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Gel electrophoresis through polyacrylamide under conditions that suppress nucleic acid folding; suitable sequencing conditions resolve adjacent nucleotide lengths.

Starch gel electrophoresis uses a starch-based gel to separate material in an electric field. The IgG chain reduction experiment uses it to compare polypeptide chains.

A gel band is a localized population of stained or otherwise detected molecules with sufficiently similar migration in one sample lane. One visible gel band need not contain only one nucleotide sequence. Two different linear DNA fragments of 375 base pairs can occupy the same unresolved gel band; equal migration supplies size evidence under suitable conditions, not a sequence determination.

Fluorescence from a bound stain can support an estimate of DNA quantity, but suitable staining and detector response matter.^[ref]

For a quantitative model with equal staining response per unit mass, background-subtracted, integrated fluorescence $I$ satisfies $I=km$. This requires an unsaturated detector and a common proportionality constant $k$; visual peak brightness alone does not supply $I$.

The amount of substance is $n=m/M$, where $M$ is molar mass. For double-stranded DNA with approximately equal average mass per base pair, $M$ is proportional to length $L$, so $n$ is proportional to $I/L$. In a constructed example, equal integrated signals from 250-base pair and 1000-base pair gel bands imply approximately equal masses but four times as many short DNA molecules. Conversely, equal numbers of those DNA molecules would give about four times the signal for the longer fragments in this model. Neither conclusion follows from darkness in a schematic drawing.

A particle beam is a directed stream of particles prepared for transport, interaction or detection. A molecular beam can contain neutral chemical atoms or molecules; an accelerator beam can contain charged electrons, protons or ions. Its direction, energy spread, spatial distribution and particle flux describe different aspects of the preparation.

A source, direction-selecting apertures or focusing elements, a transport region and a detector perform separate tasks. For a charged beam, electric fields can change its energy and magnetic fields can bend its trajectory through the Lorentz force. A neutral atomic beam requires interactions appropriate to its neutral constituents. A vacuum reduces unwanted collisions along either transport path, but it does not itself make every particle's speed equal.

A particle accelerator increases the kinetic energy of charged particles through the work of an electric field. A single electric potential difference $V$ gives an energy gain of magnitude $|q|V$ to a particle of electric charge $q$ crossing in the accelerating direction. Reusing a smaller electric potential difference many times can give a much larger final kinetic energy without requiring the whole apparatus to withstand the equivalent single voltage. A magnetic field can return the particles to the accelerating region: magnetic forces do no work, but they make repeated energy gains possible. The cyclotron turns this separation between bending and acceleration into a particularly elegant machine.

A DNA ligase is an enzyme that joins appropriately juxtaposed DNA ends by forming phosphodiester bonds.

The pyruvate dehydrogenase complex converts pyruvate into acetyl-CoA, releasing carbon dioxide and reducing NAD+ to NADH. Several catalytic components and enzyme cofactors couple decarboxylation, group transfer and oxidation within one assembly. It links glycolysis to the citric acid cycle, so control of the complex regulates the entry of carbohydrate-derived carbon into oxidative metabolism. A shared reaction intermediate can be passed between component active sites rather than diffusing freely through the cell. ^[ref]

An acid phosphatase catalyses hydrolysis of phosphate esters under acidic conditions; its lysosomal enzyme latency supplied evidence for lysosomes.

An acid hydrolase is an enzyme that catalyses hydrolysis most effectively under acidic conditions; lysosomes contain multiple kinds.

A restriction enzyme cleaves DNA at or near recognized sequence patterns. Many type II systems produce reproducible fragments useful in genetic engineering, while a corresponding DNA modification system protects the host sequence. Different recognition patterns and cut positions can produce blunt ends or single-stranded overhangs. Thus recognition specificity and the physical end structure are separate properties important for assembling DNA fragments. ^[ref]

An enzyme inhibitor lowers an enzyme's reaction rate. In reversible enzyme inhibition, reducing free inhibitor concentration can restore activity; slow release can make this difficult to distinguish experimentally from irreversible inactivation. Competitive inhibition and mixed inhibition describe different changes in enzyme kinetics; pure noncompetitive inhibition is a special case of mixed inhibition, not a name for every inhibitor that binds away from an active site.^[ref]

The useful question is how adding substrate changes the inhibition. The model below connects binding to a measurable reaction rate, predicts when more substrate can overcome inhibition, and supplies examples for comparison with an enzyme inhibition initial-rate assay. Its inhibition constants are explicitly defined; neither a binding cartoon nor one reduced reaction rate by itself determines a mechanism.

A protease catalyses hydrolysis of peptide bonds in proteins or peptides. Different proteases recognize different sequences or structures, and some cut within a chain while others remove terminal residues. Digestion, signalling activation and controlled protein degradation all use this chemistry. The sequence specificity of chymotrypsin, for example, differs from indiscriminate breakdown of every peptide bond. ^[ref]

Trypsin is a serine protease: an enzyme that performs proteolysis by catalysing peptide bond hydrolysis. It preferentially cuts on the C-terminus side of lysine and arginine amino acid residues, leaving the selected amino acid residue in the preceding fragment.^[ref]

The bond being broken is the backbone amide linkage, rather than the lysine or arginine amino acid side chain. A formal connectivity equation for hydrolysis isHere $R^1$ and $R^2$ stand for the connected portions of the original peptide. Actual terminal protonation and electric charge depend on pH; the equation displays connectivity. Water supplies the elements needed to form the two new ends, while the enzyme is regenerated.

Selective cutting turns an unwieldy protein into shorter peptides, making peptide mapping useful for comparing proteins. In cell culture, trypsin also helps detach adherent biological cells: the HeLa culture viability experiment provides a concrete example of its use and subsequent stopping of proteolysis. The same enzyme can therefore serve both chemical analysis and preparation of a biological cell suspension.

Papain is an enzyme used for proteolysis, including limited Papain digestion of IgG.

It is a cysteine protease: a catalytic cysteine participates directly in peptide-bond hydrolysis. Limited digestion can cleave accessible regions while preserving folded domains, which is why carefully interpreted fragment patterns can reveal aspects of antibody architecture. ^[ref]

Lactate dehydrogenase couples pyruvate-to-lactate reduction to NADH-to-NAD+ oxidation.

Pyruvate kinase catalyzes phosphate transfer from phosphoenolpyruvate to ADP, producing pyruvate and ATP in glycolysis.

A scientist who studies insects. An entomologist can connect observations of development, behavior or population change with questions in physiology, ecology, agriculture or disease transmission.