Chapter 6 - An Introduction To Metabolism

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Metabolism

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the totality of an organism’s chemical processes; an emergent property of life that arises from specific interactions between molecules within the orderly environment of the cell

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Catabolic pathways

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Degradative processes in which complex molecules are broken down into simpler molecules; one major component of catabolism is cellular respiration, in which sugar glucose is broken down into carbon dioxide and water

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Anabolic pathways

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Processes that consume energy to build complicated molecules from simpler ones (e.g. synthesis of proteins from amino acids)

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Energy coupling

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the transfer of energy from catabolism to anabolism;
energy that is produced through catabolic processes (downhill) is used to drive anabolic processes (uphill)

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Bioenergetics

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the study of how organisms manage their energy resources

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Energy

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the capacity to do work; the ability to rearrange a collection of matter

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Kinetic Energy

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the energy of motion

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Potential Energy

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the energy that matter possesses because of its location or structure

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Chemical Energy

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a form of potential energy; stored in molecules because of the structural arrangement of the atoms in those molecules

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Thermodynamics

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the study of energy transformation that occur in a collection of matter

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First law of thermodynamics

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states that the energy of the universe is constant; energy can be transferred and transformed, but it can be neither created nor destroyed

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Second law of thermodynamics

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every energy transfer or transformation increases the entropy (disorderliness) of the universe; an organism takes in organized forms of matter and energy from the surroundings and replaces them with less ordered forms; when a spontaneous process occurs in a system, the stability of that system increases (e.g. when water flows downhill, its system increases in stability)

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Free energy

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the portion of a system’s energy that can perform work when temperature is uniform throughout the system; free energy (G) = the system’s total energy (H) – temperature Kelvin (T) x entropy (S)
G=H-TS

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Exergonic Reation

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a reaction that proceeds with a net release of free energy; spontaneous reactions

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Endergonic Reaction

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a reaction that absorbs free energy from the surroundings; nonspontaneous reactions

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Energy coupling

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the use of an exergonic process to drive an endergonic process

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ATP (Adenosine triphosphate)

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molecule used to power cellular processes; closely related to one type of nucleotide found in nucleic acids; bonds between phosphate groups can be broken by hydrolysis to yield energy and ADP (adenosine diphosphate)

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Phosphorylated intermediate

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through the help of enzymes, the free phosphate ion from ATP is transferred to another molecule within the cell; this avoids loss of the free energy and is the key to energy coupling within the cell; this intermediate is more reactive than the original molecule

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Enzymes

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catalytic proteins

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Catalyst

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a chemical agent that changes the rate of a reaction without being consumed by the reaction

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Activation energy

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the energy required to break the bonds in the reactant molecules; initial investment of energy for starting a reaction

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Substrate

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the reactant an enzyme acts on

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Active site

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typically a pocket or groove on the surface of the protein; a limited region of the enzyme that actually binds to the substrate; usually formed by only a few of the enzyme’s amino acids, with the rest of the protein molecule providing a framework that reinforces the configuration of the active site

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Induced fit

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an induced change in the conformation of the enzyme that allows it to bind more snuggly to the substrate; brings chemical groups of the active site into positions that enhance their ability to catalyze the chemical reaction

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Cofactors

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nonprotein helpers required by some enzymes for catalytic activity; may be bound tightly to the active site as permanent residents, or they may bind loosely and reversibly along with the substrate; some of these are inorganic compounds

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Coenzyme

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organic cofactors are more specifically called coenzymes

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Competitive inhibitors

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inhibitors that closely resemble the normal substrate molecule and compete for admission into the active site; reduce the productivity of enzymes by blocking the substrate from entering active sites; this is reversible by increasing the amount of substrate

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Noncompetitive inhibitors

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inhibitors that do not directly compete with normal substrate at the active site; impede enzymatic reactions by binding to another part of the enzyme; causes enzyme to change its conformation, rendering the active site unreceptive to substrate or leaving the enzyme less effective at catalyzing the conversion of substrate to product

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Allosteric site

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a site remote to the active site where regulatory molecules can bind to an enzyme and change its shape and function

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Feedback inhibition

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the switching off of a metabolic pathway by its end-product, which acts as an inhibitor of an enzyme within the pathway

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Cooperativity

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if an enzyme has two or more subunits, this interaction with one substrate molecule triggers the same favorable conformational change in all other subunits of the enzyme; amplifies the response of enzymes to substrates

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Apoenzyme

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an enzyme that is devoid of its necessary cofactor and is thus catalytically inactive

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Holoenzyme

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an enzyme that contains its necessary cofactor and is thus catalytically active

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Zymogen

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an enzyme that is secreted in an inactive form; cleaved under certain physiological conditions to the active form of the enzyme