AP BIO UNIT 3 PART 1

Metabolism

All chemical reactions in an organism.

Metabolic pathways

A series of chemical reactions that build or break down complex molecules, proceeding from a substrate through intermediates to a product.

Catabolic pathways

Metabolic pathways that release energy by breaking down complex molecules into simple compounds.

Anabolic pathways

Metabolic pathways that consume energy to build complex molecules from simple compounds.

Energy

The ability to do work, which organisms need to survive and function.

Kinetic energy

Energy associated with motion.

Thermal energy

Energy associated with the movement of atoms and molecules.

Potential energy

Stored energy.

Chemical energy

Potential energy available for release in chemical reactions.

Thermodynamics

The study of energy transformations in matter.

First Law of Thermodynamics

The principle stating that energy cannot be destroyed or created, but it can be transferred.

Second Law of Thermodynamics

The principle stating that energy transformation increases entropy (disorder) in the universe, as some energy is unusable and often lost as heat.

Free energy

A concept used by scientists to determine the likelihood of reactions in organisms or if reactions are energetically favorable, calculated as $\Delta G = \Delta H - T\Delta S$.

Exergonic reactions

Chemical reactions that release free energy, are spontaneous, and have $\Delta G < 0$ (e.g., cellular respiration).

Endergonic reactions

Chemical reactions that absorb free energy, are not spontaneous, and have $\Delta G > 0$ (e.g., photosynthesis).

Mechanical work

A type of cellular work involving movement, such as the motion of flagella in sperm.

Transport work

A type of cellular work that pumps substances across membranes against spontaneous movement.

Chemical work

A type of cellular work that drives the synthesis of molecules, such as building polymers from monomers.

Adenosine triphosphate (ATP)

A molecule composed of adenine, ribose, and three phosphate groups that organisms use as a source of energy to perform work.

Phosphorylation

The transfer of a released phosphate group from ATP to another molecule to give it energy.

Enzymes

Protein molecules that catalyze (speed up) reactions by lowering activation energy without being consumed by the reaction.

Active Site

The specific region of an enzyme where the complementary substrate binds, held in place by weak interactions.

Enzyme-Substrate Complex

The temporary complex formed when a substrate binds to the active site of an enzyme before being converted into products.

Induced Fit

The conformational change in an enzyme's active site that allows molecules to bind better.

Enzyme Catabolism

A reaction pathway in which an enzyme facilitates the breakdown of molecules, releasing energy.

Enzyme Anabolism

A reaction pathway in which an enzyme assists in building complex molecules.

Cofactors

Inorganic molecules, consisting of metals, that can be bound loosely or tightly to assist enzyme function.

Coenzymes

Organic cofactors that assist enzyme function, such as vitamins.

Enzyme Inhibitors

Molecules that reduce the activity of specific enzymes through permanent or reversible binding.

Permanent Inhibition

Inhibition occurring when an inhibitor attaches to an enzyme via covalent bonds (e.g., toxins and poisons).

Reversible Inhibition

Inhibition occurring when an inhibitor binds to an enzyme using weak interactions.

Competitive Inhibitors

Inhibitors that reduce enzyme activity by blocking substrates from binding to the active site, which can be reversed by increasing substrate concentration.

Noncompetitive Inhibitors

Inhibitors that bind to a site other than the active site (allosteric inhibition), altering the shape of the active site and preventing substrate binding.

Allosteric Site

A regulatory binding site on an enzyme distinct from the active site.

Allosteric Regulation

The mechanism by which molecules bind via noncovalent interactions to an allosteric site to change the shape and function of the active site, continuing or pausing processes so ATP is not wasted.

Allosteric Activator

A molecule that binds to an allosteric site and stabilizes the enzyme shape so that the active site remains open.

Allosteric Inhibitor

A molecule that binds to an allosteric site and stabilizes the enzyme shape so that the active sites are closed (inactive).

Cooperativity

A form of allosteric regulation where substrate binding to one active site stabilizes the active form and changes the shape of the other active sites.

Feedback Inhibition

A metabolic pathway control mechanism in which the final product binds to an early enzyme to render its active site inactive.

Photosynthesis

The biological process that converts light energy into chemical energy.

Autotrophs

Organisms that produce their own food (organic molecules) from simple substances in their surroundings.

Heterotrophs

Organisms that are unable to make their own food and must live off of other organisms.

Cyanobacteria

Early photosynthetic prokaryotes that oxygenated the Earth's atmosphere.

Mesophyll

The cells that make up the interior tissue of leaves where chloroplasts are found.

Stomata

Pores located in leaves that allow $CO_2$ in and oxygen out.

Stroma

The aqueous internal fluid surrounded by the double membrane of the chloroplast.

Thylakoids

Individual membrane-bound structures inside a chloroplast that make up grana and contain chlorophyll.

Chlorophyll

The green pigment located within the thylakoid membrane that absorbs light.

Redox Reaction

A chemical reaction involving the complete or partial transfer of one or more electrons from one reactant to another.

Oxidation

The loss of electrons ($e^-$) by a substance during a redox reaction, making it less negative.

Reduction

The gain of electrons ($e^-$) by a substance during a redox reaction, making it more negative.

Light Reactions

The first stage of photosynthesis, occurring in the thylakoids, that converts solar energy into chemical energy in the forms of ATP and NADPH.

Calvin Cycle

The stage of photosynthesis occurring in the stroma that synthesizes sugar.

Photons

Discrete particles of energy that make up light and travel in waves.

Wavelength

The distance from one crest of a light wave to the next crest.

Chlorophyll a

The primary photosynthetic pigment directly involved in the light reactions, displaying a blue/green color.

Chlorophyll b

A yellow/green accessory pigment that broadens the spectrum of light absorbed for photosynthesis.

Carotenoids

Yellow/orange accessory pigments that broaden the color spectrum driving photosynthesis and absorb excess light energy to protect chlorophyll.

Photoprotection

A process where carotenoids absorb and dissipate excess light energy that could otherwise damage chlorophyll or interact with oxygen.

Photosystems

Light-collecting units located in the thylakoid membrane composed of a reaction center and surrounding light-capturing complexes.

Reaction Center

A complex of proteins associated with a special pair of chlorophyll a molecules and a primary electron acceptor.

Light-Capturing Complexes

Pigment molecules associated with proteins that act like an antenna to direct photon energy toward the reaction center.

Photosystem II (PS II)

A photosystem functioning first in linear electron flow that contains a P680 reaction center absorbing light at $680\,nm$.

Photosystem I (PS I)

A photosystem with a P700 reaction center that absorbs light at $700\,nm$.

Linear Electron Flow

The pathway where excited electrons pass from Photosystem II to Photosystem I via an electron transport chain.

ATP Synthase

An enzyme complex that couples the diffusion of $H^+$ across the thylakoid membrane to the formation of ATP.

NADP+ Reductase

An enzyme that catalyzes the transfer of electrons from ferredoxin (Fd) to $NADP^+$, reducing it to NADPH.

Stomata

Small pores that serve as the principal means of gas exchange in vascular plants, opening to allow $CO_2$ to enter and water and oxygen to escape.

Guard cells

A pair of banana-shaped cells that control the opening and closing of leaf stomata.

Stomata density

The number of stomata per unit area of a leaf.

Desiccation

Drying out caused by excessive evaporation, particularly when water is unavailable under drought conditions.

Photolysis

The reaction where $H_2O$ splits into electrons, $2H^+$, and oxygen, which immediately bonds with another oxygen atom to make $O_2$.

Electron transport chain (ETC)

A pathway that allows electrons to flow from photosystem II to photosystem I.

Proton pump

A transport mechanism that uses energy from electron transport to move $H^+$ against its gradient from the stroma into the thylakoid lumen.

NADP+ Reductase

An enzyme that reduces $NADP^+$ by adding electrons to form NADPH, which is then sent to the Calvin Cycle.

ATP Synthase

An enzyme that couples the diffusion of $H^+$ to produce ATP from ADP and inorganic phosphate.

Photosynthesis

The process performed by plants, algae, and some bacteria that transforms light energy from the sun into chemical energy stored in glucose.

Glucose

A simple sugar produced by photosynthesis that stores chemical energy which cells transfer to ATP for cellular processes.

Chloroplast

The organelle in which photosynthesis occurs, composed of thylakoid membrane structures and stroma.

Thylakoids

Flat membrane sacs located inside the chloroplast.

Grana

Stacks of thylakoids found inside the chloroplast.

Stroma

The fluid-filled space surrounding the thylakoids within the chloroplast.

Chlorophyll

A green pigment located inside the thylakoid membrane that absorbs light energy from the sun to power photosynthesis.

Light-dependent Reaction

The stage of photosynthesis that takes in light energy and directly requires light.

Light-independent Reaction (Calvin Cycle)

The stage of photosynthesis that produces glucose and does not directly require light.