Lecture Outline

                      Growing Old With Molecular Mayhem

           A.   Free radicals are molecules with extra electrons.

                  1.   The "extra" electrons have been stripped from other atoms in the cell.

                  2.   Free radical are highly reactive and can alter normal cellular function..

           B.   The enzymes superoxide dismutase and catalase can eliminate one of the most common free radicals—O2-, but these enzymes decrease in quantity as we age.

           C.   Metabolism refers to the cell's capacity to acquire energy and use it to build, store, break apart, and eliminate substances in controlled ways.

 

          6.1      Energy and the Underlying Organization of Life

           A.   Defining Energy

                  1.   Potential energy is the capacity to make things happen, to do work.; it can also be called chemical energy, measured in kilocalories.

                  2.   Kinetic energy is the energy of motion; it includes heat energy.

           B.   What Can Cells Do With Energy?

                  1.   Energy from the sun or from organic substances becomes coupled to thousands of energy-requiring processes in cells.

                  2.   Cells use the energy to perform chemical, mechanical, and electrochemical work.

           C.   How Much Energy Is Available?

                  1.   First law of thermodynamics  states that the total amount of energy in the universe is constant; it cannot be created nor destroyed; it can only change form.

                  2.   Energy cannot be produced by a cell; it can only be borrowed from someplace else.

                  3.   Energy can be of high quality, that is, highly concentrated and usable; or it can be of low quality, such as heat that is released into the universe.

           D.   The One-Way Flow of Energy

                  1.   Second law of thermodynamics  states that the spontaneous direction of energy flow is from high- to low-quality forms.

                  2.   Each conversion produces energy (usually heat) that is unavailable for work.

                  3.   As systems lose energy they become more disorganized; the measure of this disorder is called entropy.

                  4.   The world of life (plant and animal) maintains a high degree of organization only because it is being resupplied with energy from the sun.

 

          6.2      Energy Inputs, Outputs, and Cellular Work

           A.   Cells and Energy Hills

                  1.   Endergonic (“energy in”) reactions require energy input resulting in products with more  energy than the reactants had; for example: photosynthesis.

                  2.   Exergonic (“energy out”) reactions release energy such that the products have less  energy than the reactants had; for example: cellular respiration.

           B. ATP Couples Energy Inputs With Outputs

                  1.   ATP is composed of adenine, ribose, and three phosphate groups.

                          a.   Energy input links phosphate to ADP to produce ATP (phosphorylation).

                         b.   ATP can in turn donate a phosphate group to another molecule, which then becomes primed and energized for specific reactions.

                  2.   ATP's role is like currency in an economy: earning ATP during exergonic reactions and spending it during endergonic ones.

                  3.   ADP can be recycled to ATP very rapidly in the ATP/ADP cycle.

           C.   Some Electron Transfers Drive ATP Formation

                  1.   Electrons are transferred in nearly every reaction that harnesses energy for use in the formation of ATP.

                  2.   In plant cells sunlight energy drives electrons from water molecules to initiate the reactions that will eventually produce carbohydrates.

                  3.   In aerobic respiration, the degradation of glucose releases energy that can be transferred to ATP.

 

          6.3      Cells Juggle Substances as Well as Energy

           A.   Participants in Metabolic Reactions

                  1.   Reactants  are substances that enter reactions.

                  2.   Intermediates  are the compounds formed between the start and the end of a pathway.

                  3.   Products  are the substances present at the conclusion of a pathway.

                  4.   Energy carriers  are mainly ATP.

                  5.   Enzymes  are proteins that catalyze (speed up) reactions.

                  6.   Cofactors  are small molecules and metal ions that help enzymes by carrying atoms or electrons.

                  7.   Transport proteins  are membrane-bound proteins that participate in adjusting concentration gradients that will influence the direction of metabolic reactions.

           B.   What Are Metabolic Pathways?

                  1.   Metabolic pathways form series of reactions that regulate the concentration of substances within cells by enzyme-mediated linear and circular sequences.

                  2.   In biosynthetic pathways, small molecules are assembled into large molecules; for example, simple sugars are assembled into complex carbohydrates.

                  3.   In degradative pathways, large molecules such as carbohydrates, lipids, and proteins are broken down to form products of lower energy. Released energy can be used for cellular work.

           C.   Are the Reactions Reversible?

                  1.   Chemical reactions can proceed from reactants to products, which, if they are allowed to accumulate, will convert back to reactants.

                  2.   The direction of reaction depends on concentrations and the collision of molecules.

                  3.   When a reaction approaches chemical equilibrium, the forward and reverse reactions proceed at equal rates

                          a.   There is no net  change in concentrations.

                         b.   Every reaction has its own ratio of products to reactants at equilibrium.

           D.   No Vanishing Atoms at the End of the Run

                  1.   The law of conservation of mass  states that the total mass of all substances entering a reaction equals the total mass of all the products.

2.     This is why you must always "balance" a chemical equation by having an equal number of atoms of each element on both sides of the arrow.

 

6.4         Electron Transfer Chains in the Main Metabolic Pathways

           A.   Energy is released from storage molecules (such as glucose) in controlled steps via a series of intermediate molecules.

                  1.   Electrons released during bond breaking are transferred stepwise through the components of electron transport systems located on various cell membranes.

                  2.   Each time a donor gives up an electron it is oxidized; if it gains, it is reduced.

                  3.   Coenzymes are large organic molecules such as NAD+, FAD, and NADP+ that transfer protons and electrons from one substrate to another.

           B.   Electron transfer chains are similar to staircases where electrons flow down the steps from the top (most energy) to the bottom (least energy), releasing a small amount at each step.

           C.   The energy is harnessed to move hydrogen ions, which in turn establish pH and electric gradients necessary for ATP production.

 

          6.5      Enzymes Help With Energy Hills

           A.   Enzymes are catalytic molecules that alter the rate of a chemical reaction.

           B.   Enzymes have four features:

                  1.   Enzymes speed up reactions.

                  2.   Enzymes can be reused.

                  3.   Enzymes, at least some of them, can recognize both reactants and products in order to catalyze a reaction in both directions.

                  4.   Enzymes are very selective about the substrates to which they will bind and thereby bring about change.

           C.   Enzymes increase the rate of a reaction by lowering the activation energy (the amount of energy needed to get a reaction going).

 

          6.6      How Do Enzymes Lower Energy Hills?

           A.   The Active Site

                  1.   Enzymes increase the rate of reactions by creating a microenvironment that is energetically more favorable for the reaction.

                  2.   Each enzyme molecule has an active site where the substrate binds to the enzyme during a reaction.

           B.   Transition at the Top of the Hill

                  1.   Activation energy brings the reactive chemical groups into alignment so that chemical bonds can be broken, created, and rearranged.

                  2.   The substrate is brought to its transition state, the point when a reaction can occur.

           C.   How Enzymes Work

                  1.   Binding energy helps bring about the transition state by four mechanisms:

                          a.   Helping substrates get together;

                         b.   Orienting substrates in positions favoring reaction;

                          c.   Shutting out water;

                         d.   Inducing changes in enzyme shape (induced-fit model).

           D.   About Those Cofactors

                  1.   Cofactors are nonprotein groups that bind to many enzymes and make them more reactive.

                  2.   Inorganic metal ions such as Fe++ also serve as cofactors when assisting membrane cytochrome proteins in their electron transfers in chloroplasts and mitochondria.

            E.   Why Are Enzymes So Big?

                  1.   A large molecule affords structural stability.

                  2.   The extensive folding of the polypeptide chains puts amino acids and functional groups in locations and orientations that favor interaction with water and substrate.

 

          6.7      Enzymes Don't Work in a Vacuum

           A.   How Is Enzyme Activity Controlled?

                  1.   Some controls regulate the number of enzyme molecules available by speeding up/slowing down their synthesis.

                  2.   Allosteric enzymes have (in addition to active sites) regulatory sites where control substances can bind to alter enzyme activity; if this control substance is the end product in the enzyme’s metabolic pathway, feedback inhibition occurs.

           B.   Do Temperature and pH Affect Enzymes?

                  1.   Because enzymes operate best within defined temperature ranges, high temperatures decrease reaction rate by disrupting the bonds that maintain three-dimensional shape (denaturation occurs).

                  2.   Most enzymes function best at a pH near 7 (pepsin in the stomach is an exception); higher or lower values disrupt enzyme shape and halt function.

 

          6.8      Focus On Health:  Beer, Enzymes, and Your Liver

 

          6.9      Light Up the Night—and the Lab—with Enzymes

           A.   Fireflies use enzymes (luciferase) to produce light by bioluminescence.

           B.   Researchers transferred genes for bioluminescence into strains of Salmonella  so that the course of infection could be tracked by visualization.