Chemistry 301 Introduction to Biochemistry

Study Guide :: UNIT 2

Energy

Overview

Living organisms are made up of cells, and cells contain many biochemical components such as proteins, lipids, and carbohydrates. As one can imagine, living cells are not random collections of molecules, but maintain a high order of organization. Living organisms require energy to maintain order; in the nonliving world, there is a universal tendency to increasing disorder. This unit will cover the fundamental concepts of energy and how energy is harnessed and utilized in the cell.

The unit is divided into five lessons:

Learning Objectives

After completing this unit, you should be able to:

1. define “energy” and “entropy.”
2. differentiate between oxidation and reduction reactions.
3. describe catabolic and anabolic processes.
4. explain the role of phosphorylation in ATP synthesis.
5. explain the basic principle of thermodynamics and calculate Gibbs Free Energy for an equation.
6. compare exergonic, endergonic, and equilibrium reactions.

Glossary

A good definition identifies the thing described, and says something about where it is found and how it works. Each of the following definitions is incomplete. As you work through this and later units, you should develop a complete definition for the terms in each glossary.

Lesson 1: Energy Reactions

Overview/Objectives

After completing this lesson, you should be able to:

1. explain “oxidation”, “reduction”, “catabolic”, and “anabolic” reactions.
2. demonstrate an understanding of the role of ATP in providing energy.

Readings and Activities

1. In Chapter 2 Energy, read “Introduction,” “Oxidative Energy,” “Oxidation vs. Reduction in Metabolism,” and “Energy Coupling” (pages 25–28 in the textbook).
2. For additional information on metabolic strategies, watch the two video lectures:
   • #20 Biochemistry Metabolic Controls/Energy Lecture for Kevin Ahern’s BB 450/550

   • #21 Biochemistry Glycolysis Lecture for Kevin Ahern’s BB 450/550

     (There are also links to these on page 26 of the textbook).

Commentary

Living organisms are composed of cells, which contain many biochemical components that are involved in a number of integrated and complex reactions and processes to sustain life. Unlike non‑living systems, which tend to proceed from order to disorder, cells need to maintain order and balance in their processes. To do this, cells require the input of energy. Depending on the cell type, energy may come from the sun (photosynthetic organisms) or from food sources (heterotrophic organisms).

Getting energy from food is achieved by a process called oxidation. Oxidation is the loss of electrons by a molecule (increase in oxidation state). Conversely, reduction is the gain of electrons (decrease in oxidation state).

A redox reaction (reduction‑oxidation) is a chemical reaction whereby the oxidation states of atoms are changed by the transfer of electrons between them. What this means is that the reaction will have an oxidation and a complementary reduction process. The molecule that loses an electron is referred to as “oxidized” and the molecule that gains an electron is “reduced.”

Many important biological processes involve redox reactions. For example, the breakdown of glucose in the human body to get ATP for energy, which is part of cellular respiration (covered in Unit 6), involves the oxidation of glucose to carbon dioxide and the reduction of oxygen to water:

C₆H₁₂O₆ + 6 O₂ → 6 CO₂ + 6 H₂O

Glucose (C₆H₁₂O₆) loses electrons (oxidized) to form carbon dioxide (CO₂) and oxygen (O₂) is reduced to form water (H₂O). You can see that the molecules and the changes are conserved within the system.

The more reduced a carbon atom is (more electrons), the more energy can be released when it is oxidized. As shown in the text, palmitic acid has less oxygen per carbon than glucose, and so when palmitic acid is fully oxidized it generates more ATP than glucose. In contrast, the more oxidized a carbon atom is (less electrons), the more energy is takes to reduce it. See the first figure on page 26 of the text.

Carbon is the most commonly oxidized energy source. Oxidation releases energy in the form of ATP, which can be used to drive processes that require an input of energy (energy coupling). Catabolic reactions are those that generate energy and anabolic reactions are those that require energy. Catabolic and anabolic reactions are coupled in living organisms. See the second figure on page 26 of the text.

An overview of the two processes follows:

Catabolic → oxidative → release energy
Anabolic → reductive → use energy

Coupling of reactions involves enzymes. When energy (ATP) for a reaction is needed, an enzyme can bind ATP and the other molecule(s) involved in the reaction. Hydrolysis of the ATP (removal of phosphate ATP → ADP + P_i) provides energy for the enzyme to catalyze the reaction on the molecule(s).

This commentary draws on the Wikipedia page Redox.

Study Questions

1. Define “oxidation” and “reduction.”
2. What is a redox reaction? Why are redox reactions common in biological systems?
3. In the combustion of wood, oxygen from the air transfers electrons to the carbon in the wood. Is the oxygen being oxidized or reduced?
4. Are catabolic reactions usually oxidative or reductive? Are anabolic reactions usually oxidative or reductive?
5. Is the utilization of glucose to produce ATP catabolic or anabolic? Is synthesis of nucleic acids catabolic or anabolic?
6. What is the role of enzymes in energy coupling?

If you wish to discuss any of these questions or need assistance with the material, please contact your Academic Expert (AE) by emailing the Student Success Centre at  fst_success@athabascau.ca.

Lesson 2: Thermodynamics

Overview/Objectives

After completing this lesson, you should be able to:

1. Explain the basic principle of thermodynamics as it pertains to biochemical systems.
2. Describe the two laws of thermodynamics.
3. Differentiate between entropy and energy.
4. Define Gibbs Free Energy and calculate the change in Gibbs Free Energy (ΔG).
5. Demonstrate an understanding of the difference between endergonic, exergonic, and equilibrium reactions.
6. Demonstrate an understanding of thermodynamic equations.

Readings and Activities

1. Read “Entropy and Energy” and “Gibbs Free Energy” (pages 28–31 in the textbook).
2. For additional information on metabolic strategies, watch the two video lectures.
   • #20 Biochemistry Metabolic Controls/Energy Lecture for Kevin Ahern’s BB 450/550

   • #21 Biochemistry Glycolysis Lecture for Kevin Ahern’s BB 450/550

     (The links for these videos are also provided in Lesson 1 Energy Reactions, and on page 26 of the textbook.)

Commentary

All living things are composed of biomolecules. To sustain life, the cells of a living body constantly form new molecules or break down existing ones. These continual changes of biomolecule structure (“dynamics”) use energy or release energy, or both; the process usually results in the production of heat (“thermo‑”). The measurement of energy change is therefore known as “thermodynamics.”

The first law of thermodynamics states that energy can be exchanged between physical systems as heat and work.

The second law of thermodynamics states that entropy, a measurement of the molecular disorder in a system, exists and that isolated systems increase in entropy.

The change in entropy of a system depends on the initial and final states. In an irreversible reaction, entropy would increase. In a reversible process, entropy is conserved.

Enthalpy is the amount of energy in a thermodynamic system and is equivalent to the total heat content of a system.

As mentioned in the text, living cells are not isolated systems and, to counter the tendency to disorder, a cell needs to use energy. Energy for the cell is often in the form of high‑energy phosphate molecules such as ATP, GTP, CTP, and UTP. ATP is the most common form of energy used by the cell. Hydrolysis of the phosphate bonds in ATP and other phosphate molecules releases energy.

Gibb’s Free Energy is a measurement of thermodynamic potential. It is important to note that the maximum amount of work/energy from a closed system can only be realized in a completely reversible reaction. The equation is:

ΔG = H − TS

where ΔG is Gibb’s Free Energy, H is enthalpy (joule), T is temperature (in kelvin), and S is entropy (joule/kelvin).

The change in Gibbs Free Energy can be used to determine whether a given chemical reaction can occur spontaneously. A negative ΔG indicates a spontaneous reaction, while a positive ΔG indicates a reaction cannot occur spontaneously.

At standard temperature and pressure, every system will attempt to achieve a minimum of free energy. ΔG is reduced by increased entropy (S) and excess heat (T).

Cells must work within the laws of thermodynamics, which sets limitations on their biochemical reactions. When you consider how cellular processes must interact and balance, it makes sense that the ΔG value is critical, because it determines whether or not a reaction will go forward.

ΔG = ΔH − TΔS

As explained in the text:

The equation can be modified at pH 7 considering substrates and products in a reaction to determine ΔG:

ΔG = ΔG°′ + RT ln([B]^b/[A]^a)

where A is the substrate and B is the product and b and a are integers.

With multiple substrates and products (aA + cC ↔ bB + dD), it becomes:

where:

ΔG°′ is the Standard Gibbs Free Energy. This is the change in energy that occurs when all products and reactants are at standard conditions and pH = 7. This value is constant for a given reaction. This can be calculated using the equilibrium equation for a system at chemical equilibrium:

ΔG°′ = −RT ln K

where K = equilibrium constant (also known as K_eq)(unitless)

Temperature is a constant in biological reactions. Since ΔG°′ is also a constant for a particular reaction, then ΔG is dependent on the ratio of [products]/[reactants]. If a reaction is in standard conditions where everything except protons is at 1 M (molar), the RT ln ([products]/[reactants]) term is zero, so the ΔG°′ value will determine the direction of the reaction. This is why a negative ΔG°′ indicates an energetically favourable reaction (releases energy) and a positive ΔG°′ indicates an energetically unfavourable one (requires energy).

Increasing the ratio of [products]/[reactants] causes the value of the natural log (ln) to become more positive (less negative), so ΔG is more positive. Decreasing the ratio of products to reactants causes ln to become more negative (less positive) and ΔG to become more negative. In a closed system, ΔG will always move towards zero or equilibrium.

In biological systems, some reactions may be “coupled” to drive an unfavourable reaction. For example, the reaction of glucose with fructose to form sucrose has a ΔG value of +5.5 kcal/mole and will not occur spontaneously. However, the breakdown of ATP to form ADP and inorganic phosphate (P_i) has a ΔG value of −7.3 kcal/mole, coupling these reactions, so that glucose binds with ATP to form glucose‑1‑phosphate and ADP creates an overall ΔG of −1.8 kcal/mole. The glucose‑1‑phosphate can bond fructose, yielding sucrose and inorganic phosphate. Coupling reactions to alter the Gibbs Free Energy is a basic principle behind enzymatic action in biology.

ΔG is expressed in kcal or kcal/mole or joules/mole and ΔG°′ is expressed in joules.

Some information in this commentary is from the Wikipedia pages Thermodynamics, Gibbs free energy, and Biological thermodynamics.

Study Questions

1. Outline the first and second laws of thermodynamics.
2. What is entropy? How does an increase in entropy affect the value of ΔG?
3. What does a negative ΔG mean for a reaction? A positive ΔG value? What if the ΔG value is zero?
4. In a biological system, how can reactions be coupled to turn an unfavourable reaction (positive ΔG) into a favourable one (negative ΔG)?

5. Calculate ΔG for the following reaction:

   Glutamate + NH₃ ⇄ glutamine + H₂O

   where the reaction occurs at 293 kelvin, the change in heat is 19,070 calories, and the change in entropy is 90 cal/k.

   Is this reaction endergonic or exergonic?

6. Use the equilibrium equation ΔG°′ = −RT ln K_eq to calculate ΔG°′ for the following reaction:

   Pyruvate + NADH ⇄ Lactate + NAD⁺

   This reaction occurs at 298 K and the equilibrium concentrations of the above products and reactants are as follows:

   pyruvate: 20 μM
   NADH: 30 μM
   Lactate: 60 μM
   NAD⁺: 10 μM
   R = 8.314 J · K⁻¹

   Is this reaction endergonic or exergonic?

If you wish to discuss any of these questions or need assistance with the material, please contact your Academic Expert (AE) by emailing the Student Success Centre at  fst_success@athabascau.ca.

Lesson 3: Cellular Phosphorylations and Electron Transport

Overview/Objectives

After completing this lesson, you should be able to:

1. Demonstrate an understanding of the role of ATP in energy generation and utilization.
2. Describe the three types of phosphorylation mechanisms in the cell.
3. Describe the structure and function of ATP synthase.
4. Describe the synthesis of ATP by oxidative phosphorylation.
5. Summarize the function of the electron transport chain.
6. Describe the sequence of components of the electron transport chain.
7. Explain why NADH and FADH₂ yield different amounts of ATP.
8. Define the term “oxidative phosphorylation.”
9. Use the “chemiosmotic hypothesis” to explain how the energy from electron transport is “coupled” to ATP synthesis.
10. Name the two mechanisms proposed for proton transport.
11. Explain why aerobic ATP production is much more efficient than anaerobic production.
12. Identify one advantage of anaerobic glycolysis over aerobic metabolism.

Readings and Activities

1. Read “Cellular Phosphorylations,” “Substrate‑Level Phosphorylation,” “Electron Transport/Oxidative Phosphorylation,” “ATP Synthase,” “Photophosphorylation,” and “Electron Transport in Chloroplasts versus Mitochondria” (pages 31–38 of the textbook).

2. You can also watch the video lectures on Energy and on Photosynthesis:

   Energy:

   • #32 Biochemistry Nerve Transmission/Mitochondria Lecture for Kevin
   • #33 Biochemistry Electron Transport/Oxidative Phosphorylation Lecture for Kevin Ahern’s BB

   • #34 Biochemistry Oxidative Phosphorylation/Respiratory Control Lecture for Kevin Ahern’s BB 451/551

     (Links to these are also provided on page 32 of the textbook.)

   Photosynthesis:

   • #34 BB 350 Photosynthesis - Kevin Ahern’s Biochemistry Online

     (A link to this is also provided on page 35 of the textbook.)

Commentary

ATP (adenosine triphosphate) is the molecule essential for providing energy for cellular processes. Chemical energy is stored in the phosphoanhydride bond of ATP. This is considered to be a high energy bond, but it is not high energy because it is hard to break; it is in fact quite easy to break this bond. It is the electrons that are high energy.

Hydrolysis of ATP into ADP and P_i is highly exergonic, releasing 30.5 kJ/mol. Further hydrolysis of ADP into AMP and P_i can release more energy. ATP hydrolysis can be coupled with other energetically unfavourable reactions in the cell to make them more favourable (−ΔG). See page 31 in the text for a figure of adenine nucleotides showing the phosphate bonds and the resonance stabilization between them. This resonance stabilization makes the products (ADP and P_i) lower in energy than the reactant (ATP), which favours the reaction to proceed (exergonic). Also the high energy charge density associated with the three phosphate units of ATP acts to destabilize the molecule, which makes it higher in energy.

Triphosphates such as ATP are made by phosphorylation reactions and there are three types of these reactions.

Some information in this commentary is taken from the Wikipedia page ATP hydrolysis.

Substrate Level Phosphorylation

Substrate level phosphorylation does not contribute the most ATP made in the cell, but it provides additional energy to the cell to carry out reactions. ATP is synthesized directly from ADP and a reactive intermediate, usually a high energy phosphate‑containing molecule. An example is in glycolysis with the formation of pyruvate and ATP from phosphoenolpyruvate (PEP) and ADP:

Phosphoenolpyruvate + ADP ↔ pyruvate + ATP

PEP donates a phosphate to ADP to form ATP and pyruvate. This reaction has a very high negative ΔG (−31.4 kJ/mol). What this means is that PEP (reactant) has a higher energy than ATP (product), which drives the reaction to the formation of ATP.

As noted in the textbook, other triphosphates (GTP, UTP, TTP) can be synthesized by substrate level phosphorylation as well. In some reactions in the cell, these triphosphates can be interchanged in substrate level phosphorylations by the enzyme nucleoside diphosphate kinase (NDPK).

Electron Transport/ Oxidative Phosphorylation

Electron Transport Chain (NADH/FADH₂ → ATP)

As we will see in Unit 6, Metabolism I, NADH and FADH₂ are high energy compounds produced by the citric acid cycle in the matrix of the mitochondrion. Thus, they are readily available to the enzymes of the electron transport chain, which are located within the inner membrane of the mitochondrion. The electron transport chain is a series of protein complexes that transfers electrons to the final acceptor, O₂. A proton gradient across the membrane is generated by the pumping of H⁺ and this is used to phosphorylate ADP to ATP and generate energy. This is known as oxidative phosphorylation. See page 32 of the text for an illustration of the location of this system in the mitochondria and the structure of a mitochondria.

There must be redox balance in vivo. This fact means that the reduced compounds, NADH and FADH₂, must donate their electron pairs to recycle as NAD⁺ and FAD to keep the citric acid cycle going. Without the electron transport chain, the citric acid cycle cannot function.

The electron transport chain consists of six redox reactions. The electron pair on NADH is passed sequentially to (reduces) various organic compounds and metalloenzymes and finally oxygen:

To interpret the above diagram, consider two linked pairs at a time. For example, NADH (from the citric acid cycle) donates electrons to the oxidized form of complex I. Complex I is now reduced and ready to donate electrons to the oxidized form of coenzyme Q, while NAD⁺ is ready to return to the citric acid cycle for another pair of electrons.

Oxygen, the ultimate electron pair acceptor, is converted to water and removed from the system. A constant supply of oxygen carries away the electron pairs that have travelled down the electron chain. This removal converts the preceding carriers to their oxidized forms, ready to receive more electrons.

The electron transport chain carriers have a redox potential, meaning they are able to accept electrons. Coenzyme Q and cytochrome c, two components of the electron transport chain, are relatively small molecules that travel freely through the membrane. These two molecules donate their electrons with little loss of energy.

Complexes I, III, and IV of the electron transport chain are relatively large, immobile enzyme complexes. There is a large change in energy between the electrons accepted by these complexes and those donated by them. The energy difference is used to produce ATP from ADP + P_i.

Complex II is a multi‑enzyme complex that contains covalently bound FAD. This is the same FAD that is converted to FADH₂ by the citric acid cycle. Complex II can therefore be considered part of both the citric acid cycle and the electron transport chain.

Besides redox balance, there must also be chemical balance. NADH and FADH₂ lose hydronium ions (protons) in the process of donating their electrons. An interesting feature of the electron transport chain is that protons are pumped outside the mitochondrion. This proton pumping is an important feature of ATP production, as we will see in the next lesson. See page 34 of the text for a figure of the electron transport chain.

The mitochondrial protein that binds ADP and P_i and then releases ATP (ATP synthase) is physically distinct from the redox‑carrying proteins of the electron transport chain. The problem, then, is “How does the redox energy of the electron transport chain convert ADP + P_i to ATP?”

Several theories have been developed to try to explain this anomaly. Mitchell’s chemiosmotic hypothesis is the only one with experimental backing, but even it has problems. Proton pumping (according to Mitchell) arises when a reduced organic compound donates its electrons to a metalloenzyme and discards its electrons outside the mitochondrion. The metalloenzyme in turn reduces another organic compound, which picks up electrons inside the mitochondrion, and so on.

The experimental difficulty with this hypothesis is there are far more metallo‑redox enzymes in the electron transport chain than there are organic redox molecules. That is, there are not enough H⁺ carriers to pump protons out of the mitochondrion. To get around this difficulty, Mitchell indicates that the pumped protons do not all have to come from the redox carriers; some can come from amino acids on the proteins themselves. The overall message here is that the pumping of protons creates a gradient that provides the energy for ATP synthase to make ATP.

ATP‑synthase is a very large multi‑enzyme complex. Many thousands of these complexes project, much like lollipops, from the mitochondrial membrane toward the matrix (see the second figure on page 34). ATP‑synthase has binding pockets for both ADP and P_i. The proton motive force is thought to create conformational changes in ATP‑synthase. These conformational changes provide the energy to couple ADP and P_i.

Photophosphorylation

Photophosphorylation occurs in photosynthetic organisms; instead of the energy coming from the oxidation of compounds, the energy comes from the sun. Otherwise, this form of ATP synthesis is similar to oxidative phosphorylation. The figures on pages 35 and 36 of the text illustrate the similarities between oxidative phosphorylation and photophosphorylation. Both systems utilize an electron transport chain, creation of a proton gradient, and ATP synthase.

ATP synthase uses the proton gradient to generate ATP from ADP and P_i. Photophosphorylation differs from ATP synthase in the source of energy (light from the sun), H₂O as source of electrons instead of FADH₂ and NADH, the direction and movement of protons, and the use of NADP⁺ as terminal electron acceptor instead of O₂. Photons from the sun interact with chlorophyll molecules in chloroplasts. H₂O is split and an electron is passed along the chain. Photons interact with photosystem I and II and provide energy for the process. Protons are pumped to create a gradient and the electron is passed to the final acceptor NADP⁺ which becomes NADPH.

Study Questions

1. Why is the hydrolysis of ATP a highly exergonic reaction?
2. What is the basis for ATP generation through substrate‑level phosphorylation?

3. Would the following reaction favour synthesis of ATP? Why or why not?

   Phosphoenolpyruvate (PEP) + ADP ↔ Pyuvate + ATP

4. How does the generation of a proton gradient contribute to synthesis of ATP in electron transport?
5. What are the three forms/states of ATP synthase and what is the function of each state?
6. Why can you not hold your breath indefinitely?
7. Suppose a patient oxidized NADH regardless of whether ADP was present or not. What symptoms might the patient have?
8. Define photophosphorylation. What is the main difference between oxidative phosphorylation (electron transport) and photophosphorylation (photosynthesis)?
9. Why are mitochondria functional only if the inner membrane is intact, while the integrity of the outer membrane is less crucial?

If you wish to discuss any of these questions or need assistance with the material, please contact your Academic Expert (AE) by emailing the Student Success Centre at  fst_success@athabascau.ca.

Lesson 4: Energy Efficiency

Overview/Objectives

After completing this lesson, you should be able to:

1. Demonstrate an understanding of why cells are not completely energy efficient.
2. Compare the net ATP input and output of glycolysis and gluconeogenesis.

Readings and Activities

1. Read “Energy Efficiency” (page 38 in the textbook).

Commentary

As we will learn in Unit 6, glycolysis is the pathway of reactions that is responsible for the catabolic breakdown of glucose into pyruvate. This pathway results in the production of 2 ATP molecules for energy. The anabolic pathway responsible for the synthesis of glucose is gluconeogenesis, which uses 4 ATPs and 2 GTPs. These pathways run almost the reverse of each other and are coordinately regulated. Low amounts of ATP in the body will drive the process of glycolysis and high amounts will induce gluconeogenesis. See page 38 of the text for a figure of these pathways side by side.

As discussed in the textbook, the body is not completely energy efficient. You can see that gluconeogenesis requires more energy than glycolysis generates. This inefficiency in the body is why we have to eat. In addition, the inefficiency serves the function of producing heat, which keeps our bodies warm.

However, we also know that electron transport yields more ATP. Unit 6 will present the citric acid cycle and you will learn how this connects glycolysis and electron transport for ATP generation (38 ATP).

Study Questions

1. Why are cells not 100% energy efficient in their energy use? How do the yields of glycolysis and gluconeogenesis illustrate this concept?
2. How does eating contribute to equalizing the energy input and output of glycolysis and gluconeogenesis?
3. How does the amount of ATP in the cell drive the processes of glycolysis and gluconeogenesis?

If you wish to discuss any of these questions or need assistance with the material, please contact your Academic Expert (AE) by emailing the Student Success Centre at  fst_success@athabascau.ca.

Lesson 5: Metabolic Controls

Overview/Objectives

After completing this lesson, you should be able to:

1. Discuss the role of metabolic controls on energy consumption and generation in the cell.
2. Explain how muscles have maintain energy stores for use.

Readings and Activities

1. Read “Metabolic Controls of Energy,” and “Molecular Backups for Muscles” (pages 39–40 of the textbook).

Commentary

In the last lesson, we discussed how glycolysis and glyconeogenesis run the opposite of each other. This is an example of a futile cycle; however, as mentioned in the last lesson, is not exactly a futile cycle because it is highly regulated and which pathway is turned on is dependent on the concentration of ATP.

A futile cycle is defined as a cycle in which two metabolic pathways run simultaneously in opposite directions, producing no net effect except the production of heat. Futile cycles are also called substrate cycles. As the textbook explains, these types of cycles are rare in the body, as they would not serve much of a function except an overall loss of ATP and the production of heat. Therefore, most pathways in the body are not futile cycles, and pathways are intricately regulated overall. However, a few examples of futile cycles do serve the specific function of producing heat (thermal homeostasis):

• in brown adipose tissue of young mammals:  thermal homeostasis
• insect flight muscles: to generate rapid heat
• in hibernating animals: periodic arousal from torpor (reduced body temperature and metabolic rate)

Some information here is from the Wikipedia page Futile cycle.

Animals require that energy stores be accessible on demand. Muscles are the best example of this. Because muscle contraction requires ATP, for muscles to respond, muscles need stores of energy in addition to ATP. This is accomplished by having creatine phosphate and glycogen available for quick release of glucose and ATP. Creatine phosphate is a high energy compound, and the formation of creatine and ATP is highly energetically favoured (ΔG − 43.1 kJ/mol).

Creatine + ATP ↔ creatine phosphate + ADP

In a resting muscle cell, ATP is abundant and ADP is low; this drives the reaction to the right forming creatine phosphate, which is not energetically favourable (ΔG + 12.6 kJ/mol). During muscle contraction, ATP levels fall and ADP levels rise. The reaction reverses to synthesize ATP. This is another example of coupling reactions to make an unfavourable reaction energetically feasible. In addition, this is a unique mechanism muscle cells have to ensure there is enough ATP.

Study Questions

1. What is a futile cycle? What do they produce? Give an example of an animal process that relies on a futile cycle.
2. How are muscles able to have stores of energy readily available for use? Explain the mechanism.

If you wish to discuss any of these questions or need assistance with the material, please contact your Academic Expert (AE) by emailing the Student Success Centre at  fst_success@athabascau.ca.

Answers to Unit 2 Study Questions

Lesson 1 Energy Reaction

1. Oxidation is the loss of electrons by a molecule (increase in oxidation state). Reduction is the gain of electrons (decrease in oxidation state).
2. A redox reaction is one in which there is reduction and oxidation, because the oxidation states of atoms are changed between the reactants and products by an exchange of electrons between the reactants and products. They are common in biological systems because they allow the molecules and changes to be conserved within the system.
3. In the combustion of wood, the oxygen is being reduced because it is losing electrons to the carbon in the wood.
4. Catabolic reactions are oxidative and anabolic reactions are reductive.
5. The utilization of glucose to produce ATP is catabolic, and the synthesis of nucleic acids is anabolic.
6. The role of enzymes in energy coupling is to provide energy for the reaction by binding ATP and the other molecules involved in the reaction. Using the ATP for energy and hydrolyzing the ATP to ADP + P_i the enzyme can catalyze the reaction.

Lesson 2 Thermodynamics

1. The first law of thermodynamics states that energy can be exchanged between systems as heat and work. The second law of thermodynamics states that entropy, or disorder, increases in isolated systems.
2. Entropy is a measurement of the molecular disorder in a system, in joules/kelvin. In an irreversible reaction, entropy increases; and in a reversible reaction, entropy is conserved. An increase in entropy reduces the value of ΔG.
3. A negative ΔG means a reaction is favourable, exergonic (energy releasing), and spontaneous. A positive ΔG value means a reaction is unfavourable, endergonic (energy requiring), and non‑spontaneous. If the ΔG value is zero, the reaction is at equilibrium.
4. In a biological system, a reaction that is highly spontaneous (−ΔG value) can be coupled with a reaction that is non‑spontaneous (+ΔG) and, if the difference between these two reactions is still a negative value, then the reactions will proceed.
5. The ΔG for this reaction equals −7,300 calories. This reaction is exergonic.
6. ΔG°′ is equal to zero joules. This reaction is neither endergonic nor exergonic; it is at equilibrium.

Lesson 3 Cellular Phosphorylations and Electron Transport

1. The hydrolysis of ATP is a highly exergonic reaction, because the electrons in the bond are high energy. The high charge density of the three phosphate units in ATP acts to destabilize the molecule, making it higher in energy. The resonance stabilization between the phosphate groups makes the products (ADP and P_i) lower in energy than the reactant (ATP). This means the reaction to ATP is favoured to proceed and exergonic.
2. The basis for ATP generation through substrate‑level phosphorylation is that ATP is synthesized directly through ADP and a reactive intermediate which is usually a high‑energy phosphate‑containing molecule. An example is the formation of pyruvate and ATP from phosphoenolpyruvate (PEP) and ADP.
3. The following reaction would favour synthesis of ATP, because PEP is a high‑energy phosphate‑containing molecule. PEP donates a phosphate to ADP to form ATP and the resulting product is pyruvate. PEP has a higher energy than ATP which drives the reaction to the formation of ATP.
4. The generation of a proton gradient contributes to the synthesis of ATP in electron transport by providing the energy for ATP synthase to make ATP.
5. The three forms/states of ATP synthase are:
   • Loose (L):  binds ADP + P_i
   • Tight (T): squeezes the ADP + P_i together to form ATP
   • Open (O): releases the ATP into the mitochondrial matrix.
6. You cannot hold your breath indefinitely because humans are aerobes and require oxygen. Without a supply of oxygen, energy metabolism ceases because oxygen is required as the final electron acceptor for the electron transport chain and eventual ATP synthesis.
7. In these circumstances, a patient might show an elevated temperature and an inability to sustain prolonged physical exercise. The energy that the electron transport chain would normally convert to ATP is lost as heat. The amount of ATP available is less than it would be with a normal person.
8. Photophosphorylation is the synthesis of ATP using light from the sun as a source of energy. The main difference between oxidative phosphorylation (electron transport) and photophosphorylation (photosynthesis) is that  the electrons produced from the oxidation of biological molecules is the source of energy in oxidative phosphorylation, and light is the source of energy in photosynthesis.
9. Mitochondria are only functional if the inner membrane is intact, because the inner membrane keeps the protons out to establish and maintain the gradient used to drive ATP synthase. The only protons allowed to cross the inner membrane via ATP synthase.

Lesson 4 Energy Efficiency

1. Cells are not 100% energy efficient in their energy use, because some reactions may use more energy than they produce. The inefficiency in the capture of energy in reactions serves the function of producing heat.
2. Eating contributes to equalizing the energy input and output of glycolysis and gluconeogenesis by providing additional energy. The synthesis of glucose (gluconeogenesis) takes more energy than the utilization of glucose (glycolysis). To have that additional energy, we must eat to provide more fuel and energy through the breakdown (oxidation) of glucose.
3. High amounts of ATP induce gluconeogenesis (synthesis of glucose), because there is energy available and this process requires energy. Low amounts of ATP in the cell drive the process of glycolysis (breakdown of glucose) to provide ATP to the cell.

Lesson 5 Metabolic Controls

1. A futile cycle is where two metabolic pathways run simultaneously in opposite directions producing no net effect except the production of heat. They produce not function except heat and ATP loss. One example of an animal process that relies on a futile cycle is: thermal homeostasis in brown tissues of young mammals (also insect flight muscles for heat, and arousal from torpor in hibernating animals).
2. Muscles are able to have stores of energy ready for use by storing creatine phosphate. When muscles are resting ATP is high and this drives the synthesis of creatine phosphate and ADP. When muscles begin to contract ATP levels fall and the reaction of creatine phosphate and ADP runs in reverse to create creatine and ATP.

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