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An Introduction To Metabolism

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I.                     The Chemistry of life is organized into metabolic pathways.

Metabolism - totality of an organism's chemical processes.

-                                  Property emerging from specific molecular interactions in the cell.

-                                  Concerned with managing cellular resources; material and energy

Metabolic reactions organized into 2 pathways:

1.                              Catabolic pathways - Release energy by breaking down complex molecules into simpler molecules. (Cellular Respiration)

2.                              Anabolic pathways - Consume energy to build complicated molecules from simpler ones. (Photosynthesis)

These reactions may be coupled, so that energy released from a catabolic reaction can be used to drive an anabolic reaction.

 

II.                   Organisms transform energy

Energy = the capacity to do work.

Kinetic Energy = Energy in the process of doing work.

-                                  Heat is KE expressed in random movement of molecules.

-                                  Light energy is KE because it powers photosynthesis.

Potential Energy = Energy that matter possess because of it location or arrangement

-                                  Chemical energy is PE stored in molecules because of the arrangement of nuclei and electrons in its atoms.

 

Energy can be transformed from one form to another:

-                                  KE of sunlight can be transformed into PE found in the bonds of molecules.

-                                  PE in the chemical bonds of gas can be transformed into KE to make the engine run

 

III.                  The energy transformations of life are subject to two laws of thermodynamics

Thermodynamics = The study of energy transformations.

First Law of Thermodynamics = Energy can be transferred and transformed but it cannot be created or destroyed.

Second Law of Thermodynamics = Every energy transfer or transformation makes the universe more disordered (every process increases the entropy of the universe)

Entropy = Quantitative measure of disorder that is proportional to randomness (designated by the letter S)

Closed System = Collection of matter under study which is isolated from its surroundings.

Open system = System in which energy can be transferred between the system and its surroundings.

 

The entropy of a system may decrease, but the entropy of the system plus it surroundings must always increase.  Highly ordered living organisms do not violate the second law because they are open systems.  For example,  animals:

-                                  Maintain highly ordered structure at the expense of increased entropy of their surroundings.

-                                  Take in high energy molecules as food and extract chemical energy to create and maintain order.

-                                  Return to the surroundings simpler low energy molecules and heat.

 

Energy can be transformed but part of it is dissipated as heat which is largely unavailable to do work.  Heat energy can perform work if there is a heat gradient resulting in heat flow from warmer to cooler.

 

The quantity of energy in the universe stays the same but the quality of heat does not.

 

IV.  Organisms life at the expense of free energy

A.    Free Energy: A criterion for spontaneous change

        Not all of a systemís energy is available to do work.  The amount of energy that is available to do work is described as free energy.  Free energy (G) is related to the systemís total energy (H) and its entropy (S) in the following way:

        G = H - TS where G = Gibbs free energy - energy available to do work.

                                       H = enthalpy or total energy

                                       T = Temperature in Kelvin

                                       S = Entropy

        Free energy (G) is the portion of a systemís energy available to do work; is the difference between the total energy(H) and the energy not available for doing work (TS)

B.    Significance of Free Energy:

        Indicates the maximum amount of a systems energy which is available to do work.

        Indicates whether a reaction will occur spontaneously or not.

        A spontaneous reaction is one that will occur without additional energy.

        In a spontaneous process the free energy of a system decreases

        A decrease in enthalpy and an increase in entropy reduce the free energy of a system and contribute to the spontaneity of a process.

        A high temperature enhances the effect of an entropy change.  Greater kinetic energy of molecules tends to disrupt order as the chances for random collisions increase.

        Enthalpy and entropy changes in a system have an opposite effect on free energy,  temperature may determine whether the reaction will be spontaneous or not. (i.e. protein denaturation by increased temperature.)

        High energy systems including high energy chemical systems are unstable and tend to change to a more stable state with a lower free energy.

C.   Free Energy and Equilibrium

        There is a relationship between chemical equilibrium and the free energy change of a reaction.

        As a reaction approaches equilibrium, the free energy of the system decreases (spontaneous and exergonic reaction)

        When a reaction is pushed away from equilibrium, the free energy of a system increases (nonspontaneous and endergonic)

        When a reaction reaches equilibrium G = 0, because there is no net change in the system

Metabolic Disequilibrium - since many metabolic reactions are reversible, they have the potential to reach equilibrium.

        At equilibrium, G = 0 so the system can do no work.

        Metabolic disequilibrium is a necessity of life; a cell at equilibrium is dead.

        In the cell, these potentially reversible reactions are pulled forward away from equilibrium, because the products of some reactions become reactants for the next reaction in the pathway.

        During cellular respiration, a steady supply of high energy reactants such as glucose and removal of low energy products such as carbon dioxide and water, maintain the disequilibrium necessary for respiration to proceed.

D.   Free energy and Metabolism

        Reactions can be classified upon their free energy changes.

            Exergonic reaction = A reaction that proceeds with a net loss of free energy.

            Endergonic reaction = An energy-requiring reaction that proceeds with a net gain of free energy; a reaction that absorbs free energy from its surroundings.

        Exergonic reactions:

1.      Products have less free energy than the reactant molecules.

2.      Reaction is energetically downhill

3.      Spontaneous reaction.

4.      G is negative

5.      -G is the maximum amount of work the reaction can perform.

        Endergonic reactions:

1.     Products store more free energy than reactants.

2.     Reaction is energetically uphill

3.     Non-spontaneous reaction

4.     G is positive

5.     +G is the minimum amount of work required to drive the reaction.

V.  ATP Powers cellular work by coupling exergonic to endergonic reactions

A.    ATP is the immediate source of energy that drives most cellular work which includes:

1.     Mechanical work such as beating of cilia, muscle contraction, cytoplasmic flow, and chromosome movement during mitosis and meiosis.

2.     Transport work such as pumping substances across membranes.

3.     Chemical work such as endergonic process of polymerization.

B.    The structure and hydrolysis of ATP

ATP = Adenosine Triphosphate = nucleotide with unstable phosphate bonds that the cell hydrolyzes for energy to drive endergonic reactions.

Adenine - a nitrogenous base

Ribose - a five carbon sugar

Chain of three phosphate groups

        Unstable bonds between the phosphate groups can be hydrolyzed in an exergonic reaction that releases energy.

        When the terminal phosphate bond is hydrolyzed, a phosphate group is removed producing ADP.

        Under standard condition in the laboratory, this releases -31KJ/mol

        In a living cell, this reaction releases - 55 kJ/mol = about 77% more than under standard conditions.

        The terminal phosphate bonds of ATP are unstable so the products of the hydrolysis reaction are more stable than the reactant.

        Hydrolysis of the phosphate bonds is thus exergonic as the system shifts to a more stable state.

B.  How ATP performs work

        Exergonic hydrolysis of ATP is couples with endergonic process by transferring a phosphate group to another molecule.  This transfer is enzymatically controlled.

        The molecule acquiring the phosphate becomes more reactive (phosphorylation)

 

C.   The Regeneration of ATP

        ATP is continuously regenerate by the cell.

        Process is rapid 107 molecules used and regenerated/sec/cell

        Reaction is endergonic

        Energy to drive the endergonic regeneration of ATP comes from the exergonic process of cellular respiration.

 

VI.  Enzymes speed up metabolic reactions by lowering energy barriers.

A.     A catalyst is a chemical agent that changes the rate of a reaction without being consumed. 

B.     An enzyme is a catalytic protein.

C.    The Activation Energy Barrier

1.      Chemical reactions require bond making and breaking.

2.      Reactant molecules must absorb energy for the bonds to break and the products must release energy when new bonds form.

3.      The free energy of activation or activation energy is the energy needed to break the bonds of the reactants. (EA)

4.      Usually provided in the form of heat.

5.      Increases the speed of the molecules.

D.    Enzymes and the Activation Energy

1.      Proteins, DNA and other complex molecules have free energy and are able to decompose spontaneously.

2.      Heat could be used but often, that would kill the cell.

3.      An enzyme speeds up a reaction by lower the activation energy to get to the transition state faster.

4.      An enzyme cannot change the rG for the reaction nor can it change it from an endergonic reaction to an exergonic reaction.

5.      They only speed up what would occur anyway.

VII.  Enzymes are substrate-specific

A.     The substrate is the reactant an enzyme acts on.

B.     The enzyme binds to the substrate.

C.    While joined, the enzyme converts to the substrate to the products

D.    An enzyme can distinguish its substrate from even closely related compounds such as isomers.

E.     The active site is the region of the enzyme that binds to the substrate.

F.     It is typically a pocket or groove on the surface that is formed only by a few of the enzymeís amino acids while the rest of the molecule forces the conformation to stay the same.

G.    Induced fit of the enzyme forces the enzyme to change to the shape of the substrate which makes it fit even more snug.

H.     It brings chemical groups of the active site into positions that enhance their ability to catalyze the reaction.

VIII.  The active site is an enzyme's catalytic center

A.     The substrate is held in the active site by weak interactions such as hydrogen bonds and ionic bonds. 

B.     Side chains of the amino acids catalyze the conversion.

C.    The new products leave the active site and the enzyme is able to bond again.

D.    An enzyme can act on about 1000 substrates per second.

E.     They do not change shape at all.

F.     Most metabolic reactions are reversible.

G.    The rate at which the reaction takes place is a function of the initial concentration of the substrate.

IX.  A cells chemical and physical environment affects enzyme activity

A.     Effects of Temperature and pH

1.      Enzymes have an optimal temperature and pH where they work at their optimum level.

2.      This is because the conformation of the protein is at its best.

3.      Most human enzymes react best at 35-40 oC and pH 6-8

B.     Cofactors

1.      Many enzymes require nonprotein helpers for catalytic activity.

2.      Cofactors may be bound tightly to the active site as permanent residents or they may bind loosely and reversibly along with the substrate.

3.      Some are inorganic like metal ions like zinc, iron, and copper.

4.      If the cofactor is organic, it is called a coenzyme.

5.      Most vitamins are coenzymes.

C.    Enzyme Inhibitors

1.      Certain chemicals selectively inhibit the action of specific enzymes.

2.      If an inhibitor attaches to the enzyme by covalent bonds, inhibition is usually irreversible.

3.      It is reversible if the inhibitor binds using weak bonds.

4.      Some reversible inhibitors resemble the normal substrate molecule and compete for admission into the active site. And are called competitive inhibitors because they reduce the productivity of the enzymes by blocking the substrates from entering.

5.      This can be overcome by increasing the concentration of the substrates.

6.      Noncompetitive inhibitors do not directly compete but they impede enzymatic  reactions by binding to another part of the enzyme and cause the enzyme to change its conformation making the active sit unreceptive.

7.      Some poisons act by inhibiting enzymes.

8.      Antibiotics are inhibitors for specific bacteria.

9.      Penicillin blocks the active site of an enzyme that many bacteria use to make their cell walls.

10. Selective inhibition and activation of enzymes by molecules naturally present in the cell are essential mechanisms in metabolic control.

X.  The Control of Metabolism

A.     Metabolic control often depends on allosteric regulation

1.      The regulatory noncompetitive inhibitors change an enzymeís shape and function by binding weakly to an allosteric site, a specific receptor site on some part of the enzyme molecule remote from the active cell.

2.      The effect of this allosteric regulation may inhibit or stimulate

3.      Allosteric regulation

a.      Most allosterically regulate enzymes are constructed from two or more polypeptide chains or subunits.

b.      Each subunit has its own active site and allosteric sites are often located where the subunits are joined.

c.      The binding of an activator to an allosteric site stabilizes the conformation that has a functional active site, whereas the binding of an allosteric inhibitor stabilizes the inactive form.

d.      The activity of an allosteric enzyme changes in response to fluctuating concentrations of the regulators.

4.      Feedback Inhibition.

a.      This is the switching off of a metabolic pathway by its end products  which acts as an inhibitor of an enzyme within the pathway.

b.      It slows down its own synthesis by allosterically inhibiting the enzyme from the very first step of the pathway.

c.      This prevents the cell from wasting chemical resources to synthesize more than necessary.

5.      Cooperativity

a.      This is a mechanism that amplifies the response of enzymes to substrates by priming the enzyme to accept more.