chapter 8

Question 1

what is the citric acid cycle/Krebs cycle or tricarboxylix acid (TCA cycle)?

Answer 1

• major step in aerobic metabolism
  
  • the next step after glycolysis for glucose
  • crossroads of various metabolic pathways
  • does generate some ATP directly (through GTP) but its main value is that it generates several electron-carrying molecules that are fed into the electron transport chain to generate realtvely huge amounts of ATP

Question 2

in eukaroytes where does the citric acid take place and where does it take plays in prokaryotes?

Answer 2

• mitochondrial matrix in eukaryotes
• cytosol in prokaryotes

Question 3

before entering the citric acid cycle, pyruvate must be converted into?

Answer 3

• acetyl-coA in the mitochondria, in a special area called the pyruvate dehydrogenase complex (PDC) and results in 1 NADH and 1 CO₂, which corressponds to the oxidative decarboxylation of pyruvate

Question 4

why is the PDC called a “complex”?

Answer 4

• it contains 3 distinct enzymes that are physically linked with eahcother (pyruvate dehydrogenase being most important, dihydrolipoyl transacetylase, and dihydrolipoyl dehydrogenase) and 5 coenzymes that are derived form vitamin B

Question 5

acetyl-coA then enters the citric acid cycle which is made from?

Answer 5

• produced via glycolysis, beta oxidation of fatty acids, and produced from amino acids

Question 6

each turn of the citric acid cycle generates?

Answer 6

• 1 GTP, 3 NADH, 1 FADH₂, and 2CO₂

Question 7

the basic idea of the citric acid cycle is that?

Answer 7

• the 2-C molecule acetyl-CoA joins with the 4-C molecule oxaloacetate to form a 6-C molecule known as citrate (the deprotonated form of citric acid)
  
  • citrate then undergoes a series of redox and decarboxylation reactions to generate the products of the citric acid cucle
  • the final product is the 4-C compound oxaloacetate, which joins acetyl-CoA to start the process again

Question 8

what is step 1 of the TCA?

Answer 8

• pyruvate dehydrogenation complex:
  
  • pyruvate is decarboxylated and CoA is added to the resulting 2-C molecule, generating acetyl-coA. this process also generates 1 NADH

Question 9

what is step 2 of the TCA?

Answer 9

• oxaloacetate (4C) + acetyl-CoA (2C) → citrate (6C)
  
  • catalyzed by citrate synthase
  • it is highly energetically favourable, and is essentially irreversible

Question 10

what is step 3 of the TCA?

Answer 10

• citrate (C6) → isocitrate (6C)
  
  • catalyzed by aconitase
  • reversible isomerization step in which a hydroxyl group gets moved around

Question 11

what is step 4 of the TCA?

Answer 11

• isocitrate (6C) → oxalosuccinate (6C) → alpha-ketoglutarate (5C)
  
  • catalyzed by isocitrate dehydrogenase
  • first time in the cycle where we lose a C; the decarboxylation of oxalosuccinate results in 1 CO₂. this also produces 1 NADH. it is rate limiting and irreversible

Question 12

what is step 5 of the TCA?

Answer 12

• alpha-ketoglutarate (5C) → succinyl-CoA (4C)
  
  • catalyzed by alpha-ketoglutarate dehydrogenase, and involves the release of 1 CO₂
  • this involes the loss of a C, produces 1 NADH and is irreversible

Question 13

what is step 6 of teh TCA?

Answer 13

• succinyl-CoA (4C) → succinate (4C)
  
  • catalyzed by succinyl-CoA synthetase and allows 1 GTP to be synthesized (GTP is functionally equivalent to ATP)

Question 14

what is step 7 of the TCA?

Answer 14

• succinate (4C) → fumarate (4C)
  
  • this redox reaction is catalyzed by succinate dehydrogenase
  • the oxidation of succinate is couples with the reduction of FAD to FADH₂

Question 15

what is step 8 of the TCA?

Answer 15

• fumarate (4C) → oxaloacetate (4C)
  
  • reversible hydration reaction catalyzed by fumarase

Question 16

what is step 9 of the TCA?

Answer 16

• malate (4C) → oxaloacetate (4C)
  
  • produces 1 NADH
  • under standard conditions, this reaction is extremely unfavourable but Le Chateliers principle comes into play because after this step is completed, the product oxaloacetate is immediately consumed in step 1 of the TCA which is very favourable so concentrations of oxaloacetate are kept very low which pushes the reaction to the right

Question 17

what is the pneumonic for the intermediates of the TCA?

Answer 17

“Can I keep selling sex for money officer?”

C - citrate

I - isocitrate

K - alpha-ketoglutarate

S- succinyl-CoA

S- succinate

F- fumarate

M- malate

O - oxaloacetate

Question 18

before the electron transport chain, how much ATP has been generated?

Answer 18

• a net of 2 ATP from glycolysis and 2 GTP- one from each of the two pyruvate molecules produced from each glucose

Question 19

where is the electron transport chain located?

Answer 19

• inner mitochondrial membrane in eukaryotes and in the cell membrane of prokaryotes that carry out aerobic respiration
  
  • its basic task is to get energy in the form of ATP form the electron carriers NADH and FADH₂, from which NAD⁺ and FAD are regenerated

Question 20

what happens in the ETC?

Answer 20

• a series of redox reactions transfers the electrons from NADH/FADH₂ to O₂ which is the final acceptor and is ultimately reduced to water
  
  • when NADH/FADH₂ are oxidized to NAD⁺ and FAD and the hydrogens that are lost as are being broken up into protons and electrons. the electrons are passed on to reduce oxygen and the protons are pumped into the intermembrane space. the resulting imbalance in charge is known as the proton gradient and it is a way of storing electrochemical energy. this electrochemical energy- more specficially, the controlled flow of H⁺ back into the mitochondrial matrix is used to power the enzyme ATP synthase, which catalyzes the formation of ATP from ADP and P_i

Question 21

how many complezes are embedded in the ETC?

Answer 21

• 4 embedded in the inner membrane, known as complexes I, II, III, IV and the electrion carriers uniquinone (Q) and cytochrome C

Question 22

How electrons transferred through the complexes?

Answer 22

• the ‘transfer’ of electrons is accomplished by them being handed from a carrier that “wants” them relatively less to a carrier that “wants” them relatively more
  
  • this means that electrons are transferred from compounds with lower reduction potentials to compounds with higher reduction potentials
    
    • in eukaryotic cells, the final electron acceptor is oxygen which menas that the reduction potential for O₂ → H₂O is higher than that of any of the other reduction half-reactions involved

Question 23

what is complex I?

Answer 23

• AKA NADH dehydrogenase
  
  • converts NADH to NAD⁺
  • in this reaction the electron is transferred to the electron carrier ubiquinone (Q) with an overall reaction of NADH + H⁺ + Q → NAD⁺n+ QH. at the same time 4 protons are transferred from the mitochondrial matrix into the intermembrane space; as such complex I begins to generate the proton gradient that ultimately powers ATP synthase

Question 24

what is complex II?

Answer 24

• specifically deals with HAD/FADH₂ and is a point of overlap with the TCA
  
  • complex II consists of succinate dehydrogeanse which is a membrane-bound enzyme that catalyzes the converstion of succinate to fumarate in the TCA generating FADH₂.
    
    • in complex II FADH₂ delivers more electrons to Q, generating QH₂

Question 25

what is complex III?

Answer 25

* electrons get passed from QH₂ to the electron carrier known as cytochrome c, regenerating Q and resulting in the reduced form of cytochrome c. * Q carries 2 elecgtrons while cytochomr c carries 1 * the transfer of electrons from Q to cytochomr C is accomponied by the translocation of 4 protons into the intermembrane space per molecule of QH₂

Question 26

what is complex IV?

Answer 26

* where the electron trnasport chain ends * cytochrome c transfers electrons to O₂, reducing H₂O.

Question 27

what is the oxidized form of Q?

Answer 27

* ubiquinone and the reduced form is uniquinol * the partially reduced form, which exists as an intermediate is known as ubisemiquinon and is an example of seminquinone

Question 28

what is cytochrome c?

Answer 28

* a larger molecule classified as a hemeprotein (12 kDA) * the mechanism of electron shuttling is for the iron atom to alternatate between +2 and +3 oxidization states

Question 29

the cell uses the enrgy generated by the energetically favourable redix reactions of the ETC to?

Answer 29

* push protons into the intermembrane space * the resulting proton gradient powers ATP synthase * a complex enzyme with multiple subunits that interact closely with eachother to capture the energy of the proton gradient as efficiently as possible * ATP synthase catalyzes ATP production and that the energy provided by the proton gradient is directly used to disoldge already-synthesized ATP from the enzyme to keep the process moving

Question 30

what is the stoichiometry of the electron transport chain?

Answer 30

* 2.5 molecules of ATP per NADH and 1.5 molecules of ATP per HADH₂

Question 31

how much energy is generated from glucose?

Answer 31

* 30 ATP *

Question 32

the TCA and oxydative phosphorylation are upregualted when?

Answer 32

* the cell needs more ATP, as reflected by a relatively high level of ADP present in the cell

Question 33

the TCA is also subject to negative feedback, in which certain products inhibit the upstream steps in the process:

Answer 33

* the first regulaotry step of the TCA is the production of acetyl-coA * pyruvate is converted to acetyl-CoA by the pyruvate dehydrogenase complex (PDC) and is upregualted by high levels of AMP, CoA and NAD⁺ which are all signs that the cell needs to make more energy. it is down regulated by ATP and NADH, which indicate that the cell has access to ample energy, as well as by acetyl-coA, in a classic example of negative feedback * the final major regulator of the PDC is the presence of high levels of fatty acids. this reflects the fact that fatty acids are metabolized to acetyl-CoA so they can be potential acetyl-CoA molecules that signifiy that there is no need for the PDC to be especially active

Question 34

teh TCA is also regulated at 3 major exergonic steps:

Answer 34

* the initial step in the cycle in which citrate is formed, is upregualted by high elvels of ADP and is downregualted by ATP and NADH and by citrate and succinyl-coA which are the immediate and slightly downstream products of this reaction * the conversion of isocitrate to alpha-ketoglutarate is downregulated by ATP and upregulated by ADP * the formation of succinyl-coA from alpha-ketoglutarate is downregulated by succinyl-CoA and NADH

Question 35

how is oxidative phosphorylation regulated?

Answer 35

* upregualted (largely via upstream elements, such as the TCA and glycolysis) when a relatively large amount of ADP is present indicating the cell needs energy and is slowed down when abundant ATP is present

Question 36

what substances interfere with the ETC and oxidative phosphorylation?

Answer 36

* cyanide and carbon monoxide, both of which interfere with cytochrome c oxidase * without this step, the whole process breaks down