BIOL 141: Chapters 6 to 10 - Comprehensive Review

Comprehensive vocabulary flashcards covering cell structure and organelles, membrane transport, metabolism and enzymes, cellular respiration, and photosynthesis.

Light Microscope

An optical instrument invented ~400 years ago that uses beams of visible light focused by glass lenses to examine whole cells and large internal cellular structures.

Electron Microscope

A microscope invented ~90 years ago that utilizes focused beams of electrons to provide approximately 100X better resolution than a light microscope, allowing visualization of ultrastructural cell components.

Transmission Electron Microscope (TEM)

A type of electron microscope that directs an electron beam through an ultra-thin specimen section to generate flat, two-dimensional (2D) images of internal cellular anatomy.

Scanning Electron Microscope (SEM)

A type of electron microscope that scans an electron beam across the gold-coated surface of a specimen to generate detailed three-dimensional (3D) images of surface topography.

Surface Area-to-Volume Ratio

The mathematical relationship ($\text{surface area} / \text{volume}$) that sets an upper limit on cell size; as a cell expands, volume grows proportionately faster than membrane surface area, reducing transport efficiency.

Nucleoid

The dense, non-membrane-bounded region in a prokaryotic cell where its circular DNA chromosome is localized.

Chromatin

The complex of genomic DNA and associated histone proteins that constitutes eukaryotic chromosomes within the nucleus.

Ribosomes

Non-membranous complexes of ribosomal RNA (rRNA) and proteins that carry out protein synthesis either freely suspended in the cytosol or bound to the endoplasmic reticulum.

Rough Endoplasmic Reticulum (Rough ER)

The portion of the endomembrane system studded with ribosomes on its outer surface that manufactures proteins destined for secretion or membrane insertion and packages them into transport vesicles.

Smooth Endoplasmic Reticulum (Smooth ER)

The membrane-bound network lacking ribosomes that synthesizes lipids (including steroids and phospholipids), metabolizes carbohydrates, detoxifies drugs and poisons, and stores calcium ions ($Ca^{2+}$).

Golgi Apparatus

An organelle of stacked, flattened membranous sacs (cisternae) with distinct cis and trans faces that receives, modifies, sorts, and packages macromolecules from the ER for secretion or intracellular delivery.

Lysosome

A membrane-enclosed digestive sac of hydrolytic enzymes maintained at an acidic pH that degrades food particles, engulfs pathogens, and recycles damaged cellular organelles.

Autophagy

The intracellular recycling process in which a cell sequesters and delivers damaged organelles or cytosol to lysosomes for enzymatic breakdown and monomer recycling.

Central Vacuole

A large membrane-bound vesicle prominent in mature plant cells that stores water and nutrients, degrades waste, and maintains hydrostatic turgor pressure against the cell wall.

Cristae

Infoldings of the inner mitochondrial membrane that expand surface area for housing electron transport chain protein complexes and ATP synthase.

Cytoskeleton

A dynamic network of protein fibers—microtubules, intermediate filaments, and microfilaments—extending through the cytoplasm that provides mechanical support, anchorage, and tracks for vesicle movement.

Extracellular Matrix (ECM)

The external meshwork surrounding animal cells consisting of glycoproteins, glycolipids, and proteoglycans that mediates cell-to-cell signaling, recognition, and adhesion.

Amphipathic Molecule

A chemical compound possessing both a hydrophilic (polar, water-soluble) region and a hydrophobic (nonpolar, water-insoluble) region, such as a membrane phospholipid.

Fluid Mosaic Model

The accepted model of membrane structure depicting proteins as distinct, functional entities bobbing laterally within a fluid bilayer of amphipathic phospholipids.

Selective Permeability

The property of cellular membranes allowing certain substances (such as small nonpolar molecules like $O_2$ and $CO_2$) to diffuse freely while impeding ions and large polar solutes.

Osmosis

The passive diffusion of free water across a selectively permeable membrane toward the region with a higher solute concentration.

Tonicity

The ability of an extracellular solution to cause a cell to gain or lose water, determined by the concentration of non-penetrating solutes relative to the cell's interior.

Hypertonic Solution

A surrounding solution having a higher solute concentration than the cell interior, exerting greater osmotic draw and causing animal cells to shrivel and plant cells to plasmolyze.

Hypotonic Solution

A surrounding solution having a lower solute concentration than the cell interior, causing net water entry that causes animal cells to lyse and plant cells to become turgid.

Facilitated Diffusion

The spontaneous, passive movement of polar molecules or ions down their concentration gradient across a membrane through specific transmembrane transport proteins without energy expenditure.

Aquaporins

Specialized transmembrane channel proteins that facilitate the rapid, high-volume passage of water molecules across cellular membranes.

Active Transport

The energy-requiring transport of a solute against its concentration or electrochemical gradient across a biological membrane, mediated by carrier proteins and driven by ATP hydrolysis.

Sodium-Potassium Pump

An electrogenic transmembrane carrier protein that hydrolyzes ATP to export three $Na^+$ ions and import two $K^+$ ions per cycle against their steep concentration gradients.

Cotransport

A transport mechanism in which the active transport of one solute down its gradient (such as $H^+$) drives the simultaneous uphill transport of a second solute (such as sucrose) across a membrane.

Exocytosis

A form of bulk active transport where internal secretory vesicles migrate to and fuse with the plasma membrane, releasing their macromolecular contents into the extracellular space.

Pinocytosis

A non-specific type of endocytosis ('cell drinking') wherein the plasma membrane invaginates to ingest droplets of extracellular fluid and dissolved solutes within tiny coated vesicles.

Receptor-Mediated Endocytosis

A selective endocytic mechanism whereby specific extracellular ligands (such as LDL particles) bind membrane receptor proteins, triggering inward budding of coated pits into transport vesicles.

Metabolism

The comprehensive collection of all chemical reactions occurring within an organism, coordinating catabolic degradation and anabolic biosynthesis via enzyme-mediated steps.

Catabolic Pathway

A metabolic route that releases free energy by breaking down complex, bond-rich organic molecules into simpler molecules, exemplified by cellular respiration.

Anabolic Pathway

A metabolic route that consumes free energy to assemble complex macromolecules (such as proteins or carbohydrates) from simpler building blocks.

First Law of Thermodynamics

The principle of conservation of energy stating that energy can be transformed or transferred from one form to another, but it cannot be created or destroyed.

Second Law of Thermodynamics

The thermodynamic principle establishing that every spontaneous energy conversion increases the net entropy (disorder) of the universe, releasing unusable energy as heat.

Free Energy ($G$)

The portion of a biological system's energy that is capable of performing work under uniform cellular temperature and pressure conditions.

Exergonic Reaction

A spontaneous, energetically favorable reaction characterized by a net release of free energy and a negative change in free energy ($\Delta G < 0$).

Endergonic Reaction

A nonspontaneous, energetically unfavorable reaction that absorbs free energy from its surroundings, yielding a positive change in free energy ($\Delta G > 0$).

Energy Coupling

The bioenergetic strategy of driving an endergonic process forward by coupling it directly to the favorable free energy released by an exergonic reaction, primarily via ATP.

Adenosine Triphosphate (ATP)

The cellular energy currency composed of adenine, ribose, and three negatively charged phosphate groups whose terminal phosphoanhydride bond releases energy upon hydrolysis.

Activation Energy ($E_A$)

The initial threshold amount of energy that must be absorbed by reactants to destabilize their chemical bonds and push them into the transition state.

Active Site

The specialized, pocket-like catalytic cleft of an enzyme composed of specific amino acid residues where substrate molecules bind and undergo conversion to products.

Induced Fit Model

The model of enzyme-substrate interaction wherein substrate binding induces a subtle conformational shift in the enzyme active site that tightens the fit and catalyzes bond alteration.

Cofactor

Any non-protein chemical compound or inorganic ion (such as $Fe$, $Cu$, $Zn$, or $Mg^{2+}$) required by an enzyme for catalytic function; organic cofactors are coenzymes.

Competitive Inhibitor

A regulatory substance with a structure mimicking the natural substrate that reduces enzyme activity by directly competing for and occupying the active site.

Noncompetitive Inhibitor

An inhibitor that reduces catalytic rate by binding to an allosteric regulatory site away from the active site, inducing a conformational change that lowers catalytic efficiency.

Cellular Respiration

The multi-stage aerobic catabolic process wherein fuel molecules (such as glucose) are systematically oxidized to $CO_2$ and $H_2O$, driving the generation of up to $32\,\text{ATP}$.

Oxidation

The complete loss or partial removal of electrons from a substance during a chemical redox reaction.

Reduction

The complete gain or partial addition of electrons to a substance during a chemical redox reaction.

Nicotinamide Adenine Dinucleotide ($NAD^+$)

A key coenzyme and mobile electron acceptor derived from niacin that is reduced to NADH by accepting two high-energy electrons and one proton from organic fuel molecules.

Glycolysis

The ten-step metabolic pathway in the cytosol that splits 1 six-carbon glucose into 2 three-carbon pyruvates, yielding a net of $2\,\text{ATP}$ and $2\,\text{NADH}$ independently of oxygen.

Substrate-Level Phosphorylation

The direct synthesis of ATP catalyzed by soluble enzymes that transfer a reactive phosphate group directly from a phosphorylated substrate molecule to ADP.

Pyruvate Oxidation

The transition reaction in the mitochondrial matrix where each pyruvate is converted to acetyl CoA by pyruvate dehydrogenase, releasing $CO_2$ and producing NADH.

Citric Acid Cycle (Krebs Cycle)

The cyclic eight-step metabolic furnace in the mitochondrial matrix that oxidizes acetyl CoA to $CO_2$, generating $2\,\text{ATP}$, $6\,\text{NADH}$, and $2\,\text{FADH}_2$ per starting glucose.

Oxidative Phosphorylation

The terminal stage of cellular respiration in the inner mitochondrial membrane where the electron transport chain and chemiosmosis couple electron transfer to synthesize $26\text{--}28\,\text{ATP}$.

Chemiosmosis

The coupling mechanism that harnesses the potential energy stored in an electrochemical proton ($H^+$) gradient across a membrane to drive ATP synthesis via ATP synthase.

ATP Synthase

A rotary enzyme complex embedded in the inner mitochondrial and thylakoid membranes that channels the downhill flow of $H^+$ to phosphorylate ADP and inorganic phosphate into ATP.

Lactic Acid Fermentation

An anaerobic pathway in animal muscle and certain microbes where pyruvate accepts electrons from NADH to form lactate, regenerating $NAD^+$ to sustain glycolysis at $2.1\%$ efficiency.

Alcohol Fermentation

An anaerobic pathway in yeast where pyruvate is decarboxylated to acetaldehyde and subsequently reduced by NADH to produce ethanol and $CO_2$, regenerating $NAD^+$.

Autotrophs

Organisms that sustain themselves without consuming other living beings, utilizing sunlight or inorganic energy to synthesize organic molecules from $CO_2$.

Heterotrophs

Organisms that obtain organic carbon and chemical energy by consuming other organisms, their by-products, or decomposing organic matter.

Stomata

Microscopic pores on leaf surfaces regulated by guard cells that permit carbon dioxide ($CO_2$) influx while releasing oxygen ($O_2$) and water vapor.

Thylakoid

A flattened, chlorophyll-bearing membranous sac inside a chloroplast organized into stacks called grana, serving as the site of light-dependent photosynthetic reactions.

Stroma

The dense fluid-filled compartment of the chloroplast surrounding the thylakoid network, housing enzymes responsible for the carbon-fixing Calvin cycle.

Chlorophyll a

The central light-capturing pigment in photosynthetic oxygenic organisms, possessing a magnesium-centered porphyrin ring and a $-\text{CH}_3$ group, which absorbs blue-violet and red wavelengths.

Carotenoids

Accessory photosynthetic pigments that broaden light absorption and safeguard the photosynthetic apparatus through photoprotection by dissipating excessive, damaging light energy.

Light Reactions

The initial stage of photosynthesis occurring in thylakoid membranes that converts absorbed solar energy into chemical bond energy as ATP and NADPH while photolysing water to release $O_2$.

Photophosphorylation

The light-driven production of ATP from ADP and inorganic phosphate via chemiosmosis during the light-dependent reactions of photosynthesis in chloroplasts.

Photosystem II (PS II)

The first photosystem functioning in linear electron flow, featuring a reaction-center chlorophyll pair ($P680$) that splits water to supply electrons to the primary transport chain.

Photosystem I (PS I)

The photosystem functioning second in linear electron flow, utilizing a reaction-center chlorophyll pair ($P700$) to transfer electrons down a secondary chain to reduce $NADP^+$ into NADPH.

Calvin Cycle

The anabolic, cyclic metabolic pathway in the chloroplast stroma that uses ATP and NADPH to reduce fixed atmospheric carbon into glyceraldehyde 3-phosphate (G3P) sugar.

Rubisco

Ribulose bisphosphate carboxylase-oxygenase; the stroma-localized enzyme that catalyzes the initial fixation of atmospheric $CO_2$ to ribulose bisphosphate (RuBP) in the Calvin cycle.

Photorespiration

A wasteful metabolic pathway triggered on hot, dry days when closed stomata cause $O_2$ accumulation, prompting rubisco to bind $O_2$ instead of $CO_2$ and consuming ATP without making sugar.

C4 Plants

Plants that avoid photorespiration by spatially segregating carbon fixation into four-carbon compounds in mesophyll cells before releasing $CO_2$ into bundle-sheath cells for the Calvin cycle.

CAM Plants

Succulent plants that minimize photorespiration and water loss through temporal separation, opening stomata at night to fix $CO_2$ into organic acids and releasing it to the Calvin cycle by day.