Cellular and Molecular Biology: Evolution, Genetics, DNA Structure, Replication, and Microbiology

Comprehensive vocabulary flashcards covering the evolutionary framework, phylogenetics, testing of Darwin's postulates, the Human Genome Project, the history of genetics, DNA structure, the enzymology of DNA replication, and microbial physiology.

Provisional Nature of Science

The foundational scientific principle that all scientific concepts, theories, and models are open to revision or replacement when confronted with new experimental or observational data.

TACK Superphylum

An archaeal superphylum comprising Thaumarchaeota, Aigarchaeota, Crenarchaeota, and Korarchaeota that shares features with eukaryotes previously thought to be eukaryotic-specific, including proteins for cytokinesis, cell shape determination, protein recycling, and membrane remodelling.

Asgard Archaea

A group of archaea identified by Hug et al. (2016) through comparative sequencing of $16$ ribosomal proteins as the closest known prokaryotic relatives of eukaryotes.

Intromission Theory

The optical framework described by Alhazen (Abū ʿAlī al-Ḥasan ibn al-Ḥasan ibn al-Haytham) in the Kitāb al-Manāẓir (Book of Optics) demonstrating that vision occurs in the brain when light travels in straight lines and reflects from external objects into the eyes, overturning Plato's emission theory.

Principle of Parsimony (Occam's Razor)

A guiding heuristic attributed to William of Ockham stating that when faced with multiple explanations for an observation, one should select the hypothesis requiring the fewest assumptions until contradictory data arise.

Darwin's Postulates of Natural Selection

The three logical principles underlying evolution by natural selection: (1) individuals within a species are variable; (2) at least some of this variation is heritable; and (3) reproduction is non-random, with individuals bearing favourable variations reproducing the most.

Darwin's Finches (John Gould Illustration)

Specimens of Galápagos finches collected by Charles Darwin and illustrated by ornithologist John Gould (1845) demonstrating variation in beak size and shape among closely related island populations.

Artificial Selection in Brassica oleracea

The process by which selective breeding of wild mustard generated distinct agricultural crops by selecting specific plant structures: terminal buds (cabbage), lateral buds (Brussels sprouts), stems (kohlrabi), leaves (kale), flower clusters (cauliflower), and flowers/stems (broccoli).

Synapomorphy

A shared derived character state that evolved in the most recent common ancestor of two or more taxa and is used in cladistics to establish monophyletic groups.

Autapomorphy

A derived phenotypic trait unique to a single terminal taxon that does not provide grouping information for inferring relationships with other taxa.

Homology

Structural or genetic similarity between different taxa attributable to inheritance from a shared common ancestor, such as the mammalian forelimb bones found in human hands and whale flippers.

Homoplasy

A shared phenotypic similarity between taxa that did not originate from a common ancestor, typically arising independently via convergent evolution (such as streamlined bodies and fins in fish, marine reptiles, and whales).

Monophyletic Group (Clade)

A cladistic grouping that comprises an ancestral lineage and all of its descendants, definable by a single cut across a phylogenetic tree.

Paraphyletic Group

A taxonomic group containing a common ancestor and some, but not all, of its descendants, such as traditional classifications of 'fish' (which exclude tetrapods) or 'Reptilia' (which exclude birds).

Involucrum

A thickened, dense bony structure of the auditory bulla that serves as a cetacean synapomorphy specialized for underwater hearing.

Astragalus (Talus)

The double-pulley ankle bone that acts as a diagnostic synapomorphy of artiodactyls, providing morphological evidence linking early fossil whales (Pakicetus) to terrestrial artiodactyls.

Daphne Major Geospiza fortis Study

Field research conducted by Rosemary and Peter Grant (1976–1978) demonstrating natural selection in action: a severe drought reduced seed abundance and increased seed hardness, causing directional selection that increased the average beak depth of surviving medium ground finches.

Melanism in Hyla orientalis

An adaptive evolutionary shift documented by Burraco and Orizaola (2022) wherein Eastern tree frogs inhabiting the Chornobyl exclusion zone exhibit darker skin coloration than frogs from outside the zone, driven by the protective role of melanin against ionizing radiation.

Genetic Drift

Random fluctuations in allele frequencies within a population across successive generations due to stochastic sampling error during gamete transmission, exerting its strongest effects in small populations.

Long-Term Evolution Experiment (LTEE)

An experimental evolution investigation initiated by Richard Lenski on February 24, 1988, propagating $12$ isolated populations of Escherichia coli ($6\,\text{Ara}^+$ and $6\,\text{Ara}^-$) by daily $1/100$ serial transfers in glucose-limited medium containing citrate.

$\text{Cit}^+$ Phenotype

A novel metabolic capability that evolved in the Ara-3 population of Lenski's LTEE through gene duplication of the citrate transporter, deregulating its expression and allowing aerobic utilization of citrate.

Gene Flow

The transfer of genetic alleles between previously separated populations resulting from the migration of breeding individuals or the movement and fertilization of gametes (such as pollen).

London Underground Mosquito (Culex molestus)

A subterranean mosquito lineage that diverged from the aboveground bird-biting Culex pipiens pipiens, characterized by biting mammals, breeding continuously without a required blood meal, mating in enclosed spaces without swarming, and remaining active during winter.

Big Bird Lineage

A distinct, reproductively isolated homoploid hybrid species that arose on Daphne Major following the arrival in 2016 of an immigrant male Geospiza conirostris from Isla Española ($100\,\text{km}$ away), which mated with local Geospiza fortis females and subsequently inbred.

Whole-Genome Shotgun Sequencing

The genomic sequencing strategy employed by J. Craig Venter's laboratory at TIGR to publish the first complete organismal cellular genome, Haemophilus influenzae Rd ($1.8\,\text{Mbp}$), in 1995.

Human Genome Project (HGP)

An international scientific effort proposed in 1986, started in 1990, and completed on April 14, 2003, which sequenced $99\%$ of the euchromatic human genome at $99.99\%$ accuracy, discovering that only ~$1.5\%$ of the $3.2 \times 10^9\,\text{bp}$ genome encodes ~$22,000$ proteins.

BRCA1 Gene

A human tumor suppressor gene encoding a DNA repair protein whose pathogenic mutations increase lifetime breast cancer risk from $12.5\%$ to $60-90\%$ and ovarian cancer risk from $1.9\%$ to $11-40\%$.

Central Dogma of Molecular Biology

The sequence-hypothesis framework formulated by Francis Crick (1958, 1970) asserting that residue-by-residue information transfers from DNA to RNA and from RNA to protein, but cannot transfer out of protein back into nucleic acid or protein.

Law of Segregation (Mendel's First Law)

The genetic principle stating that the two coexisting hereditary factors (alleles) of an individual for any given trait separate during gamete formation so that each gamete carries only one allele.

Chromosome Theory of Inheritance

The concept advanced by Walter Sutton (1902) following cytological studies of Brachystola magna grasshoppers, postulating that Mendel's paired hereditary factors reside on homologous maternal and paternal chromosomes that segregate during meiosis.

Sex-Linked Inheritance

The pattern of inheritance established by Thomas Hunt Morgan (1910) using white-eyed Drosophila melanogaster, demonstrating that the eye color gene resides on the X chromosome and is absent from the Y chromosome.

Tetranucleotide Hypothesis

The incorrect structural model proposed by Phoebus Levene (~1909, ~1930) claiming that DNA consists of simple, repeating four-base units with outward-facing bases, leading early biochemists to reject DNA as the genetic material.

Chargaff's Rules

Empirical base ratios formulated by Erwin Chargaff (1950) establishing that in native double-stranded DNA, the proportion of adenine equals thymine ($\text{\%}A = \text{\%}T$) and guanine equals cytosine ($\text{\%}G = \text{\%}C$), while the total $\text{\%}GC$ content varies among species.

Photo 51

The X-ray diffraction photograph of hydrated B-form DNA taken in 1952 by Rosalind Franklin and Raymond Gosling, displaying an unambiguous cross-shaped pattern indicative of a helical structure.

B-DNA

The standard physiological conformation of DNA characterized by a right-handed double helix, a diameter of ~$2\,\text{nm}$, base pairs spaced $0.34\,\text{nm}$ apart, and $10.5$ base pairs per turn ($3.6\,\text{nm}$ pitch).

Major Groove

The wider and deeper of the two helical depressions running along the outer surface of B-DNA, where functional chemical groups of the base pairs are exposed and accessible to sequence-specific DNA-binding proteins.

Z-DNA

A left-handed double-helical conformation of DNA that forms under physiological conditions in alternating purine-pyrimidine tracts, with a diameter of ~$1.8\,\text{nm}$ and $12$ base pairs per helical turn.

A-DNA

A right-handed double-helical form of DNA found under low-hydration conditions, featuring a diameter of ~$2.6\,\text{nm}$, $11$ base pairs per turn, and a base tilt of $20^\circ$ relative to the central axis.

Semi-Conservative Replication

The mechanism of DNA replication wherein each newly produced duplex comprises one intact parental strand and one newly synthesized daughter strand.

CsCl Equilibrium Density Gradient Centrifugation

An ultracentrifugation method introduced by Matthew Meselson and Franklin Stahl (1958) that generates a density gradient to resolve heavy ($^{15}\text{N}$), hybrid ($^{14}\text{N}/^{15}\text{N}$), and light ($^{14}\text{N}$) isotopic DNA species.

Nearest-Neighbour Frequency Analysis

An enzymatic method devised by Arthur Kornberg using $\alpha\text{-}^{32}\text{P}$-labeled dNTPs and specific phosphodiesterase digestion to transfer the radioactive phosphate to the adjacent $5'$ nucleotide, proving that the two DNA strands are antiparallel.

DNA Polymerase I (Pol I)

A bacterial polymerase isolated by Arthur Kornberg that possesses $5' \rightarrow 3'$ DNA polymerase, $3' \rightarrow 5'$ proofreading exonuclease, and $5' \rightarrow 3'$ primer-removal exonuclease activities, primarily involved in DNA repair and Okazaki fragment processing.

DNA Polymerase III (Pol III)

The primary bacterial replisome polymerase discovered by Thomas Kornberg, characterized by high synthesis rates when clamped (~$1000\,\text{bases/s}$), $3' \rightarrow 5'$ proofreading exonuclease activity, and an absence of $5' \rightarrow 3'$ exonuclease activity.

Proofreading ($3' \rightarrow 5'$ Exonuclease)

A catalytic activity localized in the palm domain of replicative DNA polymerases that excises terminal mispaired nucleotides to generate a correctly base-paired $3'\text{-OH}$ primer terminus before elongation resumes.

Okazaki Fragments

Short stretches of DNA synthesized discontinuously in the $5' \rightarrow 3'$ direction on the lagging strand, measuring ~$1000-2000$ nucleotides in E. coli and ~$100-200$ nucleotides in eukaryotes.

DNA Primase

A rifampicin-sensitive DNA-directed RNA polymerase that synthesizes short RNA primers (~$10-12$ nucleotides) complementary to template DNA to initiate both leading-strand and lagging-strand synthesis.

$\beta$ Clamp (Sliding Clamp)

A ring-shaped homodimeric protein complex loaded onto DNA by the clamp loader that anchors the Pol III core to the template, increasing its processivity to allow synthesis of long DNA stretches.

Trombone Model

The architectural model of the bacterial replisome where the lagging strand template forms a loop that expands and releases during each cycle of Okazaki fragment synthesis, allowing the two tethered Pol III cores to synthesize DNA synchronously.

Single-Stranded DNA-Binding Protein (SSB)

A protective replisome protein that binds selectively to exposed single-stranded DNA to prevent nuclease degradation and prevent the formation of disruptive intramolecular stem-loop structures.

Type II Topoisomerase (DNA Gyrase)

An ATP-dependent bacterial enzyme that relieves positive supercoiling ahead of the replication fork by generating a double-strand break, passing a DNA loop through the break, and resealing the cut to introduce negative supercoils.

Type I Topoisomerase

An enzyme that binds negatively supercoiled DNA, makes a transient nick in a single DNA strand, allows swivel relaxation, and religates the strand to yield relaxed DNA.

Topoisomerase IV

A bacterial type II topoisomerase that resolves catenated (interlinked) circular daughter chromosomes following bi-directional DNA replication.

Telomerase

A ribonucleoprotein reverse transcriptase carrying an internal RNA template that elongates the $3'$ ends of eukaryotic lagging-strand templates, preventing progressive chromosome shortening during cell division.

Photolithoautotroph

A metabolic classification for organisms (such as cyanobacteria and plants) that capture energy from light, use inorganic compounds (such as $\text{H}_2\text{O}$) as electron donors, and fix inorganic $\text{CO}_2$ as their primary carbon source.

Chemoorganoheterotroph

A metabolic classification for organisms (such as Escherichia coli and animals) that derive energy from chemical bonds and utilize organic compounds as both electron donors and carbon sources.

Chemolithoautotroph

A metabolic classification for organisms (such as Thiobacillus spp.) that derive energy from chemical bonds, utilize reduced inorganic compounds as electron donors, and fix inorganic $\text{CO}_2$ as a carbon source.

Defined Medium (Synthetic Medium)

A microbial growth medium in which the exact chemical identity and concentration of every constituent substance is known and specified.

Complex Medium

A nutrient-rich culture medium containing chemically undefined biological digests (such as yeast extract and peptone in Luria broth), useful for cultivating organisms whose exact nutritional requirements are uncharacterized.

Selective Medium

A culture medium formulated with specific chemical agents or physical conditions that permit the proliferation of designated microorganisms while inhibiting the growth of non-target organisms.

Differential Medium

A culture medium incorporating biochemical indicators that allow visually distinguishable growth patterns (such as coloration) to differentiate specific microbial metabolic traits among colonies.

Total Viable Count

A quantitative microbiological enumeration technique that calculates the number of viable, dividing bacterial cells in a sample by counting colony-forming units (CFU) grown after serial dilution plating.