CELL

Anotações:

• Up to 50% of the membrane can be proteins

1. Fluid
   1. Dynamic at 37º

      Anotações:

      • biomembrane as to be able to move things around
   2. 2 dimensional fluids
      1. Lateral diffusion

         Anotações:

         • within the leaflet Phospholipids in one leaflet can move within that leaflet with ease common, easy, rapid
      2. Transverse Diffusion

         Anotações:

         • Between bilayers is very slow & unlikely you never get flip-flopping you rarely get phospholipid from one leaflet going into the other
   3. Temperature & composition dependent
      1. Fluidity regulation
         1. Sterols, cholesterol
            1. break apart van der waal interactions = more fluid
         2. Composition of phospholipids
         3. # of double bonds
         4. # of phospholipids
         5. Proteins
            1. transmembrane proteins break van der waal forces = more fluid
   4. Measuring fluidity
      1. FRAP

         Anotações:

         • using fluorescent proteins proteins in PM are potentially floating around & laterally diffusing in the PM bleached area cannot be seen on microscope recovery- does bleached area recover some of it's fluorescence?
         1. Goal: look for recovery

            Anotações:

            • only way to look for recovery is if proteins from periphery diffuse into this area & recover fluorescence protein diffusion related to amount of diffusion in the membrane more fluid = more recovery
            1. Graph

               Anotações:

               • Certain level of fluorescence, which is 100% (starting point) when you bleach, it drops to 0 (100-0 real quick) look for recovery, which eventually plateaus you end up with 50% recovery in this case, which means 50% are motile & 50 are non-motile 50% of the membrane has fluidity
               1. reason for non-motility
                  1. protein linked to cytoskeleton, which is tethered to membrane & does not let proteins move
2. Closed compartments
   1. membrane-bound organelles
   2. Plasma membrane
      1. Cytosolic face
         1. Internal

            Anotações:

            • BUT FOR VESICLE MEMBRANE CYTOSOLIC = EXTERNAL FACE
      2. Exoplasmic face
         1. proteins in lumen
         2. Carbs are found exclusively here
3. Asymmetric

   Anotações:

   • ASYMMETRY TILL YOU DIE
   1. Present with all proteins, not just lipid bilayer
   2. Proteins within membrane are same orientation
      1. Cadherins have binding domain in EC domain ALWAYS
   3. ETC
   4. Membrane proteins
      1. integral

         Anotações:

         • Proteins go through PM sizes of domain vary
         1. transmembrane domain

            Anotações:

            • most important domain inner part of lipid bilayer transmembrane made up of hydrophobic amino acids it has fatty acid carbon tails
            1. Spans lipid bilayer, hydrophobic region
            2. Different structures
               1. Alpha helix

                  Anotações:

                  • chain of amino acids making a simple little helix 20-25 amino acids
               2. Beta barrel

                  Anotações:

                  • complex structure hydrophobic amino acids make it to span the membrane
            3. cytosolic side
               1. Arg & lys
                  1. Help anchor the protein

                     Anotações:

                     • if you try to pull protein through membrane, these charged proteins resist going into hydrophobic region
            4. Exoplasmic side
               1. glycosylated

                  Anotações:

                  • can add sugars to transmembrane proteins on extracellular domain
         2. Cytosolic & exoplasmic domain
      2. peripheral

         Anotações:

         • Proteins somehow attached to membrane Does not tell you anything about its function
         • Example: Dystrophin is bound to transmembrane protein You never find dystrophin outside of a cell
         1. attached non-covalently to something that is covalently linked to membrane

            Anotações:

            • Ionic interactions, hydrogen bonds protein-protein interactions van der waals forces
         2. Attached to transmembrane protein, integral membrane protein or lipid-linked
            1. integral protein can be linked to cytoskeleton via peripheral membrane protein
            2. ECM can be bound by peripheral membrane protein
               1. ECM can bind to integrins, which are transmembrane protein, thus making it a peripheral membrane protein
      3. Lipid-Linked

         Anotações:

         • Proteins physically linked to one of the phospholipids on the membrane
         1. Acylation

            Anotações:

            • N-term Glycine linked to phosphate
         2. Prenylation

            Anotações:

            • C terminal Cysteine or one that is close to C-terminal domain
         3. GPI linked

            Anotações:

            • Link to exterior surface
            1. PI (phosphlipd & phoshoglyceride)

               Anotações:

               • In order to link protein to membrane you have to link to PI LINK IS CALLED GPI ANCHOR
            2. have a signal on their C-term so they can be linked to GPI anchor
            3. Doesn't have to be transmembrane domain
               1. Some NCAM have GPI anchors

                  Anotações:

                  • NCAM = IG superfamily molecules have transmembrane domain, others have GPI anchors remember: both are cell adhesion molecules but they can do different things
                  1. does not interact with cytoskeleton

                     Anotações:

                     • NCAM transmembrane molecules do interact with cytoskeleton
      4. INSERTION OF PROTEINS INTO MEMBRANE
         1. Translation of any protein starts in cytosol

            Anotações:

            • ribosome is in cytosol
            1. Need signal to leave cytosol

               Anotações:

               • not necessarily sequence specific
               • WHENEVER YOU HEAR SIGNAL IT IS BEING TAKEN TO ER
               1. Topogenic sequences

                  Anotações:

                  • found in proteins that can be translated
                  • Its not the exact amino acids that are signals, its the shapes they form, which are recognized by other proteins such as signal recognition particles
                  1. N terminal Sequence

                     Anotações:

                     • found on N-term & is cleaved Recognized by signal recognition particle- taken to ER
                  2. Signal Anchor Sequence (SA)

                     Anotações:

                     • anchored in ER N-term signal that is NOT cleaved
                  3. Hydrophobic C-terminus

                     Anotações:

                     • acts as a signal to get protein to ER
                     1. Tail-anchored protein
                        1. translation starts at N-terminal in the cytoplasm
                           1. after translation finishes, a Hydrophobic C terminus made

                              Anotações:

                              • Occurs in cytosol, which has a hydrophilic environment
                              1. Protein folds to get out of hydrophilic environment of cytosol
                                 1. Forms a structure recognized by GET3

                                    Anotações:

                                    • GET 3 in cytoplasm GET 1 & 2 - ER MEMBRANE
                                    1. GET3 recognizes C terminus
                                       1. Docks with Get 1 & 2 and uses ATP to shove hydropobic tail into ER membrane
                                          1. Result: protein that has hydrophobic C term tail in the membrane and N term domainin cytosol
                                             1. DOES NOT HAVE EXTRACELLULAR DOMAIN BUT HAS TRANSMEMBRANE DOMAIN
                  4. Stop-transfer/Membrane anchor (STA)

                     Anotações:

                     • Where-ever its being transferred, we transfer & stop it anchor it there
                  5. Type 1, 3, 4B the N terminal are luminal
                  6. Type 2 & 4A N terminal is cytosolic
         2. TYPES OF PROTEINS

            Anotações:

            • ALL TYPES OF PROTEINS ARE TRANSMEMBRANE PROTEINS
            1. Synthesis of Type I

               Anotações:

               • typical transmembrane proteins has hydrophobic domain
               • N term sign go into lumen & is cleaved C term remains in the cytoplasm
               1. translation occurs in cytoplasm N terminal translated first
                  1. N term signal is hydrophobic & begins to fold (stops translation)
                     1. Signal recognized by signal recognition particles (goes to ER)
                        1. N term goes via translocon into ER lumen
                           1. N term sequence cleaved- mature protein does not have signal
                              1. Translation continues into ER lumen
               2. hydrophobic domain = STA,
            2. Synthesis of TYPE II & III

               Anotações:

               • No n terminal signal they have integral signal
               1. translation starts in cytosol with N term domain
                  1. make N term domain, until you hit SA, which tells you to go to ER

                     Anotações:

                     • signal region = hydrophobic it becomes the transmembrane domain , but the thing is you already have this N terminal domain translated
                     1. Does the N term domain stay in cytosol, or do you shove it into the lumen?

                        Anotações:

                        • depends on charges around the SA SA = hydrophobic, its going to be in the membrane
                        • cytosolic amino acids are often charged, which helps anchor the protein in the membrane & helps get protein to the right side of the matrix
                        1. TYPE II
                           1. Positive charged amino acids on N term side
                              1. N term stays in cytosol
                                 1. translocon flips translation & lets C term domain go into lumem
                        2. Type III
                           1. No/very little charge on amino acids on N term domain
                              1. N term goes into lumen
                                 1. Charged amino acids on Carboxyl term side of SA thus it stays in cytosol
            3. Synthesis of Type IV
               1. STA means protein stops transferring into ER
                  1. Protein goes back & forth between signal, STA, signal, STA
                     1. in & out of ER
                        1. # of domains varies & position of N term domain can be cytosolic or luminal
      5. Transport across Membrane
         1. Passive Diffusion
            1. partition coefficient AND concentration gradient

               Anotações:

               • membranes are semi permeable & allow small uncharged molecules through
               1. partition - measures hydrophobicity of molecule

                  Anotações:

                  • How soluble a molecule is VS how soluble it is in an aqueous solution
                  • how fast a moelcule goes through biomembrane
                  1. relatively high coefficient

                     Anotações:

                     • some solubility in membrane
                     • remember: do not want it too lipid soluble
                     1. K = 0, not cross
            2. no energy

               Anotações:

               • driven by existing concentration different across PM or any membrane HIGH TO LOW
         2. Active Transport
            1. Needs energy
            2. primary active transport
            3. secondary active transport

               Anotações:

               • uses a situation that's already arisen using primary transport
               • doesn't really require ATP, so not necessarily ATP powered
               1. Antiporters
               2. Symporters
                  1. Na/Glucose

                     Anotações:

                     • Na high outside cell- (+) charge Glucose = outside cell High glucose = inside cell, energy source for cells
                     • want more glucose inside cell, but you already have a high concentration of it Glucose moves against its gradient, which requires energy
                     • Energy is provided by symporter & uses the fact that Na wants to come in (down its gradient) Glucose uses the energy provided by Na
                     1. 2 free energies

                        Anotações:

                        • 1) Concentration gradient of Na more sodium outside, it wants to get inside
                        • 2) Charge gradient of cell positive charge on outside of cell
                        • Both energies enough to move 2 Na down & 1 glucose against gradient
               3. Use already established graident to tranport themselves

                  Anotações:

                  • Use one molecule that goes with concentration gradient & one against gradient
            4. pumps that use ATP to move molecules against concentration gradient

               Anotações:

               • ions are charged, cannot get them across the membrane, need to pump ions
               1. V & F

                  Anotações:

                  • responsible for pumping, they use ATP to pump H+ across membrane
                  • Important in mitochondria & chloroplasts, that is where a lot of H gets pumped around for ATP synthesis
               2. ABC type

                  Anotações:

                  • Move variety of small molecules
                  1. Have ATP binding cassette

                     Anotações:

                     • specific domain that binds ATP in specific way
                  2. Not restricted to ions
                  3. Can flip from one leaf to other

                     Anotações:

                     • need ATP
                  4. CFTR

                     Anotações:

                     • just pumps Cl-
               3. P

                  Anotações:

                  • move different types of ions two types first one is called muscle-calcium ATPase
                  1. Muscle ATPase pumps 2 Ca out of cytoplasm per ATP

                     Anotações:

                     • in this case it pumps it into SR as soon as you trigger muscle contraction
                     • Calcium release is voltage gated channel, as soon as calcium comes out P-class pump kicks in & gets it back into SR
                     1. END: cystosol has little or no Ca

                        Anotações:

                        • pump works against concentration gradient END: lots of Ca in SR, so when channel opens again Ca can flow out
                  2. Na/K ATPase pumps 3 Na out per 2 K in per ATP

                     Anotações:

                     • working all the time in our cells
                     • Lots of Na outside of the cell & K inside of cell because pump is always working - pumps ions against concentration gradient
                     1. Antiporter
         3. Facillitated transport
            1. pore/channel

               Anotações:

               • holes in membrane formed by some sort of protein
               1. Selective
                  1. proteins line at pore, creating holes through membrane

                     Anotações:

                     • keep things out, let things in
                     1. K+ resting channel
                        1. K+ can go through the membrane leaving water molecules behind

                           Anotações:

                           • but its bound to water molecules, so it has to have the right driving force
                           • in this example: bound to 4 oxygen molecules, so it has to break bond with all 4 in order to pass through channel
                           1. Needs concentration gradient
                              1. channel's have oxygen that are same spacing as water shell
                                 1. K+ release itself from water & binds to Oxygen lining channel
                                    1. goes through channel & once its released to other side it picks up water molecules again
                                       1. Channel specific to K+, because if you look at Na even though it has hydration shell it is different size & spacing
                                          1. Results in creation of membrane potential
                                             1. more positive on one side
            2. Uniporter

               Anotações:

               • movement of one molecule
               1. Glucose binds to one side of uniporter (GLUT1)
                  1. conformational change, opens up, allows glucose to enter
            3. gate

               Anotações:

               • something that opens & closes
               1. opened/closed
                  1. GLUT1 is basically a gate
               2. LIgand gated channel

                  Anotações:

                  • still with a concentration gradient
               3. Voltage gated channels

                  Anotações:

                  • opens with change in membrane potential
                  1. EXAMPLE: channel that releases Ca+ from SR in response to nerve impulses
                     1. nerve impulses travel down muscle cell & trigger voltage chennel on SR
                        1. opens & calcium comes down concentration gradient
            4. concentration gradient

               Anotações:

               • HIGH TO LOW moving through pore/channel such as protein-lined, so they don't come into contact with hydrophobic interior
            5. faster than passive
            6. Saturable

               Anotações:

               • only certain number of molecules can get through in any period of time
               • limit to the speed
         4. uniporter, symporter, antiporter

            Anotações:

            • do not tell you about type of transport, just the number of molecules & which way they are moving
            1. uni
               1. one mole moving
            2. sym
               1. two molecules moving same direction
            3. Anti
               1. two molecules moving different direction
         5. Co-transporter In Epithelial Cells
   5. Leaflets
4. Semi-permeable
   1. Small & uncharged or hydrophobic
      1. YES YOU CAN ENTER
   2. Large &/or hydrophilic
      1. NO. DIPSHIT
      2. Ions & glucose

Anotações:

• main component is phospholipid

1. Micelles
2. Liposomes

   Anotações:

   • CELL IS A LARGE LIPOSOME its a hallow sphere, where all of the tails form a bilayer structure
   1. lipid bilayer is not just a lipid
      1. Transmembrane proteins

         Anotações:

         • transmembrane receptors such as cadherins & integrins have transmembrane domains Dystrophin links transmembrane protein to cytoskeleton
         1. Transmembrane domain is the most imporatant domain
      2. Peripheral proteins
      3. EC domains

         Anotações:

         • integrins have domains outside of the cell to allow it to bind to ECM
      4. Composed of two leaflets

         Anotações:

         • row of phospholipids on each side hydrophobic tails facing inside
         1. lipid composition varies within each half of bilayer

            Anotações:

            • depending on composition, certain properties arise
            1. EXAMPL: PC or PE can be used in the membrane

               Anotações:

               • If PC is cyclindrical & PE has a comb-like structure, then you get bilayers of different shapes PC would form a straight bilayer, but as soon as you put in PE (tail wider than head), you introcude curves
3. Fatty Acid

   Anotações:

   • basic building block of phospholipid Cx:y x = carbon molecules y = double bonds
   1. Phosphoglyceride
      1. Base = glycerol

         Anotações:

         • 2 esterified fatty acids attached to glycerol
      2. different heads groups, ALL attached by a phosphate

         Anotações:

         • depending on head group you have PE, PC, PS, PI
      3. Plasmalogen

         Anotações:

         • One of its fatty is not esterified
   2. Saturated vs. unsaturated
      1. Temperature

         Anotações:

         • Humans = 37ºC Palmitate (C16:0)- TM = 63ºC at 37 it forms a fat (solid) thus not a good building block
         1. longer chain = higher TM

            Anotações:

            • more carbons interact with each other, if you stack them together there are van der waal interactions TEMPERATURE CANNOT BE TOO HIGH BECAUSE IT BECOMES A SOLID AT 37ºC
         2. More double bonds = lower TM

            Anotações:

            • double bonds introduce kinks, you cannot stack them & as a result get less attraction between chains becomes more liquid
            1. Cis double bonds
      2. PM is semi-fluid because it uses combination of saturate & unsaturated
   3. Sphingolipids
      1. base = sphingosine

         Anotações:

         • 3 carbons that kind of look like glycerol sphingosine already has this carbon chain, so you are only adding ONE fatty acid
      2. Glycolipid

         Anotações:

         • sugar group as polar head
      3. can/cannot use phosphate group

         Anotações:

         • can be a phospholipid if there is no phosphate used to attached head group its just a sphingolipid
   4. Sterols

      Anotações:

      • 4 ring hydrocarbons intercalate themselves into lipid bilayer with polar hydroxyl groups facing same direction as polar head groups
      1. Cholesterol
      2. No long carbon chain (tail)
      3. Thickness may change
         1. PC + cholesterol = thickens membrane
         2. Sphingomylein + cholesterol = does not change thickness