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2015-11-19 15:46:40
Test #3
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  1. H zone
    In the H zone there is only myosin but in the middle of the H zone myosing molecules interlink.The dark portion of the H zone is due to that overlap of myosin and actin
  2. Actin
    Thin filament
  3. Heavy meromyosin (HMM)
    Composed of two identical heavy sub units
  4. Light meromyosin (LMM)
  5. Optical Tract
  6. Emphysema
    Long term chronic lung disease.
  7. Elastin
    This is the key protein in the extracellular matrix surrounding your aveoli and bronchioli and lungs. Elastin is a structural protein. Elastin folds into a random coil. Elastin also surrounds your blood vessels. Tissues in your body that change shape in your body dramatically and often. Breathing stretches the the random coil of the Elastin molecule out when you inhale; when your exhale the Elastin returns to it regular random coiled conformation. Cells in regions of tissue that are constantly changing shape like the lungs produce an enzyme called elastase
  8. Elastase
    a certain amount of elastase is being releases to remove/ digest some of the damaged elastin cause by the constant stretching and relaxing. Elastase is a protease ( enzyme that breaks up proteins and peptide bonds) and its substrate is Elasti. It breaks up and digests some of the Elastin that gets damaged and the elastin will be replaced.
  9. Inhibitions off Elastase
    Elastase is produced with an inhibitor that is produced naturally by the body to control the activity of that portease. But if the inhibitor is not properly functioning( mutatation that causes the inhibitor to not be able to bind to the Elastase or presents the inhibitor from being secreted at all), the Elatase can digest away unnecessary amounting of Elastase causing great expansion of whatever tissue it is located in.)The Tissue/ organ now fails to function properly.
  10. Smoking and Elastase
    The chemicals in smoke leads to a single change in the methonine (s) residue of the Elastase. It oxididizes a single methionine residue (side chain) causes the Elastase inhibitor to no longer bind to the Elastase. Too much Elastin goes into the extracellular matrix.
  11. Clot
    A interlink of fibrin and blood platelets. Plateletes bound in a mesh work of firbin,
  12. Blood clotting
    certain proteins always present in our blood ready to perform the cascade effect of blood clotting. Need repose rapidly, locally, and proportional to the size of the damage. Two pathways lead to blood clot formation ( intrinsic pathways "stabbed" vs. extrinsic pathway "blunt force")
  13. Fibrinogen
    made up of 6 polypeptide chains. This is present in the highest concentration in the blood stream. Key elements in this overall protein structure is the globular domains (Gamma & Beta) and they have binding sites for other fibrin molecules. Fibrin will bind to fibrin.Thrombin causes this activation
  14. Fibrin
    Fibrin with short polypeptide stretches, made up of charged amino acids. The negative charges of the fibrinopeptides help to keep the fibrin soluble in its aqueous environment (blood; less hydrogen bonds). The charges also prevent the polymerization. One fibrinogen repells the other. In response to blot force trauma or being stabbed Thrombin (protease) cuts all the fibrinopeptides.This Fibrin does not repel each other anymore and it is less soluble ( No it is  fribrin). The ends that are created after the fibrinopeptides are cut is Gly-Pro-Arg sequence. These sequences can bind to the binding site of the globular firbrin binding site of firbin
  15. Fibrinopeptides
    Charge amino acids strectehes that are apart of the fibrinogen structure.
  16. Gly-Pro-Arg sequence
    Sequenc of amino acids inside the blunt cut ends of fibrin after the fibrino peptides are cut off my thrombin
  17. Transglutaminase
    cross links fibrin molecules that are congregated together (mesh work). Transglutaminase is an enzyme that forms covalent bonds between individual fibrin molecules.Glutamine and Lysine are linked together in a covalent bond. Ttranglutaminase creates a surface that prevents exsanguniation, impervious to mildew and rot, prevent infectious particles from entering, lastly create a surface in which cells can migrate to fix the tissue you damaged. Activated by Thrombin! Thrombin activates the crosslink of fibrin moleculees
  18. Cascade examples
    • Bloodclotting
    • Digestion
  19. Thrombin
    Activated Fibrinogen to Fibrin and also activate transglutaminase. Thrombin triggers the crosslinking of the Firbin molecules ; the covealent bond between glutamine and lysine residues form the covelent crosslink that helps to make the clot or the scab much more durable. Thrombin is a serine protease.
  20. Prothrombin
    Domain structure for prothrombin is much larger than it has to be. Made from 4 domains the Serine protease domain, two kringle domains, and a Gla domain.
  21. Kringle domains
    Big linkers that connect the serine domain to the Gla domain.
  22. Gla domain
    part of the domain structure for prothrombin and contains a great amount of glutamic acid residues. Glutamic acid is a good chelator of calcium, it binds to calcium well. By adding an extra carboixy group to the glatmic acid residues in the gla doamin, it become an even better calcium chelator. The structure that is created when the glutamic acid residues are(Post translationally modify them by adding or  combined) with the carboixyl groups is called gamma(Υ) carboxyglutamate residue.This structure has the additon of an extra CO2. The Gamma carboxyglutamate helps to binds more calcium ions. a
  23. Enzymes responsible for making the post translational modification of Gla domain
    The enzyme that makes this post translational modification of the glutamin acid residues in the gla domain to gamma carboyglutamate is a Vitamin K dependent enzyme. Vitamin k is a protetic group with a carboxylating enzynme.
  24. Rat posion and Vitamin k
    Rat poison contains molecules that look like Vitamin K thus they get into the active site of the Gla domain enzyme replace the vitamin K and they prevents the production of Gamma carboxy glutamate;there is only regular glutamate residues; which means that it cannot bind calcium as well and when it doesn't bind calcium as well what it cant do is this Gla domain all the little platelets that are incorporated into the scab, the Gla domain anchors itself into those little platelets as they are circulating through the blood.The Gla domain bring prothrombin with them to the wound site. If there is not postranslational modification and you do not bind calcium, it cannot anchor. So when the platetletes arrive there is no prothrombin and because there is no prothrombin, you cannot activate the fibriniogen into fibrin and you cannot get that meshwork or scab to form. Hemorrhaging occurs since prothrobim does no end up at the wound site.
  25. How does the zinc prosthetic group operate ?
    The zinc prothetic group is in the active site of carbonic anhydrase and it is held there by histidine . The active site of carbonic anhydrase is directly in the center . Histidine coordinates the Zinc atom. Scientist made synthestic molecule that accepts zinc and this molecule with zince attached was able to accelrate the conversion of CO2 to bicarbonate.
  26. How was it verified that Histidine played a vital role in the active site of carboniic anhydrase? ( Test for the important amino acid side chains in the active site of carbonic anhydrase?
    The reaction of CO2 with H2O with this enzyme at low Ph shows relatively no activity but at higher ph values the activity increased. Histidine has the ability to change side chains fron neutral to positively charged
  27. What allows the contraction of the sarcomere to occur?
    Optical Tract experiment
  28. Optical tract experiment
    Involves both actin and myosin. Take an actin filament and stretch it between two ceramic beads. Then the two beads are suspended a good distance apart to get an appropriate stretch. The laser beams hold the beads in place as well as measures the pull or stress of the beads. It can detect the movement of the bead. There is another bead that have heavy meromyosin in between the two beads holding the actin and the goal is to get a single dimer of heavy meromyosin on the third bead in the middle to attach to the actin filament.This is all done in a buffer and this system is supplied with ATP. The ATP will bind to the globular domain of the myosin and then the myosin will hydrolyze and go through the changes that it regularly does in a sarcomere.The two head of the meryomyosin grab on to the actin and attempt to walk on it. But instead of them moving the actin filament will move relative to this location of the bead and it will be and the laser beams will detect the movement. The distance over time is collected for the movement of the actin and there is a large distance jump at a particular time that indicate a step like movement. Each step is the same distance and takes the same amount of time to take place and this gave insight into how the interactipon between myosin and actin are occuring.
  29. 5 step mechanism of actin and mysosin when one ATP is hydrolyzed
    • Myosin binds well to actin when ADP is in the active site; actin and myosin has a high affintiy for each other. 
    • If ATP is added to the system it replaces the ADP in the system.
    • Myosin afinity for actin decreases when ATP is in the active site and it lets go of actin. The secon thing that occurs when ATP binds to myosin is a major conformational change between the mysoin globular domain and its fibrous domain.These is a 90 degree shift of the fibrous region as a result of ATP being in the active site of myosin.
    • Step 3. Globular domain that is released from the actin will now hydrolyze the ATP bringing in a water molecule that is in the binding site and turns it into ADP and a Release in energy with a removal of the gamma phosphate. ADP in the active site there is an increase in affinity for actin by myosin and the myosin rebind to the actin. The rebinding of the myosin to the actin cause the inorganic phosphate to be released from the active site
  30. Power stroke
    When myosin has hydrolzyed ATP in its active site and when it begins to rebind to the actin the rebinding causes the release of the inorganic phosphate and the mysoin changes back to it s original conformation ( back (90 degrees). Power stroke either propel the myosin molecule along the actin or moves the actin filament relative to the myosin by one step. The power stroke is conformational change and only one step.
  31. ADP and ATP
    • Determines to conformation of the myosin head relative to it fibrous domain 
    • Also determines the binding of the actin to the myosin.
  32. Lever arm
    • single alpha helical region. The level arm moves 
    • Switch II and I 
    • The difference in the location of the lever arm 
    • P-looop reacts to whether there is two or three phosphates in the active site. The P-loop makes a very small change in its location that conformational change is transmitted through the polly peptide chain to the two switches.Switch I has a small change then Switch II which reacts with the relay helix then the large change happens in the lever arm.
  33. Changes that occur when ATP binds to myosin relative to how ADP binds to myosin
    Tested this by creating an ADP analog that acts like ATP but locks myosin in the conformation that it would have with ATP in the binding site. People were able to see the conformation differenceo of myosin and ADP binding and ATp binding.
  34. Trypomyosin
    Regulate the interactions between actin an myosin so that contraction isn't going on all the time.The Tropomyosin is a protein that wraps around the actin filament.
  35. Troponin complex
    • way of moving trypopmyosin out of the way. Consist of three different protein TNC TNI and TNT
    • TNc- binds calcium; when ca2+ binds it goes through a conformational shift that results in tropomyosin being moved out of the way.
    • TNI binds to actin 
    • TNT binds to tropomyosin
    • when you want muscle to move you brain tells your sarcomplasmic recticulum to release ca2+
  36. Sarcoplasmic Recticulum
    • Ca2+ storage compartment of the muscle cell. 
    • A nerve impulse tell the S.R. to release Calcium, calcium then binds to TNC to move tropomyosin out the way so that the contraction mechanism can proceed. So that your muscles can move.
    • depolarization is an action potential.
  37. Levels of complexity for motor protein
    • monomer- one single polypeptide chain; an enzyme capable of catalyzing a reaction on its own(protease)( dimers trimer or tetramers) lowest level of organization
    • 2) Protein complexes- transcribe a gene. proteins of different types, multisubunit complex involved in translation
    • ribosomes- large multisubunit machines used to assemble proteins
    • 3)organelles- hundred of different proteins coming together in a sub-cellular organelle. Function of producing energy for the cell. they have their own set of genes to caode for their own set of protein. " own organism inside the cell" 
    • 4) highest level of complexity is filaments that help to form scaffolding and a communication system for the cell.
  38. Filaments
    Involved in providing a scaffolding and a communication for the cell. They spread throughout the cell. The cytoskeleton providning structure for the cell preventing rapid changes in shape, connecting cell to outside environment anchor between the cyoskelton through the membrane to extracellular matrix components.holds cells together
  39. How is the cyotskelton used as a communication system (railway system )?
    • Motor protein- moving things around inside the cell. Different levels in the cyotskelton. The first level is the micro filament(i.e. actin)polymer of different subunints.
    • Second level - intermediate filaments(i.e. keratin) dimers are trimers of alpha helical coiled helices; strong durable enzymatic proteins.
    • third level- microtubles
  40. Microtubules
    • polymers that are a hollow cylinder. Made up of two type of sub units alpha and beta tubulin.
    • Tubulin subunits bind one onto the other and leave a hollow hole in the middle.
    • It provides a network of tubulns that spread throughout the cell that are either temporary or permanent
    • micro tubule form by one end anchoring in an MTOC
    • Micro tubules are GTPases that bind and hydrolyze GTP
    • They bind GTP.
    • When GTP is there the next sub unit of tubulin is more likely to bind so that the microtubule can grow.Once as the sub unit at the end hydrolyzes the GTP the microtuble will begin to fall apart.
  41. MTOC
    Microtubule organizing center. where micro tubules anchor
  42. Dynamic instability
    The disassembling and reassembling of the microtubule subunits. back and forth formation and dissassembling of microtubules.
  43. Eukaryotic Cillia or flagellum
    permanent microtubules. Struturally flagellum and cilia are made up of a series of micrtubules. That set of microtubules together are referred to as an axonin
  44. axonin
    • series of microtubles that make up cilia or flagellum:
    •  Microtubules dimer (fused together) in the cross section of a flagellum . then two indivudal microtubles riunning down the middle. this arrangement gives the flagellum and the microtubules the structure. cell moves due to the movement of the flagellum.
  45. Nexin
    protein connecting individual dimers of microtubles
  46. Radial spoke
    Connecintg outer dmers to the center microtubules is a protein
  47. dynein
    • running up and down the microtubules is the motor proteins. It is an ATPase. Acts like myosin w/ actin. reaches out and grabs the structural protein (tubulin). It binds to it, it hydrolyzes ATP it goes through power stroke type mechanism then it releases. 
    • They crawl along microtubule
    • the Dyneins causer micro tubules to bend and then snap back.
    •  Has six active sites 
    • These active sites goes through similar ATP hydrolysis.
  48. Kinesin
    • Uses microtubles as a substrate for walking
    • kinesin is a tetramer: two globular heads, alpha helical coiled helix, and a bind region on the tail
    • moves molecules around cell for us
    • Kinesin walk along the microtubles and carrything like neurotrasmitter across the cell. 
    • Kinesin walks from minus to plus end.
    • Kinesin moves via the hydrolysis of P-loop ATPase.
    • Has a p-loop, two switches, a relay helix and then relay helix is connected to the neck linker where the major conformational change will take place.
  49. Neck linker
    • connected to the switches which is connected to the p-loop which does the ATp hydrolysis for the kinesin. The necklinker causes the major conforamtional change that causes the kinesin to crawl along the microtubules.
    • Depends on what is on the active site.
    • if ATP is in the active site the P-loop pushes the Necklinker has a 90 degree change in position
  50. ATP ADP and kinesin binding to tubulin
    ADP in the active site binds weakly to tubulin. When ATP is in the active site that when it strongly bends to tubulin.Doesnt let go. ATP bind gets the globular domain that was behind to switch forward. Globular domain with ADP will losely bind. The release and binding or simultaneous. The release of the phosphate and AtP put into the other domain and this means the same conformational change and step. The ATP binds to one globular domain once as the phosphate is being released from the other domain thus as the affinity for one gets stronger and the affinity of the other gets weaker it causes that quick step forward.
  51. Prokaryotic flagella
    • multiiple flagella that are wrapped together and form one large super flagella
    • Clockwise is reverse and causes tumbling
    • Counterclockwise is efficient movement
  52. tumbling
    Tumbling when bacterial flagella are spread out.
  53. Flagellum
    • This motor protein uses proton motore force. A difference in Ph is what will be powering this. The ph outide a bacterial cell is lower for outside the cell than in the cell. this ph difference powers the spinning of the motors.
    • anchored into the membrane that seperaate cyotplasm from extrcellular region.
  54. Falgelluin
    Subunits that make up flagella
  55. Mot A and B
    motor A and B. Stationary do not spin but they are the pathway through which the protons will move. They are refereed to as half channel. Provides protons with a channel to come from outside of the bacterial cell to the inside of the bacterial cell. Half channels dont allow the proton to come directly in.
  56. Proton motor force
    The protion gradient inside and outside the cell is different for bacterial cells thus they use the proton gradient to power the spinning of the flagellum.
  57. Fli G
    • Individual proteins that make up the MS ring
    • Key for the fli G subunit is the aspartic residue right inthe middle.
    • The aspartic residue is negatively charges and and binds with the proton, move a bit and then outs it in the half channel causing the ms ring to spin.
  58. What causes the tumbling in the prokaryote ?
    Tumbling and direction of bacertiral flagellar momvement is regulated by a protein called Chey Y
  59. Chey Y
    • a protein that regulates the flaggular motor movement of a bacterial cell. 
    • The way that the motor is spinning is dependent on the binding of Chey Y to the motro
    • The Chey Y binds preferably when it is phosphorylated.'(reversible phosphorylation regulatory mechanism)
    • out membrane is a receptor that binds things to the membrane of the bacterial cell.causes random tumbling every once ina while. 
    • Chey Y will not bind to motor meaning that the motor will keep gooing counter clockwise and the Chey Y is dephosphorylated. when there is a good stimulus in the environment
    • Chey Y is ecessively phosphorylated when there is a deleterios factor inthe environment that causes tumbling and change in direction to get away.
  60. Features of membranes :sheetlike
    • sheetlike: no very thick 60-100 angstroms. and only a few molecules thick. They spread out.
    • made of lipids and protein (50/50)
    • fluid "mosacic" constantly moving around very rapidly but held together well enough because of van der waals interactions. 
    • Asymmetric: tell the outside from inside. test this by glycoclylation
    • electrically polarized: Their is a charged differential inside and outside of membrane.
  61. moiety
    Both the lipids and proteins that make up the membrane have a hydrophillic portion on the outside interacting with the environment and a large hydrophic region inside the membrane, basically interacting with each other. membranes do not need energy because of these interacting
  62. Proteins an membrane
    Protein make holes in the membranes.
  63. glycosolation
    the addition of sugar groups to the protein on the outside of a membrane.
  64. Make up of membrane
    • fatty acid- long hydrocarbon chains with terminal carboxylic acid groups. Carboxylic acid group is the hydrophobis portion.
    • fatty acids are usually even number between 14 and 24 (16 and 18 most common) because you use 2 carbon in the krebs cycle. If you are going to use fatty acids for energy to use for krebs cycle ti create ATP.
  65. Melting point and fatty acids
    • affected by length of the tail and amount of unsaturation 
    • shorter tail has lower melting point
    • saturated- no double bonds have lower melting point.
  66. fatty acids
    named from omega carbon
  67. Amphipathic
    They have both a hydrophobic and hydrophillic moiety or part
  68. how to make a Phospholipid
    • Start with a glycerol backbones. that that backbone you add two fatty acid chains to the third carbon you add a phosphorylated alcohol ( hydrophilic portion)
    • Fatty acids tails facinging and alchol facing the water
    • All the alcohols added to the glycerol are hydrophillic.
  69. Sphingosine
    • Amino alcohol with a long unsaturated hydrocarbon tail.
    • Used to make a phosphlipid. building block for spingomyelin.
  70. spingomyelin
    • Shingosine with addition of hydrophillic and hydrophobic portions.
    •  Add anothes hydrophobic tail to the spingosine and to the other end we will asterify phosphorocholine 
    • for the phospoglycerid instead of adding a hydrophillic
  71. Phophogylcerides
    attach group of glucose or gulactose sugars that to the Shingosine backbone and add another fatty acid tail but the hydrophillic moiety will be the sugar units.
  72. Cholesterol
    Found in the Eukarytic cell membranes. Is a large ring structure. No cholesterol in prokaryotes. Only has a small hydrophillic moiety the hydroxyl group at the end. If you want to increase the rigidity of a membrane at cholesterol.
  73. Components of membranes
    • Phospholipids
    • Glycolipids
    • Cholesterol
  74. Mi cell
    • a single molecule. Mi cells interact with water and help.
    • Contains one fatty acid chain and has a hydrophillic head and a hydrophobic tail.
    • Mi cells help to clean grease from cells, dishes clothing.
    • They are apart of soaps
  75. Membranes
    Membranes pack together so densely they for sheetlike structures. they wrap around and have a inner aqueous compartment. makes a bilayer. A cell. This molecule does not allow everything to pass through.Different environment outside than inside.Bilayer cells form spontaneously
  76. What can get across experiment and what cannot? how well do they do their job?
    • Experiment- a solution with glycine soluablized in it and at the bottom of the beaker are phospholipids. By applying a sonicator to the glycine solution with phospholipids at the bottom of the beaker 9 not interacting necause the lipids are at the bottom and the aqueous at the top.
    • the sonicator ( small metal probe) sends out waves of energy in the form of sound. that go through the water stir up the lipids that are on the bottom and gently ,mix them with the liquid on top.  those lipids associate with each other in big sheet that found around and form large sheets and these sheets have aqueous compartments on the inside. The sheets form spheres with aqueous compartments inside. At this point we have the same concentration of glycine inside as well as outside. We are going to use gel filtration to seperate cells we made and put them in a new environment with glycine on the ouside. The time how long it take for eht glycine to get out of the vesicle. We are testing the permeableility of the membrane to glycine molecules and we can go this with many other molecules.
  77. Aqueous compartment to see permeability of molecule to lipid bilayer
    Two aqueous compartment that are seperate by a divier with a small hole that had a lipid membrane painted on the little hole. Out electrode in the aqueeous compartments and see how long it take for the molecules to diffuse across.
  78. Permeability coefficent of the lipid bilayer
    Units are cm per second across the membrane. The permeability of the molecules that are going across the membrane. the lower the permeability coefficent the less likely to get across the membrane.

    • the membrane is selectively permeable against positively charged molecules such as K=, Na+, and them Cl-. 
    • One of the most permeable molecules is indole , Urea, and Glycerol. and water gets across the membrane with aa high permeability coefficient simply because there is so much of it. 
    • More hydrophobic in nature they are more permeable. more hydrophillic they are less permeable.
    • Less polar you are more likely to get across membrane
  79. What proteins are in the membranes?
    • By simply isolating the membrane the proteins came with them. 
    • Technique for isolating proteins required that they be soluble however membrane bond proteins are not very soluble to water because they live in the bi layer(hydrophobic environment) . This requires detergents to replace the membrane surround the protein keep them soluble then allow them to undergo gel filtration  and other technique to separate them.
  80. Two broad categories of proteins associated with membrane?
    • Integral membrane proteins- if you need to disrupt the membrane to isolate it.
    • Transmembrane proteins- span the entire membrane from one side to the other.
    • peripheral membrane proteins: The proteins are bound to the intergral membrane protein. We do not need to disrupt the membrane to get them just the bond between the integral proteins and themselves.
  81. momst common structurl motif for spaning a membrane
    Alpha helix.take about 20 amino acids to get across a memebrane.
  82. integral membrane proteins
    most common way to get across a membrane is an alpha helix and you need about 20 amino acids ( hydrophobic ones) to do so.
  83. Two ways to span a membrane
    • hydrophobic alpha helices
    • Or beta sheet membranes like porin that form hole in the membrane that certain sized molecules can fit through. Hydrophillic ones point into the pore.
  84. Protoglandin H2 synthetase.
    • an example of an integral membrane protein that is not a trans membrane protein.
    •  signaling molecule that can circulate and get things like cirulation and immune response dilation of capillaries that are associates with response to damage to tissues because this hydrophillic signaling molecule has been produced.
    • It catalyzes 
    • enzyme targeted by aspirin
    •  when damage is done to cells the membranes become disrupted 
    • substrate called Archidonate. Takes this that is evident that damage is taking place and turns it into something that can circulate in your blood stream and alert other parts of your body that you are hurt.It needs to convert this hydrophobic molecule into a hydrophillic molecule.
    •  Part of it the protoglandin hs synthetase is anchored in the membrane and the rest is on the outside. The Archidonate is in the membrane and there is a channel through the enzyme down to the active site that is originally hydrophobic, but the active site goes through the reaction necessary to convert the substrate into hydrophobic product and then that product is sent out to the other side. Serine 530is in the active site of pro- H2-synthetase and when aspirin is taken , it is an inhibitor and prevents the serine from being active and inflammation and pain can be reduce becase the signaling molecule will not be able to be converted to a hydrophillic molecule and turn on inflammation responses of the body.
  85. Two step from changing archidonate
    From hydrophobic to hydrophillic
  86. Proteins that travel with membrane but are not associated
    • It is possible that you can have a protein that travels around a membrane and is always associated with the membrane but is not associated with another membrane and is not anchored there. Take proteins and add to the hydrophobic groupslike palmitoyl group,farnesyl group, and GPI (glycophosphatidylinositol).Postranslationally modified by covelently attaching extremely hydrophobic groups.
    • absolutely non of the proteins are in the membrane
  87. prenyl groups
    • Take protein and add to them hydrtophobic groups. super hydrophobic groups added to proteins so that they can associate with the membrane without being anchored to them.
    • Palmitoyl
    • Farnesyl
    • glycophophotidainostidol(GPI)
    • these hydrophobic groups insert themselves into the membrane althought the protein itself is not in the membrane
  88. How to determine if a protein is a transmembrane protein?
  89. Transfer energu]y associated with the protein willingness to stay in a membrane or get out
    Positive hydrophobic transfer energy is very high and positive  and will not leave the mebrane.
  90. Hydropathyplot 
    Hydropathy index
    • Ex- glylcophorin is a protein associated with red blood cells. make RBC more soluble so they slide thorough membrane easily.
    • windows of 20 amino acids are take of a protein and the transfer energy is added up . We are looking for a very big number to display that there is alot of hydrophobic acids in that window of 20 amino acids. There is a criterion level of 84 which tells you that it is hioghkly likely that this is a transmembrane domain. that is the domain that anchor the protein to the membrane. an exception is porine because the hydropethy index for porin is below the 84 free energy transfer energy .
  91. experiments to display that molecules are moving in a membrane
    • Photobleaching experiment:
    • Took flourecent dye and labeled the outer surface of the cell. take a laser beam and shoots it at a specific region of the cell. The laser beam washes out the florescence of the dye and bleaches a specific portion of the cell. This part is "bleached". Then we watch how long it takes for the flourescene molecules that are in the membrane to move around to that bleached area. That is called the recovery time.When you bleach the cell the recovery time was extremely rapid. proves that there is rapid movement through the membrane.Discovered is that this idea of a fluid mosaic . The receptors in the surface of the cell can respond to where the signal is coming from. the fluidity of the membrane allow the receptors to respond to the signal. lipis facilitate that movement.
    • Movement for the most part occurs within the layer that that lipid is found. Very rapid lateral diffusion but it does not do tranverse diffusion.this is because you have a hydrophillic moiety that would cause disruptive interaction.
  92. Pumps
    pumps need energy to transport molecules. they also undergo conformational changes. Take molecules from one side of the membrane and move it to the other side of the membrane  against its gradient. that why the energy is required. Energy can be in the form of ATP, light, or another gradient.
  93. NA+ K+ pump
    • ATP is used to go against this gradient.
    • More sodium outside, more potassium inside.
  94. Fox glove plant
    produced a toxin to help treat congestive heart failure.
  95. Channels
    • get their names because they are selective to those particular ions. 
    • Channels are set up to incorporate crtain amino acids that line the channel or or barriers for certain channelsand if it were not for that selectivity our cells would not function properly.
  96. Action Potential
    • Movement of information from one neuron to the other.
    • Electrical signal until it reaches the synapse, there is the release of neurotransmitter. Kinesin gets the vesicels from presynaptic to post synaptic. This leads to the depolarization of the membrane. More positive charges outside than inside. High potassium inside and low Na+ inside. We have a gradient. A charge disparity determine 175 milivoltages across the membrane bases on the disproportionate.
    • Acetylcholine binding to this receptor causes the depolarization.
  97. Electric Fish
    • Fish with electric organ in head the emits a low voltage high amphage current into the water that has two purpose : shock any predator or stun  a prey item tio paralyze it temporarily so that it can eat it.
    • In that electric organ is an acetylcholine receptor (high concentration)
    •  to inhibit the receptors you can use the venom of a cobra. Cobra toxin has a high affinity for these receptors.
  98. Cobra toxin
    Use for affintiy chromotography to isolate the acetylcholine recptors because it is an inhibitor.
  99. Acetylcholine receptor
    • large multisubunit protein the receptors is composed of 5 subunits. Two alphas, gama, beta, and delta. the alpha subunits are the one that bind choline thatis refered tpo as the ligand. channel will open and close based in the bind of acetyl choline (ligand).
    •  Ligand gated channel
  100. Ligand
    relatioveky small protein that binds to a larger molecules.acetyle choline is the ;ligand .
  101. Patch clamp experiment
    • involve taking a piece of the membrane of the cell and clamping it to the tip of a pitpette.
    • They pipette takes up some of the membrane along with the acetylcholine receptors.Goal to have a membrane covering the tip of this clamp.You can out an electrode inside or ourside and you can see what the current is moving through the tip of the pipette. The data that is generated shows the resistance of the current moving through the pipette tip. when it is closed it is at its baseline. Whenit is open the current move easily and you get a spike in the membrane potential. during this short time of a spike in the membrane potential thousands of ions move through the channel.
    •  expoeriment proved that when acetylcholine was supplied there was opening of the channels temporarily for a short time then they would reclose. only positive ions were moving thoughout
  102. Two option in Patch clamp experiement
    • whole cell mode- the receptors are outside and there is a small suction hole for the pipette.
    • Excised patch mode- receptor is on the inside the pipette. 
    • * necessary to know which of the two patch clamp experiment done because you supply the ligand where the receptor is.
  103. difference between opened and close acetylcholine receptor
    • the conformational change that takes place has to do with the rotation of the subunit relative to each other. Once the acetylcholine binds to the aplha subunits it leads to the slight rotation of the alpha subunits  and that is transmitted to the other subunits so that they all end up rotating a little bit. 
    • Also which type of amino acid side chains are facing the center of the channel.
    • In the closed conformation the channels is blocked by large hydrophobic side chains. but rotations cause large hydrophobic sidechains to move out of the way in the open conformation ( when ligand is bound). Replaced by small hydrophillic side chains polar groups that allow ions to pass rapidly through the channel.
    • Na+ in K+ out
    •  This channel is selective for just positive ions because there is a ring near the entrance of the channel of negatively charges amino acid side chains this repels negatively charges ions (i.e cl-)
  104. What type of selectivity do acetylcholin receptor have
    Charged based selectivity from tjhe set pf negative charge amino acid side chains at the entrance of the channel that repel other negatively charged ions
  105. Acetylcholineesterase
    digests neurtransmitters and prevents it from being permanently active
  106. Transporting signal down the post synaptic membrane
    Using Na+ and K+ but not with channels that both ions can pass through it but rather individual channels. The main difference is that the channels for the Na+ and the K+ are not ligand gated they are ion gated channels. The change in voltage and depolarization with the acetylcholine receptor induced is now going to regulate whether or not these two channels are opened or closed. Wave of opening and closing
  107. Na+ channel
    • Opens first leads to further depolarization down the side of the neuron. This is counterbalanced by the opening of the K+ channel which helps to reestablish the polarization. Na+ is depolarizing
    •  the Na+ channel is blocked by tetrodotoxin
    • Na+ channel is ione gain protein, one gaint gene all linked together with 4 repeats, 6 transmemberane alpha helices
  108. K+ channel
    • Repolarizing/ Restoring. Both Na+ and K+ channel are located up and down the neuron.
    • so that the signal can be transported from the action potential.
  109. What blocks the Na+ channel?
    • Tetrodotoxin- made by the puffer fish.
    • Neurotoxin.
  110. Uses of tetrodotoxin?
    • Used to isolate Na+ channels so that they can be isolated and characterized.
    • Used in Affinity Chromatography.
  111. What was proven when patch clamp was done on the sodium channels?
    • Proved that it is not a ligand because the ligands could not get the channels to open. however, as you went from polarized to depolarized the channels would open more frequently.
    • Na+ is a voltage gated channel. Difference is voltage is what regulates the opening and closing.
  112. S4 helix
    • One of the helices that make up the Na+ channel, the one that seems to undergo the most conformation changing. This responds the most to the change in voltage of the Na+ channnel.
    • In the S4 helix there are positve charges ( lysines (k) and Arginines (R)) that interact with the negative charges .
    • These positive negative charges are helping to maintain a certain position of the helix in the mebrane.
    • In response to depolarization. the S4 helix would rotate up and the inidvidual interacts would change and therefor the conformation/ location of the S4 helix would change and open up the channel so that the Na+ can get through.
  113. What makes the Na+ channel Selective for Na+?
    • Its a size thing ;-)
    • Size selectivity. 
    • Na must remain bound to water. 
    • K+ has a large radius than Na+.Therefore when K+ is bound to Na+ it is too large to pass through the NA+ channel.
  114. Response to the depolarization of the acetylcholine recpetor?
    • 1)The electrical signal to open up Na+ so that sodium can get inside the cell, Na+ opens up for a couple millseconds .But then you get a propogatoion, depolarization of the Na+ channel going down the neuron as the action potential continues. 
    •  2) After this is balance between Na+ and K+ is restored by opening the K+- channel.
  115. Calcium channel
    Found in the SR and releases Ca2+ that is used for muscle contraction has a very similar structure to Sodium.
  116. Difference between K+Channel and Na+ channel
    • Same six alpha helica strcuture as Na+ channel except it only occurs once and does not repeat. 
    • K+ has a shalker attached to it.
  117. Shaker potassium Channel
    • Zap fruit fly with X-rays to cause mutations
    • and these mutatiopns can be passed down from one generation to the other.
    • Mutations in the shaker potassium channel which caused them to shake (literaally)
    • when an action potential was initated in these flies, Nat channel worked put the K+ would initally function properly but then it couldn't shut itself off. the K+ would continue to flow and the result of this excess flowing of K is the shaking.
    • Time after depolarization in mini seconds shows that the K+ channel in the deletion mutant ( shaker k+ channel mutation) 
    • It wwas disciovered that a second of the gene was missing. A bunch of amino acids were eleminated from the Skaker potassium channel.
    • This cane be semi cured by taking this section of genes that are missing from the deletion mutant, from the wild type " normal functioning protein" and inserting it into the deletion mutant.
    • When this is done the function of the Potassium channel is almost returned to normal.
  118. K+ channels
    • It is a tetramer. 
    • Transmembrane alpha helices 
    • As you move through the channel the potassium channel move through the aqueous portion of the channel. There is a point where the K+ has to dehydrate. This is done by narrow portion containing certain amino acids that are able to bind to the K+. These amino acids are (threonine, glycine) and are capable of binding K+ as it passes through the channel.
    • K+ cannot pass through with water attached to it.
    • Sodium is kept from going through the K+ channel because K+ aligns perfectly to the side chains that are present there and not Na+.
    • The radius of K+ allows this reaction and binding to take place in a lower energy state. In order for K+ give up its water it does it more readily that sodium. K+ ha s a higher hydration free energy.
    • Hydration energy selectivity
    • When the K+ gets to the other side of the channel it rehydrates. Kind of like a "wash"
    • There is no gain or loss of energy as K+ moves through the channel as opposed to the Na+ the "wash " causes a loss in energy.
    • S4 helix changes location channel opens temporarily. K+ wants to rush OUT.
    •  The repulsion of the positive charge actually gets the flow of K+ moving out..
  119. Difference between open and closed in the postassium channel
    • Structurally the S4 helix is pretty far away from the channel however the conformational change of the S4 helix leads to the opening and closing of the channel.
    • S4 is still voltage gates in the K+ channel and still has to do positive negative charge interactions with the alpha helices.
  120. Inactivation domain
    • The amino acids in the Shake K+ channel protein , a globular domain. depicted as a ball. on a short flexible bit of amino acids sequence (chain)
    • Marriage model
    • There are charges associated with the ball and charges associated with the underside of the pore. Once the channel opens, the ball and Inactivation domain is going to flip up and clog the K channel.
    • Until the membrane repolarizes and the protein goes back to closed conformation waiting for the next action potential. 
    • The inactivation domain set of amino acid where the ones deleted in the shaker flies.
  121. Gap junction (connexon)
    • Situation in your body where the cells are going to respond to stimuli and need a concerted response from a great number of cells. You want an electrical impulse in one area to be felt or heardall over. 
    • Protein that are inserted  into the membrane of two adjacent cells and they connect between the gap of cells.
    • can open and close in reponse to ceertain conditions. 
    • when they are open. individual cells become a network of connected cells. 
    • Happens in heart (i.e. pace maker- one impulse felt by a variety of muscles; uterus when you are ready to give birth- contraction of uterus;)
    • Gap junction produce pores.
    •  produced by cells that are apart of a tissue that want to be able to communicate very rapidly with one another. they need to be able to instantaneously have every cell in that particular tissue to know what is going on. (heart, muscles) 
    • stimulating one or a few triggers all.
    • Signal is a electrical signal in the form of ions. Ions fit through gap junctions.
    • Size selectively of pored of gap junctions ( only as big as 1000 daltons)
    • Gap junction prevent large proteins like Rnas and MRNA from getting through thus individual cells can still mainttain their own microenvirionemtn even though the communicate.
  122. Connexin
    • Proteins that make up gap junctions.
    • Each cell is going to produce 6 connexin molecules which are going to arrange themselves in a half channel that is going to go through the membrane of that cell and extend  out into the intercellular space.
    • Both half channel produce 6 subunits and when they come together (12 subunits) make up a gap junction or connexon..
  123. Shutting off Gap jjunctions
    If connected to dieing cell needs shutting off of gap junctions
  124. Two conformations in gap junctions
    • Open and close gap junction
    • dependent on calcium levels in the cell. 
    • extreme extended levels of calcium tend to be a sign that something is going wrong in the cell. If intracellular calcium stay high for a long period of time. Ca2+ ions will bind to the sub units of the gap junction and lead to a conformational change that closes off the pore. Decreasse of Ca2+ can lead to reopening and going back top normal
  125. Aquaporin
    • Channel for salivation
    • Water transport channel
    • present in all cells but are concentrate din salivary glands, tear ducts, kidney cells (places where water is exchanged more rapid than normal.)
    • Allow 1 million water molecules per second to pass through
    • strucutre is alpha helical sections/motifs that cross the memebrane
    • at the center of the channels are hydrophillic molecules/ residues in the center of pore.These attract water molecules and make it easy for them to pass through.
    • Proton gradients established. Created a hole in the membrane that lets water through. As it turns out, many of the hydrophillic residues are positively charges and the positive charges prevent proton from getting through the pore through repulusion.
  126. Signal Transduction Pathway
    Method of communication used by cells in which extracellular signals are converted to intracellular signals . It generates a cascade of cellular responses. It is activated when a signaling substance like a hormone converts message ultimately into a physiological response.
  127. Protein Phospotase
    Removes Orthro phosphate from phpsphorylated protein by hydrolysis