OpenStem

@openstem · Joined Jul 2026

7420 public items8 groups

Flashcards9 cards

Describe the physical principle by which optical tweezers trap and manipulate a micron-scale bead attached to a single biomolecule, and how this enables force-extension measurements.1 / 9

Optical tweezers use a tightly focused laser beam to trap a dielectric (typically polystyrene or silica) microsphere near the beam's focal point: the steep intensity gradient near the focus creates a gradient force pulling the higher-refractive-index bead toward the region of highest light intensity, while scattering force pushes it slightly along the beam axis, together producing a stable three-dimensional trap whose effective stiffness (typically approximated as a linear, Hookean restoring force for small displacements) can be precisely calibrated.

Biology

Biology · L5 · Biophysics and Single-Molecule Methods

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Flashcards9 cards

Describe the chromosome conformation capture (3C) technique and how it is scaled up into Hi-C to map genome-wide chromatin contacts.1 / 9

Chromosome conformation capture (3C) formaldehyde-crosslinks chromatin in its native folded state, digests the crosslinked DNA with a restriction enzyme, then performs intramolecular proximity ligation under dilute conditions (favoring ligation between crosslinked, spatially adjacent fragments over random intermolecular ligation), so that DNA fragments far apart in linear sequence but close together in 3D space become joined into a single ligation product detectable by locus-specific PCR.

Biology

Biology · L5 · Chromatin and 3D Genome Organization

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Flashcards9 cards

Explain the chemistry of a cytosine base editor (CBE) and why it does not require a double-strand break to install a point mutation.1 / 9

A cytosine base editor fuses a catalytically impaired Cas9 nickase (Cas9 D10A, which nicks only the non-target strand) to a cytidine deaminase domain (derived from APOBEC or AID family enzymes) and a uracil glycosylase inhibitor (UGI). The deaminase converts cytosine to uracil within the single-stranded DNA exposed in the R-loop formed when the guide RNA binds its target, at a position set by the editing window (typically protospacer positions 4-8 counting from the PAM-distal end).

Biology

Biology · L5 · Advanced CRISPR Genome Editing

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Flashcards9 cards

Describe the biosynthesis of N-linked glycans, from the dolichol-phosphate-linked oligosaccharide precursor through en bloc transfer and initial ER trimming.1 / 9

N-linked glycosylation begins with stepwise assembly of a 14-sugar oligosaccharide precursor (Glc3Man9GlcNAc2) on the lipid carrier dolichol phosphate, embedded in the ER membrane, built up by a series of glycosyltransferases acting first on the cytoplasmic face and then, after the growing chain flips to the luminal face, on the ER luminal side.

Biology

Biology · L5 · Glycobiology

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Flashcards9 cards

Contrast 16S rRNA amplicon sequencing with shotgun metagenomic sequencing as strategies for profiling a microbial community.1 / 9

16S rRNA amplicon sequencing PCR-amplifies one or more hypervariable regions (commonly V3-V4) of the universally conserved bacterial/archaeal 16S ribosomal RNA gene using conserved-region primers, then sequences the amplicons to assign taxonomy; it is inexpensive and works from very low-biomass or degraded samples, but resolves taxonomy typically only to the genus level, cannot directly detect non-bacterial community members, and is subject to primer bias and variable 16S copy number across taxa.

Biology

Biology · L5 · Metagenomics and Microbial Ecology

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Flashcards9 cards

Describe the electron transport pathway through Complexes I, III, and IV, and identify which complexes translocate protons across the inner mitochondrial membrane.1 / 9

Complex I (NADH:ubiquinone oxidoreductase) oxidizes NADH, passing electrons through a flavin mononucleotide cofactor and a chain of iron-sulfur clusters to reduce ubiquinone to ubiquinol, translocating 4 protons per pair of electrons. Complex III (cytochrome bc1) oxidizes ubiquinol and, via the Q cycle, passes electrons to cytochrome c while translocating 4 protons per electron pair. Complex IV (cytochrome c oxidase) oxidizes cytochrome c and reduces molecular oxygen to water at a binuclear heme a3-CuB center, translocating 2 protons per electron pair (plus consuming 2 additional matrix protons in water formation, contributing further to the charge gradient).

Biology

Biology · L5 · Advanced Mitochondrial Bioenergetics

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Flashcards9 cards

Explain the amyloid cascade hypothesis of Alzheimer disease, including the roles of APP processing, amyloid-beta aggregation, and downstream tau pathology.1 / 9

The amyloid cascade hypothesis proposes that accumulation of amyloid-beta peptide, generated by sequential cleavage of amyloid precursor protein (APP) by beta-secretase (BACE1) and then gamma-secretase (a complex including presenilin as the catalytic subunit), is the initiating event in Alzheimer disease pathogenesis; amyloid-beta42, the more aggregation-prone cleavage product, self-assembles into soluble oligomers and eventually insoluble extracellular plaques.

Biology

Biology · L5 · Mechanisms of Neurodegeneration

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Flashcards9 cards

Explain why a gene tree inferred from a single locus can differ in topology from the true species tree, and name the two principal biological processes responsible.1 / 9

A gene tree traces the ancestry of a single genomic locus, while a species tree traces the branching history of the populations/species themselves; because different loci across the genome can have genuinely different underlying genealogical histories, a single gene tree is not guaranteed to match the species tree topology even when both are estimated without any error.

Biology

Biology · L5 · Phylogenomics and Comparative Genomics

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Flashcards9 cards

Describe the TIR1/AFB auxin co-receptor mechanism and how it triggers rapid transcriptional derepression of auxin-responsive genes.1 / 9

Auxin (indole-3-acetic acid) is perceived by a co-receptor mechanism in which the F-box protein TIR1 (or one of its AFB paralogs), a substrate-recognition subunit of an SCF-type E3 ubiquitin ligase complex, directly binds auxin as a 'molecular glue' that increases TIR1's affinity for Aux/IAA repressor proteins — auxin therefore acts not by inducing a conformational change in a separate receptor but by promoting a protein-protein interaction between TIR1 and its substrate.

Biology

Biology · L5 · Advanced Plant Molecular Biology

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Flashcards9 cards

What is the site frequency spectrum (SFS), and how does its shape differ under neutral demographic equilibrium versus a recent population expansion?1 / 9

The site frequency spectrum tabulates, across all polymorphic sites in a sample, how many sites have a derived (or minor) allele at each possible frequency count in the sample, summarizing the genome-wide distribution of allele frequencies and serving as a compact statistic for demographic and selective inference.

Biology

Biology · L5 · Population Genomics and Selection

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Flashcards9 cards

State Anfinsen's thermodynamic hypothesis and describe the experimental evidence (the ribonuclease A refolding experiment) that supported it.1 / 9

Anfinsen's thermodynamic hypothesis holds that a protein's native, functional three-dimensional structure is (for many single-domain proteins) the thermodynamically most stable conformation under physiological conditions, and that this structure is determined entirely by the protein's amino acid sequence — meaning a denatured protein should be able to spontaneously refold to its correct native structure without any additional information, given the right solution conditions.

Biology

Biology · L5 · Protein Folding and Molecular Chaperones

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Flashcards9 cards

Contrast bottom-up and top-down proteomics workflows, including what each measures and its principal limitation.1 / 9

Bottom-up (shotgun) proteomics digests proteins into peptides (typically with trypsin, cleaving C-terminal to lysine/arginine) before mass spectrometry, then infers protein identity from peptide spectra; it offers high sensitivity and throughput but loses direct information about which proteoform or combination of co-occurring modifications was present on an intact protein molecule (the protein inference problem).

Biology

Biology · L5 · Proteomics and Mass Spectrometry

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Flashcards9 cards

What design properties must a tissue engineering scaffold balance, and how do natural (e.g. collagen, decellularized matrix) and synthetic (e.g. PLGA, PEG) scaffold materials differ in meeting them?1 / 9

An effective scaffold must provide sufficient mechanical strength to support the target tissue during regeneration, a degradation rate matched to the rate of new tissue formation (neither dissolving before the tissue can support itself nor persisting so long that it impedes remodeling), adequate porosity and pore interconnectivity for cell infiltration, nutrient/waste diffusion, and eventual vascularization, and appropriate surface chemistry to support cell adhesion without provoking a chronic foreign-body immune response.

Biology

Biology · L5 · Regenerative Medicine and Tissue Engineering

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Flashcards9 cards

Describe the stepwise assembly of the spliceosome (E, A, B, Bact, B*, C complexes) on a pre-mRNA intron.1 / 9

Biology

Biology · L5 · RNA Biology, Splicing, and Noncoding RNA

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Flashcards9 cards

Define a network motif in a gene regulatory network and describe the feed-forward loop (FFL) as a canonical example.1 / 9

A network motif is a small subgraph pattern (a specific arrangement of a few nodes and edges) that recurs in a regulatory network far more often than expected in a randomized network with the same degree distribution, implying it has been selected for a specific dynamical function.

Biology

Biology · L5 · Systems Biology and Network Modeling

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Flashcards9 cards

What are cancer-associated fibroblasts (CAFs), and by what mechanisms do they promote tumor progression?1 / 9

Cancer-associated fibroblasts are a heterogeneous, activated fibroblast population within the tumor stroma, arising from resident fibroblasts, pericytes, mesenchymal stem cells, or epithelial cells via transdifferentiation, typically marked by alpha-smooth muscle actin and FAP (fibroblast activation protein) expression, though CAF subtypes vary considerably in marker expression and function.

Biology

Biology · L5 · Tumor Microenvironment and Metastasis

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Flashcards9 cards

Describe how RIG-I-like receptors (RIG-I, MDA5) distinguish viral RNA from host RNA in the cytoplasm, and the downstream signaling that leads to type I interferon production.1 / 9

RIG-I preferentially recognizes short double-stranded RNA bearing an uncapped 5' triphosphate or diphosphate group, a chemical signature present on many viral RNA replication intermediates but absent from host cytoplasmic mRNA, which is 5' capped; MDA5 instead recognizes longer double-stranded RNA structures, together giving the RIG-I-like receptor family broad but discriminating coverage of RNA virus replication intermediates.

Biology

Biology · L5 · Advanced Virus-Host Interactions

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Quiz3 questions

Which one is a living thing?

AA toy carBA puppyCA rockDA spoon

Biology

Biology · L1 · Living or Not?

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Quiz3 questions

Which body part do you use to hear sounds?

AEyesBNoseCEarsDHands

Biology

Biology · L1 · Your Five Senses

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Quiz5 questions

Which part of the plant soaks up water from the soil?

ALeavesBRootsCPetalsDStem

Biology

Biology · L1 · Plants and How They Grow

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Quiz5 questions

Which animal group has fur or hair and feeds its babies milk?

ABirdsBFishCMammalsDInsects

Biology

Biology · L1 · Animal Groups

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Quiz5 questions

Which habitat is covered in snow and ice most of the year?

ADesertBArcticCRainforestDPond

Biology

Biology · L1 · Habitats and Homes Quiz

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Quiz5 questions

What does your heart do?

AHelps you smellBPumps blood around your bodyCHelps you seeDDigests your food

Biology

Biology · L1 · Your Amazing Body

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Quiz5 questions

Which drink is best for your body every day?

ASodaBWaterCSugary punchDCandy juice

Biology

Biology · L1 · Staying Healthy Quiz

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Quiz5 questions

What is a baby dog called?

APuppyBKittenCCalfDFoal

Biology

Biology · L1 · Baby Animals and Growing Up Quiz

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Quiz5 questions

What do we call an animal that only eats plants?

ACarnivoreBHerbivoreCOmnivoreDProducer

Biology

Biology · L1 · Food Chains in Nature Quiz

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Quiz5 questions

What do many trees do in autumn (fall)?

AGrow bright new flowersBLose their leavesCGrow much taller overnightDTurn into evergreen trees

Biology

Seasons and Living Things Quiz

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Quiz5 questions

What do plants use to make their own food?

ASunlight, water, and airBOther animalsCRocks and sandDOther plants

Biology

Plants, Animals, and Living Things Quiz

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Quiz5 questions

How many legs does an insect have?

A4B6C8D10

Biology

Biology · L1 · Bugs and Minibeasts Quiz

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Quiz5 questions

Why do people have two eyes instead of one?

ASo one eye can rest while the other worksBSo the brain can judge how far away things areCSo eyes can change colorDSo people can see in the dark

Biology

Biology · L1 · Your Five Senses Quiz

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