BIOL 1020: Enzymes, Metabolic Pathways, Cellular Respiration, and Photosynthesis

Comprehensive practice flashcards defining key vocabulary across metabolic principles, cellular respiration, and photosynthesis covered in Lectures 11-13.

Metabolism

The totality of an organism's chemical reactions, representing an emergent property of life that arises from orderly molecular interactions within the cell.

Catabolic Pathways

Metabolic pathways that release energy by breaking down complex molecules into simpler compounds, such as cellular respiration breaking down glucose.

Anabolic Pathways

Metabolic pathways that consume energy to synthesize complex molecules from simpler ones, such as the synthesis of proteins from amino acids.

Bioenergetics

The study of how organisms manage their energy resources.

Kinetic Energy

The form of energy associated with the relative motion of objects or particles.

Thermal Energy (Heat)

Kinetic energy associated with the random movement of atoms or molecules.

Potential Energy

The energy that matter possesses because of its location or structure.

Chemical Energy

The potential energy available for release in a chemical reaction.

Isolated System

A system unable to exchange either energy or matter with its surroundings, exemplified by liquid in a thermos.

Open System

A system in which energy and matter can be transferred between the system and its surroundings; all living organisms are open systems.

First Law of Thermodynamics

The principle of conservation of energy stating that the amount of energy in the universe is constant; energy can be transferred and transformed, but it cannot be created or destroyed.

Second Law of Thermodynamics

The physical law stating that every energy transfer or transformation increases the entropy (disorder) of the universe.

Entropy

A thermodynamic measure of molecular disorder or randomness in the universe.

Free Energy ($\Delta G$)

The portion of a biological system's energy that can perform work when temperature and pressure are uniform throughout the system, given by $\Delta G = \Delta H - T\Delta S$.

Exergonic Reaction

A spontaneous chemical reaction that proceeds with a net release of free energy ($\Delta G < 0$).

Endergonic Reaction

A nonspontaneous chemical reaction that absorbs free energy from its surroundings ($\Delta G > 0$).

Energy Coupling

The management of energy resources in a cell through the use of an exergonic process to drive an endergonic one.

Phosphorylated Intermediate

A recipient molecule that covalently bonds to a phosphate group transferred from $ATP$, making it more reactive and less stable.

Enzyme

A biological catalyst (typically a protein) that speeds up metabolic reactions by lowering activation energy barriers without being consumed.

Activation Energy ($E_A$)

The initial free energy required to contort reactant molecules so their chemical bonds can break and a reaction can begin.

Active Site

The specific region of an enzyme molecule to which a substrate binds and where catalysis takes place.

Induced Fit

The slight conformational change of an enzyme's active site upon substrate binding that brings chemical groups into positions to enhance catalytic capability.

Cofactors

Nonprotein enzyme helpers that can be inorganic (such as metal ions) or organic.

Coenzyme

An organic cofactor required for an enzyme to function properly, frequently including vitamins.

Competitive Inhibitors

Molecules that reduce an enzyme's productivity by binding directly to the active site in competition with the substrate.

Noncompetitive Inhibitors

Inhibitors that bind to an enzyme at a site separate from the active site, altering the enzyme's conformation so the active site functions less effectively.

Allosteric Regulation

Regulation of a protein's function wherein a regulatory molecule binds to one site and affects protein activity at a different site.

Cooperativity

A mechanism of allosteric activation where substrate binding to the active site of one subunit locks all other subunits into the active conformation.

Feedback Inhibition

A metabolic control mechanism in which the final end product of a pathway binds allosterically to an early enzyme, shutting down its own synthesis.

Oxidation

The complete or partial loss of electrons from a substance in a redox reaction.

Reduction

The complete or partial addition of electrons to a substance in a redox reaction, thereby reducing its positive charge.

Reducing Agent

The electron donor in a redox reaction that becomes oxidized.

Oxidizing Agent

The electron acceptor in a redox reaction that becomes reduced.

$NAD^+$ (Nicotinamide Adenine Dinucleotide)

A coenzyme electron shuttle that acts as an oxidizing agent in respiration by accepting two electrons and one proton to form $NADH$.

Substrate-Level Phosphorylation

The direct enzymatic transfer of a phosphate group from an organic substrate to $ADP$ to form $ATP$, occurring in glycolysis and the citric acid cycle.

Glycolysis

A ten-step metabolic pathway in the cytosol that oxidizes glucose into two molecules of pyruvate, generating a net yield of $2\,\text{ATP}$ and $2\,\text{NADH}$ without using $O_2$.

Pyruvate Oxidation

The multi-step reaction linking glycolysis to the citric acid cycle within the mitochondrial matrix, converting each pyruvate into acetyl-CoA, $CO_2$, and $NADH$.

Citric Acid Cycle

An eight-step pathway in the mitochondrial matrix that decomposes acetyl-CoA into $CO_2$, producing $1\,\text{ATP}$ (or $GTP$), $3\,\text{NADH}$, and $1\,\text{FADH}_2$ per turn.

Oxidative Phosphorylation

The production of $ATP$ using energy derived from redox reactions in the electron transport chain and chemiosmosis; produces nearly $90\%$ of cellular $ATP$.

Chemiosmosis

The energy-coupling mechanism that utilizes energy stored across a hydrogen ion ($H^+$) gradient across a membrane to drive cellular work, such as phosphorylation of $ADP$.

Proton-Motive Force

The potential energy stored in the electrochemical gradient of $H^+$ generated across the inner mitochondrial or thylakoid membrane.

ATP Synthase Structure

A molecular machine comprising a stator anchored in the membrane, a rotating membrane rotor driven by flowing $H^+$, an internal rod, and a catalytic knob that phosphorylates $ADP$ to $ATP$.

Alcohol Fermentation

An anaerobic catabolic pathway in yeast where pyruvate is converted to ethanol in two steps, releasing $CO_2$ and regenerating $NAD^+$ to sustain glycolysis.

Lactic Acid Fermentation

An anaerobic process where pyruvate is directly reduced by $NADH$ to form lactate with no release of $CO_2$, regenerating $NAD^+$ for continued glycolysis.

Obligate Anaerobes

Organisms that carry out only fermentation or anaerobic respiration and cannot survive in the presence of molecular oxygen ($O_2$).

Facultative Anaerobes

Organisms, such as yeasts and many bacteria, capable of surviving by using either fermentation or cellular respiration depending on oxygen availability.

Photoautotrophs

Organisms (including plants, algae, and cyanobacteria) that use sunlight to synthesize organic molecules directly from $CO_2$ and inorganic precursors.

Heterotrophs

Biospheric consumers that sustain life by obtaining organic molecules from other organisms.

Mesophyll Cells

The primary photosynthetic tissue in leaves, containing about $30\text{--}40$ chloroplasts per cell.

Stomata

Microscopic leaf pores through which carbon dioxide ($CO_2$) enters and oxygen ($O_2$) exits.

Stroma

The dense fluid matrix enclosed by the two chloroplast envelope membranes, surrounding the thylakoids and housing the Calvin cycle.

Thylakoids

Interconnected membranous sacs within chloroplasts that segregate the stroma from the thylakoid space, stack into grana, and house the light-capturing pigments.

Absorption Spectrum

A graphical representation plotting a pigment's light absorption as a function of wavelength across the spectrum.

Action Spectrum

A profile plotting the relative effectiveness of different wavelengths of radiation in driving a process, such as oxygen production in photosynthesis.

Engelmann's Experiment

An 1883 demonstration illuminating a filamentous alga with light split by a prism; aerobic bacteria congregated around regions illuminated by violet-blue and red light, identifying peak photosynthetic activity.

Chlorophyll Molecule Structure

Photosynthetic pigment structure featuring a light-absorbing porphyrin ring with a central magnesium atom and a hydrophobic hydrocarbon tail that anchors into thylakoid membranes.

Carotenoids

Accessory pigments in chloroplasts that absorb excessive light energy that would otherwise damage chlorophyll or form reactive oxidative species.

Photosystem

A light-harvesting complex in thylakoid membranes consisting of pigment-protein complexes that capture photon energy and pass it to a central reaction-centre complex.

Photosystem II (PS II)

The photosystem that functions first in linear electron flow, with reaction-centre chlorophyll $a$ ($P680$) that splits water to replace lost electrons, generating $O_2$.

Photosystem I (PS I)

A light-capturing complex with a reaction-centre chlorophyll $a$ known as $P700$ (absorbing best at $700\,\text{nm}$), passing energized electrons toward $NADP^+$ reductase.

Linear Electron Flow

The primary photosynthetic pathway during light reactions that utilizes both PS II and PS I to generate both $ATP$ and $NADPH$, while splitting water and releasing $O_2$.

Cyclic Electron Flow

An alternate route of electron flow using only PS I, where electrons cycle through ferredoxin back into the cytochrome complex, producing $ATP$ without generating $NADPH$ or releasing oxygen.

Rubisco

Ribulose-1,5-bisphosphate carboxylase/oxygenase; the enzyme that catalyzes carbon fixation in Phase 1 of the Calvin cycle by attaching $CO_2$ to ribulose bisphosphate (RuBP).

Calvin Cycle

The stroma-based anabolic cycle of photosynthesis composed of carbon fixation, reduction, and RuBP regeneration; fixes three $CO_2$ molecules per net synthesis of one glyceraldehyde 3-phosphate (G3P).