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Week 2 Class and Book Notes Combined

by: Luke Holden

Week 2 Class and Book Notes Combined BIOL 4610

Marketplace > Clemson University > BIOL 4610 > Week 2 Class and Book Notes Combined
Luke Holden

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These notes are from week 2 and are more lecture heavy than book heavy since she went into great detail. Good organization of the lecture notes.
Cell Biology
Susan Chapman
Class Notes
Membrne, Proteins
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This 11 page Class Notes was uploaded by Luke Holden on Wednesday September 7, 2016. The Class Notes belongs to BIOL 4610 at Clemson University taught by Susan Chapman in Fall 2016. Since its upload, it has received 29 views.


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Date Created: 09/07/16
Week Two Lecture and Book Notes Combined Chapter 2 and (8/30 - 9/1) The Mosaic Part of the Model Continued  Why have proteins carry specific molecules across? o To be selective o It is important  Example / Chapter Opener Water flows through each of the four complexes It is crucial because: 10 /10 more molecules come across o  The permeability gradient: o Permeable molecules  Gases: CO2, N2, O2  Ethanol o Slightly Permeable  Water Urea o Impermeable  Large uncharged polar molecules  Glucose, Fructose  Ions  K Mg Ca Cl HCO3 HPO4  Charged Polar Molecules  Amino Acids, ATP, Glucose 6 Phosphate, Proteins, Nucleic Acids o ALL THINGS IN RED NEED SOME SORT OF TRANSPORT PROTEIN.  3 Categories of Transport:  Passive/ Simple Diffusion  Facilitated Diffusion  Active Transport Passive/ Simple Diffusion Distinguishing Characteristics  No energy  The concentration gradient is the driver  No protein required!!! Relationships of Simple Diffusion  Increase Polarity=Decrease the hydrophobicity= Decrease the Permeability  Increase Size= Decrease the permeability  Closer the Charge is to Zero= Increase the permeability  Increase the Partition Coefficient= Increase Permeability  Increase the Partition Coefficient= Increase Fatty Acid Chains  Increase the Partition Coefficient= Increase nonpolar Important Concepts  Molecules of no net charge have their movement determined by their concentration gradients  Charged molecules are determined on their electrochemical gradient (going back to net charge of zero)  Water diffuses faster than expected  ALWAYS GOING TOWARDS EQUILIBRIUM  ALWAYS GOING TOWARDS NO FREE ENERGY  RATE OF SIMPLE DIFFUSION IS DIRECTLY PROPORTIONAL TO THE CONCENTRAITON GRADIENT Facilitated Diffusion Characteristics:  No energy required still  Down concentration gradient  Requires a transport protein Types of proteins  Uniporter Carrier o Specific o Provide a hydrophilic pathway through the membrane  Therefore the partition coefficient is irrelevant o No energy required o Reversible o Why is it different than simple?  SO MUCH FASTER  it never enters the hydrophobic core of the membrane  There is a max point in which molecules are going into or out of the cell at constant rate because the protein cannot handle anymore. (Vmax)  This achieved when all proteins are moving at their max rate across the cell.  It is reversible based on the concentration gradient.  Highly specific  Affinity of a protein for a certain molecule is measured by Km is the concentration at which transport is 1/2 o Example: Glut 1: This is the uniporter that carries glucose into/out of the blood cell.  Integral protein with 12 transmembrane segments that forms a cavity with hydrophilic side chains  glucose concentration is kept low on the inside of the cell at most times   How it works: 1. T1 conformation is open to the outside of cell 2. Glucose comes and binds to GLUT 1 3. The binding of glucose cause the protein to change conformation to the inside of the cell 4. The glucose is released which cause the cell to conform back into T1  This porter is reversible o This is done by glucose binding to the protein from the inside and the protein will transport it back out o So if glucose is transported into the cell why does it not rebind to the protein and cause a conformational shift back out?  This is because the glucose is immediately reacted with hexokinase and phosphorylated to yield glucose 6- phosphate.  Since the proteins are specific the molecule cannot renter the cytoplasm Channel Proteins  Facilitate diffusion by hydrophilic transmembrane channels  3Types of Channels: o Ion Channels – Transmembrane proteins that allow rapid passage of specific ions  small pores with a hydrophilic inside  different channels for different proteins  selectivity is based on the side chains (point into the cell) and the size of the ion  Faster than a uniporter  This is because no conformation change is needed  Structure:  Four identical subunits, each containing two conserved membrane-spanning α helices, called by convention S5 and S6, and a shorter P, or pore segment.  The p segment is where the action happens as it connects all four sub units and provides an ion sensitivity filter (short α helix that extends into the small pore  The ion falls into the vestibule (safe area before it goes into the cell.   Functions of Ion Channels  Signaling  salt balance in the lungs  Cystic Fibrosis o Malfunctioning chloride pump o Cystic fibrosis affects the cells that produce mucus, sweat, and digestive juices. It causes these fluids to become thick and sticky. They then plug up tubes, ducts, and passageways. o Symptoms vary and can include cough, repeated lung infections, inability to gain weight, and fatty stools. o o Gated Channels:  Open and close in response to a stimulus  Voltage-gated channels open and close in response to changes in membrane potential  Ligand-gated channels are triggered by the binding of certain substances to the channel protein  Mechanosensitive channels respond to mechanical forces acting on the membrane o Porins  Selective holes in the membrane  formed by multipass transmembrane proteins called porins  β barrels  Hydrophilic interior  Hydrophobic exterior  aquaporin  porins just big enough for water to pass though  Gates on the porins contain: highly conserved arginine and histidine residues, as well as the two asparagine residues whose side chains form hydrogen bonds with transported water molecules. Active Transport Characteristics:  Requires Energy (ATP or another molecule across the membrane)  Moves solutes against their concentration gradients  Requires a transporter Divided into two categories:  Indirect Active Trasport o This harness the power generated by the movement of a solute down its concentration gradient to move another back across o Example: Na/glucose symporter/ Cotransport / Secondary Active transport: These transport proteins line the walls of the intestine that take up glucose with the uptake of Na o This can be either symporters or antiporters o NO ATP HYDROLYSIS OCCURS o Ion gradients drive indirect active transport:  Sodium for animals  Protons for plants fungi and bacteria  They ions go down their concentration gradient driving indirect transport o Despite ATP not direct being used, ions are typically shoved out of the cell by direct transport and brought back in through indirect transport o can be used for export as well as uptake o Glucose uptake requires energy  Despite glucose being indirectly brought across the membrane, it still needs a steep gradient of sodium to do so  This is made possible by the Na/ K pump. Therefore these proteins are called sodium-dependent glucose transporters (SGLT)  Steps of the Symporter SGLT:  2 Na atoms bind to the protein from the outside  Glucose then binds  Conformational change from outside to inside  2 Na release from protein (locks symporter) (they are then forced back out of the cell via Na/ K pump)  glucose will release and allow the protein to change back o More examples of Indirect  GLUT 1 on erythrocytes is a Uniporter  Anion exchange protein for Cl- in and HCO3- out is an antiporter  If an anion is not present the protein will stop  1:1 ratio  The waste CO2 from the tissue enters the erythrocyte via diffusion and then it is converted into carbonate by carbonic anhydrase (this builds up one side of the gradient  As it is pushed out along its gradient, the Cl- is brought in  “Ping Pong”- The Chloride binds to one side (serves across the membrane) where the bicarbonate binds and (comes right back across)  Direct Active Transport o going up the concentration gradient o The use of some type of energy to transport stuff across is direct o Unidirectional o Usually hydrolysis of ATP  Called ATPase/ ATPase pump (clever right?)  Reaction is coupling an endergonic process( movement of solutes against their concentration gradient) at the expense of an exergonic reaction (hydrolysis of ATP) o 3 Main Functions  Get those nutrients in  Get that crap (waste) out  And get everything back to normal (restore equilibrium) o The ATPases  P- type  Large family  reversibly phosphorylated on a specific aspartic acid residue  eight to ten transmembrane 3-gments  Inhibited by: Vanadate VO 4 (Looks like phosphate)  What they move: o H pump in plants and fungi o Sodium Potassium pump in higher eukaryotes o Hydrogen potassium pump Apical plasma membrane in stomach o Calcium pump of eukaryotic cells o Calcium pump in sarcoplasmic reticulum membrane in muscle  5 Sub families o P1- found in all organisms and transport heavy metal ions o P2- Responsible for ion gradients across membranes of eukaryotes and play a role in muscle contraction and acidification of gastric juices o P3- plants and fungi that acidify medium o P4- pump hydrophobic molecules such as fatty acids or cholesterol however, they transport them by flipping them across the membrane. not transporting them all the way across o P5- transport cations  V –Type  pump protons into organelles  2 multi subunit components an integral and peripheral  Where they at: o Vacuolar proton pumps membranes in plants yeast and fungi o Endosomal and lysosomal membranes in animal cells o Plasma membranes of osteoclasts and kidney tubule cells  F-Type  Very similar to the V-type!!  REVERSIBLE o In this case (ATP synthase) protons going down their gradient makes ATP o THEREFORE: THE GRADIENT GENERATED BY ATP CAN BE USED AS AN INVESTMENT TO MAKE MORE ATP!!!  2 subunits one integral (0 ) and peripheral (Contains ATP binding site) (1 )  Transports protons  Where they are at: o Bacterial plasma membrane o Inner mitochondrial membrane o Thylakoid membrane of the chloroplast  ABC- Type ATPases  ATP Binding Cassette  Cassette in this example is referring to the catalytic domain of the protein where ATP is hydrolyzed  Large family as well  Structure: o 4 domains (2 are really hydrophobic in membrane) o Other 2 Associated with the cytoplasmic side and bind ATP o The segments spanning the plasma membrane have 6 walls all forming a channel for the solute to pass through  Medical? o ABC can pump antibiotics outs o MDR (multidrug resistance)- can pump lots of not alike drugs out of cell causing them to be resistant  Examples  Na/K pump (P-Type) o At rest POTASSIUM IS HIGER ON THE OUTSIDE OF THE CELL AND SODIUM IS HIGHER ON THE INSIDE o 2 Conformations  E1- open to the INSIDE = (3 sodium at a time )affinity for Na  E2- open to the outside= (2 Potassium at a time) affinity for potassium o Responsible for asymmetric distribution o Contains 3 subunits, alpha beta and gamma  alpha is on the cytoplasmic side and binds ATP and Na o Steps:  In E1 3 Na bind  triggers ATP to bind  E1E2  3 Na release and now it is K’s turn  Bind of K triggers the dephosphorylating of the alpha subunit  E2E1  K releases


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