Exam 3 November 18 Lecture

Question 1

What is an overview of oxidative respiration?

Answer 1

carbon fuel + O2 → CO2 + H2O + ENERGY

carbon fuel from glucose, other carbs, amino acids, and fatty acids) (CO2 from TCA cycle and H2O from ETC

Question 2

How is oxidative phosphorylation achieved?

Answer 2

achieved by a series of removal of electrons (on coenzymes like NADH and FADH2) from carbohydrates and intermediates (oxidation) → the electrons pass through carriers NADH and FADH2 to the ETS and this drives ATP synthesis by oxidative phosphorylation

Question 3

Where does the TCA cycle, ETS, and oxidative phosphorylation occur?

Answer 3

TCA cycle starting from pyruvate occurs in the mitochondrial matrix (inside the inner membrane) while the ETS and oxidative phosphorylation occurs on the inner surface of the inner mitochondrial membrane

Question 4

What reactions occur in the cytosol?

Answer 4

glycolysis, gluconeogenesis, pentose phosphate pathway, and glycogen metabolism

Question 5

What are the 3 main steps of oxidative phosphorylation?

Answer 5

1. electrons from NADH and FADH2 are transferred to O2 (oxidation)
2. creation of the proton gradient (which will pump protons to intermembrane space which will drive ATP synthesis through the ATP synthase)
3. ATP synthase produces ATP using the proton gradient (phosphorylation)

Question 6

What is the energy yield of oxidative phosphorylation?

Answer 6

2.5 mol of ATP per 1 NADH and 1.5 mol of ATP per 1 FADH2 → FADH2 comes into complex 2 so it skips proton transferring step so less protons are transferred and less ATP is created

Question 7

What is the role of redox coenzymes?

Answer 7

living organisms utilize redox coenzymes as high energy electron carriers (examples are NADH and FADH2) → this is coupled with oxidation of another molecule (a carbon intermediate in metabolism)

Question 8

What are the two nicotinamide coenzymes?

Answer 8

NAD(H) and NADP(H)

Question 9

What are the levels of NAD(H) and NADP(H) in the cytosol?

Answer 9

[NAD+] > [NADH]

[NADPH] > [NADP+]

Question 10

Enzymes that only work in one direction evolve what?

Answer 10

evolve a specificity for either NAD+ or NADP+

Question 11

What are properties of nicotinamide coenzymes (NADH and NADPH)?

Answer 11

1. co-substrates and bind to enzymes transiently like other substrates
2. highly polar and water soluble so they cannot cross the mitochondrial membrane

Question 12

What are the sources and uses of NADH?

Answer 12

sources: glycolysis, TCA cycle, fatty acid oxidation
uses: generation of ATP by oxidative phosphorylation

Question 13

What are the sources and uses of NADPH?

Answer 13

sources: pentose phosphate pathway
uses: reducing cofactor in anabolic reactions

Question 14

What are the two flavin coenzymes?

Answer 14

FAD (flavin adenine nucleotide) and FMN (flavin mononucleotide)

Question 15

What are the properties of flavin coenzymes?

Answer 15

1. hydrophobic since they are buried deep in hydrophobic clefts in proteins
2. serve as prosthetic groups → don’t bind transiently like NAD(H) and NADP(H) and instead is constitutively bound to the enzyme it regulates

Question 16

What are the key differences between NAD+/NADP+ and FAD/FMN?

Answer 16

NAD+/NADP+: bind to enzymes transiently like other substrates and are highly polar and water soluble
FAD/FMN: serve as prosthetic groups in enzymes and the flavin ring system is very hydrophobic

Question 17

What does coenzyme A resemble?

Answer 17

a phosphoanhydride-linked dinucleotide similar to FAD, NAD+, and NADP+

Question 18

What is the role of coenzyme A?

Answer 18

acts as an acyl carrier without being oxidized → animals can make all the parts of coenzyme A EXCEPT for the pantothenic acid (vitamin B5) so we have to get it from the diet

Question 19

The ETC is composed of how many complexes?

Answer 19

four

Question 20

What happens at Complex I?

Answer 20

1. electron transfer form NADH to ubiquinone (coenzyme Q) → so NADH comes in and gets oxidized to NAD+ + H+ and then donates electron to the complex

Question 21

What happens at Complex II (succinate dehydrogenase)?

Answer 21

1. succinate to ubiquinone (coenzyme Q)

2. part of the TCA cycle

Question 22

What happens at Complex III?

Answer 22

ubiquinol to cytochrome c

Question 23

What happens at Complex IV (cytochrome c oxidase)?

Answer 23

cytochrome c to O2

Question 24

What complex does FADH2 enter in at?

Answer 24

complex II which does not transfer any protons across the intermembrane space → is the only complex that doesn’t do that (FADH2 gets oxidized to FAD)

Question 25

What does both complex I and complex II do?

Answer 25

they both donate electrons to coenzyme Q (also known as ubiquinone)

Question 26

What happens at complex III and complex IV?

Answer 26

complex III: transferring electrons to cytochrome c complex IV: also known as cytochrome c oxidase which enables the conversion of oxygen to water and the electrons are recaptured in the water molecule

Question 27

How many protons are transported at each complex?

Answer 27

``` complex I: 4 complex II: 0 complex III: 2 complex IV: 4 total: 10 protons (from oxidation of NADH) ```

Question 28

How many protons is required for ATP synthase to generate 1 ATP?

Answer 28

usually 3-4 protons but is 4 protons in our case even though it should be 3

Question 29

What is the energy yield of oxidative phosphorylation?

Answer 29

2. 5 mol of ATP per 1 NADH → 10 H+ | 1. 5 mol of ATP per 1 FADH2 → 6 H+

Question 30

What is the role of the ATP synthase?

Answer 30

synthesizes ATP from ADP using the proton gradient and is described as a "turbine engine" with 3 stages (open, loose, tight)

Question 31

What happens at each stage of the ATP synthase?

Answer 31

loose: where ADP and a phosphate bind open: ATP comes out tight: ATP is formed by proximity 1 H+ induces 1 rotation so 3 H+ would make sense, but experimentally, it is 3-4 H+ → 4 H+ to create 1 ATP

Question 32

What is the role of cyanide in the ETC?

Answer 32

cyanide inhibits cytochrome c oxidase (Complex IV)

Question 33

If cyanide poisoning occurs, would the pH of the intermembrane space increase or decrease?

Answer 33

if less H+ are transported to the intermembrane space since complex IV is blocked, pH will increase!

Question 34

What effect would cyanide have on ATP synthesis?

Answer 34

ATP synthesis decreases because of the lack of gradient since ATP synthesis is driven by the proton gradient

Question 35

What are the role of uncouplers?

Answer 35

they prevent the proton gradient from resulting in energy and uncouples electron transport from ATP synthesis and transports back to the matrix

Question 36

What is the importance of uncouplers?

Answer 36

oxygen is consumed without ATP synthesis so energy is lost as heat

Question 37

Where are uncouplers found?

Answer 37

in hibernating animals and in brown adipose tissue (found in newborn babies)

Question 38

What was the importance of the synthetic uncoupler 2,4-dinitrophenol?

Answer 38

1. used as a diet pill in the 1930s for weight loss 2. could cause fatal hyperthermia which was a problem in which patients got too overheated 3. discontinued in 1938 due to its dangerous side effects

Question 39

What is UCP-1?

Answer 39

1. expressed in brown adipose tissue which plays a major role in non-shivering thermogenesis, especially in newborns (helps them regulate temperature) 2. located in the inner mitochondrial membrane 3. dissipates the proton gradients → uncouples electron transport from ATP synthesis

Question 40

What are reactive oxygen species?

Answer 40

dangerous but natural side effects of electron transport which can lead to protein oxidation, lipid oxidation, and DNA damage that causes oxidative stress → pro-inflammatory markers → inflammation related diseases like cancer, diabetes, atherosclerosis, and arthritis

Question 41

Reactive oxygen species (ROS) occurs mainly in which complex?

Answer 41

complex IV since cytochrome c oxidase (complex IV) catalyzes the reaction of oxygen to water and the intermediates (ROS) are highly reactive and can cause the following cellular damages: lipid peroxidation, damages to proteins, and DNA damage

Question 42

What are the three main ROS created in each round of electron transport?

Answer 42

1. superoxide (O2-) 2. hydrogen peroxide (H2O2) 3. hydroxyl radical (OH・)

Question 43

What are the two main defenses against ROS?

Answer 43

1. cellular enzymes | 2. diet

Question 44

What are the cellular enzymes used as defense against ROS?

Answer 44

1. superoxide dismutase (SOD) and catalase → primary defense mechanism 2. glutathione peroxidase → uses glutathione as a reductant and oxidized glutathione is reduced by glutathione reductase using NADPH (so OH radical is converted to water)

Question 45

What is the role of SOD and catalase compared to glutathione peroxidase?

Answer 45

SOD and catalase take part in the first 2 steps from superoxide to hydrogen peroxide to hydroxyl radical while glutathione peroxidase takes care of the hydroxyl radical in the end to convert it to water

Question 46

How can the diet be a defense against ROS?

Answer 46

antioxidants such as vitamins (vitamins C, E, and β-carotene) and the foods we eat (green tea, red wine, blueberries)

Question 47

The more ROS we are exposed to, the more the _____.

Answer 47

systems are unable to keep up (aka the defenses against ROS)

Question 48

How are ROS and diabetes related?

Answer 48

too much intracellular glucose leads to the overproduction of the superoxide by mitochondria

Question 49

What cells are especially vulnerable to ROS?

Answer 49

cells that cannot restrict the uptake of glucose: retina → diabetic retinopathy kidney → diabetic nephropathy peripheral nerves → diabetic neuropathy

Question 50

How can a light touch feel like a needle?

Answer 50

due to hyperglycemia which can lead to oxidative stress and creates lots of ROS → increases inflammatory signaling and activation of pro-inflammatory cytokines, leading to inflammation which will trigger the senses of neuropathies → common in diabetic patients since they can't properly regulate their glucose levels