The net hydrogen bonding polarities of polypeptides sum to zero, with equivalent numbers of hydrogen bond donors and acceptors. Polyglucose has an excess of hydrogen bond acceptors over donors. Polynucleotides have a large excess of acceptors over donors. Is it possible to relate the functional roles of biopolymers to their structures? First, one must attempt to accurately describe biological functions. What does each biopolymer type do?
There are no bright lines—functional roles are not rigidly proscribed by polymer type.
The enormous diversity in the chemical transformations of biological systems are catalyzed and regulated primarily by proteins. Protein contributes enzymes, enzyme inhibitors, structural fibers, adhesives, pumps, pores, switches, and receptors.
RNA is used for temporal and specific information transfer i. By contrast, DNA appears to be used exclusively for long-term and bulk information storage i. On the whole, polynucleotides maintain, record, read and transmit sequence information. Polysaccharides contribute structure along with energy storage and elaborate recognition. Ribozymes Kruger et al. However, thus far there has been no observation of a biological RNA-only ribozyme that is formally enzymatic; there are no RNA-only biological ribozymes that turn over Kruger et al. All RNA-only catalytic elements discovered thus far in biological systems perform suicide single turn-over phosphoryl transfer functions.
By contrast, highly abundant and critically important ribonuclear protein ribozymes protein-assisted ribozymes , with RNA-only catalytic sites, do turn over and are thus fully enzymatic. These RNP ribozymes include the ribosome Khaitovich et al. No catalytic function of polysaccharide has been observed thus far, to our knowledge. DNA and RNA both fold and assemble to form double helices with central cores of paired and stacked nucleobases, framed by external, anionic backbones. DNA and RNA appear similar in chemical representations, differing only by a single atom on the backbone and by a methyl group on one base.
There are over 40 examples of this motif in the large ribosomal subunit of prokaryotes Hsiao et al. These base—backbone interactions promote folding of RNA into local stem-loops, which are often further stabilized by tertiary interactions Fig. Biological DNA, by contrast, is generally restrained to base—base associations, forming long, monotonous double helices Fig.
RNA holds a gun to its own head. In addition, the N1 and N2 of the guanine form a hydrogen bond with a phosphate oxygen of the backbone. RNA folds into elaborate three-dimensional structures. In panels a and b, hydrogen bonding groups that do not form hydrogen bonds are omitted for clarity. The rate of RNA self-cleavage is modulated by local structure, flexibility, pH, and interactions with cations. Thus, the RNA and DNA backbones have distinctive lability profiles, which depend on many factors including on the chemistry of the cleavage process.
Westheimer suggested that phosphates dominate molecular biology because phosphate is a kinetically trapped e. While correct, in our view this analysis should be extended to incorporate the role of phosphate in mechanochemical coupling. All biopolymerization reactions utilize phosphorylated or pyrophosphorylated intermediates Figs.
Biopolymers and Cell
Phosphorylated intermediates appear to be necessary for the mechanochemical coupling required for processive polymerization. Translocation is energy-driven; the nascent polymer translocates relative to the polymerization enzyme.
The strength, directionality, and unipolarity of hydrogen bonding and electrostatic interactions between phosphate and protein cause linkage of phosphate association to protein conformation Rice et al. We Williams have previously proposed that formalisms for describing mutualisms on levels of cells, organisms, and ecosystems also apply to biopolymers Lanier et al.
Mutualisms are everywhere in the biosphere and are fundamentally important in evolution, ecology, and economy Moran ; Bronstein ; Douglas ; Gray The mutual benefit, exchange of proficiencies, persistence, interdependence, co-evolution, and parasitism that characterize relationships on cellular, organismal, and ecological levels have direct parallels in the behaviors of biopolymers. A mutualism is a persistent and intimate interaction that benefits multiple interactors Douglas Evolutionary change of one partner triggers change of the other.
Mutualisms were previously understood to operate at the levels of cells, organisms, ecosystems, and even societies and economies. The eukaryotic cell is a culmination of mutualism between simpler prokaryotic cells Sagan ; Poole and Gribaldo ; Gray Essentially every species on Earth is involved in mutualisms.
Biopolymers satisfy all of the formalisms of mutualism. Biopolymers protect each other from hydrolysis and synthesize each other. Biology requires polymers. Biopolymers allow processes of folding and assembly to be detached from the required investment of free energy.
Advances in Physicochemical Properties of Biopolymers (Part 2)
For biopolymers, prior free energy investment in synthesis is distributed over time and space, offsetting the subsequent cost of folding and assembly. Biopolymers appear to spontaneously fold and assemble, only because of prior free energy investments. For small molecules, by contrast, assembly and investment are directly coupled.
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The free energy of assembly is paid in real time, during molecular assembly. Therefore, small molecules cannot achieve the elaborate folds and assemblies, based on conditional self-complementarity, that appear to come naturally to biopolymers. The data surveyed here suggest that polypeptide, polynucleotide, and polysaccharide arose by co-evolution. Biopolymer universalities, including i synthesis by condensation and degradation by hydrolysis, ii folding by pre-organization and self-complementarity, iii homogeneous and heterogeneous assembly, and iv protection by folding or homogeneous assembly selfishness and v protection by heterogeneous assembly mutualism , point to simultaneous origins in a shared environment.
In contrast to the consensus, this model suggests that early selection operated at the level of hydrolytic degradation mitigated by folding and assembly , rather than at the level of synthesis. We Hud have proposed that the thermodynamic driver for synthesis and degradation on the ancient Earth would have been cycling water activity Forsythe et al.
Biopolymers Application Notes
Synthesis by condensation dehydration is favored in low water activity day and degradation by hydrolysis is favored in high water activity night. Molecular self-interest is chemical persistence. Persistence of biopolymers in a hydrolytic environment is enhanced by folding and assembly.
Self-complementarity is therefore an expression of self-interest, a method to escape from hydrolysis, a path to survival, and a property universal to biopolymers. Extremely stable folds and assemblies could persist for some period but ultimately form molecular dead-ends. It seems likely that our small set of surviving biopolymers were chemically selected from diverse competing polymers Hud et al. Biopolymers, as indicated by spider webs, DNA nanodevices, chromatin, the ribosome, and cellulose, are masters of folding and assembly. Loser polymer types, which were less accomplished at folding and assembly, were forced into hydrolytic extinction.
If so, ancestral polymers, which dominated in early stages, would have been supplanted by more successful second- or third-generation polymers. Their system , a heterogeneous, functionally integrated, self-maintained, quasi-stationary state allowing for increases in complexity and elaboration, is a chemically vague but reasonable description of our shared environment of cycling water activity and co-evolution, with chemical selection at the level of degradation.
Although biopolymer types are traditionally studied and taught in isolation of each other, we believe that DNA, RNA, polypeptide, and polysaccharide are best understood in the context of their shared attributes and key differences. Recognition of biopolymer universalities explains their structures and functions and points to their origins.
Only by examining biopolymers in context can we hope to achieve a reasonable understanding of the fundamental molecules of life. The authors thank Drs. Gary Schuster and Roger Wartell for helpful discussions. Skip to main content Skip to sections.