Topic 6 - Bioenergetics Flashcards

Question

What is phosphoryl transfer potential?

Answer 1

Phosphoryl transfer potential --\> examines the ease at which a phosphate group can be lost from a molecule. It is a relative measure (Phosphoryl transferred from a compound to water). Greater phosphoryl transfer potential --\> more energetically favourable for the hydrolysis of the phosphate group.

Answer 2

High phosphoryl transfer potential is due to the structural differences between ATP and it hydrolysis products. 1. Resonance stabilisation --\> Products (inorganic Pi has greater resonance stabilisation) 2. Electrostatic repulsion --\> negative charges close together in ATP molecule. 3. Entropy increase --\> entropy of products is greater 4. Stabilisation due to hydration --\> H₂O stabilizes products --\> makes reverse reaction less favourable.

Answer 3

1. Phosphate anhydride 2. Enol Phosphate 3. Some thioesters 4. Some compounds containing N-P bonds --\> phosphoguanidines.

Answer 4

~ --\> indicates high energy bond.

Answer 5

ATP ≈ -30 KJ mol^-1 More than -30 KJ mol^-1(more negative) --\> high energy phosphate compound Less than -30 KJ mol^-1(more positive) --\> low energy phosphate compound

Answer 6

Use high energy compounds and couple the reactions in order to synthesize ATP.

Answer 7

The transfer of the phosphoryl group from a compound with a large ΔG value to ADP yielding ATP.

Answer 8

1. ATP is intermediate in energy --\> serves as an energy conduit between super high energy and low energy phospho-compounds. 2. The highly exergonic phosphoryl transfer reactions of nutrient degradation are coupled to the synthesis of ATP from ADP + Pi

Answer 9

1. Early stages of carbohydrate breakdown to produce low energy phosphate compounds. 2. Interconversion of nucleoside triphosphates. 3. Muscle contraction and active transport against the concentration gradient. 4. Phosphoanhydride cleavage followed by pyrophosphate cleavage provides extra energy for fatty acyl-CoA synthesis and nucleic acid biosynthesis.

Answer 10

1. Substrate level phosphorylation 2. Oxidative phosphorylation

Answer 11

Phosphotransferase enzyme that catalyzes the interconversion of adenine nucleotides (ATP, ADP, and AMP). 2ADP \<----\> ATP + AMP

Answer 12

Note --\> Atp is a free energy transmitter, not a reservoir. - ATP pool supplies energy for about 1 minute - At rest --\> the average human turns over ATP at a rate of approximately 1.5kg/hour - The brain only has a few seconds supply of ATP.

Answer 13

Phosphocreatine acts as a reservoir for ATP formation (muscle and nerve cells). ATP + creatine \<-----\> Phosphocreatine + ADP

Answer 14

2ADP \<-----\> ATP + AMP When we exercise large quantities of ATP are used up which results in high ADP concentration and low ATP concentrations. Normally, ATP concentrations in cells are very low but when the reaction above is activated during exercise --\> AMP concentrations increase --\> this activates al energy producing pathways (glycolysis) --\> Hence, AMP acts as a signal of low energy which stimulates the oxidation of nutrients.

Answer 15

They are all ATP derivatives. Note --\> All nucleotide triphosphates are energetically equivalent but ATP is the primary cellular energy carrier.

Answer 16

4 electrons

Answer 17

It is impermeable --\> nothing can simply diffuse through.

Answer 18

1. Large molecules are broken down, absorbed and distributed --\> no useful energy produced. 2. Break down molecules into simple units --\> acetyl unit of acetyl CoA. 3. ATP is produced by complete oxidation of the acetyl unit.

Answer 19

- Phosphate esters are thermodynamically unstable but kinetically stable - Stability due to negative charges that make them resistant to hydrolysis without the action of enzymes --\> enzymes can then manipulate energy release --\> results in regulatory molecules (Kinases and phosphatases) - No other element has the same properties and it is also abundant.

Answer 20

The electron carriers capture electrons and thus store the cell's reducing power.

Answer 21

Yes, it can take place in both environments.

Answer 22

Before cycle --\> Pyruvate dehydrogenase transfer pyruvate to CoA to form acetyl-CoA. 1. Acetyl-CoA donates 2 carbons to the cycle --\> from pyruvate added to oxaloacetate --\> enzyme citrate synthase. 2. a) Dehydration reaction (water released) --\> Enzyme Aconitase (contains an Fe and S atom) 2. b) Hydration (Water taken in) --\> enzyme aconitase 3. Oxidative decarboxylation (1st) (NADH+H⁺ released)--\> enzyme isocitrate dehydrogenase --\> requires NAD⁺ as a coenzyme. 4. Oxidative decarboxylation (2nd) (NADH+H⁺ released) --\> releases CO₂ --\> enzyme Isocitrate dehydrogenase --\> Utilizes co-enzyme A. 5. Substrate level phosphorylation (GDP to GTP which is latter enzymes convert to ATP later) --\> Enzyme succincyl - coenzyme synthase --\> Note enzyme CoA is regenerated. 6. Dehydrogenation --\> Succinate dehydrogenase (dependent on FAD --\> hence FADH₂ is created) 7. Hydration (Water taken in) --\> Fumerase 8. Dehydrogenation --\> Malate dehydrogenase --\> reuqires to presence of NAD⁺so NADH +H⁺ is released. Note --\> Steps and picture don't always match.

Answer 23

Main products --\> per pyruvate 3 x NADH 1 X FADH₂ They generate reducing power.

Answer 24

- Operates when ATP is needed - High levels of ATP and/or NADH inhibit the citrate synthetase (first step of cycle). - Conversely --\> high levels of ADP and or NAD⁺ activate isocitrate dehydrogenase. - Low levels of ATP or high levels of acetyl CoA speed up the cycle to give energy.

Answer 25

Citric acid cycle is controlled by levels of Ca²⁺ concentration in the matrix. For example... High concentrations in the cytosol caused by an increase in muscle activity increase Ca²⁺ levels in the matrix which activates enzymes for the citric acid cycle.

Answer 26

Using redox reaction we can use the transfer of electrons between species to do useful work. The ability of an organism to carry out redox reactions depends on the redox state of the environment or its reduction potential.

Answer 27

The reduction potential is a measure of the tendency of a chemical species to acquire electrons and thus be reduced. It is measured in Volts, millivolts or E (1mv = 1 E) The more positive the potential is --\> the greater the species affinity for electrons is and thus has a greater tendency to be reduced.

Answer 28

Electrons flow from the **low** to **high** reduction potential.

Answer 29

Standard reduction potential is measured under standard conditions and is defined relative to a standard hydrogen electrode --\> which is arbitrarily given a potential of 0 volts.

Answer 30

Electron transport chain is located in the inner mitochondrial membrane. 1. Complex 1 In the membrane, you find Quinine --\> highly hydrophobic molecule that is dissolved and diffuses freely in the inner membrane space. 2. Complex 2 3. Complex 3 Note between Complex 3 and 4 there is a hydrophilic cytochrome c molecule located on the outside of the membrane. 4. Complex 4

Answer 31

**1.** NADH donates two electrons to complex 1. They are accepted FMN (FMN + 2H⁺ + 2e^- ---\> FMNH₂) **2.** FMN donates one electron to FeS (it can only accept one electron). --\> Results in the formation of quinone FMNH. (Note there are multiple FeS entres --\> mammalian complex 1 has 7) **3.** The FeS centres donate the electrons to quinine --\> this is possible as there are quinine pools located in the non-polar region of the membrane. **4.** Quinine gets reduced by complex 1 and acts as an electron carrier to complex 3 (Note --\> it hangs around till it is fully reduced.)

Answer 32

What is FMN? - A prosthetic group of flavoproteins which is like FAD without the adenine nucleotide. - FMN can accept two electrons from NADH - But FMN can only give away one electron at a time --\> results in the formation of a radical intermediate called a semiquinone.

Answer 33

What is FES? Iron-sulfur centres which are prosthetic groups to proteins (each has 1-4 iron atoms). They can only transfer one electron but there are multiple centres as mentioned. Note --\> cytochromes have a haem prosthetic group which absorbs light --\> absorption of light can determine whether oxi- or red- occurs.

Answer 34

**Quinine** (also known as CoQ, Q, ubiqionone and Q10) - Reduced to quinol in a 2 electron reduction reaction Q + 2e^- + 2H⁺ ---\> QH₂ - It is an extremely hydrophobic molecule so it dissolves within the fatty acid part of the membrane ----\> thus it can diffuse freely along the plane of the membrane.

Answer 35

Complex III --\> CoQ, cytochrome c reductase 1. Reduced Q donates 2 electrons into complex III 2. One electron goes to FeS and the other goes to a low-affinity cytochrome b. 3. a) FeS donates its electron to cyt C1 b) The electron is transferred from the low to high-affinity cytochrome b and subsequently returned to Q. 4. cyt C₁ donates its electron to cytochrome C. 5. Cytochrome C acts a mobile electron carrier thatis reduced by Complex III and oxidised by complex IV.

Answer 36

Cytochrome C It is a small water-soluble molecule with a haem group. It attaches to the outside of the membrane on the side of the intermembrane space. It acts as a mobile electron carrier between complexes III and IV.

Answer 37

Complex IV --\> Cytochrome oxidase The complex contains 3 copper atoms --\> two in clusters Cu_A and one is Cu_B. 1. Cytochrome C donates its electrons to complex IV --\> accepted by CuA. 2. The electrons are passed down to Cytc a and then Cytc a₃ (Both are identical but they are found in different environments giving them different redox potentials). 3. Oxygen accepts electrons from cytochrome a3 and along with protons produces water --\> oxygen acts as the final electron acceptor. 4. Complex iv translocates 8 protons (8 are taken up from the matrix) --\> 4 are pumped into the intermembrane space, the others are chemical protons used for water formation.

Answer 38

Succinate 2 reductase - Succinate dehydrogenase - Situated between complex I and III but is not a transmembrane protein, only partially embedded in the matrix side of the bilayer - Oxidises FADH2 to FAD, producing two electrons --\> The electrons are fed directly into Q.

Answer 39

**Complex 1** - Complex 1 is L shaped with a large hydrophobic portion and a large hydrophilic portion - The Q chamber which is long, narrow and enclosed binds the two regions - Q chamber is linked to one channel through a funnel of charged residues which continue along the entire membrane domain. - The polar residues become surrounded by water to form a continuous hydrophilic axis spanning the entire domain - The hydrophobic region has many vertical half channels made of vertical helices - One set is exposed to the matrix, the other to the inner membrane space - Horizontal helices connect to vertical helices on matrix side and β hairpin (βH) helices link the vertical helices on the inner membrane space.

Answer 40

1. NADH donates electrons to FMN which then donates them to Q. (Hydrophilic part) 2. Q^2- is generated which interacts with the negatively charged amino acid residues. 3. Creates conformation changes in the long α helices and β hairpins (vertical and horizontal helices). 4. This causes changes in the pKa of the amino acids 5. Allows protons from the matrix to bind to amino acids, dissociate in the water-filled channel and enter the intermembrane space. **Note** For every two electrons which are accepted by Quinone = 4H⁺ Q^2- will take up protons from the matrix and form QH₂ ANIONIC Q IS THE DRIVING FORCE

Answer 41

The substituents linked to the ring (prosthetic groups) --\> Heme c, heme a, etc.

Answer 42

1. Generates a pH gradient --\> Higher pH in the matrix 2. Generates a voltage gradient inside is -ve and outside is +ve. Together both these forces are known as the electrochemical proton gradient which exerts a proton motive force (mV)

Answer 43

Complex I, III and IV can transport protons across the membrane. Complex I --\> Proton pump mechanism Complex III --\> Q cycle Complex IV --\> proton pump mechanism

Answer 44

ATP synthase 1. ADP + Pi --\> ATP --\> Synthesis of a phospho-anhydride bond 1. F1 (segment) is in the matrix and F0 (segment) is in the membrane. 3. There is a stalk region which interconnects the subunits. 4. **F1** catalyses ATP hydrolysis - F1 (α3β3γδε) - Made up of homologous α &β (both have different conformations) subunits which alternate in a ring around the γ centre/stalk - Three nucleotide binding sites are present at αβ interfaces, mainly involving β subunit residues - γ creates asymmetry --\> different interactions with α and β subunits - β contains the catalytic site for ATP synthesis. - Mg²⁺ will bind to the nucleotides in all the subunits - ATP synthase, without the presence of a proton gradient, will catalyse the reverse reaction and hydrolyse ATP to ADP **5. F0** (a1b2c9-10) - The membrane containing F0 is leaky to protons however inhibitors can interact with F0 to block the leaky properties - Number of c depends on the species - Also contains accessory peptides e.g. d, F6 and OSCP

Answer 45

Rotation requires a rotor which rotates with respect to a stator. Rotor --\> γ,ε and C ring complex Stator --\> α, β and δ

Answer 46

ATP synthesis 1. Translocation of protons by F0 2. Catalysis of phosphoanhydride bond of ATP by F1 3. Coupling of dissipation of proton gradient with ATP synthesis which requires both subunits interacting

Answer 47

How ATP is synthesized by the F1 subunit - 3 homologous subunits which are conformationally different. - Classified as Loose (bind to loosely -\> no catalytic activity), tight (tight binding --\> catalytically active) and open (Catalytically inactive) - Has γ in the centre _Process_ 1. ATP is bound to tight 2. ADP + Pi will bind to L and induce conformational changes in the three subunits 3. ADP.Pi now are tightly bound in the T catalytic site and can form ATP 4. ATP in T is now in O so is released So.... L --\> Initial binding of ADP + Pi T --\> Reaction is catalyzed to form ATP O --\> ATP released

Answer 48

**Rotation** Rotor= γε-C12 ring Stator=ab2-α3β3δ - Rotational motion is due to the passage of protons from the outside (I.M.S) to the inside (Matrix) - Suggested that the b.δ complex prevents the α3β3 assembly from rotating with the γ subunit. - Coiled coils span the membrane with a central aspartic acid with a neutral charge (C subunits) --\> Two proton path channels are formed in this subunit c - Subunit a has a cytosolic half channel and a matrix half channel --\> they interact directly with the c subunit. **Process** 1. Aspartic acid is protonated (by proton from I.M.S), serine can rotate. 2. Rotation --\> aspartate moves into contact with the membrane and then the other half channel throughout the rotation. 3. The proton then dissociates and leaves the matrix half channel.

Answer 49

ATP will form and hang around the enzyme, it will only leave the catalytic site when protons flow through. The proton gradient is present to release ATP from ATP synthase rather than form the ATP itself.

Answer 50

This occurs when there is still electron transfer but no ATP production. This is because the energy from the proton motive force is simply dissipated as heat.

Answer 51

UNCOUPLING REAGENTS - Need to be Lipid soluble and dissolve in the membrane. - Tend to be weak acids - Example --\> Dinitrophenol --\> proton dissociates from OH^-.

Answer 52

Uncoupling proteins -\> inner mitochondrial membrane Example: Thermogenin -\> Found in brown adipose tissue --\> Found in all new-born mammals and all hibernating animals - Functions as a proton carrier blocking the electrochemical gradient formation so ΔG dissipates as heat --\> results in ‘Non shivering thermogenesis’ - Costly in terms of energy but the heat generated warms up the new-borns who are not yet able to shiver (lack muscles) - Inhibition by purine but the inhibition is overcome by free fatty acids but presence of the fatty acids activates it.

Answer 53

1. Noradrenaline (controls fatty acid concentration in brown adipose) binds to a receptor. 2. Adenylate cyclase increase cAMP 3. cAMP activates cAMP dependant protein kinase 4. The kinase phosphorylates triacylglycerol lipase --\> activating it 5. Lipase hydrolyses the triacylglycerol into fatty acids 6. Activates and opens the Thermogenin proton channel. 7. Protons do not enter ATP synthase so does not create the electrochemical gradient 8. Heat is produced.

Answer 54

ATP and ADP can not pass inner-membrane --\> highly charged. Transported via a ATP/ADP translocase --\> Can be used for either ATP or ADP --\> when they bind there is a conformational change which moves them across the membrane. - Acts as an antiport --\> exchange of ADP and ATP (ADP can only enter if ATP exists) - Note --\> inner membrane has a positive membrane potential --\> ATP has one more negative charge than ADP --\> So ATP out and ADP in is favoured. - The exchange is driven and uses up the membrane potential --\> hugely expensive process uses up a 1/4 of the proton-motive force generated by the respiratory chain.

Answer 55

**Malate-aspartate shuttle --\>** Common in heart and liver cells. - The function is to transfer electrons of cytosolic NADH to mitochondrial NAD⁺to form NADH. - Mitochondrial NAD⁺ is reduced by cytosolic NAD⁺ through the reduction and regeneration of oxaloacetate. - Each NADH yields just over 2 ATP - The carrier proteins have no NADH interactions, only with electrons moving into the matrix. **Process** **Cytosol** --\> Oxaloacetate reduced by malate NADH to form Malate (transported via protein into Mito) **Mitochondria** --\> Malate oxidised to form NADH and oxaloacetate. - The rest of the reactions in the cycle are present to regenerate oxaloacetate

Answer 56

**Influx** --\> protein channel --\> rate of transport depends on cytosolic concentrations. **Efflux** --\> antiport with Na⁺ --\> movement is driven by sodium gradient --\> works at max velocity always --\> not impacted by cytosolic concentrations. - Set point is where rate of influx = rate of efflux. How exactly does it help maintain cytosolic levels? 1. If Cytosolic [Ca²⁺] increases --\> influx increases but efflux remains constant --\> net is towards influx so cytosolic concentration is restored (more moves in). 2. If cytosolic concentration is down, influx rate is reduced, and efflux remains constant. The net direction is efflux, so the concentration of the cytosol increases and restored (more net moves out)

Answer 57

Phosphate enters the matrix with H⁺ by an electrochemical symport mechanism --\> drive and uses up pH gradient.

Answer 58

Essential as it is a secondary messenger. Mitochondria can store and release it, so it communicates with the ER (which can also do the same) in order to control cytosolic concentration.

Answer 59

**Stage 1** is the trapping and preparation phase. No ATP is generated in this stage. In stage 1, glucose is converted into fructose 1,6-bisphosphate in three steps: phosphorylation, an isomerization, and a second phosphorylation reaction --\> function: trap the glucose in the cell and form a compound that can be readily cleaved into phosphorylated three-carbon units. **Stage 2:** ATP is harvested when the three-carbon fragments are oxidized to pyruvate.

Answer 60

Glucose enters the cell via glucose transporters. Hexokinase phosphorylates glucose to form glucose-6-phosphate. Reason for this: Glucose 6-phosphate cannot pass through the membrane because of the negative charges on the phosphoryl groups, and it is not a substrate for glucose transporters. Addition of the phosphoryl group facilitates the eventual metabolism of glucose into three-carbon molecules with high-phosphoryl-transfer-potential.

Answer 61

Hexokinase, like adenylate kinase and all other kinases, requires Mg²⁺ (or another divalent metal ion such as Mn) for activity. Glucose induces a large conformational change --\> hexokinase consists of two lobes the move closer together when glucose binds --\> this closes the cleft and surrounds the glucose molecule with protein ---\> except for -OH on carbon 6 --\> the closing of the cleft makes the environment more non-polar --\> favours reaction between -OH group and terminal phosphoryl group --\> plus the closing of the cleft allows the enzyme to discriminate against water as water molecules are not near the active site --\> this allows for phosphorylation of glucose.

Answer 62

Isomerization of glucose 6-phosphate to fructose 6-phosphate. Straight chain of glucose has an aldehyde on carbon 1 whereas the fructose has a ketone on carbon 2. Hence, the isomerisation is a conversion between an aldose to a ketose. Catalyzed by phosphoglucose isomerase --\> takes several steps as it has to open the ring structure in order to catalyze the reaction.

Answer 63

Fructose-6-phosphate is phosphorylated using ATP to form Fructose-1,6-bisphosphate. This reaction is catalyzed by phosphofructokinase (PFK), an allosteric enzyme that sets the pace of glycolysis.

Answer 64

Fructose 1,6-bisphosphate is cleaved into glyceraldehyde 3-phosphate (GAP) and dihydroxyacetone phosphate (DHAP), completing stage 1 of glycolysis. This reaction, which is readily reversible, is catalyzed by aldolase --\> enzyme derives its name from the nature of the reverse reaction, an aldol condensation.

Answer 65

Triosephosphate isomerase catalyzes the isomerization of DAHP into GAP. This has to be done as DAHP cannot continue in the glycolytic pathway --\> if not converted ATP will be lost. The reaction is rapid and reversible --\> normally at equilibrium there is 96% of DAHP --\> but subsequent reactions in glycolysis remove the product --\> driving the reaction to the RHS.

Answer 66

Conversion of glyceraldehyde 3-phosphate into 1,3-bisphosphoglycerate (1,3-BPG), a reaction catalyzed by glyceraldehyde 3-phosphate dehydrogenase. Sum of two processes: the oxidation of the aldehyde to a carboxylic acid by NAD⁺ and the joining of the carboxylic acid and orthophosphate to form the acyl-phosphate product. This creates a molecule with a high phosphoryl-transfer potential.

Answer 67

- The first reaction is thermodynamically favourable --\> Free energy change of -50 KJ mol^-1. - The second reaction is thermodynamically unfavourable --\> Free energy change of +50 KJ mol^-1 The two processes must be coupled so that the favourable aldehyde oxidation can be used to drive the formation of the acyl phosphate How are they coupled? The key is an intermediate, formed as a result of the aldehyde oxidation, that is linked to the enzyme by a thioester bond. Thioesters are high-energy compounds found in many biochemical pathways (Section 15.4). This intermediate reacts with orthophosphate to form the high-energy compound 1,3-bisphosphoglycerate. The thioester intermediate is higher in free energy than the free carboxylic acid is. The favourable oxidation and unfavourable phosphorylation reactions are coupled by the thioester intermediate, which preserves much of the free energy released in the oxidation reaction. We see here the use of a covalent enzyme-bound intermediate as a mechanism of energy coupling.

Answer 68

1,3-Bisphosphoglycerate is an energy-rich molecule with a greater phosphoryl-transfer potential than that of ATP. Thus, 1,3-BPG can be used to power the synthesis of ATP from ADP. Phosphoglycerate kinase catalyzes the transfer of the phosphoryl group from the acyl phosphate of 1,3- bisphosphoglycerate to ADP. The formation of ATP in this manner is referred to as substrate-level phosphorylation because of the phosphate donor. Background info --\> energy released of the oxidation of glyceraldehyde-3- phosphate to 3-phosphoglycerate is temporarily trapped as 1,3-bisphosphoglycerate --\> energy powers the transfer of a phosphoryl group from 1,3-bisphosphoglycerate to ADP to yield ATP.

Answer 69

Rearrangement reaction --\> The position of the phosphoryl group shifts in the conversion of 3-phosphoglycerate into 2-phosphoglycerate, a reaction catalyzed by phosphoglycerate mutase. Generally --\> Mutase is an enzyme catalyzes the intramolecular shift of a chemical group, such as a phosphoryl group.

Answer 70

**Dehydration of 2-phosphoglycerate** introduces a double bond, creating an enol. Enolase catalyzes this formation of the enol phosphate phosphoenolpyruvate (PEP). Dehydration reaction increases the transfer potential of the phosphoryl group --\> because the phosphoryl group traps the molecule in its unstable enol form --\> when the phosphoryl group has been lost --\> molecule forms the more stable ketone (pyruvate). Hence, the difference in stability between the enol and the ketone form creates the high phosphoryl transfer potential.

Answer 71

Substrate level phosphorylation --\> ADP to ATP Irreversible transfer of a phosphoryl group from phosphoenolpyruvate to ADP is catalyzed by pyruvate kinase. **Extra** --\> The formation of pyruvate from 2-phosphoglycerate is, in essence, an internal oxidation-reduction reaction; carbon 3 takes electrons from carbon 2 in the conversion of 2-phosphoglycerate into pyruvate. Compared with 2-phosphoglycerate, C-3 is more reduced in pyruvate, whereas C-2 is more oxidized.

Answer 72

The cell has limited amounts of NAD⁺ so the cell must regenerate it for glycolysis to proceed. 1. During anaerobic conditions --\> The regeneration of NAD⁺ in the reduction of pyruvate to lactate or ethanol sustains the continued process of glycolysis under anaerobic conditions. Fermentation (ethnaol) --\> 1. decarboxylation first to form acetaldehyde (In H⁺ / Out CO₂) 2. reduction from acetaldehyde to ethanol (In NADH / Out NAD⁺) Fermentation (latic acid) --\> 1. Reduction of pyruvate to form lactate (In NADH / Out NAD⁺) 2. TCA cycle/E.T.C --\> The NAD⁺ required for this reaction and for the oxidation of glyceraldehyde 3-phosphate is regenerated when NADH ultimately transfers its electrons to O₂ through the electron transport chain in mitochondria.

Answer 73

1. A major area of fructose metabolism is the liver --\> Fructose is phosphorylated --\> fructose to fructose 1-phosphate by fructokinase. Fructose 1-phosphate is then split into glyceraldehyde and dihydroxyacetone phosphate an intermediate in glycolysis. 2. In other tissues, such as adipose tissue --\> fructose can be phosphorylated to fructose 6-phosphate by hexokinase --\> enter the glycolytic pathway.

Answer 74

Galactose is converted into glucose 6-phosphate in four steps. 1. Galactose to galactose-6-phosphate --\> galactokinase. 2. Galactose-6-phosphate then attains a uridyl group from uridine diphosphate glucose (UDP-glucose) --\> Enzyme: galactose 1-phosphate uridyl transferase. Products: UDP-galactose and glucose 1-phosphate 3. Enzyme UDP-Galactose-4-epimerase --\> galactose moiety of UDP-galactose is then epimerized to glucose 4. Finally, glucose 1-phosphate, formed from galactose, is isomerized to glucose 6-phosphate by phosphoglucomutase.

Answer 75

The glycolytic pathway has a dual role: it degrades glucose to generate ATP and it provides building blocks for biosynthetic reactions.

Answer 76

Fuel molecules are carbon compounds that are capable of being oxidized that is, of losing electrons. The citric acid cycle includes a series of oxidation-reduction reactions that result in the oxidation of an acetyl group to two molecules of carbon dioxide. This oxidation generates high-energy electrons that will be used to power the synthesis of ATP. Note --\> The citric acid cycle doesn't produce a lot of ATP by itself --\> instead removes electrons from acetyl CoA and uses these electrons to reduce NAD⁺ and FAD to form NADH and FADH_2.

Answer 77

Pyruvate is oxidatively decarboxylated by the pyruvate dehydrogenase complex to form acetyl CoA. Pyruvate + CoA + NAD⁺ --\> acetyl CoA + CO₂ + NADH + H₂ The pyruvate dehydrogenase complex is a large, highly integrated complex of three distinct enzymes.

Answer 78

Condensation of a four-carbon unit, oxaloacetate, and a two-carbon unit, the acetyl group of acetyl CoA. Oxaloacetate reacts with acetyl CoA and H₂O to yield citrate and CoA. The first step is an aldol reaction (produces citryl CoA --\> energy-rich due to thioester bond) which is followed by a hydrolysis reaction (driving reaction --\> pushes reaction forward) --\> both catalyzed by citrate synthase.

Answer 79

Because citrate synthase catalyses the first reaction that initiates the citric acid cycle it is important that side reactions (hydrolysis of acetyl CoA to acetate and CoA) be minimized. Citrate synthase exhibits sequential, ordered kinetics: oxaloacetate binds first, followed by acetyl CoA. The reason for the ordered binding is that oxaloacetate induces a major structural rearrangement leading to the creation of a binding site for acetyl CoA --\> catalyzes condensation reaction. Newly formed citryl CoA induces additional structural changes in the enzyme, causing the active site to become completely enclosed. Hence, how is waste hydrolysis prevented? How does it distinguish between acetyl-CoA and Citryl CoA. - Acetyl CoA can only bind when OAA is bonded - residues crucial for hydrolysis are only properly aligned until Citryl CoA is present.

Answer 80

Hydroxyl group is not properly situated for oxidative decarboxylation in the next step --\> citrate has to undergo isomerization. Isomerization of citrate is accomplished by a dehydration step followed by a hydration step. The result is an interchange of an H⁺ and an OH^_. The enzyme catalyzing both steps is called aconitase because cis-aconitate is an intermediate.

Answer 81

Oxidative decarboxylation First of four oxidation-reduction reactions in the citric acid cycle. The oxidative decarboxylation of isocitrate is catalyzed by isocitrate dehydrogenase. 1. Oxidation --\> Isocitrate to Oxalosuccinate 2. Decarboxylation --\> Oxalosuccinate to alpha-ketoglutarate The intermediate in this reaction is oxalosuccinate, an unstable beta-ketoacid. While bound to the enzyme, it loses CO₂ to form alpha-ketoglutarate. Produces first high-transfer-potential electron carrier --\> NADH.

Answer 82

Oxidative decarboxylation reaction, the formation of succinyl CoA from alpha-ketoglutarate. Catalyzed by the a-ketoglutarate dehydrogenase complex --\> an organized assembly of three kinds of enzymes

Answer 83

Cleavage reaction of the thioester bond --\> removes CoA Coupled with the phosphorylation of a purine nucleoside diphosphate, usually ADP. This reaction, which is readily reversible, is catalyzed by succinyl CoA synthetase (succinate thiokinase). Note --\> ADP or GDP can be used for the phosphorylation Depends on the needs of the cells/tissue --\> large amounts of cellular respiration, (skeletal and heart muscle) the ADP-requiring isozyme predominates. In tissues that perform many anabolic reactions, such as the liver, the GDP-requiring enzyme is common. Note --\> nucleoside diphosphokinase enzyme can be used to interconvert between GTP and ATP.

Answer 84

Succinate is oxidized to fumarate by succinate dehydrogenase. The hydrogen acceptor is FAD rather than NAD⁺. FAD is the hydrogen acceptor in this reaction because the free-energy change is insufficient to reduce NAD⁺ .

Answer 85

Hydration of fumarate to form L-malate. Fumarase catalyzes a stereospecific trans addition of H⁺ and OH^_ . The OH group adds to only one side of the double bond of fumarate; hence, only the L isomer of malate is formed.

Answer 86

Malate is oxidized to form oxaloacetate This reaction is catalyzed by malate dehydrogenase and NAD⁺ is again the hydrogen acceptor. The standard free energy for this reaction, unlike that for the other steps in the citric acid cycle, is significantly positive (+29.7 KJ mol^-1) --\> oxidation of malate is driven by the use of the products—oxaloacetate by citrate synthase and NADH by the electron transport chain.

Answer 87

Isotope-labeling studies have revealed that the two carbon atoms that enter each cycle are not the ones that leave. The two carbon atoms that enter the cycle as the acetyl group are retained during the initial two decarboxylation reactions and then remain incorporated in the four-carbon acids of the cycle. The two carbons that enter the cycle as the acetyl the group will be released as CO₂ in subsequent trips through the cycle.

Answer 88

The evidence is accumulating that the enzymes of the citric acid cycle are physically associated with one another. The close arrangement of enzymes enhances the efficiency of the citric acid cycle because a reaction product can pass directly from one active site to the next through connecting channels, a process called substrate channelling.

Answer 89

Pyruvate dehydrogenase converts pyruvate into acetyl CoA - This is an irreversible step --\> can't get pyruvate from acetyl CoA. 1. High concentration of products --\> decreases the reaction rate --\> Acetyl CoA + NADH --\> informs the enzyme that the energy needs of the cell have been met or that FAs are being degraded to produce energy --\> prevents wasting glucose. 2. Phosphorylation of pyruvate dehydrogenase by pyruvate dehydrogenase kinase (PDK) switches off the activity of the complex --\> this is revered (switching complex back on) --\> dehydrogenase phosphatase (PDP) Summary --\> Muscle cells At rest --\> High NADH/Acetyl CoA/ATP --\> decreases reaction rate + phosphorylation switches of complex. (visa-versa)

Answer 90

The first control site is isocitrate dehydrogenase. The enzyme is allosterically stimulated by ADP, which enhances the enzyme’s affinity for substrates. In contrast, ATP is inhibitory. The reaction product NADH also inhibits isocitrate dehydrogenase by directly displacing NAD⁺ .

Answer 91

A second control site in the citric acid cycle is alpha-ketoglutarate dehydrogenase, which catalyzes the rate-limiting step in the citric acid cycle. Alpha-Ketoglutarate dehydrogenase is inhibited by succinyl CoA and NADH, the products of the reaction that it catalyzes. In addition, alpha-ketoglutarate dehydrogenase is inhibited by a high energy charge. Thus, the rate of the cycle is reduced when the cell has a high level of ATP

Answer 92

The **outer membrane** is quite permeable to most small molecules and ions because it contains mitochondrial porin --\> voltage-dependent anion channel (VDAC) --\> controls flux of metabolites --\> usually anionic species such as phosphate, chloride, organic anions, and the adenine nucleotides. The **inner membrane** --\> impermeable to nearly all ions and polar molecules --\> large family of transporters shuttles metabolites such as ATP, pyruvate, and citrate across the inner mitochondrial membrane.

Answer 93

Complex I --\> NADH-Q oxidoreductase Complex II --\> succinate-Q reductase Complex III --\> Q-cytochrome C oxidoreductase Complex IV --\> Cytochrome C oxidase

Answer 94

Coenzyme Q or ubiquinone Ubiquinone is a hydrophobic quinone that diffuses rapidly within the inner mitochondrial membrane --\> it carriers electrons from complex I to complex III by reduced Q. FADH₂ gets oxidized at complex II --\> electrons get passed to Q which then transfers them to complex III. Ubiquinone is soluble in the membrane, a pool of Q and QH₂ , the Q pool, is thought to exist in the inner mitochondrial membrane --\> however recent research has shown that Q pool is confined to the respirasome (supercomplex containing all the complexes)

Answer 95

Coenzyme Q is a quinone derivative with a long tail consisting of five carbon isoprene units that account for its hydrophobic nature --\> number of isoprene units differs on the species --\> mammalian form contains 10 isoprene units (coenzyme Q₁₀) It may exist in several oxidation states. - Fully oxidized --\> two keto groups - Oxidation of one electron and one proton --\> semiquinone (QH) - Semiquinone can lose a proton to form a semiquinone radical anion (Q^.-) - Fully reduced state --\> 2 e^-and 2 H⁺ --\> ubiquinol (QH₂)

Answer 96

The second special electron carrier is a protein. Cytochrome c, a small soluble protein, shuttles electrons from Complex III to Complex IV.

Answer 97

Iron–sulfur clusters or iron–sulfur proteins (also called nonheme iron proteins) play a critical role in a wide range of reduction reactions in biological systems. Several different types are known: 1. Single iron ion is tetrahedrally coordinated to the sulfhydryl groups of four cysteine residues of the protein. 2. Second kind, denoted by 2Fe-2S, contains two iron ions, two inorganic sulfides, and usually four cysteine residues. 3. Third type, designated 4Fe-4S, contains four iron ions, four inorganic sulfides, and four cysteine residues

Answer 98

Contains both 2Fe-2S and 4Fe-4S clusters. Iron ions in these Fe-S complexes cycle between Fe²⁺ (reduced) and Fe³⁺ (oxidized) states.

Answer 99

1. Binding of NADH --\> transfer of its two high potential electrons to the flavin mononucleotide (FMN) prosthetic group --\> creates reduced form FMNH₂ . Note --\> The electron acceptor of FMN, the isoalloxazine ring, is identical with that of FAD. 2. Electrons are then transferred from FMNH₂ to a series of iron–sulfur clusters the second type of prosthetic group in complex I. ] 3. Eventually, these electrons get used to reduce Coenzyme Q --\> QH₂ .

Answer 100

Protein is L-shaped --\> region sticking out into the matrix (hydrophilic) and an inner-membrane region (hydrophobic) **Membrane region** Has four proton half-channels consisting, in part, of vertical helices --\> One set of half channels are on the matrix side whereas the others are on the inner membrane space side. The Vertical helices on the matrix side are linked by a long horizontal helix --\> connects the matrix half channels. The cytoplasmic half-channels are joined by a series of beta-hair-pin-helix connecting elements (BH). An enclosed Q-chamber --\> site where Q accepts electrons exists between the junction of the hydrophilic and hydrophobic region of the protein Finally, a hydrophilic A.A. funnel connects the Q chamber to a water-lined channel (into which the half channels open) that extends the entire length of the membrane-embedded portion.

Answer 101

1. When Q accepts two electrons from NADH, generating Q^2-. 2. Negative charges on Q^2- interact electrostatically with negatively-charged amino acid residues in the membrane-embedded arm, causing conformational changes in the long horizontal helix and the BH elements. 3. Changes in conformation of the vertical helices --\> which changes the pKa of the amino acids. 4. This allows protons to bind to the amino acids --\> and then dissociate into the water-lined channel and finally enter the intermembrane space. Hence --\> flow of two electrons from NADH to NAD⁺ --\> pumps four protons into the inner-membrane space (proton motive force) + reduced Q^2- accepts two protons to form QH₂ --\> leaves protein complex so that more Q molecules can bind.

Answer 102

FADH₂ enters the electron-transport chain at the second protein complex (integral membrane protein) of the chain. In citric acid cycle --\> oxidation of succinate to fumarate by succinate dehydrogenase --\> produces FADH₂ Succinate dehydrogenase is also part of complex II. 1. Electrons from FADH₂ are transferred to Irons-sulfur centres. 2. Subsequently, they are passed on to Q to form QH_2. Note --\> no protons pumped --\> so more ATP is produced from NADH oxidation.

Answer 103

Electrons from QH₂ are passed on to complex III --\> flow of electrons through this complex leads to the transport of 2H⁺ --\> due smaller thermodynamic driving force. Contains two types of cytochromes --\> b and c₁ . Note --\> cytochrome is an electron-transferring protein that contains a heme prosthetic group. The two types of cytochromes contain a total of three heme groups: - two hemes with cytochrome b --\> b_L(low affinity) and b_H (high affinity) - one heme group with cytochrome c_1. These identical heme groups have different affinities due to the different polypeptide environments that they are found in. The protein also has a Iron-sulfur center (2Fe-2S) which is coordinated by two histidine rather than cysteine residues --\> stabilizes the center and increases its reduction potential --\> so that it can readily be reduced by QH₂

Answer 104

QH₂ passes two electrons to complex III but it only can accept one. Overall --\> Two QH₂ molecules bind to the complex consecutively, each giving up two electrons and two H₂--\> These Protons are released on the cytoplasmic side of the membrane. 1. First QH₂ binds to first Q binding site (Q_o) --\> releases it electrons which travel through the compelx to different destinations. - One electron --\> 2Fe-2S cluster --\> cytochrome c₁ --\> then to Cytochrome C turning it into its reduced form. --\> free to diffuse to complex IV. - The second electron passes through two heme groups (low to high affinity) --\> used to reduce oxidized ubiquinone in second binding site to form semiquinone radical anion. 2. Now fully oxidized Q in first binding site leaves to enter Q pool. 3. A second molecule of QH₂ binds to the Q_oof complex III and reacts in the same way as the first --\> one e^-to Cyto C whereas, the other is used to reduce Q radical to an anion (second binding site). 4. On addition of the second electron, the anion takes up two protons from the matrix side --\> The removal of these two protons from the matrix contributes to the formation of the proton gradient As a whole --\> Four protons are released on the cytoplasmic side, and two protons are removed from the mitochondrial matrix.

Answer 105

In one Q cycle, two QH₂ molecules are oxidized to form two Q molecules, and then one Q molecule is reduced to QH₂ . The problem of how to efficiently funnel electrons from a two-electron carrier (QH₂) to a one-electron carrier (cytochrome c) is solved by the Q cycle. The cytochrome b component of the reductase is, in essence, a recycling device that enables both electrons of QH₂ to be used effectively.

Answer 106

Last of the three proton-pumping assemblies of the respiratory chain --\> catalyzes the transfer of electrons from the reduced form of cytochrome c to molecular oxygen. The complex consists of 13 subunits --\> it also has two heme A groups and three copper ions (arranged in two copper centers)

Answer 107

An electron flows from cytochrome c to CuA/CuA, to heme a, to heme a3, to CuB, and finally to O₂ Heme a3 and CuB are directly adjacent. Together, heme a3 and CuB form the active centre at which O₂is reduced to H₂O.

Answer 108

1. 2 Cytochrome C is oxidized and releases two electrons --\> they flow down an electron-transfer pathway within cytochrome c oxidase, one stopping at CuB and the other at heme a₃ . 2. Both centres are in the reduced state so they can now bind to an oxygen molecule. 3. When it binds the O₂ obtains the 2 electrons from the centres in order to form a peroxide bridge between CuB and Heme a₃ . 4. Two more molecules of cytochrome C are oxidised and the released electrons travel to the active center. 5. Addition of two electrons plus 2 H⁺ is used to reduce the oxygens to -OH (forms CuB²⁺-OH and Fe³⁺-OH). 6. Reaction with two more H⁺ ions allows the release of two molecules of H₂O and resets the enzyme to its initial, fully oxidized form. Note --\> the four protons come from the matrix --\> directly contribute to proton gradient. Also note that during this entire process the complex transports another 4 protons into the inner-membrane space --\> total of 8 protons removed from matrix --\> mechanism not clear.

Answer 109

4 electrons are needed for this reduction which equates to four molecules of cytochrome c.

Answer 110

Partial reduction generates hazardous compounds. In particular, the transfer of a single electron to O₂ forms superoxide ion, whereas the transfer of two electrons yields peroxide. Prevented by... the catalyst does not release partly reduced intermediates. Cytochrome c oxidase meets this crucial criterion by holding O₂ tightly between Fe and Cu ions.

Answer 111

Superoxide dismutase --\> This enzyme scavenges superoxide radicals by catalyzing the conversion of two of these radicals into hydrogen peroxide and molecular oxygen. The hydrogen peroxide formed by superoxide dismutase and by other processes is scavenged by catalase, a ubiquitous heme protein that catalyzes the dismutation of hydrogen peroxide into water and molecular oxygen.

Answer 112

Proton motive force (Δp) = Chemical gradient (ΔpH) + charge gradient (ΔΨ)

Answer 113

Can be described as a ball on a stick. Stick = F₀ subunit --\> inner mitochondrial membrane Ball = F₁ subunit --\> produdes into matrix --\> catalytic activity of ATPase. **F₁ subunit --\>** hydrophilic segment Five types of polypeptide chains (α₃ , β_3,γ, δ, ε) with the indicated stoichiometry α and β subunit make up the bulk of the subunit --\> form hexameric ring --\> arranged alternately --\> homologous to each other --\> Both bind nucleotides but only the β subunits are catalytically active. Below the α and β subunits is a central stalk consisting of the γ and ε proteins --\> γ long helical coiled coil that extend into the center of the hexamer --\> γ breaks the symmetry of the α and β subunits --\> forms different interactions --\> different conformation. **F₀subunit --\> hydrophobic** F₀contains the proton channel of the complex Channel --\> a ring comprising from 8 to 14 c subunits that are embedded in the membrane. A single a subunit binds to the outside of the ring. **General** The F₀ and F₁subunits are connected in two ways: by the central stalk and by an exterior column. The exterior column consists of one a subunit, two b subunits, and the ε subunit.

Answer 114

ATP synthases associate with one another to form dimers, which then associate to form large oligomers of dimers. This association stabilizes the individual enzymes to the rotational forces required for catalysis and facilitates the curvature of the inner mitochondrial membrane.

Answer 115

ADP^3-+ HPO₄^2- + H⁺ \<---\> ATP^4- + H₂O Terminal oxygen atom of ADP attacks the Pi --\> forms a pentacovalent intermediate --\> dissociates to form ATP and H₂O.

Answer 116

The role of the proton gradient is not to form ATP but to release it from the synthase.

Answer 117

Since there are 3 Beta subunits --\> Beta subunits are the only sites that are catalytically active --\> Hence, there are three active sites on the enzyme, each performing one of three different functions at any instant. At any one moment... Loose active site --\> This conformation ADP + Pi bind (note --\> can not release once bound) Tight active site --\> Bind to ATP with high avidity --\> it converts ADP + Pi into ATP. (note --\> can not release once bound) Open active site --\> has a more open conformation and can bind or release adenine nucleotides. Note --\> rotation of the γ subunit by 120 degrees --\> changes the conformation of the Beta subunits --\> thus also changing their function (L, T or O).

Answer 118

(1) the moving unit, or rotor, consists of the c ring and the stalk (Gamma, epsilon subunits) (2) The stationary unit, or stator, is composed of the remainder of the molecule.

Answer 119

General steps are (1) ADP and Pi bind (2) ATP synthesis (3) ATP release. Basically... 1. ADP + Pi bind to the O- form site 2. The stalk rotates by 120 degrees which converts the O site into an L site --\> traps the substrates --\> can't leave. 3. Another rotation converts it into the T site --\> catalyzes the conversion into ATP. 4. One more rotation converts it back into the O form which allows the ATP to be released.

Answer 120

Stationary a subunit is located next to the ring consisting of 8-14 subunits. **A subunit** - a subunit contains two hydrophilic half-channels that do NOT span the membrane --\> protons can move into either of these channels but they are unable to pass the membrane. - a subunit is positioned so that each half channel can interact with one c subunit in the ring structure. **C subunits** - Structure of c subunit --\> each polypeptide forms a pair of alpha-helices that span the membrane --\> glutamic acid is found in the middle of the polypeptide. - When glutamate is charged --\> not protonated --\> it will not move into the membrane. - Key to proton movement --\> Proton-rich environment --\> cytoplasmic side (Inner membrane space) --\> proton will enter and bind to glutamate. BUT in the proton-poor environment --\> matrix side --\> the half-channel releases a proton.

Answer 121

1. The cytoplasmic half channel is deprotonated. 2. Proton from the Intermembrane space enters the half channel and protonates the glutamate residue. 3. The ring structure rotates clockwise --\> movement of protons through the half channels from the high proton concentration of the cytoplasm to the low proton concentration of the matrix powers the rotation of the c ring. Note --\> a subunit remains stationary throughout the entire process. 4. The protonated glutamic acid residue is now in the matrix half-channel. 5. Glutamic acid gets deprotonated --\> releases H⁺ into the matrix.

Answer 122

C ring is tightly linked to the subunits in the stalk --\> hence as the c ring turns --\> the stalk rotates as well --\> allows ATP synthesis through the binding-change mechanism (allows the process to continue --\> otherwise no ATP will be released or no new ADP + Pi will bind). Note --\> the two b chains on the exterior are used to prevent the hexamer ring rotating in sympathy with the c ring structure.

Answer 123

Range from 8-14 --\> changes between species. This number is significant because it determines the number of protons that must be transported to generate a molecule of ATP. i.e. 8 subunits --\> 8 protons for 360 degree turn --\> each turn produces 3 ATP molecules. If you had 14 subunits --\> 14 protons for a full turn --\> less efficient. Vertebrates have 8 subunits --\> most efficient.

Answer 124

Electrons from NADH pump enough protons to generate 2.5 molecules of ATP, whereas those from FADH₂ yield 1.5 molecules of ATP.

Answer 125

The inner mitochondrial membrane is impermeable to NAD⁺ and NADH. Solution --\> transport electrons from NADH not NADH itself --\> Glycerate 3-phosphate shuttle. 1. Transfer of a pair of electrons from NADH to dihydroxyacetone phosphate --\> to form glycerol 3-phosphate --\> catalyzed by a glycerol 3-phosphate dehydrogenase in cytoplasm 2. Glycerol 3-phosphate dehydrogenase moves into the inner-membrane space of the mitochondria. 3. Reoxidized back to dihydroxyacetone phosphate --\> catalyzed by an enzyme that is on the surface of the inner mitochondrial membrane (glycerol 3-phosphate dehydrogenase). 4. Electron pair from glycerol-3-phosphate is transferred to a FAD prosthetic group on the enzyme -\> converted to FADH₂. 5. Electrons then used to reduce Q to form QH₂ . Note --\> 1.5 ATP is produced rather than the expected 2.5 from NADH because FAD is the electron acceptor. This method of electron transfer is predominant in muscles --\> allows the cell to maintain high levels of oxidative phosphorylation.

Answer 126

About 30 molecules of ATP are formed when glucose is completely oxidized to CO₂ . The calculation showed below.

Answer 127

When ADP concentration rises, as would be the case in active muscle, the rate of oxidative phosphorylation increases to meet the ATP needs of the muscle. The regulation of the rate of oxidative phosphorylation by the ADP level is called respiratory control or acceptor control. The rate of oxygen consumption by mitochondria increases markedly when ADP is added and then returns to its initial value when the added ADP has been converted into ATP.

Answer 128

1. At low concentrations of ADP, as in a resting muscle, NADH and FADH₂ are not consumed by the electron-transport chain. The citric acid cycle slows because there is less NAD⁺ and FAD to feed the cycle. 2. As the ADP level rises and oxidative phosphorylation speeds up, NADH and FADH₂ are oxidized, and the citric acid cycle becomes more active --\> more NAD⁺andFAD to feed into the cycle.

Answer 129

Inhibitory factor 1 (IF1), specifically inhibits the potential hydrolytic activity of the F₀F₁ of ATPase. Scenario --\> tissue deprived of oxygen - This will stop the electron transport chain/generation of proton motive force --\> there is no terminal electron acceptor - Consequently --\> ATPase will hydrolyze ATP instead ---\> role of IF1 is to prevent the wasteful hydrolysis of ATP.

Topic 6 - Bioenergetics Flashcards

(158 cards)