Basic Molecules of Life

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  1. Two options for passive transport via proteins
    • channel proteins 
    • carrier proteins
  2. How do channel proteins work
    • they are the simpler of the two
    • diffusion, they open and things that are permeable enter
  3. How do carrier proteins work
    Facilitated diffuision, they bind to the protein changing its conformation or shape and then bring it apart. This speeds its diffusion across the bilayer
  4. Which membrane channel is always open? What's the most common variation of such channels
    • Leak channel
    • Potassium Leak channels
  5. What are two things that will determine the direction K+ will flow
    • concentration gradient 
    • electrical gradient
  6. ______ ______ ion channels open when the ligand binds to the transmembrane protein. State three examples
    • Ligand gated ion channels 
    • neurotransmitters like ACTH, glutamate, glycine
  7. What happens to the ligand gated ion channel when the ligand unbinds
    transmembrane protein changes conformation and is no longer permeable
  8. What influences the opening and closing of cells voltage gated sodium channels
    changes in voltage
  9. In facilitated diffusion, the higher the _______ of for ex sodium, the faster the rate of diffusion
  10. If you have equal amounts of sodium on both sides of the membrane, how much diffusion will occur?
    Zero, the concentration gradient demands flow from high to low concentration
  11. If you increase glutamate on one side of the membrane, as the carrier protein, diffusion will increase and eventually top off. This occurs with ____ and not with ____  why?
    • facilitated diffusion
    • diffusion
    • The number of proteins can carry a finite amount of glutamate and will eventually reach a maximum of how many they are transporting.
    • This maxing out of the rate of transportation wouldn't occur with diffusion because it goes until a balance is reached uninhibited by any protein count
  12. Active transport implies _____ _____ and movement from _____ to ____. This will directly or indirectly cost _____
    • energy spending 
    • low to high 
    • energy
  13. Active transport gradient is a combination of _____ & _____ gradients
    electrical & concentration gradients
  14. Three types of integral proteins involved in active transport
    • uniporters
    • symporters
    • antiporters
  15. Uniporters transports ______ at a time and are always ______ ______ transporters. They cannot utilize another molecules _____ _____ _____, they have to have their own. The molecules are transported ______ their concentration gradient
    • one type of molecule
    • primary active transporters
    • pirmary active transport
    • against
  16. Symporters transport ____ molecules in ____ direction(s). They are transported ______ their concentration gradient
    • two types of molecules 
    • the same
    • against
  17. Antiporters transport
    Transports two types of molecules in opposite directions against their concentration gradients
  18. In primary active transport, when ATP is broken down by _______, what is left?
    • hydrolysis
    • ADP+Pi+free energy
  19. In secondary active transport, a molecule uses a ______ gradient and the ______ ______ ______ transport of another molecule. No ____ is directly used.
    • concentration gradient
    • primary active transport
    • ATP
  20. Na++/K+ pump (story)
    • Different conformations of the same transmembrane protein set the stage for the story of how allow molecules in and out.
    • Step1: 3 Na+s and 1 ATP (all on the inside) bind intracellulary to the receptors on Keep in mind [Na+] is low on the inside and high on the outside of the cell
    • Step2: Once they bind, ATP will be hydrolyzed and the phosphate (Pi) will remain, while ADP wanders away
    • Step3: When this happens, due to the phosphorylation and the energy from breaking the bond, the molecule will change its shape and Na+ will go to the outside.
    • Step4: The change in shape/ conformation of our protein will then lead to binding sites (2) becoming available for K+ Keep in mind [K+] is low on the outside and high on the inside
    • Step5: The K+ binding leads to yet another conformational change that transports 2 K+s into the cell
    • Step6: The phosphate because of this shape change is no longer attracted to the protein's receptor.
    • Step7: This will lead to available sites for 3 more Na+s and a new ATP molecule to bind to the inside of the cell and restart the cycle. This repeats until you die
  21. The most important pump in the body, it maintains gradients, etc
    Na/K pump
  22. The ratio of the Na/K pump
    3Na++ (pumped out of the cell) to 2K+ (pumped in to the cell)
  23. Electrogernic means
    making a charge differential
  24. What nature of transport is the Na/K pump
    Active transport
  25. Phosphates change the _____ & _____ of proteins.
    shape & activity
  26. Phosphorylate
    to put a phosphate on another molecule
  27. The energy from the breaking of the bond in ATP-ADP is also _____ to the molecule and _____ when its gone
    • transferred
    • released
  28. Three things necessary for secondary active transport
    • a concentration gradient
    • a primary active transporter
    • a symport (**pg 40)
  29. 3 differences between primary active transport & secondary active transport
    • Primary uses ATP
    • secondary uses potential energy aka concentration gradients 
    • secondary is dependent on another active transport while primary is not
  30. What type of transport is high to low?
    Facilitated diffusion
  31. If diffusion is going against a concentration gradient and uses ATP it is _____ ____ ____
    primary active transport
  32. If diffusion goes against a concentration gradient and doesn't use ATP it is _____ _____ _____
    secondary active transport
  33. If movement occurs simply by opening and closing and things diffusing through, it must be a ?
    channel protein (maybe leakage if perpetually open)
  34. Why does a cell become positive?
    voltage gated sodium channels
  35. Macromolecules like _____, _____, ____ & _____ will not fit through our transmembrane proteins. How can they get in and out of cells?
    • nucleic acids 
    • lipids
    • proteins
    • carbs
    • endocytosis & exocytosis
  36. ______ & ______ are exhibited at the start of neurotransmission. The plasma membrane folds in or invaginates
    around the material and is ______ by forming a vesicle. Later, the synaptic vesicle filled with hormones fuses with the plasma membrane from inside the cell and is _______
    • endocytosis & exocytosis
    • endocytosed 
    • exocytosed
  37. How do cells know how to behave differently, for example reacting to smelling something that causes nausea?
    Signal transduction pathway
  38. Signal transduction pathways _____ signals, can modify ___ _____ and will either use _____ _____ receptors or ______ receptors. Signal transduction pathways are activated by _____.
    • amplify 
    • DNA transcription
    • membrane bound receptors 
    • cytoplasmic receptors 
    • hormones
  39. Why are steroids able to get through the plasma membrane of the phospholipid bilayer and not ions?
    The charge on ions make for a difficult time getting through plasma membrane. However, with the nonpolar steroids, lipids etc they slide right through and bind to receptors that are cytoplsamic.
  40. Some signals are polar and can only get through the phospholipid bilayer via _______ ______ receptor
    transmembrane protein receptor
  41. Metabotropic aka
    g-protein linked receptor
  42. ACTH uses a ______ receptor. What would be this type of receptor's agonist be?
    • nicotinic
    • nicotine
  43. ACTH binds to the channel protein and causes a ________ change to the protein
  44. NMDA receptors are ______ proteins, specifically _____ proteins. ______ is their primary signal. These receptors allow ions to flow, particularly ___
    • transmembrane/integral proteins
    • channel proteins
    • glutamate 
    • Ca++
  45. Name 2 characteristics of the inactive state of g-protein coupled receptors
    • ligand has not binded to the transmembrane protein
    • alpha sub unit has a GDP attached
  46. Cascade (story) of the active g-protein coupled receptors (7)
    • Ligand is bound
    • Receptor protein changes
    • Interaction between the g-protein and the receptor
    • The GDP falls off and floats away
    • Fresh new GTP attaches to the alpha sub unit
    • When the ligand binds, the protein's affinity for GDP drops to nothing and it gains an affinity for GTP
    • Alpha sub unit shuttles over to the effector protein and because a GTP is attached, it is activated.
  47. ______ catalyze reactions that remove phosphates while ______ catalyze reactions that add phosphates
    • Phosphotases
    • Kinases
  48. cAMP is a __ ____
    2nd messenger
  49. Gi signaling cascade (story G-inhibitory signaling) (7)
    • Ligand (ACTH) binds to and interacts with the g-protein receptor
    • The GDP falls away and GTP binds to the alpha sub unit
    • Alpha sub unit shuttles to the effector protein
    • The effector protein (enzyme) for Gi signaling is called adenylyl or adenylate cyclase (AC)
    • AC catalyzes a reaction that converts ATP into cAMP
    • ATP binds to the enzyme's active cite and is converted into cAMP & two inorganic phosphates
    • Gi is inhibitory so it'll slow or inhibits the production of cAMP
  50. Gs signaling (cascade story G-stimulatory signaling) Pt 1
    • Ligand (Norepinephrine) binds to and interacts with the g-protein receptor
    • The GDP falls off and a new GTP binds to the alpha sub unit
    • Alpha sub unit shuttles to the effector protein
    • The effector protein (enzyme) for Gs signaling is also called adenylyl cyclase
    • Alpha sub units stimulates AC to convert ATP into cAMP (Gs signaling will increase or amplify cAMP production)
    • At this point there are two possible things cAMP can do at this point
  51. Gs signaling (cascade story G-stimulatory signaling) Pt2: The two possible things cAMP can do when produced by AC (2,8)
    *=not going to be tested
    It can bind to an ion channel: 

    • Ion channel opens up calcium/sodium comes in
    • Cell becomes more (+)

    It can bind to/ activate a protein kinase (PKA):

    • PKA has 2 catalytic domains and 2 regulatory domains
    • In the inactive state (regulatory sub units attached), catalytic domains can't do their jobs. Since it’s a kinase, we know the job is to phosphorylate
    • cAMP is released and will bind to regulatory domain 
    • affinity of PKA to regulatory subunits goes to zero, freeing the catalytic subunit
    • catalytic subunit begins to phosphorylate (the end of the story that will be tested) 
    • *Catalytic subunits is transported to the nucleus' nuclear pores if it has a nuclear localization signal
    • *It phophorylates its target (a molecule called Creb)
    • *Creb helps make new protein transcripts (via transcription) that allow us to form new memories, like remembering Creb.
  52. Nicotonic receptors are ___ channels and Muscarinic (_____ cells) are ______ ______
    • ion channels
    • pacemaker cells
    • g-protein coupled
  53. Gq/11 signaling (cascade story) (6) Pt1
    • Ligand (Norepinephrine/epinephrine) binds to and interacts with the g-protein receptor
    • The GDP falls off and a new GTP binds to the alpha sub unit
    • Alpha sub unit shuttles to the effector protein
    • Effector protein for Gq/11 signaling is phospholipase C
    • Phospholipase C is an enzyme that catalyzes a reaction that affects the bonds of a molecule called PIP2 which ends up breaking it up
    • PIP2 can be broken into 2 molecules (2nd messengers): IP3 and DAG
  54. Gq/11 signaling (cascade story) Pt2 IP3 & DAG's story (6,3)
    *=not going to be tested
    IP3's story:

    • IP3 will float to the endoplasmic reticulum (which stores calcium in its lumen)
    • *if calcium levels aren't highly regulated in the lumen, the cell could die. Ca++ can be pumped in or out of the cell via active transport
    • Ca++ doesn't stay outside the lumen for long, through uniporters, it will be returned.
    • IP3 floats to/ binds to the receptor of the channel protein in ER and it opens allowing calcium to flow out.
    • Ca++ (a 2nd messenger) activates protein kinase C (PKC)
    • PKC phosphorylates

    DAG's story:

    • PIP2 is broken into DAG
    • DAG activates a PKC
    • PKC phosphorylates
  55. Lithium can inhibit ____ production
  56. Tyrosine is a transmembrane _____/____ that is not ______ ______.
    • protein/enzyme
    • g-protein coupled
  57. On the receptor tyrosine kinase protein, we have molecules. In one domain we have a _____/_____, in the ______ domain we have ____
    • receptor/ligand
    • cytoplasmic domain 
    • tyrosines
  58. Tyrosine kinase cascade story (7)
    • Ligands exist as dimers (two identical molecules linked together)
    • Both ligands bind to receptors
    • leads to dimerizing of receptor tyrosine kinase proteins (aka the proteins become bound to one another)
    • Dimerization of these kinases is necessary in order for them to phosphorylate: (this is called autophosphorylation: kinase phosphorylates itself)
    • Fully phosphorylated tyrosine kinase or activated by converting ATP into ADP and Pi
    • Now relay proteins can bind and be modified in different areas (no phosphate transfer)
    • This can lead to up to 10 different cellular responses
    • You can stop this process by introducing phosphotases which will remove the phosphates until another ligand binds
  59. _____ production occurs when we are stressed
  60. Cortisol is able to get into the membrane of nuclei because it is ______.
  61. Cytoplasmic receptors cascade story (6)
    • Cortisol gets in by finding a cytoplasmic receptor aka "cortisol" receptor.
    • The receptor is bound to a chaperone protein (inactive state)
    • Cortisol binds to receptor and the receptor's affinity for chaperone protein drops to zero
    • Chaperone protein is released and the newly bound pair translocates (goes to the nucleus). Keep in mind cortisol & cytoplasmic receptor need a nuclear localization signal.
    • Once inside the nucleus, it can modify transcription
    • New mRNA is formed which leads to new proteins that are involved in that stress response
  62. When we have an activated alpha sub unit, how do we return to the deactivated state? (4)
    • As long as a GTP is attached to the sub unit, reactions with AC or Phospolipase C will continue to yield cAMP or IP3s/DAGs
    • This is regulated by an enzyme called GTPase
    • It catalyzes a reaction that converts GTP to GDP
    • Once the conversion occurs, the GDP returns to its regulatory subunit (beta or gamma subunits)
  63. How do we stop cAMP production?
    • A phosphodiesterase will convert cAMP to AMP
    • AMP is not a 2nd messenger: phosphorylation/ion channel opening stops
  64. Phosphodiesterase and GTPase are examples of ______ that keep these systems balanced
  65. Signal amplification story (ballpark figures)
    • One hormone/neurotransmitter binds to one receptor coupled to g-proteins (containing alpha subunits)
    • While bound, it can activate many (maybe 10) alpha subunits w/ GTPs attached
    • They shuttle of to AC and AC can convert up to 5000 cAMP molecules
    • 5000 cAMPs can activate 25,000 PKAs
    • Protein kinase As can lead to 2,500,000 phosphorylations of proteins
    • Moral of the story: one signal can cause massive changes to the brain/ don’t do drugs
  66. LSD, PCP, cocaine can all lead to _____ _____ story because they utilize _____ ____ cascades
    g-protein cpld cascades

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Basic Molecules of Life
2016-10-06 06:24:17
Week 1
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