Energy Within the Cell

Metabolic reactions

1. exergonic - release energy

2. endergonic - absorb energy

Activation energy - energy required for reaction to proceed

Enzymes

1.         General - biological catalysts which speed up metabolic reactions by lowering activation energy so reactions can proceed at biological temperatures; made of protein; often named for the substrate with the suffix “ase.” e.g., an enzyme which digests protein is a protease; one that digests lipids is a lipase.

            a.         active site - the area of the enzyme where the reaction actually occurs. The active site is like a pocket into which the substrate fits. There is specificity between the enzyme and substrate because of the shape of the active site. “It’s all about shape, Baby!”

            b.         substrate - usually only one substrate is ‘recognized’ by a given enzyme. The shape of substrate must match the shape of the enzyme active site.

            c.         ‘Induced Fit’ model - when substrate enters the active site, the shape of the site changes to induce a better fit between the substrate and the enzyme.

            d.         cofactors - additional factors required for the enzyme to function; inorganic - e.g., Fe, Zn, K.

            e.         coenzymes - additional factors required for the enzyme to function; organic - usually synthesized from vitamin precursors.

2.         Factors affecting the rate of enzyme-catalyzed reactions:

            a.         Temperature - as with non-catalyzed reactions, the reaction rate increases with increasing temperature because the kinetic energy of the molecules is greater and closer to the activation energy. Also, the increased molecular movement means more frequent collisions between molecules. This is advantageous for homeotherms because they can maintain body temperature close to the optimum temperature for enzymes. Why does enzyme activity decrease dramatically above a certain temperature?

            b.         pH - a change in pH (i.e., [H⁺]) affects the tertiary structure of proteins. Because there is such high specificity between the active site and the substrate, if the shape of the active site changes, it will no longer match the substrate as well. Why does enzyme activity have an optimum pH?

            c.         [S] - with increasing substrate, the enzyme spends less time “looking” for substrate and more time catalyzing reactions; Why does enzyme activity plateau at a certain [S]?

3.         Enzyme regulation - to be efficient, the cell must be able to control enzyme activity.

            a.         Inhibition - enzyme activity is slowed

                        i.         competitive - an inhibitor binds to the active site, preventing the binding of substrate.

                        ii.        non-competitive - an inhibitor binds to a site other than the active site and causes a conformational change in the enzyme so the active site shape no longer matches that of the substrate.

                        iii.       allosteric - binding of an inhibitor to the “allosteric site,” (separate from the active site) causes a conformational change in all the active sites of that enzyme molecule.

                        iv.       feedback inhibition - an end-product from a chain of reactions is an inhibitor of an enzyme in the chain. This is an efficient way of building in self-regulation to a series of reactions.

                                    (1)       competitive - as above

                                    (2)       non-competitive - as above

                                    (3)       allosteric - as above

            b.         Activation - enzyme activity is increased

                        i.         allosteric - binding of an activator to the allosteric site improves the fit between substrate and active site.

                        ii.        precursor activity - a precursor of an enzyme’s substrate activates that enzyme. Think of this as a means of priming an enzyme to function more quickly when the substrate is about to be present.

                        iii.       cooperativity - the binding of substrate to one active site induces a favorable change in the shape of other active sites of that enzyme molecule; think of this as similar to allosteric activation.

Energy Transformation and Storage

1.         ATP

            a.         photosynthesis and cellular respiration are opposite processes

            b.         energy is stored as ATP

                        i.         ATP closely resembles the nucleotide adenine

                        ii.        made from a sugar, a base, and 3 phosphates

            c.         the conversion of ATP to ADP is reversible

            d.         the three negatives of the phosphate group make it unstable; the energy is held within the phosphate bond. The transfer of the phosphate bond (i.e., the phosphate group) to another molecule transfers energy to that molecule. The energy is released from ATP to do work and the resulting ADP can then be recharged with energy and used again.

            e.         when the phosphate is lost from a molecule, energy is released; when the phosphate is added to a molecule, energy is stored Where does this energy come from?

2.         Oxidation/reduction - these reactions involve the transfer of electrons

            a.         electrons in the bonds of molecules contain energy

            b.         electrons can be transferred from one molecule to another and the energy captured by doing so. This transfer is called oxidation and reduction.

            c.         oxidation - a loss of electrons; reduction - a gain of electrons

            d.         energy is released when electrons move toward electronegative atoms (such as oxygen); energy must be added to pull electrons away from electronegative atoms. Why do electrons move?

            e.         oxidation is always accompanied by a net release of energy, producing products that are more stable than the reactants

            f.         in cells, this energy is captured by ADP to form ATP; the resulting phosphate makes ATP quite unstable and to regain stability it must lose the phosphate (i.e., the energy)

            g.         H⁺ and electrons (and their energy) are removed from glucose and accepted by NAD⁺ which becomes NADH (a reduction); NADH is the carrier of electrons

Cellular Respiration

Cellular Respiration - C₆H₁₂O₆ + 6O₂ ➝ 6CO₂ + 6H₂O

1.         Glycolysis Why is everything after step 3 multiplied by 2?

            a.         occurs in the cytosol, outside the mitochondrion

            b.         note in step 5 that the energy released from the oxidation was used to attach a phosphate to PGAL. The resulting 2 phosphate compound immediately gives up one of the phosphates to ADP and two ATP are created. The cell has capitalized on the fact that oxidation reactions release energy.

            c.         pyruvic acid (or pyruvate) is the starting material for the next step (the Krebs cycle) and it enters the mitochondrion where that occurs

            d.         Anaerobic (fermentation) vs. Aerobic Respiration - which one the cell performs depends on whether oxygen is present or absent

                        i.         the net energy gain in fermentation is 2 ATP; c.f. 36 in aerobic respiration

                        ii.        pyruvate is the electron acceptor to oxidize NADH to NAD+

                        iii.       NAD+ is then available to oxidize more glucose

                        iv.       if no O₂ is present, the ETC stops; therefore pyruvate accepts electrons to form lactic acid. This causes muscle pain and cramping.

                        v.         because the pyruvate does not enter the Krebs cycle, there is still a lot of energy which is not removed from the fuel. This is evident in yeast fermentation where the end product is alcohol - a high energy fuel. Why is never more than ~12-14% alcohol?

2.         Krebs Cycle

            a.         after glycolysis, most of the energy in glucose is still there, very little was removed by glycolysis; remember the energy yield.

            b.         in the presence of O₂ pyruvate enters the mitochondrion to be used in the Krebs cycle

            c.         the purpose of the Krebs cycle is to produce NADH - the electron carrier

            d.         notice that CO₂ is a highly oxidized, therefor low energy, product. Where did the energy go?

3.         Electron Transport Chain

            a.         high energy electrons carried by NADH are delivered to the ETC

            b.         the electrons are passed to stronger and stronger electron acceptors and, each time, energy is released and used to make ATP (note: the ETC does not actually make any ATP)

            c.         the final electron acceptor is oxygen which combines with H⁺ to form water. Note that water is a low energy product which shows that most of the energy in the original fuel has been extracted.

            d.         the overall net energy yield from cellular respiration is 36 ATP/glucose molecule.

Photosynthesis

1.         General

            a.         6CO₂ + 6H₂O ➝ C₆H₁₂O₆ + 6O₂ - note that the reaction is the reverse of cellular respiration

            b.         light energy is captured by low energy CO₂ and converted into high energy C₆H₁₂O₆

            c.         it was long believed that CO₂ was split up so that C was incorporated into glucose and O₂ was released. Actually, C goes into glucose and O into glucose and water (as a product); water (as a reactant) is split to yield the oxygen product

            d.         redox - in cellular respiration electrons move from high energy glucose to O₂ making low energy water; in photosynthesis, low energy water is split and electrons move to CO₂ making high energy glucose; solar energy provides the “power” needed for the reduction

2.         Leaf structure

            a.         grana

            b.         thylakoid

            c.         stroma

Two Phases of Photosynthesis

1.         Light reactions - occur in thylakoid membrane

            a.         absorbing energy - Why do plants look green if they absorb red and blue light?

                        i.         pigment molecules are arranged in photosystems of a few hundred. These arrangements are called an antenna complex

                        ii.        a photon of light strikes a pigment molecule and an electron absorbs the energy, becoming excited. The energy of this electron is passed from one molecule to another until it reaches the reaction center chlorophyll. There, the primary electron acceptor captures the energy in a redox reaction before it is lost.

            b.         Electron Flow

                        i.         photosystem II absorbs light energy and the energy is transferred to the primary electron acceptor

                        ii.        electrons from photosystem II are replaced by splitting water

                        iii.       electrons are passed along an electron transport chain to photosystem I and the energy is used to make ATP (note: as in cellular respiration, the ETC does not actually make any ATP)

                        iv.       electrons in pigment molecules of photosystem I are excited again by absorbing light energy and are used to reduce NADP+ to NADPH

                        v.         electrons are replaced by those coming down the electron transport chain fro photosystem II.

2.         Carbon Fixation (Calvin Cycle) - occurs in the stroma - the purpose is to reduce low energy CO₂ into high energy glucose. The energy needed comes from the ATP produced by the light reactions while the electrons needed come from the NADPH produced by the light reactions. That is, the light reactions function to provide some of the materials needed by the Calvin cycle.

            a.         Carbon Fixation

                        i.         a carbon from CO₂ is attached to a 5C compound to form a 6C compound

                        ii.        the 6C compound breaks in half

            b.         Reduction

                        i.         each 3C compound gets another phosphate and is reduced by NADPH

            c.         Regenerate starting compound

                        i.         some 3C product is used to make glucose and other compounds

                        ii.        some is used to regenerate the starting material