BIOL 2107 Chapter 6

Metabolism & Metabolic Pathways

• Metabolism - totality of an organism’s chemical reactions

• Metabolic pathways - begin with a specific molecule and end with a product; each step is catalyzed by a specific enzyme

Catabolic and Anabolic Pathways

• Catabolic pathways - release energy by breaking down complex molecules into simpler ones; the energy is then able to cellular work

  • Glucose is broken down into CO2 & H2O

• Anabolic pathways (biosynthetic pathways) - consume energy to build complex molecules from simpler ones

  • Proteins are synthesized from amino acids

Energy, Work, and Bioenergetics

• Energy - the capacity to cause change

  • Exists in various forms

• Work - the movement of matter against opposing forces, such as gravity and friction

• Bioenergetics - study of how energy flows through living organisms

Six Forms of Energy

• Kinetic - energy of motion

• Thermal - kinetic energy associated with random movement of atoms and molecules

• Heat - thermal energy in transfer from one object to another

• Light - type of energy that can be harnessed to perform work

• Potential - energy that matter possesses because of its location or structure

• Chemical - potential energy available for release in a chemical reaction

• Energy can be converted from one form to another

Thermodynamics, Open Systems, and Closed/Isolated Systems

• Thermodynamics - study of energy transformations

• Open System - energy and matter can be transferred between the system and its surroundings

  • Organisms are open systems

• Closed/Isolated System - exchange with the surroundings cannot occur

The First Law of Thermodynamics

• Energy can be transferred ad transformed, but it cannot be created nor destroyed

  • A.K.A. “The Principle of Conservation of Energy”

The Second Law of Thermodynamics

• Every energy transfer or transformation increases the entropy of the universe

  • Entropy - measure of molecular disorder

Spontaneous and Nonspontaneous Processes

• Spontaneous processes - occur without energy input; can happen quickly or slowly

  • For a process to occur spontaneously, it must increase the entropy of the universe

• Nonspontaneous processes - lead to a decrease in entropy; energy must be supplied

Biological Order and Disorder

• Individual cells and whole organisms create ordered structures from less organized starting materials and replace ordered forms of matter and energy with less ordered forms

• Energy flows into an ecosystem in the form of light and exits in the form of heat

• Organisms are islands of low entropy in an increasingly random universe

Free Energy

• Free Energy - the portion of a system’s energy that can do work when temp and pressure are uniform throughout, as in a living cell

Free-Energy Change (delta G), Spontaneity, and Chemical Equilibrium

• delta G = G (final state) - G (initial state)

  • Reactions with a negative delta G are spontaneous

• Spontaneous reactions can be harnessed to perform cellular work

• Chemical Equilibrium - state of maximum stability, in which the forward and reverse reactions occur at the same rate

  • Spontaneous reactions occur when it is moving toward equilibrium

Exergonic and Endergonic Reactions

• Endergonic Reactions - absorb free energy from its surroundings, is nonspontaneous, and delta G is positive

  • The magnitude of delta G is the quantity of energy required to drive the reaction

• Exergonic Reactions - proceed with a net release of free energy, is spontaneous, and delta G is negative

  • delta G represents the maximum amount of work the reaction can perform

Cells. Equilibrium, and Metabolism

• Cells are not in equilibrium; hey are open systems experiencing a constant flow of materials in and out

  • Metabolism is never at equilibrium

• A catabolic pathway in a cell releases free energy in a series of reactions

• The product of each reaction is the reactant for he next, preventing the system from reaching equilibrium

Energy Coupling

• Energy Coupling - the use of exergonic process to drive an endergonic one

  • Most energy coupling in cells is mediated by ATP

ATP

• ATP (adenosine triphosphate) - composed of ribose (sugar), adenine (a nitrogenous base), and a chain of three phosphate groups

  • In addition to its role in energy coupling, ATP is also used to make RNA

ATP hydrolysis

• Bonds between the phosphate groups of ATP can be broken down by hydrolysis

• ATP hydrolysis - releases energy and produces ADP (adenosine diphosphate) and inorganic phosphate

• The energy released comes from the chemical change to a state of lower free energy, not from the phosphate bonds themselves

• ATP hydrolysis releases a lot energy due to the repulsive force of the three negatively charged phosphate groups

• The triphosphate tail of ATP is the chemical equivalent of a compressed spring

How ATP Works

• Chemical work in the cell is powered by ATP hydrolysis

• Energy released by the exergonic reaction of ATP hydrolysis used to drive endergonic reactions

• ATP drives endergonic reactions by phosphorylation, transferring a phosphate group to another molecule, such as a reactant; the recipient molecule is a phosphorylated intermediate

• Coupled reactions are exergonic

• Transport and mechanical work in the cell are also powered by ATP hydrolysis

• ATP hydrolysis leads to a change in a protein’s shape and often its ability to bind to other molecules; this can occur via a phosphorylated intermediate or noncovalent bonding between ATP and a protein

The Regeneration of ATP

• ATP is a renewable resource that is regenerated by addition of a phosphate group to ADP

  • The energy to phosphorylate ADP comes from catabolic reactions in the cell

• The ATP cycle is a revolving door through which energy passes during its transfer from catabolic to anabolic pathways

Catalysts and Enzymes

• Catalyst - a chemical agent that speeds up a reaction without being consumed by the reaction

• Enzyme - a macromolecule that acts as a catalyst; most enzymes are proteins

Activation Energy

• Activation Energy (Ea) - the energy required to start a reaction by breaking binds in the reactant molecules

How Enzymes Speed up Reactions

• Activation energy is often supplied by heat in the form of thermal energy that reactant molecules absorb from the surroundings

• Heat is a nonselective catalyst and high temps can denature proteins

• Instead of relying on heat, organisms carry out catalysis to selectively speed up reactions

• Enzymes catalyze reactions by lowering the barrier without being consumed

• Enzymes do not affect the change in free energy (delta G); they only speed up reactions that would eventually occur without them

Substrate Specificity of Enzymes

• Enzymes are specific for the reactions they catalyze

• Substrate - the reactant molecule on which an enzyme acts

• The enzyme binds to its substrate, forming an enzyme-substrate complex

• Most enzyme names end in -ase

• Active Site - the region on the enzyme to which the substrate binds

• Enzyme specificity results from the fit between the shape of the active site and the substrate

  • Enzymes change shape due to chemical interactions with the substrate

• Induced Fit - binding of the substrate that brings chemical groups of the active site together

Catalysis in the Enzyme’s Active Site

• Substrates are held to an enzyme’s active site by weak interactions, such as hydrogen bonds

• The active site lowers the Ea and converts substrates to products

  • Can do this by:

    • Orienting substrates correctly

    • Straining substrate bonds

    • Providing a favorable microenvironment

    • Covalently bonding to the substrate

• After releasing products, the active site is available to bind with more substrate molecules

• At enzyme saturation (when all enzymes are bonded with substrates), reaction speed can only be increased by adding more enzyme

Cofactors

• Cofactors - nonprotein molecules that help carry out processes that are difficult for amino acids

  • May be inorganic or organic

• Coenzyme - organic cofactor

  • Most vitamins act as coenzymes or as the raw material from which coenzymes are made

Cells Regulating Metabolic Pathways

• Cells tightly regulate metabolic pathways by

  • Switching on or off the genes that encode specific enzymes

  • Regulating the activity of enzymes once formed

Allosteric Regulation

• Allosteric Regulation - when a regulatory molecule binds to a protein at one site and affects the protein’s function at another site

  • May inhibit or stimulate an enzyme’s activity

Cooperativity

• Cooperativity - the binding of one substrate molecule to the active site of one subunit locks all other subunits into the active shape

  • Amplifies the response of enzymes to substrates

Feedback Inhibition

• Feedback Inhibition - the end product of a metabolic pathway shuts down the pathway

  • Prevents a cell from wasting chemical resources by synthesizing more product than is needed