BIOL 1P93: Chemical Basis of Life, Metabolism, Cellular Respiration, and Cell Biology

Comprehensive vocabulary flashcards covering the chemical foundations of biology, biomolecules, thermodynamic principles, enzyme kinetics, cellular respiration pathways, and cellular anatomy and membrane transport.

Kinetic Energy

Energy that is actively performing work or associated with movement.

Potential Energy

Stored or inactive energy possessed by an object as a result of its position relative to other objects.

Atomic Number

The number of protons in an atom's nucleus, which is unique to each chemical element and indirectly gives the number of electrons in an electrically neutral atom.

Atomic Mass Number

The total sum of protons and neutrons contained within an atom's nucleus.

Atomic Weight

A value approximately equal to the mass number of an element's most abundant isotope, calculated as a weighted average.

Isotopes

Atoms of the same element that share the same atomic number (protons and electrons) but differ in their atomic mass due to varying numbers of neutrons.

Radioactivity

The spontaneous process of atomic decay occurring in unstable, heavy isotopes as they decompose into more stable isotopes.

Molecule

Any chemical structure composed of two or more atoms held together by chemical bonds.

Compound

A specific class of molecule formed when two or more different chemical elements bond together.

Valence Shell

The outermost electron shell of an atom that participates in bonding and determines chemical behavior.

Rule of Eights

The chemical guideline stating that atoms are chemically stable and inert when their outermost valence shell contains $8$ electrons, with the exception of the first shell which fills at $2$ electrons.

Ionic Bond

A chemical bond formed by the complete transfer of electrons from one atom to another, producing positively charged cations and negatively charged anions that attract one another.

Covalent Bond

A chemical bond formed when reacting atoms share pairs of valence electrons to fill their outer electron shells.

Nonpolar Covalent Bond

A covalent bond wherein electrons are shared equally between atoms, rendering the molecule electrically neutral.

Polar Covalent Bond

A covalent bond wherein electrons are shared unequally due to differing electronegativities, establishing positive and negative poles on the molecule.

Hydrogen Bond

A weak intermolecular attraction formed when a hydrogen atom covalently bound to an electronegative atom is attracted to an electronegative atom, such as oxygen or nitrogen, on another polar molecule.

Van der Waals Forces

Weak, short-range, distance-dependent electrostatic attractions between atoms or molecules generated by temporary fluctuations in electron distribution.

Dehydration Synthesis

A chemical condensation reaction in which monomers are covalently linked into polymers accompanied by the removal of a water molecule ($H_2O$).

Hydrolysis

A cleavage reaction in which covalent bonds in polymers are broken down into monomers via the enzymatic addition of a water molecule ($H_2O$).

High Heat Capacity of Water

The property of water whereby it absorbs or releases substantial quantities of heat before changing temperature, thereby stabilizing and buffering body temperature.

Electrolyte

An ionic compound, such as a salt, that completely dissociates into ions in water and conducts electrical currents in solution.

Acid

A substance that acts as a proton donor by dissociating in aqueous solution to liberate hydrogen ions ($H^+$).

Base

A substance that acts as a proton acceptor by dissociating in aqueous solution to liberate hydroxyl ions ($OH^-$).

Buffer

A chemical compound or system that maintains homeostatic pH by taking up or releasing hydrogen ions in response to pH fluctuations.

Glycosidic Bond

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

Saturated Fat

A lipid containing fatty acid chains with only single covalent carbon-carbon bonds, resulting in straight chains that solidify at room temperature.

Unsaturated Fat

A lipid containing fatty acid chains with one or more double covalent carbon-carbon bonds, forming kinks that prevent tight molecular packing and keep the oil liquid at room temperature.

Trans Fat

An oil that has been artificially solidified by the industrial addition of hydrogen atoms across double bond sites, associated with increased cardiovascular risk.

Phospholipid

An amphipathic lipid consisting of a hydrophilic, charged phosphate-containing head and two hydrophobic fatty acid tails that self-assembles into cellular membranes.

Steroid

A lipid molecule characterized by four fused, interlocking hydrocarbon rings, synthesized from cholesterol as a precursor.

Selenocysteine

The recognized 21st amino acid that can be biologically incorporated into polypeptide chains during protein synthesis.

Primary Protein Structure

The linear sequence of amino acids in a polypeptide chain determined by peptide bonds.

Secondary Protein Structure

Localized repetitive twisting or folding patterns of the polypeptide backbone stabilized by hydrogen bonds, forming either an alpha ($\alpha$) helix or beta ($\beta$)-pleated sheet.

Tertiary Protein Structure

The overall three-dimensional globular conformation of a single polypeptide chain, stabilized by side-chain hydrogen bonds, ionic bonds, hydrophobic interactions, Van der Waals dispersion forces, and disulfide bridges.

Quaternary Protein Structure

The biological structure formed by the structural assembly and coordination of two or more independent polypeptide subunits.

First Law of Thermodynamics

The law of conservation of energy stating that energy cannot be created or destroyed, only transformed from one form to another.

Second Law of Thermodynamics

The thermodynamic law stating that any energy transfer increases the entropy (disorder) of a closed system, reducing the quantity of usable energy available to do work.

Enthalpy ($H$)

The total energy of a thermodynamic system, mathematically represented in Gibbs free energy calculations as $H = G + TS$.

Exergonic Reaction

A spontaneous reaction in which free energy is released into the system, characterized by a negative change in Gibbs free energy ($\Delta G < 0$).

Endergonic Reaction

A non-spontaneous reaction that requires a net input of free energy to proceed, characterized by a positive change in Gibbs free energy ($\Delta G > 0$).

Activation Energy ($E_A$)

The initial amount of energy required to strain chemical bonds in reactants to reach the transition state and initiate a chemical reaction.

Induced Fit Phenomenon

The conformational adaptation an enzyme undergoes upon substrate binding that tightens the active site pocket and strains bonds to accelerate catalysis.

Michaelis Constant ($K_M$)

The substrate concentration at which an enzyme-catalyzed reaction proceeds at half of its maximal velocity ($\frac{V_{\max}}{2}$); inversely proportional to enzyme-substrate affinity.

Competitive Inhibitor

A molecule that directly competes with the substrate by binding to the active site of an enzyme, increasing the apparent $K_M$ without changing $V_{\max}$.

Noncompetitive Inhibitor

A molecule that binds to an allosteric site on an enzyme rather than the active site, inducing a conformational change that decreases $V_{\max}$ while leaving $K_M$ unaffected.

Prosthetic Group

A small non-protein molecule permanently bound to an enzyme that is required for its catalytic activity.

Coenzyme

An organic cofactor that temporarily participates in an enzymatic reaction and leaves the reaction chemically unchanged.

Agonist

A drug or ligand that binds to a specific target receptor or allosteric site and enhances its normal biochemical activity.

Antagonist

A drug or ligand that binds to a receptor or enzyme active site to block its normal physiological activity.

Substrate-Level Phosphorylation

The direct enzymatic transfer of a phosphate group from a phosphorylated organic metabolic substrate to ADP, generating ATP.

Chemiosmosis

The mechanism of ATP synthesis wherein energy stored in an electrochemical proton ($H^+$) gradient across a membrane drives the phosphorylation of ADP by ATP synthase.

Feedback Inhibition

A negative feedback regulatory mechanism where high concentrations of a metabolic pathway's final product allosterically inhibit an early rate-limiting enzyme in that pathway.

Phosphofructokinase

The allosteric enzyme that catalyzes step 3 of glycolysis, converting fructose-6-phosphate to fructose-1,6-bisphosphate; serves as the primary rate-limiting step regulated by ATP binding.

Pyruvate Dehydrogenase

The multienzyme complex in the mitochondrial matrix that decarboxylates pyruvate into an acetyl group, generates NADH, and attaches coenzyme A to produce acetyl CoA.

Electron Transport Chain

A series of membrane-embedded protein complexes and electron carriers in the inner mitochondrial cristae that accept electrons from NADH and $FADH_2$, releasing energy to pump protons ($H^+$) into the intermembrane space.

ATP Synthase

A rotary transmembrane enzyme composed of membrane-embedded c subunits and non-membrane subunits ($1\,\epsilon, 1\,\gamma, 1\,\delta, 3\,\alpha, 3\,\beta$) that synthesizes ATP from ADP and $P_i$ as protons flow through its channel.

Anaerobic Respiration

A cellular respiration pathway that utilizes a membrane electron transport chain with an inorganic terminal electron acceptor other than oxygen, such as nitrate ($NO_3^-$) in Escherichia coli.

Fermentation

The anaerobic catabolism of organic nutrients to synthesize ATP purely via substrate-level phosphorylation while using organic molecules to regenerate $NAD^+$ from NADH without net oxidation.

Fluid-Mosaic Model

The structural framework describing the plasma membrane as a dynamic, fluid bilayer of phospholipids embedded with mobile proteins, glycoproteins, and glycolipids.

Transmembrane Protein

An integral membrane protein that extends entirely through the phospholipid bilayer, possessing hydrophobic alpha-helices embedded in the membrane interior.

Crenation

The cellular shrinkage that occurs when an animal cell loses water by osmosis after being placed in a hypertonic environment.

Osmotic Lysis

The osmotic swelling and rupturing of an animal cell that occurs when water rushes into the cytoplasm in a hypotonic environment.

Uniporter

A membrane transport protein that transfers a single ion or solute molecule across the phospholipid bilayer in one direction.

Symporter

A membrane cotransporter that couples the movement of two or more different ions or solutes across the membrane in the same direction.

Antiporter

A membrane transport protein that moves two or more different ions or solute molecules in opposite directions across the lipid bilayer.

$$Na^+/K^+\text{-ATPase}$$

An active transport antiporter pump that hydrolyzes ATP to export $3\,Na^+$ ions from the cytosol and import $2\,K^+$ ions into the cell against their concentration gradients.

Phagocytosis

A form of endocytosis termed 'cell eating' in which a cell projects pseudopodia to engulf large solid matter, such as bacteria or cellular debris, into a membranous phagosome.

Pinocytosis

A form of non-specific endocytosis termed 'cell drinking' in which invaginations of the plasma membrane enclose droplets of extracellular fluid.

Nucleolus

A dense, dark-staining structure within the cell nucleus dedicated to the transcription of rRNA and assembly of ribosomal subunits.

Chromatin

The diffuse nuclear complex of genomic DNA wrapped around histone proteins that condenses into distinct chromosomes during cellular division.

Rough Endoplasmic Reticulum

A continuous system of membranous tubules studded with ribosomes that synthesizes, folds, and modifies proteins destined for secretion or membrane insertion.

Smooth Endoplasmic Reticulum

A network of membranous tunnels lacking ribosomes that performs lipid and steroid synthesis, carbohydrate metabolism, and drug detoxification.

Golgi Apparatus

A cellular organelle consisting of stacks of flattened membranous sacs that receives transport vesicles from the rough ER to modify, sort, and package proteins.

Lysosome

A membrane-bound organelle filled with hydrolytic digestive enzymes that degrades damaged organelles, extracellular debris, and phagocytosed pathogens.

Peroxisome

A membranous organelle housing oxidase enzymes that neutralize metabolic toxins and free radicals, converting them into hydrogen peroxide ($H_2O_2$) and then water ($H_2O$).

Microtubules

Hollow cytoskeletal cylinders measuring $25\,\text{nm}$ in diameter composed of alpha- and beta-tubulin, functioning in organelle transport, chromosome movement, and ciliary motion.

Intermediate Filaments

Rope-like cytoskeletal proteins measuring $10\,\text{nm}$ in diameter composed of fibrous proteins like keratin and lamin that provide mechanical stability and cellular anchorage.

Actin Filaments

Cytoskeletal fibers measuring $7\,\text{nm}$ in diameter formed from intertwined actin polymers that facilitate amoeboid movement, cytokinesis, and muscle contraction.