General Biology: Energy, Metabolism, Cellular Communication, and Genetics

Comprehensive vocabulary flashcards covering bioenergetics, cellular respiration, photosynthesis, signal transduction, cell division, meiosis, and Mendelian genetics.

Kinetic Energy

The energy of motion, which includes thermal energy (the kinetic energy of molecules moving).

Potential Energy

Energy stored in position or configuration; within molecules, chemical potential energy is stored in bonds, where weaker bonds with equally shared electrons possess high potential energy and stronger bonds with unequally shared electrons possess low potential energy.

Standard Free-Energy Change Equation

The mathematical relationship used to calculate change in Gibbs free energy: $\Delta G = \Delta H - T\Delta S$, where $\Delta H$ is change in enthalpy, $\Delta S$ is change in entropy, and $T$ is temperature in Kelvin.

Exergonic Reaction

A spontaneous chemical reaction in which free energy is released ($\Delta G < 0$) and products have less free energy than reactants.

Endergonic Reaction

A non-spontaneous chemical reaction requiring an input of free energy ($\Delta G > 0$) in which products have more free energy than reactants.

Energy Coupling

The pairing of an exergonic reaction (such as ATP hydrolysis, $\Delta G = -7.3\,\text{kcal/mol}$) with an endergonic reaction to make the overall coupled reaction spontaneous with a net negative $\Delta G$.

Activation Energy ($E_a$)

The initial kinetic energy barrier required to strain chemical bonds, align colliding reactants in a precise orientation, and overcome electron repulsion so that reactants can reach the transition state.

Transition State

An unstable, high-energy intermediate configuration of reactants occurring at the peak of the activation energy barrier during a chemical reaction.

Induced Fit

The conformational change that an enzyme undergoes upon substrate binding, which closes the active site more tightly around the substrate to facilitate the reaction.

Cofactors

Inorganic ions, such as $\text{Zn}^{2+}$, $\text{Mg}^{2+}$, and $\text{Fe}^{2+}$, that interact reversibly with enzymes to assist catalytic activity.

Coenzymes

Organic non-protein molecules, such as $\text{NADH}$ and $\text{FADH}_2$, that interact reversibly with enzymes to assist in transferring chemical groups or electrons.

Prosthetic Groups

Non-amino acid atoms or molecules that are permanently bound to proteins or enzymes, essential for their functional activity.

Competitive Inhibition

A mechanism of enzyme regulation where an inhibitor molecule resembles the substrate and competes directly for binding at the active site, preventing substrate access.

Allosteric Regulation

A regulatory process where an effector molecule binds to an allosteric site away from the active site, inducing a conformational change that shifts the enzyme between a high-affinity active state (allosteric activation) and a low-affinity inactive state (allosteric inhibition).

Feedback Inhibition

A type of metabolic pathway control in which the end product binds to an allosteric site on an enzyme early in the pathway (such as threonine deaminase or phosphofructokinase), inhibiting its activity when product levels are high.

Ribozymes

RNA molecules that function as biological catalysts, such as RNA components of ribosomes that catalyze peptide bond formation or RNAs that catalyze RNA cutting and splicing.

Catabolism vs. Anabolism

Catabolism refers to metabolic pathways that break down larger molecules into smaller ones, releasing energy; anabolism refers to metabolic pathways that synthesize larger complex molecules from smaller ones, consuming energy.

Substrate-Level Phosphorylation

The direct synthesis of ATP by an enzyme transferring a phosphate group from a phosphorylated donor substrate molecule directly onto ADP.

Glycolysis

A series of 10 cytosolic reactions that oxidizes 1 glucose ($6\text{C}$) into 2 molecules of pyruvate ($3\text{C}$), yielding a net gain of $2\,\text{ATP}$ (4 generated, 2 used) and $2\,\text{NADH} + 2\,\text{H}^+$.

Pyruvate Oxidation

A step taking place in the mitochondrial matrix where pyruvate is converted to acetyl-CoA, releasing $\text{CO}_2$ and transferring electrons to reduce $\text{NAD}^+$ to $\text{NADH}$.

Citric Acid Cycle

A cyclical series of reactions in the mitochondrial matrix that oxidizes the acetyl group of acetyl-CoA to $\text{CO}_2$, generating $3\,\text{NADH}$, $1\,\text{FADH}_2$, and $1\,\text{ATP}$ (via GTP) per turn.

Chemiosmosis

The movement of hydrogen ions ($\text{H}^+$) across a membrane down their electrochemical proton gradient through ATP synthase to power the phosphorylation of ADP into ATP.

ATP Synthase

A molecular rotary turbine composed of an embedded $F_o$ subunit that conducts protons and a catalytic $F_1$ subunit joined by a rotor shaft and stator that synthesizes ATP in mitochondria and chloroplasts.

Fermentation

An anaerobic metabolic pathway that transfers electrons from $\text{NADH}$ to an organic acceptor (yielding lactate or ethanol and $\text{CO}_2$), which regenerates $\text{NAD}^+$ to keep glycolysis running in the absence of oxygen.

Oxygen Requirements for Microbial Growth

Classification of organisms based on oxygen tolerance: obligate aerobes require oxygen; facultative anaerobes grow aerobically or anaerobically (growing best with oxygen); obligate anaerobes are poisoned by oxygen because they lack catalase and superoxide dismutase (SOD).

Phosphofructokinase

A key regulatory enzyme in glycolysis that is allosterically inhibited by high levels of ATP and NADH (and citrate), and stimulated by ADP or AMP.

Chlorophyll Molecule Structure

A photosynthetic pigment consisting of a light-absorbing porphyrin ring head containing a central magnesium ($\text{Mg}$) atom and a nonpolar hydrocarbon tail that anchors it into the thylakoid membrane.

Carotenoids

Accessory photosynthetic pigments (such as $\beta$-carotene) that absorb blue and green light, transmit yellow, orange, or red light, and help protect plants by dissipating excess energy.

Photosystem

A light-harvesting complex in thylakoid membranes composed of an antenna complex (pigment molecules that absorb photons and transmit energy via resonance) and a reaction center containing special chlorophyll $a$ molecules and a primary electron acceptor.

Oxygenic Photosynthesis

The photosynthetic process in Photosystem II that oxidizes water ($2\,\text{H}_2\text{O} \rightarrow 4\,\text{H}^+ + 4\,\text{e}^- + \text{O}_2$) to replace electrons transferred from the P680 reaction center, releasing molecular oxygen.

Cyclic Electron Flow

An alternative electron pathway in photosynthesis involving only Photosystem I where electrons cycle through ferredoxin, the plastoquinone pool, and the cytochrome complex back to P700, pumping protons to generate extra ATP without producing NADPH or $\text{O}_2$.

Rubisco

Ribulose 1,5-bisphosphate carboxylase/oxygenase; the most abundant protein on Earth, which catalyzes the fixation of $\text{CO}_2$ to ribulose 1,5-bisphosphate (RuBP) in the Calvin cycle.

Photorespiration

A wasteful metabolic process occurring when rubisco binds $\text{O}_2$ instead of $\text{CO}_2$, producing one molecule of 3-phosphoglycerate and one molecule of 2-phosphoglycolate, consuming ATP and releasing previously fixed $\text{CO}_2$.

$C_4$ Pathway

An adaptation to minimize photorespiration that separates carbon capture and the Calvin cycle spatially: PEP carboxylase fixes $\text{CO}_2$ into a $4\text{C}$ organic acid in mesophyll cells, which is transported to bundle sheath cells to release concentrated $\text{CO}_2$ to rubisco.

CAM (Crassulacean Acid Metabolism)

A photosynthetic adaptation in desert plants that separates carbon fixation and the Calvin cycle temporally by opening stomata to capture $\text{CO}_2$ into $4\text{C}$ malate at night, and releasing $\text{CO}_2$ to the Calvin cycle during the day.

Autocrine Signaling

A form of local cell communication in which a cell secretes a regulatory molecule that binds to receptors on its own plasma membrane, eliciting a response in itself.

Paracrine Signaling

A form of local cell communication in which a secreting cell releases signaling molecules into the extracellular fluid to act on nearby target cells.

Endocrine Signaling

Long-distance cellular communication where specialized cells secrete hormones that travel through the circulatory system to elicit responses in distant target cells.

G-Protein-Coupled Receptor (GPCR)

A major class of cell-surface receptors characterized by seven transmembrane $\alpha$-helical domains that activate an intracellular heterotrimeric G protein by exchanging bound GDP for GTP upon ligand binding.

Cyclic AMP (cAMP)

A common intracellular second messenger produced from ATP by the enzyme adenylyl cyclase, which subsequently activates protein kinase A (PKA) to initiate a phosphorylation cascade.

$\text{IP}_3$ and DAG Pathway

A signaling cascade where activated phospholipase C cleaves the membrane phospholipid $\text{PIP}_2$ into diacylglycerol (DAG) and inositol trisphosphate ($\text{IP}_3$); $\text{IP}_3$ triggers $\text{Ca}^{2+}$ release from the ER, which together with DAG activates protein kinases.

Receptor Tyrosine Kinase (RTK)

A cell-surface receptor whose monomeric subunits bind signaling molecules, dimerize, and trigger autophosphorylation of tyrosine residues in their cytoplasmic kinase domains.

Ras Protein

A monomeric G protein linked to RTKs via adapter proteins that binds GTP and initiates a three-step MAP (mitogen-activated protein) kinase cascade that regulates genes controlling cell division.

Nitric Oxide ($\text{NO}$) Signaling

A paracrine signaling process in endothelial cells where acetylcholine activates $\text{Ca}^{2+}$/calmodulin and NO synthase to produce $\text{NO}$, which diffuses into smooth muscle cells, activates guanylyl cyclase to produce cyclic GMP, and induces vessel relaxation.

Crosstalk

The interconnected integration between different signaling pathways, where components of one pathway stimulate or inhibit another pathway, modulating the overall cellular response.

Nucleosome

The basic structural unit of eukaryotic chromatin packaging, consisting of DNA double helix wound around an octamer core of histone proteins ($2$ molecules each of H2A, H2B, H3, and H4), stabilized by histone H1 into a $10\text{-nm}$ to $30\text{-nm}$ fiber.

Euchromatin vs. Heterochromatin

Euchromatin is loosely packed, transcriptionally active chromatin; heterochromatin is densely packed, transcriptionally inactive chromatin.

Ploidy

The number of complete chromosome sets in a cell or organism, such as haploid ($n$), diploid ($2n$), or polyploid ($3n$, $4n$, etc.).

Cell Cycle Phases

The ordered sequence of cell replication consisting of Interphase ($G_1$ growth, $S$ DNA synthesis, and $G_2$ mitotic preparation) and M phase (mitosis and cytokinesis).

Kinetochore

A specialized protein complex assembled at the centromere of each sister chromatid that binds to kinetochore spindle microtubules during prometaphase and metaphase.

Cytokinesis in Plants vs. Animals

In animal cells, cytokinesis occurs through an actin-myosin contractile ring that pinches the membrane to create a cleavage furrow; in plant cells, Golgi vesicles fuse along the spindle equator to construct a cell plate.

p53 Protein

A tumor suppressor protein acting at the $G_1$ checkpoint that arrests the cell cycle when DNA damage is detected to allow repair, or induces apoptosis if damage cannot be repaired.

Cyclin-Dependent Kinases (Cdks)

Protein kinases that regulate the cell cycle checkpoints; they are active only when bound to specific regulatory cyclin proteins, phosphorylating target proteins to drive cell cycle progression.

Proto-oncogenes vs. Oncogenes

Proto-oncogenes are normal genes that stimulate cell growth and division; when mutated into hyperactive oncogenes, they cause uncontrolled cell proliferation.

Binary Fission

The asexual mode of cell division in prokaryotes where the single circular bacterial chromosome replicates beginning at the origin ($\text{ori}$), and the cell divides into two identical cells.

Synapsis and Bivalent

The tight side-by-side pairing of homologous chromosomes during early prophase I of meiosis, forming a four-chromatid structure known as a bivalent (or tetrad).

Crossing-Over

The physical exchange of genetic segments between non-sister chromatids of homologous chromosomes occurring at chiasmata during prophase I of meiosis.

Independent Assortment (Meiosis)

The random orientation and segregation of maternal and paternal homologous chromosome pairs at the metaphase I plate during meiosis, producing $2^n$ possible chromosome combinations in gametes.

Nondisjunction and Aneuploidy

Nondisjunction is the failure of homologous chromosomes (in meiosis I) or sister chromatids (in meiosis II) to separate properly, resulting in aneuploid gametes ($n+1$ or $n-1$) that cause trisomy (e.g., Down syndrome) or monosomy (e.g., Turner syndrome) upon fertilization.

Alternation of Generations

A plant life cycle that alternates between a multicellular diploid sporophyte ($2n$) phase that produces haploid spores by meiosis and a multicellular haploid gametophyte ($n$) phase that produces gametes by mitosis.

Gene Locus

The specific physical position or site on a chromosome where a particular gene is located.

Principle of Segregation

Mendel's first law stating that the two alleles of a gene carried by a diploid individual separate during gamete formation, such that half of the gametes carry one allele and half carry the other.

Testcross

A genetic cross between an individual showing the dominant phenotype (unknown genotype) and a homozygous recessive individual to determine if the dominant individual is homozygous or heterozygous.

Incomplete Dominance

An inheritance pattern in which the heterozygous phenotype is an intermediate blend between the homozygous dominant and homozygous recessive phenotypes (e.g., red and white snapdragons producing pink offspring).

Codominance

An inheritance pattern in which both alleles are fully and distinctly expressed in the heterozygote (e.g., $I^A I^B$ genotype resulting in AB blood type).

Epistasis

A gene interaction in which alleles at one gene locus mask or inhibit the phenotypic expression of alleles of a different gene at a distinct locus (such as coat color in Labrador retrievers producing a $9:3:4$ ratio).

Pleiotropy

The condition in which a single gene influences multiple, seemingly unrelated phenotypic traits or bodily systems (e.g., the sickle-cell hemoglobin allele causing diverse organ complications).

Polygenic Inheritance

The inheritance of quantitative characters (such as human height) that are controlled by the additive effects of two or more distinct genes, resulting in continuous phenotypic variation.