Chapter 14

• Oxidative phosphorylation - ADP + Pi ->ATP THIS IS INNER MEMBRANE

• Electron transport equation- NADH + ½ O2+H+->NAD+ +H2O NET OF INNER TRANSPORT

• Biological oxidation is important so humans don’t combust spon

-famously and the energy in the bonds are in small dosages

• O2 is important for biological oxidation so there is a place for

Energy to go

• Citric acid cycle> NADH dehydrogenase>Quinone>cytocromeC(REDUCED)>cytocrome C oxidase(OXIDIZE)

MEMORIZE THIS

Chapter 14BCONT

• First is reduced and then oxidized

• redox(mV) to free energy(kJ/mole)

• E’delta=mV, G0=kJ/mole

• The more positive redox potential the stronger acceptor more NEGATIVE BETTER DONOR

• n=#ofelectrons

• CAVEAT redox potential can be influenced by redox conc3entration

• Heme group attached to c cytocrome

• Copper is critical to complex 4

• Iron sulfur cluster

• Q(noOH), QH(1OH), QH2(2OH)

• None, semi, all

• MATRIX ARM -electron transport

• MEMBRANE ARM-proton pumping

• Proton highways are good and 40X fast but its non-selective , we dont know if its unidirectional

• When 2 H+ joins Q it becomes QH2

• Through cytocrome reductase QH2>iron sulfur cluster>cytocrome b>hemebh>heme bL>cytocrome c1>cytocrome c

• none>semi then semi>all

• Cytocrome C passes through cu and then heme

• iron/sulfur>su>heme

• Cytocreme C can indicate cell death

• FAD from succinate dehydrogenase donates to Q

CH 14C

• 1 glucose > 2 pyruvate+2NADH(1.5ATP)+2ATP GLYCOLYSIS

• 2pyruvate>2acetyl coA+2NADH(2.5 ATP per) PYRUVATE DEHYDROGENASE

• 2acetyl CoA>6NADH+2FADH2+2GTP CAC

• 2pyruvate > 8NADH+2FADH2 (1.5 ATP)+2GTP NET MITOCONDRIA

• 1 palmitoyl CoA-> 8Acetyl CoA +7NADH +7 FADH2 FATTY ACID OXIDATION

• 8 Acetyl CoA.>24 NADH + 8 FADH2 +8 GTP CAC

• 1 palmitoyl CoA >31 NADH +15FADH2 +8 GTP NET RESULT MITOCONDRIA

• NADH has 2 values because LOCATION CHANGES

• 

• ATP hydrolysis is -30.5kJ/mole

• -54kJ is Gdelta or 1ATP

• Nadh to oxygen is spontaneous

• 14 protons in total

• Only 61.4% of energy reaches the next stage

• - delta G is coupled with positive and for example NADH oxidation and creation of the proton gradient are energetically coupled

• Diffusion of the proton gradient-and generation of atp synthase+

• Long arm is stator in ATP synthase

• There is a rotor stalk

• As the protons move they loose their negative and is pushed into the matrix

• The stator holds F1 stable so the F1 can catalyzize atp synthesis

• Each bump in the images is created by hairpin protien (F0)

• 13-15 hairpins but can be as low as 8-9 or 21-23(F0)

• You need 1 proton for every hairpin

• The difference in charge drives the rotor around

• There are dimers that stabilize the atp syntheses

• There is a sink for atp synthase

• 8000 revolutions per minute,3 atp per turn

• ADP/ATP cotransporter

• The inter membrane space will be the more positive side

• ATP being negative drives directionality

• Bacteria use proton to pump nutrients into the cell and ATP

• In anerobic atp pumps and Na but no gradient is established

CHAPTER 14 D

• Stroma = matrix

• Thylakoids= cristae

• ATP in plants is produced in the stroma and consumed

• The high level electrons get excited and water replaces those electrons

• Dark reactions are dependent on the products of light

• Carboxylation, take the product 5C +1C=6C/2=3C molecules

• Rubisco fixes the carbon

• Reduction is gain of electrons and remodeling of bonds 6 3 Carbon molecules NADPH is in the bond energy , 5 continue because we keep one to break down

• REGENERATION 5 * 3C +ATP from light

• Carboxylation is CO2+ribulose 1,biphosphate>w/rubisco intermediate +H2O2 molecules of 3-phosphoglycerate

• 

• Review the photo system video

• 100 per second

• Mn cluster splits the water for electrons to be excited into the zscheme

• Photo system 2 only has one pathway that’s used rapid

• 

• The alpha rotor has 12 subunits=12 - charged residues

• Every time a proton enters the hairpin is moved one over

• How many protons are needed to turn =how many subunits there are

• Every 12 protons 3 ATP

• Ancient origin ATP synthesis (used originally for protons not ATP) first then ETC and then they’d are combined

• Started from ancestral fermenting minimal atp and H2S synthesis’s

• Purple non sulfur bacteria used something like cytochrome c but it wasn’t

CHAPTER 16A

• Freeway system made out of ants

• Cytoskeleton maintains org,cell structure , cell shape changes,cell movement, and intracellular trafficking of vesicles/organelles, cell division

• Cytoskeleton react in response to a lot of signals

• Repolarize-rebuild cell skeleton

• Actin and microtubules are dynamic to refunctionung

• All filaments need 1000 monomeric subunits and though they are structurally simple prokaryotes have ace steal versions of these filaments

• Actin fibers can be like a fishing line, very versatile

• Microtubules have + or - ends

• All of these filaments can interact to make and maintain a mature cell cytoskeleton

• Intermediate filaments are made of a-helical region its coiled together until dimer becomes a Teramer and it is no longer parallel

• This is a really strong 32 protein chains and it is a very strong

• Mesenchymal cells muscle and keratin

• Nuclear laminate give tremendous structural support unless it’s phosphorylated and it falls apart

• Epidermal IF keratin filaments connect through desmosomes or hemidesmosomes

• EBS rapid blistering due to tetramers not being able to form into protofilaments

• Axons IFs-

• Actin filaments, most abundant proteins in animals, all cells need it, 7nm , used as a reference control in everything and thin mesh work

• Repeat overly short lived , creates striated muscles

• Dynamic burst of polymerazation makes the cell move really quickly

• G-Actin -globular actin is a mono subunit

• It is a spherical contact had atp Imbedded inside the gactin

• Factin- there is a + and - end

• Suitable pool of charged g-actin ATP

• Add more readily to the + end

• You cannot depolymerize from the middle

• Polymerization happens in one configuration

• Origin of actin actin and myosin bonds and

• Myosin creates a barb and the plus end is more barbed

• The process of polymerizing 1.lag phase2.growth phase3.equilibrium phase lots of gactin to factin

• Lag phase - nucleation it’s rryl long

• The growth phase occusd as a monomer add to the exposed ends of the growing filaments,causing filament elongation

• If a gactin needs to be added then it needs to be removed, balanced

• We run out of free subunits and it hits an equilibrium

• Disassembly is more favorable at the - end

• Once they are in the polymer there is no difference in the - and + surface

• The plus end is more stable because they ATP binds initially (glue) that does not happen to the negative end

• If depolymerazes because of a time differential

• Critical concentration is higher for the ATP bound + side then the ADP bound - side

• Hydrolysis is not nessecarg

• Treadmilling when the actin filaments results when assembly at the plus end is concomitant with depolymerization at the minus end

CHAPTER 16 B

• 

• Arp2 and 3 very actin related

• Arp3/2 bind to NPF and clicks both into a active state so it can bind to a uncleared actin filament (ON MINUS END)

• ARPS kind of glue onto the edge (70° angle) these make branched formations

• ADP it’s pushed into the NPF and the actins dissasociatw.

• Profilin is opposed by thyomisin

• Forms clamp the actin and myosin to the membrane (associated with the plus end)

• Uniform Z disks lead to striating

• Tropomodilin and CapZ prevent polymerization and depolarizing

• We can use coffilin to break off actin filament ends(induces severe twisting)

• Creates new ends to deassamble more rapidly

• Filament is gel forming and brain relies on it

• I. Fibrin it’s exclusively structural

• Periventrical heterotrophia-seisures

• Myosin a ton binding protien 

• Listeria bacteria-pathogenic food poisoning coops actin array and pull the subunits to breaking 

• You can generate force by the actin by densly pushing things to the front

• Focal adhesions via integrins to move the leading edge

• All of the cell Mobility is myosin dependent 

• Cell moves like this

• Coffilin will twist the actin filaments to have Arp fill in to make it very large 

• Amobeid cell membrane is facilitated by external sensing and feedback, they hunt for pathogens and commit eating so it can use the actins from them 

• Ratchet is used to describe the actin filaments moving forward and not back 

• Profilin recruits actins

• Capping protien binds to plus end to stop it Arp is the branch

• These factor give polarity and allow the cell to move 

• A lot of feedback crll regulation

• Myosin is an allosteric binding protien that depends on polarity and atp Adele activity, + end directed, actin dependent

• Myosin and actin work together to perform cellular functions: vesicle translocation,cytoplasmic streaming,cell locomotion, and muscle contraction

• Allosteric-protien with a binding site so the structure can conform to it

• Atp and ADP stay in their pocket tnad it effect the relative shape

• Myosin is highly concerned

• 2myosinnprotiens will be interwoven

• Myosin 1-the bilayer is attaching to the cortical actin to hydrolyze atp

• Myosin 5- the carbon binding protien da drag and grab vesicles by “walking” and it has a 35nm  distance(draw this )

• Myosin 2- has 2 heavy subunits with a coil coil terminus

• The neck regions diversify the force

• These are regulated , from the center there is a bare zone 

• 50-60 myosin heads 

  CHAPTER 19

• Cadenerin based protiens respond to adherin junctions

• How one cell is connected to another

• Cells anchor to other junctions based off cadaherins

• High calcium is needed for cadaherims to link and then anchor to the cytoskeleton

• Under tension protiens are extended to reduce stress on the molecule

• The actin support cell connections, important and weak, useless without adherin junction

• Adherin junction can generate force and bend and pull tubes out

• Desmosomes cell cell anchoring junctions they are embedded within the plasma membrane with

• Integrins is like cadaherins but it binds to the extracellular material

• Tight Junction- elaborate array of protien, function is to seperate spaces that are created by a layer of cells, separates interstitial and blood stream(Tupperware lid) creates a seal

• Series of protiens stitched together (clodins and aculin ) with lateral attachments across

• Channel forming junctions or gap junctions- connects cytosol , chemical synapses, only 1000 daltons can pass small ions and molecules can pass

• Gap junctions that are small stack together

• The ECM is diverse and complicated mixture, its secreted and it can be structural or space filling,

• Makes you durable and promotes compression resistance

• Fibrous protiens provide tensile resistance

• 

• Hyluranan forms the backbone for bigger complex of things like heparin that ca. dock on the hyluran complex

• Collagen- an example of a fibrous protien that can provided tensile strength via GAG and it’s usually made of a chain of amino acid, fhe partner chains are woven together

• Hydroxylation gives collagen distinctive folding patterns.

• Ex bone defects,dwarfism, nasal laminate will fail in the kidenehs , and all sorts of problems that come from a lack of calllahdn

• Collagen is dependent on vitamin C as a cofactor

• Elastin- forms cross links and are coiled up to allow streachimess and relaxation and prevents the other end without tearing ping or ripping

• Finromectim and other multi adhesive protiens all of domains can be switched out via alternitive splicing

• Fibromectins bind integrins

• Arg protiens allow the integrity protiens allow the cell being knit into the and then show it to. E

• Basal lamina is exclusive to the epithelial cells

• The key assembly factor that is growing into the cell did 3 rd protien call dystroglucan,indigenous,,perfect

• Integrity bind the cell to the extracellular ,atria

• Connected to cell with intermembrane filaments, and anchoring junctions

• Inactive integrity- makes internal and external signals on the alpha and beta site inactive anchoring

• Lateral cross linking protiens mediate binding