General Biology: Chemical Basis of Life and Cell Biology

Comprehensive practice flashcards covering the chemical foundations of life, atomic structure, bonding, water chemistry, biological macromolecules (carbohydrates, lipids, proteins, and nucleic acids), cell theory, microscopy, cellular organelles, the endomembrane system, cytoskeleton, and intercellular junctions.

Theory of Vitalism

The historical doctrine proposing that living organisms are governed by a unique vital force that does not exist in non-living matter, implying organic compounds could only originate within living systems and could not be synthesized in a laboratory.

Friedrich Wöhler (1828)

The German chemist who synthesized the organic compound urea from the inorganic precursor ammonium cyanate in $1828$, directly disproving the theory of vitalism.

Hermann Kolbe (1845)

The chemist who synthesized acetic acid directly from inorganic elements in $1845$, providing further evidence against vitalism.

Jöns Jacob Berzelius

The scientist who coined the chemical term isomerism to describe compounds having identical molecular formulas but different structural arrangements.

Condensation Reaction

A chemical reaction in which two monomers combine to form a larger polymer; when this process results in the net loss of a water molecule, it is specifically termed a dehydration reaction.

Hydrolysis Reaction

A chemical reaction that breaks covalent bonds within polymers, splitting them into monomers by adding a molecule of water ($\text{R}_1\text{-}\text{R}_2 + \text{H}_2\text{O} \rightarrow \text{R}_1\text{-OH} + \text{H-}\text{R}_2$).

Functional Group

A specific cluster of atoms exhibiting characteristic chemical structures and properties, such as amino ($-\text{NH}_2$), carbonyl ($-\text{CO}$), carboxyl ($-\text{COOH}$), hydroxyl ($-\text{OH}$), methyl ($-\text{CH}_3$), phosphate ($-\text{PO}_4^{2-}$), sulfate ($-\text{SO}_4^-$), and sulfhydryl ($-\text{SH}$).

Monosaccharide

The simplest monomeric unit of carbohydrates with the general formula $\text{C}_n(\text{H}_2\text{O})_n$, such as pentoses ($\text{C}_5\text{H}_{10}\text{O}_5$ ribose, $\text{C}_5\text{H}_{10}\text{O}_4$ deoxyribose) and hexoses ($\text{C}_6\text{H}_{12}\text{O}_6$ glucose, fructose, and galactose), which exist primarily in cyclic ring forms in aqueous solutions.

Glycosidic Bond

The covalent linkage formed between two monosaccharide units via a dehydration reaction to create disaccharides (such as sucrose, maltose, and lactose) and polysaccharides.

Starch

A moderately branched energy-storage polysaccharide produced by plants, composed of glucose monomers joined by linear $\alpha\text{-}1,4\text{-glycosidic}$ linkages and branching $\alpha\text{-}1,6\text{-glycosidic}$ linkages.

Glycogen

A highly branched polysaccharide used for energy storage in animal tissues, characterized by frequent $\alpha\text{-}1,6\text{-glycosidic}$ branch points that increase its aqueous solubility.

Cellulose

An unbranched, linear structural polysaccharide composed of glucose monomers linked by $\beta\text{-}1,4\text{-glycosidic}$ bonds, providing rigidity and tensile strength to plant cell walls.

Triglyceride

A lipid macromolecule formed through dehydration reactions linking one molecule of glycerol to three fatty acid chains via ester bonds, functioning primarily in long-term energy storage.

Saturated Fatty Acid

A fatty acid hydrocarbon chain devoid of double bonds where all carbon atoms are fully bonded to hydrogen atoms, permitting linear chains to pack tightly via Van der Waals forces to form solids at room temperature (e.g., stearic acid in beef fat).

Unsaturated Fatty Acid

A fatty acid hydrocarbon chain containing one or more carbon-carbon double bonds ($\text{C}=\text{C}$) that induce kinks, disrupting Van der Waals interactions and maintaining liquidity at room temperature (e.g., oleic acid in olive oil).

Phospholipid

An amphipathic lipid consisting of a glycerol backbone attached to two hydrophobic fatty acid tails and a hydrophilic head containing a negatively charged phosphate group linked to a nitrogen-containing polar group; the primary building block of cellular bilayers.

Steroid

A nonpolar lipid characterized by a core carbon framework consisting of four interconnected hydrocarbon rings (three six-membered rings and one five-membered ring), exemplified by cholesterol.

Wax

A highly nonpolar, hydrophobic lipid compound consisting of an ester formed from a long-chain fatty acid and a long-chain alcohol, serving as waterproof protective coatings on plants and structural material in bee hives.

Nucleotide

The structural monomer of nucleic acids, consisting of three covalently linked components: a five-carbon pentose sugar, a phosphate group attached at the $5'$ carbon, and a nitrogenous base attached at the $1'$ carbon.

Purine vs. Pyrimidine

The two classes of nitrogenous bases in nucleic acids: purines feature fused double-ring structures (adenine and guanine), whereas pyrimidines consist of single-ring structures (cytosine, thymine in DNA, and uracil in RNA).

Zwitterion

The dipolar, electrically neutral ionic form assumed by an amino acid in aqueous solution at neutral $\text{pH} = 7$, where the amino group is protonated ($-\text{NH}_3^+$) and the carboxyl group is deprotonated ($-\text{COO}^-$).

Peptide Bond

The covalent carbon-nitrogen ($\text{C-N}$) bond linking the carboxyl carbon of one amino acid to the amino nitrogen of another, formed during ribosomal translation via a dehydration reaction.

Primary Protein Structure

The precise linear sequence of amino acids in a polypeptide chain, extending from the N-terminus (free amino group) to the C-terminus (free carboxyl group).

Secondary Protein Structure

Repetitive localized polypeptide conformations, primarily the $\alpha\text{-helix}$ and $\beta\text{-pleated sheet}$, stabilized by intra-chain or inter-chain hydrogen bonds between backbone carbonyl oxygen and amino hydrogen atoms.

Tertiary Protein Structure

The complex three-dimensional folding of a single polypeptide chain, stabilized by interactions among side chain (R) groups including hydrogen bonds, ionic bonds (salt bridges), hydrophobic clustering, covalent disulfide bridges, and Van der Waals forces.

Quaternary Protein Structure

The multi-subunit structural arrangement formed when two or more distinct polypeptide chains associate through non-covalent or covalent interactions (e.g., hemoglobin formed as a heteromultimer of two $\alpha$ and two $\beta$ subunits).

Sickle-Cell Hemoglobin Mutation

A genetic disease resulting from a point mutation altering primary protein structure: at position $6$ of the hemoglobin $\beta$ globin chain, hydrophilic glutamic acid ($\text{Glu}$) is replaced by hydrophobic valine ($\text{Val}$), causing proteins to aggregate into fibers.

Atomic Number

The fundamental characteristic of a chemical element defined as the exact number of protons located within its atomic nucleus.

Atomic Mass

The average mass of an element's atom measured in Daltons ($\text{Da}$) or atomic mass units ($\text{a.m.u.}$), roughly equal to the total number of protons and neutrons in the nucleus.

Isotope

One of multiple structural variants of the same chemical element sharing the same atomic number (protons) but differing in the number of neutrons and atomic mass, such as $^{12}\text{C}$, $^{13}\text{C}$, and radioactive $^{14}\text{C}$.

Avogadro's Number

The fundamental constant defining the quantity of entities in one mole of any chemical substance, equal to $6.02214076 \times 10^{23}$ (commonly rounded to $6.022 \times 10^{23}$) particles.

Major Chemical Elements of the Human Body

The four predominant elements comprising approximately $96.5\%$ of human body mass: oxygen ($65\%$), carbon ($18.5\%$), hydrogen ($9.5\%$), and nitrogen ($3.5\%$).

Electronegativity

The intrinsic ability of an atom participating in a chemical bond to attract shared pairs of electrons toward its own nucleus.

Nonpolar Covalent Bond

A covalent bond formed between two atoms having an electronegativity difference ($\Delta \text{electronegativity}$) of less than $0.4$, resulting in equal electron sharing without partial charges (e.g., $\text{C-C}$ and $\text{C-H}$).

Polar Covalent Bond

A covalent bond between atoms whose electronegativity difference falls between $0.4$ and $1.8$, causing unequal electron sharing and generating partial negative ($\delta^-$) and partial positive ($\delta^+$) charges (e.g., $\text{O-H}$ and $\text{N-H}$).

Ionic Bond

An electrostatic attraction between a positively charged cation and a negatively charged anion, occurring when the electronegativity difference exceeds $1.8$ and electrons are fully transferred (e.g., $\text{Na}^+$ and $\text{Cl}^-$).

Hydrogen Bond

A weak intermolecular electrostatic attraction formed between a partially positive hydrogen atom covalently bonded to an electronegative atom and another electronegative atom (typically oxygen or nitrogen).

Van der Waals Dispersion Forces

Weak, short-range electrostatic attractions that develop between nonpolar atoms or molecules due to temporary, fluctuating asymmetrical distributions of electrons that induce transient dipoles in neighboring atoms.

Amphipathic Molecule

A chemical molecule possessing both a hydrophilic (polar or charged) region and a hydrophobic (nonpolar) region, such as phospholipids, detergents, and bile acids.

Micelle

A spherical aggregate formed by amphipathic molecules in aqueous environments, with hydrophilic heads oriented outwardly toward water and hydrophobic hydrocarbon tails sequestered within the interior core.

Molarity ($\text{M}$)

A quantitative unit of solution concentration defined as the number of moles of dissolved solute per liter of total solution ($\text{M} = \text{moles of solute} \div \text{liters of solution}$).

Specific Heat

The quantity of heat energy required to raise the temperature of $1\,\text{g}$ of a substance by $1\,^\circ\text{C}$; water possesses an unusually high specific heat due to hydrogen bonding, enabling it to resist rapid thermal fluctuations.

Cohesion and Adhesion

Complementary physical properties of water: cohesion refers to the hydrogen-bonding of water molecules to each other, generating surface tension, while adhesion is the attraction of water molecules to other polar surfaces.

pH Scale

A negative logarithmic measure of hydrogen ion concentration defined by $\text{pH} = -\log_{10}[\text{H}^+]$, where pure water possesses a neutral $\text{pH} = 7$ ($[\text{H}^+] = 10^{-7}\,\text{M}$), and each integer change signifies a $10\text{-fold}$ change in acidity.

Bicarbonate Buffer System

A physiological chemical equilibrium ($\text{CO}_2 + \text{H}_2\text{O} \rightleftharpoons \text{H}_2\text{CO}_3 \rightleftharpoons \text{H}^+ + \text{HCO}_3^-$) that prevents abrupt fluctuations in human blood pH, maintaining it strictly within the range of $7.35\text{--}7.45$.

Cell Theory

The biological doctrine formulated by Matthias Schleiden ($1838$), Theodor Schwann ($1839$), and Rudolph Virchow stating that all organisms consist of one or more cells, the cell is the fundamental unit of life, and all new cells originate from pre-existing cells via cell division.

Microscope Resolution

The capacity of an optical system to distinguish two adjacent structures as distinct and separate entities, measuring clarity; light microscopes have a resolution limit of approximately $0.2\,\mu\text{m}$, whereas transmission electron microscopes resolve down to $2\,\text{nm}$.

Transmission Electron Microscope (TEM)

A microscope that directs a beam of electrons through an ultrathin, stained biological specimen to yield high-resolution ($\sim 2\,\text{nm}$) cross-sectional micrographs of internal cellular ultrastructure.

Scanning Electron Microscope (SEM)

A microscope that sweeps an electron beam over the metal-coated surface of an intact specimen to produce detailed three-dimensional images of external cellular topography.

Protobiont

A hypothetical pre-cellular ancestor consisting of an aggregate of abiotically formed macromolecules enclosed within a boundary membrane, representing the third stage in the prebiotic origin of life.

Nucleoid

The non-membrane-enclosed region within the cytoplasm of prokaryotic cells where the genetic material (chromosomal DNA) is concentrated.

Nucleolus

A prominent, non-membrane-bound dense region within the eukaryotic nucleus dedicated to the transcription of rRNA and the assembly of ribosomal subunits.

Ribosome

A cellular ribonucleoprotein complex responsible for polypeptide synthesis; prokaryotes possess $70\text{S}$ ribosomes ($50\text{S}$ large and $30\text{S}$ small subunits), while eukaryotes possess $80\text{S}$ ribosomes ($60\text{S}$ large and $40\text{S}$ small subunits).

Rough Endoplasmic Reticulum

A network of flattened, ribosome-studded membrane cisternae involved in the synthesis, glycosylation, and cotranslational sorting of proteins targeted for the endomembrane system, lysosomes, or extracellular secretion.

Smooth Endoplasmic Reticulum

A ribosome-free membranous network functioning in the biosynthesis of lipids, steroids, and phospholipids, carbohydrate metabolism, calcium ion ($\text{Ca}^{2+}$) sequestration via SERCA pumps, and enzymatic detoxification of toxic organic compounds.

Golgi Apparatus

A polarized stack of membrane-bound cisternae consisting of cis, medial, and trans compartments that modifies, glycosylates, proteolytically processes, sorts, and packages cargo proteins and lipids into transport vesicles.

Signal Recognition Particle (SRP)

A cytosolic ribonucleoprotein complex that recognizes and binds to an emerging hydrophobic ER signal peptide on a translating ribosome, temporarily halting translation and docking the ribosome onto an ER membrane receptor.

Lysosome

A eukaryotic endomembrane digestive organelle containing acid hydrolases active at $\text{pH} \approx 5$, responsible for degrading endocytosed macromolecules, cellular debris, and damaged organelles via autophagy.

Peroxisome

A metabolic organelle that utilizes molecular oxygen to oxidize toxic compounds, yielding hydrogen peroxide ($\text{H}_2\text{O}_2$) as an intermediate ($\text{RH}_2 + \text{O}_2 \rightarrow \text{R} + \text{H}_2\text{O}_2$), which is subsequently decomposed into water and oxygen by catalase ($2\text{H}_2\text{O}_2 \rightarrow 2\text{H}_2\text{O} + \text{O}_2$).

Central Vacuole

A prominent fluid-filled organelle in plant cells that stores water, enzymes, and inorganic ions, exerting hydrostatic turgor pressure against the cell wall to maintain structural stiffness.

Contractile Vacuole

A specialized organelle found in freshwater protists (e.g., Paramecium) that periodically accumulates and expels excess hypoosmotic water to prevent osmotic cellular swelling and lysis.

Endosymbiotic Theory

The evolutionary theory asserting that eukaryotic semiautonomous organelles evolved from ancient endosymbiotic prokaryotes engulfed by ancestral cells: mitochondria originated from proteobacteria, while chloroplasts originated from cyanobacteria.

Microfilaments (Actin Filaments)

Cytoskeletal fibers measuring $7\,\text{nm}$ in diameter formed from two intertwined helical strands of actin monomers, dynamic in lengthening and shortening, and collaborating with the motor protein myosin to drive muscle contraction and cytokinesis.

Intermediate Filaments

Rope-like cytoskeletal polymers measuring $10\,\text{nm}$ in diameter that provide persistent tensile strength and mechanical stability, exemplified by keratins in epithelial tissues and nuclear lamins lining the inner nuclear membrane.

Microtubules

Hollow cytoskeletal cylinders with a diameter of $25\,\text{nm}$ composed of polymerized $\alpha\text{-tubulin}$ and $\beta\text{-tubulin}$ heterodimers, organizing spindle apparatuses during mitosis and forming the core elements of cilia, flagella, and centrioles.

Axoneme

The internal structural arrangement of eukaryotic cilia and flagella comprising an arrangement of nine outer doublet microtubules encircling a central pair ($9+2$ array), propelled by dynein motor protein arms.

Centrosome

The primary microtubule-organizing center (MTOC) in animal cells, consisting of a pair of mutually perpendicular centrioles, each constructed from nine peripheral triplets of microtubules.

Tight Junction

An occluding animal cell junction composed of claudin proteins forming continuous seals between adjacent plasma membranes, preventing the leakage of extracellular solutes across epithelial layers (e.g., in the urinary bladder and skin).

Desmosome

An anchoring animal cell junction consisting of transmembrane cadherin proteins linked to intracellular protein plaques and keratin intermediate filaments, conferring strong mechanical adhesion against shear stress in heart and skin tissues.

Gap Junction

A communicating animal cell junction formed by ring-like complexes of six connexin proteins (connexons) creating an open hydrophilic channel between neighboring cells to allow direct diffusion of ions and small signaling molecules.

Plasmodesma

A membrane-lined cytoplasmic channel perforating the plant cell wall, establishing cytoplasmic continuity and facilitating symplastic transport of water and small solutes between adjacent plant cells.

Extracellular Matrix (ECM)

An intricate network of extracellular proteins (such as collagen and fibronectin) and carbohydrate-rich proteoglycans that binds animal cells together, provides structural support, and mediates intercellular communication.