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Water# - Biology

Water# - Biology


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Water is a unique substance whose special properties are intimately tied to the processes of life. Water solvates or "wets" the cell and the molecules in it, plays a key role as reactant or product in an innumerable number of biochemical reactions, and mediates the interactions between molecules in and out of the cell. Many of water’s important properties derive from the molecule's polar nature, which can be tracked down to the polar molecules whose dipole originates from its polar covalent bonds between hydrogen and oxygen.

In BIS2A, the ubiquitous role of water in nearly all biological processes is easy to overlook by getting caught up in the details of specific processes, proteins, the roles of nucleic acids, and in your excitement for molecular machines (it'll happen). It turns out, however, that water plays key roles in all of those processes and we will need to continuously stay aware of the role that water is playing if we are to develop a more functional understanding. Be on the lookout and also pay attention when your instructor points this out.

In a liquid state, individual water molecule interact with one another through a network of dynamic hydrogen bonds that are being constantly forming and breaking. Water also interacts with other molecules that have charged functional groups and/or functional groups with hydrogen bond donors or acceptors. A substance with sufficient polar or charged character may dissolve or be highly miscible in water is referred to as being hydrophilic (hydro- = “water”; -philic = “loving”). By contrast, molecules with more nonpolar characters such as oils and fats do not interact well with water and separate from it rather than dissolve in it, as we see in salad dressings containing oil and vinegar (an acidic water solution). These nonpolar compounds are called hydrophobic (hydro- = “water”; -phobic = “fearing”). We will consider the some of the energetic components of these types of reactions in other another chapter.

Figure 1. In a liquid state water forms a dynamic network of hydrogen bonds between individual molecules. Shown are one donor-acceptor pair.
Attribution: Marc T. Facciotti (original work)

Water's solvent properties

Since water is a polar molecule with slightly positive and slightly negative charges, ions and polar molecules can readily dissolve in it. Therefore, water is referred to as a solvent, a substance capable of dissolving other polar molecules and ionic compounds. The charges associated with these molecules will form hydrogen bonds with water, surrounding the particle with water molecules. This is referred to as a sphere of hydration, or a hydration shell and serves to keep the particles separated or dispersed in the water.

When ionic compounds are added to water, the individual ions interact with the polar regions of the water molecules, and the ionic bonds are likely disrupted in the process called dissociation. Dissociation occurs when atoms or groups of atoms break off from molecules and form ions. Consider table salt (NaCl, or sodium chloride). A dry block of NaCl is held together by ionic bonds and is difficult to dissociate. When NaCl crystals are added to water, however, the molecules of NaCl dissociate into Na+ and Clions, and spheres of hydration form around the ions. The positively charged sodium ion is surrounded by the partially negative charge of the water molecule’s oxygen. The negatively charged chloride ion is surrounded by the partially positive charge of the hydrogen on the water molecule. One may imagine a model in which the ionic bonds in the crystal are "traded" for many smaller scale ionic bonds with the polar groups on water molecules.

Figure 2. When table salt (NaCl) is mixed in water, spheres of hydration are formed around the ions. This figure depicts a sodium ion (dark blue sphere) and a chloride ion (light blue sphere) solvated in a "sea" of water. Note how the dipoles of the water molecules surrounding the ions are aligned such that complementary charges/partial charges are associating with one another (i.e., the partial positive charges on the water molecules align with the negative chloride ion whereas the partial negative charges on the oxygen of water align with the positively charged sodium ion).
Attribution: Ting Wang - UC Davis (original work modified by Marc T. Facciotti)

Note: possible discussion

Consider the model of water dissolving a salt crystal presented above. Describe in your own words how this model can be used to explain what is happening at the molecular level when enough salt is added to a volume of water that the salt no longer dissolves (the solution reaches saturation). Work together to craft a common picture.

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Properties of Water: AP® Biology Crash Course Review

Attention: This post was written a few years ago and may not reflect the latest changes in the AP® program. We are gradually updating these posts and will remove this disclaimer when this post is updated. Thank you for your patience!


Freshwater biology

Freshwater biology is the scientific biological study of freshwater ecosystems and is a branch of limnology. This field seeks to understand the relationships between living organisms in their physical environment. These physical environments may include rivers, lakes, streams, ponds, lakes, reservoirs, or wetlands. [1] Knowledge from this discipline is also widely used in industrial processes to make use of biological processes involved with sewage treatment [2] and water purification. Water presence and flow is an essential aspect to species distribution and influence when and where species interact in freshwater environments. [1]

In the UK the Freshwater Biological Association [3] based near Windermere in Cumbria was one of the early institutions to research the biology of freshwater and promote the concepts of trophism in lakes and demonstrated the process of migration from oligotrophic water through mesotrophic to marsh.

Freshwater biology is also used to study the effects of climate change and increased human impact on both aquatic systems and wider ecosystems. [4]

  1. ^ ab Castillo-Escrivà, Andreu Aguilar-Alberola, Josep A. Mesquita-Joanes, Francesc (2017-06-01). "Spatial and environmental effects on a rock-pool metacommunity depend on the landscape setting and dispersal mode". Freshwater Biology. 62 (6): 1004–1011. doi:10.1111/fwb.12920. ISSN1365-2427.
  2. ^Open University - Sewage treatment processes
  3. ^The Freshwater Biological Association web site
  4. ^
  5. Rockström, Johan Steffen, Will Noone, Kevin Persson, Åsa Chapin, F. Stuart Lambin, Eric F. Lenton, Timothy M. Scheffer, Marten Folke, Carl (2009). "A safe operating space for humanity" (PDF) . Nature. 461 (7263): 472–475. doi: 10.1038/461472a . PMID19779433.

This ecology-related article is a stub. You can help Wikipedia by expanding it.


The Biological Importance of Water

The first topic that I covered in AS Level Biology was about molecules of biological importance. Water is a substance that is in great abundance on this planet, and it holds some significant importance to our lives. Without it, we could not live, and not simply because we would die of thirst. Some of the notes here are also relevant to AS Chemistry, but be careful, as different specifications might ask for information on different anomalous properties, so make sure you check your exam syllabus!

The Properties of Water

A water molecule consists of two hydrogen atoms and an oxygen atom however, the electrons in the covalent bonding are not shared equally. The oxygen atom has a greater electronegativity, meaning that it has a greater pull on the electrons. Due to this each water molecule has slightly negative and slightly positive regions.

The negative and positive ends of water molecules attract each other to form hydrogen bonds. These hydrogen bonds give water many of its unique properties. Compounds with molecules similar to the size of water are usually gases. Since each water molecule can form hydrogen bonds with up to 4 other water molecules, water is a liquid at room temperature.

Polar and ionic substances have an electrostatic charge, so they are attracted to the charges on water molecules and dissolve readily. Non-polar substances, such as oil, do not dissolve in water, as they do not have charged molecules. When a salt dissolves in water, the ions separate and a layer of water molecules form around the ions. These layers prevent ions or polar molecules from clumping together, keeping the particles in solution.

At an interface between air and water, a water molecule on the surface forms hydrogen bonds with other molecules around and below it, but not with air molecules above it. The unequal distribution of bonds produces a force called surface tension this causes the water surface to contract and form a surprisingly tough film or ‘skin’.

Water is at its most dense at 4 o C. When water freezes the hydrogen bonds between the molecules forms a rigid lattice, that holds the molecules further apart then in liquid water. Ice, having expanded when freezing, is less dense than its liquid counterpart and so floats on water.

Water is ‘wet’ because it sticks to things. This is because its molecules can form hydrogen bonds with other polar substances. This is called adhesion. The attraction between molecules of similar substances is called cohesion. In this way water molecules stick together which allows water to enter and move along very narrow spaces, in a process called capillarity.

Water has a high specific heat capacity meaning that it needs to gain a lot of energy to raise its temperature. Conversely it also needs to lose a lot of energy to lower its temperature. Water’s specific heat capacity is 4.2 kJ/g/ o C

Water has a high latent heat of vaporisation which means a lot of energy is required to evaporate it. When it evaporates, water draws thermal energy out of the surface it’s on, which can be observed in sweating.

Water also has a high latent heat of fusion meaning that at 0 o C water must lose a lot of thermal energy before it freezes, thus liquid water can reach temperatures of down to -10 o C before it forms ice.

It is transparent to sunlight.

It has a relatively high density compared to air.

It is difficult to compress.

It conducts electricity (when it contains dissolved ions)

See if you can think of ways that these properties are important to life.

An important part of A Level Biology is being able to write a clear and concise essay on the topics you have covered, particularly as many exam boards set an essay question in each of their papers. Below is an example essay on the importance of water.

The Biological Importance of Water

Water has several unique properties that make it vital not only for human beings, but for all living organisms to survive. The most noticeable of its physical properties is that it is a liquid at room temperature, which is unusual for compounds with molecules of a similar atomic composition. This is due to the hydrogen bonds that form between each water molecule, and up to four others. Water being a liquid at room temperature provides a marine environment for organisms to live in, and also provides a liquid environment inside cells, which holds significant importance as metabolic reactions that are key to life take place in solution.

Water molecules are dipolar, meaning they have a positively charged and a negatively charged region. The charges of these areas attract polar and ionic substances that are dissolved in it, and the water molecules form a layer around each charged ion, keeping the substance in solution. Water is known as the ‘universal solvent’, this is because it dissolves much more substances than most common solvents. This is of vital significance as all of the metabolic reactions essential for life take place in solution in the cytoplasm of living cells.

Another property caused by water molecules being dipolar is that water is adhesive, and this adhesion makes water stick to other polar substances, effectively making it ‘wet’. This allows water to move upwards through the very narrow xylem of tall plants, such as trees, against gravity. Continuous columns of water can also be pulled up to the top of trees due to its high tensile strength, meaning that water columns do not break easily. Also important to plants is water’s transparency. Water, being transparent and colourless transmits sunlight, enabling aquatic plants to photosynthesis, and also enabling us to see, as our eyes are coated in water.

There are also many thermal properties that make water so essential for life, for example its very high specific heat capacity, 4.2kJ/g/ o C . This means that a lot of energy needs to be gained, or lost, in order to change the temperature of water, and so the environment inside organisms resists temperature changes that could cause it damage. Water also has a high latent heat of vaporisation which means mean that water needs a lot of energy to evaporate, and so draws this thermal energy from the surface it is on, cooling it as the water evaporates from it (this can be observed when we sweat to cool ourselves). Water’s high latent heat of fusion prevents the liquid environment of cells from freezing, and tearing the cells apart, as liquid water temperatures can drop to around -10 o C before it begins to freeze.


Friday, October 28, 2016

Are hydrophobic protein surfaces like big or small hydrophobes?

It seems to me that a paper on protein denaturation by Michele Vendruscolo at Cambridge, Stefano Gianni at the University of Rome La Sapienza, and their colleagues will repay careful study (C. Camilloni et al., Sci. Rep. 6, 28285 2016 – paper here). The researchers use MD simulations to model observed NMR shifts during hot and cold denaturation, and thereby to gain insight into transition-state structures, changes in hydration and thermodynamic parameters. This enables them to characterize in some detail the differences between hot and cold denaturation: the former has more secondary structure, being more influenced by hydrophobic interactions. In effect this points to the existence of two alternative folding mechanisms from denatured states. What’s more, water molecules at the protein surface have the same number of hydrogen bonds on average as those in the bulk. This is what theory predicts for small hydrophobes ( 7 ps, some as much as 20 ps. These waters tend to be located in concavities on the protein surface and make fewer hydrogen bonds with surrounding waters than do molecules in the bulk. Moreover, waters near hydrophobic groups tend to be slower on average than those near hydrophilic groups. But although misfolding exposes more of the hydrophobic surface, it also means that these hydrophobic regions are less concave, and so the water dynamics is somewhat faster on average and there are fewer of the “ultraslow” sites.


Water reorientational decay times seen in simulations of native (left) and misfolded (right) bovine α-lactalbumin.

A somewhat comparable exercise is conducted for B-DNA by James Hynes and Damien Laage at the ENS Paris and colleagues (E. Duboué-Dijon et al., JACS 138, 7610 2016 – paper here). And there are some commonalities: while the hydration water is generally rather slower to reorient than in the bulk, the waters confined in the narrow minor groove are much more significantly retarded (relaxation times 30-85 ps). Moreover, there is considerable heterogeneity, and some of this comes from coupling of the macromolecular fluctuations with the water dynamics, especially in the minor groove. In other words, there does not seem in this case to be slaving of biomolecular dynamics to those of the solvent, but more or less the reverse.


Water reorientational times on the minor and major grooves of the B-DNA dodecamer (CGCCAATTCGCG)2

Lorna Dougan at Leeds and colleagues have found evidence of a low-density form of water at low temperatures (285-238K), which might be related to the putative phase transition separating low- and high-density liquids in the metastable regime (J. J. Towey et al., JPCB 120, 4439 2016 – paper here). They keep the water liquid by mixing it with the cryoprotectant glycerol. Neutron scattering and simulation show that at low temperatures the mixture segregates at the nanoscale, and the water nanophase has greater tetrahedral ordering than the bulk.

Predicting protein structure from sequence data often draws on information on homologous structures or fragments from the Protein Data Base. But such homologies cannot always be spotted, or might not be present in the database, or might not be reliable. Peter Wolynes and colleagues at Rice have developed a scheme for predicting structures ab initio, without bioinformatics input, using what they call the atomistic, associative memory, water mediated structure and energy model (AAWSEM) (M. Chen et al., JPCB 120, 8557 2016 – paper here). This uses coarse-grained simulations at the whole-protein level while drawing on atomistic simulation of fragments – and crucially, incorporates water-mediated interactions in the folding process. It’s a smart approach to the folding problem that draws on the biological reality – the fact that protein folding is funneled to make it evolutionarily robust to small variations in sequence – rather than brute-force number-crunching.

Water mediation is thought to be important too for the aggregation of amyloid fibrils. Samrat Mukhopadhyay and colleagues at the Indian Institute of Science Education and Research in Mohali have used time-resolved fluorescence measurements on the human prion protein (PrP) to investigate how (V. Dalal et al., ChemPhysChem 17, 2804 2016 – paper here). They find that water hydrating the amyloid-competent oligomers has mobility retarded by three orders of magnitude relative to the bulk, perhaps because of entrapment in the collapsed polypeptide chains. They say that this water might create a hydrogen-bonded network that stabilizes the partly unfolded, molten oligomer conformation and acts as a scaffolding for the assembly of oligomers into fibrils.


Proposed role of ordered water molecules in the misfolding and amyloid formation of PrP – and in protein misfolding diseases more generally.

Antiviral drugs against influenza B could work by blocking the proton-conducting channel BM2, but no such have yet been devised. Mei Hong at MIT and colleagues have used NMR to investigate the mechanism of proton transport in BM2 and the role of hydration, and to elucidate the differences with AM2 from influenza A (J. K. Williams et al., JACS 138, 8143 2016 – paper here). The His19 residue in BM2 remains unprotonated to lower pH than the corresponding His 37 in AM2, but increasing channel hydration in acidic conditions seems to enhance proton transport to His 19 from water molecules.

Why trehalose acts as a cryoprotectant of protein structure still isn’t fully understood. Jan Swenson and coworkers at Chalmers University of Technology in Göteborg try to develop a comprehensive picture by looking at how trehalose affects the protein glass transition, denaturation temperature, and solution viscosity (C. Olsson et al., JPCB 120, 4723 2016 – paper here). They study the myoglobin-trehalose-water system using DSC and viscometry. In short, their results seem to exclude the picture in which trehalose displaces water in the solvation shell on the contrary, they suggest that the protein retains one or two layers of water within a stabilizing water-trehalose matrix. This would be consistent with an apparent lack of coupling between the trehalose-water matrix dynamics and the stability of the native protein.


Schematic of the interactions between water, trehalose and protein.

That picture of a lack of direct interaction between trehalose and proteins – the disaccharide is in fact preferentially excluded from the protein hydration layer – is also the general context for an experimental study by Christina Othon of Wesleyan University in Connecticut and colleagues of trehalose bioprotection (N. Shukla et al., JPCB 120, 9477 2016 – paper here). Using ultrafast fluorescence spectroscopy for two fluorescent probes, they see a slowdown of water reorganizational dynamics at relatively low trehalose concentrations (0.1-0.25 M, well below the vitrification threshold). At these concentrations, there is around 7 water layers between osmolyte molecules. These results therefore support an indirect mechanism for cryoprotection. Sucrose has much the same effect, but less markedly, the researchers say.

The interaction between two hydrophobic particles in water is generally attractive: this is simply the (water-mediated) hydrophobic effect. But Alenka Luzar and coworkers at Virginia Commonwealth University show that this interaction can become repulsive (B. S. Jabes et al., JPC Lett 7, 3158 2016 – paper here). Such repulsion has been seen before in simulations of fullerenes and carbon nanotubes in water, and has sometimes been attributed to specific structural changes in the water. But Alenka and her colleagues show that it can be explained purely as a geometric effect of the thermodynamic cost of formation of a liquid-vacuum interface bridging the hydrophobic particles (in these calculations, pure and propyl-terminated graphitic nanoparticles) when drying occurs in the intervening space. This process can be modeled with a straightforward, bulk-like Young-type calculation of the surface free energies.

Nanoconfinement effects on water structure and properties are investigated by Vrushali Hande and Suman Chakrabarty of the National Chemical Laboratory in Pune through simulations of water inside reverse micelles and water-in-oil nanodroplets (Phys. Chem. Chem. Phys. 18, 21767 2016 – paper here). For the reverse micelles the interface is (negatively) charged, and the deviations from bulk-like behaviour are longer-ranged for orientational order than they are for translational ordering. These effects are far less pronounced for nanodroplets in oil, where the interface is hydrophobic, indicating that electrostatic influences on the hydrogen bonding are more pronounced than spatial confinement per se.

Also on nanoconfinement: quite why water has an enhanced mobility in carbon nanotubes remains a matter of some debate. Using IR spectroscopy, Pascale Roy at the Synchrotron Soleil in Gif-sur-Yvette and colleagues suggest that it may be due to unusually “loose” hydrogen-bond networks among water molecules inside the nanotubes (S. D. Bernadina et al., JACS 138, 10437 2016 – paper here). They look at nanotubes with diameters of 0.7-2.1 nm, in which the water varies from single-file chains to multilayers, and find a spectroscopic signature of “loosely bonded water” in all cases – in the latter seeming to correspond to waters in the outer layers with dangling OH bonds pointing towards the nanotube walls.

The distance dependence of the hydrophobic force between two hydrophobic walls is investigated in MD simulations by Biman Bagchi and colleagues at the Indian Institute of Science in Bangalore (preprint arxiv.1608.04107). They find a bi-exponential force law, with correlation lengths of 2 nm and 0.5 nm, and a crossover close to 1.5 nm. This behaviour is mimicked by the tetrahedral order parameter, but I’m not entirely clear what the authors’ mechanistic explanation is.

Of course, the issue with many studies of this kind is that your results might only be as good as your model. Angelos Michaelidies and colleagues at UCL offer an overview of the extent to which density-functional theory supplies a good description of water, from small clusters to the bulk (M. J. Gillan et al., JCP 144, 130901 2016 – paper here). In particular they consider how well different functional forms of exchange-correlation terms perform, and what role many-body terms play. Looks like essential reading for anyone using DFT to model aqueous systems.

Many-body effects are also central to a study by Shelby Straight and Francesco Paesani at UCSD of influences of water’s dipole moment on the hydrogen-bond network of pure water (JPCB 120, 8539 2016 – paper here). They use simulations to predict the infrared spectra of HOD in H2O, and in particular the shape of the OD stretch. They find that the calculated spectral diffusion of this vibrational frequency depends rather strongly on exactly how one truncates a many-body expansion of the water dipole.

How effectively can hydration be described with a coarse-grained model? Bill Jorgensen and colleagues consider the performance of one attempt to balance accuracy and speed that mixes all-atom and coarse-grained descriptions – the so-called AAX-CGS model, in which all-atom solutes are solvated with coarse-grained water (X. C. Yan et al., JPCB 120, 8102 2016 – paper here). The approach works well for hydrophobic and halogenated alkane solutes, less so for those that are more polar or engage in hydrogen bonding (amines, alcohols). But the efficiency of the calculations beats that of all-atom simulations by about an order of magnitude or more.

Why are ion hydration free energies asymmetric with respect to ion charge? Rick Remsing and John Weeks investigate that question using an analytical model for calculating hydration free energies that involves gradually “turning on” the ion-solvent Coulomb interaction (JPCB 120, 6238 2016 – paper here). This enables them to see why the Born solvation model fails to capture the asymmetry: in short, it works well enough for slowly varying Gaussian charge distributions but not for the abrupt, delta-function-like distributions in ion cores. Only in the latter case is the asymmetry in response to ion charge recovered.


Operation Water Biology (OWB) is a series of eight lesson plans designed for use with students in grades 9-12. OWB directly connects with science, chemistry and biology curricula and covers several different aspects of drinking water treatment. The major topics are chlorine, chloramine, ammonia and iron. For each of these there is a discussion explaining what it is and its importance to drinking water treatment. There are also lab activities for each which allow students to work with small amounts of these substances and see them in action. Students will demonstrate the idea of chlorine demand, create chloramine through a simple chemical reaction, test local samples of drinking water for chlorine and ammonia, and filter water samples with iron oxidized by different processes to determine if one is superior. Every lesson includes additional suggested activities and resources, along with references to other sources of information.

Generally, sponsored Operation Water Biology kits are sent to schools every second Monday from mid-September until the beginning of November and the beginning of March until the end of May. Purchased kits are usually sent on the same dates, but teachers can request that they be sent as soon as possible and we will do our best to accommodate their request.

The cost of an Operation Water Biology kit is $170 and includes all of the materials necessary to conduct the experiments. Many school kits are available free of charge as a result of different sponsors. However, if there is not a sponsored kit available for your school or you want a kit right away it is best to purchase a kit.

Or, phone us at 1-306-934-0389 to pay for your kit with Visa or MasterCard.

Or, mail a cheque payable to Safe Drinking Water Foundation to:

Safe Drinking Water Foundation
#1-912 Idylwyld Drive North
Saskatoon, SK S7L 0Z6


Water# - Biology

All living things need water to stay alive, and plants are living things! Plants, however, need much more water than many living things because plants use much more water than most animals. Plants also contain more water than animals - plants are about 90% water. The amount of water a plant needs depends on the type of plant, how much light the plant gets, and how old the plant is. When plants are not watered properly they wilt. This is because of something called turgor, which is water pressure inside the cells that make up the plant's skeleton. Water enters a plant through its stem and travels up to its leaves. When a plant is properly hydrated, there is enough water pressure to make the leaves strong and sturdy when a plant doesn't get enough water, the pressure inside the stems and leaves drops and they wilt.

Plants also need water for photosynthesis. Photosynthesis is what plants do to create their food, and water is critical to this process. Water enters a plant's stem and travels up to its leaves, which is where photosynthesis actually takes place. Once in the leaves water evaporates, as the plant exchanges water for carbon dioxide. This process is called transpiration, and it happens through tiny openings in the plant's leaves, called stomata. The water from the leaves evaporates through the stomata, and carbon dioxide enters the stomata, taking the water's place. Plants need this carbon dioxide to make food. Transpiration - this exchange of water for carbon dioxide - only occurs during the day when there is sunlight. This is why you might find dew on plants in the morning.

The plants contain a lot of water because all night long water has been entering through the stem and being pulled into the leaves where it can't evaporate. Since the water doesn't evaporate at night, the water has no where to go so it remains on the leaves as dew.

When water evaporates from a plant during transpiration it cools the plant, in the same way the humans sweat to cool off in the heat. A mature house plant can transpire its body weight daily. This means it gives off a lot of water! If people needed that much water, an adult would drink 20 gallons of water a day.

Actually, all living things need water because life requires a LOT of chemical reactions. The chemicals are usually dissolved in water. Also, plants put the water together with carbon dioxide to make sugar. This takes energy, which plants get from light.

Water also helps plants stand up tall, even when they aren’t made of wood. They don’t have bones, but they do have cell walls and water pressure. Water comes up from the roots, but carbon dioxide doesn’t. How do you think plants get carbon dioxide?

The plants need water because the reactions that take place in the cell to make energy require a watery medium.

Plants need water for the same reason that all living things do: to dissolve the chemicals they use to do their biology. Plants also use a water current up the plant for transport, which evaporates water out the leaves, so they need water for that reason, too. Lastly, water is used to make sugar, and plants store energy in the form of sugar.


PH, Buffers, Acids, and Bases

The pH of a solution indicates its acidity or alkalinity.

litmus or pH paper, filter paper that has been treated with a natural water-soluble dye so it can be used as a pH indicator, to test how much acid (acidity) or base (alkalinity) exists in a solution. You might have even used some to test whether the water in a swimming pool is properly treated. In both cases, the pH test measures the concentration of hydrogen ions in a given solution.

Hydrogen ions are spontaneously generated in pure water by the dissociation (ionization) of a small percentage of water molecules into equal numbers of hydrogen (H + ) ions and hydroxide (OH – ) ions. While the hydroxide ions are kept in solution by their hydrogen bonding with other water molecules, the hydrogen ions, consisting of naked protons, are immediately attracted to un-ionized water molecules, forming hydronium ions (H30 + ). Still, by convention, scientists refer to hydrogen ions and their concentration as if they were free in this state in liquid water.

The concentration of hydrogen ions dissociating from pure water is 1 × 10 -7 moles H + ions per liter of water. Moles (mol) are a way to express the amount of a substance (which can be atoms, molecules, ions, etc), with one mole being equal to 6.02 x 10 23 particles of the substance. Therefore, 1 mole of water is equal to 6.02 x 10 23 water molecules. The pH is calculated as the negative of the base 10 logarithm of this concentration. The log10 of 1 × 10 -7 is -7.0, and the negative of this number (indicated by the “p” of “pH”) yields a pH of 7.0, which is also known as neutral pH. The pH inside of human cells and blood are examples of two areas of the body where near-neutral pH is maintained.

Non-neutral pH readings result from dissolving acids or bases in water. Using the negative logarithm to generate positive integers, high concentrations of hydrogen ions yield a low pH number, whereas low levels of hydrogen ions result in a high pH. An acid is a substance that increases the concentration of hydrogen ions (H + ) in a solution, usually by having one of its hydrogen atoms dissociate. A base provides either hydroxide ions (OH – ) or other negatively charged ions that combine with hydrogen ions, reducing their concentration in the solution and thereby raising the pH. In cases where the base releases hydroxide ions, these ions bind to free hydrogen ions, generating new water molecules.

The stronger the acid, the more readily it donates H + . For example, hydrochloric acid (HCl) completely dissociates into hydrogen and chloride ions and is highly acidic, whereas the acids in tomato juice or vinegar do not completely dissociate and are considered weak acids. Conversely, strong bases are those substances that readily donate OH – or take up hydrogen ions. Sodium hydroxide (NaOH) and many household cleaners are highly alkaline and give up OH – rapidly when placed in water, thereby raising the pH. An example of a weak basic solution is seawater, which has a pH near 8.0, close enough to neutral pH that marine organisms adapted to this saline environment are able to thrive in it.

The pH scale is, as previously mentioned, an inverse logarithm and ranges from 0 to 14 ([link]). Anything below 7.0 (ranging from 0.0 to 6.9) is acidic, and anything above 7.0 (from 7.1 to 14.0) is alkaline. Extremes in pH in either direction from 7.0 are usually considered inhospitable to life. The pH inside cells (6.8) and the pH in the blood (7.4) are both very close to neutral. However, the environment in the stomach is highly acidic, with a pH of 1 to 2. So how do the cells of the stomach survive in such an acidic environment? How do they homeostatically maintain the near neutral pH inside them? The answer is that they cannot do it and are constantly dying. New stomach cells are constantly produced to replace dead ones, which are digested by the stomach acids. It is estimated that the lining of the human stomach is completely replaced every seven to ten days.

Watch this video for a straightforward explanation of pH and its logarithmic scale.

So how can organisms whose bodies require a near-neutral pH ingest acidic and basic substances (a human drinking orange juice, for example) and survive? Buffers are the key. Buffers readily absorb excess H + or OH – , keeping the pH of the body carefully maintained in the narrow range required for survival. Maintaining a constant blood pH is critical to a person’s well-being. The buffer maintaining the pH of human blood involves carbonic acid (H2CO3), bicarbonate ion (HCO3 – ), and carbon dioxide (CO2). When bicarbonate ions combine with free hydrogen ions and become carbonic acid, hydrogen ions are removed, moderating pH changes. Similarly, as shown in [link], excess carbonic acid can be converted to carbon dioxide gas and exhaled through the lungs. This prevents too many free hydrogen ions from building up in the blood and dangerously reducing the blood’s pH. Likewise, if too much OH – is introduced into the system, carbonic acid will combine with it to create bicarbonate, lowering the pH. Without this buffer system, the body’s pH would fluctuate enough to put survival in jeopardy.

Other examples of buffers are antacids used to combat excess stomach acid. Many of these over-the-counter medications work in the same way as blood buffers, usually with at least one ion capable of absorbing hydrogen and moderating pH, bringing relief to those that suffer “heartburn” after eating. The unique properties of water that contribute to this capacity to balance pH—as well as water’s other characteristics—are essential to sustaining life on Earth.

To learn more about water. Visit the U.S. Geological Survey Water Science for Schools All About Water! website.


Harry Jabs is educated with two masters’ degrees in physics, from Germany and Texas A&M University. Currently he is senior scientist at the Institute for Frontier Science in Emeryville, California. He is a multidisciplinary researcher and engineer who has developed novel technologies in such diverse areas as energy, nano/bio-technology, electronics, computer hardware and software, detector systems, and fluid handling.

– Title Of Talk –

Influences on Chiral Symmetry Breaking During Crystallization of Salts from Aqueous Solution