CHEMISTRY REVIEW

 

General Chemistry

Elements are the simplest form of matter; cannot be broken down further by either physical or chemical means.

 

Compounds are made up of two or more elements combined in definite quantities and in definite proportions by chemical bonds.

 

Substances are pure forms of matter that cannot be separated or purified further by physical means; include compounds and elements.

 

Mixtures contain two or more substances in indefinite quantities and indefinite proportions.

 

Atoms are the smallest particles of matter that can enter into chemical reactions.Elements are composed of atoms.

 

Molecules are the smallest particles of matter that can have independent existence. Molecules can contain one atom, two atoms, or more than two atoms.

 

Atomic number is the number of protons in the nucleus of an atom of an element.

 

Mass number is the sum of the protons and the neutrons in the nucleus of an atom of an element.

 

Atomic mass or atomic weight is the average mass of a very large number of atoms of an element and is a mixed fraction.

 

The mass number of the most abundant isotope of any element is determined by rounding the atomic mass of the element to the nearest whole number.

 

The number of neutrons in the nucleus of an isotope of an element is equal to the difference between the mass number and the atomic number.

 

An atom, by definition, is a neutral particle and must have the same number of electrons as protons.

 

The nucleus of an atom is the center of the atom where all the mass of the atom resides. It contains the protons and the neutrons.

 

The electrons are arranged in orbitals which are arranged in main energy levels or shells which surround the nucleus of the atom.

 

Particle

Relative Mass

Electrical Charge

Proton

one dalton

+ 1

Neutron

one dalton

none

Electron

negligible

- 1

 

Chemical bonds:

Names of Bonds

Particles Bound

††††††† Nature or How formed

†††††††††††† Relative Strength

Ionic bonds

ions

electrical charge from electron transfer

strong

Covalent bonds

atoms

††† sharing of electrons

strong

Non-polar covalent

atoms

equal sharingof electrons

strong††

Polar covalent bonds

atoms

unequal sharing of electrons

strong†††

Hydrogen bonds

polar molecules

††† partial electrical charges on atoms

weak

Hydrophobic Interactions

nonpolar molecules

repelled by water

very weak

 

 

 

 

Valence is the ability of an atom of an element to form covalent bonds.Some common valences of a few elements are:

Element†††††††††††††††† Valence

Carbon†††††††††††††††††† ††† ††††††††††† 4

Hydrogen††††††††††††† ††† ††††††††††† 1

Oxygen††††††††††††††††† ††† ††††††††††† 2

Nitrogen††††††††††††††††††††††††††††††† 3, 5

Phosphorus††††††††† ††††††††††††††† 5

Sulfur†††††††††††††††††††† ††††††††††††††† 2, 4, 6

 

 

The universe is composed of matter and energy.Matter is anything that has mass and occupies space.Energy is the ability to do work.

†††† Matter is composed of mixtures and pure substances.Mixtures can be separated into their components by physical means, but lack definite components or definite proportions of their components, or both.Pure substances cannot be separated into components by physical means.Pure substances may be elemental substances, called elements, or compound substances, called compounds.

†††† Elements are substances that cannot be broken down by chemical means.Elements are made up of atoms, which are the smallest particles of matter that can enter into chemical reactions.

†††† Over 200 elements are known to exist in the universe.These elements have been arranged into a periodic table.The periodic table arranges the elements by atomic number into periods, or horizontal rows, based upon periodicity, or repetition of chemical properties.

The periodic table also arranges elements into vertical columns called families, based upon the similarities of their chemical properties.Some useful families of elements to know are the alkali metals of column I, the alkaline earth metals of column II, the halogens of column VII, and the noble gases of column VIII.

†††† Some elements are said to be very electronegative, or to have very high electronegativity values.Other elements have very low electronegativity values.Generally, metals are low in electronegativity, while nonmetals are higher in electronegativity than metals.Elements high on the periodic table are more electronegative than elements lower on the periodic table.Elements on the right side of the periodic table are more electronegative than elements on the left side of the table.The most electronegative elements are F>O>N>Cl>S>P.The least electronegative elements are the metals of the lower left part of the periodic table.

†††† Elements can be chemically combined into compounds, therefore, a compound consists of two or more elements combined, in definite proportions, by chemical means.Compounds may be formed by combining atoms of their constituent elements by ionic bonds or by covalent bonds.

†††† Ionic bonds are formed by the transfer of one or more electrons from an atom of one element to an atom of another element.Ionic bonds are usually formed between a metal and a halogen or a metal and a group of highly electronegative elements.Ionic compounds exist as crystals of ions attracted by electrical forces in definite proportions, but in indefinite numbers.Because the numbers of ions in crystals are indefinite, ionic compounds are represented by empirical formulas.Empirical formulas express the ratios of atoms of the constituent elements in the smallest ratios of whole numbers of atoms of each element present.

†††† Covalent bonds are formed by the sharing of electrons between two atoms.Sharing of electrons can occur between two atoms of the same element, as in H2, N2, O2, F2, and Cl2 or between atoms of different nonmetals such as H2O, CO2, CH4, NH3, etc.

†††† Molecules are the smallest particles of matter that have independent existence.Molecules may consist of single atoms in the case of the noble gases, whose atoms will not normally combine chemically with each other or with atoms of other elements.Noble gases are said to be inert.

†††† Molecules usually consist of two or more atoms of an element, such as H2, N2, O2, F2, and Cl2, or two or more atoms of more than one element, such as H2O, CO2, CH4, NH3, etc.Molecules are represented by molecular formulas because each molecule contains definite numbers of atoms in definite ratios.

†††† Covalent bonds may involve approximately equal sharing of electrons, such as between two atoms of the same element, or between atoms of two elements which are nearly equally electronegative, such as carbon and hydrogen.

Bonds involving equal or nearly equal sharing of electrons are called non-polar covalent bonds.

†††† Molecules composed mostly of non-polar covalent bonds are usually non-polar molecules.Non-polar compounds have a fairly even distribution of electrons throughout their molecules, and therefore, there is no significant excess electrical charge at any point in the molecule.Thus, no electrical attractions occur between these kinds of molecules and other molecules.They are not attracted to water, will not mix with water, and are said to be water-hating or hydrophobic.

†††† Covalent bonds between elements that are very different in electronegativity values, such as oxygen and hydrogen, involve an unequal sharing of electrons.Covalent bonds resulting from an unequal sharing of electrons are called polar covalent bonds.Such an uneven sharing of electrons causes an uneven distribution of electrical charge throughout the molecule, resulting in a partial negative charge on atoms of the more electronegative element and a partial positive charge on atoms of the least electronegative element.Molecules having an unequal distribution of electrical charges are called polar molecules.

†††† Compounds with a significant percent of polar covalent bonds are called polar compounds and their molecules are called polar molecules.Water, or H2O, is the best known example of a polar compound.Some other polar compounds are ammonia, NH3, carbon dioxide, CO2, some alcohols, some organic acids, and many other compounds.These polar compounds are attracted to water andmix well with water, therefore they are said to be water-loving or hydrophilic.

†††† When two or more molecules containing hydrogen and one highly electronegative element approach each other, a weak electrical attraction occurs among the molecules.This attraction exists because of the uneven distribution of electrical charges within the individual polar molecules.These forces of attraction between polar molecules containing hydrogen are called hydrogen bonds.

†††† When several non-polar, hydrophobic molecules are surrounded by water molecules, the hydrophobic molecules are repelled by the water and are attracted to one another.The very weak forces of attraction among the hydrophobic molecules are called hydrophobic attractions.

 

†††† Water is the most abundant compound on the surface of the earth.It is also one of the most important compounds in maintaining and preserving life on the earth.Most organisms consist mainly of water, usually between 70 and 95 percent water.

†††† Water owes its physical properties that make it so important to life to itís unique chemical composition.This gives it a relatively low density and the ability to form hydrogen bonds with itís own molecules and those of other non-polar compounds.These physical properties include, most importantly, the fact that water exists as a liquid over a very wide range of temperatures within which bio-molecules can function satisfactorily, a high heat capacity for itís molecular weight, a high heat of fusion (melting), and high heat of vaporization.These properties enable water to assist living organisms in maintaining a relatively constant range of temperatures in their internal environments.

†††† Water has other properties that are uniquely essential for life such as the fact that the solid state of water (ice) is less dense that itís liquid state.This property helps to prevent ponds and streams form freezing throughout in winter.

†††† The ability of water molecules, through their polarity, to hydrate, or surround ions, polar molecules and macromolecules, makes water an excellent solvent for a wide range of substances.The ability of water to dissolve and dissociate ionic and polar compounds leads to the formation of solutions of these substances or solutes.

Water molecules may also dissociate, or separate into two ions.These are called H30+ or hydronium ions and OH- or hydroxyl ions.When water is pure, only one molecule in ten million will dissociate into hydronium and hydroxyl ions.One in ten million is 1x10-7, so we say that the concentration ofhydronium ion is 1x10-7and the negative logarithm of 1x10-7 is 7.†††††††

†††† Mathematicians use the letter p to represent the negative logarithm of a number.The negative logarithm of the hydronium ion concentration is called pH, and the pH of pure water is 7.†† So for pure water, pH=7.Acids, when dissolved in water,increase the hydronium ion concentration and the negative logarithm gets smaller.Therefore, the more acidic a solution is, the smaller the pH number.For acidic solutions the pH may be anything less than 7.

†††† Alkaline substances or bases increase the hydroxyl ion concentration and decrease the hydronium ion concentration.Therefore, the more alkaline, or basic, a solution is, the larger the pH number.For basic solutions, the pH may be anything between 7 and 14.

 

 

 

 

Organic Chemistry and Biochemistry

 

Organic chemistry is the study of compounds of carbon or organic compounds.Carbon is important in forming the compounds found in living organisms because carbon atoms can form strong covalent bonds with each other.Indeed, the hardest substance known, diamond, is composed of carbon atoms covalently bonded into three-dimensional crystals.

†††† The organic compounds of living organisms contain the elements carbon, hydrogen, oxygen, nitrogen, phosphorus and sulfur.Some organic compounds that are not found in living organisms, but were formed from compounds in long buried, dead organisms by heat and pressure are the hydrocarbons. Hydrocarbons consist of only two elements, carbon and hydrogen, and an understanding of the composition and structure of the hydrocarbons is important to our understanding of the molecules of life.

 

††† Hydrocarbon molecules are formed from atoms of hydrogen and carbon joined by covalent bonds.Since carbon and hydrogen are relatively close on the electronegativity scale, simple hydrocarbons are nonpolar organic compounds and will undergo hydrophobic interactions with one another and with other nonpolar compounds.The hydrophobic or water-hating nature of hydrocarbon is important to our understanding of the function ofbiochemical compounds that contain hydrocarbon chains in cellular structures such as membranes.

††† Hydrocarbons may contain varying numbers of carbon atoms.The simplest hydrocarbon molecule is methane, CH4, composed of one carbon atom and four hydrogen atoms.Hydrocarbons that contain more than one carbon atom have carbon atoms joined by one or more covalent bonds with hydrogen atoms filling the remaining valences of the carbon atoms.

††† Hydrocarbon molecules that contain four or more carbon atoms may be arranged in straight chains or branched chains.Thus, it is possible for large hydrocarbon molecules to have the same molecular formula, but different structural formulas.Molecules having the same molecular formula, but different properties are called isomers, and molecules having the same molecular formula, but different structural formulas are called structural isomers.The simplest examples of such molecules are n-butane and isobutane, both of which have the molecular formula C4H10, but n-butane has a straight chain of carbon atoms and isobutane has a branched chain.

 

Carbon atoms may also form double bonds with each other.Since carbon has a valence of four, that is each carbon atom can form four, and only four, bonds with other atoms, double bonds between carbon atoms reduce the number of bonds available for bonding to hydrogen atoms.Hydrocarbons with one or more double bonds between carbon atoms are said to be unsaturated, because they could hold more hydrogen atoms if they did not have any double bonds.Hydrocarbons, which have only single bonds between carbon atoms, contain all of the hydrogen atoms they can hold.These hydrocarbons are said to be saturated.

 

†††† Many of the most important molecules in living organisms are very complex molecules called macromolecules.Macromolecules consist of many simpler molecules joined together by special covalent bonds.These special covalent bonds form between the simpler molecules by the removal of a molecule of water, so the reaction is called condensation.Synthesis means to make complex molecules by joining simpler molecules, so condensation is also called dehydration synthesis.

†††† Macromolecules also must be broken down by living organisms.The process of breaking down a macromolecule into simpler molecules by replacing the water and breaking the bond is called hydrolysis.

†††† Lipids are an important class of macromolecules that are greasy to the touch, insoluble in water, and are mostly hydrophobic.Lipids include the triglycerides, the waxes, the sterols, and the phospholipids.

†††† Triglycerides are made by joining three fatty acids to glycerol by dehydration synthesis.Glycerol is a trihydroxy alcohol, meaning that it has three hydroxyl groups that can form three bonds with organic acids such as fatty acids.Fatty acids are organic acids that have very long hydrocarbon chains making them hydrophobic.

†††† Triglycerides are often called fats and oils.Fats and oils are used by cells for long-term storage of energy.Fats have saturated fatty acids and are generally solids at room temperature.Oils contain unsaturated fatty acids and are generally liquids at room temperature.

†††† Waxes are composed of long-chained alcohols joined to fatty acids by condensation, therefore they are hydrophobic.Waxes help to protect external surfaces of organisms.

†††† Sterols are cyclic compounds, that is, they have multiple rings of carbon atoms in their structure.The most abundant sterol is cholesterol which is a cell wall component of some microorganisms,a component of plasma membranes of most organisms, and is an intermediate in the synthesis of the steroid hormones of humans and other mammals.

†††† Phospholipids are composed of a phosphate group, an amine called choline, glycerol, and two long-chained fatty acids all chemically bound into one macromolecule.Phospholipids are the major component of cell membranes, and are arranged in two layers.Because the phosphatidyl choline head end of the phospholipid is hydrophilic, it faces outward toward the water inside or outside of the cell.The fatty acid tail end of the phospholipid molecule is hydrophobic and turns inward toward the tails of the adjacent layer of phospholipid molecules.This arrangement is called a phospholipid bilayer.

†††† Other types of macromolecules are called polymers.Polymers consist of many repeating units of simpler molecules called monomers bound together by dehydration synthesis.Polysaccharides, polypeptides, and polynucleotides are all examples of polymers that are essential to life.

†††† Polysaccharides are polymers made up of monomers called monosaccharides, or simple sugars.Monosaccharides that have three carbon atoms per molecule are called trioses.†† Two important trioses are glyceraldehyde and dihydroxy acetone.

†††† Pentoses are monosaccharides that have five carbon atoms per molecule. Ribose, deoxyribose, and ribulose are pentoses.

†††† Hexoses are monosaccharides that have six carbon atoms per molecule.Glucose, fructose,and galactose are hexoses.

†††† The disaccharides include some of the most abundant sugars in nature.Disaccharides are composed of two hexoses bound together by condensation.Sucrose, or table sugar consists of glucose and fructose.Lactose, or milk sugar consists of glucose and galactose.Maltose, or malt sugar consists of glucose and glucose molecules bound together.

†††† Most polysaccharides contain glucose or some derivatives of glucose as the monomers.Some important polysaccharides are starches that serve as energy storage in cells, cellulose, found in the cell walls of plants, and chitin, found in some cell walls and arthropod exoskeletons.

†††† Foods containingmonosaccharides, disaccharides, and some polysaccharides are called carbohydrates because they contain carbon, hydrogen and oxygen in approximately a 1:2:1 ratio.

†††† Polypeptides are polymers which, when biologically active, are classified as proteins.

Pol;ypeptides contain amino acids as their monomers.When amino acids are bound through dehydration synthesis, the bond is called a peptide bond, thus when many amino acids are joined by peptide bonds, the resulting polymer is a polypeptide.

†††† Proteins function in cells as enzymes, integral proteins and peripheral proteins of cell membranes, as structural components of tissues such as collagen, as carriers of oxygen and carbon dioxide in the blood such as hemoglobin and in muscle cells as myoglobin.The antibodies, or immunoglobulins, of the immune system are also proteins.

†††† Polynucleotides, better known as nucleic acids, are polymers whose monomers are called nucleotides.Nucleotides consist of three components: a phosphate, a pentose, and a nitrogen-containing base.

 

Macromolecules

 

Macromolecule††††††††††††††††††† Monomers or Building blocks††††††††† Location††††††††††††††† Functions

 

Lipids

††††† Triglycerides†††††††††††††††††† fatty acids and glycerol††††††††††††††††††††† specialized cells††† long term energy storage

††††† Waxes††††††††††††††††††††††††††††† fatty acid and long alcohol†††††††††††††† surfaces†††††††††††††††† protection

††††† Sterols††††††††††††††††††††††††††††† cyclic hydrocarbon rings††††††††††††††††††† cell walls††††††††††††††† protection

††††††††††††††††††††††††††††††††††††††††††††††††††††††††††††††††††††††††††††††††††††††††††††††††††††††††††††††† membranes††††††††††† strength††††††††††††††††††††††††††††††††

††††† ††††††††††††††††††††††††††††††††††††††††††††††††††††††††††††††††††††††††††††††††††††††††††††††††††††††††† blood††††††††††††††††††††† steroid hormones

††††† Phospholipids††††††††††††††††††††††††††††††† Phosphate, choline, glycerol, f.a.ís†† membranes††††††††††† separation of compartment††††††††††

 

Carbohydrates

††††† Polysaccharides†††††††††††† monosaccharides†††††††††††††††††††††††††††††††† in cells††††††††††††††††††† short term energy storage

††††† Disaccharides†††††††††††††††† monosaccharides†††††††††††††††††††††††††††††††† in cells, fluids††††††† short term energy storage

 

Proteins

††††† Polypeptides†††††††††††††††††† amino acids†††††††††††††††††††††††††††††††††††††††††† in cells, fluids††††††† enzymes, structure,

transfer, digestion, etc.

 

Nucleic acids††††††††††††††††††††††† nucleotides†††††††††††††††††††††††††††††††††††††††††† in cells††††††††††††††††††† information transfer

 

 

Nucleic Acids

 

Nucleic Acid†††††††† Pentose††††††††††††††††† Nitrogen-containing Bases†††††††††††††† †††††††††††††† Location†††††††††††††††

DNA†††††††††††††††††††††† deoxyribose††††††††† adenine, guanine, cytosine, thymine††††††††††††††††††††††††††††††† chromosomes, plasmids

RNA†††††††††††††††††††††† ribose†††† †††††††††††††† adenine, guanine, cytosine, uracil†††††††††††††††††††† nucleolus, ribosomes, and

††††††††††††††††††††††††††††††††††††††††††††††††††††††††††††††††††††††††††††††††††††††††††††††††††††††††††††††††††††††††††††††††††††††††††††††† cytoplasm


 

 

†††† There are two kinds of nucleic acids: ribose nucleic acid, or RNA, and deoxyribose nucleic acid, or DNA.The nucleotides of RNA contain the pentose ribose and the bases adenine, guanine, cytosine, and uracil.The nucleotides ofDNA contain deoxyribose and adenine, guanine, cytosine and thymine.

†††† DNA is found in the chromosomes and in plasmids of cells.DNA functions in the transmission of inherited traits from one generation to the next and in directing all of the metabolic activities of cells.

†††† RNA is found in the nucleolus, in ribosomes, and in solution in the cytoplasm.It functions in the synthesis of proteins.