Bio 93: From Atoms to Cells - Lectures 2 through 9 Comprehensive Review

Comprehensive practice flashcards matching the vocabulary style for Bio 93 (Lectures 2 through 9), covering atomic structure, water chemistry, macromolecules, membrane transport, organelle biology, cytoskeletal dynamics, and cell signaling.

Matter

Anything that takes up space and has mass; all organisms and biological systems are composed of it.

Element

A substance that cannot be broken down into other substances by chemical reactions, composed of only one type of atom.

Essential Elements

The approximately $25\%$ of the $92$ natural elements that an organism needs to live a healthy life and reproduce.

Four Dominant Elements of Living Matter

Carbon ($\text{C}$), Oxygen ($\text{O}$), Nitrogen ($\text{N}$), and Hydrogen ($\text{H}$), which make up approximately $96\%$ of all living matter.

Trace Elements

Elements indispensable for life but required in minute quantities, including iron ($\text{Fe}$), iodine ($\text{I}$), zinc ($\text{Zn}$), and copper ($\text{Cu}$).

Atom

The smallest unit of matter that retains all the unique chemical properties of an element.

Compound

A substance consisting of two or more different elements combined in a fixed ratio, exhibiting emergent properties distinct from its constituent elements.

Molecule

Two or more atoms held together by covalent bonds, which can consist of the same element or different elements.

Potential Energy (Atomic)

The energy that matter possesses because of its location or spatial arrangement; electrons have potential energy based on their distance from the positively charged nucleus.

Electron Shell

An energy level of electrons at a characteristic average distance from the nucleus; the first shell holds up to $2$ electrons, while the second and third hold up to $8$ electrons each.

Valence Electrons

Electrons residing in the outermost electron shell (valence shell) that dictate the chemical reactivity and bonding capacity of an atom.

Covalent Bond

A strong chemical bond formed when two atoms share one or more pairs of valence electrons to complete their outer shells.

Electronegativity

The attraction of a particular atom for the shared electrons of a covalent bond.

Nonpolar Covalent Bond

A covalent bond in which electrons are shared equally between two atoms of similar electronegativity, such as $\text{C}-\text{C}$ or $\text{C}-\text{H}$.

Polar Covalent Bond

A covalent bond between atoms that differ significantly in electronegativity, pulling shared electrons closer to the more electronegative atom and creating partial charges ($\delta^+$ and $\delta^-$).

Ionic Bond

A chemical bond resulting from the mutual electrostatic attraction between oppositely charged ions formed by the complete transfer of one or more valence electrons.

Hydrogen Bond

A noncovalent attraction between a hydrogen atom covalently linked to an electronegative atom (like $\text{O}$ or $\text{N}$) and another nearby electronegative atom.

Hydration Shell

The sphere of water molecules surrounding each dissolved ion when an ionic compound dissolves in an aqueous solution.

Dissociation of Water

A reversible reaction where a hydrogen atom leaves its electron behind to transfer as a proton ($\text{H}^+$) to another water molecule, generating a hydronium ion ($\text{H}_3\text{O}^+$) and a hydroxide ion ($\text{OH}^-$).

Tetravalence of Carbon

The ability of carbon, having $4$ valence electrons, to form $4$ covalent bonds in tetrahedral geometry, making complex organic molecular diversity possible.

Hydrocarbons

Organic molecules composed exclusively of carbon and hydrogen linked by nonpolar covalent bonds, serving as energy-rich frameworks.

Hydroxyl Group

A chemical functional group consisting of a hydrogen atom covalently bonded to an oxygen atom ($-\text{OH}$); polar and characteristic of alcohols.

Carbonyl Group

A functional group consisting of a carbon atom double-bonded to an oxygen atom ($>\text{C}=\text{O}$), found in ketones and aldehydes (aldoses and ketoses).

Carboxyl Group

A functional group consisting of a single carbon double-bonded to an oxygen atom and also bonded to a hydroxyl group ($-\text{COOH}$); acts as an organic acid by donating $\text{H}^+$.

Amino Group

A functional group consisting of a nitrogen atom bonded to two hydrogen atoms ($-\text{NH}_2$); acts as a base by picking up an $\text{H}^+$ from solution.

Sulfhydryl Group

A functional group consisting of a sulfur atom bonded to a hydrogen atom ($-\text{SH}$); two groups can interact to form covalent cross-linking disulfide bridges in proteins.

Phosphate Group

A functional group consisting of a phosphorus atom covalently bonded to four oxygen atoms ($-\text{OPO}_3^{2-}$); confers negative charge and reacts with water to release energy.

Methyl Group

A nonpolar, unreactive functional group consisting of a carbon atom bonded to three hydrogen atoms ($-\text{CH}_3$), acting as a recognizable tag on biological molecules.

Polymer

A long macromolecule built from many similar or identical building blocks (monomers) linked together by covalent bonds.

Dehydration Reaction

A chemical reaction in which two monomers become covalently bonded to each other with the concurrent loss of a water molecule.

Hydrolysis

A chemical reaction that breaks the covalent bond between monomers in a polymer through the addition of a water molecule.

Monosaccharide

The simplest carbohydrate monomer, generally having a molecular formula that is some multiple of $\text{CH}_2\text{O}$, such as glucose.

Glycosidic Linkage

A covalent bond formed between two monosaccharides through a dehydration reaction.

Lactose Intolerance

A condition characterized by bloating, cramps, and diarrhea caused by lack of the digestive enzyme lactase needed to break down the disaccharide lactose.

Cellulose

A structural polysaccharide comprising unbranched polymers of glucose joined by $\beta\text{-1,4-glycosidic linkages}$, reinforced by hydrogen bonds to form plant cell walls.

Glycogen

An extensively branched glucose storage polysaccharide found in the liver and muscle tissues of animals.

Triacylglycerol

A lipid formed by esterifying three fatty acid molecules to a three-carbon glycerol backbone via dehydration reactions; also known as a fat.

Saturated vs. Unsaturated Fatty Acid

Saturated fats have no double bonds and pack tightly as solids at room temperature; unsaturated fats possess one or more cis double bonds causing kinks that keep them liquid.

Trans Fats

Unsaturated fats containing trans double bonds produced synthetically during the partial hydrogenation of vegetable oils, linked to coronary heart disease.

Steroid

A lipid molecule characterized by a carbon skeleton consisting of four fused rings with varying chemical functional groups attached.

Amino Acid

An organic molecule containing an alpha carbon, an amino group ($-\text{NH}_2$), a carboxyl group ($-\text{COOH}$), a hydrogen atom, and a variable side chain (R group).

Peptide Bond

The covalent bond joining the carboxyl group of one amino acid to the amino group of an adjacent amino acid, formed by a dehydration reaction.

Primary Structure

The specific, linear sequence of amino acids in a polypeptide chain, encoded directly by nucleotide sequences in DNA.

Secondary Structure

Repetitive localized coils ($\alpha$ helices) or folds ($\beta$ pleated sheets) within a polypeptide, stabilized by hydrogen bonds along the polypeptide backbone.

Tertiary Structure

The overall three-dimensional conformation of a single polypeptide, stabilized by interactions among R groups including hydrogen bonds, ionic bonds, hydrophobic interactions, and disulfide bridges.

Disulfide Bridge

A strong covalent bond formed when the sulfhydryl groups ($-\text{SH}$) of two cysteine monomers oxidize to form a cross-link ($-\text{S}-\text{S}-$).

Quaternary Structure

The overall protein structure resulting from the specific aggregation and noncovalent stabilization of two or more polypeptide subunits.

Sickle-Cell Disease

A genetic blood disorder caused by a single base change in DNA leading to a valine substitution for glutamic acid at position 6 of the $\beta$-globin chain, causing hemoglobin fiber aggregation.

Denaturation

The structural unraveling of a native protein into an inactive conformation caused by changes in pH, high salt concentration, or elevated temperature.

Chaperone Proteins

Protein complexes that assist in the proper folding and refolding of other proteins by providing a favorable isolated environment within the cell.

Ubiquitin

A small regulatory protein that covalently tags damaged or misfolded proteins as a "kiss of death" to target them for proteasomal degradation.

Proteasome

A large cylindrical protein complex that recognizes ubiquitin-tagged proteins and degrades them into short peptide fragments using active proteases.

Multiple Myeloma

A cancer of plasma B cells in bone marrow that overproduces misfolded antibodies and relies heavily on proteasomes to prevent apoptosis.

Nucleotide

The monomer building block of nucleic acids, consisting of a five-carbon pentose sugar, a nitrogenous base, and one to three phosphate groups.

Phosphodiester Linkage

The covalent bond joining adjacent nucleotides by connecting the $3'$ carbon of one sugar to the $5'$ carbon of the next through a phosphate group.

Pyrimidines

A class of nitrogenous bases characterized by a single six-membered ring; includes cytosine ($\text{C}$), thymine ($\text{T}$), and uracil ($\text{U}$).

Purines

A class of nitrogenous bases characterized by a six-membered ring fused to a five-membered ring; includes adenine ($\text{A}$) and guanine ($\text{G}$).

Prokaryote

A type of cell lacking a membrane-enclosed nucleus and membrane-bound organelles, harboring its circular chromosome in an unbound nucleoid region.

Eukaryote

A type of cell possessing a double-membrane-bound nucleus containing linear chromosomes, as well as distinct membrane-bound cytoplasmic organelles.

Fluid Mosaic Model

The structural model of cell membranes depicting proteins drifting laterally in or on a fluid bilayer of phospholipids.

Amphipathic Molecule

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

Lateral Drifting

The rapid planar movement of phospholipids and unanchored proteins within the leaflet of a cellular membrane.

Membrane Fluidity Buffer

The function of cholesterol in animal membranes that reduces fluidity at moderate temperatures but hinders close packing and solidification at low temperatures.

FRAP (Fluorescence Recovery After Photobleaching)

An experimental technique that measures the rate of lateral diffusion by bleaching a spot of fluorescently tagged molecules with a laser and recording fluorescence return.

Frye-Edidin Experiment

A landmark 1970 cell fusion experiment demonstrating that human and mouse membrane proteins diffuse and intermix laterally within 1 hour after heterokaryon formation.

Integral Membrane Protein

A protein permanently embedded within the lipid bilayer, typically spanning the membrane with hydrophobic alpha-helical segments.

Peripheral Membrane Protein

A protein loosely bound to the surface of the membrane or to integral proteins, not embedded in the lipid bilayer's hydrophobic core.

Transmembrane Domain

An amphipathic alpha helix traversing the lipid bilayer, exposing nonpolar side chains to fatty acid tails and clustering polar groups internally.

Membrane Sidedness

The asymmetrical distribution of proteins, lipids, and carbohydrates across the bilayer, established as vesicle lumen contents become the extracellular face upon fusion.

Glycolipid

A membrane lipid covalently attached to an oligosaccharide chain, facing the extracellular side for cell recognition and signaling.

Glycoprotein

A membrane-spanning or peripheral protein covalently bonded to carbohydrate chains, projecting into the extracellular space for recognition.

ABO Blood Group Antigens

Carbohydrate chains attached to lipids and proteins on red blood cell membranes, synthesized by glycosyltransferase enzymes.

CD4 and CCR5

Host cell surface receptors that the envelope glycoproteins of HIV bind to mediate viral entry into immune cells.

ACE-2 Receptor

Angiotensin-converting enzyme 2, a cell-surface receptor protein bound by the SARS-CoV-2 spike protein during coronavirus entry.

TMPRSS2

A host cell surface protease that cleaves both ACE-2 and the viral spike protein, triggering SARS-CoV-2 fusion and cellular entry.

CAR T-Cell Therapy

A cancer immunotherapy where patient T cells are genetically engineered to express a synthetic Chimeric Antigen Receptor targeting tumor antigens.

Selective Permeability

The property of membranes allowing nonpolar hydrophobic molecules ($\text{O}_2, \text{CO}_2$) to cross freely while impeding ions and large polar molecules.

Passive Transport

The spontaneous movement of substances across a biological membrane down their concentration gradient without cellular energy expenditure.

Diffusion

The thermal motion of particles resulting in the net movement of a substance down its concentration gradient from high to low concentration.

Osmosis

The passive diffusion of free water molecules across a selectively permeable membrane from lower solute concentration to higher solute concentration.

Tonicity

The ability of a surrounding solution to cause a cell to gain or lose water, depending on the concentration of nonpenetrating solutes.

Hypertonic Solution

A surrounding solution with a higher nonpenetrating solute concentration than the cell, causing net water loss and cellular shriveling.

Hypotonic Solution

A surrounding solution with a lower nonpenetrating solute concentration than the cell, causing net water uptake and cellular swelling or lysis.

Isotonic Solution

A surrounding solution having the same nonpenetrating solute concentration as the cell, resulting in no net water flow across the membrane.

Facilitated Diffusion

The passive transport of polar molecules or ions across a membrane down their concentration gradient assisted by specific transmembrane proteins.

Aquaporins

Tetrameric channel proteins that facilitate the rapid bidirectional diffusion of up to $3\text{ billion}$ water molecules per second across membranes.

Gated Ion Channel

A channel protein that opens or closes its pore in response to a specific stimulus, such as ligand binding or electrical voltage change.

Active Transport

The carrier-protein-mediated movement of a substance across a membrane against its concentration gradient, requiring cellular energy like ATP hydrolysis.

Sodium-Potassium Pump

An electrogenic carrier protein that uses the hydrolysis of one ATP to export $3\text{ Na}^+$ ions and import $2\text{ K}^+$ ions against their gradients.

Membrane Potential

The difference in electrical charge (voltage) across a cell's plasma membrane, typically around $-70\text{ mV}$ inside animal cells at rest.

Electrochemical Gradient

The combination of an ion's chemical concentration gradient and electrical membrane potential that drives its passive diffusion across a membrane.

Proton Pump

The primary electrogenic pump in plants, fungi, and bacteria that actively hydrolyzes ATP to export $H^+$ ions, generating membrane potential.

Cotransport

A transport mechanism in which the downhill diffusion of one solute drives the uphill active transport of a second solute against its concentration gradient.

Exocytosis

The secretion of cellular molecules by the fusion of internal transport vesicles with the plasma membrane, releasing cargo outside the cell.

Phagocytosis

A type of endocytosis ("cell eating") wherein a cell engulfs large particles or microbes by extending pseudopodia and packaging them in food vacuoles.

Pinocytosis

A form of endocytosis ("cell drinking") in which the plasma membrane invaginates non-specifically to take in extracellular fluid droplets and recycle membrane components.

Receptor-Mediated Endocytosis

A specialized endocytic mechanism where specific extracellular solutes bind cell-surface receptors, concentrating into clathrin-coated pits that bud into vesicles.

Familial Hypercholesterolemia

An inherited disease caused by defective LDL receptors, preventing cholesterol uptake and leading to severe blood vessel plaque deposition.

Endosymbiont Theory

The evolutionary theory stating that mitochondria and chloroplasts originated as independent prokaryotes engulfed by an ancestral eukaryotic cell.

Mitochondria

Semiautonomous double-membrane organelles that generate the majority of cellular ATP through the Krebs cycle and oxidative phosphorylation.