Water Molecules

11 Key excerpts on "Water Molecules"

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  Water

  The Forgotten Biological Molecule

  • Denis Le Bihan, Hidenao Fukuyama, Denis Le Bihan, Hidenao Fukuyama(Authors)
  • 2016(Publication Date)
  • Jenny Stanford Publishing

    (Publisher)

  Chapter 1 THE WATER MOLECULE, LIQUID WATER, HYDROGEN BONDS, AND WATER NETWORKS Martin Chaplin Department of Applied Science, London South Bank University, Borough Road, London SE1 0AA, UK [email protected] 1.1 INTRODUCTION Water (H 2 O) is often perceived to be a perfectly ordinary substance because it is transparent, odorless, tasteless, and ubiquitous. We interact with it all the time in our everyday lives, and it is, not surprisingly, the most studied material on earth. Unfortunately, we often erroneously think that the properties of liquids are those that we ind for liquid water and the changes we see as water changes to steam or ice as those commonly found among other liquids. These assumptions are much mistaken as the properties of liquid water are unique, because it is considerably different from other liquids. Liquid water is the most extraordinary substance, and life on earth and its probability elsewhere in the universe cannot have evolved or continue without it. Organisms consist mostly of liquid water, and this water performs many functions. Therefore it cannot be considered simply as an inert diluent. It transports, lubricates, reacts, enables, stabilizes, signals, structures, and partitions. The living world should be thought of as an equal partnership between the biological molecules and water where each is required and structured by the other. Water: The Forgoen Biological Molecule Edited by Denis Le Bihan and Hidenao Fukuyama Copyright © 2011 by Pan Stanford Publishing Pte. Ltd. www.panstanford.com 4 The Water Molecule, Liquid Water, Hydrogen Bonds, and Water Networks Figure 1.1 The water molecule. Water Molecules have the molecular formula H 2 O. The “average” water molecule has two mirror planes (in the plane of the picture and vertically through the oxygen atom at a right angle) and a twofold axis of symmetry (vertically through the oxygen atom).

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  Biomolecular Electronics

  Bioelectronics and the Electrical Control of Biological Systems and Reactions

  • Paolo Facci(Author)
  • 2014(Publication Date)
  • William Andrew

    (Publisher)

  The recognition of the role of water as one of the main players in biology refers exactly to its role not only as the milieu of choice for life to exist, rather as an essential ingredient for biological phenomena, reactions and systems to take place. In this sense, water should really be considered itself a biological molecule as in the case of any other biomolecule or biomolecular assembly that has its own native structure and functional properties thanks exactly to the involvement of water. Water not only drives and stabilizes molecular structures, but is actively involved in biomolecular functionality, providing, probably, the simplest, paradigmatic exemplification of system biology, where biological structure and function are not inherent to the single biomolecule, but rather to the macromolecule-water system. In other terms, it is meaningless to consider native biomolecular structure and function separately from the presence and the role of water since, as such, they would be simply non-existent. Albeit a detailed analysis of the role of water in biomolecular systems is beyond the scope of this book, in the next sections we will focus on water’s controlling influence over protein and nucleic acid structure and function, neglecting that over cellular activity. The interested readers will find exhaustive readings about the role of water in cellular activity in the literature (see, e.g., Chaplin 2004). 3.4. Water and biomolecules As we have mentioned, water is an integral part of many biomolecules. In particular, water–protein interactions determine and shape the free-energy landscape that governs the folding, structure, stability and activity of proteins (Halle, 2004). In what follows we will see in some detail the role of water in these various contexts. 3.4.1. Protein folding Proteins fold rapidly into well-defined three-dimensional shapes that constitute native structures. These depend on the primary structure, or sequence, of their amino acids

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  Chemical and Functional Properties of Food Components

  • Zdzislaw E. Sikorski(Author)
  • 2006(Publication Date)
  • CRC Press

    (Publisher)

  3.2.6 W ATER IN B IOLOGICAL M ATERIALS 3.2.6.1 Properties Water behaves differently in different environments. Properties of water in hetero-geneous systems, such as living cells or food, remain a field of debate (Mathlouthi, 2001; Rückold et al., 2003). Water Molecules may interact with macromolecular components and supramolecular structures of biological systems through hydrogen bonds and electrostatic interactions. Solvation of biomolecules such as lipids, pro-teins, nucleic acids, or saccharides resulting from these interactions, determines their molecular structure and function. Various physical techniques, such as nuclear magnetic resonance (NMR), x-ray diffraction, and chemical probes (exchange of H by D), indicate that there is a layer of water bound to protein molecules, phospholipid bilayers, and nucleic acids, as well as at the surface of the cell membranes and other organelles. Water associated at the interfaces and with macromolecular components may have quite different properties from those in the bulk phase. Water can be expected to form locally ordered structures at the surface of water-soluble, as well as water-insoluble macromolecules and at the boundaries of the cellular organelles. Biomac-romolecules generally have many ionized and polar groups on their surfaces and tend to align near polar Water Molecules. This ordering effect exerted by the mac-romolecular surface extends quite far into the surrounding medium. According to the association–induction theory proposed by Ling (1962), fixed charges on macromolecules and their associated counterions constrain water mole-cules to form a matrix of polarized multilayers having restricted motion, compared with pure water. The monolayer of Water Molecules absorbed on the polar sorption site of the molecule is almost immobilized and thus behaves, in many respects, like part of the solid or like water in ice. It has different properties from additional water layers defined as multilayers.

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  Foods That Harm, Foods That Promote Health

  A Biochemical and Nutritional Perspective in Health and Disease Prevention

  • Stefan A. Hulea and Mirela Ahmadi, editors, Mirela Ahmadi(Authors)
  • 2021(Publication Date)
  • Universal Publishers

    (Publisher)

  Chapter III

  Water, the big, little understood player in biological systems

  Mirela Ahmadi

  From where it all originated…

  I t is a truism to say that water is the foundation of all life on earth. Water is a critical nutrient without which humans can only live for a few days. And yet we polluted the rivers and oceans of this planet to the point where our own existence is threatened. It is only the belief and hope that man’s inner good, before it’s too late will reverse this state of affairs for the benefit of future generations and life itself on planet Earth.

  3.1. Water structure and properties

  Since water is such a fascinating molecule whose physical and chemical properties are critical for life to exist as we know it, we thought appropriate to refresh the memory of readers on some of the basic features of water structure and properties. Water is one of the smallest molecules on Earth. One liter of water at 25° C weighs 997 g and contains some 33 trillion molecules. Water exhibits unexpected physical properties such as higher boiling point, melting point, heat of vaporization, surface tension and dielectric constant. These properties set water apart from other hydrides of elements close to oxygen in the periodic table, namely N(NH3 ), S(H2 S) and F(HF).

  The high values of the above properties suggest that high intermolecular forces are at work in liquid water as well as ice. The water molecule is electrically neutral but because of differences in electronegativity between the oxygen atom and the hydrogen atoms it behaves as an electric dipole (Fig. 3.1.A ). The water dipoles attract one another and the strength of this attraction is less than the one in the chemical bond between the oxygen atom and the hydrogen atom. This attraction form the basis of hydrogen bonding. The hydrogen (H) bond is weaker and somewhat longer than the H-O bond (Fig. 3.1.B ). The lifespan of a H bond is extremely short, one picosecond (10-12

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  Water in Biological and Chemical Processes

  From Structure and Dynamics to Function

  • Biman Bagchi(Author)
  • 2013(Publication Date)
  • Cambridge University Press

    (Publisher)

  7 An essential chemical for life processes: water in biological functions Water Molecules play diverse roles in facilitating biological processes that are aided by their unique features mentioned in Chapter 1. The dynamic and spatial heterogeneity in the hydration shell of proteins facilitates many important processes, such as enzyme functions, molecu- lar recognition, and protein association, to name a few. Water plays another role in facilitating drug–DNA intercalation, as discussed below. While some of these actions have been discussed extensively in the literature, the direct participation of Water Molecules where one of the oxygen–hydrogen bonds is broken and the resulting proton and hydroxyl anion are used as chemicals seems to have escaped much articulation, even though these steps can influence the kinetics of the catalysis pro- cesses profoundly. In fact this is really impressive chemistry because, as we discussed in Chapter 4, the breaking of the oxygen–hydrogen covalent bond to create a hydroxyl anion and a proton is a rare process in bulk water, but this occurs apparently in an effortless manner in enzyme catalysis. We cannot stop without mentioning its inevitable role in photo- synthesis. In this chapter we try to congregate a few specific examples where water plays a role as a direct collaborator in the functioning of the biological world. 7.1 Introduction We all know that water controls chemical and physical changes in the biological world in both direct and indirect fashions. This was recognized long ago by Leonardo da Vinci, who termed water a “vehicle of natural changes”. It is also termed, albeit less poetically, a “lubricant of life”. What, however, was probably not recognized earlier is that water actively and directly participates in (that is, not just mediates or lubricates) a large number of biological processes, making their occurrence possible in the first place.

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  Biochemical Ecology of Water Pollution

  • Rose Marie O. Mendoza(Author)
  • 2019(Publication Date)
  • Arcler Press

    (Publisher)

  Nevertheless, this material is generally concentrated in just one chapter and its significance is hardly ever emphasized elsewhere. For example, chapters on nucleic acids and proteins, often talk about functional and structural details of these macromolecules with little importance given to the omnipresent effects of the surrounding water (Bernett, 1969; Laing, 1987). Some other areas, for example, metabolism, frequently ignore the several functions of water completely. This lack of prominence often results from the multidisciplinary nature of literature on water and the complexity in bringing together the extensive but frequently thinly-spread available information (Pauling, 1960; Petillo & Lerner, 1993). At first glance, water appears to be a fairly simple molecule, comprising of two hydrogen atoms which are attached to an oxygen atom. However, its size belies the intricacy of its properties, and these characteristics appear to ideally fit into the requirements of a carbon-based life (Bondi, 1964; Shannon, 1976). Organisms are mostly composed of liquid water, which is responsible for performing several functions and must never be considered just an inert diluent. However, despite much investigation, several properties of water are perplexing. Often, it is stated that life is dependent on the anomalous properties of water. Specifically, in organisms, the huge heat capacity, as well as high content of water, play a role in thermal regulation by preventing local temperature fluctuations (Isaacs et al., 1999; 2000; Bartha, Kapuy, Kozmutza, & Van Alsenoy, 2003). The high dormant heat of evaporation provides resistance to dehydration and significant evaporative cooling. Owing to its small size, polarity, and high dielectric constant, water is an excellent solvent, particularly for ionic and polar compounds and salts (Rao, Biochemical Characteristics of Water 45 1972; Oss & Good, 1996; Van Oss, Giese, & Good, 2002; McMurry, 2014).

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  Visualizing Microbiology

  • Rodney P. Anderson, Linda Young, Kim R. Finer(Authors)
  • 2020(Publication Date)
  • Wiley

    (Publisher)

  From a chemical perspective, water is a most unusual molecule, existing naturally in all three physical states within the given temperature range on Earth: as ice, liquid water, and water vapor. Water is a bent molecule composed of one oxygen atom and two hydrogen atoms joined with polar covalent bonds. Despite its simple structure, water is vital to all organisms. Water’s Unique Properties Because water contains polar covalent bonds, it is a polar mol- ecule, which means one end has a slight positive charge and A group of plastic reaction wells used for the diagnosis of HIV infection Reshma P. Shetty 32 CHAPTER 2 An Introduction to the Chemical Basis of Life special features, or emergent properties, that make it uniquely essential for all living things. The first emergent property of water linked directly to its potential for hydrogen bond formation is its lower den- sity as a solid than as a liquid (Figure 2.7b). This is why, the other end has a slight negative charge even though it is electrically neutral overall. Water’s polar nature allows it to participate in extensive hydrogen bond formation with other molecules, often with other Water Molecules (Figure 2.7a). These collective molecular interactions confer on water a set of Negative pole Positive pole Electron pair (–) (+) H H Intermolecular hydrogen bonds –20° F Ambient air temperature Water temperature 40° F FIGURE 2.7 Water’s emergent properties The polarity of water enables it to interact with itself and other polar molecules. These interactions allow water to have emergent properties. MICROBIOLOGY INSIGHT a. Hydrogen bonding between Water Molecules Water’s emergent properties are due to its ability to form numerous hydrogen bonds. Electronegative oxygen pulls the electron pair close, resulting in negative and positive regions or a polar molecule. Consequently, hydrogen bonds form between the slightly positive hydrogen of one water and the slightly negative oxygen of another.

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  Water on Earth

  Physicochemical and Biological Properties

  • Christophe Lécuyer, Christophe Lécuyer(Authors)
  • 2013(Publication Date)
  • Wiley-ISTE

    (Publisher)

  Chapter 1

  Water: A Molecule Endowed with Extraordinary Physicochemical Properties

  1.1. Molecular geometry and electrical properties

  A water molecule consists of an oxygen atom bonded to two hydrogen atoms. In water, each hydrogen atom is bound to the oxygen by a pair of electrons. However, only two of the six outer-shell electrons of oxygen are used to form covalent bonds, the remaining four being organized into two non-bonding pairs (Figure 1.1 ). The four electron pairs surrounding the oxygen tend to arrange themselves as far from each other as possible in order to minimize repulsions between these clouds of negative charge. However, the two non-bonding pairs exert a strong repulsion against the two covalent bonding pairs, which results in a deformed tetrahedral geometry with a angle of 105° instead of the theoretical angle of 109°. As a result, the H2 O molecule is electrically neutral even though the electrical charges are not distributed uniformly. Indeed, a negative charge is associated with the oxygen atom while the hydrogen atom carries a positive charge (Figure 1.2 ). This electronic configuration defines the polar structure of Water Molecules, which consequently have a mutual attraction and tend to stick together.

  This process is called “hydrogen bonding” and explains why water is a liquid instead of a gas under standard conditions (close to the Earth’s surface pressure and temperature conditions). In comparison to a covalent bond, the hydrogen bond is so weak that the timescale of its life expectancy is in the order of the picosecond (10−12 s), therefore explaining the low molecular viscosity of water (

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  Water and Life

  The Unique Properties of H2O

  • Ruth M. Lynden-Bell, Simon Conway Morris, John D. Barrow, John L. Finney, Charles Harper, Ruth M. Lynden-Bell, Simon Conway Morris, John D. Barrow, John L. Finney, Charles Harper(Authors)
  • 2010(Publication Date)
  • CRC Press

    (Publisher)

  It maintains macromolecular structure and medi-ates molecular recognition, it activates and modulates protein dynamics, it provides a switchable communication channel across membranes and between the inside and outside of proteins. Many of these properties do seem to depend, to a greater or lesser degree, on the special attributes of the H 2 O molecule, in particular its ability to engage in directional, weak bonding in a way that allows for reorientation and reconfiguration of discrete and identifiable three-dimensional structures. Thus, although it seems entirely likely that some of water’s functions in biology are those of a generic polar solvent rather than being unique to water itself, it is very hard to imagine any other solvent that could fulfill all of its roles—or even all of those that help to distinguish a generic polypeptide chain from a fully functioning protein. The fact that fully folded proteins moved from an aqueous to a nonaqueous environment may retain some of their functionality does not alter this, and does not detract from the centrality of water for life on earth. That, however, is not the same as saying that all life must be aqueous. At least with our present (incomplete) state of knowledge about pivotal concepts such as the hydrophobic interaction, it is not obvious that any one of the functions of water in biology has to stand as an irreducible aspect of a living system. It is certainly possible to imagine, and even to make, 133 artificial chemical systems that engage in some form of information transfer—indispensable for inheritance and Darwinian evolution—in nonaqueous media. Moreover, life in water has some well publicized drawbacks 134 —perhaps most notably the sol-vent’s reactivity, raising the problem of hydrolysis of polymeric structures and of basic building blocks such as sugars. How the first pseudo-biological macromolecules on the early earth avoided this problem is still something of a puzzle.

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  Water

  A Matrix of Life

  • Felix Franks(Author)
  • 2007(Publication Date)
  • Royal Society of Chemistry

    (Publisher)

  There is still a tendency to think of crystallographically ordered water as ‘the’ hydration, neglecting the facts that all Water Molecules are subject to more or less rapid exchange with water in the bulk and that not all Water Molecules exist in the ordered state. As regards the role of water in promoting or maintaining a particular biopolymer configurational state, it cannot be emphasised too strongly that stability is a matter of the free energy of the whole system, and not of the apparent structure. Structural biology literature, especially as it pertains to nucleic acids, suffers from some confusion between structure and thermodynamics, especially where labile, non-covalently bonded hydration structures are involved. Water Hydration and the Molecules of Lfe 135 forms an integral part of all ordered biological structures, helical and otherwise, a factor that must be taken into account in any adequate description of such a system. This caveat is of particular importance for descriptions of nucleotides, because of their highly charged nature. Lipid Thermotropism and Lyotropism Lipids are included here because, together with the biopolymers, they constitute the basic building blocks of biological structures. They differ from the other, polymeric species described in this chapter because, by comparison, they are ‘small’ molecules. The structures formed by lipids are stabilised by noncovalent interactions, resulting from hydration and steric factors. In the main they are derivatives of glycerol in which one, two or all three -OH groups have been replaced by acyl chains and ionogenic or polar groups. Some other molecules that are also often classified as lipids include steroids, e.g. cholesterol. Within the context of this chapter, pride of place goes to those polar lipids that are the main constituents of biological membranes.

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  Water Relations of Foods

  Proceedings of an International Symposium held in Glasgow, September 1974

  • R Duckworth(Author)
  • 2012(Publication Date)
  • Academic Press

    (Publisher)

  It is accepted that the properties of liquid water—even at high temperatures—reflect an unusually expanded arrangement of centers at the molecular level. This non-close packing feature is even more extreme for ice. Our immediate concern is what can be said about the molecular arrangement of Water Molecules in the presence of biopolymers. The relevant experimental evidence now comes from three sources: (1) high resolution X-ray and neutron diffraction from protein crystals; (2) n.m.r. dipolar and quadrupolar splitting in oriented systems; (3) i.r. bandwidths and dichroism from hydrated films. We can anticipate that new information will soon be available from self-diffusion studies and inelastic neutron scattering. The high resolution diffrac-tion studies of protein crystals are approaching atomic resolution. Water Molecules have been located as part of the repeating structural unit. Typically 5-20 Water Molecules per protein are found localized often at active sites. A careful study of chymotrypsin (Birktoft and Blow, 1972) found 51 Water Molecules, 16 of which were inside the protein. About 10 Water Molecules are incorporated in carbonic anhydrase and subtilisin. We can suspect that these Water Molecules move with the proteins when the crystals are dissolved and that they contain the water protons seen in the low frequency n.m.r. dispersion experiments. Considerably larger numbers of Water Molecules can be seen in the interstitial regions of the protein crystals. There are large uncertainties here, because at 2-3 Â resolution the water oxygens are quite indistinct. There are several reports of 100-300 such oxygens being identifiable [see Kuntz and Kauzmann (1974)]. No readily apparent water structure is associated with these surface waters. They appear to be serving as proton donors and proton acceptors for the hydrogen bonding sites on the protein surface, as we have come to expect from the spectroscopic studies.

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