Chapter 6: Energy

6.1 Energy

Energy

1. What is Energy
   - Living things can’t grow, reproduce, or exhibit any of the characteristics of life without a ready supply of energy.
   - Energy is the capacity to do work.
   - Eg. Light energy comes from the sun; electrical energy powers kitchen appliances; and heat energy warms out houses.

1. Kinetic Energy
   - Is the energy of objects in motion.
   - All moving objects have kinetic energy.
   - Thrown baseballs, falling water, and contracting muscles have kinetic energy.

2. Potential energy
   - Is stored energy.
   - Eg. water behind a dam, or a rock at the top of a hill, or ATP
   - Can be potential energy that can be converted to kinetic energy.
   - Chemical energy is in the interactions of atoms, one to the other, in a molecule.
   - Glucose has much more energy than its breakdown products, carbon dioxide and water.

B) Two laws of thermodynamics

All about converting energy

1. The first law: Law of conservation of energy

• Says that energy cannot be created or destroyed but can only be changed from one form to another.

  • Eg 1. Burning coal to power a locomotive.

    • The chemical energy of coal is converted to heat energy and then heat energy is converted to kinetic energy in a steam engine.

  • Eg 2. Similarly, the potential energy of coal or gas is converted to electrical energy by power plants.

  • Eg 3. Chemical energy in the food we eat is changed to the chemical energy of ATP,

    • This ATP is potential energy that is converted to mechanical energy in muscle contraction.

2. The second law of thermodynamics: Law of loss of energy?
   - Energy cannot be changed from one form to another without a loss of usable energy.

• Usually heat/sound being lost.

• Eg 1. 25% of the chemical energy of gasoline is converted to the motion of a car.

  • 75% is lost as heat.

• Eg. 2 When muscles convert the chemical energy ATP to the mechanical energy of contraction, some of this energy becomes heat right away.

  • Heat is lost to the environment and heat dissipates, it can never be converted back to a form of potential energy.

C) Entropy

• Law of randomcy and chaos

• Entropy is a measure of randomness or disorder.

  • Eg 1. A neat room has a low entropy

  • Eg 2. A messy room has high entropy

• Eventually, a neat room becomes messy.

• All energy conversions eventually result in heat loss.

  • Eg 1. ATP is an organized, usable form of energy that has a low entropy.

  • Eg 2. Heat is an unorganized, less stable form of energy and has a high entropy.

• It takes an input of usable energy to keep your room neat.

• It takes a constant input of usable energy from the food you eat to keep you organized.

• Very rarely low entropy

6.2 Metabolic Reactions and Energy

1. Metabolic reactions

• Metabolism is the sum of all the reactions that occur in a cell.

• Reactants are substances that participate in a reaction.

• Products are substances that form from a reaction.

• Eg A +B -> C+D,

• (Reactants) (products)

• In chemistry or biochemistry, free energy is part of the reaction.

• The energy in a reaction was discovered by Josiah Gibbs who coined the term energy with the letter “G”

• ΔG shows the change in energy during a reactions

2 Types of energy reactions:
1) Exergonic (Exothermic)

A+B > energy than C+D

• Exergonic reactions are ones in which ΔG is negative

• This means energy is released during a reaction.

• This type of reaction is called a “spontaneous reaction” or a reaction that does not require us to feed it energy to occur.

2) Endergonic (Endothermic)

A+B < energy than C + D

• Endergonic reactions are where ΔG is positive.

• This means energy needs to be added to the reaction for it to proceed.

• Without the addition of energy, the reaction will not proceed.

• Chemistry calls this an endothermic reaction.

Exergonic RXN
A + B -> C + D + (+686 kcal)

Endergonic RXN
A+B + (+686 kcal) -> C + D

2. Coupled Reaction (Exer AND ender)

• ATP (Adenosine Triphosphate) is an energy molecule

• When ATP is broken down: ATP -> ADP + P (release energy)

• This is an exergonic reaction

• The energy released is used to help drive endergonic reactions that require the input of energy

  • Eg. nerve conduction, muscle contractions, and protein synthesis

• In coupled reactions, the energy released by an exergonic reaction is used to drive an endergonic reaction.

• The body is supplied with glucose from your food.

• Cellular respiration in the mitochondria produces EXERGONIC reactions that changes ADP + P = ATP

  • Energy comes from glucose (exergonic) breaks down and releases energy into the endergonic reaction for ADP to turn into ATP

3. ATP

• Conversion of energy into usable forms usually results in some heat loss

• But ATP releases just enough energy so only a minimal amount of energy is wasted.

  • E.g. pay for something with cash but no change back.

    • $100 for a lollipop? 

    • $100 at ATP 

• ATP is coupled with endergonic reactions so the energy released goes directly into an endergonic reaction.

• 3 functions of ATP.

1. Chemical work

• Supplies the energy needed to synthesize macromolecules that make up the cell.
  Eg. protein synthesis

2. Transport work.

• Supplies the energy needed to pump substances across the plasma membrane.
  Eg. Active transport.

3. Mechanical work

• Supplies the energy needed to permit muscles to contract, cilia and flagella to beat, chromosomes to move, and so forth.

4. Structure of ATP

• ATP is a nucleotide composed of 3 parts:

1. The base adenine

2. Sugar ribose (Adenine + ribose = adenosine)

3. Three phosphate groups

• ATP is called a “high-energy” compound because a phosphate group is easily removed.

• One molecule of ATP hydrolysis into ADP + P produces 7.3 kcal/mol of energy.

6.3 Metabolic Pathways

1. Metabolic pathways

• A metabolic pathway is a series of reactions

• C6H12O6 +6 O2 ——>6 CO2+ 6 H2O

• Cellular respiration is composed of multiple reactions that are simplified into one overall equation.

• Each step in the reaction requires a different enzyme.

• An enzyme is a protein molecule that speeds up reactions by reducing activation energy (catalyzes a reaction)

• Enzymes end with -ase.

• Brings together particular molecules and causes them to react with one another.

• Without an enzyme, the molecules may not find each other easily.

• An enzyme is not part of the reaction but facilitates the reaction between 2 reactants

• The reactants are called substrates.

• Not part of reaction

2. Energy of Activation

• Reactions are caused by the collision of molecules.

• Without catalysts or enzymes, the chances of collisions are much lower.

• To increase the chances of collisions, energy is added.

• Activation Energy (Ea): The energy added to cause molecules to collide/react with one another.

• Enzymes help lower Ea by helping reactants meet so less energy is required to cause collisions

• Without an enzyme, the Ea required is much higher or less chance for a reaction to occur.

3. Enzyme -substrate complexes

• Enzyme + substrate -> Enzyme - substrate complex -> Enzyme + |

• The enzyme has a specific binding site based on the enzyme called the ACTIVE SITE

• The enzyme and substrate fit together like a lock and key.

• The enzyme uses an induced fit model because the enzyme 

• Once the reaction has been completed, the product(s) is released and the active site returns to its original shape.

• Only a small amount of enzyme is needed in a reaction because enzymes are generally not used up during the reaction.

• Every reaction in a cell requires its specific enzyme.

• Enzymes are named for their substrates, as in the following examples:
  
  

4. Factors affecting enzymatic speed

• It is imperative that enzymatic reactions proceed quickly.

• f reactions occur too slowly, critical products may not be produced fast enough causing complications or even death.

• Eg. Liver produces catalase which breaks down hydrogen peroxide.
  2 H2O2 -> 2H2O + O2

• This reaction occurs 600,000X per second.

• There are certain things that affect the reaction rate:

1.  Substrate Concentration

• Higher concentration of substrate = more collisions between substrate and enzyme.

• But the increase in reaction rate plateaus when all the enzymes are saturated.

2. Temperature

• Higher temperature results in faster moving substrate which increases the chances of collision between enzyme and substrate.

• But if temperatures are too high, enzymes will denature and break its bonds causing it to lose its active binding site.

• The enzyme becomes inactive.

3. PH

• Each enzyme also has an optimal pH (usually around 6-8)

• Pepsin: pH 2 (stomach

• Trypsin: pH 8 (intestines)

• If pH is too extreme, it could denature the enzyme leading to breaking of amino acid bonds leading to a loss of active binding site.

• This renders the enzyme inactive.

4. Enzyme Concentration

• The amount of enzymes decides the rate of reaction.

• More enzymes = faster reaction rate

• When enzymes are produced, they must be turned on to activate.

• When they are no longer, they need to be turned off.

• Genes must be turned on to increase the concentration

• Phosphorylation: is the addition of phosphate groups to the enzyme.

• Eg. The enzyme kinase phosphorylates the protein to turn it on.

• Doesn’t start at 0 because the reaction does not need enzymes to start; enzymes just speed up the reaction.

5. Enzyme inhibition

• Inhibitors are molecules that bind to the enzyme in some way to prevent or reduce the rate of substrate binding to enzyme

• 2 Types of enzyme inhibition:

1.  Competitive Enzyme Inhibition

• When another molecule (resembles the substrate) competes with the substrate for the enzyme active site.
  

• Will slow down the reaction. Can be reversible or non-reversible.

• More inhibitors–slower its gonna get

2. Non-competitive enzyme inhibition

• A molecule binds to another site on the enzyme called the allosteric site. (inhibitor binding site)

• This changes the shape of the enzyme’s active site so it cannot bind to the substrate thus stopping the reaction

• The activity of the enzyme can be regulated by its product.

• When enough of the product is made, it binds to the enzyme’s allosteric site.

• Binding to the enzyme’s allosteric site causes the active site to change shape so the substrate cannot bind.

• This is called FEEDBACK INHIBITION

• Once the product is used up, the product doesn’t bind to the allosteric site and more products can be produced.

• Eg. poisons

• Eg. Cyanide is an inhibitor for an enzyme cytochrome c oxidase (irreversible)

• HCN (hydrogen cyanide) is a lethal irreversible inhibitor of enzyme action in humans.

• Eg2. Lead (Pb⁺⁺) and other heavy metals (like mercury (Hg ⁺⁺) and cadmium) are non-competitive inhibitors that cause poisoning when they bind irreversibly to enzymes and make them denature.

• Eg3. Penicillin blocks the active site of an enzyme unique to bacteria (irreversible)

6) Enzyme Structure

• An enzyme is made of two parts

1. Apoenzyme

• A protein part (frame of a car)

• Function is to provide a binding site for a specific substrate

2. Helper parts (wheels, seats, etc)

• A non protein molecule that binds to the apoenzyme to assist in the enzyme substrate complex binding process

• 2 Types:

  • Cofactors and Coenzymes

6.4 Oxidation and Reduction

Redox: Na loses electron to make Cl

• Lose electron = oxidize

• Cl gains an electron = reduction

1. REDOX (movement of electrons)
   Reduction/Oxidation Reactions (REDOX RXNs)

• LEO (lose electrons oxidation) 

• GER (gain electrons reduction)

OR

• OIL (oxidation is loss)

• RIG (reduction is gain)
  
  i) IONIC REDOX RXNS

• In ionic reactions, 1 element loses electrons and 1 gains electrons.

• Eg. Na+ + Cl - -> NaCl

• Na has been oxidized (loses electrons)

• Cl has been reduced (gains electrons)

II) COVALENT REDOX RXN (movement of hydrogen) 

• In covalent reactions, there are no physical loss of electrons because electrons are shared.

• But REDOX rxns can still occur in some covalent rxns.

• In covalent reactions, compounds will lose a hydrogen atom.

• Technically, you lose 1p+ and 1e- when you lose 1 H Atom.

• Any compound that loses an H undergoes oxidation because you have lost 1e-

• Any compound that gains an H undergoes reduction because you have gained 1 e-.

• In coupled reactions, ATP energy from exergonic reactions are released.

• The energy is given to endergonic reactions to help it synthesize macromolecules (anabolic reactions)

• But the transformation of ATP requires a REDOX reaction where electrons (in the form of hydrogen) are transferred.

• The REDOX reactions occur during cellular respiration and photosynthesis.

2. Photosynthesis

• Hydrogen atoms transferred from water to carbon dioxide.

• Water has been oxidized to produce oxygen.

• Carbon dioxide has been reduced to create glucose.

• Water is a low energy molecule.

• Glucose is a high energy molecule.

• Endergonic reaction that requires energy

• Energy comes from the SUN as solar energy.

• Captured by chloroplasts.

• A coenzyme of oxidation-reduction called NADP (nicotinamide adenine dinucleotide phosphate)

• NADP carries a positive charge and is written as NADP+

• During photosynthesis, NADP+ accepts electrons and hydrogens from water and passes by way of a metabolic pathway to CO2.
  
  Step 1: Calvin Cycle

• CO2 enters the chloroplast and enters the Calvin cycle.

• CO2 is reduced into glucose

• NADPH and ATP is oxidized into NADP+ and ADP

Step 2: Light Reactions

• Consists of several multistep reactions called Photosystem I and Photosystem II and the ETC (Electron Transport Chain)

  • H2O enters the light reaction and is oxidized.

  • NADP+ and ADP from Calvin Cycle also enters the light reaction and is reduced.

  • Oxygen is produced and leaves the chloroplast.

3. Aerobic Cellular Respiration
   - Cellular respiration is the opposite of photosynthesis.
   - Glucose has been oxidized (lost hydrogen atoms) to produce CO2.
   - Oxygen has been reduced (gained hydrogen atoms) to produce H2O.
   - Glucose is a high energy molecule.
   - Water is a low energy molecule.
   - This is an exergonic reaction where energy has been released.
   - A coenzyme called NAD (nicotinamide adenine dinucleotide) is needed. NAD accepts electrons (hydrogen) from glucose products and then later passes them on to oxygen and reduces it to produce water.
   - NAD accepts electrons (hydrogen) from glucose products and then later passes them on to oxygen to make water.
   - NAD carries a positive charged and is written as NAD+

Step 1: Glycolysis

- Occurs in the cytoplasm
- Glucose converted into pyruvate.

• Produces 2 ATP

• Produces 2 NADH which enters the mitochondria to the ETC

• Pyruvate enters the mitochondria and is converted into Acetyl CoA

Step 2: Citric Acid Cycle/Krebs Cycle
- Acetyl CoA enters the Krebs Cycle

• Oxygen enters mitochondria

• Produces more NADH which goes to the ETC

• Produces 2 ATP and CO2 which goes to the cytoplasm.

Step 3: ETC (Electron Transport Chain)
- NADH goes through ETC to produce 34 ATP which goes to the cytoplasm.

• Oxygen enters the mitochondria and H2O is produced and leaves the mitochondria.

• After 1 glucose molecule undergoes cellular respiration, 36-38 ATP is produced (2+2+31 or 34 ATP).