Chapter 6

6.1 The Flow of Energy in Living Systems 

• Thermodynamics

  • The branch of chemistry concerned with energy changes 

  • Means “heat changes” 

• Energy 

  • The capacity to do work 

  • Two states of energy: 

    • Kinetic energy 

      • Energy of motion; moving objects perform by causing other matter to move 

    • Potential energy 

      • Stored energy; objects that are not entirely moving but have the potential to do so 

  • Energy exists in many forms:

    • Mechanical energy, heat, sound, electric current, light, or radioactive radiation 

    • Heat is the most convenient form of measurement 

      • Kilocalorie (kcal/Cal) is the most common, which is equal to 1000 calories (cal) 

        • One calorie is the heat required to raise the temperature of one gram of water one degree Celsius 

• Sun

  • Provides the energy for life (approx 40 million billion calories per second) 

    • Plants, algae, and photosynthetic bacteria capture only a fraction of this energy through photosynthesis 

• Covalent bond

  • The strength of a covalent bond is measured by the energy required to break it 

    • Ex: it takes 98.8 kcal to break one mole of C-H bonds in organic molecules 

• Oxidation-reduction reactions (redox reactions) 

  • OIL RIG [oxygen is losing (electrons), reduction is gaining (electrons)] 

  • Reduced molecule has a higher level of energy than oxidized form 

  • Oxidation and reduction reactions always take place together 

6.2 The Laws of Thermodynamics and Free Energy 

• Two laws of thermodynamics

  • First law: 

    • Energy cannot be created or destroyed, it can only go from one form to another form (potential to kinetic or vice versa)

      • Ex: Jason devouring peyton’s gyatt

        • Jason is transferring the potential energy from Peyton’s gyatt to himself, just like how Peyton’s gyatt got its energy from a hawk tuah 

        • Also energy dissipates into the environment, as heat (the measure of the random motion of molecules), after each conversion 

    • Total amount of energy in the universe remains constant 

  • Second law: 

    • Entropy (disorder) is continuously increasing

      • Disorder is more likely than order 

      • Energy transfers from a more ordered, but less stable form, to a less ordered, and more stable form 

    • More and more of the universe’s finite potential energy is being converted to kinetic energy 

• G = H - TS

  • This equation is used to find the total free energy, where: 

    • G is free energy, the energy available to do work in any system

    • H is enthalpy, energy contained in a molecule’s chemical bonds 

    • T is the temperature in kelvin 

    • S is entropy

• ΔG = ΔH - TΔS

  • This equation is used to find the change in free energy from a reaction 

    • When ΔG is positive, it is an endergonic reaction, a reaction that requires an input of energy 

      • Enthalpy (H) is higher or the entropy (S) is lower 

      • Endergonic reactions DO NOT proceed spontaneously 

    • When ΔG is negative it is an exergonic reaction, a reaction that releases excess free energy as heat 

      • H is lower or S is higher 

      • Exergonic reactions PROCEED spontaneously 

    • The reaction occurs spontaneously when TΔS  is greater than ΔH 

    • Endergonic reaction would become an exergonic reaction in reverse and vice versa 

      • Equilibrium constant is when the reaction is at equilibrium

• Activation energy 

  • The energy needed to break existing bonds to initiate a chemical reaction 

    • Rate of exergonic reaction is proportional to the amount of activation energy needed 

      • Reactions with more activation energy tend to proceed slowler because fewer molecules succeed in overcoming the initial energy hurdle 

• Catalysis 

  • The process of lowering the activation energy 

  • Catalysts are the substances that accomplish this 

    • They accelerate both the forward and reverse reactions, by the same amount, so, it doesn’t alter the proportions of reactant to product 

    • They cannot violate the basic laws of thermodynamics 

6.3 ATP: The Energy Currency of Cells 

• ATP (adenosine triphosphate) 

  • Powers almost every energy-requiring process in cells 

• Structure 

  • Ribose, a 5-carbon sugar

  • Adenine, an organic molecule, composed of two carbon-nitrogen rings 

  • A chain of 3 phosphates 

• Energy storage 

  • Energy lies within the really unstable bonds between the phosphates in the triphosphate group

    • They are highly negatively charged and strongly repel from each other 

  • The bonds holding them together have a low activation energy and are easily broken by hydrolysis 

    • They release a considerable amount of energy when the bonds are broken (7.3kcal/mol) , and the energy is used to perform work 

      • Hydrolysis of ATP has a negative ΔG 

    • In most reactions of ATP, only the outermost phosphate bond is hydrolyzed, cleaving the phosphate group at the end: ATP then becomes adenosine diphosphate (ADP) and an inorganic phosphate  (P_i)

      • Both of the two terminal phosphates can be hydrolyzed, leaving behind adenosine monophosphate (AMP)

• ATP hydrolysis drives endergonic reactions

  • Cleavage of the terminal phosphate releases energy that supplies the endergonic reaction’s energy needs 

• ATP cycle 

  • Exergonic reactions synthesize ATP from ADP + P_i, and then hydrolysis of ATP provides energy for endergonic reactions 

  • Most cells don’t maintain a huge supply of ATP 

6.4 Enzymes: Biological Catalysts 

• Enzymes can exists as active or inactive conformation aka allosteric enzymes 

• Enzymes alter the activation energy

  • 3D shape of an enzyme allows it to temporarily associate between substrates, the molecule undergoing the reaction 

    • Bridges two substrates together in the correct orientation, or stressing specific chemcal bonds, to lower the A.E

  • The enzyme isn’t changed or consumed in the reaction, so only a little bit is needed, and it can be used over and over 

• Active sites 

  • Actives sites are the clefts/pockets found on enzymes 

    • Substrates binds to enzymes on these sites, forming a enzyme-substrate complex 

      • After fitting perfectly, amino acid side groups from the enzyme interact chemically with the with the substrate to lower the A.E. needed to break the bonds 

      • The substrates have now been converted into products and dissociates from the enzyme

      • The cycle repeats with the next one 

• Multienzyme complexes 

  • Several enzymes catalyzing different steps of a reaction associated with one another in noncovalently bonded assemblies

    • The product of one reaction can be delivered to the next enzyme instantly 

    • Possibility of unwanted side reactions is eliminated because the substrate never leaves the complex during its passage 

    • All of the reactions that take place within the complex can be controlled as a unit 

• Nonprotein enzymes 

  • Ribozymes 

    • RNA catalysts 

    • Two types:

      • Intramolecular ribozymes

        • Folded structures and catalyze reactions on themselves 

      • Intermolecular ribozymes 

        • Act on other molecules without being changed themselves 

• Factors affecting enzyme function 

  • Temperature

    • Optimum tempeature where the enzyme-catalyzed reaction is the most efficient

      • Humans is between 35-40 degrees celsius  

    • Below this temp, there are less collisions between enzymes & substrates 

    • Above this temp, the forces to maintain the enzyme’s shape against the increased random movement of the atoms, become weaker and are disrupted 

  • pH

    • Optimum pH usually ranges from 6-8

    • Changing the concentration of hydrogen ions shifts the balance between positively and negatively charged amino acid residues, disrupting the bonds and the 3D shape 

  • Salinity 

    • Adds or removes cations (+) and anions (-)

    • Disrupts bonds and 3D shape 

  • Inhibitors and activators 

    • A substance that binds to an enzyme and decreases its activity 

    • Occurs in two ways: 

      • Competitive inhibitors

        • Substrates compete for the same active site, and once occupied, they prevent other substrates from binding 

      • Noncompetitive inhibitors 

        • Bind to the enzyme that’s NOT the active site, changing the enzyme shape, and making it unable to bind with other substrates 

    • Allosteric sites

      • Most noncompetitive inhibitors bind to this site 

      • Serve as on/off switches

        • Switch the configuration of the enzyme to active or inactive 

    • A substance that binds to allosteric sites and reduces enzyme activity is called an allosteric inhibitor 

    • Allosteric activator

      • Bind to allosteric sites to keep an enzyme in its active configurations, increasing enzyme activity

  • Enzyme cofactors

    • Additional chemical components that assist enzyme function

    • Nonprotein, inorganic molecules

    • Metal ions 

    • Bound within enzyme molecule 

  • Coenzymes 

    • Nonprotein, organic molecules 

    • Vitamins 

      • B₆ and B₁₂

    • Bind temporarily or permanently to enzyme near active site 

6.5 Metabolism: The Chemical Description of Cell Function 

• Metabolism

  • All of the chemical reactions carried out by an organism 

• Anabolism/Anabolic reactions 

  • Reactions that use energey to make or transform chemical bonds 

• Catabolism/Catabolic reactions 

  • Reactions that harvest energy when chemical bonds are broken 

• Biochemical pathways 

  • Product of one reactions becomes the substrate of another reaction

  • These are the organaztional units of metabolism 

• Feedback inhibition

  • End products of the pathway binds to an allosteric site on the enzyme that catalyzes the first reaction of the pathway 

    • The end product goes back to the beginning of the pathway and prevents other substrates to bind because it binds to an allosteric site