Biological and Molecular Organization of Life

Vocabulary practice flashcards covering cell theory, taxonomy, microbiology, virology, biomolecules, structural biochemistry, and basic genetics based on lecture notes.

Taxonomy

The branch of biology concerned with the identification and classification of living organisms.

Binomial Nomenclature

The universal classification system devised by Carolus Linnaeus that uniquely identifies a species using two names: the genus (e.g., Homo) and the species epithet (e.g., sapiens).

Three Domains of Life

The primary taxonomic groups consisting of Bacteria (unicellular prokaryotes), Archaea (ancient prokaryotes adapted to extreme environments), and Eukarya (divided into protists, fungi, plants, and animals).

Cell Theory

The foundational biological doctrine updated by Virchow (1855) stating that all living organisms are composed of one or more cells, the cell is the smallest functional unit of life, new cells arise only from pre-existing cells, genetic material (DNA) is passed on via cell division, and all vital metabolic functions take place inside cells.

Virion

An individual, fully formed infectious viral particle located outside a host cell, capable of surviving temporarily in the external environment.

Bacteriophage

A virus that specifically infects bacteria, typically featuring a head (capsid) containing DNA, a collar, a central core sheath, a baseplate, and tail fibers.

Capsid

The protective protein shell surrounding viral nucleic acid, composed of repeating protein subunits called capsomeres that self-assemble into helical, icosahedral, or complex structures.

Class I Viruses (Baltimore)

Double-stranded DNA ($dsDNA$) viruses that utilize the host cell's DNA polymerase for genomic replication and host RNA polymerase for transcription (e.g., Herpesvirus, Adenovirus, Poxvirus).

Class VI Viruses (Baltimore)

Single-stranded RNA reverse-transcribing ($ssRNA\text{-}RT$) viruses, such as HIV, that use a viral reverse transcriptase enzyme to convert single-stranded RNA into DNA, which then integrates into the host cell genome as a provirus.

Lytic Cycle

A viral replication pathway in which a virulent virus immediately hijacks host cell metabolism, replicates its nucleic acid, synthesizes structural proteins, and releases progeny virions by destroying (lysing) the host cell.

Lysogenic Cycle

A viral replication pathway in which a temperate virus integrates its viral DNA into the host chromosome as a profage, remaining latent and replicating silently along with host cell division until an environmental trigger initiates the lytic cycle.

Reverse Transcriptase

A viral enzyme unique to retroviruses that synthesizes a complementary strand of DNA using a single-stranded viral RNA template.

Provirus

The viral DNA intermediate formed by reverse transcription that has been integrated into the host cell's nuclear DNA genome.

Plasmids

Small, circular, self-replicating extrachromosomal DNA molecules found in prokaryotes, categorized into metabolic, resistance, and conjugation plasmids.

Peptidoglycan (Murein)

A structural polymer consisting of alternating aminosugars N-acetylglucosamine (NAG) and N-acetylmuramic acid (NAM) linked by $\beta\text{-1,4}$ glycosidic bonds and cross-linked by amino acid chains, forming the rigid bacterial cell wall.

Gram Staining

A differential staining procedure that distinguishes Gram-positive bacteria (purple, due to a thick peptidoglycan wall retaining crystal violet-iodine complex) from Gram-negative bacteria (pink, due to a thin peptidoglycan layer and an outer lipopolysaccharide membrane decolorized by alcohol and counterstained by safranin).

Archaea

A domain of prokaryotic organisms lacking peptidoglycan in their cell walls, possessing ether-linked membrane lipids, and frequently thriving in extreme environmental conditions as thermophiles, halophiles, or methanogens.

Bacterial Transformation

A mechanism of horizontal gene transfer in which a competent bacterial cell takes up free DNA or RNA fragments from its environment released by dead, lysed bacteria and integrates them into its genome.

Bacterial Conjugation

The direct horizontal transfer of genetic material (usually plasmids) between two bacterial cells via direct physical contact mediated by a sex/conjugation pilus using a rolling circle replication mechanism.

Bacterial Transduction

A mechanism of horizontal gene transfer in which a bacteriophage virus transfers a fragment of host DNA from one bacterium to another during viral infection.

Fluid Mosaic Model

The structural model of biological membranes proposed by Nicolson in 1972, describing a dynamic phospholipid bilayer containing embedded proteins and carbohydrates capable of lateral movement.

Glycocalyx

A carbohydrate-rich coating located on the extracellular face of the plasma membrane, composed of glycoproteins, glycolipids, and proteoglycans, involved in cell recognition, protection, and blood type determination.

Endosymbiotic Theory

An evolutionary theory stating that eukaryotic organelles such as mitochondria and chloroplasts originated from free-living aerobic or photosynthetic prokaryotes that were engulfed by a larger ancestral host cell.

Glycogen

A highly branched storage polysaccharide in animals composed of glucose monomers connected by $\text{alpha-1,4}$ glycosidic bonds with $\text{alpha-1,6}$ branch points occurring every $8$ to $10$ residues.

Starch

A plant storage polysaccharide consisting of unbranched amylose ($\text{alpha-1,4}$ glycosidic bonds) and branched amilopectin ($\text{alpha-1,4}$ and $\text{alpha-1,6}$ glycosidic bonds with branches every $24$ to $30$ glucose residues).

Cellulose

An unbranched structural polysaccharide in plant cell walls composed of $\beta\text{-D-glucose}$ monomers joined by $\beta\text{-1,4}$ glycosidic bonds.

Zwitterion

A dipolar amino acid ion present at neutral pH, containing a positively charged amino group ($\text{-NH}_3^+$) and a negatively charged carboxyl group ($\text{-COO}^-$) with a net charge of zero.

Peptide Bond

A planar, polar, covalent bond formed between the carboxyl group of one amino acid and the amino group of another via a condensation reaction, removing one molecule of water.

Primary Structure of Proteins

The specific linear sequence of amino acids joined together by covalent peptide bonds in a polypeptide chain.

Secondary Structure of Proteins

Regular local folding patterns within a polypeptide chain, such as $\text{alpha-helices}$ and $\beta\text{-sheets}$, stabilized by hydrogen bonds between non-consecutive backbone residues.

Tertiary Structure of Proteins

The overall three-dimensional shape of a single polypeptide chain, stabilized by side-chain ($R$ group) interactions including ionic bonds, hydrogen bonds, hydrophobic interactions, and covalent disulfide bridges between cisteines.

Kinase

An enzyme that catalyzes the transfer of a phosphate group from ATP to a specific amino acid residue (serine, threonine, or tyrosine) on a target protein.

Phosphatase

An enzyme that removes a phosphate group from a target protein through a hydrolysis reaction (dephosphorylation).

Triglycerides

Nonpolar, hydrophobic lipids formed by three fatty acids esterified to a single glycerol molecule via condensation reactions, serving as long-term energy storage.

Phospholipids

Amphipathic membrane lipids consisting of a glycerol molecule linked to two hydrophobic fatty acid tails and a hydrophilic phosphate head group bonded to a small polar molecule like choline.

Steroids

Non-saponifiable lipid molecules containing a characteristic core structure of four fused carbon rings (cyclopentanoperhydrophenanthrene), such as cholesterol and steroid hormones.

Phosphodiester Bond

The covalent link in nucleic acids formed between the 5' phosphate group of one nucleotide and the 3' hydroxyl group of the adjacent sugar monomer.

B-DNA

The standard right-handed double-helical conformation of normal cellular DNA, characterized by antiparallel strands, a diameter of $2\text{ nm}$, a helical pitch of $3.4\text{ nm}$ ($10\text{ bp}$ per turn), and complementary base pairing.

Ubiquitination

A post-translational modification in which ubiquitin molecules are sequentially attached to target protein lysine residues via E1, E2, and E3 enzymes to target the protein for degradation by the proteasome.

Anabolism

Endergonic metabolic processes involving the synthesis of complex molecules from simpler precursors, requiring an input of chemical energy.

Catabolism

Exergonic metabolic processes involving the enzymatic breakdown of complex organic molecules into simpler compounds, releasing usable chemical energy.

Nuclear Envelope

A double-membrane system surrounding the eukaryotic cell nucleus, consisting of an outer membrane continuous with the rough endoplasmic reticulum and an inner membrane supported by the nuclear lamina, pierced by nuclear pore complexes.