Biological Chemistry and Cell Biology Vocabulary

Comprehensive vocabulary flashcards covering the chemical context of life, chemical bonding, and cell structure and function from Chapter 2 and Chapter 6.

Matter

Anything that takes up space and has mass.

Element

A substance that cannot be broken down to other substances by chemical reactions.

Compound

A substance consisting of two or more elements in a fixed ratio, possessing characteristics different from those of its constituent elements.

Trace Elements

Elements required by an organism in minute quantities, making up less than $0.01\%$ of body mass.

Atomic Number

The number of protons in the nucleus of an atom, unique to each element.

Mass Number

The total sum of protons plus neutrons in the nucleus of an atom.

Isotopes

Two or more atoms of the same element that have the same number of protons but differ in their number of neutrons.

Valence Electrons

Electrons located in the outermost shell (valence shell) of an atom that interact with other atoms to determine chemical behavior.

Octet Rule

The tendency of atoms to react by sharing, losing, or gaining electrons so that their outermost shell contains $8$ electrons for maximum stability.

Valence

The number of unpaired electrons needed to complete an atom's outermost shell, which equals the number of covalent bonds the atom can form.

Covalent Bond

A strong, stable chemical bond formed by the sharing of a pair of valence electrons by two atoms.

Single Covalent Bond

A covalent bond in which two atoms share one pair of valence electrons.

Double Covalent Bond

A covalent bond in which two atoms share two pairs of valence electrons.

Electronegativity

An atom's measure of attraction for the shared electrons in a covalent bond.

Nonpolar Covalent Bond

A type of covalent bond in which electrons are shared roughly equally between two atoms of similar electronegativity.

Polar Covalent Bond

A covalent bond between atoms that differ in electronegativity, leading to unequal electron sharing and partial charges ($\delta+$ and $\delta-$).

Ion

An atom or group of atoms that has gained or lost one or more valence electrons, acquiring a net electrical charge.

Cation

A positively charged ion formed when an atom has fewer electrons than protons.

Anion

A negatively charged ion formed when an atom has more electrons than protons.

Ionic Bond

A chemical bond resulting from the electrostatic attraction between oppositely charged ions (a cation and an anion).

Hydrogen Bond

A weak chemical bond formed when a hydrogen atom covalently bonded to a strongly electronegative atom ($\delta+$) is attracted to another electronegative atom ($\delta-$) in a different molecule.

van der Waals Interactions

Weak, transient attractions between molecules resulting from momentary, unsymmetrical electron distributions that create temporary positive and negative charge regions.

Chemical Equilibrium

The state in a reversible chemical reaction where the forward and reverse reaction rates are equal, resulting in no net change in reactant and product concentrations.

Cell Theory

The foundational biological principle stating that all organisms are composed of one or more cells, the cell is the basic unit of organization, and all cells arise only from pre-existing cells.

Light Microscope (LM)

An optical instrument that passes visible light through a specimen, capable of magnifying effectively up to approximately $1{,}000$ times its actual size.

Scanning Electron Microscope (SEM)

A microscope that focuses a beam of electrons onto the surface of a specimen to produce detailed three-dimensional surface images.

Transmission Electron Microscope (TEM)

A microscope that focuses an electron beam through a thin section of a specimen to study internal cellular ultrastructure.

Cell Fractionation

A technique that uses differential centrifugation to break apart cells and separate major organelles for biochemical analysis.

Prokaryotic Cell

A simple type of cell lacking a nucleus and membrane-bound organelles, typically $1\text{--}10\,\mu\text{m}$ in size, with a single circular DNA chromosome located in a nucleoid.

Eukaryotic Cell

A complex cell type, generally $10\text{--}100\,\mu\text{m}$ in size, characterized by linear chromosomes housed inside a membrane-bound nucleus and possessing membrane-bound organelles.

Nucleoid

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

Surface Area-to-Volume Ratio

A critical physical constraint on cell size that decreases as cell volume grows faster than its membrane surface area, limiting metabolic exchange.

Microvilli

Long, thin plasma membrane projections supported by microfilaments that increase a cell's surface area for absorption with minimal volume increase.

Nucleus

The organelle in eukaryotic cells enclosed by a double membrane that houses chromatin, DNA replication machinery, and transcription machinery.

Chromatin

The complex of DNA and associated proteins that makes up eukaryotic chromosomes.

Nucleolus

A dense structure inside the eukaryotic nucleus where ribosomal RNA (rRNA) is synthesized and ribosome subunits are assembled.

Nuclear Envelope

A double membrane, composed of inner and outer lipid bilayers perforated by pore complexes, that encloses the nucleus.

Nuclear Lamina

A netlike array of protein filaments (lamins) lining the inner surface of the nuclear envelope that maintains nuclear shape.

Ribosomes

Non-membrane-bound cellular particles composed of rRNA and protein that carry out protein synthesis (translation) in the cytosol or on the rough ER.

Endomembrane System

A collection of eukaryotic membranes (nuclear envelope, ER, Golgi apparatus, lysosomes, vesicles, vacuoles, plasma membrane) that regulates protein traffic and carries out metabolic tasks.

Endoplasmic Reticulum (ER)

An extensive membranous network continuous with the outer nuclear membrane, divided into tubular smooth ER and sac-like rough ER.

Smooth ER

The portion of the endoplasmic reticulum lacking ribosomes; functions in lipid synthesis, drug and toxin detoxification, and calcium ion ($\text{Ca}^{2+}$) storage.

Rough ER

The portion of the endoplasmic reticulum studded with bound ribosomes; functions in synthesizing membrane, secreted, and lysosomal proteins, as well as protein glycosylation.

Golgi Apparatus

An organelle consisting of stacks of flattened membranous sacs (cisternae) with structural polarity (cis and trans faces) that modifies, sorts, and packages proteins and lipids into transport vesicles.

Lysosome

A membrane-bound digestive organelle in animal cells and protists containing acidic hydrolytic enzymes that digest macromolecules, engulfed pathogens, or damaged organelles.

Central Vacuole

A large, membrane-bound organelle in mature plant cells that stores water, ions like potassium and chloride, and macromolecules while helping maintain cell turgor.

Contractile Vacuole

A specialized organelle found in freshwater protists that pumps excess water out of the cell to maintain osmotic balance.

Phagocytosis

A type of endocytosis where a cell engulfs a large particle, food organism, or foreign cell, forming a food vacuole or phagosome that fuses with a lysosome.

Autophagy

A lysosomal recycling process in which a cell packages its own damaged organelles or cytoplasmic components into vesicles for degradation and reuse.

Tay-Sachs Disease

A fatal genetic lysosomal storage disorder caused by the absence of a single hydrolytic enzyme, leading to lipid accumulation in brain tissue.

Endosymbiont Theory

The theory stating that mitochondria and chloroplasts originated as prokaryotic cells engulfed by an ancestral eukaryotic cell, forming a mutually beneficial symbiotic relationship.

Mitochondria

Double-membrane-bound organelles present in nearly all eukaryotic cells that serve as the site of cellular respiration and ATP generation.

Cristae

Infoldings of the inner mitochondrial membrane that house electron transport chains and increase surface area for ATP synthesis.

Mitochondrial Matrix

The fluid-filled compartment enclosed by the inner mitochondrial membrane, containing mitochondrial DNA, circular chromosomes, free ribosomes, and enzymes.

Chloroplasts

Photosynthetic organelles in plants and algae surrounded by a double membrane and containing chlorophyll, thylakoid membranes, and stroma.

Thylakoid

A flattened, membranous sac inside a chloroplast, stacked into grana, where light-absorbing chlorophyll pigments are housed.

Stroma

The dense fluid within the inner chloroplast membrane surrounding the thylakoid membrane system, containing chloroplast DNA and ribosomes.

Peroxisomes

Single-membrane metabolic compartments that perform oxidative reactions to break down fatty acids and detoxify harmful compounds.

Cytoskeleton

A dynamic network of protein fibers (microtubules, microfilaments, intermediate filaments) extending throughout the cytoplasm that functions in cell support, shape, transport, and motility.

Microtubules

Hollow cytoskeleton rods $25\,\text{nm}$ in diameter made of tubulin dimers ($\alpha$-tubulin and $\beta$-tubulin) that shape cells, guide vesicle transport, and separate chromosomes during cell division.

Centrosome

A structure located near the nucleus in animal cells that functions as a microtubule-organizing center (MTOC) and contains a pair of centrioles.

Microfilaments

Solid cytoskeleton rods $7\,\text{nm}$ in diameter composed of twisted double strands of actin subunits that bear tension, support cell shape, drive muscle contraction with myosin, and form pseudopodia.

Intermediate Filaments

Fibrous cytoskeleton proteins coiled into cables $8\text{--}12\,\text{nm}$ in diameter (such as keratins and lamins) that bear tension, anchor organelles, and form the nuclear lamina.

Extracellular Matrix (ECM)

An elaborate extracellular meshwork of glycoproteins (collagen, proteoglycans, fibronectin) secreted by animal cells for support, adhesion, movement, and signaling.

Plasmodesmata

Membrane-lined channels perforating plant cell walls that connect the cytoplasm of adjacent cells, allowing water, solutes, and small molecules to pass.

Tight Junctions

Animal cell intercellular junctions that form continuous seals around adjacent cells, preventing leakage of extracellular fluid across cell layers.

Desmosomes

Anchoring junctions in animal tissues that fasten cells together into strong sheets, anchored by intermediate filaments.

Gap Junctions

Communicating junctions in animal cells consisting of membrane proteins surrounding a pore, providing cytoplasmic channels for direct transfer of ions and small molecules between cells.