Bioenergetics

Patcharee Boonsiri

For Education Only

Cell is the smallest unit of life. Metabolic processes that occur in cells help keeping the organism alive.

In this ebook, there are 4 chapters.

Chapter 1 Bioenergetics :

Living organisms use energy for their functions and they have the metabolic pathway to produce energy.

Chapter 2 Thermodynamics :

The laws of Thermodynamics are about conservation of energy and the order/disorder in living organisms.

Chapter 3 Gibbs’ free energy :

This help predicting direction of the chemical reactions in cells.

Chapter 4 High energy compound ATP :

ATP is the energy currency for the living organisms.

Part 1 Bioenergetics

What are the 4 essential things the cells need? 1.molecular building blocks 2.chemical catalysts 3.genetic information 4.energy

The activities of living things require energy.

The energy help the cells to perform functions such as growth, maintaining balance of the body or called homeostasis, repair, reproduction, movement, and defense. This means that all living organisms must obtain and use energy for their life.

What is energy? Energy is ability to do work. Each cell can convert fuel to energy in the form that our bodies can use.

Unit of Energy: Calorie, Joule (SI unit) 1 cal = 4.184 J

There are 2 forms of energy 1.Potential energy - is stored energy ( for example, chemical, concentration gradient, electrical potential energy) 2.Kinetic energy - energy that is actively engaged in doing work (for example, radient, thermal, mechanical energy)

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What is work? Work is the use of energy to drive all processes other than heat flow. Work = force x distance

Examples of biological works. 1.Synthetic work 2.Mechanical work 3.Electric work 4.Concentration work 5.Heat production 6.Bioluminescence

What is (are) the energy source for living cells?

The first source of energy is from sunlight. The plants use sunlight for photosynthesis. Some animals eat plants. We eat both plants and animals. We get energy from these food. Energy in the molecules of carbohydrate, protein and lipid is stored in the form of the chemical bonds. We can say that energy is derived from the chemical bond energy in food molecules.

Why do we eat everyday? This is because our cells require a constant supply of energy to generate and maintain the biological order in our body. Please notice that energy passes through an ecosystem in one direction only.

Cells release the energy stored in their food molecules through a series of oxidation reactions.

For oxidation reaction, electrons are transferred from one molecule to another.

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Food molecules act as electron donors.

Animals consume food to obtain energy. Carbohydrates, lipids, proteins, and nucleic acids provide chemical energy for them. During food breakdown (catabolism), product of oxidation rx. has a lower energy than the donor molecule. At the same time, e- acceptor molecules capture some energy lost from the food molecule and store it for later use. When carbon atoms from food molecule are fully oxidized at the end of the rx.  they are released as CO2 Cells do not use the energy from oxidation rx. as soon as it is released but convert it into ATP and NADH.

Plants convert light energy from the sun into chemical energy stored in molecules by photosynthesis. During photosynthesis, the green plants capture light energy and convert water, CO2, and minerals into oxygen and energy-rich organic compounds.

What is “bioenergetics” ?

Bioenergetics is the study of the transformation of energy in living organisms. - Living organisms acquire and transform energy in order to perform biological work.

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Energy flows into an ecosystem in the form of light and exits in the form of heat. Therefore, bioenergetics is the study of how organisms manage their energy resources through metabolic pathways.

How do the food (chemical source of energy) metabolized?

Chemical source can be metabolized by metabolic network system. Metabolism in our body is a network of chemical reactions, called pathways. Some of these chemical reactions occur spontaneously and release energy whereas the other chemical reactions are non-spontaneous and require energy in order to proceed.

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Metabolism is the totality of an organism’s reactions that arise from interactions between molecules.

All of the chemical reactions that take place inside cells are the cell’s metabolism. Metabolism help organisms to transform the chemical energy stored in molecules into energy that can be used for cellular processes.

Catabolic pathway- breakdown complex molecules into simpler molecules.

Anabolic pathway - form complex molecules from simpler molecules; biosynthesis requires energy input.

Part 1 – conclusion Cells need energy to accomplish the tasks of life Energy sources are obtained in the form of sunlight and food molecules

Eukaryotic cells make energy-rich molecules (ATP and NADH) via energy pathways including photosynthesis, glycolysis, Krebs’ cycle, and oxidative phosphorylation

Excess energy is stored in polysaccharides (starch and glycogen) and lipids

Part 2 –Thermodynamics

Thermodynamics is the study of energy transformations. Thermodynamics involved with the flow and interchange of heat, energy and matter in a system of interest.

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The advantage of Thermodynamics is that it predicts whether a reaction will occur spontaneously.

Cells are not in equilibrium

Living organisms are open systems. They can exchange energy and matter with surroundings. The open systems involve with a constant flow of materials in and out, preventing metabolic pathways from reaching equilibrium. A catabolic pathway in a cell releases free energy in a series of reactions.

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How is the energy conserved in living organism?

An organism’s metabolism transforms matter and energy according to the laws of thermodynamics. There are 3 laws of Thermodynamics. In biological systems, we usually involve with the 1st and the 2nd law of Thermodynamics.

The 1st law of Thermodynamics (Conservation of energy) Energy can be transferred and transformed, but it cannot be created or destroyed.

For example, You are transforming chemical energy from food into kinetic energy for cycling. Plants convert the energy of sunlight (radiant energy) into chemical energy stored in organic molecules.

Energy flow through living systems such as cells. Human body is an open system. It can exchange both energy and matter with its surroundings.

Can cells use 100% of energy from food?

Transfer of energy, in the 1st law, is not 100% efficient. It releases thermal energy or heat.

What is enthalpy?

Enthalpy (H) is the heat absorb or lost of a chemical system at constant pressure.

For the chemical reactions, measuring enthalpy is difficult. It is easier to measure enthalpy change or ∆H.

When a chemical reaction releases heat, e.g. dissolving NaOH in distilled water, it is exothermic reaction and has a negative ∆H.

When a chemical reaction absorbs heat, e.g. wash your skin with alcohol, it is endothermic reaction and has a positive ∆H.

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What is entropy? According to the 1st law of Thermodynamics, energy cannot be created or destroyed, but it can change from more-useful forms into less-useful forms. In most cases, this unusable energy is in the form of heat.

Heat that does not do work goes towards increasing the randomness (disorder) of the universe called entropy (S).

The 2nd law of Thermodynamics The universe tends toward greater disorder.

Any process, including a chemical reaction, will proceed in a direction that increases the entropy of the universe.

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Systems tend to proceed from ordered to disordered states (increase entropy)

Energy is needed to make ordered state. Therefore, the 1st Law of Thermodynamics tells us about conservation of energy among processes, while the 2nd Law of Thermodynamics tells us about the directionality of the processes, that is, from lower to higher entropy.

ΔS is + or – or 0?

The cells are organized into tissues, and the tissues into organs. Your body maintains homeostasis to keep you alive. We try to maintain “the order” in our body. For example, amino acids can form proteins. Protein structure is highly order compare to amino acids. ΔS of this process is -ve which means you need energy to synthesis proteins from amino acids (which are building blocks of proteins). When living organism die, proteins are degrade to amino acids. The proteins which are large, complex biomolecules are converted into a lot of small, simple amino acid molecules. In this event, ΔS = +ve which means that the rx. occur spontaneous.

ΔS = +ve the rx.occur spontaneous ΔS = - ve the rx. occur in opposite direction ΔS = 0 the rx.occur is in equilibrium

Part 2 – conclusion The 1st law of Thermodynamics Energy cannot be created or destroyed Energy can be transferred and transformed During every energy transfer or transformation, some energy is unusable, often lost as heat

The 2nd law of Thermodynamics The disorder (entropy) in the universe is continuously increasing Living systems use energy to maintain order. This increase the entropy of the universe

Part 3 – Gibb’s free energy and energy coupling

What is “free energy”?

Free enegy (G) is the energy available to do work when temperature and pressure is uniform throughout the system, as in a living cell.

The following formula shows the relationship between the 1st and the 2nd law of Thermodynamics.

ΔG = ΔH - TΔS

Unit of ΔG and ΔH is J/mol or cal/mol Unit of ΔS is J/mol.K or cal/mol.K

ΔG during the rx is influenced by • Temperature • Pressure • Initial concentration of substrate and product • pH of solution

ΔG o is different from ΔG o’ The standard condition of both of them are as follows: temp. 25oC (298 Kelvin). pressure 1 atm, initial conc. of 1 M for all reactants and products. At pH 7 , we add the prime (‘) .

ΔG predicts direction of rx ΔG is directly related to Keq or chemical equilibrium constant. We can calculate Keq from the chemical reaction here.

If Keq is large, the products are favored.

ΔG = - RTln Keq = -2.303 RT logKeq

When Keq > 1, ΔG is less than, 0, the process is exergonic and will proceed spontaneously in the forward direction to form more products.

When Keq = 1, ΔG is greater than 0, the process is endergonic and not spontaneous in the forward direction.

When Keq < 1, ΔG equals, 0, the system is in equilibrium and the concentrations of the products and reactants will remain constant

For the chemical reactions

Endergonic reactions are the reactions that required an input of energy. Reactants have more free energy than the products.

Exergonic reactions are the reactions that that release energy. Reactants have less free energy than the products.

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Why enzymes are needed for biochemical reaction?

Enzyme is a biological catalys. Enzyme catalyzes the reaction in our body, then the reaction can go faster than the reaction without enzyme.

Enzyme help lowering activation energy (Ea) of the reactions. Enzyme also help increasing Keq of the reactions.

Enzyme cannot change ΔG of the reaction.

ΔG can tell that the rx. can occur but cannot tell the rate (how fast) of rx.

https://ka-perseus-images.s3.amazonaws.com/2d4f6af428b1bd852cd959c199227e1e85e6577b.png How can we make the unfavorable reaction occur?

Glucose + Pi Glucose-6 P + H2O ΔGo’ = +14 kJ/mol ATP + H2O ADP + Pi ΔGo’ = -30.5 kJ/mol Glucose + ATP Glucose-6 P + ADP ΔGo’ = - 17 kJ/mol

Living organisms have the ability to couple exergonic and endergonic reactions. By coupling reaction (with ATP), the overall chemical process is made exergonic so it can occur spontaneously due to –ve ΔG.

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A living system’s free energy is energy that can do work under cellular conditions (break and form chemical bonds). Gibbs’ free energy (G) – in a cell, the amount of energy contained in a molecule’s chemical bonds (temp and pressure constant) Change in free energy (ΔG) • Endergonic - any reaction that requires an input of energy • Exergonic - any reaction that releases free energy

Living organisms have the ability to couple exergonic and endergonic reactions Part 4 – high energy compound

Most of oxidation-reduction (redox) reaction in general chemistry involved the flow of electron (e-) from one compounds to the other compounds. Oxidation is loss of e- Reduction is gain of e-

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In living organisms, the processes of metabolism need help of high energy molecules. The main purpose of these high energy molecules is to transfer either inorganic phosphate groups (Pi) or hydride (H-) ions.

The Pi are used to make high energy bonds with many of the intermediates of metabolism. These bonds can then be broken to yield energy and then driving the metabolic processes.

Hydride ions can be transferred from one intermediate to another resulting in a net oxidation or reduction of the intermediate.

Oxidation is a loss of hydride (or hydrogen) Reduction is a gain of hydride (or hydrogen).

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Adenosine triphosphate (ATP) ATP is the energy currency for living organisms. The goal of catabolism is to synthesize ATP. After the body used ATP, ATP is then break- down into adenosine diphosphate (ADP) and Pi .

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Why ATP (adenosine triphosphate) is called “energy currency” ?

1.Electrostatic repulsion of the positively charged phosphates of phosphoanhydride bonds.

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2.Resonance stabilization : When the phosphoanhydride bonds are broken there is an increased stability due to the resonance of that product's structure

Conversion from ATP to ADP is an important reaction for the supplying of energy for life processes

In a cell, the ratio of ATP to ADP concentrations is called the "energy charge" .

If there is more ATP than ADP, the cell can use ATP to do work. If there is more ADP than ATP, the cell must synthesize ATP via oxidative phosphorylation.

ATP can be synthesized by

1.Substrate level phosphorylation Phosphate group is directly added to ADP to form ATP.

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2.Oxidative phosphorylation This occur at the inner membrane of mitochondria.

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NADH and FADH2 (from metabolic pathways) are reduced forms of high energy molecules or called reducing equivalent. They donate their electrons to the electron carriers of the electron transport chain (ETC). After oxygen get electron (oxygen is the final electron acceptor in this process) ATP is produced by oxidative phosporylation.

Electron transport chain and oxidative phosphorylation

Electron transport chain and oxidative phosphorylation capture the energy in the redox potential of NADH and FADH2 result in ATP production.

Electron is transported from Complex I (or II)  III  IV  V, create concentration and pH gradients.

This look like series of sequential oxidation/reduction (redox) reactions. In each reaction, an electron donor is oxidized and an electron acceptor is reduced. During these processes, protons (H+) are pumped out (from the matrix to intermembrane space of mitochondria). This cause the different in proton concentration (or we can called proton gradient or pH gradient) between the matrix and intermembrane space.

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Oxidative phosphorylation is the process of making ATP by using the proton gradient generated by the electron transport chain. Proton motive force then drives proton to go back to the matrix through the ATP synthase.

Therefore, release of the energy in the gradient back through the membrane through the protein ATP synthase can drive ATP synthesis.

In electron transport chain, flow of electrons is spontaneous and thermodynamically favorable.

Electrons flow downhill and spontaneously moving from molecules that are strong e- DONORS to strong e- ACCEPTORS (oxygen is the very strong acceptors). That means e- move from high energy state to low energy state. The next carrier has greater affinity for electrons than the previous as you can see the standard reduction potential in the Tables.

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Why there are many steps in electron transport chain ?

We need proton gradient from many steps of electron transport chain. Only one step is not possible for us to get enough proton gradient.

How can ATP synthase generate ATP ?

F0F1 ATP Synthase uses the proton gradient energy for the synthesis of ATP.

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Proton flow through the Fo channel  C unit rotates  conformation change  ATP synthesized.

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Part 4 Conclusion ATP is the energy currency of living cell. ATP ADP + Pi (exergonic rx.) can couple with many endergonic rx.

We get NADH and FADH2 (reducing equivalents which can give e- to complex in electron transport chain) from metabolism e.g. glycolysis, Kreb’s cycle

In electron transport chain, e- pass from complex I, II, III, IV and O2 is the final e- acceptor.

ATP synthase use energy from proton gradient to generate ATP (oxidative phosphorylation).

Acknowledgements We appreciate and thank the websites that provide the figures for this e-book. This e-book is for education only.