OpenStem

@openstem · Joined Jul 2026

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List the major categories of prezygotic isolating mechanisms.1 / 10

Prezygotic mechanisms prevent mating or fertilization from occurring at all: habitat isolation (populations occupy different habitats and rarely meet), temporal isolation (breeding at different times of day, season, or year), behavioral isolation (differing courtship displays or mating signals not recognized between groups), mechanical isolation (incompatible reproductive structures), and gametic isolation (sperm and egg are incompatible at a biochemical level even if mating is attempted, as in many broadcast-spawning marine invertebrates).

Biology

Biology · L4 · Reproductive Isolation and Species Boundaries

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Distinguish endothermy from ectothermy, and homeothermy from poikilothermy.1 / 10

Endothermy vs ectothermy describes the heat source: endotherms generate most of their body heat metabolically (e.g. via mitochondrial uncoupling and shivering), while ectotherms rely mainly on external heat sources and behavior. Homeothermy vs poikilothermy describes the outcome: homeotherms keep body temperature nearly constant, poikilotherms let it fluctuate with the environment. Most endotherms are homeothermic and most ectotherms are poikilothermic, but the two axes are logically independent (e.g. some fish are regional endotherms yet still poikilothermic overall).

Biology

Biology · L4 · Thermoregulation Mechanisms

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Distinguish osmoconformers from osmoregulators.1 / 10

Osmoconformers (mostly marine invertebrates) keep their internal osmolarity matched to that of the surrounding seawater, so they face no net osmotic gradient and expend little energy on osmotic work, but they cannot tolerate large salinity changes. Osmoregulators (most vertebrates) actively maintain an internal osmolarity different from their environment using energy-dependent transport, which costs more but allows them to occupy habitats with fluctuating or extreme salinity, such as freshwater or estuaries.

Biology

Biology · L4 · Osmoregulation and Excretion

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What are the core components of a eukaryotic RNA polymerase II promoter, and what is the role of the TATA box?1 / 10

The core promoter includes the transcription start site and nearby elements such as the TATA box (a conserved AT-rich sequence typically ~25-30 base pairs upstream of the start site in many genes). The TATA box is bound by TATA-binding protein (TBP), a subunit of the general transcription factor TFIID, which nucleates assembly of the rest of the general transcription machinery (TFIIA, B, D, E, F, H) and RNA polymerase II into the preinitiation complex. Not all genes have a strong TATA box; many, especially housekeeping genes, instead use alternative core elements (e.g. Initiator, DPE) for polymerase recruitment.

Biology

Biology · L4 · Promoters, Enhancers, and Transcription Factors

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What structural components are shared by essentially all viruses, and which components are present only in some?1 / 10

Every virus has a genome (DNA or RNA, single- or double-stranded) enclosed within a protein capsid built from repeating protein subunits (capsomeres), which protects the genome and, in many viruses, mediates initial attachment to a host cell. Some viruses additionally have an envelope, a lipid bilayer derived from host membrane and studded with viral glycoproteins, acquired as the virus buds through a host membrane; enveloped viruses generally require the envelope to remain intact for infectivity and are more sensitive to desiccation and detergents than non-enveloped viruses, which rely on a more physically robust capsid alone.

Biology

Biology · L4 · Virus Structure and Replication Strategies

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Describe the lac operon regulatory mechanism in E. coli, including the roles of the repressor, inducer, and catabolite activator protein.1 / 5

The lac operon comprises lacZ, lacY, and lacA under a single promoter. In the absence of lactose the LacI repressor binds the operator (O1, O2, O3 sites) and blocks transcription. Allolactose (the true inducer, formed from lactose by β-galactosidase) binds LacI, causing allosteric release from the operator.

Biology

Biology · L5 · Gene Regulation & Epigenetics

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Derive the Hardy–Weinberg genotype frequencies from allele frequencies p and q.1 / 5

Let A and a be two alleles with frequencies p and q = 1 − p respectively (so p + q = 1). Under random mating, gametes pair independently. Treating gamete union as sampling with replacement:

Biology

Biology · L5 · Population Genetics

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What structural feature is shared by all ATP-dependent chromatin remodeling complexes, and how does it couple ATP hydrolysis to nucleosome mobilization?1 / 9

All four remodeler families (SWI/SNF, ISWI, CHD, INO80) share a Snf2-family ATPase motor built from two RecA-like lobes homologous to DExH-box helicases. ATP binding and hydrolysis in the cleft between the lobes drives a conformational cycle that translocates DNA relative to the histone octamer — the motor engages DNA roughly two helical turns from the nucleosome dyad and pumps a DNA loop across the octamer surface, propagating as a wave that repositions the nucleosome without releasing histone–DNA contacts entirely.

Biology

Biology · L5 · Chromatin Remodeling Complexes & the Histone Code

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Outline the mechanism by which the lncRNA Xist silences an entire X chromosome in cis.1 / 9

Xist is transcribed from the X-inactivation center (Xic) on the future inactive X and, unlike most lncRNAs, acts exclusively in cis — it does not diffuse to the homologous active X. Xist RNA coats the chromosome from which it is transcribed, spreading outward from the Xic through direct RNA–chromatin contacts assisted by proteins such as SPEN/SHARP, which recruits the NCoR/SMRT–HDAC3 corepressor complex to trigger initial histone deacetylation and Pol II eviction.

Biology

Biology · L5 · Non-Coding RNA and Genomic Imprinting

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Contrast short-read (Illumina) and long-read (PacBio, Oxford Nanopore) sequencing platforms in terms of read length, throughput, per-base error rate, and characteristic use cases.1 / 10

Illumina sequencing-by-synthesis produces reads of 50-300 bp with very high per-base accuracy (Q30, roughly 0.1% error) and very high throughput (hundreds of gigabases per run at low per-base cost), dominated by substitution errors. It is the workhorse for SNP/small-indel calling, RNA-seq, and population-scale resequencing.

Biology

Biology · L5 · Next-Generation Sequencing

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What is a genome-wide association study (GWAS), and what statistical model is typically fit at each variant to test for association with a binary disease phenotype?1 / 10

A GWAS tests hundreds of thousands to millions of common genetic variants (typically SNPs) across the genome for statistical association with a trait or disease in a large cohort, without any prior hypothesis about which genes are involved.

Biology

Biology · L5 · Genome-Scale Analysis

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In X-ray crystallography, why must a protein be crystallised, and what physical quantity is actually measured in the diffraction experiment?1 / 9

A single protein molecule scatters X-rays far too weakly to detect. A crystal is a periodic lattice of billions of identically oriented copies of the molecule; their scattered waves interfere constructively only along discrete directions defined by the lattice (Bragg's law, nλ = 2d sinθ), amplifying the signal into measurable diffraction spots (reflections).

Biology

Biology · L5 · Experimental Structure Determination

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What problem do molecular chaperones solve, and why is co-translational folding especially vulnerable to this problem?1 / 10

A nascent polypeptide emerging from the ribosome exposes hydrophobic core residues that, in the folded native state, would be buried away from solvent. In the crowded cytoplasm (protein concentrations of 200–300 mg/mL), these exposed hydrophobic surfaces are strongly prone to non-specific aggregation with other unfolded or partially folded chains before folding can complete.

Biology

Biology · L5 · Molecular Chaperones & Protein Quality Control

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Distinguish a proto-oncogene from an oncogene in terms of gene dosage and dominance.1 / 10

A proto-oncogene is a normal cellular gene (often encoding a growth factor, receptor, signal transducer, or transcription factor) that promotes proliferation under tight regulatory control. An oncogene is a mutant, constitutively active or overexpressed allele of that gene. Oncogenic activation is functionally dominant — a single mutant allele, in the presence of a normal wild-type allele, is sufficient to drive transformation, in contrast to the typically recessive behavior of tumor-suppressor loss.

Biology

Biology · L5 · Oncogenes and Tumor Suppressors

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What are the six original hallmarks of cancer proposed by Hanahan and Weinberg (2000), and what two enabling characteristics were later added?1 / 9

The 2011 update added genome instability and mutability, and tumor-promoting inflammation as enabling characteristics that accelerate acquisition of the core hallmarks, plus deregulated cellular energetics (the Warburg effect) and evading immune destruction as emerging hallmarks.

Biology

Biology · L5 · The Hallmarks of Cancer

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What is central tolerance, and where does the deletion of self-reactive T cells occur?1 / 9

Central tolerance is the process by which developing lymphocytes with receptors reactive to self-antigens are purged or functionally silenced within the primary lymphoid organs before entering the peripheral repertoire. For T cells this occurs in the thymic medulla, where double-positive (CD4+CD8+) thymocytes that have survived positive selection encounter self-peptide–MHC complexes presented by medullary thymic epithelial cells (mTECs) and dendritic cells.

Biology

Biology · L5 · Immune Tolerance

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Which transcription factor and signature cytokines define the Th1 helper T-cell lineage, and what is its principal effector role?1 / 8

Th1 differentiation is driven by IL-12 (from activated dendritic cells/macrophages) and IFN-γ signalling through STAT4 and STAT1 respectively, which together induce the master regulator T-bet (TBX21). T-bet reinforces IFN-γ production and represses alternative lineage programmes, creating a positive feedback loop.

Biology

Biology · L5 · Cytokine Signaling Networks

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Describe the two-step mechanism by which NMDA receptor activation requires both glutamate binding and postsynaptic depolarization — the basis of coincidence detection.1 / 10

NMDA receptors are simultaneously ligand-gated and voltage-gated. At resting membrane potential, an extracellular Mg2+ ion occludes the channel pore, so glutamate binding alone is insufficient to permit ion flow. Only when the postsynaptic membrane is substantially depolarized — typically by concurrent, strong AMPA receptor activation from repetitive presynaptic firing — is the Mg2+ ion electrostatically expelled from the pore, permitting Ca2+ and Na+ influx.

Biology

Biology · L5 · Synaptic Plasticity

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Describe the amyloidogenic processing pathway of amyloid precursor protein (APP) that generates amyloid-beta (Aβ) peptides in Alzheimer's disease.1 / 10

APP is processed via two competing pathways. In the non-amyloidogenic pathway, alpha-secretase cleaves APP within the Aβ domain, precluding Aβ formation. In the amyloidogenic pathway, beta-secretase (BACE1) first cleaves APP at the N-terminus of the Aβ domain, releasing soluble APPβ and leaving a membrane-bound C99 fragment.

Biology

Biology · L5 · Neurodegenerative Disease Mechanisms

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What is deep homology, and why did it force a revision of how comparative biologists think about morphological novelty?1 / 10

Deep homology is the conservation of the same underlying gene regulatory circuitry across lineages whose morphological structures are not themselves homologous by classical criteria — the structures may have arisen independently, but the genetic machinery that builds them was inherited from a common ancestor and redeployed. The Pax6/eyeless case is paradigmatic: insect compound eyes and vertebrate camera eyes were long treated as textbook convergent evolution, yet both are built under the control of orthologous Pax6-class transcription factors. Deep homology reframes 'independent evolution' claims — the toolkit gene is homologous even when the resulting organ's architecture is not, so morphological convergence at the anatomical level can sit atop genetic conservation at the regulatory level.

Biology

Biology · L5 · The Conserved Developmental Toolkit

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What is heterochrony, and why is it treated as a distinct category of evolutionary mechanism from changes in gene content?1 / 10

Heterochrony is evolutionary change in the relative timing or rate of developmental events between an ancestor and its descendant — the same developmental program runs, but earlier, later, faster, slower, or for a longer or shorter duration. It is mechanistically distinct because it requires no new genes and no new gene products, only altered regulation of when and how long existing developmental processes operate; a shift in a single regulatory threshold (e.g., the timing of growth-plate closure or of onset of sexual maturity) can cascade into substantial morphological divergence, making heterochrony a comparatively 'cheap' route to evolutionary novelty.

Biology

Biology · L5 · Mechanisms of Morphological Evolution

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State the neutral theory's core claim about the rate of molecular evolution, and identify the population-genetic result it rests on.1 / 10

Kimura's neutral theory holds that the overwhelming majority of nucleotide substitutions fixed over evolutionary time are selectively neutral or nearly neutral, not adaptive. It rests on the classical result that, for a strictly neutral allele, the rate of substitution per generation equals the neutral mutation rate μ, independent of population size — because a larger population produces proportionally more new neutral mutations (2Nμ per generation, diploid) but each has proportionally lower probability of fixation (1/(2N)), and the two effects exactly cancel.

Biology

Biology · L5 · The Molecular Clock

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What is the fundamental distinction between distance-based and character-based methods of phylogenetic tree construction?1 / 10

Distance-based methods first reduce the full character (sequence) data to a single pairwise distance matrix and then build a tree that best fits those distances (e.g. minimizing total branch length or satisfying additivity). Character-based methods instead evaluate candidate trees directly against the original character-state data (individual sites), retaining information about which specific characters support which groupings rather than collapsing everything into a scalar distance.

Biology

Biology · L5 · Phylogenetic Tree Construction

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What is a standardized biological part (e.g., a BioBrick), and why does standardization matter for genetic engineering at scale?1 / 10

A standardized biological part is a DNA sequence encoding a defined biological function (promoter, RBS, coding sequence, terminator) that is characterized under a common set of conditions and packaged with uniform physical interfaces (e.g., BioBrick RFC10 flanking restriction sites: EcoRI/XbaI upstream, SpeI/PstI downstream) so parts can be assembled interchangeably without re-engineering junctions.

Biology

Biology · L5 · Synthetic Biology Design Principles

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Describe the general design of a whole-cell biosensor for environmental heavy-metal detection, using the arsenic biosensor as an example.1 / 10

A whole-cell biosensor couples a natural or engineered ligand-responsive transcription factor to a reporter output. The classic arsenic biosensor places a fluorescent or bioluminescent reporter (e.g., gfp, the lux operon) under control of the arsenic-responsive promoter PADS, repressed by ArsR in the absence of arsenite and de-repressed once arsenite binds ArsR and releases it from the operator.

Biology

Biology · L5 · Synthetic Biology Applications

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Define totipotency, and identify the specific developmental window during which totipotent cells exist in the mammalian embryo.1 / 10

A totipotent cell can generate every cell type of the resulting organism, including both the embryonic lineages (all three germ layers) and the extraembryonic lineages (trophectoderm/placenta, primitive endoderm/yolk sac). In mammals, totipotency is restricted to the zygote and the blastomeres of the very early cleavage-stage embryo, up to approximately the 8-cell stage in humans.

Biology

Biology · L5 · Stem Cell Types and Potency

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What did Takahashi and Yamanaka demonstrate in 2006, and what are the four original Yamanaka factors?1 / 10

Takahashi and Yamanaka showed that forced retroviral expression of just four transcription factors, Oct4, Sox2, Klf4, and c-Myc, collectively OSKM, is sufficient to reprogram a terminally differentiated mouse fibroblast into an induced pluripotent stem cell functionally and molecularly resembling an embryonic stem cell.

Biology

Biology · L5 · Reprogramming and Regenerative Biology

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List at least six of the widely cited 'hallmarks of aging' and briefly describe one of them in mechanistic detail.1 / 9

Biology

Biology · L5 · Aging Biology and Cellular Senescence

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Describe the core molecular machinery of macroautophagy, from autophagosome nucleation through the ULK1 and PI3K class III complexes to elongation via the ATG12-ATG5-ATG16L1 and LC3 conjugation systems.1 / 9

Autophagy initiation begins with activation of the ULK1 complex (ULK1, ATG13, FIP200, ATG101), which is directly inhibited by mTORC1 phosphorylation under nutrient-replete conditions and activated by AMPK phosphorylation under energy stress; active ULK1 phosphorylates and activates the class III PI3K complex (VPS34, Beclin-1, VPS15, ATG14L), generating phosphatidylinositol-3-phosphate at the nucleation site that recruits downstream effectors and marks the site of the forming isolation membrane (phagophore).

Biology

Biology · L5 · Autophagy and Cell Death Pathways

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Contrast the Needleman-Wunsch and Smith-Waterman dynamic programming algorithms for pairwise sequence alignment.1 / 9

Needleman-Wunsch performs global alignment, requiring the entire length of both input sequences to be aligned end to end (permitting gaps throughout); it initializes the dynamic programming matrix with gap penalties along the first row and column and always traces back from the bottom-right corner, making it appropriate when the two sequences are expected to be similar in length and homologous over their full extent.

Biology

Biology · L5 · Bioinformatic Sequence Analysis

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