BIO 190A EXAM 2 TERMS

Energy

The ability to promote change or do work

Kinetic energy

Energy associated with relative motion

Potential energy

Stored energy due to structure or location

First law of thermodynamics

Energy cannot be created or destroyed, but can be transferred or transformed

Second law of thermodynamics

Any energy transfer or transformation increases the entropy (degree of disorder) of a system

Entropy

A measure of the degree of disorder or randomness in a system

Free energy (G)

Usable energy; the amount of energy available to do work

Free-energy change (ΔG)

The difference in free energy between reactants and products that determines whether a reaction occurs spontaneously

Exergonic reaction

A spontaneous reaction where ΔG < 0 and free energy is released

Endergonic reaction

A non-spontaneous reaction where ΔG > 0 that requires an input of free energy

Enzyme

A protein catalyst that speeds up chemical reactions without being consumed

Activation energy (EA)

The initial input of energy required to achieve the transition state and start a chemical reaction

Transition state

An unstable, high-energy state where bonds are strained and ready to break/form products

Active site

The specific location on an enzyme where substrates bind and the chemical reaction occurs

Substrate

A reactant molecule that binds specifically to the active site of an enzyme

Induced fit

Conformational changes an enzyme undergoes upon substrate binding to bind the substrate more tightly

Affinity

The degree of attraction between an enzyme and its substrate

Vmax

The maximal velocity or reaction rate of an enzyme-catalyzed reaction when saturated with substrate

KM

The substrate concentration at which the reaction velocity is half of its maximal value (Vmax)

Reversible inhibitor

An inhibitor that noncovalently binds to an enzyme to reversibly decrease its activity

Competitive inhibitor

An inhibitor that binds directly to the enzyme's active site, competing with the substrate

Noncompetitive inhibitor

An inhibitor that binds to an allosteric site (outside the active site) to decrease enzyme activity

Allosteric site

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

Cofactor

An inorganic ion (such as Fe2+ or Mg2+) required for an enzyme to function properly

Coenzyme

An organic, non-protein molecule (often derived from vitamins) required for enzyme function

Prosthetic group

A small molecule permanently attached to the surface of an enzyme to aid function

Metabolic pathway

A coordinated series of chemical reactions in a cell catalyzed by specific enzymes

Catabolic reaction

A metabolic pathway that breaks down larger molecules into smaller ones; typically exergonic

Anabolic reaction

A metabolic pathway that synthesizes larger molecules from smaller ones; typically endergonic

Energy intermediate

A molecule such as ATP or NADH directly used to store and transfer energy in cellular processes

Oxidation

The removal of electrons from an atom or molecule

Reduction

The addition of electrons to an atom or molecule

Redox reaction

A chemical reaction involving the transfer of electrons from one molecule to another

Cellular respiration

The process by which living cells obtain energy from organic molecules to produce ATP

Glycolysis

The first stage of respiration; breaks 1 glucose into 2 pyruvate, yielding 2 net ATP and 2 NADH

Pyruvate oxidation

The breakdown of 2 pyruvate into 2 acetyl CoA, 2 CO2, and 2 NADH

Citric acid cycle

Cyclic pathway that oxidizes 2 acetyl groups to produce 4 CO2, 6 NADH, 2 FADH2, and 2 ATP (via GTP)

Oxidative phosphorylation

Uses high-energy electrons from NADH/FADH2 to create an H+ gradient that drives ATP synthesis

Electron transport chain (ETC)

Protein complexes and organic molecules in the inner mitochondrial membrane that transfer electrons and pump H+

Final electron acceptor

The terminal molecule in the electron transport chain (O2 in aerobic respiration) that accepts electrons

H+ electrochemical gradient

Transmembrane gradient of proton concentration and electrical charge that stores potential energy

ATP synthase

A rotary enzyme that utilizes the flow of H+ across a membrane to synthesize ATP from ADP and Pi

Chemiosmosis

The synthesis of ATP driven by the electrochemical gradient of H+ across a membrane

Substrate-level phosphorylation

Direct transfer of a phosphate group from an organic substrate to ADP to form ATP

Anaerobic

An environment or process that occurs in the absence of oxygen

Nitrate reductase

An enzyme used by anaerobic bacteria like E. coli that uses nitrate (NO3-) as a final electron acceptor

Fermentation

Anaerobic breakdown of organic molecules to produce ATP solely via glycolysis by regenerating NAD+

Photosynthesis

The process capturing light energy to synthesize carbohydrates from CO2 and H2O

Autotroph

An organism that produces its own organic food molecules from inorganic sources

Heterotroph

An organism that must consume organic molecules from its environment for sustenance

Chloroplast

The organelle in plant and algal cells where photosynthesis takes place

Chlorophyll

The green photosynthetic pigment found in chloroplasts that absorbs light energy

Stroma

The fluid-filled region of the chloroplast enclosed by the inner membrane and surrounding the thylakoids

Thylakoid

A flattened, fluid-filled membranous sac inside chloroplasts where light reactions take place

Stomata

Microscopic pores on leaf surfaces that open and close to allow gas exchange (CO2/O2) and water transpiration

Light reactions

The first stage of photosynthesis occurring in thylakoid membranes; produces ATP, NADPH, and O2

Calvin cycle

The second stage of photosynthesis occurring in the stroma; uses ATP and NADPH to fix CO2 into carbohydrates

Light

A form of electromagnetic radiation composed of photons traveling as waves

Electromagnetic radiation

Energy that travels through space in the form of synchronized electric and magnetic oscillations

Photon

A discrete packet or particle of light energy

Excited state

An unstable, high-energy state of an electron after absorbing a photon of light

Chlorophyll a

The primary photosynthetic pigment in plants and algae that absorbs blue-violet and red light

Chlorophyll b

An accessory photosynthetic pigment that transfers absorbed light energy to chlorophyll a

Carotenoids

Accessory pigments that absorb blue and green light, appearing yellow, orange, or red

Absorption spectrum

A graph showing the wavelengths of light absorbed by a specific pigment

Action spectrum

A graph showing the rate of photosynthesis across different wavelengths of visible light

Photosystem I (PS I)

A protein-pigment complex in thylakoid membranes that absorbs light to generate NADPH

Photosystem II (PS II)

The initial complex in linear electron flow that oxidizes water, releases O2, and pumps H+

Linear electron flow

The combined noncyclic pathway of PS II and PS I generating ATP, NADPH, and O2

Photophosphorylation

The synthesis of ATP driven by light-activated electron transport in chloroplasts

Cyclic electron flow

An alternative pathway using PS I and the ETC to generate only ATP without producing NADPH or O2

Light-harvesting complex

Pigment molecules bound to proteins that absorb photons and transfer energy via resonance energy transfer

Reaction center

The specialized site in a photosystem containing P680 or P700 where light-driven redox reactions occur

Resonance energy transfer

The non-radiative transfer of excitation energy from one pigment molecule to an adjacent one

P680

The special pair of chlorophyll a molecules in the PS II reaction center that releases high-energy electrons

Z scheme

The model depicting the progression of an electron's energy levels across PS II and PS I during photosynthesis

Rubisco

Ribulose-1,5-bisphosphate carboxylase/oxygenase; the key enzyme that catalyzes CO2 fixation in the Calvin cycle

RuBP

Ribulose-1,5-bisphosphate; the 5-carbon acceptor molecule that binds CO2 in the first step of the Calvin cycle

Glyceraldehyde-3-phosphate (G3P)

The 3-carbon sugar produced by the Calvin cycle used to synthesize glucose and other organic molecules

Carbon fixation

The enzymatic incorporation of inorganic carbon (CO2) into an organic molecule

C3 plants

Plants that fix carbon solely via rubisco into a 3-carbon intermediate (3-phosphoglycerate)

Photorespiration

A wasteful metabolic process occurring when rubisco fixes O2 instead of CO2, releasing CO2 and consuming ATP

C4 plants

Plants that spatially separate carbon fixation (forming 4-carbon oxaloacetate) from the Calvin cycle

CAM plants

Plants that open stomata at night to fix CO2 into organic acids and run the Calvin cycle during the day

Cell communication

The process by which cells detect, interpret, and respond to signals in their environment

Signal

An extracellular agent (chemical molecule, light, temperature) that influences cell properties or activity

Direct intercellular signaling

Signaling where molecules pass directly between the cytosols of adjacent cells via gap junctions

Contact-dependent signaling

Signaling requiring physical contact between membrane-bound ligands and receptors of adjacent cells

Autocrine signaling

Signaling where a cell secretes molecules that bind to receptors on its own surface or neighboring identical cells

Paracrine signaling

Signaling where a cell secretes molecules that affect target cells in the immediate close vicinity

Endocrine signaling

Long-distance signaling where hormones are secreted into the bloodstream to reach distant target cells

Receptor

A cellular protein that specifically binds a signaling molecule (ligand) to initiate a response

Ligand

A signaling molecule that binds specifically and noncovalently to a complementary receptor protein

Receptor activation

The initial signaling step where ligand binding induces a conformational change in the receptor

Signal transduction

The sequence of intracellular biochemical events that converts an extracellular signal into a specific response

Cellular response

The altered physiological activity (e.g., enzyme activation, gene expression) resulting from a signaling cascade

Conformational change

A change in the three-dimensional tertiary structure of a protein upon binding a ligand or substrate

Dissociate

The reversible unbinding or separation of a ligand from its receptor

Equilibrium

The state where the rate of ligand binding to receptor equals the rate of ligand dissociation

Dissociation constant (Kd)

The equilibrium constant measuring the affinity between a receptor and its ligand; [ligand] at 50% receptor saturation