AP BIO Energy/enzymes and Photosynthesis

Thermal Energy: Thermal energy has two parts: 1) the chemical energy in the bonds of molecules and 2) kinetic energy from the movement of molecules.

Temperature: The average kinetic energy of molecules.

Heat: The flow of kinetic energy between objects or places.

Metabolism: All of the biological chemical reactions.

Metabolic Pathway: A series of chemical reactions that result in a product. Each step in the pathway is helped along by a different enzyme.

Catabolism: Metabolic pathways that release energy. Catabolism is a degradative process, breaking down molecules.

Anabolism: Metabolic pathways that use energy to create complex molecules. This is also known as a biosynthetic process.

Entropy: A measure of disorder or randomness in a system.

The First Law of Thermodynamics: Energy can only be converted from one form to another, it cannot be created or destroyed.

The Second Law of Thermodynamics: All systems tend toward a state of increased entropy. While parts of a system can become more ordered, that requires energy to be added to the system from somewhere else. Transforming energy results in the loss of usable energy in the form of heat.

Spontaneous Process: A process that occurs naturally without the need for external energy input. Spontaneous processes tend to increase disorder.

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Exergonic Pathway: A chemical reaction where the change in Gibbs Free Energy is negative. This means the reaction increases entropy and happens spontaneously. The product molecules are lower energy and degradative.

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Endergonic Pathway: A chemical reaction where the change in Gibbs Free Energy is positive. This means the reaction decreases entropy and requires energy input. The product molecules are higher energy.

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Energy Coupling: Exergonic reactions provide energy for endergonic reactions. This energy transfer is mediated by ATP.

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Adenosine Triphosphate (ATP): A nucleoside consisting of ribose, adenine, and three phosphates. The hydrolysis of ATP releases an inorganic phosphate and energy.

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Substrate Level Phosphorylation: An enzyme moves a phosphate from ATP to a molecule, creating an unstable, high energy, phosphorylated intermediate that is more likely to react.

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Enzyme: A protein that acts as a biological catalyst. Enzymes speed up the rate of a chemical reaction by lowering activation energy, but they are not consumed in the reaction and do not alter the overall change in Gibbs Free Energy. Ribozymes are an exception, as they are RNA enzymes, not proteins.

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Activation Energy: The initial input of energy that is required to start a chemical reaction. Enzymes lower the amount of activation energy required to start a reaction.

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Substrate: The reactant that an enzyme binds to.

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Active Site: The specific location on an enzyme where a substrate binds.

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Induced Fit: When a substrate or active site is altered to form a better fit between them.

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Competitive Inhibitor: Molecules that are similar in structure to the substrate and can bind to the enzyme's active site. This blocks the substrate from binding and inactivates the enzyme.

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Allosteric Site: A binding site on an enzyme that is different from the active site, where activators and inhibitors can bind.

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Allosteric Regulation: The regulation of enzyme activity by the binding of molecules (activators or inhibitors) to the allosteric site.

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Activator: Increases the activity of an enzyme by stabilizing it in its active form.

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Inhibitor: Decreases the activity of an enzyme by stabilizing it in its inactive form.

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Feedback Inhibition: An allosteric regulation mechanism where the end product of a metabolic pathway inhibits the activity of the first enzyme in that pathway.This prevents the overproduction of the product.

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Cofactor: A non-protein molecule or atom that is needed for the enzyme to function properly.

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Coenzyme: An organic cofactor. Many coenzymes are vitamins or vitamin derivatives.21

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Denatured Enzyme: An enzyme that has lost its three-dimensional shape. This is usually irreversible and the enzyme must be recycled Denaturation can occur when the enzyme is exposed to extreme temperatures, pH, or high salt concentrations.

Photoautotroph: An organism that uses photosynthesis to make its food.

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Photo refers to light.

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Auto refers to self.

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Troph refers to feeder.

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Photosynthesis: The process where organisms capture energy from the sun and convert it into chemical energy in the form of sugars.

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Chlorophyll: The green pigment that is essential for photosynthesis. Chlorophyll is a mutant pigment. When chlorophyll absorbs energy from the sun, its electrons jump out of the molecule. This makes chlorophyll special, because in normal molecules the electrons would give off the energy and return to their normal energy level.

Photosystem: A cluster of pigment molecules. Energy absorbed by pigments in the photosystem is passed to chlorophyll a as heat.

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Electron Transport Chain: A series of proteins that are embedded in a membrane. Each time a protein passes an electron to its neighbor, a small amount of energy is lost from the electron. Protein pumps use this energy to move H+ ions, creating a strong electrochemical gradient.

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Electrochemical Gradient: A difference in concentration and electric charge across a membrane. This creates a store of potential energy.

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ATPase: An enzyme that uses energy to create ATP. ATPase is perched at the end of a channel protein and captures the kinetic energy of H+ flow.

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Proton Pump: A protein that uses energy to move protons (H+ ions) across a membrane.

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NADPH: An electron carrier. NADP collects an electron and H+ to become NADPH. NADPH carries energized electrons to power the Calvin Cycle.

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Light Dependent Reactions: The first stage of photosynthesis. Light dependent reactions take place in the thylakoids. During this stage, light is absorbed by pigments in photosystems, energized electrons exit chlorophyll and run the electron transport chain, energized electrons are carried by NADPH to power the Calvin cycle, proton pumps in the electron transport chain create an electrochemical gradient of H+, and protons flowing past ATP synthase make ATP, which is used to run the Calvin cycle.

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Light Independent Reactions (Calvin Cycle): The second stage of photosynthesis, which can take place even at night. Light independent reactions use the energy from the light dependent reactions (ATP and NADPH) to run an anabolic glucose production pathway. The Calvin Cycle takes place in the stroma. During this stage, energy runs an anabolic glucose production pathway.

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Carbon Fixation: The first step of the Calvin cycle, where atmospheric carbon dioxide is attached to an organic molecule called RuBP. This is how inorganic carbon dioxide is converted to organic carbon.

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Rubisco: An enzyme involved in the Calvin cycle. Rubisco helps atmospheric carbon dioxide attach to RuBP.

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Stroma: The fluid that fills the center of the chloroplast. The stroma is where the Calvin cycle occurs.

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Thylakoid: Membrane-bound compartments found within chloroplasts. Thylakoids are where the light dependent reactions of photosynthesis take place.

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Cyanobacteria: Photosynthetic bacteria. Cyanobacteria have photosystems and electron transport chains embedded in folds of their cell membranes. They use oxygenic photosynthesis, like plants