Biology 1001: General Biology Midterm Review

Comprehensive practice vocabulary flashcards covering the key concepts, cellular structures, biological macromolecules, thermodynamic principles, and metabolic pathways from Biology 1001 lectures.

Emergent properties

Novel properties that arise at each higher level of biological organization due to the arrangement and interactions of parts as complexity increases.

Reductionism

An approach that reduces complex biological systems to simpler, more manageable units for study, providing an incomplete view of life when used alone.

Systems biology

An approach that models the dynamic behavior of biological systems by studying interactions among the system's parts across all levels of organization.

Cell theory

The fundamental theory stating that all living organisms are composed of cells, and that the processes of living organisms are based on the functioning of cells.

Eukaryotic cell

A type of cell characterized by having membrane-enclosed organelles and a membrane-enclosed nucleus containing genetic material, found in domain Eukarya.

Prokaryotic cell

A simpler and smaller cell lacking a membrane-enclosed nucleus and membrane-enclosed organelles, characteristic of organisms in domains Bacteria and Archaea.

Gene expression

The entire process by which information encoded in a gene directs the transcription of messenger RNA ($\text{mRNA}$) and translation into a specific sequence of amino acids to produce a protein.

Bioinformatics

The use of computational tools to store, organize, and analyze large volumes of biological data, such as $\text{DNA}$, $\text{RNA}$, and protein sequences.

Negative feedback

A primary form of biological regulation in which an accumulation of an end product slows down or reduces the initial stimulus of the pathway, such as insulin signaling.

Positive feedback

A form of biological regulation in which an end product speeds up or reinforces its own production, increasing the response, such as platelet aggregation during injury.

Natural selection

The evolutionary mechanism wherein individuals with inherited traits best suited to their local environment have higher reproductive success, leading to adaptation over generations.

Inductive reasoning

A type of logical thinking in which broad generalizations are derived from a large number of specific observations.

Deductive reasoning

A form of logic in which specific results are predicted from general premises or hypotheses (commonly structured as "if… then" statements).

Scientific theory

A broad, comprehensive explanation of aspects of the natural world that is supported by a large body of evidence and generates new testable hypotheses.

Valence

The bonding capacity of an atom, generally equal to the number of unpaired electrons in its outermost (valence) shell; carbon has a valence of $4$.

Hydrocarbon

An organic molecule consisting solely of carbon and hydrogen atoms connected by nonpolar covalent bonds, making it hydrophobic and capable of storing large amounts of energy.

Structural isomers

Compounds that have the same molecular formula but differ in the covalent arrangements of their carbon skeletons.

Cis-trans isomers

Organic molecules that differ in arrangement of atoms around an inflexible double bond; cis isomers have groups on the same side, while trans isomers have groups on opposite sides.

Enantiomers

Molecules that are mirror images of each other and cannot be superimposed, differing in spatial arrangement around an asymmetric carbon bonded to four different groups.

Functional groups

Specific chemical groups attached to a carbon skeleton that participate directly in chemical reactions and contribute to molecular shape, size, charge, and function.

Dehydration reaction

A chemical reaction in which two molecules become covalently linked to each other with the simultaneous removal of a water molecule ($H_2O$); facilitates polymerization.

Hydrolysis

A chemical process that breaks covalent bonds between monomers in a polymer through the addition of a water molecule ($H_2O$).

Glycosidic linkage

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

Starch

A storage polysaccharide in plants consisting entirely of glucose monomers joined by $\alpha$ 1-4 linkages, existing in unbranched (amylose) or branched (amylopectin) forms.

Glycogen

An extensively branched glucose storage polysaccharide found in the liver and muscle tissue of animals, hydrolyzed to release glucose when fuel is needed.

Cellulose

A structural polysaccharide comprising the tough cell walls of plant cells, composed of glucose monomers joined by $\beta$ 1-4 glycosidic linkages that form straight, parallel microfibrils held by hydrogen bonds.

Chitin

A structural polysaccharide made of glucose monomers modified with nitrogen-containing groups, found in arthropod exoskeletons and fungal cell walls.

Triacylglycerol

A lipid molecule composed of three fatty acids linked to one glycerol molecule by ester linkages formed via dehydration reactions.

Saturated fatty acid

A fatty acid in which all carbons in the hydrocarbon chain are joined by single covalent bonds, maximizing hydrogen atoms; packs tightly and is solid at room temperature.

Unsaturated fatty acid

A fatty acid possessing one or more double bonds (usually cis) in its hydrocarbon chain, causing a kink that prevents tight packing and keeps it liquid at room temperature.

Phospholipid

An amphipathic lipid made of glycerol joined to two hydrophobic fatty acid tails and a hydrophilic head consisting of a phosphate group, forming bilayer membranes in cells.

Steroid

A lipid characterized by a carbon skeleton composed of four fused rings, exemplified by cholesterol, which serves as a precursor for vertebrate sex hormones.

Polypeptide

A polymer of amino acids joined together in a specific sequence by covalent peptide bonds between carboxyl and amino groups.

Primary structure

The unique linear sequence of amino acids in a polypeptide chain, determined directly by inherited genetic information.

Secondary structure

Regions of repetitive coiling or folding in a polypeptide backbone stabilized by hydrogen bonds between the repeating backbone constituents ($\alpha$ helix and $\beta$ pleated sheet).

Tertiary structure

The overall three-dimensional shape of a polypeptide resulting from interactions among the amino acid side chains (R groups), including hydrophobic interactions, ionic bonds, hydrogen bonds, and disulfide bridges.

Quaternary structure

The functional biological structure of a protein that arises from the aggregation of two or more distinct polypeptide subunits.

Phosphodiester linkage

The covalent bond joining the $3'\text{-OH}$ group of one nucleotide's pentose sugar to the $5'\text{-phosphate}$ group of the adjacent nucleotide, constructing the sugar-phosphate backbone.

Antiparallel

The arrangement in a $\text{DNA}$ double helix where the two complementary polynucleotide strands run in opposite $5' \rightarrow 3'$ directions relative to one another.

Fluid mosaic model

The accepted model of cell membrane structure, depicting the membrane as a mosaic of individual protein molecules drifting laterally within a fluid bilayer of phospholipids.

Integral proteins

Transmembrane proteins that penetrate the hydrophobic interior of the lipid bilayer, typically possessing hydrophobic $\alpha$-helical domains spanning the membrane.

Peripheral proteins

Membrane proteins that are not embedded in the lipid bilayer but are loosely attached to the extracellular or cytoplasmic surface of the membrane.

Selective permeability

A fundamental property of biological membranes that enables them to regulate the passage of substances, allowing some to cross more easily than others.

Diffusion

The spontaneous movement of particles of any substance so that they spread out into available space down their concentration gradient, requiring no expenditure of energy.

Osmosis

The diffusion of free water across a selectively permeable membrane from a region of lower solute concentration to a region of 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 relative to the cell's interior.

Plasmolysis

A phenomenon in walled cells placed in a hypertonic environment where the cell shrivels and its plasma membrane pulls away from the cell wall.

Facilitated diffusion

Passive transport of polar molecules or ions across a biological membrane down their concentration gradient via specific transmembrane transport proteins (channels or carriers).

Active transport

The movement of a substance across a biological membrane against its concentration or electrochemical gradient, mediated by specific carrier proteins and requiring energy expenditure (usually ATP hydrolysis).

Sodium-potassium pump

An animal cell transport protein that hydrolyzes $\text{ATP}$ to pump three $\text{Na}^+$ ions out of the cell for every two $\text{K}^+$ ions moved into the cell against their concentration gradients.

Electrochemical gradient

The combined diffusion gradient of an ion, driven by both a chemical concentration force and an electrical membrane potential force.

Cotransport

A mechanism in which a transport protein couples the downhill diffusion of one solute to the uphill transport of a second solute against its concentration gradient.

Exocytosis

The cellular secretion of biological molecules by the fusion of vesicles from the endomembrane system with the plasma membrane.

Phagocytosis

A type of endocytosis where a cell engulfs a large particle or microorganism by extending pseudopodia around it and packaging it into a membranous food vacuole.

Pinocytosis

A type of endocytosis in which droplets of extracellular fluid containing dissolved solutes are gulped into tiny vesicles formed by plasma membrane infoldings.

Receptor-mediated endocytosis

A specialized pinocytic process where receptor proteins on the cell surface bind specific ligands, clustering in coated pits to internalize bulk quantities of dilute molecules.

Nuclear lamina

A netlike array of protein filaments lining the inner surface of the nuclear envelope that mechanically supports the shape of the nucleus.

Nucleolus

A prominent non-membranous structure within the eukaryotic nucleus where ribosomal $\text{RNA}$ ($\text{rRNA}$) is synthesized and assembled with proteins into ribosomal subunits.

Smooth ER

The portion of the endoplasmic reticulum devoid of ribosomes, active in lipid synthesis, carbohydrate metabolism, calcium storage, and poison/drug detoxification.

Rough ER

The portion of the endoplasmic reticulum studded with ribosomes on its outer surface, responsible for synthesizing secretory proteins and manufacturing cell membrane phospholipids.

Golgi apparatus

An organelle composed of flattened stacks of membranous cisternae that receives, modifies, stores, sorts, and ships products from the endoplasmic reticulum.

Lysosome

A membrane-enclosed digestive sac containing acidic hydrolytic enzymes that animal cells use to hydrolyze macromolecules, engulfed food particles, and damaged organelles.

Cristae

The intricate inner foldings of the mitochondrial membrane that increase surface area for the enzymes and protein complexes that participate in cellular respiration.

Thylakoids

Flattened, interconnected sacs inside a chloroplast that contain chlorophyll; stacks of thylakoids form structures called grana.

Microtubules

Hollow rods measuring approximately $25\,nm$ in diameter made of tubulin dimers ($\alpha$-tubulin and $\beta$-tubulin) that shape the cell, guide organelle movements, and separate chromosomes during cell division.

Microfilaments

Thin, solid rods about $7\,nm$ in diameter composed of two intertwined strands of actin proteins, functioning in bearing tension, muscle contraction, amoeboid movement, and cytoplasmic streaming.

Intermediate filaments

Cytoskeletal fibers measuring $8\text{--}12\,nm$ in diameter constructed from coiled cables of fibrous proteins (such as keratins), specialized for bearing tension and anchoring the nucleus and organelles.

Catabolic pathways

Metabolic breakdown pathways that release energy by dismantling complex organic molecules into simpler compounds, such as glucose breakdown in cellular respiration.

Anabolic pathways

Biosynthetic metabolic pathways that consume energy to build complicated molecules from simpler components, such as synthesizing a polypeptide from individual amino acids.

First law of thermodynamics

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

Second law of thermodynamics

The physical law stating that every energy transfer or transformation increases the entropy (disorder) of the universe, with some energy inevitably lost as thermal energy (heat).

Free energy (G)

The portion of a biological system's energy that can perform work under conditions of uniform temperature and pressure; calculated by $\Delta G = \Delta H - T\Delta S$.

Exergonic reaction

A spontaneous chemical reaction characterized by a net release of free energy ($\Delta G < 0$).

Endergonic reaction

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

Energy coupling

The cellular strategy of using an exergonic process (predominantly $\text{ATP}$ hydrolysis) to drive an endergonic chemical process.

Activation energy ($E_A$)

The initial investment of energy required to contort reactant molecules into an unstable transition state where existing chemical bonds can break.

Active site

The restricted region of an enzyme molecule, usually a specific pocket or groove formed by a few amino acids, where the substrate binds and catalysis occurs.

Induced fit

The subtle conformational change in an enzyme's active site upon substrate entry, bringing catalytic chemical groups into precise alignment to catalyze the reaction.

Competitive inhibitor

A regulatory substance that mimics the normal substrate and competes directly for binding at the enzyme's active site, reducing productivity.

Noncompetitive inhibitor

A substance that impedes enzymatic reactions by binding to an alternative allosteric site on the enzyme, changing the enzyme's conformation so the active site functions less effectively.

Redox reaction

A chemical reaction involving the complete or partial transfer of one or more electrons from one reactant to another; oxidation involves electron loss and reduction involves electron gain.

Glycolysis

A ten-step metabolic pathway occurring in the cytosol that splits one molecule of glucose ($C_6H_{12}O_6$) into two molecules of pyruvate, generating a net of $2\,\text{ATP}$ and $2\,\text{NADH}$.

Oxidative phosphorylation

The production of ATP using energy derived from the redox reactions of the mitochondrial electron transport chain coupled with chemiosmosis, accounting for approximately $90\%$ of cellular respiration ATP.

Fermentation

A catabolic pathway that harvests chemical energy through substrate-level phosphorylation via glycolysis without an electron transport chain and without oxygen, using pyruvate or a derivative as the electron acceptor to regenerate $\text{NAD}^+$.