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A polysaccharide is a polymer built from many linked monosaccharide units. Cellulose provides a structural example. See Biology 2e: polysaccharides.

Polystyrene is a polymer used as a calibration-standard family in organic-solvent size-exclusion chromatography. Its hydrodynamic size in a specified solvent supplies a conditional SEC molar mass calibration for other dissolved chains.

Polyuridylic acid is an RNA polymer whose nucleotides all carry uracil.

A fluorinated polymer whose polar crystalline phases can exhibit piezoelectricity and pyroelectricity.

A polymer containing pyrrolidone groups, widely used as a soluble stabilizer or capping agent. In silver nanostructure synthesis its adsorption can affect facet growth and aggregation. Residual polymer can also create electrically resistive nanowire junctions.

A poor solvent favors effective attraction between polymer segments relative to solvent contacts. A dilute flexible chain tends to contract, and sufficiently unfavorable conditions produce a compact polymer globule. Solvent quality depends on the polymer, solvent and temperature. The simple Flory–Huggins solution theory identifies the poor-solvent side of the theta condition with $\chi >1/2$; this does not guarantee that every finite-density mixture is inside its spinodal.

Journal of polymer Science: polymer Symposia 65, 173–192.

Publisher: doi.org/10.1002/polc.5070650116

The primary-paper abstract reports light-scattering and viscometry characterization of relatively stiff synthetic polymers in solution.

A radical chain reaction regenerates a radical during propagation. Initiation supplies free radicals; propagation consumes one and produces another; termination removes chain-carrying free radicals. This explains why one initiating event can lead to many product-forming chemical reactions. The chain-growth polymerization article develops the corresponding growth of polymers.

For polymer mass concentration $c$, the leading ideal chain pressure is $RTc/M_n$. Plotting $\Pi /c$ against $c$ and extrapolating removes the leading virial correction. The intercept has units of energy per mass; without the measurement temperature it determines $M_n/T$, not an absolute molar mass.

Consistent orientation of constitutionally unsymmetrical repeat units along a polymer chain.

Reptation is the snake-like motion of a long polymer through the constraints imposed by neighboring chains or a fixed porous matrix. A tube model restricts large transverse motion while allowing curvilinear motion along the chain contour. For a flexible chain with additive segment friction, contour diffusion scales as $N^{-1}$ and the time to renew a contour of length proportional to $N$ scales as $N^3$. With coil size squared proportional to $N$, this gives a centre-of-mass diffusion coefficient proportional to $N^{-2}$. Applying this tube picture to weak-field DNA gel electrophoresis gives an inverse-length mobility over its appropriate regime; field-induced orientation and trapping can invalidate that simple law.

An experimental comparison joined a two-ended diol chain, HOPCLOH, with a bifunctional isocyanate, at reported isocyanate-to-diol ratio $1.14:1$. The researchers used oven-dried $25\mathrm{mL}$ round-bottom flasks and an IKA RET magnetic hotplate with a metal carrier. They varied solvent, concentration, reaction temperature ($50$ or $61{}^{\circ }\mathrm{C}$), and duration ($1$ or $8\mathrm{h}$).^[ref]

A Bruker $500\mathrm{MHz}$ NMR spectroscopy instrument measured residual hydroxy group-adjacent signal relative to an ester signal. Independently, size-exclusion chromatography used ResiPore columns at $70{}^{\circ }\mathrm{C}$, a refractive-index detector, and polystyrene calibration. Figure 8 reports sharply increasing apparent number-average molar mass beyond the reported conversion $0.95$. A deliberately water-exposed isocyanate comparison reproduced a $1625\mathrm{c}{\mathrm{m}}^{-1}$ infrared spectroscopy band assigned to urea-containing products. The authors warn that tiny residual NMR spectroscopy signals reduce integration precision.^[ref]

The inference is increasing chain size alongside depletion of reactive groups, consistent with step-growth polymerization. It is not an exact measurement of $X_n$ in the toy model. The feed contains already extended diol chains: counting their constituent repeat units differs from counting each feed molecule as one unit. Their varying molar masses, calibration against a different polymer, residual starting material, and competing chemical reactions further obstruct a direct conversion-to-$X_n$ substitution. Report which functional groups the conversion readout measures before comparing it with stoichiometric imbalance in step growth.

Useful proposed controls, distinct from the reported water comparison, are pre-reaction spectra and matched mixtures omitting each joining partner in turn. Keep solvent, heating, and signal normalization matched. Disappearance of an isocyanate signal in the omitted-diol control would reveal competing consumption rather than establish chain joining. Agreement between residual-group and independently calibrated chain-size readouts is stronger evidence than calculating both quantities from the same Carothers equation.

Ribonucleic acid, or RNA, is a nucleotide polymer whose nucleotide sequence can both carry information and organize a working molecular shape. Its backbone contains alternating ribose sugars and phosphate groups connected through covalent bonds. Its usual nucleobases are adenine A, uracil U, guanine G, and cytosine C. Thus RNA uses U where DNA uses T; its ribose also differs chemically from DNA's deoxyribose. See NHGRI: RNA.

In transcription, an enzyme uses one DNA strand as a template for RNA. For example, the DNA template $3^{\prime }\text{-}\mathrm{TACGG}\text{-}{5}^{\prime }$ specifies $5^{\prime }\text{-}\mathrm{AUGCC}\text{-}{3}^{\prime }$ in RNA. The base pairing rules now include A–U rather than A–T, while G–C remains. This RNA matches the other DNA strand's $5^{\prime }$-to-$3^{\prime }$ lettering after T is replaced by U. Identifying the template strand matters: replacing T by U in an arbitrarily chosen DNA strand is not a general method for deriving the RNA product. See Alberts et al., Molecular Biology of the Cell: from DNA to RNA.

RNA is often a single strand, but single-stranded does not mean straight or entirely unpaired. Complementary regions within one RNA molecule can undergo base pairing, bringing distant positions together. Consider the illustrative twelve-nucleotide nucleotide sequence $5^{\prime }\text{-}\mathrm{GCAUUUUUAUGC}\text{-}{3}^{\prime }$. Pair positions 1 with 12, 2 with 11, 3 with 10, and 4 with 9. The resulting stem-loop has four base pairs: G–C, C–G, A–U, U–A. Positions 5–8 remain unpaired in the loop. Both arms belong to the same continuous backbone, and the paired arms have the directions of antiparallel nucleic acid strands.

The diagram proposes a possible pairing pattern, not a prediction that this short RNA must adopt that shape under every condition. Actual RNA folding depends on additional interactions, temperature, ions, and associated proteins; the full three-dimensional arrangement contains more information than the drawn base pairs. The example's purpose is to show how a linear nucleotide sequence can specify contacts within itself.

Different RNA roles make this flexibility useful. Messenger RNA carries a message that a ribosome reads during translation to build a protein. Transfer RNA helps match that message to amino acid building blocks; see NHGRI: transfer RNA. Ribosomal RNA forms structural and catalytic parts of the ribosome. Other RNA participates in gene regulatory networks, changing how strongly genes are expressed. Many RNA molecules therefore function without being translated into proteins; for some genes, functional RNA is the product itself.

Most strikingly, some folded RNA acts as an enzyme: these catalytic RNA molecules are ribozymes. The ribosome's bond-forming active site is built from RNA, although the complete ribosome also contains proteins. Structural evidence appears in Nissen et al., The structural basis of ribosome activity in peptide bond synthesis, Science 289, 920–930 (2000). RNA therefore connects a readable record with physical recognition, regulation, and catalysis: the same kind of polymer can be a message, an adaptor, or part of molecular machinery.

A ribozyme is an RNA molecule whose folded structure provides catalysis of a chemical reaction. A protein enzyme builds its active site from an amino acid chain; a ribozyme builds a working active site from RNA, sometimes with metal ions and associated proteins. Base pairing can help recognize a substrate, but recognition alone does not establish catalysis: the RNA must promote chemical conversion. A passive messenger RNA template being read by a ribosome is not thereby a ribozyme. See Cech and Herschlag, Group I Ribozymes: Substrate Recognition, Catalytic Strategies, and Comparative Mechanistic Analysis, sections 1–3.

The surprise is that an information-bearing polymer can also perform chemistry. Examples include the self-splicing group I intron of Tetrahymena thermophila and the catalytic RNA component of bacterial RNase P, discussed below. The ribosome supplies an everyday example: its peptide bond-forming active site is made of ribosomal RNA, although the complete machine also contains proteins. Nissen and colleagues examined structures of a large ribosome subunit with substrate analogues and found RNA contacting those analogues at the catalytic centre. This supports an RNA active site, not a claim that isolated ribosomal RNA can carry out all of biological translation. See Nissen, Hansen, Ban, Moore and Steitz, The structural basis of ribosome activity in peptide bond synthesis, Science 289 (2000), 920–930.

For the Tetrahymena group I intron, RNA splicing removes the intron and joins its flanking exons. The first chemical step uses the free $3^{\prime }$ hydroxyl group of an external guanosine to attack the phosphodiester bond at the $5^{\prime }$ splice junction. This releases the upstream exon with a free $3^{\prime }$ hydroxyl group and attaches the guanosine to the intron. That newly freed hydroxyl group then attacks the phosphodiester bond at the other splice junction, joining the exons and releasing the linear intron. Each step exchanges one backbone connection for another; it is not simply separation of base pairs. See Cech, Zaug and Grabowski, 1981: the phosphoester-transfer mechanism.

The motivating experiment began with an unexpected control. As Cech recounts, Zaug purified a ribosomal RNA precursor from Tetrahymena using a detergent and phenol extraction, then compared test tubes with and without added cell nucleus extract. Incubation in salts and nucleotides released the same amount of small intron RNA in both cases, detected by gel electrophoresis. Repetition made a missing ingredient or accidental omission less plausible. Activity also survived treatments intended to destroy proteins. Nevertheless, absence of added extract did not by itself exclude a tightly attached, resistant protein, or prove that the small RNA had been newly excised rather than released from an already processed complex. See Thomas R. Cech, 1989 Nobel lecture, pp. 655–659: the unexpected control and alternative explanations.

An independent chemical readout addressed the latter problem. Cech mixed precursor RNA with phosphorus-32-labelled guanosine bearing three phosphate groups (GTP), and used gel electrophoresis followed by exposure to X-ray film to locate the label. Label appeared in the excised intron with magnesium present; it was absent when magnesium was omitted or labelled ATP replaced the labelled guanosine reagent. This experiment is described in Cech, 1989 Nobel lecture, pp. 657–658: labelled-guanosine controls. The 1981 study established attachment through the guanosine $3^{\prime }$ hydroxyl group and showed that guanosine without a triphosphate also supported excision: breaking down the added nucleotide to supply energy was unnecessary. See Cech, Zaug and Grabowski, In vitro splicing of the ribosomal RNA precursor of Tetrahymena, Cell 27 (1981), 487–496: primary abstract. Separately, sequencing and terminal analysis found an extra $5^{\prime }$ guanosine absent from the corresponding DNA sequence. See Zaug and Cech, The intervening sequence excised from the ribosomal RNA precursor of Tetrahymena contains a 5-terminal guanosine residue not encoded by the DNA, Nucleic Acids Research 10 (1982), 2823–2838. Together, incorporation and sequence evidence support a new covalent bond, beyond a change in how RNA associates.

Kruger, Grabowski, Zaug, Sands, Gottschling and Cech's 1982 test removed dependence on a precursor purified from Tetrahymena. They cloned the intron and adjacent exons into a DNA template, made precursor RNA with purified bacterial RNA polymerase under conditions suppressing RNA splicing, and removed proteins by detergent–phenol extraction. Denaturing gel electrophoresis separated precursor species. Purified precursor was then incubated with the guanosine reagent, magnesium and salt; matched samples without this incubation supplied a precursor baseline. Their standard assay used $10\mathrm{mM}$ magnesium chloride, $0.1\mathrm{mM}$ of that guanosine reagent, $100\mathrm{mM}$ ammonium sulfate and a buffer solution at pH $7.5$, for $30$ minutes at temperature $37{}^{\circ }\mathrm{C}$, with specified variations in individual experiments. Gel electrophoresis and radioactive-film detection showed excised intron RNA; sequencing verified its $5^{\prime }$ junction. See Kruger et al., Self-Splicing RNA, Cell 31 (1982), 147–157, figures 3–4 and Experimental Procedures.

Excision alone could leave disconnected exons. To test joining, the authors paired labelled RNA with DNA spanning the joined-exon sequence, removed exposed RNA with enzymes, and separated the protected pieces by denaturing gel electrophoresis. Spliced samples yielded protected RNA long enough to span the junction. See Kruger et al., 1982, figure 6: independent evidence for exon ligation. The experimental logic matters: an intron-sized band identifies a candidate product, while sequence and junction assays test its chemical identity.

These controls support sufficiency of the prepared RNA under the assay conditions. They do not show that every RNA self-splices, or that proteins are dispensable inside a biological cell. Many group I introns use proteins to help attain an active fold. See Cech and Herschlag, Group I Ribozymes, section 6: protein facilitation. Nor does a failed assay necessarily identify an inactive nucleotide sequence: unsuitable ions, pH, or temperature can prevent a working active site from forming.

The distinction between self-processing and repeated use became especially clear with bacterial RNase P. In 1983 Guerrier-Takada, Gardiner, Marsh, Pace and Altman separated the RNA and protein components of RNase P from two bacteria. Purified RNA cleaved precursor transfer RNA under conditions containing $60\mathrm{mM}$ magnesium ions, or $10\mathrm{mM}$ magnesium ions plus $1\mathrm{mM}$ spermidine. The protein components alone had no catalytic activity. At $5$–$10\mathrm{mM}$ magnesium without spermidine, both components were needed. Thus the comparison demonstrated an RNA catalyst while also explaining why protein assistance could matter under other conditions. RNase P produces the mature $5^{\prime }$ end of transfer RNA by removing its leader; it acts on a separate substrate and can be used again. See Guerrier-Takada et al., The RNA moiety of ribonuclease P is the catalytic subunit of the enzyme, Cell 35 (1983), 849–857: primary abstract.

Self-splicing demonstrates RNA chemistry, but one precursor completing one rearrangement is not yet evidence for catalytic turnover: repeated conversion of separate substrates by a regenerated catalyst. The self-splicing precursor changes its own connectivity and incorporates external guanosine. In 1986 Zaug and Cech showed that a shortened Tetrahymena intron RNA could cleave and rejoin separate short RNA substrates in a sequence-dependent reaction. This demonstrated an RNA enzyme acting beyond its own self-processing. See Zaug and Cech, The intervening sequence RNA of Tetrahymena is an enzyme, Science 231 (1986), 470–475: primary abstract.

Read the second figure as a counting argument. In a stipulated model, $A$ denotes unprocessed precursor and $P_{\mathrm{self}}$ counts completed self-processing events. Set $A(0)=R_0$, $P_{\mathrm{self}}(0)=0$ and $dA/d\tau =-A$. The exponential function solution gives $P_{\mathrm{self}}/R_0=1-e^{-\tau }$, never exceeding one. Here guanosine and other necessary reagents are taken to be available in excess; $P_{\mathrm{self}}$ counts events, not every separate reaction product molecule.

For a second stipulated model, let an unchanged ribozyme $R$ perform $R+S⟶R+P$ on a separate substrate $S$. Assume the effective law of mass action $dS/dt=-kRS$, no reverse reaction, no ribozyme loss and no inhibited or long-lived bound states. Set $R=R_0$, $S(0)=5R_0$, $P(0)=0$ and $\tau =k{R}_{0}t$. Then $S/R_0=5e^{-\tau }$ and $P/R_0=5(1-e^{-\tau })$, with $S+P=5R_0$. At $\tau =1$, self-processing gives about $0.632$ completed events per initial RNA, whereas the regenerated ribozyme gives about $3.161$ reaction product molecules per initial ribozyme. More than one substrate conversion per initial ribozyme, with appropriate background and identity controls, is evidence for turnover. Product accumulation below that threshold alone cannot distinguish a reusable catalyst from one-shot chemistry. These models illustrate that distinction; actual enzyme kinetics can include folding delays, binding, saturation and product release.

A polymer conformation model assigning allowed torsional states and statistical weights to successive backbone bonds. Correlations between torsional states can represent local stiffness beyond the fixed-angle, uniformly rotating freely rotating chain.

An overdamped bead-spring model of polymer dynamics with local friction and no long-range hydrodynamic interaction. For an ideal unentangled chain of $N$ identical frictional units, the centre-of-mass diffusion coefficient is proportional to $N^{-1}$ and the longest internal relaxation time to $N^2$. A tagged segment has an intermediate-time mean-square displacement proportional to $t^{1/2}$ before ordinary whole-chain diffusion dominates. Entanglement adds constraints beyond this model.

In a flexible crosslinked polymer network, deformation restricts the configurations of chain segments between cross-links. The resulting decrease of entropy produces a restoring entropic force. For an ideal affine Gaussian network, the shear modulus is $G={\nu }_s{k}_{B}T$, where ${\nu }_s$ is the number density of elastically active strands. A nearly incompressible isotropic rubber has Young's modulus $E\simeq 3G$. At fixed network density within the rubbery regime, both increase approximately linearly with absolute temperature. This statement does not describe crossing the glass transition or chemical degradation.

An analytical form of gel electrophoresis using an anionic surfactant and a polymer gel to separate proteins predominantly by chain size under denaturing conditions. Western blot separation often uses SDS-PAGE; the resulting apparent mass and subsequent antibody binding provide complementary, incomplete evidence about identity.

SEC molar mass calibration measures standards under the same column, solvent, and temperature conditions as the unknown. Over a suitable fractionation interval, a common empirical approximation iswhere $M_{\mathrm{ref}}$ specifies the molar mass unit and $b$ has inverse-volume units. Interpolation is conditional on the standards' size–molar mass relationship. SEC measures access associated with hydrodynamic size, so a branched polymer, an extended chain, and a compact protein need not share that relationship.

In this model the $80,000$, $40,000$, and $20,000\mathrm{g}\mathrm{mo}{\mathrm{l}}^{-1}$ standards have hydrodynamic radii $2\sqrt{2}$, $2$, and $\sqrt{2}\mathrm{nm}$ and elute at $7$, $9$, and $11\mathrm{mL}$. An unknown at $8\mathrm{mL}$ would be assigned $M_{\mathrm{app}}=40,000\sqrt{2}\mathrm{g}\mathrm{mo}{\mathrm{l}}^{-1}$ by this calibration. But a $40,000\mathrm{g}\mathrm{mo}{\mathrm{l}}^{-1}$ species that expands from $2$ to $2\sqrt{2}\mathrm{nm}$ elutes at $7\mathrm{mL}$ and is assigned $80,000\mathrm{g}\mathrm{mo}{\mathrm{l}}^{-1}$ without gaining any mass. The numbers demonstrate ambiguity, rather than predict a real unfolding transition.

Changes in conformational isomerism, protein folding, protein denaturation, and protein aggregation can therefore shift peaks. Association usually increases size; compaction can reduce size at unchanged molar mass. Adsorption creates a different ambiguity: delayed elution need not indicate a smaller species. A different solvent can change both polymer coil dimensions and interactions with the packing. The SEC protein conformation experiment tests these alternatives with additional detectors.

In ideal SEC pore access, geometric exclusion changes the fraction of pore liquid a solute can occupy. Diffusion permits entry into and exit from accessible pores; the through-flow chiefly transports the sample between packing particles. A hydrodynamic radius is a useful size descriptor, but actual pore entry also depends on shape and pore geometry. A flexible polymer coil is not a rigid ball with a perfectly sharp entry diameter.

The extra delay is best understood as extra accessible storage, rather than a prescribed longer streamline. Pore visits are reversible and random. An entirely excluded species samples the SEC void volume; a sufficiently small nonbinding species samples the SEC total accessible liquid volume. Intermediate species lie between these limits. Larger hydrodynamic size generally means earlier elution within the column's SEC fractionation range.