  120. When there is no Ptc, ___.
    Smo is found in endosomal vesicles
  121. Upon Hh binding to Ptc, ___.
    Smo is released and localizes to the cell membrane
  122. Smo multimers may be required for ___.
    high level signaling
  123. With Hh present, Ci__ is processed to ___.
    • 155
    • Weak activator - Ci^act
    • Strong activator - Ci*
  124. If no Hh is present, Ci__ is formed.
    75
  125. How is Ci phosphorylated?
    • PKA
    • Glycogen synthase Kinase 3-beta
    • Casein Kinase 1-gamma
  126. Upon phosphorylation, Ci is ___ by ___, a ___.
    • ubiquitinated
    • Slimb (supernumerary limbs
    • proteosome for cleavage
  127. Describe Coastal 2 (Cos2)
    • Possibly a microtubule-motor
    • Interacts with Smo
    • Responsible for moving Smo
  128. How do Cos2 and Smo interact?
    • Cos2 binds Fu to Smo
    • Their interaction is critical for hh pathway signalling
  129. Where does Cos2 move Smo?
    • cell membrane upon Hh pathway activation.
    • Intracellular vessicles in the absence of Hh ligand
  130. Describe Fused (Fu)
    • Has kinase activity, i.e. might phosphorylate Cos2 and Su(Fu) upon Hh pathway activation.
    • Binds to Cos2 and Su(Fu) via carboxy terminus domain
  131. Describe Suppressor of Fused
    • May be antagonistic to Fu
    • No a.a. homology to known proteins
    • Binds Fu and Ci, but not Cos2
  132. What evidence is there that Su(Fu) and Fu might be antagonistic?
    Su(Fu)- and Fu- flies yield a wt phenotype
  133. What are possible functions of Su(Fu)?
    • May inhibit Ci activation
    • Nuclear translocation of Ci
    • Transcriptional regulation in vertebrates
  134. Describe Hh pathway at no/low [Hh].
    • Ptc on cell membrane repressing/sequestering Smo at vesicle with HSC-A inactive.
    • HSC-R on MT picking up vesicle leading to truncated Ci^75 by Su(Fu).
    • Ci^75 to nucleus as repressor
  135. Describe Hh pathway at medium [Hh].
    • Hh binds Ptc at cell membrane permitting Smo/HSC-A to go to cell membrane
    • HSC-R not at MT
    • HSC-A allows Ci^act into Nucleus for low activation with possible low amount of Ci^75.
  136. Describe Hh pathway at high [Hh].
    • Hh sequesters Ptc to vesicle permitting Smo Multimer/HSC-A to go to cell membrane
    • Fu phosphorylates Cos2/SuFu
    • SuFu leaves HSC
    • Cos2 drives Ci to Smo
    • HSC-R not present/inactivated.
    • HSC-A allows Ci* to be processed untruncated into Nucleus by SuFu for high activation
  137. Research shows that Hh signalling malfuction is responsible for:
    • Formation of tumors
    • Survival of tumors
  138. In mammals, absence of Hh leads to ___.
    • Gli forms MT-attached complex with Fu and SuFu
    • Gli remains in cytoplasm
  139. In mammals, if Hh is present, ___.
    • Hh binds to Ptc
    • Smo is activated (no longer supressed)
    • Processing of Gli is activated
    • Gli is translocated to nucleus
  140. In mammals, the negative feedback regulators in the Hh pathway are ___.
    Ptch, Hip, Gli
  141. What genes are for cell proliferation?
    • Cyclins D1 and D2 (mammalian) -> mitosis
    • cMyc
  142. What are three target proteins?
    • Cyclin B - Mitotic P Factor (MPF) - nuclear translocation
    • P21 inhibition - tumor supression
    • PDGF pathway activation (MAPK) - cell division
  143. What are two types of genetic problems w.r.t. cancer?
    • LOF for tumor supression - Ptc and SuFu
    • Overespression of oncogenes - Shh and Smo
  144. LOF of SuFu leads to ___.
    medulloblastoma
  145. LOF of Ptc1 leads to ___.
    cell nevus carcinoma
  146. Heterozygous Ptc mice ___.
    develop tumors
  147. Blocking Smo blocks ___.
    binding of Hh
  148. What should be inhibited for cancer treatment?
    Smo, Gli
  149. What are inhibitors of Smo?
    • Cyclopamine - binds to Smo, but difficult to synthesize and toxic
    • KAAD - modified cyclopamine - less toxic
  150. How do you inhibit Gli?
    • Forskolin - PKA activator - used in different pathways as well
    • RNAi - Not feasible for treatment

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