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Ch 8: An Introduction to Metabolism - Coggle Diagram
Ch 8: An Introduction to Metabolism
Concept 8.1: An organism’s metabolism transforms matter and energy
Metabolism: the totality of an organism’s chemical reactions. It is an emergent property of life that arises from orderly interactions between molecules
Metabolic Pathway: a specific molecule is altered in a series of steps to produce a product. Each step is catalyzed by a specific enzyme, a macromolecule that speeds up a specific reaction
Catabolic pathways: release energy by breaking down complex molecules into simpler compounds. Cellular respiration, the breakdown of glucose in the presence of O₂, is an example of a pathway of catabolism (“downhill” reaction).
8.2: Like a multistep open hydroelectric system, a catabolic pathway in a cell releases free energy in a series of reactions
8.3: Free energy needed to phosphorylate ADP comes from exergonic breakdown reactions (catabolism)
Anabolic pathways consume energy to build complex molecules from simpler ones. For example, the synthesis of protein from amino acids is an anabolic pathway (“uphill” reaction).
8.1: The chemical reactions of metabolism are reversible, but never reach equilibrium in a living cell
Bioenergetics: the study of how energy flows through living organisms
Energy: the capacity to cause change, can be used to do work—move matter against opposing forces, such as gravity and friction. Energy exists in various forms. Living cells must transform energy from one form to another to do the work of life
Kinetic energy: energy associated with motion. Moving objects perform work by imparting motion to other matter. For example, water gushing through a dam turns turbines
Thermal energy: the kinetic energy associated with random movement of atoms or molecules. Thermal energy in transfer from one object to another is called heat. Light is another type of energy that can be harnessed to do work, such as photosynthesis
Potential energy: energy that matter possesses because of its location or structure. For example, water behind a dam possesses energy because of its altitude above sea level. Molecules possess energy due to the arrangement of electrons in bonds between their atoms
Chemical energy: potential energy available for release in a chemical reaction. Complex molecules, such as glucose, are high in chemical energy because energy is released as they are broken down to simpler products
Thermodynamics: the study of energy transformations in a collection of matter
Isolated System: the liquid in a thermos bottle, is unable to exchange energy or matter with its surroundings
Open System: energy and matter can be transferred between the system and its surroundings
First Law of Thermodynamics: the energy of the universe is constant. Energy can be transferred and transformed, but it cannot be created or destroyed. The first law is also called the principle of conservation of energy
The Second Law of Thermodynamics: During every energy transfer or transformation, some energy is converted to thermal energy and lost as heat, becoming unavailable to do work. According to the second law of thermodynamics, every energy transfer or transformation increases the entropy of the universe and entropy is a measure of molecular disorder, or randomness
Spontaneous processes: occur without energy input; they can happen quickly or slowly.
Spontaneous reactions do not need added energy, but they can be slow enough to be imperceptible
Nonspontaneous Processes: decrease entropy are nonspontaneous; they require an input of energy
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 do work when temperature and pressure are uniform throughout the system, as in a living cell
ΔG = change in free energy
The magnitude of ΔG determines the quantity of energy required to drive an endergonic reaction
ΔG is negative for all spontaneous processes
ΔG is zero or positive for nonspontaneous processes
ΔG = Gfinal state – Ginitial state
ΔH = change in enthalpy (total energy)
ΔS = change in entropy
T = Temperature in Kelvin (K)
Change equation: ΔG = ΔH – TΔS
Equilibrium: the point at which forward and reverse reactions occur at the same rate, describes a state of maximum stability. Systems never spontaneously move away from equilibrium. A process is spontaneous and can perform work only when it is moving toward equilibrium
exergonic reaction (“energy outward”): proceeds with a net release of free energy to the surroundings. In exergonic reactions, the products store less free energy than the reactants. Because ΔG is negative, exergonic reactions occur spontaneously
8.3: In an exergonic reaction, the formation of new bonds releases more energy than was invested in breaking the old bonds
endergonic reaction (“energy inward”): absorbs free energy from the surroundings. In endergonic reactions, the products store more free energy than the reactants. Because ΔG is positive, endergonic reactions are non-spontaneous
CONCEPT 8.3: ATP powers cellular work by coupling exergonic reactions to endergonic reactions
Cell Work
Chemical work—pushing endergonic reactions
Transport work—pumping substances across membranes against the direction of spontaneous movement
Mechanical work—such as beating cilia or contracting muscle cells
Cellular work (mechanical, transport, and chemical) is powered by ATP hydrolysis
Cell energy
energy coupling: Cells manage energy resources to do work through the use of this exergonic process to drive an endergonic one. Most energy coupling in cells is mediated by ATP.
Overall, the coupled reactions are exergonic
ATP (adenosine triphosphate) is composed of ribose (a sugar), adenine (a nitrogenous base), and three phosphate groups. In addition to energy coupling, ATP functions as one of the nucleoside triphosphates used to make RNA
Transport and mechanical work in the cell are also nearly always powered by ATP hydrolysis
ATP hydrolysis causes a change in protein shape and binding ability
ATP is regenerated by addition of a phosphate group to adenosine diphosphate (ADP)
The shuttling of inorganic phosphate and energy is called the ATP cycle; it couples energy-yielding processes to energy-consuming ones
In the cell, energy from the exergonic hydrolysis of ATP is used to drive endergonic reactions
Phosphorylation: transfer of a phosphate group from ATP to another molecule, is typically used to power endergonic reactions
The recipient molecule, a phosphorylated intermediate, is more reactive (less stable, with more free energy) that the original molecule
CONCEPT 8.4: Enzymes speed up metabolic reactions by lowering energy barriers
catalyst: a chemical agent that speeds up a reaction without being consumed by the reaction
catalysis: the process by which a catalyst selectively speeds up a reaction without itself being consumed
An enzyme catalyzes a reaction by lowering the EA barrier enough for the reaction to occur at moderate temperatures
An enzyme cannot change ΔG; it only speeds up a reaction that would eventually occur anyway
enzyme: a macromolecule (typically protein) that acts as a catalyst to speed up a specific reaction
enzyme’s substrate: the reactant that an enzyme acts on
The rate of an enzyme-catalyzed reaction can be sped up by increasing substrate concentration
The enzyme binds to its substrate, forming an enzyme-substrate complex
While bound, the catalytic activity of the enzyme converts substrate to product
The ACTIVE SITE is the region on the enzyme, often a pocket or groove, that binds to the substrate
The complementary fit between the shape of the active site and the shape of the substrate is responsible for enzyme specificity
When the substrate enters the active site, the enzyme changes shape slightly, tightening around the substrate like a handshake. This INDUCED FIT results from interactions (and weak bonds) between chemical groups on the substrate and the active site. It brings the chemical groups of the active site into positions that enhance catalysis of the reaction
When all enzyme molecules have their active sites engaged, the enzyme is saturated
If the enzyme is saturated, the reaction rate can only be sped up by adding more enzyme
The conversion of substrate to product happens rapidly, and product is released from the active site
Because enzymes emerge from reactions in their original form, small amounts can have huge metabolic impacts
Enzymes use a variety of mechanisms to lower EA
Substrates may be oriented to facilitate the reaction
Substrates may be stretched to make the bonds easier to break
The active site may provide a microenvironment that favors the reaction
Amino acids in the active site may participate in the reaction
Activity
Enzyme activity can be affected by general environmental factors, such as temperature and pH
It can also be affected by chemicals that specifically influence the enzyme
Denaturization
Each enzyme has an optimal temperature at which it catalyzes its reaction at the maximum possible rate
Up to this point, the reaction rate increases with increasing temperature; beyond this point the rate of reaction begins to drop
Enzymes begin to denature at temperatures (or pHs) beyond their optimum
Evolution
Enzymes are proteins encoded by genes
Changes in genes (mutations) lead to changes in the amino acid composition of the enzyme
Altered amino acids, particularly at the active site, can result in novel enzyme activity or altered substrate specificity
If a mutation results in a new enzyme function that is beneficial to the organism, natural selection will favor the mutated allele
activation energy (EA): The initial energy needed to break the bonds of the reactants
Heat in the form of thermal energy absorbed from the surroundings often supplies activation energy
Molecules become unstable when enough energy is absorbed to break bonds; this is the transition state
The activation energy provides a barrier that determines the rate of spontaneous reactions
For some reactions, EA is low enough that thermal energy at room temperature is sufficient to overcome the activation barrier
Most reactions have high EA, and need additional energy (usually heat) to reach the transition state
Cofactors: nonprotein helpers that bind to the enzyme permanently, or reversibly with the substrate
Organic cofactors are called coenzymes
Enzyme Inhibitors
Certain chemicals selectively inhibit the action of specific enzymes
If an inhibitor forms covalent bonds with the enzyme, then the inhibition is usually irreversible
Many inhibitors bind to the enzyme by weak interactions, resulting in reversible inhibition
Competitive inhibitors: closely resemble the substrate, and can bind to the enzyme’s active site
Enzyme productivity is reduced because the inhibitor blocks the substrate from entering the active site
Increasing substrate concentration can overcome this type of inhibition
Noncompetitive inhibitors: bind to another part of the enzyme, away from the active site
Binding of the inhibitor causes the enzyme to change shape, making the active site less effective at catalyzing the reaction
Toxins and poisons are often irreversible enzyme inhibitors
Other examples include pesticides and antibiotics
CONCEPT 8.5: Regulation of enzyme activity helps control metabolism
Regulation of metabolic pathways
Cells can regulate metabolic pathways by switching on or off the genes that encode specific enzymes, or by regulating the activity of existing enzymes
Allosteric regulation occurs when a regulatory molecule binds to a protein at one site and affects the protein’s function at another site
This type of regulation may either inhibit or stimulate enzyme activity
Most allosterically regulated enzymes are made from polypeptide subunits, each with its own active site
The complex oscillates between two shapes, one catalytically active and the other inactive
An activating or inhibiting molecule may bind to a regulatory site, often located where the subunits join
The binding of an activator stabilizes the shape that has functional active sites, whereas the binding of an inhibitor stabilizes the inactive form of the enzyme
In COOPERATIVITY, substrate binding to one active site triggers a shape change in the enzyme that stabilizes the active form for all other sites
This mechanism amplifies the response by priming the enzyme to act on additional substrate molecules more readily
feedback inhibition: the end product of a metabolic pathway shuts down the pathway
Feedback inhibition prevents a cell from wasting chemical resources by synthesizing more product than is needed
Compartmentalization of the cell: helps to bring order to metabolic pathways
In some cases, the enzymes for several steps in a metabolic pathway form a multienzyme complex
Some enzymes have fixed locations and act as structural components of particular membranes