Basic Chemistry

Energy and Matter

     Energy is roughly defined as the ability to do work (i.e. movement, cause chemical or physical changes, etc.).  Energy exists as two forms, kinetic energy, which is the energy of motion and activity, and potential energy, which is stored or at rest.  Matter is defined as anything which has mass and occupies space.  The building blocks of matter are called elements.  Ninety-two elements occur naturally, and these, plus eighteen which have been  artificially produced, are classified in the Periodic Table of Elements, according to size, number of particles, and mass.   The smallest complete component of an element is called the atom, and the number of atoms which compose a substance is the mass of that substance.  The atom is composed of three basic types of particles; protons, which carry a net positive electrical charge, electrons, which carry a net negative electrical charge approximately equal to that of the proton, and neutrons, which have no electrical charge.  The smallest atom, hydrogen, is composed of a single proton which resides in a region called the nucleus, and a single electron which moves or orbits around the proton.  The electron carries a great deal of energy which is released to produce movement approaching the speed of light, but since it is attracted to the positively charged proton, it orbits along a path around the nucleus.  The space between the electron and the nucleus of the atom is called its energy level, since it takes a certain amount of energy to maintain a specific distance.  The greater the amount of energy carried by an electron, the farther away from the nucleus of an atom it will orbit.  Electrons arrange themselves into pathways called orbitals, and each orbital can hold a specific number of electrons.  The first orbital, which is closest to the nucleus of the atom, can hold only two electrons.  The second can hold eight, and so on.  If an atom has more or less electrons in its outermost orbital than eight or some multiple of eight, it is chemically active, since it can either lose, gain, or share those electrons with other atoms, forming a molecule.  The outermost orbital is called the valence (bonding) orbital.  Atoms which have valence orbitals containing the maximum number of electrons, such as helium, neon, argon, xenon, and radon are chemically inert, since they do not need to gain or lose electrons to fill or remove an orbital.  Since these elements exist in a gaseous state, they are often called noble gasses.

     The number of protons in the nucleus of an atom is called the atomic number, and this is generally also equivalent to the number of electrons orbiting the nucleus.  Hydrogen is said to have an atomic number of 1, since there is only one proton in its nucleus and only one orbiting electron.  The atomic mass of an atom is the sum of the number of protons and neutrons in the nucleus.  Hydrogen has an atomic number of 1, since its nucleus only contains a single proton.  Helium has an atomic number of 2, and an atomic mass of 4, since its nucleus is composed of two protons and two neutrons.  Neutrons act as a type of "nuclear glue" since they carry no charge.  In the absence of the two shielding neutrons, helium's protons would repel one another and the atom would disintegrate.  This is also true of the atoms of other elements, which have increasingly larger atomic numbers and masses.

Isotopes and Ions

     If an atom has more or less neutrons in its nucleus than protons, it is called an isotope.  Isotopes can be of great interest to scientists, since many of them have a tendency to lose the excess neutrons and energy.  For example, the carbon atom, which has an atomic number of 6 and an atomic mass of 12, can exist as several isotopes.  Carbon 14 (14C) contains two more neutrons and has a known rate of decay which is measured according to its half-life, or the amount of time necessary for the atom to lose approximately one-half of its mass, of about 5600 years.  By measuring the amount of 14C in a sample such as a fossilized bone, scientists are able to estimate how old the sample is.

     Ions are elements which have either more or less than the normal number of electrons filling their valence orbital.  This excess or lack of electrons gives a normally neutral atom an electrical charge which is either positive or negative.  For example, sodium normally has eleven electrons, so there is only one electron in its valence orbital.  Chlorine has seventeen electrons, seven of which compose its valence orbital.  Sodium serves as an electron donor, releasing its extra electron to chlorine, the electron recipient.  This changes sodium into a cation (Na+), or positively charged atom, and chlorine into an anion (Cl-), or negatively charged atom, and forms an ionic bond between the two atoms, producing sodium chloride (table salt).  Ionically bonded compounds are very hard to break physically, but can be dissociated (pulled apart) by charged solvents such as water.

Covalent Bonds

     Another means by which chemically reactive elements can fill their outermost valence orbitals is through the formation of covalent (sharing) bonds.  In this type of chemical bond, electrons are shared between the valence orbitals of two or more atoms.  This sharing of electrons can either be equal, such that there is no residual electrical charge, or unequal, resulting in weak residual charges on opposite ends of the molecule.  Molecules which carry no charge are called nonpolar, while those which have charges are said to be polar.  Covalent bonds can be single, when only one pair of electrons is shared, double, when two pairs are shared, or multiple, when more than two pairs are shared.  The strength of the bond depends on how many pairs are shared.


     A molecule of water (H2O) is composed two hydrogens and one oxygen atom.  Each hydrogen gains an electron from oxygen, filling its valence orbital, while oxygen receives two electrons, one from each hydrogen, raising the number of electrons in its valence orbital from six to eight, thus satisfying the rule of octets for that atom.  The resulting molecule takes on a bent shape, wherein the two hydrogen atoms lie at an angle to one another of about 104.5o owing to the unequal affinity for electrons by the nucleus of the larger oxygen and two small hydrogens and the repulsive forces exerted by the protons in each of the three atoms.  The sharing is thus unequal, since at any time there could be as many as ten electrons surrounding the oxygen, but only two surrounding each of the hydrogens.  This establishes polarity, with the oxygen end of the molecule more negative and the hydrogen end more positive.  The water molecule is thus analogous to a bar magnet having negative and positive poles.  It tends to be attracted by the more negative oxygen end to positive charges, and to negative charges by the more positive hydrogens.  When the hydrogen end is attracted to the partially negative end of another polar molecule, a hydrogen bond can be formed which only lasts for milliseconds.  Alone, a single hydrogen bond is very weak, but many of these can form at any one time and the net bond can be very strong.  This explains the ability of water to dissociate ionic compounds and pull other polar molecules apart from one another when substances are dissolved, such as when sugar is placed in water.  It also explains the biologically important aspects of water such as cohesion of water molecules allowing them to cling together to produce surface tension and adhesion of water molecules to other polar compounds, high specific heat caused by the release of heat when hydrogen bonds form and absorption of heat when they break, and high heat of vaporization, or the amount of heat necessary to initiate the physical change of water from a liquid to a gas.

     The interaction of water with ionic, polar and nonpolar compounds is of great biological significance.  When a charged molecule, such as an ionically bonded compound like salt is dissociated, water molecules quickly surround the cationic sodium and anionic chlorine atoms, forming hydration shells which prevent the ions from forming new associations with one another.  When nonpolar compounds which do not form hydrogen bonds are placed in water, they are pushed aside by water molecules which tend to form hydrogen bonds with one another.  Nonpolar compounds are thus referred to as hydrophobic (water fearing).  Conversely, polar molecules are pulled apart from one another as hydration shells form due to the tendency of the water molecules to form hydrogen bonds with the molecules rather than one another.  These compounds are thus said to be hydrophyllic (water loving).  The movement of water molecules across structures such as the plasma membrane of a cell is influenced by this interaction, since cell membranes are composed of both hydrophobic and hydrophyllic components.

Acids and Bases

     In liquid form, water is composed of molecules which interact with one another owing to their dipolar structure.  Water molecules do not, however, remain joined together as H2O, rather the relatively weak bonds between single hydrogen atoms in water molecules are continuously breaking and reforming.  This means that at any time, there could be free hydrogen protons (H+) called hydronium ions, as well as an equal number of OH- molecules called hydroxide ions present in the solution.  If the number of hydroxide and hydronium ions present in a solution is equal, as is the case for pure, deionized water, the solution is essentially neutral with respect to its electrical charge.  Alternatively, if a substance dissociates in water such that the concentration of H+ ions is greater than that of the OH- ions present,  the solution has a net positive charge and is said to be acidic.  If the reverse is true, with more OH- than H+, the solution is said to be basic.  A measure of the number of hydrogen ions present in a solution can be provided by the pH scale, which represents pH as the negative logarithm of molar H+ concentration.  The number of H+ ions is equal to an exponent of log base 10, but on the scale the exponent is written as a positive number.  Pure water has an H+ concentration of 10-7 ions, meaning that at any one time there are as many OH- as H+ present, therefore its pH value is 7.  The pH scale ranges from about 14 (10-14 H+ moles per liter; strongly basic), to 0 (10-1 moles per liter; strongly acidic).  Most living cells can only operate properly across a narrow range of pH values close to a neutral pH since overly acidic or basic environments alter the shape of proteins necessary for essential life activities.  To balance alterations in external and internal pH balance, cells rely on buffers, compounds which freely donate H+ ions when pH is too high or take away excess H+ ions when the pH is too low.

States of Matter

     The physical states of matter include liquids, solids, gasses, and plasma.  Individual atoms and molecules are in constant motion, and the amount of motion is directly associated with the amount of free energy (usually in the form of heat) present in the system.  While the basic chemical makeup of a substance can change, the matter from which it is composed does not.  Changes in the state in which matter exists can either be physical, owing to the spacing of atoms and/or molecules as a consequence of the amount of energy present, or chemical, wherein the interactions between atoms or molecules change.  In a physical change the amount of energy which each atom or molecule has is either increased or decreased and the spacing between these changes.  For example, if liquid water is cooled, the amount of free energy decreases, and water molecules begin to slow down.  In time, enough free energy can be removed from the system to cause the molecules to lie very close together and express little movement.  As a consequence, the water changes in its physical state from a liquid to a solid called ice.  Keep in mind, however, that the chemical structure of the water (H2O) is not altered in any way, only the amount of the free energy of movement expressed by the water molecules.  By giving ice more free heat energy, the water molecules begin to move more rapidly and will eventually return to the liquid state.  Giving  liquid water even more energy, raising the temperature to 100o C, will make the molecules move so rapidly that they will leave the liquid state and enter the gaseous state as water vapor.

     Chemical changes occur when the actual atomic makeup of molecules is altered.  Such changes occur as chemical reactions, wherein existing bonds between atoms are broken, or new bonds are formed.  Reactions which break bonds between atoms or molecules release energy, generally in the form of heat.  These are called exergonic reactions.  Conversely, endergonic reactions store energy in the form of new chemical bonds.  The storing and releasing of energy in small, manageable amounts is vital to the proper metabolic functioning of cells.

     Chemical reactions which occur within living cells generally occur as one or more of three basic types.  Exchange reactions occur when atoms or parts of molecules are exchanged between two molecules.  For example, when sodium hydroxide (NaOH) is mixed with hydrochloric acid (HCl), there is an exchange of atoms between the two reactants, resulting in the formation of two products, water (H2O) and sodium chloride (NaCl).  Written in chemical notation, this how the reaction appears:

                                            NaOH + HCl  --------> NaCl + H2O

     Note that the number of atoms in the products of the exchange reaction are exactly the same as the number in both of the reactants.  Condensation (dehydration) reactions occur when two or more molecules are linked together through the removal of water molecules.  This type of reaction is necessary in living cells to build new molecules for structure and as storage products.  Hydrolysis reactions are the opposite of condensation reactions, because they involve the addition of water to break large biological molecules apart, releasing the energy store within the bonds of their component parts.  Both condensation and hydrolysis are reactions which usually do not occur spontaneously in living cells, but must be stimulated by a group of very specialized protein compounds called enzymes.

Organic Chemistry

     All living things are composed of compounds which contain carbon (C), hydrogen (H), oxygen (O) and nitrogen (N).  These are referred to as organic compounds.  The carbon atom has four valence electrons in its outmost shell, and can form single, double, or triple covalent bonds either with other carbon atoms, or with other elements, forming a complex skeleton.  The structures which can be formed by these associations can be quite complex, ranging from linear to ring-shaped.  Structure is important, because it conveys upon the organic compound characteristics which allow it to interact with others in ways which give rise to important cell components and metabolic activity.  Organic compounds are generally composed of subunits called monomers, which can be joined together by condensation, or split apart by hydrolysis.  When two or more monomers are linked together, they form polymers which can be quite large. There are four basic categories of organic compounds; carbohydrates, lipids, proteins, and nucleic acids.


     This category of organic compounds is composed of carbon, hydrogen, and oxygen atoms bonded together in a ratio of 1:2:1 (carbon:hydrogen:oxygen).  Carbohydrates serve as a source of energy, serve to store energy, and as structural components for cells.  The smallest complete subunit of a carbohydrate is called a monosaccharide, which may have a minimum of three carbon atoms, or a maximum of six.  Glucose and fructose are examples of six-carbon monosaccharide (sugar monomer) compounds which are important to cells.  They are called isomers, since both have the same chemical formula (C6H12O6), but have different three-dimensional arrangements of atoms.  By enzymatically removing and -OH group from glucose and an H+ from fructose, the two can be  linked to form a disaccharide (a type of polymer; polysaccharide) called sucrose, which is common table sugar.

     Mono- and disaccharide compounds can be broken down relatively easily by cells to release energy stored between chemical bonds.  Larger polysaccharides are generally used as storage compounds or structural components of cells, based on their shapes.  For example, starch is a complex polysaccharide composed of long chains of glucose molecules linked together by condensation. Starch is used as an energy storage compound by organisms such as plants.  Many living things, including humans, have the enzymes necessary for the hydrolysis of starch into glucose, but do not have the enzymes necessary for the hydrolysis of another compound called cellulose, which plants and algaes use as structural components of their cell walls.  Cellulose is chemically identical to starch, but its individual glucose monomers are linked together differently.  Thus cellulose is an isomer of starch, chemically the same, but structurally different.  Some protists and bacteria have the necessary enzymes to break cellulose down, and many of these have evolved symbiotic relationships with animals.  For example, termites and large herbivores such as cows rely upon their stomach microflora such as the ciliate protist Trichonympha to break down the cellulose into glucose, which can then be used by the host organism as a source of energy.  If the microflora are excluded from the digestive process, both hosts would be unable to break cellulose down, and would starve.


     Lipids are also composed of carbon, hydrogen, and oxygen, but not in the exact ratio of 1:2:1.  The most common forms of lipids are fats, waxes, and oils.  These compounds have carbon backbones which are either linear or ring-shaped.  Lipids provide energy storage (one molecule of a fat can store twice as much energy between its chemical bonds than a molecule of glucose), structural components of cells, insulation in multicellular organisms, lubrication, and protection.  Some lipid-containing compounds such as mucus and cerumin (ear wax) are bacteriostatic, since they inhibit the growth of many bacterial species and trap the organisms so that they cannot colonize the host.  Lipids can also serve as chemical messengers which elicit changes in cell activity.  Many hormones, such as testosterone, are lipid compounds.

     Fats and oils are examples of triglycerides, lipids composed of fatty acid monomers bonded to glycerol.  Fats are solids at room temperature since they are composed of fatty acids which have hydrogens single-bonded to most of the carbon atoms composing the backbone.  Such fatty acids are said to be saturated.  Saturated lipids are very hard to hydrolyze, and can build up in the blood vessels of humans, leading to the formation of plaques which block the flow of blood.  Conversely, oils are liquids which are generally unsaturated, since some of the carbon atoms form double bonds with one another, leaving no valence electrons available for forming bonds with hydrogen atoms.

     Sterols are ring-shaped lipids.  These can serve as the basic components of hormones, and can act as units to maintain the structural integrity of the cell membrane.  Animal cells contain the sterol cholesterol, while fungal cells contain ergosterol.  This distinction is important clinically, since it can be used to produce antimicrobial compounds which are selectively toxic (i.e. will attack pathogenic fungi while causing no toxic side-effects to the host).

     Phospholipids are composed of two fatty acid "tails" bonded to a phosphate (-PO4) group "head".  These are key components of the cell membrane of plants, animals, protists, and bacteria, but not of the archaebacteria, whose membranes are composed of fatty acids bonded to hydrocarbon compounds rather than glycerol.  The polar/nonpolar nature of the phospholipid molecule facilitates an orientation wherein the phosphate head faces water either outside of the cell or inward toward the cytoplasm, while the nonpolar fatty acid tails face inward toward one another in a double-layered structure.  Though each phospholipid subunit is independent of the other, this interaction with water helps maintain the integrity of the cell membrane.


     Proteins are long-chain polymers or polypeptides, which are composed of monomer subunits called amino acids.  Each amino acid has two ends, a carboxyl group composed of carbon, hydrogen, and oxygen, and an amino group composed of nitrogen and hydrogen.  When two amino acids are joined by condensation, hydroxide is removed from the carboxyl group of one, and a hydrogen ion from the amino group of the other.  A carbon- nitrogen peptide bond is then formed which links the two together.  Since each amino acid has its own specific three-dimensional architecture, peptide bonding results in folding or bending of the growing polypeptide chain.  The sequence of amino acids, called the primary structure (1o) of the protein, is important since it determines the shape and ultimately the function of the protein.  The secondary structure (2o) is the way the protein arranges itself into folds or pleated sheets.  The tertiary structure (3o) refers to the three-dimensional appearence the protein assumes, and the quartenary structure (4o) refers to how each protein interacts with others in the formation of very complex molecular structures.

     Proteins form many major structural components of the cell, often forming complexes with other organic molecules such as lipids and carbohydrates.  They serve in the production of components for cellular recognition, movement, and transport of substances into and out of the cytoplasm of the cell.  Many also are vital to metabolism as enzymes which catalyze chemical reactions both for the building and breaking down of molecules in and outside of the cell.   Without the activity of enzymes, the cell would be incapable of living processes.

Nucleic Acids

     Another group of molecules essential for life to occur are called nucleic acids.  These are large, long-chain molecules composed of carbon, oxygen, nitrogen, hydrogen, and phosphorus.  Nucleic acids function in the storage, transport, and processing of cellular information by maintaining a molecular code for the production of polypeptides which ultimately become structural proteins and enzymes.  Each nucleic acids is composed of a five carbon sugar, bonded to a phosphate group. Also bonded to the sugar is a molecule called a nitrogenous base, which is one of five types: adenine, thymine, cytosine, guanine, or uracil. The combination of phosphate, sugar, and nitrogenous base is called a nucleotide, which is the basic monomer of the nucleic acid.

     Each nucleotide is joined to another by a 3'-5' glycosidic covalent bond.  These bonds form when the phosphate group from one nucleotide is bonded by condensation to either the third  or the fifth carbon atom on the sugar molecule.  Unless the nucleic acid is circular, as in prokaryotes, this leaves unbonded portions on each side of the sugar-phosphate backbone referred to as the 3' (-OH)  and the 5' (P) ends.  This conveys directionality to the molecule, which is important to the  way it interacts chemically with other molecules when it is replicated, and during the process which gives rise to new polypeptides called protein synthesis.

     The two categories of nucleic acids found in cells are deoxyribonucleic acid (DNA), and ribonucleic acid (RNA).  DNA generally occurs as a double-stranded molecule, composed of chains of nucleotides bonded by 3'-5' glycosidic bonds to form nucleosides.  The nucleosides are joined together by hydrogen bonding which forms between the nitrogenous bases adenine, thymine, guanine, and cytosine on each strand.  Adenine and guanine are double-ringed bases called purines, while thymine and cytosine are single-ringed bases called pyrimidines.  Adenine and thymine can form two hydrogen bonds, while guanine and cytosine can form three, so these pairs bond to one another specifically in a complementary fashion.  The order in which nucleotide bases align themselves on a nucleoside confers information ultimately about how amino acids are linked together to form polypeptides.  Each individual sequence of nitrogenous bases which carries this information is called a gene, and all of these combined compose the genetic code carried by each living cell.

     RNA generally occurs as a single nucleoside with a sugar-phosphate backbone linked by 3'-5' glycosidic bonds.  Its five-carbon sugar, ribose, contains an additional oxygen atom not found in the sugar deoxyribose found in DNA.  Additionally, RNA is composed of the bases adenine, guanine, and cytosine, but does not contain the pyrimidine thymine.  Replacing thymine is the nitrogenous base uracil, which can also form two hydrogen bonds when linked to adenine.  RNA can be found in three forms, messenger RNA (mRNA) which carries the information concerning the sequence of amino acids contained within a gene to the site of cellular protein synthesis, transfer RNA (tRNA) which carries amino acids to the site, and ribosomal RNA (rRNA), which acts with protein in structures called ribosomes to enzymatically combine amino acids into polypeptides.  In order for the cell to survive, both RNA and DNA must act together to produce new proteins which enable growth, repair, and metabolism to occur properly.

Cooperative Activities

I. Test Yourself: Use this link to quiz yourself about basic chemistry.

II.  Diagram - Phosphorus has an atomic number of 15, and an atomic mass of 30.  Draw a diagram to represent this atom, including the components of the nucleus.

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