Bio Unit 2: CH: 6,7,8,9,10

Cell

The fundamental unit of life and the simplest collection of matter that can be alive.

Cell theory

All organisms are made of cells; the cell is the basic unit of life; cells come from preexisting cells.

Prokaryotic cell

A cell without a membrane-bound nucleus; includes Bacteria and Archaea.

Eukaryotic cell

A cell with a membrane-bound nucleus; includes protists, fungi, plants, and animals.

Bacteria

Prokaryotic organisms without a membrane-bound nucleus.

Cytoplasm

The region between the plasma membrane and the nucleus in eukaryotic cells.

Plasma membrane

A selective barrier surrounding the cell that controls movement of substances.

Ribosome

A cellular structure that makes proteins.

Organelle

A membrane-bound or specialized structure that performs a specific cellular function.

Microscopy

The use of microscopes to visualize structures too small to see with the unaided eye.

Light microscope (LM)

Uses visible light and glass lenses to magnify specimens.

Resolution

The ability to distinguish two objects as separate.

Sem

Scanning electron microscope that focuses electrons on a specimen's surface and produces a 3-D-looking image.

Tonicity

The ability of a solution to cause a cell to gain or lose water.

Isotonic solution

A solution with equal effective solute concentration inside and outside the cell.

Diffusion

The spontaneous movement of a substance from higher concentration to lower concentration.

Facilitated diffusion

Passive transport through a membrane protein.

Endomembrane system

A group of membranes and organelles involved in protein/lipid synthesis, modification, and transport.

Golgi apparatus

Modifies, sorts, and packages proteins and other products.

Lysosome

A membrane-bound compartment containing hydrolytic enzymes that digest macromolecules.

Vacuole

A membrane-bound compartment with various storage and maintenance functions.

Cytoskeleton

A network of protein fibers that supports cell shape, movement, and organelle positioning.

Flagellum

A cellular appendage used for movement.

Photosynthesis

The process by which plants and other organisms use light energy to make chemical energy.

Chloroplast

The organelle where photosynthesis occurs in plants and algae.

Light reactions

The photosynthetic reactions that capture light energy and produce ATP and NADPH.

Calvin cycle

The set of reactions that uses ATP and NADPH to convert CO2 into carbohydrate.

NADPH

A high-energy electron carrier produced during the light reactions.

G3P

Glyceraldehyde-3-phosphate; a three-carbon sugar produced by the Calvin cycle.

C4 plant

A plant that first fixes CO2 into a four-carbon compound to reduce photorespiration.

Cyclic electron flow

Electron flow involving only PSI that produces ATP but not NADPH or O2.

ATP

Adenosine triphosphate; a major cellular energy-carrying molecule.

Fermentation

A pathway that regenerates NAD+ so glycolysis can continue without oxygen.

Anaerobic respiration

Respiration using a final electron acceptor other than oxygen.

Oxidation

The loss of electrons or hydrogen; often associated with loss of energy.

Reduction

The gain of electrons or hydrogen; often associated with gaining energy.

Cell Theory

The foundational biological principle stating that all organisms are composed of cells, the cell is the basic structural and functional unit of life, and all cells arise from pre-existing cells.

Surface Area-to-Volume Ratio (SA:V)

The relationship between a cell's exterior surface area and its internal volume; as a cell increases in size, its volume grows proportionally faster than its surface area, limiting cell size due to transport efficiency.

Prokaryotic Cell

A single-celled organism (Bacteria or Archaea) that lacks a membrane-bound nucleus and membrane-bound organelles.

Eukaryotic Cell

A complex cell type (protists, fungi, plants, animals) containing a true membrane-bound nucleus and specialized membrane-bound organelles.

Light Microscope (LM)

An optical microscope that uses visible light and glass lenses to magnify specimens up to approximately 1,000 times, limited by a resolution of about $200\,nm$.

Scanning Electron Microscope (SEM)

A microscope that uses an electron beam to scan the gold-coated surface of a specimen, creating detailed 3D topological images.

Transmission Electron Microscope (TEM)

A microscope that passes an electron beam through ultrathin sections of a specimen to study internal cellular ultrastructure.

Nucleoid

The non-membrane-bound region in a prokaryotic cell where its genomic DNA is concentrated.

Nucleolus

A dense structure within the eukaryotic nucleus responsible for synthesizing ribosomal RNA (rRNA) and assembling ribosome subunits.

Nuclear Lamina

A net-like array of protein filaments lining the inner surface of the nuclear envelope that maintains the shape of the nucleus.

Free Ribosomes

Ribosomes suspended in the cytosol that synthesize proteins destined to function within the cytosol.

Bound Ribosomes

Ribosomes attached to the exterior of the rough ER or nuclear envelope that synthesize proteins destined for insertion into membranes, organellar packaging, or secretion.

Smooth Endoplasmic Reticulum (Smooth ER)

Membranous network lacking ribosomes; functions in lipid synthesis, carbohydrate metabolism, drug detoxification, and calcium ion ($Ca^{2+}$) storage.

Rough Endoplasmic Reticulum (Rough ER)

Membranous network studded with ribosomes; synthesizes secretory proteins and produces membrane phospholipids.

Golgi Apparatus

An organelle consisting of flattened membranous sacs (cisternae) that modifies, sorts, packages, and routes proteins and lipids received from the ER.

Cis vs. Trans Face of Golgi

The cis face is the receiving side that accepts transport vesicles from the ER; the trans face is the shipping side that dispatches modified products in vesicles.

Lysosome

A membrane-enclosed sac of hydrolytic enzymes operating at acidic pH used by eukaryotic cells to digest macromolecules, pathogens, and damaged cell components.

Autophagy

The lysosomal process of recycling a cell's own damaged organelles and macromolecules to maintain cellular health.

Central Vacuole

A large, membrane-bound organelle in mature plant cells that stores cell sap, accumulates ions, disposes of wastes, and maintains turgor pressure.

Peroxisome

A specialized metabolic compartment that transfers hydrogen to oxygen, forming hydrogen peroxide ($H_2O_2$), which is then converted to water ($H_2O$) by catalase.

Microfilaments (Actin Filaments)

Solid cytoskeletal rods ($7\,nm$ diameter) made of actin proteins; involved in cell motility, muscle contraction, cytoplasmic streaming, and cell shape support.

Microtubules

Hollow cytoskeletal tubes ($25\,nm$ diameter) composed of tubulin dimers; construct the mitotic spindle, cilia, flagella, and organelle transport tracks.

Intermediate Filaments

Fibrous cytoskeletal proteins ($8-12\,nm$ diameter) like keratin that anchor the nucleus and provide permanent structural reinforcement.

Fluid Mosaic Model

Model describing biological membranes as a fluid phospholipid bilayer embedded with a mosaic of mobile proteins, glycoproteins, and glycolipids.

Amphipathic Molecule

A molecule possessing both a hydrophilic (water-loving) region and a hydrophobic (water-fearing) region, such as a phospholipid.

Selective Permeability

The property of cellular membranes that allows certain substances to cross more easily than others.

Passive Transport

The movement of substances across a biological membrane down their concentration gradient without energy expenditure ($\Delta G < 0$).

Facilitated Diffusion

Passive transport of polar or charged molecules across a membrane aided by specific transport proteins (channels or carriers).

Aquaporin

A specialized channel protein in the plasma membrane that facilitates the rapid diffusion of water molecules.

Osmosis

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

Tonicity

The capability of a surrounding solution to cause a cell to gain or lose water.

Hypertonic Solution

A solution with a higher solute concentration than the cell, causing net movement of water out of the cell.

Hypotonic Solution

A solution with a lower solute concentration than the cell, causing net movement of water into the cell.

Plasmolysis

The phenomenon in plant cells placed in a hypertonic environment where the plasma membrane pulls away from the cell wall as water leaves.

Active Transport

The movement of a substance across a cellular membrane against its concentration gradient, requiring energy (usually ATP).

Sodium-Potassium Pump ($Na^+/K^+$ Pump)

A transport protein that actively exports $3\,Na^+$ out of animal cells and imports $2\,K^+$ into cells per ATP hydrolyzed.

Electrogenic Pump

An active transport protein that generates a net voltage or electrical potential across a biological membrane (e.g., proton pumps in plants/fungi).

Cotransport

A transport mechanism in which the downhill diffusion of one solute powers the uphill active transport of a second solute.

Exocytosis

Bulk transport process in which intracellular vesicles fuse with the plasma membrane to discharge their contents extracellularly.

Phagocytosis

A form of endocytosis ('cellular eating') where large particles or cells are engulfed by extended pseudopodia into a food vacuole.

Receptor-Mediated Endocytosis

A highly specific bulk import process triggered when specific ligands bind to receptor proteins concentrated in coated pits.

Catabolic Pathway

A metabolic pathway that releases energy by breaking down complex molecules into simpler compounds (e.g., cellular respiration).

Anabolic Pathway

A metabolic pathway that consumes energy to build complicated molecules from simpler compounds (e.g., protein synthesis).

First Law of Thermodynamics

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

Second Law of Thermodynamics

The principle stating that every energy transfer or transformation increases the entropy ($S$) of the universe.

Exergonic Reaction

A spontaneous chemical reaction that releases free energy, characterized by a negative change in free energy ($\Delta G < 0$).

Endergonic Reaction

A non-spontaneous chemical reaction that absorbs free energy from its surroundings, characterized by a positive change in free energy ($\Delta G > 0$).

Energy Coupling

The use of an exergonic process (such as ATP hydrolysis) to drive an endergonic process.

Activation Energy ($E_a$)

The initial investment of energy required to contort reactant molecules so their bonds can break and start a reaction.

Induced Fit

The subtle shape change of an enzyme's active site upon substrate binding to bind the substrate more tightly and facilitate catalysis.

Competitive Inhibitor

A substance that reduces enzyme activity by mimicking the substrate and competing directly for binding at the active site.

Noncompetitive Inhibitor

A substance that impedes enzymatic reactions by binding to an allosteric site away from the active site, altering enzyme conformation.

Allosteric Regulation

The binding of a regulatory molecule to a protein at one site that affects the function and catalytic efficiency of the protein at another site.

Feedback Inhibition

A metabolic control method in which the end product of a metabolic pathway acts as an allosteric inhibitor of an enzyme early in that pathway.

Oxidation vs. Reduction

Oxidation is the loss of electrons (or loss of hydrogen), while reduction is the gain of electrons (or gain of hydrogen).

Glycolysis

A 10-step cytosolic pathway that breaks down 1 glucose molecule into 2 pyruvate molecules, yielding a net $2\,\text{ATP}$ and $2\,NADH$ without requiring oxygen.

Substrate-Level Phosphorylation

The direct enzymatic transfer of a phosphate group from a phosphorylated substrate intermediate to ADP, forming ATP.

Pyruvate Oxidation

The conversion of pyruvate into Acetyl CoA in the mitochondrial matrix, producing $\text{CO}_2$ and $NADH$ prior to the citric acid cycle.

Citric Acid Cycle (Krebs Cycle)

An 8-step metabolic cycle in the mitochondrial matrix that completes the oxidation of acetyl CoA, generating $\text{CO}_2$, $NADH$, $FADH_2$, and ATP.

Electron Transport Chain (ETC)

A sequence of electron carrier molecules in the inner mitochondrial membrane that shuttle electrons to $\text{O}_2$, using the released energy to pump $H^+$.

Proton-Motive Force

The potential energy stored in an electrochemical gradient of hydrogen ions ($H^+$) generated across a membrane.

Chemiosmosis

An energy-coupling mechanism that uses energy stored in an $H^+$ gradient across a membrane to drive ATP synthesis via ATP synthase.

Oxidative Phosphorylation

The production of ATP using energy derived from the redox reactions of an electron transport chain and chemiosmosis.

Alcohol Fermentation

An anaerobic pathway in which glycolysis pyruvate is converted into ethanol and $\text{CO}_2$, regenerating $NAD^+$.