Biology ii chapter 6

Lecture Notes

I. The chemistry of life is organized into metabolic pathways

Metabolism = Totality of an organism’s chemical processes.

· Property emerging from specific molecular interactions within the cell.

· Concerned with managing cellular resources: material and energy

Metabolic reactions are organized into pathways that are orderly series of enzymatically controlled reactions. Metabolic pathways are generally of two types:

Catabolic pathways = Metabolic pathways which release energy by breaking down complex molecules to simpler compounds. (e.g. Cellular respiration which degrades glucose to carbon dioxide and water; provides energy for cellular work.)

Anabolic pathways = Metabolic pathways which consume energy to build complicated molecules from simpler ones. (e.g. Photosynthesis which synthesizes glucose from CO₂ and H₂0; any synthesis of a macromolecule form its monomers.)

Metabolic reactions may be coupled so that energy released from a catabolic reaction can by used to drive an anabolic one.

II. Organism transform energy

Energy = Capacity to do work.

Kinetic energy = Energy in the process of doing work (energy of motion), For example:

· Heat (thermal energy) is kinetic energy expressed in random movement of molecules.

· Light energy from the sun is kinetic energy, which powers photosynthesis.

Potential energy = Energy that matter possesses because of its location or arrangement (energy of position). For example:

· in the earth’s gravitational field, an object on a hill or water behind a dam have potential energy.,

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

Energy can be transformed from one from to another. For example:

· Kinetic energy of sunlight can be transformed into the potential energy of chemical bonds during photosynthesis.

· Potential energy in the chemical bonds of gasoline can be transformed into kinetic mechanical energy, which pushes the pistons of an engine.

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

Thermodynamics

Thermodynamics = Study of energy transformations.

First Law of Thermodynamics = Energy can be transferred and transformed, but it cannot be created or destroyed (energy of the universe is constant).

Second Law of Thermodynamics = every energy transfer or transformation makes the universe more disordered (every process increase 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 its surroundings must always increase, Highly ordered living organisms do not collate 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 complex high-energy molecules as food and extract chemical energy to create and maintain order.
• Return to the surroundings simpler low energy molecules (CO₂ and water) 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.

Combining the first and second laws; the quantity of energy in the universe is constant, but its quality is not.

IV. Organisms live at the expense of free energy

1. Free Energy: A Criterion For Spontaneous Change

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

G = G – TS

Where:

G = Gibbs free energy (energy available to do work)

H = enthalpy of total energy

T = temperature in °K (which is °C + 273)

Significance of Free Energy:

1. Indicates the maximum amount of a system’s energy, which is available to do work.

2. Indicates whether a reaction will occur spontaneously or not.

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

· In a spontaneous process, ΔG or free energy of a system decreases (ΔG<0).

· A decrease in enthalpy (-ΔH) and an increase in entropy (+ΔS) reduce the free energy of a system and contribute to the spontaneity of a process.

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

· When 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 (e.g. 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.

B.Free Energy and Equilibrium

There is a relationship between chemical equilibrium and the free energy change (ΔG) 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 system increases (non-spontaneous and endergonic reaction).

· When a reaction reaches equilibrium, ΔG = 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, ΔG == 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 metabolic pathway.

· For example, during cellular respiration a steady supply of high energy reactants such as glucose and removal of low energy products such as CO₂ H₂O, maintain the disequilibrium necessary for respiration to proceed.

C. Free Energy and Metabolism

Reactions can be classified based 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 Reaction	Endergonic Reaction
Chemical products have less free energy than the reactant molecules. Reaction is energetically downhill. Spontaneous reaction. ∆G is negative -∆ is the maximum amount of work the reaction can perform.	Products store more free energy than reactants. Reaction is energetically uphill Non-spontaneous reaction (requires energy input). ∆G is positive. +∆G is the minimum amount of work required to drive the reaction.

If a chemical process is exergonic, the reverse process must be endergonic. For example:

§ For each mole of glucose oxidized in the exergonic process of cellular respiration, 2870 kJ are released (ΔGT =-2870 kJ/mol or –686 kcal/mol).

§ To produce a mole of glucose, the endergonic process of photosynthesis requires an energy input of 2870 kJ (ΔG=+2870 kJ/mol or +686kcal/mol).

Joule (J) = 0.239 cal

Kilojoule (kJ) = 1000 J or 0.239 kcal

Calorie (cal) = 4.184 J

In cellular metabolism, endergonic reactions are driven by coupling them to reaction with a greater negative free energy (exergonic). ATP plays a critical role in this energy coupling.

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

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

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

2. Transport work such as pumping substances across membranes

3. Chemical work such as the endergonic process of polymerization

A. The Structure and Hydrolysis of ATP

ATP (adenosine triphosphate) = Nucleotide with unstable phosphate bonds that the cell hydrolyzes for energy to drive endergonic reaction. ATP consists of:

§ 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 (Adenosine diphosphate).

ATP + H₂0 ADP + P

§ Under standard conditions in the laboratory, this reaction releases –31 kJ/mol (-7.3 kcal/mol).

§ In a living cell, this reaction releases –55 kJ/mol (-13 kcal/mol)---about 77% more than under standard conditions.

The terminal phosphate nods of ATP are unstable, so:

§ The products of the hydrolysis reaction are more stable than the reactant.

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

B. How ATP Performs Work

Exergonic hydrolysis of ATP is coupled with endergonic processes by transferring a phosphate group to another molecule.

§ Phosphate transfer is enzymatically controlled

§ The molecule acquiring the phosphate (phoshporylated or activated intermediate) becomes more reactive.

§ For example, conversion of glumatic acid to glutamine:

Glu + NH₃ Gln

Glutamic acid ammonia glutamine

Two step process of energy coupling with ATP hydrolysis:

(1). Hydrolysis of ATP and phosphorylation of glumatic acid.

Glu + ATP Glu - P ₊ ADP

Unstable

Phosphorylated

Intermediate

(2.) Replacement of the phosphate with the reactant ammonia.

Glu –P + NH₃ Gln + P

Overall rG:

Glu + NH₃ Gln

ATP ADP + P rG=+14.2 kJ/mol

rG=-31.0 kJ/mol

NetrG=-16.8 kJ/mol

(Overall process is exergonic)

C. The regeneration of ATP

The cell continually regenerates ATP.

§ Process is rapid (10⁷ molecules used and regenerated/sec/cell).

§ Reaction is endergonic.

ADP + P ATP rG=+kJ/moll (+7.3 kcal/mol)

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

V. Enzymes speed up metabolic reactions by lowering energy barriers: an overview

Free energy change indicates whether a reaction will occur spontaneously, but does not give information about the speed of reaction.

_§ A chemical reaction will occur spontaneously if it releases free energy (-rG), but it may occur too slowly to be effective in living cells.

_§ Biochemical reactions require enzymes to speed up and control reaction rates.

Catalyst + Chemical agent that accelerates a reaction without being permanently changed in the process, so it can by used over and over does not alter products just ants

Enzymes- Biological catalyst’s, which are usually proteins.

Before a reaction can occur, the reactants must absorb energy to break chemical bonds. This initial energy investment is the activation energy.

Free energy of activation (Activation energy)+ Amount of energy that reactant molecules must absorb to start a reaction (EA)

Transition state + Unstable condition of reactant molecules that have absorbed sufficient free energy to react

Energy profile of an exergonic reaction

1. Reactants must absorb enough energy (EA) to reach the Transition State (uphill portion of the curve). Usually the absorption of thermal energy from the surroundings is enough to break chemical bonds.

2. Reaction occurs and energy is released as new bonds form (downhill portion of the curve).

3. rG for the overall reaction is the difference in fee energy between products and reactants in an exergonic reaction the free energy of the products is less than reactants,.

Even though a reaction is energetically favorable, there must be an initial investment of activation energy (EZZ)

The breakdown of biological macromolecules is exergonic. However, these molecules react very slowly at cellular temperatures because they cannot absorb enough thermal energy to reach transition state.,

In order to make these molecules reactive when necessary, cells us biological catalysts called enzymes, which:

§ Are usually proteins.

§ Lower EA, so the Transition State can be reached at cellular temperatures.

§ Do not change the nature of a reaction (rG), but only speed up a reaction that would have occurred anyway.

§ Are very selective for which reaction they will catalyze.

VII. Enzymes are substrate-specific: a closer look

Enzymes are specific for a particular substrate, and that specificity depends upon the enzyme’s three-dimensional shape.

Substrate = The substrate an enzyme acts on and makes more reactive.

§ An enzyme binds to its substrate and catalyzes its conversion to product. The enzyme is released in original form.

§ Substrate enzyme Enzyme-substrate complex Product +enzyme

§ The substrate binds to the enzyme’s active site.

Active site = Restricted region of an enzyme molecule which binds to the substrate.

§ Is usually a pocket or groove on the protein’s surface.

§ Formed with only a few of the enzyme’s amino acids.

§ Determines enzyme specificity which is based upon a compatible fit between the shape of an enzyme’s active site and the shape of the substrate.

§ Changes its shape in response to the substrate +induced fit

Þ As substrate binds to the active site, it induces the enzyme to change its shape.

Þ This brings its chemical groups into positions that enhance their ability to interact with the substrate and catalyze the reaction.

Induced fit = Change in the shape of an enzyme’s active site, which is induced by the substrate.

VI. The active site is an enzyme’s catalytic center: a closer look

The entire enzymatic cycle is quite rapid.

Steps in the Catalytic Cycle of Enzymes:

1. Substrate binds to the active site forming an enzyme-substrate complex. Substrate is held in the active site by weak interactions (e.g. hydrogen bonds and ionic bonds).

2. Induced fit of the active site around the substrate. Side chains of a few amino acids in the active site catalyze the conversion of substrate to product.

3. product departs active site and the enzyme emerges in its original form. Since enzymes are used over and over, they can be effective in very small amounts.

Enzymes lower activation energy and speed up reactions by several mechanisms:

· Active site can hold two or more reactants in the proper position so they may react.

· Induced fit of the enzyme’s active site may distort the substrate’s chemical bonds, so less thermal energy (lower DG) is needed to break them during the reaction.

· Active site might provide a microenvironment conducive to a particular type of reaction (e.g. localized regions of low pH caused by acidic side chains on amino acids at the active site).

· Side chains of amino acids in the active site may participate directly in the reaction.

The initial substrate concentration partly determines the rate of an enzyme-controlled reaction.

· The higher the substrate concentration, the faster the reaction – up to a limit.

· IF substrate concentration is high enough, the enzymes becomes saturated with substrate.(The active sites of all enzymes molecules are engaged.)

· When an enzyme is saturated, the reaction rate depends upon how fast the active sites can convert substrate to product.

· When enzyme is saturated, reaction rate may be increased by adding more enzyme.

VII. A cell’s chemical and physical environment affects enzyme activity: a close look

Each enzyme has optimal environmental conditions that favor the most active enzyme conformation.

A. Effects of Temperature and pH

Optimal temperature allows the greatest number of molecular collisions without denaturing the enzyme.

· Enzyme reaction rate increases with increasing temperature. Kinetic energy of reactant molecules increases with rising temperature, which increases substrate collisions with active sites.

· Beyond the optimal temperature, reaction rate slows. The enzyme denatures when increased thermal agitation of molecules disrupts weak bonds that stabilize the active conformation.

· Optimal temperature range of most human enzymes is 35°-40°C.

Optimal pH range for most enzymes is pH 6-8

· Some enzymes operate best at more extremes of pH.

· For example, the digestive enzyme, pepsin, found in the acid environment of the stomach has an optimal pH of 2.

B. Cofactors

Cofactors = Small nonprotein molecules that are required for proper enzyme catalysis.

· May bind tightly to active site.

· May bind loosely to both active site and substrate.

· Some are inorganic (e.g. metal atoms of zinc, iron or copper).

· Some are organic and are called coenzymes (e.g. most vitamins).

C.Enzyme Inhibitors

Certain chemicals can selectively inhibit enzyme activity.

· Inhibition may be irreversible if the inhibitor attaches by covalent bonds.

· Inhibition may be reversible if the inhibitor attaches by weak nods.

Competitive inhibitors = Chemicals that resemble an enzyme’s normal substrate and compete with it for the active site.

· Block active site forms the substrate.

· If reversible, the effect of these inhibitors can be overcome by increase substrate concentration.

Noncompetitive inhibitors = Enzyme inhibitors that do not enter the enzyme’s active site, but bind to another part of the enzyme molecule.

· Causes enzyme to change its shape so the active site cannot bind substrate.

· May act as metabolic poisons (e.g. DDT, many antibiotics).

· Selective enzyme inhibition is an essential mechanism in the cell for regulating metabolic reactions.

C. Allosteric Regulation

Allosteric site = Specific receptor site on some part of the enzyme molecule other than the active site.

· Most enzymes with allosteric sites have tow or more polypeptide chains, each with its own active site. Allosteric site. Allosteric sites are often located where the subunits join.

· Allosteric enzymes have two conformations, one catalytically active and the other inactive.

· Binding of an activator to an allosteric sire stabilizes the active conformation.

· Binding of an inhibitor (noncompetitive inhibitor) to an allosteric site stabilizes the inactive conformation.

· Enzyme activity changes continually in response to changes in the relative proportions of activators and inhibitors (e.g. ATP/ADP).

· Subunits may interact so that a single activator or inhibitor at one allosteric site will affect the active sites of the other subunits.

D. Cooperativity

Substrate molecules themselves may enhance enzyme activity.

Cooperativity = The phenomenon where substrate binding to the active site of one subunit induces a conformational changes that enhances substrate binding at the active sites of the other subunits.

X. Metabolic order emerges from the cells’ regulatory systems and structural organization.

Metabolic pathways are regulated by controlling enzyme activity.

A. Feedback Inhibition

Feedback Inhibition = Regulation of a metabolic pathway by its end product, which inhibits an enzyme within the pathway. For example:

Enzyme Enzyme Enzyme Enzyme Enzyme

1 2 3 4 5

Threonine A B C D Isoleucine

(Initial substrate) (End product and allosteric inhibitor of enzyme 1)

Feedback Inhibition

Prevents the cell from wasting chemical resources by synthesizing more product than is necessary.

B. Structural Order and Metabolism

Cellular structure orders and compartmentalizes metabolic pathways.

· Some enzymes have fixed locations in the cell because they are incorporated into a membrane.

· Dissolved enzymes and their substrates may be localized within organelles such as chloroplasts and mitochondria.