Chapter+8

Chapter 8: An Introduction to Metabolism

//Concept 8.1: An organism’s metabolism transforms matter and energy, subject to the laws of thermodynamics.//


 * Metabolism:** totality of an organism’s chemical reactions, comes from interaction between molecules and environment of cell. Manages material and energy of a cell.
 * Reactions are arranged in “pathways”
 * **Metabolic pathways**begin with a specific molecule, altered through steps by different enzymes.
 * o May release energy by breaking down complex molecules (**catabolic pathways**).
 * o Major pathway: cellular respiration
 * o Anabolic pathways consume energy to build complicated molecules from simple ones.
 * [[image:8883n18_04.jpg width="343" height="219"]]
 * Energy released from catabolic pathways can be stored and used for anabolic pathways.
 * **Energy:** capacity to cause change.
 * **Kinetic energy:** energy associated with motion.
 * **Heat/Thermal Energy:** kinetic energy associated with the random movement of atoms or molecules.
 * **Potential energy:** the energy matter possesses because of its location or structure (object at rest).
 * **Chemical energy:**potential energy ready for release.
 * o High amounts found in glucose
 * o Used for catabolic pathways
 * __Structures and biochemical pathways of cells enable them to release chemical energy from food to molecules, powering life processes.__
 * Organisms=energy transformers
 * **Thermodynamics:** the study of the energy transformations that occur in a collection of matter.
 * **First Law of Thermodynamics:**energy of the universe is constant, AKA principle of conservation of energy.
 * o Energy can be transferred and transformed, but cannot be created or destroyed.
 * **Second Law of Thermodynamics:**every energy transfer or transformation increases the entropy of the universe, for a process to occur spontaneously, it must increase the entropy of the universe.
 * o Much of absorbed energy is given off as heat.
 * o **Entropy:**used to measure quantity of disorder.
 * § The more random a collection of matter is arranged, the greater the entropy.
 * Spontaneous does not imply that the process occurs quickly, but that it occurs without an (additional) input of energy.
 * o Some energy becomes unusable.
 * o Only fraction is actually used to power organisms.
 * o Organisms are small islands of low entropy (may be decreasing), as long as total entropy in the universe is increasing.

//Concept 8.2: The free energy change of a reaction tells us whether or not the reaction occurs spontaneously//


 * **Free energy:** the portion of a system’s energy that can perform work when temperature and pressure are uniform.
 * Processes with negative free energy are spontaneous.
 * Systems higher in free energy are less stable.
 * o Tend to change spontaneously to a more stable state.
 * o Harnessing the downhill loss of free energy is a method of “doing work”.
 * Free energy increases when a reaction is pushed away from equilibrium.
 * When a system is at equilibrium, it contains very low free energy.

Chemical reactions can be classified as: -Greater decrease in FE=more work done
 * Exergonic:** (energy outward) proceeds with net release of energy. Free energy is negative for this reaction. Occurs spontaneously.

-Stores free energy in molecules -Positive FE -Non-spontaneous
 * Endergonic:** The reaction that absorbs free energy with its surroundings.




 * Equilibrium + Metabolism**
 * Reactions within an isolated system will eventually reach equilibrium.
 * o Cells/organisms who reach equilibrium area “dead”.
 * o Cells must have steady supply of glucose and expel waste in order to avoid equilibrium.

//Concept 8.3: ATP powers cellular work by coupling exergonic reactions to endergonic reactions.//

A cell does 3 types of major work.

//Concept 8.4: Enzymes speed up metabolic reactions by lowering energy barries.// //8.5: Regulation of enzyme activity helps control metabolism//
 * Chemical Work
 * o The pushing of endergonic reactions.
 * o E.g. synthesis from polymers to monomers
 * Transport Work
 * o The pumping of substances across membranes against the direction of spontaneous movement.
 * Mechanical Work
 * o Contraction of muscle cells
 * o Movement of chromosomes during cellular respiration
 * **Energy coupling:** The use of an exergonic process to drive and endergonic one.
 * The ATP cycle is a turnstile for energy during its transfer from catabolic to anabolic pathways.
 * Enzyme
 * A macromolecule that acts as a catalyst (speeds up reaction without being consumed during the reaction)
 * Activation Energy Barrier
 * //Free energy of activation//, or activation energy, is required to break the bonds of reactant molecule
 * In the graph below, the summit is called the unstable //transition state//, meaning they are activated and their bonds can be broken.
 * The downhill slope of the graph represents the bond formation phase of the reaction, also representing the loss of free energy
 * [[image:activationener.gif]]s
 * Activation Energy
 * Heat
 * Molecules absorb thermal energy to increase the speed of reactant molecules,helping them collide more often and more forcefully
 * Thermal absorption agitate atoms within molecules, making them more likely to break.
 * Not ideal in biological systems because it will denature proteins and kill cells and speed up **ALL** reactions (including ones not wanted)
 * Catalysts
 * Enzymes catalyze by decreasing the activation energy barrier
 * Substrates / Enzymes
 * Substrate: A reactant that an enzyme acts on
 * When substrate(s) bind with an enzyme, they form an enzyme-substrate complex.
 * Enzymes are able to catalyze the correct specific substrates by the unique three-dimensional configurations of their protein structure, a consequence of their amino acid sequence
 * The **active site** is a pocket or groove on the protein surface where catalysis actually occurs
 * **Induced fit** is a result of interactions of the amino acids and the substrates that slightly changes the protein's shape, causing the active site to fit the substrate better. It brings chemical groups of the active site into positions that enhance their ability to catalyze the chemical reaction.
 * Substrates are held in place by 'weak' interactions, like hydrogen bonds and ionic bonds.
 * Since most metabolic reactions are reversible, an enzyme can catalyze either the forward or the reverse reaction, depending which direction has the negative free energy change.
 * Enzymes work better under //optimal conditions//, with environmental factors like temperature and pH.
 * Cofactors
 * **Cofactors** are nonprotein helpers for catalytic activities, such as zinc, iron, and copper in ionic form.
 * **Coenzymes** are organic cofactors, like the most of the vitamins that act as coenzymes.
 * Enzyme Inhibitors
 * **Competitive Inhibitors** reduce productivity of enzymes by blocking substrates from entering active sites.
 * **Noncompetitive inhibitors** indirectly compete with substrates at the active sites by binding to another part of the enzyme.
 * Toxins and poisons are often irreversible enzyme inhibitors
 * Allosteric Regulation Regulation of Enzymes
 * Allosteric regulation is used to describe any case in which a protein's function at one site is affected by the binding of a regulatory molecule at a separate site.
 * Allosteric Activation / Inhibition
 * An activator stabilizes the shape that has functional active site
 * An inhibitor stabilizes the inactive form of the enzyme
 * A change in one of the subunits of the protein is transmitted to the other subunits, hence the usage of the activators / inhibitors
 * When an enzyme has more than one subunit, **cooperativity** occurs when a substrate's induced fit with one of the subunits triggers the same favorable shape change in all the other subunits of the enzyme.
 * **Feedback inhibition** occurs when a metabolic pathway is switched off by the inhibitory binding of the pathway's product and the enzyme that acts at the start of the process. For example, when the production of isoleucine accumulates, it slows down its own process ( to prevent surplus) by using feedback inhibition on the enzyme that from the first step of the reactions.
 * **Feedback inhibition** occurs when a metabolic pathway is switched off by the inhibitory binding of the pathway's product and the enzyme that acts at the start of the process. For example, when the production of isoleucine accumulates, it slows down its own process ( to prevent surplus) by using feedback inhibition on the enzyme that from the first step of the reactions.