Biochem #10 Flashcards by Stone Streeter

where does the citric acid cycle occur?

mitochondria

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what is the result of the citric acid cycle going all the way through?

3 NADH, 1 FADH2, 1 GTP (ATP), and 2 CO2

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pyruvate dehydrogenase is a ____

complex

o Pyruvate dehydrogenase complex: converts pyruvate to acetyl-CoA in mitochondria.
 Irreversible
 Pyruvate (3 Carbon) to Carbon dioxide (1 C) and acetyl-CoA (2 C)
 5 enzymes that make up the complex including 3 that function and 2 that regulate.
 Involves conversion of NAD+ to NADH
 Thioester bond is formed, which is a high-energy bond that can be used to drive other reactions forward.
 Enzymes involved in catalysis:
• 1. Pyruvate dehydrogenase (PDH): pyruvate is oxidized, yielding CO2. TPP binds covalently to remaining 2-carbon molecule producing acyl-TPP
• 2. Dihydrolipoyl transacetylase: acyl-TPP is oxidized, transferred to lipoic acid. Converted to acetyl group, then catalyzes the transfer of an acetyl group to form acetyl-CoA.
• 3. Dihydrolipoy dehydrogenase: FAD used as a coenzyme to reoxidize lipoic acid to be used In future reactions.

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how do you get acetyl-CoA from pathways other than glycolysis?

 1. Fatty Acid oxidation (Beta-oxidation):
• Activation: in the cytosol, causes a thioester bond to be formed between carboxyl groups of fatty acids and CoA-SH  fatty acyl-CoA
• Fatty acyl-CoA converted to carnitine to cross the inner mitochondrial membrane.
• Acyl-carnitine crosses, transfer of fatty acyl group to mitochondrial CoA-SH.
• Acyl-CoA is formed and then converted to acetyl-CoA via Beta oxidation.
 2. Amino Acid Catabolism:
• Certain amino acids can be used to form acetyl-CoA.
• Converted to ketone bodies and then to acetyl-CoA
 3. Ketones:
• Although acetyl-CoA is typically used to produce ketones when the pyruvate dehydrogenase complex is inhibited, the reverse reaction can occur as well.
 4. Alcohol:
• Alcohol dehydrogenase and acetaldehyde dehydrogenase convert alcohol to acetyl-CoA when it is consumed in moderate amounts.
• Buildup of NADH so this acetyl-CoA is used to synthesize fatty acids.

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steps of the citric acid cycle

o Step 1: Citrate Formation
 Acetyl-CoA and OAA combine in a reaction catalyzed by citrate synthase.
 Condensation reaction (water lost)
o Step 2: Citrate Isomerized to Isocitrate
 Citrate is isomerized via aconitase.
 Water produced and then it is used
 Switch hydrogen and a hydroxyl group.
o Step 3: alpha-ketoglutarate and CO2 Formation
 Involves isocitrate dehydrogenase, the RATE LIMITING STEP OF THE CYCLE
 Requires NAD+ and produces CO2 and NADH
o Step 4: Succinyl-CoA and CO2 Formation
 Involves the alpha-ketoglutarate dehydrogenase complex
 Requires NAD+ and produces CO2 and NADH
o Step 5: Succinate Formation
 Catalyzed by succinyl-CoA synthetase
 Production of GTP, GTP is then converted to ATP.
• GDP  GTP is driven by the energy released by thioester hydrolysis.
o Step 6: Fumarate Formation
 This step occurs on the inner membrane.
 Catalyzed by succinate dehydrogenase.
• Flavoprotein: covalently bonded to FAD, the electron acceptor in this reaction.
• The enzyme is an integral protein on the inner mitochondrial membrane.
• As succinate is oxidized to fumarate, FAD is reduced to FADH2, passes its electrons to the electron transport chain.
o Step 7: Malate Formation
 Fumarase is the enzyme
 L-malate forms in this reaction.
o Step 8: Oxaloacetate Formed Anew
 Malate dehydrogenase catalyzes the oxidation to OAA.
 NAD+ reduced to NADH

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what is the rate determining step of the citric acid cycle?

o Step 3: alpha-ketoglutarate and CO2 Formation
 Involves isocitrate dehydrogenase, the RATE LIMITING STEP OF THE CYCLE
 Requires NAD+ and produces CO2 and NADH

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specialty of succinate dehydrogenase

o Step 6: Fumarate Formation
 This step occurs on the inner membrane.
 Catalyzed by succinate dehydrogenase.
• Flavoprotein: covalently bonded to FAD, the electron acceptor in this reaction.
• The enzyme is an integral protein on the inner mitochondrial membrane.
• As succinate is oxidized to fumarate, FAD is reduced to FADH2, passes its electrons to the electron transport chain.

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how many ATP per 1 NADH

2.5

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How many ATP per 1 FADH2

1.5

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how many ATP per citric acid cycle?

from pyruvate through: 12.5 ATP

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what will have negative feedback on the citric acid cycle?

o Products of the citric acid cycle such as ATP and NADH and FADH2 will have negative feedback effects on it (and the enzymes involved).

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pyruvate dehydrogenase kinase

phosphorylates PDH and inhibits it.

• During high ATP, prevent the citric acid cycle

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pyruvate dehydrogenase phosphatase

dephosphorylates and reactivates.

• During high ADP.

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what are the control points of the citric acid cycle?

o 1. Citrate synthase:
 ATP and NADH function as allosteric inhibitors of citrate synthase.
 Succinyl-CoA and citrate also allosterically inhibit citrate synthase.
o 2. Isocitrate dehydrogenase:
 ATP and NADH
 ADP and NAD+ are allosteric activators
o 3. Alpha-ketoglutarate dehydrogenase complex
 Succinyl-CoA and NADH are inhibitors
 ATP is inhibitor
 Stimulated by ADP and calcium ions.

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what generates ATP in the electron transport chain?

flow of hydrogens (built up using electrons though)

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oxidation and reduction in electron transport chain

o Reduction potential and oxidation and reduction reactions fuel the electron transport chain.

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overview of complex I

4 H+ are pumped to the intermembrane space
 The transfer of electrons from NADH to coenzyme Q (COQ).

NADH

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overview of complex II

No hydrogen pumping occurs here

 Receives electrons from succinate which interacts with FAD that is covalently bonded to Complex II (succinate dehydrogenase is also part of complex II)

FADH2

FAD and succinate dehydrogenase are part of the complex

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overview of complex III

4 H+ are pumped to the intermembrane space

 Transfer of electrons from Coenzyme Q to cytochrome c.

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overview of complex IV

2 H+ are moved across the membrane

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how many cytochrome C are required for complete reduction of oxygen?

4 (comes from 2 reduced CoQ) or 2 NADH/2FADH2

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proton motive force

o As H+ increases in the intermembrane space, the pH drops and the voltage difference between the intermembrane space and matrix increases due to proton pumping.
 Form electrochemical gradient: a gradient that has both chemical and electrostatic properties.
• This gradient stores energy and is harnessed by ATP synthase to make ATP from ADP + P.

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electrochemical gradient

a gradient that has both chemical and electrostatic properties.
• This gradient stores energy and is harnessed by ATP synthase to make ATP from ADP + P.

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NADH shuttles

o ATP production is 30-32 because it varies due to NADH produced by glycolysis not being able to directly cross into the mitochondrial matrix.
o Shuttle mechanism: transfers the high energy electrons of NADH to a carrier that can cross the inner mitochondrial membrane.
 Depending on the shuttle mechanism, either 1.5 or 2.5 ATP are produced.
 1. Glycerol 3-phosphate shuttle: mitochondrial FAD located on the outer face of the inner mitochondrial membrane and is reduced, then gives its electrons to Complex II.
• Generates 1.5 ATP
 2. Malate-aspartate shuttle: cytosolic oxaloacetate is reduced to malate, involving the oxidation of cytosolic NADH to NAD+. Once malate crosses the inner mitochondrial membrane into the matrix, the reverse reaction occurs and mitochondrial NADH is formed. NADH can then pass along its electrons to complex I
• Generates 2.5 ATP.

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where is ATP synthase located?

• ATP synthase spans the entire inner mitochondrial membrane and protrudes into the matrix.

what is chemisomotic coupling

o F0: serves as an ion channel in which protons travel through it along the gradient back into the matrix.  As this flow occurs, chemiosmotic coupling allows the chemical energy of the gradient to be harnessed as a means of phosphorylating ADP, forming ATP. o F1: utilizes the energy released from the electrochemical gradient to phosphorylate ADP to ATP.

conformational coupling

another idea of how ATP synthase works o The relationship between the proton gradient and ATP synthesis is indirect. o ATP is released by the synthase as a result of conformational change caused by the gradient.

oxidative phosphorylation in low O2 environment

o If O2 is limited, the rate of oxidative phosphorylation decreases, and the concentrations of NADH and FADH2 increase.  Increased NADH inhibits the citric acid cycle (presence of limited O2).

oxidative phosphorylation in high O2 environment

o In the presence of adequate oxygen, the rate of oxidative phosphorylation is dependent on the availability of ADP. o Increased NADH and FADH2 increase the rate of electron transport and ATP synthesis.

what are other names for the citric acid cycle?

krebs cycle, tricarboxylic acid cycle (TCA)

where is the pyruvate dehydrogenase complex located?

mitochondrial matrix

how do the number of carbons change going from pyruvate to acetyl-CoA

3 to 2 | CO2 is also produced

what are the 5 enzymes involved in the pyruvate dehydrogenase complex

``` pyruvate dehydrogenase dihydrolipoyl transacetylase dihydrolipoyl dehydrogenase pyruvate dehydrogenase kinase pyruvate dehydrogenase phosphatase ```

pyruvate dehydrogenase

oxidizes pyruvate which yields CO2

dihydrolipoyl transacetylase

utilizes lipoic acid to produce acetyl CoA

dihydrolipoyl dehydrogenase

reforms the lipoic acid to be used in future reactions | reduces FAD to FADH2. Later, this allows NAD to be reduced to NADH

pyruvate dehydrogenase kinase vs. pyruvate dehydrogenase phosphatase

kinase inactivates the enzyme | phosphate activates it

fatty acid oxidation activation reaction

causes a thioester bond to form between fatty acid and CoA

where does beta oxidation occur?

mitochondria

how does fatty acid get into the mitochondria?

addition of CoA, replace with carnitine, carnitine shuttle, replace with CoA

how do amino acids become acetyl-CoA

deamination converts them to ketone bodies then converted to acetyl-CoA

how does alcohol factor into acetyl-CoA

it can be converted to acetyl-CoA by alcohol dehydrogenase and acetaldehyde dehydrogenase. This reaction is accompanied with NADH buildup, inhibits Krebs cycle, so acetyl coA made this way is usually used to synthesize fatty acids

what is the overall reaction of pyruvate dehydrogenase complex

pyruvate + CoA-SH + NAD+ ==> NADH + CO2 + H+ + acetyl-CoA

what are the 5 ways acetyl-CoA can be produced?

``` reverse of ketone bodies from pyruvate from alcohol from amino acids from fatty acids ```

will the citric acid cycle occur anaerobically?

even though it does not use oxygen, no | NADH and FADH2 build up which inhibits the cycle.

Mnemonic for citric acid cycle substrates

``` Can I Asl Something Special For My Oranges ```

what is involved in the reaction from acetyl-CoA to citrate

condensation and hydrolysis reaction involving acetyl-CoA, oxaloacetate, and citrate synthesis

what type of reaction forms isocitrate from citrate?

isomerization

what is the rate limiting enzyme for the citric acid cycle?

isocitrate dehydrogenase

what is common about dehydrogenase enzymes?

they transfer a H- ion to an electron acceptor (so look for high energy electron carrier being formed when this enzyme is involved)

synthetase vs. synthase

synthetase creates no covalent bonds with energy input

the hydrolysis of thioester bonds results in _____

a significant release in energy

where does fumarate formation occur?

occurs on the inner mitochondrial membrane

what enzyme in the citric acid cycle is considered a flavoprotein?

succinate dehydrogenase

flavoprotein

covalently bonded to FAD

as succinate is oxidized to fumarate, FAD is ____

reduced to FADH2

how many ATP produced from one molecule of glucose in the citric acid cycle (including pyruvate to acetyl-CoA)

how much ATP produced including all glycolysis and citric acid cycle?

30-32 depending on efficiency of the cell

what inhibits pyruvate dehydrogenase

lots of fats (fatty acid oxidation producing acetyl-CoA), ATP, NADH

what are the 3 main control points of the citric acid cycle?

citrate synthase isocitrate dehydrogenase alpha ketoglutarate dehydrogenase all inhibited by NADH, ATP, and their products activated by NAD+, ADP

what kind of ions is the alpha ketoglutarate complex activated by?

calcium

why is the production of CO2 important in the citric acid cycle

CO2 is so oxidized it allows the electrons carriers in the chain to be reduced

is it the flow of electrons or the proton gradient that produces ATP?

proton gradient

where are hydrogens moved during the electron transport chain?

from the mitochondrial matrix to the intermembrane space

what physical property determines the flow of electrons in the electron transport chain?

reduction potential

what is another name for coenzyme Q?

ubiquinone

In complex I, what are the intermediates that carry the electrons from NADH to CoQ?

FMN and Fe-S subunit

where does complex II originally get its electrons from (most original)

succinate

what is the Q cycle?

electrons travel from CoQH2 to cytochrome c

what makes CoQ and cytochrome c so special in their roles in the ETC?

they are able to carry electrons and are able to move freely in the inner mitochondrial membrane

explain the electrochemical gradient established by the ETC?

chemical: increased concentration of H+ ions in the intermembrane space electrical: more + charge in the intermembrane space results in greater voltage difference

can NADH directly cross the into the mitochondrial matrix?

how is the number of ATP generated from cytosolic NADH differ?

depends on the shuttle process: glycerol-3-phosphate shuttle: 1.5 malate-aspartate shuttle: 2.5

___ potentials increase along the ETC

reduction

what type of NADH shuttle does the heart use?

malate-aspartate because it is a highly aerobic system

are all polypeptides required for oxidative phosphorylation generated by mitochondrial DNA?

chemiosmotic coupling

allows the chemical energy of the gradient to be harnessed as a means of phosphorylating ADP and forming ATP

F0 vs. F1 in ATP synthase

F0: functions as an ion channel F1: uses the energy released from this electrochemical gradient to phosphorylate ADP to ATP.

chemiosmotic coupling vs. conformational coupling

chemi: direct conformational: indirect (conformational change occurs in between proton gradient and ATP production)

what are the key regulators of oxidative phosphorylation?

O2 and ADP

respiratory control

coordinated regulation of oxidative phosphorylation and the citric acid cycle.

what does decreased oxygen result in (with respect to oxidative phosphorylation and the citric acid cycle)?

decreased ox phosph, increased NADH and FADH2, decreased citric acid cycle

what type of bond does acetyl-CoA contain?

high-energy thioester bond

does thioester cleavage or ester cleavage release more energy?

thioester cleavage

what happens when uncoupling occurs or there is a leak in the inner mitochondrial membrane?

glycogen stores depleted, more O2 is used (trying to regenerate the gradient)

how many cytochrome c reduced required for a full water molecule to be reduced?