Energy Conversion and Thermodynamics

Energy Conversion

• Cells obtain energy in many forms, and have mechanisms that convert energy from one form to another
• Radiant energy (from the sun) is the ultimate source of energy for life
• Photosynthetic organisms capture about 0.02% of the sun’s energy that reaches Earth, and convert it to chemical energy in bonds of organic molecules.

Biological Work

• Matter is anything that has mass and takes up space
• Energy is the capacity to do work (change in state or motion of matter)
• Energy is expressed in units of work (kJ) or units of heat energy (kcal)
• 1 kcal = 4.184 kj

Potential and Kinetic Energy

• Potential energy is the capacity to do work as a result of position or state
• Kinetic energy is the energy of motion, when work is performed

Chemical Energy

• Chemical energy is the potential energy stored in chemical bonds
• Chemical energy of food molecules is converted to mechanical energy in muscle cells

Laws of Thermodynamics

• Thermodynamics governs all activities of the universe
• Biological systems are open systems that exchange energy with their surroundings

The First Law of Thermodynamics

• Energy cannot be created or destroyed
• Energy can be transferred or converted from one form to another, including conversions between matter and energy
• The energy of any system plus its surroundings is constant
• Organisms must capture energy from the environment and transform it to a form that can be used for biological work.

The Second Law of Thermodynamics

• When energy is converted from one form to another, some usable energy (energy available to do work) is converted into heat that disperses into the surroundings
• As a result, the amount of usable energy available to do work in the universe decreases over time (Entropy increases)
• Heat is the kinetic energy of randomly moving particles.

Entropy

• The measure of the disorder or randomness of energy
• Organized, usable energy has a low entropy
• Disorganized energy, such as heat, has a high entropy
• No energy conversion is ever 100% efficient
• The total entropy of the universe always increases over time.

Energy and Metabolism

• Metabolism: all chemical reactions taking place in an organism
• Includes many intersecting chemical reactions
• Anabolism: pathways in which complex molecules are synthesized from simpler substances
• Catabolism: pathways in which larger molecules are broken down into smaller ones.

Enthalpy

• Enthalpy is the total potential energy of a system
• Every specific type of chemical bond has a certain amount of bond energy (the energy required to break that bond)
• Enthalpy is equivalent to the total bond energy.

Free Energy

• Free energy is the amount of energy available to do work under the conditions of a biochemical reaction
• Enthalpy (H), free energy (G), entropy (S); and absolute temperature (T) are related by the equation: H = G + TS
• As entropy increases, the amount of free energy decreases.

Changes in Free Energy

• Changes in free energy can be measured, even though the total free energy of a system cannot
• The equation ΔG=ΔH−TΔS can be used to predict whether a particular chemical reaction will release energy or require an input of energy.

Exergonic Reactions

• Exergonic reaction: releases energy and is a “downhill” reaction, from higher to lower free energy
• ΔG is a negative number for exergonic reactions.

Endergonic Reactions

• Endergonic reaction: a reaction in which there is a gain of free energy
• ΔG has a positive value: the free energy of the products is greater than the free energy of the reactants
• Requires an input of energy from the environment.

Diffusion

• Diffusion is an exergonic process
• Randomly moving particles diffuse down their own concentration gradient-no energy input required
• A cell must use energy to produce a concentration gradient.

Free-Energy Changes and the Concentrations of Reactants/Products

• Free-energy changes in a chemical reaction depend on the difference in bond energies between reactants and products
• Also depends on concentrations of both reactants and products
• A reaction that proceeds forward and in reverse at the same time eventually reaches dynamic equilibrium.

Changes in Free Energy (cont’d.)

• If the reactants have much greater free energy than the products, most of the reactants are converted to products and vice-versa
• If the concentration of reactants is increased, the reaction will “shift to the right” and vice-versa
• The reaction always shifts in order to reestablish equilibrium.

Coupled Reactions

• Endergonic reactions are coupled to exergonic reactions
• The thermodynamically favorable exergonic reaction provides energy required to drive a thermodynamically unfavorable endergonic reaction
• In a living cell the exergonic reaction often involves the breakdown of ATP.

Coupled Reactions (cont’d.)

• Two reactions taken together are exergonic:
  • A → B ΔG = +20.9 kJ/mol (+5 kcal/mol)
  • C → D ΔG = −33.5 kJ/mol (−8 kcal/mol)
  • Overall ΔG = −12.6 kJ/mol (−3 kcal/mol)
• Reactions are coupled if pathways are altered for a common intermediate link:
  • A + C → I ΔG = −8.4 kJ/mol (−2 kcal/mol)
  • I → B + D ΔG = −4.2 kJ/mol (−1 kcal/mol)
  • Overall ΔG = −12.6 kJ/mol (−3 kcal/mol).

ATP, Energy Currency of the Cell

• Adenosine triphosphate (ATP): Nucleotide consisting of adenine, ribose, and three phosphate groups
• The cell uses energy that is temporarily stored in ATP
• Hydrolysis of ATP yields ADP and inorganic phosphate.

ATP Donates Energy

• Hydrolysis of ATP can be coupled to endergonic reactions in cells, such as the formation of sucrose
• ATP + H2O → ADP + Pi
  • ΔG = −32 kJ/mol (or −7.6 kcal/mol)
• glucose + fructose → sucrose + H2O
  • ΔG = +27 kJ/mol (or +6.5 kcal/mol)
• glucose + fructose + ATP → sucrose + ADP + Pi
  • ΔG = −5 kJ/mol (−1.2 kcal/mol).

ATP Donates Energy (cont’d.)

• The intermediate reaction in the formation of sucrose is a phosphorylation reaction: phosphate group is transferred to glucose to form glucose-P
  • glucose + ATP → glucose-P + ADP
  • glucose-P + fructose → sucrose + Pi.

Maintaining a High Ratio of ATP to ADP

• A typical cell contains more than 10 ATP molecules for every ADP molecule
• High levels of ATP makes its hydrolysis reaction more strongly exergonic, and more able to drive coupled endergonic reactions
• The cell cannot store large quantities of ATP
• ATP is constantly used and replaced.

Energy Transfer in Redox Reactions

• Energy is transferred through the transfer of electrons from one substance to another
• Oxidation: substance loses electrons
• Reduction: substance gains electrons
• Redox reactions often occur in a series of electron transfers
• For cellular respiration, photosynthesis, and many other chemical processes.

Electron Carriers Transfer Hydrogen Atoms

• Redox reactions in cells usually involve the transfer of a hydrogen atom
• An electron, along with its energy, is transferred to an acceptor molecule such as nicotinamide adenine dinucleotide (NAD+), which is reduced to NADH
• XH2 + NAD+ → X + NADH + H+.

Electron Carriers (cont’d.)

• An electron progressively loses free energy as it is transferred from one acceptor to another
• In cellular respiration, NADH transfers electrons to another molecule
  • Energy is then transferred through a series of reactions that result in formation of ATP
• NADP+ is not involved in ATP synthesis
  • Electrons of NADPH are used to provide energy for photosynthesis.

Other Important Electron Carriers

• Flavin adenine dinucleotide (FAD): nucleotide that accepts hydrogen atoms and their electrons
  • Reduced form is FADH2
• Cytochromes: proteins that contain iron
  • The iron component accepts electrons from hydrogen atoms, then transfers the electrons to some other compound.

Enzymes

• Cells regulate rates of chemical reactions with enzymes, which increase speed of a chemical reaction without being consumed by the reaction
• Example: Catalase has the highest known catalytic rate; it protects cells by destroying hydrogen peroxide (H2O2)
• Most enzymes are proteins, but some types of RNA molecules also have catalytic activity.

Activation Energy

• All reactions have a required energy of activation
• Even a strongly exergonic reaction may be prevented from proceeding by the activation energy required to begin the reaction
• Energy of activation (EA) or activation energy: the energy required to break existing bonds and begin a reaction.

Enzyme - Substrate Complex

• An enzyme controls the reaction by forming an unstable intermediate complex with a substrate
• When the ES complex breaks up, the product is released
• Enzyme molecule is free to form a new ES complex:
  • enzyme + substrate(s) → ES complex
  • ES complex → enzyme + product(s).

Active Sites

• Enzymes bind to substrates at active sites to position them close together to speed up the reaction.
• Induced fit: binding of substrate to enzyme causes a change in shape to enzyme
  • Distorts the chemical bonds of the substrate
• Proximity and orientation of reactants, plus strains in their chemical bonds, facilitate the breakage/formation of products.

Enzyme Specificity

• Enzymes are specific due to shape of active site and its relationship to the shape of the substrate
• Some are specific only to a certain chemical bond (e.g. lipase splits ester linkages in many fats)
• Scientists classify enzymes into six classes that catalyze similar reactions
• Each class is divided into many subclasses.

Cofactors

• Many enzymes require cofactors
• Some enzymes have two components: an apoenzyme and a cofactor
• Neither alone has catalytic activity
• Enzyme functions only when the two are combined.
• Cofactors may be a specific metal ion (e.g. Iron, copper, zinc, and manganese)

Coenzymes

• Coenzymes are organic, nonpolypeptide compounds that bind to the apoenzyme and serve as a cofactor
• Most are carrier molecules:
  • NADH, NADPH, and FADH2 transfer electrons
  • ATP transfers phosphate groups
  • Coenzyme A transfers groups derived from organic acids
• Most vitamins are coenzymes or components of coenzymes.

Optimal Temperature

• Each enzyme has an optimal temperature.

Heat-Tolerant Archaea

• Certain archaea have enzymes that allow them to survive in extreme habitats.

Optimal pH

• Each enzyme has an optimal pH
• Optimal pH for most human enzymes is 6 to 8.

Metabolic Pathways

• Metabolic pathway: the product of one enzyme-controlled reaction serves as substrate for the next in series of reactions
• Removal of intermediate and final products drives the sequence of reactions in a particular direction
• Enzymes can bind to one another to form a multienzyme complex that transfers intermediates in the pathway from one active site to another.

Regulating Enzymatic Activity

• The cell regulates enzymatic activity
• Gene control: a specific gene directs synthesis of each type of enzyme
  • Gene may be switched on by a signal from a hormone or other signal molecule
  • Amounts of enzymes influence overall cell reaction rate.

The Cell Regulates Enzymatic Activity (cont’d.)

• The product of one enzymatic reaction may control activity of another enzyme in a sequence of enzymatic reactions
  • When concentration of a product is low, the sequence of reactions proceeds rapidly
  • When concentration of a product is high, reactions stop.

Feedback Inhibition

• Feedback inhibition is a type of enzyme regulation in which the formation of a product inhibits an earlier reaction in the sequence.
• Removal of the allosteric inhibitor allows the enzyme to bind its substrates (enzyme is active).

Enzyme Inhibition

enzymes are inhibited by certain chemical agents:

Enzyme Inhibition

• Irreversible inhibition: inhibitor permanently inactivates or destroys an enzyme when the inhibitor combines with one of the enzyme’s functional groups, either at the active site or elsewhere
  • Many poisons are irreversible enzyme inhibitors, such as mercury and lead, nerve gases, cyanide.

Enzyme Inhibitors

• Some drugs used to treat bacterial infections directly or indirectly inhibit bacterial enzyme activity
  • Example: sulfa drugs compete with PABA for the active site of the bacterial enzyme
  • Example: penicillin and related antibiotics irreversibly inhibit the bacterial enzyme transpeptidase
• Drug resistance is a growing problem.