the citric acid cycle and oxidative phosphorylation

Question 1

what main product does glycolysis end with

Answer 1

2 pyruvates

Question 2

where is pyruvate transported to after glycolysis and under what condition

Answer 2

under aerobic condition

from the cytosol into the mitochondrial matrix

Question 3

what complex is responsible for pyruvates conversion to CO2 and the acetyl group of acetyl-CoA

Answer 3

Pyruvate dehydrogenase complex

Question 4

what is pyruvate dehydrogenase complex a complex of

Answer 4

3 enzymes:

E1 – Pyruvate dehydrogenase (acetyl transferring)

E2 – Dihydrolipoyl transacetylase

E3 – Dihydrolipoyl dehydrogenase

Question 5

what are 2 additional enzymes that are involved in these reactions, but are not part of the complex

Answer 5

• Pyruvate dehydrogenase phosphatase (PDP)
  and
• Pyruvate dehydrogenase kinase (PDK)

1- Pyruvate dehydrogenase kinase (PDK):
Phosphorylates pyruvate dehydrogenase (E1) using ATP at 3 possible sites (site 1 being the most important)
- 4 isoenzymes; PDK1, 2, 3, and 4
- Site 1: PDK2 > PDK4 ≈ PDK1 > PDK3
- Site 2: PDK3 > PDK4 > PDK2 > PDK1
- Site 3: Only PDK1 can phosphorylate

2- Pyruvate dehydrogenase phosphatase (PDP)
Reverses the effects of pyruvate dehydrogenase kinase.
- Thus, E1 is the rate-determining step
- The ratios of products and substrates of this reaction are important for regulation

Question 6

describe what the citric acid cycle is

Answer 6

The citric acid cycle is the final common pathway for the oxidation of fuel molecules​:
- Carbohydrates​
- Fats​
- Proteins​

Question 7

Carbohydrates, fatty acids and some amino acids enter the citric acid cycle as what

Answer 7

acetyl coenzyme A (acetyl CoA)

Question 8

what is the citric acid cycle also know as

Answer 8

Citrate cycle​

Krebs cycle​

Tricarboxylic acid (TCA) cycle

Question 9

anaerobic glycolysis extracts what

Answer 9

only a small amount of ATP available from Glucose

Most of the ATP is generated in metabolism generated by the aerobic processing of Glucose

Question 10

what does the citric acid cycle start with and where abouts doe sit take place

Answer 10

with the complete oxidation of glucose derivatives to carbon dioxide in a sequence of reactions

This all takes place (in eukaryotes) in the mitochondrial matrix

Question 11

what is acetyl-CoA

Answer 11

Acetyl CoA, an ‘activated’ acetyl (C2) unit (on a coenzyme) is completely oxidised to CO2 and H2O by the citric acid cycle.

Question 12

explain what must happen in order for oxidation of Acetyl-CoA to take place

Answer 12

reduction must happen to something else

Many ATP molecules can be made from reduced cofactors such as NADH and FADH2 in the electron transport chain via oxidative phosphorylation.​

• NADH = Nicotinamide adenine dinucleotide (reduced)​
• FADH2 = Flavin adenine dinucleotide (reduced)

Question 13

explain reaction 1 - citrate synthase

Answer 13

This is a condensation reaction as water is broken down

Condensation of acetyl-CoA with oxaloacetate to form a C4 molecule - citrate.​

Reaction is catalysed by citrate synthase, an allosteric enzyme that is inhibited by NADH, ATP, and succinyl-CoA.

Question 14

explain reaction 2 - aconitase

Answer 14

Citrate is isomerized

The enzyme is called Aconitase because the presumed intermediate is cis-aconitate

Question 15

explain reaction 3 - isocitrate dehydrogenase

Answer 15

The first of 4 oxidation-reduction reactions​

Isocitrate is oxidised, and there is a reduction of NAD+ with loss of a carbon atom as CO2
Isocitrate

dehydrogenase is an allosteric enzyme, which is inhibited by ATP and NADH, and activated by ADP and NAD+

Question 16

explain reaction 4 - alpha-ketoglutarate dehydrogenase complex

Answer 16

The second oxidation-reduction reaction​

α-ketoglutarate dehydrogenase - another multi-enzyme complex

Question 17

explain reaction 5 - Succinyl-CoA Synthase

Answer 17

Succinyl-CoA cleavage of its bond is linked to the phosphorylation of GDP (guanosine diphosphate)

The GTP that is produced can be used to make an additional ATP by phosphoryl transfer with ADP

• This is NOT a citric acid cycle step​. Its adjacent with the cycle

Question 18

describe Succinyl-CoA

Answer 18

is a Thioester, these are energy rich, and cleavage of this bond is linked to the phosphorylation of GDP (guanosine diphosphate)

Question 19

explain reaction 6 - succinate dehydrogenase

Answer 19

The third oxidation-reduction reaction of the citric acid cycle.​

Succinate is oxidised to fumarate and FAD is reduced to FADH2

Question 20

explain reaction 7 - fumarase

Answer 20

A condensation reaction to produce malate

Question 21

explain reaction 8 - malate dehydrogenase

Answer 21

The final oxidation-reduction reaction of the citric acid cycle​
- Malate oxidised to Oxaloacetate
- NAD+ reduced to NADH

Oxaloacetate can re-enter into reaction 1 of the cycle

Only 2 ATP is made here

Question 22

give a quick summary of the citric acid cycle

Answer 22

2x: (Occurs twice as 2 pyruvates)

Acetyl-CoA —> Citrate

Citrate —> Isocitrate (OH + H rearrangement)

Isocitrate —> α-Ketoglutarate

α-Ketoglutarate —-> Succinyl-CoA

Succinyl-CoA —————–>Succinate —-> ATP

Succinate –> Fumarate

Fumarate —> Malate

Malate —-> Oxaloacetate

Question 23

explain the 3 points of control of the citric acid cycle

Answer 23

1 - Citrate synthase
- Inhibited by ATP, NADH, and succinyl CoA
- Product inhibition by citrate​

2 - Isocitrate dehydrogenase
- Activated by ADP and NAD+
- Inhibited by ATP and NADH​

3 - α-ketoglutarate dehydrogenase complex
- Activated by ADP and NAD+​
- Inhibited by ATP and NADH
- Product inhibition by Succinyl CoA

If inhibited by ATP its activated by ADP, same with NADH and NAD

There is one control point outside the cycle​
Pyruvate dehydrogenase

Question 24

what do control points do

Answer 24

help stop the process running all the time

Question 25

what are the products of the citric acid cycle

Answer 25

The metabolism of Pyruvate has produced: - 3 NADH + H+ - 1 FADH2

Question 26

what happens to the reduced components of the citric acid cycle

Answer 26

take part in Oxidative Phosphorylation within the mitochondria: - Electron Transport Chain - Chemiosmosis

Question 27

explain The Electron Transport Chain and Chemiosmosis

Answer 27

A series of membrane bound proteins which electrons pass through in a series of redox reactions, creating energy This energy is either given off as heat or used to drive a series of proton pumps to produce a concentration gradient between the mitochondrial matrix and the intermembrane space All ATP needed to survive is coming from here

Question 28

explain complex 1 of the electron transport chain

Answer 28

Ubiquinone Oxidoreductase - NADH dehydrogenase - Flavin mononucleotide - 8 iron-sulphur (Fe-S) clusters – these accept electrons and stransfer then to one another NADH oxidised by this complex - 2 electrons transferred FMN, then to Fe-S, then to Coenzyme-Q - This energy pumps 4 protons to the intermembrane space

Question 29

explain complex 2 of the electron transport chain

Answer 29

Succinate dehydrogenase 2nd entry point into the electron transport chain - FADH2 oxidised to FAD and H+, with the electrons moved through a series of Fe-S clusters to CoQ as in Complex 1 - No protons pumped through this entry point (Same as complex 1 but for FADH2 instead)

Question 30

explain coenzyme Q in terms of the electron transport chain

Answer 30

Electron carrier – taking electrons from complex 1 and 2 to complex 3 Transfers electrons to Complex 3 through the Q Cycle

Question 31

what is coenzyme Q also known as and whats its structure

Answer 31

Also known as Ubiquinone Quinone with a hydrophobic tail

Question 32

explain complex 3 of the electron transport chain

Answer 32

Cytochrome c reductase: - Cytochrome b - Cytochrome c - Rieske subunits (contains Fe-S clusters) Cytochrome Is a Heme containing electron transport protein, so Alternate between Fe2+ and Fe3+ states ( as heme = iron) - Can only transport 1 electron at a time using the Q cycle Releases 4 proton into the intermembrane space, ( Now a total of 8 protons released into intermembrane space)

Question 33

explain the Q cycle in complex 3

Answer 33

2 steps: Cycle 1: Ubiquinol (CoQH2) binds to site 1 and donates 2 electrons that go into 2 separate pathways - 1 goes to the Fe-S clusters, and then on to cytochrome c, which is reduced - 1 goes to cytochrome b, and then on to CoQ bound at the second site, which becomes the CoQH- radical This pumps 2 H+ into the intermembrane space Cycle 2: A repeat of cycle 1 - The electron donated to cytochrome b stabilises the CoQH- radical to CoQH2 Another 2 H+ ions pumped out

Question 34

explain complex 4 of the electron transport chain

Answer 34

Cytochrome c oxidase: - Cytochrome a - Cytochrome a3 - Heme and Copper groups Oxidises cytochrome c, transferring 2 electrons to Oxygen - Which becomes water 2 protons pumped into the intermembrane space

Question 35

explain complex 5 of the electron transport chain

Answer 35

ATP Synthase, formed of : - F0 Forms a rotor mechanism that is constantly protonated and deprotonated - F1 As F0 rotes it changes the orientation and conformation of F1, catalysing the formation of ATP from ADP Every 4 H+ = 1 ATP produced (For every 1 glucose molecule about 30 ATP are roughly produced)