Chapter 3 - Cellular Metabolism

Question 1

Define autotroph

Answer 1

Autotrophs are organisms that are capable of using the sun’s energy to create organic molecules (e.g. glucose) that store that energy in their bonds. These organisms do not require an exogenous source of organic molecules.

Question 2

Define heterotroph

Answer 2

Heterotrophs are organisms that derive energy by breaking down the organic molecules made by plants and harnessing the power held in the bonds of the molecules. Heterotrophs require an exogenous source of organic molecules for energy.

Question 3

Give an example of a common autotroph. What is the overall metabolic chemical reaction of these organisms.

Answer 3

Classic autotrophs are plants, which acquire energy in the form of ATP through photosynthesis. It proceeds according to the endothermic reaction:
6 CO₂ + 6 H₂O + Energy => C₆H₁₂O₆ + 6 O₂

Question 4

Give an example of a common autotroph. What is the overall metabolic chemical reaction of these organisms.

Answer 4

Animals are heterotrophic organisms, and acquire energy by breaking high energy bonds through cellular respiration, which proceeds according to the exothermic reaction:
C₆H₁₂O₆ + 6 O₂ => 6 CO₂ + 6 H₂O + Energy

Question 5

What are energy carriers?

Answer 5

Energy carriers are molecules involved in cell respiration that serve as high energy electron shuttles between the cytoplasms and the mitochondria. Energy carriers release energy when oxidized.

Question 6

What are the four common energy carriers? What is the oxidation equation of each?

Answer 6

The four common energy carriers and their associated redox reactions are:
1) ATP
ATP => ADP + Pᵢ + 7 kcal/mol
ATP => AMP + PPᵢ + 7 kcal/mol
2) NAD⁺
NAD⁺ + H:⁻ => NADH
3) NADP⁺ 
NADP⁺ + H:⁻ => NADPH
4) FAD
FAD + 2H => FADH₂

Question 7

What is glycolysis? Where does it occur and what are the inputs and outputs?

Answer 7

Glycolysis consists of a series of anaerobic enzymatic reactions that occur in the cytoplasm where glucose is converted into two molecules of pyruvate. The energy released in this process is used to produce two ATP and two NADH molecules.

Question 8

What is the net reaction for glycolysis?

Answer 8

Glycolysis proceeds according to the following reaction:

Glucose + 2 ADP + 2 Pᵢ + 2 NAD⁺ ⟶
2 Pyruvate + 2 ATP + 2 NADH + 2 H⁺ + 2 H₂O

Question 9

What is substrate level phosphorylation and where is it utilized?

Answer 9

Substrate level phosphorylation is the transfer of a phosphate group from an organic compound to ADP. Glycolysis and the citric acid cycle utilize substrate level phosphorylation to produce ATP.

Question 10

What two paths can pyruvate take after its generation during glycolysis?

Answer 10

In anaerobic conditions pyruvate undergoes fermentation. In aerobic conditions pyruvate undergoes further oxidation through the mitochondrial electron transport chain.

Question 11

Define fermentation. What are the two major pathways of fermentation, as well as their inputs and outputs?

Answer 11

Fermentation is the process by which the cell is able to replenish NAD⁺ used during glycolysis by oxidizing NADH. Fermentation occurs in the cytoplasm.

In yeast and some bacteria, alcohol fermentation reduces pyruvate through the oxidation of NADH to form ethanol and NAD⁺. In animals and some bacteria lactic acid fermentation reduces pyruvate through the oxidation of NADH to form lactic acid and NAD⁺

Question 12

What is the net reaction for alcohol fermentation? For lactic acid fermentation?

Answer 12

Alcohol fermentation proceeds according to the following reaction:
Pyruvate (3C) + NADH + H⁺ ⟶ CO₂ + Ethanol (2C) + NAD⁺

Lactic acid fermentation proceeds according to the following reaction:
Pyruvate (3C) + NADH + H⁺ ⟶ Lactic Acid (3C) + NAD⁺

Question 13

What is a Facultative Anaerobe?

Answer 13

A facultative anaerobe is an organism that makes ATP by aerobic respiration if oxygen is present, but that can switch to fermentation when oxygen is unavailable.

Question 14

What are the three key phases of cellular respiration, and what is their order?

Answer 14

The three key phases of cellular respiration, in order from first to last, are:

1) pyruvate decarboxylation
2) the citric acid cycle (also known as the Krebs cycle or tricarboxylic acid (TCA) cycle)
3) the electron transport chain

Question 15

What is pyruvate decarboxylation? Where does it proceed and what are the net inputs and outputs?

Answer 15

Pyruvate decarboxylation is the first stage of cellular respiration and occurs in the mitochondrial matrix.

Pyruvate is oxidized to acetate, which then combines with coenzyme A to form acetyl-CoA. This process results in teh formation of one NADH per pyruvate molecule, or two NADH per glucose molecule.

Question 16

What is the net reaction for pyruvate decarboxylation?

Answer 16

Pyruvate decarboxylation proceeds according to the following reaction:

2 Pyruvate (3C) + 2 CoA + 2 NAD⁺ ⟶
2 NADH + 2 Acetyl-CoA (2C) + 2 CO₂ (1C)

Question 17

Following pyruvate decarboxylation, what organic compounds remain from one glucose molecule? What energy carriers have been generated?

Answer 17

After pyruvate decarboxylation two Acetyl-CoA (2C) molecules remain from glucose. The energy carriers at this point are:

2 ATP (glycolysis)
2 NADH (glycolysis)
2 NADH (pyruvate decarboxylation)

Question 18

What is the Citric Acid Cycle (also Krebs cycle or TCA cycle)? Where does it proceed and what are the net inputs and outputs?

Answer 18

The Citric Acid Cycle is the second stage of cellular respiration and occurs in the mitochondrial matrix.

Acetyl-CoA combines with oxaloacetate to form citric acid. This product then proceeds through a series of reactions that result in the regeneration of oxaloactetic acid and the production of three NADH, one FADH₂ and one GTP.

Question 19

What is the net reaction for the Citric Acid Cycle?

Answer 19

The overall reaction of the Citric Acid Cycle is:

2 Acetyl-CoA (2C) + 6 NAD⁺ + 2 FAD + 2 ADP + 2 Pᵢ + 4 H₂O ⟶
4 CO₂ (1C) + 6 NADH + 2 FADH₂ + 2 ATP + 4 H⁺ + 2 CoA

Question 20

Following the citric acid cycle, what energy carriers have been generated from one glucose molecule?

Answer 20

After the citric acid cycle no organic products remain from glucose. The energy carriers at this point are:

2 ATP (glycolysis)
2 NADH (glycolysis)
2 NADH (pyruvate decarboxylation)
6 NADH (TCA cycle)
2 ATP (TCA cycle)
2 FADH₂ (TCA cycle)

Question 21

What is the main purpose of the TCA cycle?

Answer 21

The major purpose of the TCA cycle is to generate high energy intermediates that can be used to make ATP. No organic products remain following the TCA cycle.

Question 22

What is the the electron transport chain? What is its function, and where is it located?

Answer 22

The electron transport chain consists of a chain of cytochromes and other proteins in the inner mitochondrial membrane that transfers electrons from NADH and FADH₂ to oxygen. The energy released from the series of oxidation reactions is used to create a proton gradient, which ATP synthase then utilizes to synthesize ATP.

Question 23

What is oxidative phosphorylation?

Answer 23

Oxidative phosphorylation is the mechanism by which the electron transport chain utilizes the oxidation of high energy electron carriers such as NADH, NADPH, and FADH₂ to phosphorylate ADP and produce ATP.

Question 24

What are the five major components of the electron transport chain?

Answer 24

The five major components of the electron transport chain, in order, are:

1) NADH dehydrogenase (Complex I)
2) Succinate-Q oxidoreductase (Complex II)
3) Carrier Q (ubiquinone)
4) b-c₁ complex (Complex III)
5) cytochrome oxidase complex (Complex IV)

Question 25

In the electron transport chain, what complexes initially oxidize NADH and FADH₂?

Answer 25

NADH is initially oxidized to NAD⁺ by FMN (flavin mononucleotide), a component of complex I. FADH₂ is initially oxidized to FAD by complex II, also known as succinate-Q oxidoreductase. Following the initial oxidation reaction, the electrons from both reactions are passed to carrier Q (ubiquinone) and proceed through the same pathway outlined above.

Question 26

What are the ATP yields by energy carrier species?

Answer 26

In the electron transport chain the ATP yields per energy carrier are
1 NADH => 2 ATP (glycolysis)
1 NADH => 3 ATP (oxidative phosphorylation)
1 FADH₂ => 2 ATP (oxidative phosphorylation)

Question 27

In the electron transport chain, what species is finally reduced, i.e. what is the final electron acceptor? What is the reaction?

Answer 27

Oxygen is the final electron acceptor in the electron transport chain, and the final product is water. It takes the electrons from cytochrome a₃, a protein in complex IV, along with two protons to make water, according to the reaction
2 H⁺ + 2e⁻ + ½ O₂ ⟶ H₂O

Question 28

How do Cyanide and dinitrophenol (DNP) interfere with the electron transport chain?

Answer 28

Cyanide blocks the final transfer of electrons to O₂, while DNP destroys the mitochondrion’s ability to generate a useful proton gradient necessary for effective ATP generation.

Question 29

What molecule is responsible for the actual phosphorylation of ADP to ATP? What drives it and what is the mechanism?

Answer 29

The oxidation of high energy carriers in the electron transport chain leads to an accumulation of protons in the intermembrane space, and so also a proton gradient (electrical and chemical gradient) across the inner mitochondrial membrane. ATP synthase couples the release of energy from the movement of protons down the energy gradient to the phosphorylation of ADP to ATP. This process is known as oxidative phosphorylation.

Question 30

Describe the ATP production per glucose molecule as broken down into the stages of cellular metabolism.

Answer 30

Glycolysis:
2 ATP invested –2 ATP
4 ATP generated +4 ATP (substrate)
2 NADH x 2 ATP/NADH +4 ATP (oxidative)

Pyruvate decarboxylation:
2 NADH x 3 ATP/NADH +6 ATP (oxidative)

Citric Acid Cycle:
6 NADH x 3 ATP/NADH +18 ATP (oxidative)
2 FADH₂ x 2 ATP/FADH₂ +4 ATP (oxidative)
2 GTP x 1 ATP/ GTP +2 ATP (oxidative)

Total +36 ATP

Question 31

What are the three alternate sources of energy?

Answer 31

The three alternate sources of energy are

1) carbohydrates - sugar polymers are broken down during digestion and stored as glycogen in the liver. Glycogen can be broken down to glucose-6-phosphate when needed.
2) fats - triglycerides are esterified to glycerol and fatty acids and subsequently fed into glycolysis and the TCA cycle, respectively.
3) proteins - the removal of the amine moiety from amino acids yields α-keto acids, many of which can be converted into acetyl-CoA or other intermediates of the TCA cycle.

Question 32

What is Glycogen? Where is it stored and what role does it play in cellular metabolism?

Answer 32

Glycogen is the form in which carbohydrates are primarily stored in the liver. Glycogen is easily converted to glucose-6-phosphate, a glycolytic intermediate, when the body needs it.

Question 33

Define fatty acid activation

Answer 33

Fats must be activated using two ATP molecules before they can be converted into acetyl-CoA by beta-oxidation and enter the citric acid cycle.

Question 34

Define beta-oxidation. What is the energy output for a typical input molecule.

Answer 34

Beta-oxidation is the metabolic process by which fatty acids are converted into acetyl-CoA in the mitochondrial matrix. Each round of oxidation generates one NADH and one FADH₂. 24 total rounds of beta oxidation are used to break down a typical 48C triglyceride, generating close to 100 ATP molecules per fat molecule.

Question 35

Pair metabolic processes with their sites of occurrence.

Answer 35

Glycolysis — cytosol
Alcohol fermentation — cytosol
Lactic acid fermentation — cytosol
Pyruvate decarboxylation — mitochondrial matrix
Citric Acid Cycle — mitochondrial matrix
Electron transport chain — mitochondrial inner membrane

Question 36

Fatty acids enter the catabolic pathway in what form?

Answer 36

Fatty acids enter the catabolic pathway in the form of acetyl-CoA via the TCA cycle. Fatty acids are first activated in the cytoplasm by cleaving an ATP into cAMP. Once activated, the fatty acid is then taken to the mitochondrial matrix where, through a series of oxidation reactions, it is converted to acetyl-CoA.

Question 37

In which part of the cell would you expect to find cytochrome c?

Answer 37

cytochrome c is found in the inner mitochondrial membrane. It is a component of the electron transport chain.

Question 38

What does the term oxygen debt refer to?

Answer 38

Oxygen debt refers to the amount of oxygen that would be needed to convert the lactic acid formed through fermentation back to pyruvate. In a way it is a measure of how far behind on oxygen the cell is.

Question 39

What chemical cascade occurs during oxygen debt, and what are the physiological effects?

Answer 39

When the cell is deprived of oxygen lactic acid fermentation occurs, which results in an increase in the amount of lactic acid and, consequently, a decrease in the pH of the cytoplasm. This, paired with the limited amount of energy (ATP) that the cell can produce in anaerobic conditions (through glycolysis), leads to fatigue. Pyruvate is used up in lactic acid fermentation in order to produce the NAD⁺ required to maintain glycolysis.

Question 40

What is the total amount of ATP yielded by the catabolism of one glucose molecule via the Krebs cycle?

Answer 40

The Krebs cycle produces 3 NADH, 1 FADH₂, and 1 GTP molecules per acetyl-CoA, which yields 3 x 3 (from NADH) + 2 x 1 (from FADH₂) + 1 (GTP) = 12 ATP molecules. Since each glucose molecule produces two acetyl-CoA molecules, 24 total ATP molecules are produced via the Krebs cycle alone.