Metabolism and Energy

Metabolism and Energy

• All living organisms require energy for survival, growth, protection, and reproduction.

• Endothermic mammals and birds need energy to maintain body temperatures.

• Prokaryotic and eukaryotic cells use ATP for cellular work.

• Mitochondria produce most of the ATP in eukaryotic cells.

• Cells can be seen as chemical factories where numerous chemical reactions occur.

• Large molecules (polymers) are built from small molecules (monomers) in some reactions.

• Polymers undergo hydrolysis into monomers in other reactions.

• Metabolism is the sum of all chemical processes within an organism.

Energy - The Ability to Do Work

• Work is done when energy moves an object against an opposing force.

• Energy is required for physical activities and cellular processes.

• Forms of energy include chemical, electrical, mechanical, light, and thermal.

• Energy is the capacity to do work, and each form can be converted.

• Batteries convert chemical energy to electrical energy.

• Flashlight bulbs convert electrical energy to light and thermal energy.

• Photosynthesis converts light energy into chemical energy (stored in sugar).

• Living organisms obtain energy from the sun through photosynthesis or by consuming energy-rich molecules via food webs.

Kinetic Energy and Potential Energy

• All energy exists as kinetic or potential.

• Kinetic energy is the energy of motion (e.g., waves, falling rocks, contracting muscles).

• Potential energy is stored energy dependent on location or chemical structure.

• Chemical potential energy is stored in electrons and protons of atoms and molecules, especially in chemical bonds.

• Chemical potential energy can be released or absorbed during chemical reactions and is stored in food molecules like glucose.

• Gravitational potential energy depends on an object's elevation and Earth's gravitational pull.

• Energy is transferred when work is done.

• A diver gains kinetic energy and loses potential energy while falling.

The First Law of Thermodynamics

• Energy cannot be created or destroyed, only converted (law of energy conservation).

• Green plants convert sunlight into chemical energy.

• Plants capture light energy and convert some of it into chemical potential energy stored in carbohydrates.

• Chemical energy is passed from plants to other organisms.

• Animals convert chemical energy to mechanical energy for movement.

• The total amount of energy in any closed system is constant.

• Energy cannot be created or destroyed; it can only be converted from one form to another.

• If a physical system gains an amount of energy, another physical system must experience a loss of energy of the same amount.

Energy and Chemical Bonds

• Conversion of energy involves breaking and forming chemical bonds.

• Potential energy of electrons depends on their distance from atomic nuclei.

• Electrons farther from the nucleus have more potential energy and reach an excited state when they absorb energy.

• Chemical bonds result from strong attraction between electrons and two nuclei.

Energy Changes during a Chemical Reaction

• Bonds break in reactant molecules (energy absorbed), and new bonds form in product molecules (energy released).

• Breaking bonds requires energy to pull electrons away from atoms, while forming bonds releases energy as electrons move closer to a nucleus.

• Combustion of methane involves breaking bonds in methane and oxygen (energy absorbed) and forming bonds in carbon dioxide and water (energy released).

• The light and thermal energy from a flame result from electrons involved in bond formation.

Bond Energy

• Bond energy measures the strength or stability of a covalent bond, measured in kJ/mol.

• A mole is approximately $6.022 \times 10^{23}$ atoms or molecules (Avogadro's number).

• Bond energy equals the energy absorbed when a bond breaks or released when it forms.

• The energy needed to break a bond reflects its relative strength (e.g., a C=O double bond is stronger than a C-H single bond).

• Table 1 lists average bond energies of common biological molecules.

• All chemical reactions involve energy absorption (bond breaking) and release (bond forming).

Activation Energy (Ea)

• Activation energy (Ea) is the minimum energy needed to start a chemical reaction by breaking bonds in reactants.

• A spark or match provides activation energy for combustion.

• The transition state is the temporary condition where bonds in reactants are breaking and new bonds are forming.

• Activation energy equals the difference between potential energy of reactants and transition state.

Exothermic and Endothermic Reactions

• Exothermic reactions release energy, resulting in products with less chemical potential energy than reactants.

• Endothermic reactions absorb energy, resulting in products with more chemical potential energy than reactants.

Estimating Energy Changes during a Chemical Reaction (Tutorial 1)

• Calculations determine energy changes in reactions like methane combustion and water decomposition.

• The net change in energy determines if a reaction is exothermic or endothermic. *Example: Combustion of Methane

  • Balanced equation: $CH<em>4 + 2O</em>2 \rightarrow CO<em>2 + 2H</em>2O$

  • Bonds broken: 4 C-H bonds and 2 O=O bonds.

  • Bonds formed: 2 C=O bonds and 4 H-O bonds.

  • Energy absorbed: $4(411 \frac{kJ}{mol}) + 2(494 \frac{kJ}{mol}) = 2632$ kJ/mol

  • Energy released: $2(799 \frac{kJ}{mol}) + 4(459 \frac{kJ}{mol}) = 3434$ kJ/mol

  • Net energy change: $3434 - 2632 = 802$ kJ/mol (exothermic)

*Sample Problem 2: Decomposition of Water
* Balanced equation: $2H<em>2O \rightarrow 2H</em>2 + O_2$
* Bonds broken: 4 O-H bonds
* Bonds formed: 2 H-H bonds and 1 O=O bond
* Energy absorbed: $4(459 \frac{kJ}{mol}) = 1836$ kJ/mol
* Energy released: $2(436 \frac{kJ}{mol}) + 1(494 \frac{kJ}{mol}) = 1366$ kJ/mol
* Net energy change: $1836 - 1366 = 470$ kJ/mol (endothermic)

• To calculate the net energy change, use: $BE<em>{released} - BE</em>{absorbed} = net \space energy \space released \space by \space reaction$
  *Sample Problem 3: Calculating the energy content of food
  C3H7COOH + 5 O2 -> 4 CO2 + 4 H2O
  *Bonds broken = 3(C-C) + 7(C-H) + 1 (C=O) +1(C-O) + 1(O-H) +5(O=O)
  *Bonds formed = 8 (C=O) + 8 (O-H)

Calculating Molar mass:

• The molar mass of a compound is the mass of one mole ($6.022*10^{23}$ molecules) of the compound.
  *For the compound NaCl the molar mass equals the mass of one mole of Na (23 g/mol) added to the mass of one mole of Cl (35.5 g/mol). Thus, the molar mass of NaCl is 58.5 g/mol.

The Second Law of Thermodynamics

• Energy transfers and conversions result in some energy becoming unusable, usually as thermal energy.

• Machines are never 100% efficient.

• Cells convert about 40% of glucose's potential energy into usable metabolic energy; the rest is lost as thermal energy.

• The release of unusable energy increases disorder (entropy) in the system.

• The total entropy of a system and surroundings increases with any change, leading to a tendency toward disorder.

• Entropy increases when large particles break down or particles spread out.

• In chemical reactions, entropy increases when:

  • solids react to form liquids or gases

  • liquids react to form gaseous products

  • the total number of product molecules is greater than the total number of reactant molecules

• Living things are highly ordered structures that require energy to maintain order.

• Cells expend energy to establish complex structures (e.g., DNA, proteins).

• Maintaining low entropy requires energy input (e.g., chemical potential energy in food, light).

• Elite athletes need energy-rich food to maintain order in their cells.

• Overall entropy of the universe increases as living systems release thermal energy and metabolic by-products.

Reasons why average person needs to ingest enought food to supply energy:
*Simply to maintain their cells in a highly ordered state.
*According to the second law of thermodynamics, the overall entropy of the system always increases.
*By-products and released energy increase the entropy of the surroundings, but the living organisms themselves maintain order.

Spontaneous Changes

• Spontaneous changes occur on their own, once underway, without continuous energy input.

• Burning a match or a diver falling are spontaneous changes once initiated.

• Non-spontaneous reactions require continuous energy input (e.g., boiling water).

• A change from a tidy room to a messy room as a spontaneous change because it can happen “on its own.”

• A change from a messy room to a tidy room is not spontaneous; it will only occur when there is a continual supply of energy—from you!

• Physical changes rates depends on temperature.

Factors Influencing Spontaneous and Non-spontaneous Changes

Gibbs Free Energy

• Free energy (G) is the energy available to do useful work.

• Free energy values indicate which reactions provide fuel for cellular work.

• $\Delta G = G<em>{final \space state} - G</em>{initial \space state}$

• A negative $\Delta G$ indicates energy released and spontaneous reaction.

• A positive $\Delta G$ indicates energy required and non-spontaneous reaction.

*Gibbs Free Energy and Spontaneity
*reactions with a negative $\Delta G$ occur spontaneously
reactions with a positive $\Delta G$ do not

• Exergonic reactions release free energy (negative $\Delta G$).

• Endergonic reactions absorb free energy (positive $\Delta G$).

• Cells couple exergonic reactions to endergonic reactions (energy coupling).
  *Example:
  C6H12O6 + 6 O2 -> 6 CO2 + 6 H2O $\Delta G$= -2870 kJ/mol of glucose oxidized. The negative $\Delta G$value indicates that the reaction is spontaneous; free energy is released during the reaction, so the products have less free energy than the reactants.

Metabolic Pathways

• Metabolic pathways are series of sequential reactions.

• In catabolic pathways, complex molecules break down into simpler compounds, releasing energy.

• In anabolic pathways, energy is consumed to build complex molecules from simpler ones.

• Overall $\Delta G$ of anabolic pathways is positive; catabolic pathways is negative.

• Endergonic steps proceed only if coupled with exergonic reactions.
  Catabolic pathway : overall $\Delta G$ <0 releases energy Anabolic pathway : overall $\Delta G$>0 requires energy

ATP: Energy Currency of the Cell

• ATP supplies energy for DNA synthesis, protein synthesis, muscle contractions, flagella motion, etc.

• ATP (adenosine triphosphate) is the universal energy currency for almost all energy-driven actions.

• ATP carries out mechanical, transport, and chemical work.

Structure of ATP: a nitrogenous base called adenine, which is linked to a five-carbon sugar called ribose, which in turn is linked to a chain of three phosphate groups.

ATP Hydrolysis and Free Energy

• ATP consists of adenine, ribose, and three phosphate groups.

• ATP contains large amounts of free energy because of its three negatively charged phosphate groups

• ATP is hydrolyzed (broken down) to ADP and inorganic phosphate (Pi), releasing free energy.

• ATP + H2O -> ADP + P +Free energy ($\Delta G$ = -30.5 Kj/mol).

• In the formula above, an H+ ion is also released during ATP hydrolysis to form Pi (inorganic phosphate).

ATP and Energy Coupling

• ATP can be moved into close contact with a reactant molecule of an endergonic reaction.
  *Process called energy coupling ( where the terminal phosphate group breaks away from the ATP and transfers to the reactant molecule)
  * Attaching a phosphate group to another organic molecule is a process called phosphorylation.
  * Requires an enzyme to bring the ATP molecule close to the reactant molecule of the endergonic reaction
  *Most of the work carried out in a cell is dependent on phosphorylation for energy.

Phosphorylation - process by which a phosphate group is transfered from ATP to another organic molecule. This process causes the molecule to gain free energy and become more reactive.

Regeneration of ATP

• Cells regenerate ATP by combining ADP with Pi, requiring free energy.

• The energy for ATP synthesis comes from the breakdown of complex molecules (carbohydrates, fats, proteins) or light energy.

• ATP is hydrolyzed and resynthesized about 10 million times per second in a typical cell.

• The ATP cycle involves continuous breakdown and resynthesis of ATP.

Why ATP is the Universal Energy Currency

*Cells use ATP as an immediate source of energy because it has specific properties that are important for the biochemical reactions that allow proper cell functioning.
*Manageable amount of energy
*Cells can use ATP as a source of energy to drive endergonic reactions

*ATP cycle couples reactions that release free energy (exergonic) to reactions that require free energy (endergonic).

Enzymes and Activation Energy

*Enzymes enable chemical reactions to proceed more readily by reducing the amount of activation energy that the reactants must overcome.

• Enzymes do not affect where a reaction “begins” or “ends,” and they do not supply energy.

  • Laws of thermodynamics help us determine whether a reaction will proceed with or without the addition of energy, but not how rapidly it will occur.
    *Enzymes combine briefly with reactant molecules, speed up the rate of a reaction, and are then released unchanged

  • Only function of the enzyme catalyst in a reaction is to lower the potential energy level of the transition state

  • Each enzyme has one or more binding sites that bind to a specific type of reactant substrate.

  • Once a substrate binds, the enzyme-substrate complex catalyzes the given chemical reaction.
    *The root of its name is often based on the substrate, and it usually ends in the suffix –ase.
    *Enzymes are biological catalysts, typically proteins.
    *Maud Menten's contribution: Developed mathematical equation to measure rates of enzyme reactions and explained enzyme kinetics.

Activation Energy as a Barrier to Chemical Reactions

*Activation energy is that boost of energy required to break the initial bonds in the reactants.
Rock in a depression example
*Molecules possesing enough energy from their movement to reach the transition state of the reaction
*In the context of thermal energy, as propane is a molecule with a great deal of ree enrgy, it spontaneosly reacts with oxygen to form carbon dioxide and water. (a spark of energy is needed break the initial bonds).

Lowering Activation Energy with Enzymes

*Do not change the chemical makeup of the products that are formed in the reaction.
Enzymes increase the rate of a reaction by lowering the activation energy of the reaction, thereby lowering the energy barrier

Enzymes DO:
*Lower the activation energy of a reaction
*Increase the rate of a spontaneos (exergonic) reaction

Enzymes DO NOT:
*Alter the products of a reaction
*Supply free energy ($\Delta$G) to a reaction
*Make an endergonic reaction proceed spontaneously

*How enzymes reduce the activation energy of a reaction.
*Substrate molecules need to be in the transition state for a reaction to proceed.
*Enzymes function as a catalyst and increase the number of reactant molecule that reach the transition state, this is done in 3 ways:
1. Enzymes may bring the molecules together
2. Expose the reactant molecules to altered charged environments that promote catalysis
3. Change the shape of the substrate molecule

*Denaturation- enzyme undergoes a process calle denaturation and loses its shape.
The specific shape of an enzyme creates its binding sites and allows it to function properly. - misshapen enzymes cannot function effectively

The active site of the enzyme can strain or distort the substrate molecule, which weakens its chemical bonds.
*This reduces the amount of energy required to break the bonds (induced-fit model).

Food as Fuel

• Both glucose and gasoline have an abundance of hydrogen in the form of carbon-hydrogen (C-H) bonds
  *There is a great deal of potential energy in both gluclose and gasolibe as a result of their structure and bond type

• Atomic principals that allow for higher potential energy:
  *For any atom, an electron that is further away from the nucleus contains more potential energy than an electron that is more closely held by the nulceus (Figure 2).
  *electrons release energy if it moves closer to a large molecule and must gain energy to be pulled away.
  *Fat molecule contain more C-H bonds that glucose, so fat contains more energy per weight compared to proteins and carbohydrates.

Energy Changes During Oxidation:

• oxidation: atom or molecule loses electrons to another atom.

  • occurs when fuel molecules, become bonded to an oxygen atom.

• reduction - occurs when an atom or molecule gains electrons.
  *In the redox reaction the atom or molecule that gains elecrons is called the oxidizing agent
  The reaction between methane and oxygen illustrates a redox reaction in which the degree of electron shareing changes.

• Oxidation reaction example:
  Methane is combined with oxygen, where:
  *Carbon BECOMES oxidized
  *Oxygen BECAMES reduced

*Energy release: Energy is released when the electrons associated with the C-H bonds in methane move closer to teh electronegative oxygen atoms that form CO2 and H2O>

Rapid combustion vs Controlled oxidation:
Molecules that can undergo combustion and burn:

• Rapid combustion is where glucose is combusted and burned

• CO2 and H20, which are produced during the complete oxidation of all organic molecules, contains no more available chemical energy
  For cellular resperation:

• Energy contained food molecule through controlled oxidation
  Energy Released is through a series of enzyme catalyzed reactions

Enzymes Facilitate the transfer of energy by:
Dehydrogenases: which facilitate the transfer of high-energy electrons from food to to molecules that act as enrgy carriers/shuttles, such as Nicotinamide adenine dinucleotide (NAD1+)
Nicotinamide adenine dinucleotide (NAD1+): At various points during cellular resperation, dehydrogenases remove two hrdrogen atoms from a substrate molecule, transferrinf the tow high-energy electrons is high, and very little energy is lost as waste thermal energy.
Efficiency of the transfer of energy between food molecules and NAD1 is high