Water Chemistry

Water Sources

According to the United States Geological Survey (USGS), 71% of the Earth’s surface is covered in water, and of that 97% are the oceans. The Earth’s water can be broken into two different categories: freshwater and salt water. Fresh water is simply water that is not salty and can be found in the planet’s surface water such as streams, lakes, and frozen as ice, but also underground in aquifers. Fresh water is stored on the surface as surface water or stored underground in aquifers as groundwater. Salt water can be found in the world’s oceans.

Figure 1.1 shows that our planet’s water sources are limited. Freshwater is much easier to use for potable (drinkable) applications because it requires more simple treatment. However, it represents only a small fraction of the Earth’s water portfolio. A large proportion of the freshwater is locked in glaciers and is not accessible. As a result, less than 1% of the water present on the planet is groundwater and surface water that can be more easily used as potable water source. Although desalination plants have become more prevalent, they are very costly and their overall environmental impacts are unknown.

The origin of a water source determines its characteristics and the presence of specific contaminants. The concentration and composition of contaminants in water is also influenced by the movements of water, which is illustrated by the water hydrologic cycle (Figure 1.2). The Water Cycle is both driven by gravity (i.e., water flows downhill) and sunlight (i.e., water evaporates and condenses).

Classification of Contaminants

According to the Safe Drinking Water Act, a contaminant is any physical, chemical, biological, or radiological substance in water. While some contaminants are harmless, others are deadly. As water condenses, runs off as surface water or percolates into the ground, it accumulates contaminants. Contaminants can even mix with water molecules in the atmosphere.

Pin It! Misconception Alert Many people think that all contaminants are manmade. They are not! Some have natural sources in the soil, such as arsenic and uranium. These can be expensive to remove because they occur naturally in the rocks around the water source.

Contaminants can be classified in several ways. One way to classify contaminants is by source:
Natural contaminants come from soil geology, erosion of soils, etc. Examples of contaminants include fluoride and arsenic.
Anthropogenic (human caused) contaminants:
Industrial contaminants vary widely and are specific to the industries that generate them. Examples of industries that generate contaminants often found in water include chemical, mining, metal, textile, food processing, petrochemical, and pulp and paper industries. Agricultural contaminants can be separated into two broad groups:
▪ Contaminants that originate from crops, such as pesticides, fertilizers, nutrients, and sediments.
▪ Contaminants that are derived from animal production, which include a variety of organic contaminants, nitrogenous chemicals, microorganisms, salts. Domestic contaminants can be separated into two groups:
▪ “Conventional” contaminants, which include microorganisms, organics, nitrogen, phosphorus, inorganics, metals, detergents, and pesticides.
▪ Pharmaceuticals and personal care products, which have been gaining attention in the water industry.

Pin It! Misconception Alert People use the words contaminants and pollutants interchangeably. What is the difference between a contaminant and a pollutant? • A contaminant is a substance that is not normally expected; • A pollutant is a substance found at a concentration that has reached a level that adversely affects the suitability of the water for its intended purpose.

Introduction to Chemistry and Matter

This chapter presents the fundamentals of chemistry, starting with an introduction on matter and its elemental constituents. Molecular arrangements and chemical bonding are then introduced, followed by examples of chemical nomenclature.

Chemistry is the study of matter—its consistency, its properties, and the changes it undergoes with other matter and energy, and considers both macroscopic and microscopic information. Macroscopic refers to substances and objects that can be seen, touched, and measured directly. Microscopic refers to the small particles that make up all matter.

Chemistry touches every area of our lives. The medicines we take, the food we eat, the clothes we wear – all these materials and more are, in some way or another, products of chemistry.

Composition of Matter

Matter can be viewed as anything that has a mass and occupies a space, i.e., that has a specific volume. Mass is defined as a measurement of the quantity of matter present.

Pin It! Misconception Alert Mass is different than weight though people commonly use them interchangeably. Mass is how much matter is present. Weight is a measure of the gravitational pull on the object. So, your weight will change if you travel to the moon, but your mass will not!

Elements and Atoms
At the center of all matter are elements. Elements are basic substances that cannot be broken down without altering their basic identities; they cannot be further simplified (e.g., hydrogen, H; oxygen, O). Each element has its own unique set of physical and chemical properties. Examples of elements include iron, carbon, and gold. An atom is the smallest part of an element that maintains the identity of that element. The center of each atom contains a nucleus made of protons (very small particles with a positive electric charge) and neutrons (very small particles, without electrical charge), with electrons (very small, negatively charged particles) that gravitate around the nucleus. Electrons have an insignificant mass compared to protons and neutrons.

Electrons gravitate around the nucleus of protons and neutrons in layers or shells (Figure 2.1). There is only a limited number of electrons per shell, as shown in Figure 2.2.

Atoms have the same number of protons and electrons; thus, atoms have a neutral electrical charge. However, most atoms tend to gain or lose electrons to complete their last electron shell and obtain a stable electron configuration. Only the Noble Gasses (such as helium, neon, and argon) do not tend to gain or lose electrons because their electron configuration is naturally stable. An atom with an unequal number of protons and electrons is called an ion. Atoms that lose electron(s) become positively charged and are called cation (e.g., sodium, Na+). Atoms that gain electron(s) become negatively charged and are called anion (e.g., chloride, Cl-). Note that only electrons are gained, lost, or shared because they are readily available; only radioactive compounds can release protons and neutrons.

Pin It! Misconception Alert Be careful distinguishing between cations and anions. An atom with an unequal number of protons and electrons is an ion. Cations are positively charged ions and anions are negatively charged ions.

The Periodic Table illustrates all elements that have been found or were synthesized to date (Figure 2.3). In this table, elements are ordered in increasing number of protons (from left to right in each row; rows are called periods) and are grouped in columns (called groups) by electron configuration. For example, chlorine appears as number 17 in the Periodic Table (i.e., its atomic number is 17), which means that it has 17 protons. Chlorine is part of the Halogen Family, which all tend to gain an electron to stabilize their last electron shell. While gaining this electron, they become negative charged (e.g., chlorine becomes chloride, Cl-). Each column represents a family, e.g., Alkali Metals (Column 1), Alkali Earth Metals (Column 2), Halogens (Column 17), and Noble Gases (Column 18). Some families are named after their first element, e.g., Boron Family (Column 13), Nitrogen Family (Column 15), and Oxygen Family (Column 16). Additional characteristics are presented later.

The valence (also called the ionic state or oxidation state) is the number of electrons gained, lost, or shared between atoms. Because all elements of a family share similar electron configuration, they all tend to have the same valence, as follows:
• Noble Gases are stable, thus their valence is 0.
• Alkali Metals tend to lose one electron, thus their valence is +1.
• Alkali Earth Metals tend to lose two electrons, thus their valence is +2.
• Elements of the Boron Family tend to lose three electrons, thus their valence is +3.
• Halogens tend to gain one electron, thus their valence is -1.
• Elements of the Oxygen Family tend to gain two electrons, thus their valence is -2.
• Elements of the Nitrogen Family tend to gain three electrons, thus their valence is -3.

Certain elements have multiple valences with different characteristics based on their valence. For example, ferrous iron, Fe2+, has lost two electrons (it has a valence of +2) and is highly soluble in water. On the other hand, ferric iron, Fe3+ (valence of +3), has lost three electrons and is insoluble in water, i.e., it forms a solid and precipitates. Trivalent chromium (i.e., chromite, also called chromium 3, Cr (III), or Cr3+) has lost three electrons and has a valence of +3. It is an essential element that helps regulate the body’s use of sugar, proteins, and fats. However hexavalent chromium (i.e., chromate, also called chromium 6, Cr (VI), or Cr6+) has lost six electrons (valence of +6) and is toxic to humans.

Electronegativity is the degree of attraction of an element for electrons; it defines an element’s affinity for electrons. Electronegativity determines whether an atom will gain, lose, or share electrons.

Molecules and Compounds

Molecules

Molecules or compounds are composed of atoms that are attached together and behave as a unit. The smallest part of a compound that maintains the identity of that compound is called a molecule. Examples of compounds include water, penicillin, and sodium chloride (the chemical name for common table salt).

Atoms will tend to combine in such ways to increase their stability and complete their electron configuration. For some molecules, this means that they will obtain a zero net electrical charge.

Chemical bonds can be grouped in two broad categories, as illustrated in Figure 2.4.

1. In an ionic bond, electrons are transferred from one atom to another. The atom that loses electron(s) becomes positively charged and is called a cation. Conversely, the atom that gains electron(s) becomes negatively charged and is called an anion. Examples of ionic bonds are shown in Table 2.5.
2. In a covalent bond, electrons are shared between atoms. The electronegativity of each atom will determine the polarity of the resulting molecule.

Sodium chloride, NaCl	1. Sodium tends to lose 1 electron to become Na+ 2. Chloride tends to gain 1 electron to become Cl- 3. Net zero charge: Na+1 + Cl-1 = NaCl0
Sodium oxide, Na2O	Sodium tends to lose 1 electron to become Na+ Oxygen tends to gain 2 electrons to become O2- Net zero charge: (2 x Na+1) + (1 x O2-) = Na2O

Homonuclear molecules: Equal attraction for the shared electron(s)	Hydrogen, H2: Single covalent bond: H ̶ H Chlorine, Cl2: Single covalent bond: Cl ̶ Cl Oxygen, O2: Double covalent bond: O = O Nitrogen, N2: Triple covalent bond: N ≡ N
Heteronuclear molecule: Unequal attraction for the shared electron(s) Example: Water, H2O	1. Hydrogen, H+ Valence of +1: Need 1 bond 2. Oxygen, O2- Valence of -2: Need 2 bonds 3. Net zero charge: (2 x H+1) + (1 x O2-) = H2O

The key differences between ionic and covalent bonds are summarized in Table 2.6 on the following page.

Ionic Bonds	Covalent Bonds
• Transfer of electron(s) from one atom to another • Tend to be inorganic • High melting point • Often solid at room temperature • Good conductor • Resulting substance is called a compound	• Electrons are shared between atoms Organic compounds • Low melting point • Solid, liquid or gas at room temperature • Poor conductor • Resulting substance is called a molecule or molecular compound

Dissociation
Molecules that result from polar covalent bond (i.e., atoms of different types that share electrons) may breakdown or dissociate. This is the case for water, H2O, which dissociates into hydrogen ion, H+, and hydroxide, OH-. The dissociation of water is measured as pH.

Chemical Names
The Period Table (Figure 2.3) presents all the elements that are known to mankind to this day.

When naming chemical molecules and compounds, the cation name is the same as the element name, as listed in the Periodic Table. The anion name, however, is not the same: the end of the element name ends in –ide. For example, chloride is the anion of the element chlorine.

Binary compounds (i.e., compounds that contain only two elements) are typically made of a metal and a non-metal. If these compounds have predictable valences, they also end in –ide, even if one element has multiple atoms: for example, magnesium chloride, MgCl2.

Metals with variable valences, such as the Transition Metals (Columns 3 through 12 of the Periodic Table, Figure 2-3), are more complex because they are followed by a symbol that reflects the valence. This was introduced earlier in Section 2.1.1. For example, trivalent chromium (i.e., chromite) has a valence of +3, and is referred to as Cr(III), or Cr3+; hexavalent chromium (i.e., chromate) has a valence of +6 and is referred to as Cr(VI), or Cr6+.

Naming acids and their derivatives is more complex and may depend on the acid’s oxidation state. Generally, the acids with the highest oxidation state end in –ic; e.g., sulfuric acid (H2SO4), nitric acid (HNO3), or phosphoric acid (H3PO4). Their salts end in –ate; e.g., sulfate (SO42-), nitrate (NO3-), or phosphate (PO42-). Acids with the next lowest oxidation state end in –ous; e.g., sulfurous acid, H2SO3. Their salts end in –ite; e.g., sulfite, SO32-. Acids with the lowest oxidation state begin in hypo– and end in –ous; e.g., hypochlorous acid, HOCl. Their salts begin in hypo– and end in –ite; e.g., hypochlorite ion, OCl-.

PHYSICAL STATES OF MATTER
States of matter are distinct forms that matter can take. They are based on how elements are arranged in matter. Matter can take four different states (Figure 2.9):

1. Solid: Volume and shape are fixed;
2. Liquid: Fixed volume, but variable shape that adapts to its container;
3. Gas: Volume and shape are variable;
4. Plasma: Variable volume and shape, with electrical charges.

The physical states of matter reflect different energy levels: solids have the lowest energy level, followed by liquids. Gases have higher energy level, and plasma have the highest energy level. In water, the first three states (i.e., solid, liquid and gas) are important.

The plasma state is often misunderstood, and although not freely existing under normal conditions on Earth, it is quite commonly generated by either lightning, electric sparks, fluorescent lights, neon lights or in plasma televisions. The Sun’s corona, some types of flame, and stars are all examples of illuminated matter in the plasma state.

Like a gas, plasma does not have definite shape or volume. Unlike gases, plasmas are electrically conductive, produce magnetic fields and electric currents, and respond strongly to electromagnetic forces. Positively charged nuclei swim in a “sea” of freely-moving disassociated electrons, similar to the way such charges exist in conductive metal, where this electron “sea” allows matter in the plasma state to conduct electricity.

A gas is usually converted to a plasma in one of two ways, either from a huge voltage difference between two points, or by exposing it to extremely high temperatures. Heating matter to high temperatures causes electrons to leave the atoms, resulting in the presence of free electrons. This creates a so-called partially ionised plasma. At very high temperatures, such as those present in stars, it is assumed that essentially all electrons are “free”, and that a very high-energy plasma is essentially bare nuclei swimming in a sea of electrons. This forms the so-called fully ionised plasma.

Chemical Equations

Bonding
When the outermost energy level of an atom is not filled by electrons, the unfilled spaces or extra electrons in the outer energy level are critical as to whether it is easier for the atom to gain or lose electrons. The most chemically stable configuration for any atom is to have its outermost shell of electrons filled. For example, an atom of sodium, Na, has one electron in its outermost energy level. This level is filled when eight electrons occupy this space. For this reason, sodium atoms find it easier to give up the one electron to have a full outermost shell. An atom of chlorine, Cl, has seven electrons in its outer most energy level. This level is filled when eight electrons occupy this space. Chlorine finds it easier to accept an electron to fill the level with electrons. Sodium and chloride combine to form salt. Sodium gives up one electron to chlorine; therefore, sodium loses an electron to acquire a completed outermost energy level and chlorine accepts the electron to have a completed outermost shell.

The valence, or combining capacity, of an atom is the number of extra or missing electrons in its outermost electron shell. Hydrogen has a valence of 1 (one unfilled space, or one extra electron), oxygen has a valence of 2 (two extra electrons), chlorine has a valence of 1 (one extra electron), and magnesium has a valence of 2 (two extra electrons).

Atoms achieve the full complement of electrons in their outermost energy shells by combining to form molecules, which are made up of atoms of one or more elements. A molecule that contains at least two different kinds of atoms, such as sodium chloride (salt), is called a compound. In sodium chloride, the omission of a subscript indicates that there are one atom of sodium and one atom of chloride. In the compound, water (H2O) the subscript 2 indicates that there are two atoms of hydrogen and the absence of a subscript for oxygen indicates that there is one atom of oxygen. Molecules hold together because the valence electrons of the combining atoms form attractive forces, called chemical bonds, between the atomic nuclei. For this reason, valence may also be viewed as the bonding capacity of an element. Because energy is required for chemical bond formation, each chemical bond possesses a certain amount of potential chemical energy.

Atoms form bonds in one of two ways. They either gain or lose electrons from their outer electron shell, or they share outer electrons. When atoms have gained or lost outer electrons, the chemical bond is called an ionic bond. When outer electrons are shared, the bond is called a covalent bond. The types of bonds that are found in molecules range from highly ionic to highly covalent.

Ionic Bonds
Atoms are electrically neutral when the number of positive charges (protons) equals the number of negative charges (electrons). When an isolated atom gains or loses electrons, the balance is upset. If the atom gains electrons, it acquires a negative charge because electrons are negatively charged. Such a negatively or positively charged atom is called an ion.

For example, sodium (Na) has 11 protons and 11 electrons, with one electron in its outer electron shell. Sodium tends to lose the single outer electron. It is considered an electron donor. When sodium donates an electron to another atom, it is left with 11 protons and 10 electrons. Sodium is positively charged, and it is called a sodium ion. It is written as Na+. Chlorine (Cl) has a total of 17 electrons, 7 of them are in the outer electron shell. This outer shell can hold 8 electrons. For this reason, chlorine tends to pick up an electron that has been lost by another atom. It is considered to be an electron acceptor. By accepting an electron, chlorine totals 18 electrons. But it has only 17 protons in its nucleus. The chloride ion for this reason has a charge of -1, and it is written as Cl-.

The opposite charges of the sodium ion (Na+) and chloride ion (Cl-) attract each other. The attraction, an ionic bond, holds the atoms together, and a molecule of table salt is formed. An ionic bond is an attraction between ions of opposite charge that holds them together to form a stable molecule. An ionic bond is an attraction between atoms in which one atom loses electrons and another atom gains electrons. Strong ionic bonds have limited importance in living cells. Weaker ionic bonds formed in aqueous (water) solutions are important in biochemical reactions in living organisms.

An atom whose outer electron shell is less than half-filled will lose electrons and form positively charged ions, called cations, such as potassium (K+), calcium (Ca+2), and sodium (Na+). When an atom’s outer shell is more than half-filled, the atom will gain electron and form negatively charged ions, called anions, such as iodide ion (I-), sulfide (S-2), chloride (Cl-).

Covalent Bonds
A covalent bond is a chemical bond formed by two atoms sharing one or more pairs of electrons. Covalent bonds are stronger and more common in living organisms that are true ionic bonds. In the hydrogen molecules, H2, two hydrogen atoms share a pair of electrons. Each hydrogen atom has one electron in the outer orbit. In order to have a full shell, one additional electron is needed. In the hydrogen molecule, the one hydrogen atom with one electron shares an electron with the other hydrogen atom so that a shared pair of electrons orbits the nuclei of each atom. The outer electron shells of both atoms are filled. Atoms that share one pair of electrons form a single covalent bond. Atoms that share two pairs of electrons form a double covalent bond, expressed as two single lines (=). A triple covalent bond is expressed as three single lines, and it occurs when atoms share three pairs of electrons.

Methane (CH4) has covalent bonding between atoms of hydrogen and carbon. The outer electron shell of the carbon atom can hold eight electrons but has only four electrons. Each hydrogen atom can hold two electrons but has only one electron in the outer orbit. In the methane molecule, the carbon atom gains four hydrogen electrons to complete its outer shell, and each hydrogen atom completes its outer shell by sharing one electron from the carbon atom. Each outer electron of the carbon atom orbits the carbon nucleus and a hydrogen nucleus. Each hydrogen electron orbits its nucleus and the carbon nucleus.

Elements like hydrogen and carbon, whose outer electron shells are half-filled, form covalent bonds easily. In living organisms, carbon almost always forms covalent bonds. Covalent bonds are formed by the sharing of electrons between atoms. Ionic bonds are formed by attrition between atoms that have lost or gained electrons and are positively or negatively charged.

Hydrogen Bonds
Another type of bond is the hydrogen bond where a hydrogen atom that is covalently bonded to one oxygen or nitrogen atom is attracted to another oxygen or nitrogen atom. These bonds are weak and do not bind atoms into molecules. They serve as bridges between different molecules or between various portions of the same molecule.

When hydrogen combines with atoms of oxygen or nitrogen, the relatively large nucleus of the larger oxygen or nitrogen atoms has more protons and attracts the hydrogen electron more strongly than does the small hydrogen nucleus. In a molecule of water (H2O), the electrons tend to be closer to the oxygen nucleus than to the hydrogen nuclei. As a result, the oxygen portion of the molecule has a slightly negative charge, and the hydrogen portion of the molecule has a slightly positive charge. When the positively charged end of one molecule is attracted to the negatively charged end of another molecule, a hydrogen bond is formed. This attraction can also occur between hydrogen and other atoms of the same molecule, especially in large molecules. Oxygen and nitrogen are the elements most frequently involved in hydrogen bonding.

Hydrogen bonds are weaker than ionic or covalent bonds. Hydrogen bonds are formed and broken relatively easily. This property accounts for the temporary bonding that occurs between certain atoms of large and complex molecules, like proteins and nucleic acids.

Molecular Weight and Moles
Bond formation results in the creation of molecules. Molecules are discussed in terms of units of measure called molecular weight and moles. The molecular weight of a molecule is the sum of the atomic weights of the atoms that make up the molecule. To relate the molecular level to the laboratory level, a unit called a mole is used.

One mole of a substance is its molecular weight expressed in grams so that one mole of water (H2O) weighs 18 grams because the molecular weight of water is 18, or
H2O: The atomic number of Hydrogen (2) is 1 and Oxygen (16) is 16 [(2 x1,H)+16,O]=18

Chemical Reactions
Chemical energy occurs whenever chemical bonds between atoms are formed or broken during chemical reactions.

Synthesis Reactions
When two or more atoms, ions, or molecules combine to form new and larger molecules, the reaction is called a synthesis reaction. To synthesize means to put together, and a synthesis reaction forms new bonds. This process most often requires energy be added to the system.

Synthesis reaction:
(A,atom, ion,ormolecule ) + (B,atom, ion,ormolecule)+ energy→(AB,newmolecule)

The combining substances, A and B are called the reactants, and the substance formed by the combination, AB, is the product. The arrow indicates the direction in which the reaction proceeds.

Pathways of synthesis reactions in living organisms are collectively called anabolic reactions, or simply anabolism. The combining of sugar molecules to form starch and of amino acids to form proteins are examples of anabolism. Anabolic reactions, in general, require an input of energy. The energy is stored in the newly formed chemical bond as potential energy (chemical energy).

Decomposition Reactions
The reverse of a synthesis reaction is a decomposition reaction. To decompose means to break down into smaller parts, and in a decomposition reaction chemical bonds are broken. Decomposition reactions split large molecules into smaller molecules, ions, or atoms. A decomposition reaction occurs:

(AB,molecule)→(A, atom, ion,molecule ) + (B,atom, ion,molecule)+energy

Decomposition reaction that occur in living organisms are collectively called catabolic reactions, or catabolism. Catabolism occurs when sucrose is broken down into simpler sugars like glucose during digestion. Bacterial decomposition of petroleum is another example of decomposition reactions. Energy is released when the chemical bonds are broken down.

Exchange Reactions
Chemical reactions are based on synthesis and decomposition. Many reactions, such as exchange reactions, are actually part of synthesis and part decomposition. An exchange reaction works

(AB,molecule) + (CD,molecule)→(AD,molecule ) + (BC,molecule)

Combustion Reactions
Combustion reactions are types of chemical reactions where compounds and oxidants react to produce heat and new products. A common combustion reaction is the reaction between oxygen and hydrocarbons to yield water and carbon dioxide:

(Oxygen) + (Hydrocarbon)→(CarbonDioxide ) + (Water )+ heat

For example:
2H2 + O2 → 2H2O + heat
CH4 + 2O2 → CO2 + 2H2O + heat

It is also common for a combustion reaction to release light and produce a flame. However, it is not necessary. For a combustion reaction to be initiated, the activation energy for the reaction must be overcome. Often combustion reactions are started with a flame, which provides the
heat to initiate the reaction. Once combustion begins, the heat that is produced sustains the reaction until the reactants are used.

In order to recognize combustion reactions, oxygen will be on the reactant side of the equation and the release of heat will be on the product side of the equation. Sometimes the fuel molecule contains oxygen. For example, the combustion of ethanol:

C2H5OH + 3O2 → 2CO2 + 3H2O

Combustion is an exothermic reaction so that it releases heat. However, sometimes the reaction proceeds so slowly that a temperature change is not noticeable. The signs that a combustion reaction occurs is the presence of oxygen as a reactant and carbon dioxide, water, and heat as products. Inorganic combustion reaction may not form the same types of products; however, they are recognizable by the reaction of oxygen. The surest method of recognizing a combustion reaction is that the products contain carbon dioxide and water.

Combustion does not always proceed to completion or 100-percent efficiency. The reactions are prone to limiting reactants. Two types of combustion reactions exist:

1. Complete Combustion: known as clean combustion where oxidation of the reactants (hydrocarbons) produces only carbon dioxide and water. The burning of candle wax, where the heat from the wick vaporizes the wax (hydrocarbon), is an example. The reaction results from the oxygen in the air so that carbon dioxide and water are the products. All of the wax burns so that nothing remains once the candle is consumed. The water vapor and carbon dioxide dissipate into the atmosphere.
2. Incomplete Combustion: incomplete combustion is the oxidation of a hydrocarbon that is incomplete or dirty. The products are carbon monoxide and carbon (soot) in addition to carbon dioxide. An example would be the combustion of coal, where soot and carbon monoxide are the products. Fossil fuels oxidize incompletely, and they release waste products.

ENERGY FLOW IN CHEMICAL REACTIONS

Chemical bonds represent stored chemical energy, and chemical reactions ultimately result in net absorption or release of energy. Reactions that release energy are called exergonic reactions. These reactions yield products with less energy than the initial reactants, along with energy that can be harvested for use. Catabolic and oxidative reactions are exergonic for the most part.

The products of energy absorbing, endergonic, reactions contain potential energy in their chemical bonds which is more than the energy that the reactants contained. Anabolic reactions are energy absorbing reactions. For example, the energy released when fuel molecules are broken down (oxidized) is captured in ATP molecules and used to synthesize complex biological molecules the body needs to sustain life.

FACTORS THAT INFLUENCE THE RATE OF CHEMICAL REACTIONS

For atoms and molecules to react, they must collide with enough force to overcome the repulsion between their electrons. Interaction between valence shell electrons cannot occur long distance. The force of collisions depends on the speed of the particles. Solid, forceful collisions between rapidly moving particles in which valence shells overlap are much more likely to cause a reaction than are collisions in which the particles graze each other.

Increasing the temperature of a substance increases the kinetic energy of its particles and the force of their collisions. Chemical reactions proceed more quickly at higher temperatures.

Chemical reactions progress more rapidly when the reacting particles are present in high numbers, concentrations, because the chance of collisions are greater. As the concentrations of the reactants declines, the reaction slows. Chemical equilibrium eventually occurs unless additional reactants are added or products are removed from the reaction site.

Smaller particles move faster than large particles and tend to collide more frequently and more forcefully. The smaller the reacting particles, the faster a chemical reaction proceeds at a given temperature and concentration.

Chemical reactions in nonliving systems can be speeded up by heating. However drastic increases in body temperature are life threatening because important biological molecules are destroyed. At normal body temperature, most chemical reactions would proceed at too slow of a pace to maintain life, if catalysts were not present. Catalysts are substances that increase the rate of chemical reactions without becoming chemically changed or part of the product. Biological catalysts are called enzymes.

ORGANIC CHEMISTRY

Organic compounds contain carbon. All organic compounds are covalently bonded molecules, and most organic compounds are large molecules. All other chemicals are considered inorganic compounds, which do not contain carbon. Inorganic compounds include water, salts, and many acids and bases. Organic and inorganic compounds are equally essential for life.

Organic materials are derived from plant fibers and animal tissues, which are produced by synthesis reactions that produce materials like rubber, plastics, and other compounds; and fermentation reactions that produce alcohols, acids, antibodies, and other compounds.

Pin It! Misconception Alert: In chemistry, the word “organic” refers to compounds containing carbon. It does not refer to organic food (e.g., grown without chemical fertilizers or pesticides).

Inorganic compounds, in contrast to organic compounds, are combustible, high in molecular weight, and sparingly soluble in water and a source of food for animal consumers and microbial decomposers.

Carbohydrates, lipids, proteins, and nucleic acids are molecules unique to living systems. Each of these molecules contain carbon and they are referred to as organic compounds. Organic compounds are distinguished by the fact that they contain carbon, and inorganic compounds are defined as compounds that lack carbon. However, carbon dioxide and carbon monoxide are carbon containing compounds but are considered inorganic compounds.

Organic molecules are large molecules. Only small, reactive parts of their structure interact with other compounds. These areas are referred to as active sites and are functional groups, such as acid groups, amines, and others.

Carbon is a special atom. No other small atom is so electroneutral. The consequence of its electroneutrality is that carbon does not lose or gain electrons. It shares them. With four valence shell electrons, carbon forms four covalent bonds with other elements, as well as with other carbon atoms. As a result, carbon helps to form long, chainlike molecules, ring structures, and other structures that are uniquely suited for specific roles in living systems.

Many biologic molecules are polymers like carbohydrates and proteins. Polymers are chainlike molecules made of many similar or repeating units, monomers, which are joined together by dehydration synthesis. During dehydration syntheses, a hydrogen atom is remove from one monomer and a hydroxyl group is removed from another monomer. The resultant products are joined together with a covalent bond, and in the process, a water molecule is released. The removal of a water molecule at the bond site occurs each time a monomer is added to the growing polymer chain.

HYDROCARBONS

In organic chemistry, any chemical compound that consists of the elements of carbon and hydrogen is a hydrocarbon. Carbon and hydrogen atoms share an electron pair forming covalent bonds in hydrocarbons. One of the special properties of carbon is its ability to form double and triple bonds.

Saturated hydrocarbons contain only the elements of carbon and hydrogen with single bonds between carbon atoms. Methane is the simplest hydrocarbon, and it is a gas produced in the anaerobic decomposition of organic compounds.

When hydrocarbon molecules include one or more double or triple bonds between some of the carbon atoms it is not possible for as many hydrogen atoms to be included in the molecule as when the bonds are single bonds. The term used to describe the presence of one or more double or triple bonds in a molecule of an organic compound is unsaturated. If the organic compound contains all single bonds, it is called saturated.

Alkanes, Alkenes, and Alkynes
Hydrocarbons are classified as unsaturated or saturated. Alkanes are a group of saturated hydrocarbons meaning that the hydrocarbon contains only single bonded carbon atoms represented as:

C-C-C-C (CnH2n+2)

Alkenes are a group of unsaturated hydrocarbons meaning that the hydrocarbon contains double carbon-carbon bonds represented as:

C=C=C (CnH2n)

Alkynes are hydrocarbons that include triple carbon-carbon bonds (CnH2n-2).

A bromine solution is used to test for unsaturation of hydrocarbon molecules. Bromine solution is orange in color. When an alkene is added to a bromine solution, the orange color disappears resulting in a colorless solution. Bromine reacts with alkenes forming a new colorless compound. This test is useful in distinguishing alkenes from alkanes because alkanes do not react with bromine solution.

Unsaturated hydrocarbons are distinguished from paraffins by the presence of multiple bonds between some carbon atoms. The multiple bonds between carbon atoms displace hydrogen atoms, creating molecules containing fewer hydrogen atoms.

Vegetable shortenings available as solid fats are produced from oils through the process of hydrogenation which adds hydrogen atoms through the addition of hydrogen gas under controlled conditions. Reducing the number of unsaturated bonds increases the melting point, converting an oil to a solid fat.

CHEMICAL STRUCTURE

The parent compound of aromatic hydrocarbons is benzene. Benzene is a 6-carbon ring with double bonds between alternate atoms. Benzene is used in the manufacture of a variety of commercial products including insecticides, plastics, solvents, explosives, and dyes.

Alcohols
Alcohols are formed from hydrocarbons by replacing one or more hydrogen atoms by hydroxyl groups (-OH). Methanol is manufactured synthetically by a catalytic process from carbon monoxide and hydrogen. It is used extensively in manufacturing organic compounds, like solvents, fuel additives, and formaldehyde. Ethyl alcohol for beverage purposes is produced through the fermentation of a variety of natural organic materials, like corn, wheat, rice, and potatoes. Industrial ethanol is produced from fermentation of waste solutions containing sugars, like blackstrap molasses and residues resulting from the purification of cane sugar.

Propanol has two isomers, the more common is isopropyl alcohol, which is widely used by industry and sold as a medicinal rubbing alcohol. The three primary alcohols have boiling points less than 100oC, and they are miscible with water.
• Methanol or methyl alcohol (CH3OH)
• Ethanol or ethyl alcohol (CH3CH2OH)
• Isopropyl alcohol or 2-Propano (CH3CH3CHOH)

Miscible liquids are homogenous when mixed together.

The derivative of benzene containing one hydroxyl group, known as phenol, has a molecular formula of C6H5OH. The formula and –ol in the name indicate the characteristics of an alcohol; however, phenol, known as carbolic acid, ionizes in water yielding hydrogen ions, and exhibits features of an acid. It occurs as natural component of wastes from coal, gas, petroleum, and a variety of industrial wastes where phenol is used as a raw material. Phenol is a strong toxin that makes the waste materials particularly difficult to treat in biological systems. Phenols impart undesirable tastes to water at low concentrations.

Aldehydes and Ketones
Aldehydes and ketones are compounds containing a carbonyl group. Formaldehyde is used to produce plastics and resins. Acetone (dimethyl ketone) is a good solvent of fats and is a common cleaning agent for laboratory glassware.
• Formaldehyde (CH2OH)
• Acetone (CH3CHCOH)

Carboxylic Acids
Organic acids contain the carboxyl group, -COOH. Carboxylic acid is the highest state of oxidation that an organic radical can achieve. Further oxidation results in the formation of carbon dioxide and water. Acids through 9-carbons are liquids, and those acids with more carbons are greasy solids, fatty acids. Organic acids are weak and ionize poorly.

Formic, acetic, and propionic acids have sharp penetrating odors, and butyric and valeric acids have extremely disagreeable odors associated with rancid fats and oils. Anaerobic decomposition of long chain fatty acids result in the production of 2 and 3-carbon acids, which are converted to methane and carbon dioxide gas in decomposition reactions.
• Formic acid (HCOOH)
• Acetic acid (CH3COOH)
• Propionic acid (CH3CH2COOH)
• Butyric acid (CH3CH2CH2COOH)
• Valeric acid (C4H9COOH)
• Caproic acid (C5H11COOH)

Basic compounds react with acids to produce salts. NaOH, sodium hydroxide, reacts with acetic acid to produce sodium acetate. Soaps are slats of long chain fatty acids. Other derivatives of carboxylic acids include esters, such as ethyl acetate and amides.
• Methylamine (CH3NH2)

ORGANIC MATTER

Biodegradable organic matter in water is classified into three categories: fats, carbohydrates, and proteins. Carbohydrates consist of sugar units containing the elements of carbon, hydrogen, and oxygen. A single sugar is known as a monosaccharide. Disaccharides are composed of two monosaccharide units. Sucrose, table sugar, is glucose plus fructose. The most prevalent sugar in milk is lactose, consisting of glucose plus galactose. Polysaccharides, long chains of sugar units, are divided into two groups: readily degradable starches, like potatoes, rice, corn, and other edible plants; and cellulose which is found in wood, cotton, paper, and similar plant tissues. Cellulose compounds degrade biologically at a slower rate than starches.

Proteins are long strings of amino acids containing carbon, hydrogen, oxygen, nitrogen, and phosphorus. They form an essential part of living tissue and constitute a diet necessary for higher life forms.

Fats refer to a variety of biochemical substances that have the property of being soluble to varying degrees in organic solvents, like ether, ethanol, acetone, and hexane, while being sparingly soluble in water. Because of their limited solubility, degradation by microorganisms is very slow. A simple fat is a triglyceride composed of a glycerol unit with short or long chain fatty acids attached.

The majority of carbohydrates, fats, and proteins in nature are in the form of large molecules that cannot penetrate the cell membrane of microorganisms. Bacteria, in order to metabolize high-molecular weight substances, must be capable of breaking down the large molecules into diffusible fractions for assimilation into the cell. The first step in bacterial decomposition of organic compounds is hydrolysis of carbohydrates into soluble sugars, proteins into amino acids, and fats into short fatty acids. Aerobic biodegradation results in the formation of carbon dioxide and water. Anaerobic digestion, decomposition in the absence of oxygen, results in the formation of organic acids, alcohols, and other liquid intermediates as well as gaseous entities of carbon dioxide, methane, and hydrogen sulfide.

Several organic compounds, like cellulose, long chain saturated hydrocarbons, and complex compounds, although available as a bacterial substrate, are considered non-biodegradable because of the time and environmental limitations of biological treatment systems. Petroleum derivatives, detergents, pesticides, and synthetic organic compounds are also resistant to biodegradation, and some of these compounds are toxic and inhibit the activity of microorganisms in biological processes.

Some waste odors are inorganic compounds, like hydrogen sulfide gas; however many odors are caused by volatile organic compounds, such as mercaptans and butyric acid. Industries may produce a variety of medicinal odors in the processing of raw materials. Surface water supplies plagued with blooms of blue green algae have fishy or pigpen odors. The cause of odors can be anaerobic decomposition, industrial chemicals, or growths of obnoxious microorganisms.

METHANE AND TRIHALOMETHANE

Chlorine is used to inhibit or destroy harmful organisms. This method of disinfection alters cell chemistry causing microorganisms to die. Chlorine is the most widely used disinfectant chemical. Chlorine is relatively inexpensive, and leaves a residual chlorine that can be measured. An increased interest in disinfection other than chlorine has developed because of the carcinogenic compounds that chlorine may form, trihalomethanes, THMs.

The exact mechanism of chlorine disinfection action is not fully understood. It is felt that chlorine exerts a direct action against bacterial cell, destroying them. Another theory is that the toxic character of chlorine inactivates the enzymes, which enable living microorganisms to use their food supply. As a result, the organisms die. However, the exact mechanism of chlorine disinfection is less important than its demonstrated effects as a disinfectant.

When chlorine is added to water, several chemical reactions take place. Some of the reactions involve the molecules of the water, and some reactions involve organic and inorganic substances suspended in the water.

Chlorine combines with organic and inorganic materials to form chlorine compounds. If chlorine is added continuously, eventually all of the materials in the water that will react with chlorine are used and the chlorine reactions stop. At this point, the chlorine demand is satisfied.

The chemical reactions between chlorine and organic and inorganic substances produce chlorine compounds. Some chlorine compounds have disinfecting properties, and some compounds do not. Chlorine also reacts with the water and produces substances with disinfecting properties. The total of all of the compounds with disinfection properties plus any remaining free, uncombined, chlorine is known as the chlorine residual. The presence of this measurable chlorine residual indicates that all possible chemical reactions with chlorine have taken place and that a sufficient available residual of chlorine is available to kill microorganisms present in the water.

When organic materials are present in water being disinfected with chlorine, the chemical reactions that take place can produce suspected carcinogenic compounds, THMs. The formation of these compounds can be prevented by limiting the amount of chlorination and by removing the organic materials before chlorination of the water.

Methane
Methane is a colorless, odorless, flammable gas, and it is the primary constituent of marsh gas and the firedamp of coal mines. It is obtained commercially from natural gas, and it is the first member of the alkane series of hydrocarbons. The formation of methane can occur through organic matter decomposition or through organic synthesis which involve microorganisms, methanogenesis. The synthesis involves anaerobic and aerobic processes. Naturally occurring methane is produced by microbial methanogenesis. This multistep process is used by microorganisms as an energy source. The net reaction is:

CO2 + 8H+ → CH4 + 2 H2O

The final step in the process is catalyzed by the enzyme coenzyme-B sulfoethylthiotransfersase. Methanogenesis is a form of anaerobic respiration used by organisms that occupy landfills, ruminants, and the guts of termites.

Trihalomethanes
Trihalomethanes are harmful by-products arising from a process of water disinfection with chlorine. Trihalomethanes are formed when organic materials react with chlorine to form chlorinated by-products. Trihalomethanes are chemical compounds where 3 of the 4-hydrogen atoms of methane are replaced by halogen atoms. Trihalomethanes (THMs) are used in industry as solvents or refrigerants. THMs are environmental pollutants, and many of them are considered carcinogenic. Trihalomethanes with all the same halogen atoms are called haloform, and they are considered to be volatile organics. Some examples of trihalomethanes are:
• Chloroform
• Bromodichloromethane
• Bromoform
• Carbon tetrachloride
• Tetrachloroethlene

Trihalomethanes are formed as a by-product when chlorine is used to disinfect drinking water. They represent a group of chemicals referred to as disinfection by-products. They result from the reaction of chlorine or bromine with organic matter present in the water being treated. THMs have been associated through epidemiological studies with adverse health effects. Governmental agencies have set limits on the amount permissible in drinking water. The EPA limits the total concentration of the four chief constituents, chloroform, bromoform, bromodichloromethane, and dibromochloromethane, referred to as total TTHMs to 80 parts per billion in drinking water.

In drinking water, THM levels tend to increase with pH, temperature, contact time with chlorine, and the level of the organic precursors. The precursors, organic material, reacts with chlorine to form THMs. One method that is used to decrease THMs is to eliminate or reduce chlorination before the filters and to reduce precursors. Since more precursors are present before filtration, the treatment process is directed toward reducing or eliminating the time chlorine is in contact with the water. If some oxidation before filtration is required, an alternative disinfectant like potassium permanganate or peroxide should be considered. This strategy is not an option if pre-chlorination is necessary to achieve the required CT, contact time, values.

The EPA has advocated that the best available technology for THM control at treatment facilities is to remove precursors through enhanced coagulation. Enhanced coagulation refers to a process of optimizing the filtration process to maximize removal of precursors. Removal is improved by decreasing pH levels to 4 or 5, increasing the feed rate of coagulants, and using ferric coagulants in place of alum.

Acetic Acid and Haloacetic Acid
Haloacetic acids (HAA) are carboxylic acids where a halogen atom takes the place of hydrogen atoms in acetic acid. In monohaloacetic acid, a single halogen replaces a hydrogen atom. Chloroacetic acid has the structural formula of CH2ClCO2H. In this manner, two chlorine atoms are present in dichloroacaetic acid where two hydrogen atoms are replaced with chlorine atoms. Dichloroacetic acid has a structural formula of CHCl2CO2H.

Haloacetic acids (HAA) are a common undesirable by-product of drinking water chlorination. Exposure to such disinfection by-products in drinking water, at high levels has been associated with undesirable health outcomes through epidemiological studies. The five most common HAAs in water are:
• Monochloroacetic acid (CLCH2COOH)
• Dichloroacetic acid (Cl2CHCOOH)
• Trichloroacetic acid (Cl3CCOOH)
• Monobromoacetic acid (BrCH2COOH)
• Dibromoacetic acid (Br2CHCOOH)

Collectively, these chemicals are called HAA5.

HAAs can be formed by chlorination, ozonation, or chloramination of water with the formation of HAAs promoted by slightly acidic water, high organic matter content, and elevated temperature. Chlorine from the water disinfection process reacts with organic matter and small amounts of bromide present in the water to produce various HAAs.

ACIDS, BASES, AND SALTS

Water is the most abundant and important inorganic compound on earth. It makes up 60 to 89-percent of the volume of most living cells, and it possesses several properties that make it vital to life. Water has a high heat capacity. Water absorbs and releases large amounts of heat before changing appreciably in temperature. This property prevents sudden changes in temperature caused by external factors, such as sun or wind exposure, or by internal conditions that release heat rapidly, such as vigorous muscle activity. As part of blood system or the environment, water redistributes heat among adjacent structures ensuing the temperature remains homeostatic.

When water evaporates, or vaporizes, water changes from a liquid to a gas, water vapor. The transformation requires that large amounts of heat be absorbed to break hydrogen bonds that hold water molecules together. This property is beneficial because as water evaporates from an object or organism large amounts of heat are removed providing efficient cooling. This property is referred to as high heat of vaporization.

Water is the best solvent in nature. It is called the universal solvent. Biological molecules do not react chemically unless they are in solution, and virtually all chemical reactions that occur in the living cells depend on water’s solvent properties. Water molecules are referred to as being polar. They orient with their slightly negative ends toward the positive ends of the solutes. . This characteristic is called polarity, and it explains the reason that ionic compounds and other small reactive molecules, such as acids and bases, dissociate in water, where their ions separating from each other and become evenly scattered in the water forming a true solution.

Water also forms layers of water molecules, called hydration layers, around large charged molecules such as protein, shielding them from the effects of other charged substances in the areas and preventing them from settling out of solution. Such protein water mixtures are biological colloids. Water is also the major transport medium because it is an excellent polar solvent. Nutrients, gases, and metabolic wastes are carried dissolved in water based fluids. Wastes are excreted form living organisms in watery fluids. Specialized molecules that lubricate organisms also use water as the dissolving medium.

Water is an important reactant in many chemical reactions. Nutrients are decomposed by adding a water molecule to each chemical bond that is broken. Decomposition reactions are more specifically referred to as hydrolysis reactions. When large carbohydrates or protein molecules are synthesized from smaller molecules, a water molecule is removed for every bond formed, a reaction that is called dehydration synthesis.

Water forms resilient cushions, cushioning around certain biological structures providing protection from physical trauma.

When inorganic salts such as sodium chloride (NaCl) are dissolved in water, they undergo ionization or dissociation. They break apart into ions. Substances labeled acids and bases demonstrate similar behavior.

An acid can be defined as a substance that dissociates into one or more hydrogen ions (H+) and one or more negative ions (anions) an acid is also called a proton donor (H+). A base dissociates into one or more positive ions (cations) that can accept or combine with protons. Sodium hydroxide (NaOH) is a base because it dissociates to release OH-, has a strong attraction for protons. Bases are among the most important proton acceptors in chemistry. A salt is a substance that dissociates in water into cations and anions, neither of which is H+ or OH-.

ACIDS
Salts, acids, and bases are electrolytes. They ionize and dissociate in water and can conduct an electrical current.

Acids have a sour taste, and they can react with or dissolve metals. The definition of an acid is a substance that releases hydrogen ions (H+) in measureable amounts. Acids are also characterized as being proton donors because a hydrogen ion is a hydrogen nucleus, or a single proton.

When acids dissolve in water, they release hydrogen ions (protons) and anions, negative charged particles. The concentration of the protons determines the acidity of the solution. The anions have little or no effect on the acidity of the solution. Hydrochloric acid (HCl) dissociates into a proton and a chloride ion:

HCl → H+, proton + Cl-, anion

Living organisms maintain a constant balance of acids and bases. If a particular acid or base concentration is too high or too low, enzymes change in shape and are no longer effective. In aqueous environments, acids dissociate into hydrogen ions and anions. Bases dissociate into hydroxide ions and cations. The more hydrogen ions that are free in a solution, the more acidic the solution. The more hydroxide ions that are free in a solution the more basic or alkaline is the solution.

Biochemical reactions are sensitive to small changes in the acidity or alkalinity of the environment in which they occur. H+ and OH- are involved in almost all biochemical processes, and any deviation from a narrow band of the normal H+ and OH- concentration dramatically modifies the systems’ functioning. Acids and bases that are formed in living systems must be kept in balance.

It is convenient to express the amount of H+ in a solution by a logarithmic pH scale that ranges from 0 to 14. The term pH means potential of hydrogen ion concentration. On a log scale, a change of one whole number has 100 times more hydrogen ions than a solution of pH 2, and a pH of 2 has 100 times more hydrogen ions than a solution of pH 3.

Acidic solutions contain more H+ than OH- and have a pH lower than 7. If a solution has more OH- than H+, it is a basic or alkaline solution. In pure water, a small percentage of molecules are dissociated into H+ and OH- ions so that it has a pH of 7. When the ion concentrations of a solution are equal, the solution has a pH of 7 and is considered to be neutral.

The pH of a solution can be changed. When substances that will increase the concentration of hydrogen ions are added to a solution, then the pH will decrease. Buffers prevent the pH of a solution from changing drastically. The pH in the environment can be altered by waste products from organisms, pollutants from industry, and fertilizers used in agricultural fields or gardens. When bacteria are grown in a laboratory, they excrete waste products such as acids that can alter the pH. If acid production were to continue, the medium where the bacteria are growing will become acidic enough to inhibit bacterial enzymes and kill the bacteria. To prevent this problem, pH buffers are added to solutions or to the natural environment to prevent changes in pH. Buffers resist a change in pH.

BASES
Bases have a bitter taste, feel slippery, and are proton acceptors. They take up hydrogen ions in measurable amounts. Common inorganic bases include the hydroxides like magnesium hydroxide and sodium hydroxide. Lye acids, hydroxides dissociate when dissolved in water. In this case, hydroxyl ions (OH-) and cations are released. Ionization of sodium hydroxide produces a hydroxyl ion and a sodium ion. The hydroxyl ion binds to a proton present in the solution. This reaction produces water and simultaneously reduces the acidity of the solution by taking up free H+ ions:

NaOH → Na+ + OH-
OH- + H+ → H2O

The term pH is used to express the intensity of an acid or alkaline solution.

SALTS AND NEUTRALIZATION
The more hydrogen ions in a solution, the more acidic the solution. The greater the concentration of hydroxyl ions, the more basic, or alkaline, the solution.

When acids and bases are mixed, they react with each other in displacement reactions to form water and a salt. For example, when hydrochloric acid and sodium hydroxide interact, sodium chloride (salt) and water are formed.

HCl + NaOH → NaCl + H2O
Acid Base Salt Water

This type of reaction is called a neutralization reaction because the joining of H+ and OH- to form water neutralizes the solution. The salt produced is dissolved in the aqueous solution and disassociated into Na+ and Cl- ions.

Salts are ionic compounds containing cations other than H+ and anions other than the hydroxyl ion, OH-. When salts are dissolved in water, they dissociate into their component ions. Sodium sulfate, Na2SO4, dissociates into two Na+ ions and one SO4-2. The salt dissociates because the ions are formed. The water overcomes the attraction between the oppositely charged ions, and they disassociate.

All ions are electrolytes which are substances that conduct an electrical current in solution. Salts dissociate in aqueous solutions into ions, and the most common salts are sodium salts. In their ionized form, salts play a vital role in nature and aqueous solutions.

BUFFERS
Organisms are extremely sensitive to slight changes in the pH of the environment. In high concentrations, acids and bases are damaging to cells. Homeostasis of acid-base balance is regulated by chemical systems called buffers.

Buffers resist abrupt and large changes in the pH of a solution by releasing hydrogen ions when the pH begins to rise and by binding hydrogen ions when the pH drops.

Chemical buffer systems react by binding hydrogen ions or by releasing hydrogen ions. The acidity of a solution reflects the free hydrogen ions and not the hydrogen ions bound to anions. Acids that dissociate completely and irreversibly in water are called strong acids. They can dramatically change the pH of a solution. Acids that do not dissociate completely, like carbonic acid (H2CO3) and acetic acid, are weak acids. Undissociated acids do not affect pH, so that acetic acid solutions are much less acidic than hydrochloric acid solution. Weak acids disassociate in predictable ways, and molecules of the intact acid are in dynamic equilibrium with the dissociated ions.

For this reason, when a strong acid is added to a solution of a weak acid the equilibrium will shift to the left and some H+ will recombine to form acetic acid. On the other hand, if a strong base is added and the pH begins to rise, the equilibrium shifts to the right and more acetic molecules disassociate to release H+ ions. This characteristic of weak acids allows them to play a role in the chemical buffer systems found in nature.

H+ acetic acid ↔ H+ + Acetic-

Bases are proton acceptors. Strong bases are those bases, like hydroxides, that dissociate easily in water and quickly bind H+ ions. Sodium bicarbonate ionizes incompletely and reversibly. Since it accepts relatively few protons, its released bicarbonate ion is considered to be a weak base.

One of the buffer system that helps to maintain the pH in aqueous solutions is the carbonic acid-bicarbonate system. Carbonic acid dissociates reversibly in aqueous solutions releasing bicarbonate ions and protons, H+. The chemical equilibrium between carbonic acid, a weak acid, and bicarbonate ion, a weak base, resists changes in pH by shifting to the right or the left as H+ ions are added to or removed from the solution:

Rise in pH
H2CO3 ↔ H+ + HCO3-
Drop in pH

As the pH rises and becomes more alkaline, the equilibrium shifts to the right, forcing more carbonic acid to dissociate. Similarly as the pH begins to drop, the equilibrium shifts to the left as more bicarbonate ions begin to bind with protons. Strong bases are replaced by a weak base, bicarbonate ion. Protons are released by strong acids and are tied up in weak acids, carbonic acid. As a result, the pH changes are much less than they would be in the absence of the buffering system.

BASIC MICROBIOLOGY PRINCIPLES

Microorganisms are living things that are too small to be seen with the unaided eye. The group includes bacteria, fungi, protozoa, and microscopic algae as well as viruses.

The majority of microorganisms help maintain the balance of living organisms and chemicals in the environment. Marine and freshwater microorganisms form the basis of the food chain in oceans, lakes, and rivers. On land, soil microbes help break down wastes and incorporate nitrogen gas from the air into organic compounds recycling chemical elements between the soils, water, life, and air. Certain microbes play important roles in photosynthesis, a food and oxygen-generating process that is critical to life on earth. Humans and animals on earth also depend on microbes in their intestines for digestion.

Microorganisms have commercial applications. They are used in the synthesis of chemical products like vitamins, organic acids, enzymes, alcohols, and other drugs. The food industry uses microbes to produce vinegar, sauerkraut, pickles, soy sauce, cheese, yogurt, bread, and alcoholic beverages.

In addition, enzymes from microbes can now be manipulated to cause the microbes to produce substances that they normally do not synthesize, including cellulose, digestive aids, and drain cleaner, plus important therapeutic substances like insulin.

A minority of microorganism are pathogenic or disease-producing.

Pin It! Misconception Alert People frequently think all microorganisms are pathogenic. But only a few are actually pathogenic or disease-producing!

BASIC NOMENCLATURE AND ORGANIZATION
The system of nomenclature and organization for microorganisms is broken down into prokaryotic cells and eukaryotic cells. Bacteria and archaea are referred to as prokaryotic cells, and fungi and protozoans are called eukaryotic cells. Viruses are a separate category of non-living things.

Bacteria are simple, single celled organisms. Because their genetic material is not enclosed in a nuclear membrane, bacterial cells are called prokaryotes.

Archaea are also prokaryotes. Archaea are often found in extreme environments such as the hot springs at Yellowstone National Park. Archaea are not known to cause disease in humans.

Fungi are eukaryotes, organisms whose cells have a distinct nucleus containing the cell’s genetic material, surrounded by a special envelope called a nuclear membrane. Organisms in this kingdom can be unicellular or multicellular. Fungi cannot carry out photosynthesis. True fungi have cell walls composed of chitin.

Protozoa are unicellular eukaryotic microbes. Protozoa have a variety of shapes and live as free entities or as parasites that absorb or ingest organic compounds from their environment.

Algae are photosynthetic eukaryotes with a variety of shapes and sexual and asexual reproductive forms. Algae are abundant in freshwater and salt water, in soil, and in association with plants. Algae need light, water, and carbon dioxide for food production and growth. They receive their energy from sunlight.

Viruses are different from the other microorganisms. They are so small that most can be seen only with an electron microscope. They are considered to be acellular. Viruses can reproduce by using the cellular machinery of other organisms. Viruses are considered to be living when they multiply within the host cells that they infect. In this sense, viruses are parasites of other forms of life. On the other hand, viruses are not considered to be living because they are inert outside living hosts.

GROWTH OF MICROORGANISMS
The requirements for microbial growth are divided into two primary categories. Physical and chemical requirements exist for microorganism to grow and reproduce. Physical aspects include temperature, pH, and osmotic pressure. Chemical requirements include sources of carbon, nitrogen, sulfur, phosphorus, oxygen, trace elements, and organic growth factors.

Differing temperatures are required for different microorganisms. Most bacteria grow only within a limited range of temperatures, and their maximum and minimum growth temperatures are about 30oC apart. They grow poorly at the high and low temperature extremes within their range. Each bacterial species grows at specific minimum, optimum, and maximum temperatures. The minimum growth temperature is the lowest temperature at which the organism will grow. The optimum growth temperature is the temperature at which the species grows best. The maximum growth temperatures are the highest temperature at which growth is possible.

Refrigeration is the most common method of preserving organic materials. It is based on the principle that microbial reproductive rates decrease at low temperatures. Microbes can survive subfreezing temperatures, they become dormant and their numbers gradually decline in low temperatures. Some species decline faster than other species.

Ph value can also encourage or discourage growth of microorganisms. Most bacteria grow best in a narrow pH range near neutrality, between pH 6.5 and 7.5. Few bacteria grow at an acidity below pH 4. For this reason, a number of foods prevent spoilage by using acids produced by bacterial fermentation. Molds and yeast grow over a greater pH range than bacteria. However the optimum pH for molds and yeast is generally below that of bacteria, usually about pH 5 to 6. Alkalinity also inhibits microbial growth.

Besides water, carbon and oxygen are important requirements for growth in microorganisms. Carbon is the structural backbone of living matter. It is needed for organic compounds that make up a living cell. Carbon makes up half of the weight of bacterial cells.

CLASSIFYING MICROBES
The classification of organisms into progressively more inclusive groups is based on phylogeny and phenotype. The nomenclature is the process of applying formal rules in the naming of organisms.

Domains
Organisms are classified by cell type in the three domain systems. Animals, plants, and fungi are kingdoms in the Domain Eukarya. The Domain Archaea includes prokaryotes that do not have peptidoglycan in their cell walls. Peptidoglycan is a building block of cell walls of bacteria. The Domain Bacteria includes the pathogenic prokaryotes as well as many of the nonpathogenic prokaryotes found in soil and water.

Bacteria are classified into five groups based on their basic shapes. These shapes include spherical (cocci), spiral (spirilla), rod (bacilli), comma (vibrios), or corkscrew (spirochaetes). These cells can exist as single cells, in pairs, chains, or in clusters.

Nomenclature
Scientific nomenclature is a binomial nomenclature so that every organism has a unique binomial identification that indicates the individual and its taxonomic placement among other organisms. Taxonomy is the science of classification. Almost 2 million organisms have been identified so far, and the estimate is that 10-100 million total organisms occupy the earth. All cellular organisms evolved from a common ancestor.

The differences observed between organisms are due to random mutation and natural selection. Organisms are organized into taxonomic categories by relatedness. Systematics/Phylogeny are the study of the evolutionary history and relatedness of organisms. Modern taxonomy is based on genetic sequence information or molecular biology.

Of all the different classification systems, the Gram stain has withstood the test of time. The Gram stain remains an important and useful technique. It allows a large proportion of clinically important bacteria to be classified as Gram positive or negative based on their morphology and differential staining properties. A Gram stain is a process during which a violet dye is applied, a decolorizing agent is applied, and then a red dye is applied. Gram positive bacteria have cell walls that will retain the violet dye. Gram negative bacteria will be red.

Phylogenetic Tree
A universal Phylogenetic Tree has been developed for living organisms that establishes a tripartite division of all living organisms– bacteria, archaea, and eukarya. The classification is based on a comparison of 16s ribosomal RNA sequences. These sequences are highly conserved and undergo change at a slow, gradual and consistent rate. They are therefore useful for making comparisons among different living organisms.

Taxonomic/Phylogenetic Hierarchy groups are based on similarities. The groups begin very general and become more restricted. DNA hybridization and rRNA sequencing are used to determine evolutionary relationships and classification. Organisms that are grouped together are based on relatedness; very general relatedness at the top, followed by more and more specific and restricted subgroups where genus is all related species, and species is a single unique organism group.

1. Kingdom Protista (unicellular eukaryotes) are algae and protozoa and they are nutritionally diverse: autotrophs, heterotrophs, and intracellular parasite.
2. Kingdom Fungi are yeasts, molds, and mushrooms that absorb organic material through their plasma membrane.
3. Kingdom Animalia are multicellular animals that ingest organic food through a mouth and have cells organized into tissues
4. Kingdom Plantae are multicellular plants that undergo photosynthesis to convert carbon dioxide and water into organic molecules, and this Kingdom has cells organized into tissues

Prokaryotic Classification-prokaryotes have two domains:

1. Bacteria are all pathogenic prokaryotes, many non-pathogenic prokaryotes, and all photoautotrophic prokaryotes
2. Archaea are all prokaryotes with walls that are not peptidoglycan, that carryout unusual metabolism and live in extreme environments, and are groupings based entirely on gene sequencing since most look similar

Prokaryotic species are defined as a population of cells with similar characteristics that do not demonstrate sexual reproduction. Pure cultures are clones because they are populations derived from a single cell. They are genetically identical. Strains are cells of the same species that are not genetically identical.

Viral Classification
Viruses do not fit into a domain system because they are acellular. They are usually only classified by Family and Genus. Viral species are defined as a population of viruses with similar characteristics (including morphology, genes, and enzymes) that occupy a particular ecological niche.

In early 2020, one virus that became very well-known was coronavirus-19, which swept the world as a pandemic. This virus was a type of coronavirus that was extremely contagious and had a wide range of symptoms. It is currently not well understood.

STRUCTURE
Prokaryotes–Structure/Function
Prokaryotes are distinguished from eukaryotes by their smaller size (0.2- 10μm), their lack of internal organelles (mitochondria), the presence of a cell wall, and their cell division by binary fission rather than mitosis. They lack introns, are not capable of endo/exocytosis, and have single-stranded circular DNA rather than multiple discrete chromosomes.

Gram positive bacteria have a large peptidoglycan structure. This structure accounts for the differential staining with Gram stain. Some Gram positive bacteria are also capable of forming spores under stressful environmental conditions such as when there is limited availability of carbon and nitrogen. Spores therefore allow bacteria to survive exposure to extreme conditions.

Gram negative bacteria have a small peptidoglycan layer but have an additional membrane, the outer cytoplasmic membrane. This membrane creates an additional permeability barrier and results in the need for transport mechanisms across it. A major component of the cytoplasmic membrane that is unique to Gram negatives is endotoxin.

Microorganism Identification
The classification is based on morphological characteristics that refer to size, shape, cellular characteristics (capsule, flagella, endospores), differential staining (Gram stain, Acid fast stain), and biochemical tests that probe for specific enzyme activities that lead to carbohydrate fermentation, nitrogen fixation, sulfur oxidation, gas production, acid production, and nitrate reduction.

Brief Chemistry of Water

• Solution

A combination of two or more substances that is so intimately mixed, that the mixture behaves as a single substance. if you take salt crystals and dissolve them in water, it is very difficult to tell that you have more than one substance present just by looking—even if you use a powerful microscope. The salt dissolved in water is a homogeneous mixture, or a solution (Figure 1.3).

(Figure 1.3) Salt and water solution

Hardness – Carbonates and sulfates of calcium and magnesium cause hardness, as do sulfate, chloride and nitrate. Very hard water inhibits lathering by soap and can build up as scale in hot water piping and water heaters.

Typical Hardness Ranges

• Soft: 0 to 17 ppm / 0 to 1 gpg
• Slightly hard: 17.1 to 60 ppm / 1 to 3.5 gpg
• Moderately hard: 61 to 120 ppm / 3.5 to 7 gpg
• Hard: 121 to 180 ppm / 7 to 10.5 gpg
• Very Hard: more than 180 / more than 10.5 gpg

Anyone preparing for a water certification test will need to know:

1. What makes “hard” water hard?

    Relative high concentrations of calcium and magnesium.

2. At what concentration (mg/L) is water considered hard?

    Water over 100 mg/L hardness is considered hard. 

Alkalinity – Alkalinity is a measure of water’s ability to neutralize acids and is due primarily to the presence of bicarbonates.

pH – pH is a measure of the hydrogen ion concentration of water. It determines if water is acidic, basic or neutral. Even slightly acidic water may be corrosive to pipes, tanks, and home plumbing.

Iron (Fe) – A high concentration of iron causes reddish-brown stains on fixtures and laundry. It may also cause a bad taste and odor in water when associated with growth of iron bacteria. It may be dissolved in ground water and not be evident until oxidized to its insoluble form by exposure to air or an oxidant or disinfectant such as chlorine.

Manganese (Mn) – High concentrations of manganese cause brownish to black stains. Like iron, it may not be apparent until the water has been exposed to oxygen or a disinfectant.

Sulfide – Hydrogen sulfide gas has a distinctive smell of rotten eggs. Depending on the water pH, temperature and hydrogen sulfide concentration, it reacts with chlorine to form sulfuric acid and elemental sulfur – a fine white powder with a bad odor.

Sodium – Sodium is a component of table salt. It may make the water taste bad and can be a health risk for people with heart problems.

Radioactivity – Radioactivity in the form of radium and uranium naturally occurs in ground water in some parts of the U.S. Radon gas is radioactive and has been found in many states. Radioactivity is a concern because of its cancer-causing characteristics.

Nitrate – Nitrate and nitrite occur in some ground water and can cause a health risk for young children and pregnant mothers. These chemicals may interfere with the ability of blood to carry oxygen through the body.

Physical characteristics also affect how water will be used. Important physical characteristics include the following:

Turbidity – Turbidity is a measurement of the light-reflecting properties of water. It is used to indicate the relative amount of suspended particles in water – those which reflect light in the turbidimeter. It is required to be monitored in all surface water systems and some ground water systems suspected of being directly influenced by surface water.

Color

Even pure water is not colorless, but has a slight blue tint to it. Color in water is caused by mineral and organic matter, and a brown shade in water often comes from rust in the water pipes. Organic matter and most contaminants are usually removed by water-supply systems, the plus side is that the water you drink likely contains a number of dissolved minerals that are beneficial for human health. And, if you have ever drunk “pure” water, such as distilled or deionized water, you would have noticed that it tasted “flat”. Most people prefer water with dissolved minerals, although they still want it to be clear.

Apparent Color – Apparent color is the color the water appears to be when you look at it. It is a combination of the true color and color imparted by suspended particles. Apparent color provides general but useful information about the water’s source and content. Apparent color is removed by filtering to remove the suspended particles to show the true color of the water. Red rusty water caused by iron oxidized iron is an example of apparent color.

True Color – This is the color remaining in water after it has been filtered to remove suspended particles. True color is caused by dissolved (in solution) organic compounds in water, commonly called tannins or lignins. Filtering will not change the true color of water. The color of tea is an example of true color.

Color in a public water supply should not be detectable (above 15 units). Three hundred units is the color of weak tea.

Temperature – Ground water sources typically have constant temperatures, although some may be warmer than others. Temperature is a useful tool for determining if ground water is directly influenced by surface water.

Taste and Odor – These characteristics are determined by the physical and chemical content of water. However, most contaminants do not impart either and cannot be detected by just smelling or looking at a glass of water.

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