Inspired by Biology: From Molecules to Materials to Machines (2008)

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D Glossary actin: Globular structural protein that serves as the monomeric subunit of micro- filaments, one of the three major components of the cytoskeleton, and of thin fila- ments that are part of the contractile apparatus in muscle cells. Actin participates in many important cellular functions, including muscle contraction, cell motility, cell division and cytokinesis, vesicle and organelle movement, cell signaling, and the establishment and maintenance of cell junctions and cell shape. actuator: Device that reads a signal and converts it to a physical action. adenosine triphosphate (ATP): Multifunctional nucleotide that is the main energy source for the majority of cellular functions. ATP transports chemical energy within cells for metabolism. It is produced as an energy source during the processes of photosynthesis and cellular respiration and consumed by many enzymes and a multitude of cellular processes, including biosynthetic reactions, motility, and cell division. adenosine triphosphatase (ATPase): Class of enzymes that catalyze the decompo- sition of adenosine triphosphate (ATP) into adenosine diphosphate (ADP) and a free phosphate ion. This reaction releases energy, which the enzyme (in most cases) harnesses to drive other chemical reactions that would not otherwise occur. This process is widely used in all known forms of life. allosteric interaction: Interaction involving an enzyme that has two binding sites: 149 

150 Inspired by Biology the active site and a site into which another molecule fits. The binding of a molecule changes the shape of the enzyme and alters its activity. amphiphile: Molecule possessing both hydrophilic (water soluble) and ­hydrophobic (water repellent) regions. amyloid: Insoluble fibrous protein aggregations sharing specific structural traits. angiogenesis: Physiological process involving the growth of new blood vessels from preexisting vessels. antigen: Molecule that stimulates an immune response. bioderivation: Using a biomaterial with desired properties to create a hybrid material, such as incorporation of biologically derived proteins for targeted drug delivery. bioinspiration: Observing a particular function performed with precision by a biological system, and then attempting to create a synthetic system that performs the same function for technological applications. The strategy devised to achieve this goal can be quite different from that employed by the biological system. biomimicry: Learning the mechanistic principle used by living systems to achieve a particular function and then attempting to copy the same strategy to achieve biomimetic function. biomineralization: Process by which living organisms produce minerals, often to harden or stiffen existing tissues. Examples include calcium carbonates in seashells and bone in mammals and birds. Boolean logic: Algebraic system of logic developed by George Boole in the mid- 19th century. It is the algebra of two values—usually 0 and 1—and three opera- tions—AND, OR, and NOT. Brownian motion: Random movement of particles suspended in a fluid or the mathematical model used to describe such random movements. cell signaling: Part of a complex system of communication that governs basic c ­ ellular activities and coordinates cell actions. 

A pp e n d i x D 151 chirality: Phenomenon in which an object or molecule cannot be superimposed on its mirror image. cytoskeleton: Cellular “scaffolding” contained within the cytoplasm that maintains cell shape, enables cellular motion, and plays important roles in both intracellular transport and cellular division. dendrimer: Repeatedly branched molecules that are characterized by their high symmetry and narrow distribution of molecular mass (low polydispersity). directed assembly: Application of external fields, such as electric, magnetic, or shear, to align assembling particles into a larger structure. fluorophore: Functional group in a molecule which will absorb energy of a specific wavelength and re-emit energy at a different (but equally specific) wavelength. The amount and wavelength of the emitted energy depend on both the fluorophore and the chemical environment of the fluorophore. foldamer: Discrete chain molecule or oligomer that adopts a secondary structure stabilized by noncovalent interactions. It is an artificial molecule that mimics the ability of proteins, nucleic acids, and polysaccharides to fold into well-defined conformations, such as helices and β-sheets. gene regulation: Cellular control of the amount and timing of changes to the appearance of the functional product of a gene. histone: Chief protein components of chromatin. It acts as spool around which DNA winds, and it plays a role in gene regulation. hydrogel: Network of polymer chains that are water-insoluble, sometimes found as a colloidal gel in which water is the dispersion medium. Hydrogels are super­ absorbent (they can contain over 99 percent water) natural or synthetic polymers. Hydrogels possess also a degree of flexibility very similar to natural tissue, due to their significant water content. lithography: Technique used to pattern or construct features on a surface. macromolecule: Molecule of high relative molecular mass the structure of which usually consists of multiply repeated units that are derived—actually or conceptu- ally—from molecules of low relative molecular mass; particularly a molecule of this kind that is of biological origin. 

152 Inspired by Biology macrophage: Cell within most tissue that originates from specific white blood cells. Its role is to engulf and then digest cellular debris and pathogens either as stationary or mobile cells and to stimulate lymphocytes and other immune cells to respond to the pathogen. magnetic resonance imaging (MRI): Noninvasive technique based on nuclear magnetic resonance (NMR) for imaging the interior of objects, often used in medicine. microtubule: Long hollow cylindrical structure composed of the protein tubulin. It is one of the components of the cytoskeleton, serves as a structural compo- nent within cells, and is involved in many cellular processes, including mitosis, c ­ ytokinesis, and vesicular transport. molecular motor: Biological molecular machine that consumes energy in one form and converts it into motion or mechanical work; for example, many protein-based molecular motors harness the chemical free energy released by the hydrolysis of ATP in order to perform mechanical work. In terms of energetic efficiency, these types of motors can be superior to currently available man-made motors. natural killer (NK) cell: Type of cytotoxic lymphocyte which is a major component of the innate immune system. NK cells play a major role in the rejection of tumors and cells infected by viruses. NK cells kill by releasing small cytoplasmic granules of proteins that cause the target cell to die by apoptosis. nuclear magnetic resonance (NMR): When an atomic nucleus in a magnetic field is exposed to photons that have an energy corresponding to the difference in energy between two possible orientations of its magnetic moment, it will resonate—that is, its magnetic moment will rapidly change orientation, in the process first absorb- ing energy and then radiating it. The frequencies at which resonances are seen in some specified magnetic field not only identify the kinds of atom responsible for them but can also provide valuable information about the molecular environment in which the atoms are found. nucleotide: Molecule that consists of three portions: a heterocyclic base, a sugar, and one or more phosphate groups. Nucleotides are the monomers of nucleic acids, with three or more bonding together in order to form a nucleic acid. Nucleotides are the structural units of RNA, DNA, and several cofactors. oligonucleotide: Short sequences of nucleotides, typically with twenty or fewer bases. 

A pp e n d i x D 153 organelle: Specialized subunit within a cell that has a specific function and is separately enclosed within its own lipid membrane. peptoid: Small proteinlike chain designed to mimic a peptide. Peptoids are closely related to their natural peptide counterparts but differ chemically in that their side chains are appended to nitrogen atoms along the molecule’s backbone, rather than to the α-carbons (as they are in amino acids). polymerase chain reaction: Technique used to amplify the number of copies of a specific region of DNA by the use of sequence-specific primers and multiple cycles of DNA synthesis, each cycle being followed by a brief heat treatment to separate complementary strands. polymersome: Bilayered membranes of amphiphilic synthetic polymers. Polymer- somes exhibit increased stability and reduced permeability compared to natural liposomes. quantum dot: Semiconductor nanostructure that confines the motion of conduc- tion band electrons, valence band holes, or excitons (bound pairs of conduction band electrons and valence band holes) in all three spatial directions. The con- finement can be due to electrostatic potentials (generated by external electrodes, doping, strain, impurities), the presence of an interface between different semi- conductor materials, the presence of the semiconductor surface, or a combination of these. ribosome: Complexes of RNA and protein found in all cells that mediate the trans- lation of messenger RNA molecules into polypeptide chains or amino acids. self-assembly: Spontaneous organization of preexisting components by the forces acting among the components. Self-assembly is generally considered a reversible process, tunable by varying a thermodynamic parameter such as temperature or density, and one that can be controlled through judicious design of the compo- nents. Typically, self-assembled structures form based on thermodynamic prin- ciples in which free energy is minimized. spectroscopy: (Usually) experimental study of the energy level of materials. More generally, a spectrum is a display of the dependence of some property of a sample as a function of some other parameter—for example, energy absorption versus energy or abundance versus molecular mass. Any experimental activity that gener- ates such plots can be described as spectroscopy. 

154 Inspired by Biology stochastic process: Opposite of a deterministic process in probability theory. Instead of dealing only with one possible “reality” of how the process might evolve under time (as is the case, for example, for solutions of an ordinary differential equation), in a stochastic or random process there is some indeterminacy in its future evolution described by probability distributions. This means that even if the initial condition (or starting point) is known, there are many possibilities the process might go to, but some paths are more probable and others less. T cell: Member of a group of white blood cells known as lymphocytes which plays a central role in cell-mediated immunity. T cells can be distinguished from other lymphocyte types, such as B cells and NK cells, by the presence of a special receptor on their cell surface that is called the T cell receptor (TCR). The abbreviation “T”, in T cell, stands for thymus since it is the principal organ for their development. transcription factor: Protein that binds to specific parts of DNA using DNA bind- ing domains and is part of the system that controls the transfer (or transcription) of genetic information from DNA to RNA.