BIOCHEM CH 18

The mitochondrial ATP synthase complex consists of two large structural components called F1 which encodes the _____, and F0 which functions as the _____.

catalytic activity; proton channel crossing the inner mitochondrial membrane

Horse Evolution under climate change : woodlands --> grasslands

change from greenhouse/hothouse world in early Cenozoic in Eocene to progressively cooler, moderate temperature world with expansion of grasslands

The ______ hypothesis. : Electron transport generates a proton-motive force (through the proton gradient). : ATP synthesis can be powered by the proton-motive force. - ATP Synthase, a molecular assembly in the inner mitochondrial membrane, carries out the synthesis of ATP. => Protons flow from the inter-membrane space back into the matrix through this assembly. => The ____ drives the synthesis of ATP by ATP Synthase.

chemiosmotic => flow of protons

Question! : Earlier, we calculated the potential for the reduction of NADH by O2 to be 1.14V. What is the ΔGo' for this reaction? : (H+ + NAD+ + 1/2O2 --> H2) + NAD+)

dGo' = -2 (96 kJ/V*mol)(1.14V) = - 218.88 kJ/mol so ~ -220 kJ/mol (so why Eo' is spontaneous if positive)

Complex II: Succinate Q Reductase : No protons are pumped through Complex ___ - The small energy change associated with this reaction is not sufficient to ...? - ΔGo' = ____ kJ/mol

: II - drive transport of protons across the inner mitochondrial membrane - (-2.9 kJ/mol)

Extinct Rhinos : tallest land mammal

: Indricotherium- Eocene

Tapirs : Vicariant distrubution dispersal or extinction?

: Malay Tapir and Brazil Tapir : probably a lot of intervening extinction; tapirs pretty common in early Cenoic in North America

Learning Check : In the following reaction, which substance loses electrons? Which substance gains electrons? What is Eo'? Is the reaction spontaneous? : H+ + NADH + 1/2O2 --> H2O + NAD+

: NAD+ oxidized, NADH : 1/2 O2 oxidized, H2O reduced : 0.32 (reversed) + 0.82 = + 1.14 V : spontaneous because Eo' is positive

Chiroptera: insectivores : ___ American families : Family? V_____

: North- as go North lose diversity in terms of various diets : Vespertilionidae

White Rhino : Order : Family : Genus : Distribution

: Perissodactyla : Rhinocerotidae : Ceratotherium

Black Rhino : Order : Family : Genus : Distribution

: Perissodactyla : Rhinocerotidae : Diceros

Tapirs : Order : Family : Genus : species distribution?

: Perissodactyla : Tapiridae : Tapirus : 3 spp Neotropical; 1 sp Malaysia

Leaf Nosed (whispering) Bats : family : genus species : ___ and ____ along Colorado River.

: Phyllostomidae : Macrotus californicus : geothermal caves, Mines

Chiroptera: Animalivores : genus and 2 species of fish eaters

: Piscivores, noctilio, pizonyx

Chiroptera: Megabats : Family? : include flying ____ - distribitution? : when are they active?

: Pteropodidae : foxes - African, Oriental, Australian : can be active day and night (diurnal)

Complex III: Q-Cytochrome c Oxidoreductase : In Complex III, the electrons from ___ are passed to _____ - QH2 + 2Cyt cox + 2H+matrix --> Q + 2Cyt cred + 4H+intermembrane

: QH2, cytochrome c

Rhino numbers

: Sumatran and Javan Rhinos soon will be extinct - not replacing themselves rapidly enough - long gestation

Chiroptera: Animalivores : frog eaters genus?

: Trachops

Chiroptera: Frugivores : 3 genuses

: Vampyressa, Centurio, Ectophylla

Chiroptera: Animalivores : rodent/bat eaters, 2 genuses

: Vampyrum, Chrotopterus

Chiroptera : second only to rodents in=mammal diversity? : look at basic morphology- bat wing

: a lot due to wings and powered flight- allowed them to explore many niches not accessible to other mammals : emphasized thoracic part of body; rear part of body decreased in size

The Q cycle explains how ...? : net reaction?

a 2 electron carrier (ubiquinol) can transfer single electrons to cytochrome c proteins.

Learning Check : What is Eo' for the spontaneous reaction between oxygen (going to H2O) and FAD/FADH2 (free coenzyme)?

+ 0.815 - (-0.219) = + 1.034 V

Proton Flow and ATP Synthesis : There are usually 10-14 c subunits per c ring. - Each 360o rotation of the c ring leads to the synthesis of ____ - If there are 10 c subunits in a particular ATP Synthase, 1 rotation will move ____ (1 per _____) in order to synthesize ____ => 10 H+/3 ATP = ~_____ formed.

- 3 ATP. - 10 protons, (c subunit), 3 ATP => 3 H+/ATP

Pathways for Oxidation of NADH and FADH2 : NADH - Electrons enter at Complex ___ - Complex ___ --> ____ --> Complex ____ --> ____ --> Complex ___ --> ____ : FADH2 - Electrons enter at Complex ___ - Complex ___ --> ___ --> Complex ___ --> _____ --> Complex ___ --> ____

- I - I, Q, III, cyt c, IV, O2 - II - II, Q, III, cyt c, IV, O2

Chiroptera: Nearctic/Neotropical Diversity : Insectivores - North American Families - family: ____ - genus: ____ => they don't _____, they ____ instead - Bracken Cave, TX: 20-40 million bats

- Molossidae - tadarida => hibernate, migrate

Results of Glycolysis and the Citric Acid Cycle : Glycolysis and the citric acid cycle: - Oxidized a carbon fuel (glucose) to CO2 - Produced ATP - Produced _____ - _______

- high-energy electrons - Electrons are carried by NADH and FADH2

How the mitochondria helps make ATP. - why is inner membrane impermeable to ADP and citrate, etc?

- they have to be transported through specific transport proteins - if impermeable, then all the hard work of generating a proton gradient from the ETC would be wasted - inner membrane is folded to maximize surface area to pack in more complex I-IV (ETC machinery) and ATPase--> more ATP per mitochondria : greater surface area

Question! (opposite of other table) : What is Eo' for the spontaneous reaction between ubiquinone and cytochrome c?

0.045 - 0.045 (reversed) = + 0.19 V

The electron transport system consists of four large protein complexes. 1. Complex I: ______ (_____). 2. Complex II: ______ (contains _____). 3. Complex III: _____. 4. Complex IV: _____

1. NADH-Q oxidoreductase (NADH dehydrogenase) 2. Succinate Q reductase; succinate dehydrogenase from the citric acid cycle 3. Q-cytochrome c oxidoreductase 4. Cytochrome c oxidase.

How to make a protein gradient: the Electron Transport Chain : Oxidation of NADH and FADH2 occurs through a series of oxidation-reduction reactions that take place in ____ complexes embedded in the ______

4 protein; inner mitochondrial membrane:

Cytochrome c Oxidase can also pump protons from the matrix. : Overall, ____ electrons are funneled to O2 to reduce it to ____, concomitantly pumping _____ out of the matrix and ____ into the inter-membrane space.

: 4, 2H20, 8 protons, 4

Chiroptera: Microbats : ___ families : good at ____ : t____? : facial specializations?

: 7 : echolocation : tragus- pointy projection in ear that is indicative of kind of echolocation they use : eyes small, uropatagium- between hind feet and tail

Chiroptera: extant diversity : about ___ species

: 916 : "Over a half of the 916 species of bats on our planet are classified as threatened or near threatened with extinction"

Controlling the Rate of the electron transport chain reactions. : Electrons do not flow through the electron transport chain to O2 unless ...? - Why? => If ATP synthesis is not occurring, protons are not ...? => The ____ builds. => Eventually, the proton gradient becomes so large that ...? => Because protons can't be pumped, the ...?.

: ADP is simultaneously phosphorylated to ATP. => flowing through ATP Synthase => proton gradient => additional protons cannot be pumped into the inter-membrane space. => electron transport chain slows down

Asian one-horned rhinos : ___ species Sumatran/Java Rhinos

: Asian/Indian Rhinos; 2

Extinct Rhinos : heaviest land mammal

: Baluchitherium- Oligocene

Extinct Rhnos : Woolly Rhino

: Coelodonta- Pleistocene (North America and Paeloarctic- had fur)

Rieske Business : Complex III contains 2 types of ..? - Cytochromes are _____ that contain _____ : Complex III also contains an _____ (_____)

: Cytochromes: b and c1 : electron-transferring proteins; heme prosthetic groups : iron-sulfur center (2Fe-2S)

Under what conditions will the rate of the electron transport chain be high? (6 conditions)

: High O2 concentration : High phosphate : High ADP : Low ATP : High NADH : Low difference in H+ across the inner mitochondrial membrane

Complex I: NADH-Q Oxidoreductase : High potential energy electrons of NADH enter the respiratory chain at Complex ____. - ____-shaped - Consists of ____ polypeptide chains - NADH + Q + 5H+matrix --> NAD+ + QH2 + 4H+intermembrane : Overall, Complex I passes along ___ e- obtained from the oxidation of ___ to ___ using a coupled reaction mechanism that results in the net movement of ____ across the membrane.

: I - L - 46 : 2, NADH, Q, 4 H+

The Role of ATP Synthase : ATP synthesis occurs at ATP Synthase even in the absence of ____ : The role of the proton gradient is not to form ATP, but to _____

: a proton gradient. : release it from the synthase. - the free energy that is required to drive ATP formation has nothing to do with forming ATP (enzyme can do this just fine) => what's really necessary is opening up the active site; active site becomes so tightly closed around ATP that essentially the reaction is in equilibrium between ATP and ADP and Pi; only when have proton motive force will active site open allowing ATP to leave

Electron transfer potential is described in terms of a substance's reduction potential (Eo'). : The tendency of ...? : Depends on - The ___ of the substance. - The ____ of the substance.

: a substance to gain electrons or lose electrons - identity - chemical environment (by changing envmt, altering its Eo'- how bad substance wants electrons)

Starting to feel like Alice going down the rabbit hole? : Rotation of the γ subunit depends on interactions between the _____

: a subunit and the c subunits in F0.

Horse Evolution : Browsers (____ teeth) --> grazers (____ teeth) : went from ____ (terrain) to _____ : When did modern horse arise?

: brachyodont and budodont --> hypsodont and lophodont : woodlands, grasslands : Pleistocene

Horse Evolution :____ --> _____ : evolution in S. America vs N. America vs Old World

: browsers --> grazers : browsers became extinct in Old World and S America : in N. America, start with Hyracotherium, get a linear replacement of genera through time but not a lot of diversity at one point in time : until reach threshold, 20 mya, go from browsing to grazing horses and all of a sudden, get an explosion of diversity- get a lot of species coexisting at one time on landscape

F0 subunit : Includes the ____ subunits arranged in a ____ : Embedded in the _____ F0 and F1 are connected in 2 ways: : By the ____ : By an exterior column consisting of the _____

: c ring 10-14 c ; ring : inner mitochondrial membrane : central γε stalk : a, b2 and δ subunits

Binding Change Mechanism : Each β subunit can perform each of 3 sequential steps in the synthesis of ATP by ____ - Binding ____ ("___" or "____" conformation) - ATP Synthesis ("___" or "____" conformation) - ATP Release ("___" or "___" conformation) : Rotation of the γ subunit drives the _____ : No two subunits are ever in the same...?

: changing conformation - ADP and Pi (L, loose)- can't let them go - T, Tight - equilibrium - O, Open- ADP and Pi can bind : inter-conversion between the conformations from L--> T --> O : conformation at the same time

Summary of the Electron Transport Chain: phew! : important about I, III and IV? : I and II are responsible for?

: complex I, III and IV are pumps and are able to transform the free energy of the redox rxns into sending protons form a low concentration to a high concentration; able to couple an energetically unfavorable reaction (transport of proton from low conc to high conc) with a more energetically favorable rxn (the transfer of an electron from a molecule with a high Eo' to a molecule with a lower Eo') : generating reduced coenzyme Q shifting the equilibrium of the Q pool from the oxidized to the reduced state; when there is a high conc of reduced coenzyme Q, it will interact with complex III and thru the Q cycle, those electrons are going to be transferred to cyt c and protons that were used to reduce coenzyme Q that came from the mit matrix are always deposited into the intermembrane space

Microbats Reproduction : ____ fertilization? : size of litter?

: delayed fertilization : 1-2 young : can breed later in the season (warm) before it gets cold and then rather than females fertilizing and growing an egg to a mature neonate, females can avoid delaying implantation until following spring : contraint on size of litter, not hollowing out bones like birds and reducing body weight - 1-2 young or else would surpass wing load

Perissodactyla: rhinocerus traits : ___ horns- no ____ - which sex has them? : teeth?

: dermal, bony core - both but size may differ : lophodont, "Pi" shaped molars

Chiroptera: Conservation Issues : ?

: disturbance/loss of roosting sites - caves: disturbance of hibernacula - abandoned mines: safety concerns - trees : disturbance/loss of watering sites- natural springs/pools, livestock tanks : white-nose syndrome (fungus)- affects particularly cave roosting bats : wind turbines- migrating bats - barotrauma- tissue damage caused by rapid air pressure changes/differentials when near moving turbine blades- cause them to explode from inside out; blade strikes also could kill them : pesticides- reduction of food base - insectivorous bat worth to agriculture (x $1000 per county)

Eo' and ΔGo' are linearly related! : ΔGo' = -nFEo' : ΔGo' is the standard free energy of the reaction in J/mol (not kJ/mol) : n equals the number of ____ in the reaction. : F is the Faraday's constant (_______) : Eo' is the _____

: electrons transferred : (96 kJ/V•mol) : reaction potential

Microbats Echolocation : frequencies bats use

: fm = frequency modulated : cf = constant frequency

How many ATP are formed via the oxidation of NADH and FADH2 in the electron transport chain? : Energy needed to form ATP via ATP Synthase originally came from the high energy electrons generated by ____ - Electrons from NADH pump enough protons to generate ~_____ - Electrons from FADH2 pump enough protons to generate ~_____

: glycolysis and the citric acid cycle. - 2.5 molecules of ATP/NADH. - 1.5 molecules of ATP/FADH2.

Perissodactyla : ____ fermentation?

: hindgut- digestive system not as efficient as cetartiodactyla; not a lot of digestion until bolus enters caecum; so must eat a lot because can't digest all of it; may be one of reasons why not as diverse as Cetardiodactla

Microbats : 5 types of diets?

: insectivores : sanguinivores : frugivores : nectarivores- pollinators : animalivores

Proton Flow is coupled to rotation of the c ring. : Each proton enters the ____, follows a complete rotation of the ____, and exits through the ____

: intermembrane half-channel; c ring; other half-channel into the matrix.

Microbats Echolation : prey/predator coevolution?

: jamming sounds-create white noise and make it difficult for bat to recognize its own echolocation signals : avoiding attacks- moths have tympanum structure that allows them to pick up bat echolocation and avoid them

An experimental system to measure the reduction potential. : explain experiment : if X has high Eo', which direction will electrons flow? : if X has low Eo', which direction will electrons flow?

: left side - X- is reduced : right side - pH 1 - H2 is in equilibrium with the protons in solution : unless the Eo' of X and H2 match, this system is not in equilibrium : to achieve equilibrium, electrons are going to flow left to right or right to left : if flows right X is reduced to X- => protons combine with H forming H2 gas : if flows left X- is oxidized to X : will achieve equilibrium when H2 gas has a pressure higher than 1 atm

Perissodactyla : teeth?

: lophodont

Horse Evolution (tree) : look at digits

: losing digits and more emphasis on 3rd digit and increase in body size; increase in tooth complexity - this trend paralleled by trend in biome structure in N. America - most of evolutionary history occurs in N. America

: In any redox reaction, one substance is oxidized (loses electrons) while another is reduced (gains those electrons). : In spontaneous redox reactions, electrons are transferred from the substance with the ____ (more _____) reduction potential to the substance with the ____ (more _____) reduction potential.

: lower, negative, higher, positive

Perissodactyla : ____ limbs?

: mesaxonic- odd toed ungulates; the axis passes between the third and fourth toes

Flying Primate Hypothesis

: neurologist thought megabats looked more similar in brain wiring to primates and dermopterans : bats are polyphyletic and wings evolved twice : but turns out that if do molecular phylogenetics, very clear support for a monophyletic group that has a common ancestor- rejects Flying Primate Hypothesis- so powered flight only evolved once - brain wiring looking similar probably convergent evolution

Question. : In the following reaction, which molecule loses electrons? : Which substance gains electrons? : What is Eo'?

: pyruvate oxidized, lactate reduced : NADH reduced; NAD+ oxidized : 0.32 (NADH reversed) + (- 0.19) = +0.13 V

Complex IV: Cytochrome c Oxidase : Complex IV catalyzes the ...?. : reaction? : ΔGo' = _____ kJ/mol (wow!)

: reduction of molecular oxygen to water : -231.8 (more negative than the reaction that was previously calculated- means not every single reaction in ETC will have negative dGo' ; dG takes into consideration concentrations; as long as have massive amount of substrate, can drive unfavorable reactions forward by sucking product up)

Some Protein Complex Trivia : Complexes I, II, and III are associated in a supamolecular complex called a _____. : Complexes ______ (but not ___) _____ from the mitochondrial matrix to the inter-membrane space

: respirasome : I, III, IV, (but not II), pump protons

Microbats : higher latitudes = ? - males and females? : long and short distance? - hibernation use ____ (anatomy)

: seasonal migrations - males and females will separate geographically after mating so males won't compete for resources (hoary bats) : other option is to not migrate long distance, just migrate short distance to find stable temperature to hibernate during cold months - brown fat for coming out of hibernation; body mass decreases

Megabats : Unspecialized ___ : diet? : big ____, poor ____ : another feature of skull? : claws on which digits?

: skulls : frugivores (mostly) : eyes, echolocation : postorbital bar : claws on two digits (rather than single digit on microbats)

Summary of Cytochrome c Oxidase Function. : remember overall pathway; why would electrons want to go from cyt c to Fe and Cu?

: stronger oxidizing agents; electron goes to CuA/CuA but heme-a wants electron more

Complex II: Succinate Q Reductase : FADH2 is formed in the citric acid cycle by the _____ reaction. - This enzyme is part of Complex ___ - FADH2 does not _____ - FADH2 passes its electrons to ___ through ____ - FADH2 + Q --> FAD + QH2

: succinate dehyrogenase - II - leave the complex - Q, two Fe-S centers -

Wild Horses in N America: ecological issues : how many are ___?

: sustainable - cattle ranchers don't like wild horses because they compete for grazing : expensive and labor intensive to round up and care for and not attractive for people to want to adopt- hard to domesticate : reintroduce predators, mountain lions?

Chiroptera: Neotropical diversity : only 1 group of ____ - Family? - __ genera, ___ species - one is __ specialist and other two are ___ specialists - most common widespread vampire bat genus species => anatomy- locomotion for getting near prey to feed?

: true vampire bats and all occur in New World - Phylostomidae - 2, 3 - bird, mammal - Desmodus rotundus - land next to prey and crawl up limb; forelimbs allow flight and hop and locomote on ground very well

There are 2 mobile electron carriers that move electrons from one complex to the next. : Coenzyme Q (_____) - ____ and ____ - Diffuses through ____ - Carries electrons from Complex __ to Complex ___ and from Complex ___ to Complex ___ : Cytochrome c - ______ protein that shuttles electrons from Complex ___ to Complex ____ - Travels through the _______

: ubiquinone - hydrophobic (because its home is in the inner membrane- not soluble in the mit matrix, only exists in hydrophobic space of inner membrane), mobile - inner mitochondrial membrane (but cannot leave) - I, III, II, III - water-soluble; III, IV - intermembrane space

Chiroptera: Nectarivores : evolved with plants that..? : 3 genuses

: want to be cross pollinated : Musonycteris, Glossophaga, Lonchophylla

F1 subunit: : Consists of 5 types of polypeptide chains (____) : α and β are arranged alternately in a ____ (β are the _____ subunits). : Between the α/β subunits and F0 is a ____ consisting of ____ - The γ protein is a long ______ that extends into the center of the _____. - It has ____ different faces/sides. - It breaks the _____.

: α, β, γ, δ, ε : hexametric ring (catalytic) : central stalk, γ and ε proteins - helical coiled coil; α3β3 hexameter - 3 - α3β3 hexamer

How to make ATP: Oxidative Phosphorylation (diagram)

ATPase-- energy coupling process - the free energy of releasing these protons from where concentration is high and low will coupled to the energetically unfavorable process of making ATP

Learning Check : Which is a correct path taken by a pair of electrons down the electron transport chain? (look at picture)

E

Chiroptera: Fossil History : Eocene, 45 mya, N America, flies, echolates : genus

Icaronycteris

Chiroptera Fossil History : Eocene, N America, flies, does not echolocate

Onychonycteris

ATP Synthase Reaction (diagram)

if purify purify ATP synthase and add ATP- will hydrolyze ATP because it's energetically favorable

Where do you guys think the protons come from anyhow? (diagram)

just know this molecule can exist in 3 forms, a totally oxidized form, a semi-reduced form where one pair of electrons has been transferred or fully reduced form

why does glyceraldehyde-3-dehydrogenase pass electrons to NAD+?

low Eo' than NAD+

How the electron transport chain works. : As electrons are passed from one carrier to the next, protons from the _____ are transferred to the _____

mitochondrial matrix, inter membrane space

Electrons are transferred successively from NADH or FADH2 to a substance with a more _____ reduction potential (more likely to ____ electrons) to the next substance with an even MORE _____ reduction potential, etc. until the electrons are finally accepted by O2, which has the MOST _____ reduction potential of all of the substances involved in the electron transport chain.

positive, gain, positive, positive

Some Reduction Potentials for biologically relevant molecules. - more negative means? - if transferring electrons to oxygen from NADH or FADH2, what does this table tell you? - if less free energy is released upon the oxidation of FADH2 than NADH=> ? (table 18.1)

remember units! V : wants to get rid of electrons : since NAD+ more negative, result in larger change in free energy than from FAD - less ATP

Perissodactyla: Horses, ____ and ____

rhinos, Tapirs

Proton Flow is coupled to _____. : Rotation of the γ subunit depends on interactions between the a subunit and the c subunits in F0.

rotation of the c ring

Learning Check : Earlier, we calculated the potential for the reduction of FADH2 by O2 to be 1.034V. What is the ΔGo' for this reaction? : (1/2O2 + FADH2 --> FAD + H2O)

slide 17

The electron transport chain generates a proton gradient. (diagram)

slide 36

Binding Change Mechanism (diagram)

slide 44

Proton Flow is coupled to rotation of the c ring. (diagram)

slide 47

a positive reduction potential means that..?

the oxidized form of a substance has higher affinity for electrons than does H2 (O2) (527)

a negative reduction potential means that..?

the oxidized form of a substance has lower affinity for electrons than does H2 (NADH) (527)

Electron Transfer Potential : In oxidative phosphorylation, the electron-transfer potential of NADH and FADH2 is converted to ...?

the phosphoryl transfer potential of ATP (free energy of hydrolysis of the phosphoanhydride bond)

what is the point of oxidation of NADH and FADH2?

to generate a proton gradient - this gradient behaves like a dam that contains potential energy - building a proton gradient is energetically unfavorable => 2nd Law of Thermodyamics tells us that if you have a gradient, that it will be higher in free energy than if there's an equal concentration of protons on each side of the membrane; will observe an energy coupling event that couples the free energy release when NADH and FADH2 are oxidized and that free energy is going to be used somehow to push protons from one side of the inner membrane to the other generating this gradient - pumping against concentration gradient

Horse Evolution and Biogeography : N America --> S America and Old World : unintentional..?

went extinct in N America late Pleistocene and had to be reintroduced to N America; unintentional rewilding event