Energy, Enzymes, and Metabolism Study Notes

Energy, Enzymes, and Metabolism

Flow of Energy

  • Thermodynamics

    • Branch of chemistry concerned with energy changes.

    • Cells are governed by the laws of physics and chemistry.

Energy Flow in Living Systems

  • Energy flows into the biological world from the sun.

  • Photosynthetic organisms capture light energy and convert it to chemical energy.

    • This process involves converting CO2 into sugars.

    • Stored as potential energy in the chemical bonds between atoms in sugar molecules.

Oxidation vs. Reduction

  • OIL RIG:

    • "Oxidation is loss; reduction is gain."

    • Oxidation: Loss of electron.

    • Reduction: Gain of electron.

    • Lower energy leads to higher energy in the electron transfer process.

Redox Reactions

  • Coupled chemical reactions that involve electron (e-) transfer.

  • Drive ATP formation.

  • When an atom or molecule gains an electron, it is reduced (electron acceptor).

  • When an atom or molecule loses an electron, it is oxidized (electron donor).

  • Oxidation and reduction events are always coupled: If one atom loses e-, another atom must gain it.

What is energy?

  • Energy is the capacity to do work (or cause change or supply heat).

  • Exists in two states:

    1. Kinetic – energy of motion.

    2. Potential – stored energy.

  • Energy can take many forms: mechanical, heat, sound, electric current, light, or radioactivity.

  • Heat is the most convenient way of measuring energy.

Potential and Kinetic Energy

  • Stored potential energy is released as kinetic energy.

  • Position affects an object’s ability to store energy.

    • Example: Electrons in an outer shell (further from the positively charged nucleus) have more potential energy.

Kinetic Energy (or Thermal Energy)

  • Energy of movement, measured as temperature.

  • Low temperature: Molecules move slowly → perceived as "cold."

  • High temperature: Molecules move rapidly → perceived as "hot."

First Law of Thermodynamics

  • Energy cannot be created or destroyed.

  • Energy can change from one form to another.

  • Total amount of energy in the universe remains constant.

  • During conversions, some energy is lost as heat.

Second Law of Thermodynamics

  • Entropy (disorder) is continuously increasing.

  • Energy transformations spontaneously convert matter from a more ordered/less stable form to a less ordered/more stable form.

  • The universe, since its formation, has held all potential energy and has become progressively more disordered.

Chemical Reactions

  • Reactions consist of reactants and products.

    • For example: ext{CO}_2 + ext{H}_2 ext{O}
      ightarrow ext{H}_2 ext{CO}_3

  • Chemical equilibrium ( ext{ΔG} = 0):

    • Forward and reverse reactions proceed at the same rate.

    • Quantities of reactants and products remain constant.

  • Endergonic reactions require energy to proceed; thus they are non-spontaneous ( ext{ΔG} > 0).

  • Exergonic reactions release energy and are spontaneous ( ext{ΔG} < 0).

Energy in Chemical Reactions

  • Endergonic reaction: Products contain more energy than reactants; extra energy must be supplied for the reaction to proceed.

  • Exergonic reaction: Products contain less energy than reactants; excess energy is released.

Free Energy

  • G = ext{Energy available to do work} (G stands for Gibbs free energy).

  • Formula: G = H - TS

    • H = enthalpy (total energy contained in a molecule’s chemical bonds).

    • T = absolute temperature (in Kelvin).

    • S = entropy (unavailable energy).

Change in Free Energy

  • Formula: ext{ΔG} = ext{ΔH} - T ext{ΔS}

  • Positive ext{ΔG}:

    • Products have more free energy than reactants.

    • Higher H or lower S.

    • Non-spontaneous, requires energy input (Endergonic).

  • Negative ext{ΔG}:

    • Products have less free energy than reactants.

    • Lower H or higher S.

    • Spontaneous (may not be instantaneous) (Exergonic).

Spontaneous Chemical Reactions

  • Spontaneous reactions proceed without any continuous external influence; no added energy is needed.

  • Determined by two factors:

    1. The amount of potential energy: Products have less potential energy than the reactants.

    2. The degree of order: Products are less ordered than the reactants.

Activation Energy

  • The extra energy required to destabilize existing bonds and initiate a chemical reaction.

  • Rate of an exergonic reaction depends on the activation energy required.

    • Larger activation energy leads to slower reactions.

  • Increased rate can occur by:

    1. Increasing energy of reacting molecules (e.g., heating).

    2. Lowering activation energy.

    3. Increasing the concentration of molecules.

Catalysts

  • Catalysts are substances that influence chemical bonds in a way that lowers activation energy.

  • They cannot violate the laws of thermodynamics or make an endergonic reaction spontaneous.

  • Do not alter the proportion of reactants turned into products.

  • Catalysts are not changed or used up in the reaction; they can be reused.

  • In living systems, enzymes serve as catalysts.

Enzymes: Biological Catalysts

  • Most enzymes are globular proteins; some are RNA.

  • The shape of an enzyme stabilizes a temporary association between substrates.

  • Enzymes are not changed or consumed in a reaction and can be used repeatedly.

  • Example: Carbonic anhydrase produces 200 molecules of carbonic acid per hour without enzyme; produces 600,000 molecules per second with enzyme.

How Do Enzymes Speed Up Reactions?

  • Enzymes lower activation energy through a precise fit of substrate into the active site.

  • Enzyme-substrate complex formation applies stress to distort bonds, lowering activation energy.

Active Site

  • Pockets or clefts on the surface for substrate binding.

  • Substrates are the molecules undergoing reaction.

  • Forms enzyme-substrate complex.

  • Induced fit: The precise fit of substrate into active site leads to stress on particular bonds to lower activation energy.

Catalytic Cycle of an Enzyme

  1. The substrate sucrose consists of glucose and fructose bonded together.

  2. The substrate binds to the enzyme's active site, forming an enzyme-substrate complex.

  3. Binding places stress on the glucose-fructose bond, which breaks the bond.

  4. Products are released, and the enzyme is free to bind other substrates.

Enzyme Function

  • The rate of enzyme-catalyzed reaction depends on substrate and enzyme concentrations.

  • Chemical or physical conditions that affect the enzyme's three-dimensional shape can influence the reaction rate, such as:

    • Optimum temperature.

    • Optimum pH.

    • Binding of regulatory molecules.

Inhibitors

  • An inhibitor is a substance that binds to an enzyme and decreases its activity.

  • Competitive inhibitor: Competes with substrate for the active site.

  • Noncompetitive inhibitor: Binds to an enzyme at a site other than the active site, causing a shape change that makes the enzyme unable to bind substrate.

Inhibition Mechanisms

  • Competitive inhibition: Interferes with the active site so that the substrate cannot bind.

  • Noncompetitive inhibition: Changes the enzyme shape, preventing substrate binding.

Allosteric Enzymes

  • Allosteric enzymes exist in active and inactive forms.

  • Most noncompetitive inhibitors bind to an allosteric site (on/off switch).

  • Allosteric inhibitor: Binds to allosteric site, reducing enzyme activity.

  • Allosteric activator: Binds to allosteric site, increasing enzyme activity.

ATP (Adenosine Triphosphate)

  • ATP is a nucleotide and is the main energy currency all cells use.

  • Composed of:

    • Ribose (five-carbon sugar).

    • Adenine (purine with two C-N rings).

    • Chain of three phosphates.

  • Key to energy storage; bonds are unstable due to highly negatively charged phosphate groups repelling each other.

  • ADP (Adenosine Diphosphate) has two phosphates.

  • AMP (Adenosine Monophosphate) has one phosphate (the lowest energy form).

ATP Cycle

  • ATP hydrolysis drives endergonic reactions; unstable bonds have low activation energy and break easily, releasing energy.

  • Not suitable for long-term energy storage; fats and carbohydrates are better.

  • Cells can store only a few seconds' worth of ATP; they continually remake ATP from ADP + Pi.

Estimated ATP Turnover

  • Even a sedentary individual turns over an amount of ATP in one day roughly equal to his or her body weight.

Metabolism

  • Metabolism is the total of all chemical reactions carried out by an organism.

  • Anabolic reactions (anabolism): Expend energy to build up larger molecules.

  • Catabolic reactions (catabolism): Harvest energy by breaking down larger molecules.

Biochemical Pathways

  • Reactions occur in a sequence where the product of one reaction becomes the substrate for the next.

  • Many steps occur in specific organelles.

Feedback Inhibition

  • End-product of a pathway increases in concentration as it is synthesized.

  • More product increases the probability of binding to an allosteric site on an enzyme, causing a change that prevents normal substrate binding.

  • Shuts down the pathway to prevent waste of raw materials and energy.

Questions on Feedback Inhibition

  • To prevent over-accumulation of the end product, interventions may involve inhibiting specific enzymes in the pathway.

    • Choices could be based on which enzyme to inhibit to effectively shut down the pathway without wasting resources.