Chemical Principles
Introduction
Chemistry is the science of interaction between atoms
and molecules.
Metabolic activities of microorganisms involve
complex chemical reactions.
Nutrients are broken down by microbes to obtain
energy and to make new cells.
The Structure of
Atoms
Atoms are the smallest units of chemical elements
that enter into chemical reactions.
Atoms consist of a nucleus, which contains protons
and neutrons, and electrons that move around the nucleus.
The atomic number is the number of protons in the
nucleus; the total number of protons and neutrons is the atomic weight.
Chemical Elements
Atoms with the same number of protons and the same
chemical behavior are classified as the same chemical element.
Chemical elements are designated by abbreviations
called chemical symbols.
About 26 elements are commonly found in living cells.
Atoms that have the same atomic number (are of the
same element) but different atomic weights are called isotopes.
Electronic Configurations
In an atom, electrons are arranged around the nucleus
in electron shell.
Each shell can hold a characteristic maximum number
of electrons.
The chemical properties of an atom are largely due to
the number of electrons in its outermost shell.
How Atoms Form Molecules
Chemical Bonds
Molecules are made up of two or more atoms; molecules
consisting of at least two different kinds of atoms are called compounds.
Atoms form molecules in order to fill their outermost
electron shells.
Attractive forces that bind the atomic nuclei of two
atoms together are called chemical bonds.
The combining capacity of an atom the number of
chemical bonds the atom can form with other atoms is its valence.
Ionic Bonds
A positively or negatively charged atom or group of
atoms is called an ion.
A chemical attraction between ions of opposite charge is called an ionic bond.
To form an ionic bond, one ion is
an electron donor and the other ion is an electron acceptor.
Covalent Bonds
In a covalent bond, atoms share pairs of electrons.
Covalent bonds are stronger than ionic bonds and are
far more common in organisms.
Hydrogen Bonds
A hydrogen bond exists when a hydrogen atom
covalently bonded to one oxygen or nitrogen atom is attracted to another oxygen
or nitrogen atom.
Hydrogen bonds form weak links between different
molecules or between parts of the same large molecule.
Molecular Weight and Moles
The molecular weight is the sum of the atomic weights
of all the atoms in a molecule.
A mole of an atom, ion, or molecule is equal to its
atomic or molecular weight expressed in grams.
Chemical Reactions
Chemical reactions are the making or breaking of
chemical bonds between atoms.
Energy in Chemical Reactions
A change of energy occurs during chemical reactions.
Endergonic reactions require energy; exergonic
reactions release energy.
In a synthesis reaction, atoms, ions, or molecules
are combined to form a larger molecule.
In a decomposition reaction, a larger molecule is
broken down into its component molecules, ions, or atoms.
In an exchange reaction, two molecules are
decomposed, and their subunits are used to synthesize two new molecules.
The products of reversible reactions can readily
revert back to form the original reactants.
How Chemical Reactions Occur
For a chemical reaction to take place, the reactants must collide with each other.
The minimum collision energy that can produce a
chemical reaction is called its activation energy.
Specialized proteins enzymes accelerate chemical
reactions in living systems by lowering the activation energy.
Important Biological Molecules
Inorganic Compounds
Inorganic compounds are usually small, ionically
bonded molecules.
Water and many common acids, bases, and salts are
examples of inorganic compounds.
Water
Water is the most abundant substance in cells.
Because water is a polar molecule, it is an excellent
solvent.
Water is a reactant in many of the decomposition
reactions of digestion.
Water is an excellent temperature buffer.
Acids, Bases, and Salts
An acid dissociates into H+ and anions.
A base dissociates into OH- and cations.
A salt dissociates into negative and positive ions,
neither of which is H+ or OH-.
Acid-Base Balance
The term pH refers to the concentration of H+ in a
solution. (pH = -log [H+])
A solution of pH 7 is neutral; at equilibrium 1 mole of pure water consists of 0.9999998 moles H2O, 0.0000001 moles H+, and 0.0000001 moles OH-. The log of the [H+] is 10-7 (count the decimal places - 101=10, 100=1, 10-1=0.1, etc.), the negative log is 7.
A pH value below 7 indicates an increase in the [H+] and shows just how acidic the solution is. For example 0.9999998 moles H2O + 0.000001 moles H+ + 0.00000001 moles OH- has a pH of 6 and the [H+] is 10 times greater than a solution with a pH of 7.
A pH above 7 indicates a reduction in the [H+] below that of pure water and the solution is referred to as alkaline, or basic.
A pH buffer, which stabilizes the pH inside a cell, can be used in culture media (pH seems to be an important environmental variable for living organisms).
A buffer consists of a mixture of a weak acid and
the salt of its conjugate base. If base is added to a buffered solution the
acid neutralizes it; if acid is added the base neutralizes it and the pH
remains constant.
Organic Compounds
Organic compounds always contain carbon and hydrogen.
Carbon atoms form up to four bonds with other atoms.
Organic compounds are mostly or entirely covalently
bonded, and many of them are large molecules.
Structure and Chemistry
A chain of carbon atoms forms a carbon skeleton.
Functional groups of atoms are responsible for most
of the properties of organic molecules.
The letter R may be used to denote the remainder of
an organic molecule.
Frequently encountered classes of molecules are R-OH
(alcohols), R-COOH (organic acids), and H2N-R-COOH (amino acids).
Small organic molecules may combine into very large
molecules called macromolecules.
Monomers are usually bonded together by dehydration
synthesis, or condensation reactions, that form water and a polymer.
Organic molecules may be broken down by hydrolysis, a
reaction involving the splitting of water molecules.
Carbohydrates
Carbohydrates are compounds consisting of atoms of
carbon, hydrogen, and oxygen with hydrogen and oxygen in a 2:1 ratio.
Carbohydrates include sugars and starches.
Carbohydrates can be classified as monosaccharides,
disaccharides, and polysaccharides.
Monosaccharides contain from three to seven carbon
atoms.
Isomers are two molecules with the same chemical
formula but different structures and properties for example, glucose (C6H12O6)
and fructose (C6H12O6).
Monosaccharides may form disaccharides and
polysaccharides by dehydration synthesis.
Lipids
Lipids are a diverse group of compounds distinguished
by their insolubility in water.
Simple lipids (fats) consist of a molecule of
glycerol and three molecules of fatty acids.
A saturated lipid has no double bonds between carbon atoms in the fatty acids, an unsaturated lipid has one or more double bonds. Saturated lipids have higher melting points than unsaturated lipids.
Phospholipids are complex lipids consisting of
glycerol, two fatty acids, and a phosphate group.
Steroids have carbon ring structures, sterols have a
functional hydroxyl group.
Proteins
Amino acids are the building blocks of proteins.
Amino acids consist of carbon, hydrogen, oxygen,
nitrogen, and sometimes sulfur.
Twenty amino acids occur naturally (um, not quite).
Amino acids exist in one of two configurations, D (right-handed)or L (left-handed), with L being the isomer always found in proteins.
By linking amino acids, peptide bonds (formed by
dehydration synthesis) allow the formation of polypeptide chains.
Proteins have four levels of structure: primary
(sequence of amino acids), secondary
(helices or pleats), tertiary (overall three-dimensional structure of a
polypeptide), and quaternary (two or more polypeptide chains).
Conjugated proteins consist of amino acids combined
with other organic or inorganic compounds.
Nucleic Acids
Nucleic acids DNA and RNA are macromolecules
consisting of repeating nucleotides.
A nucleotide is composed of a pentose, a phosphate
group, and a nitrogen-containing base.
A nucleoside is composed of a pentose and a nitrogen-containing base.
A DNA nucleotide consists of deoxyribose (a pentose)
and one of the following nitrogen-containing bases: thymine or cytosine
(pyrimidines) or adenine or guanine (purines).
DNA consists of two strands of nucleotides wound in a
double helix. The strands are held
together by hydrogen bonds between purine and pyrimidine nucleotides: AT and
GC.
Genes consist of sequences of nucleotides.
An RNA nucleotide consists of ribose (a pentose) and
one of the following nitrogenous bases: cytosine, guanine, adenine, or uracil.
Adenosine Triphosphate
(ATP)
ATP stores chemical energy for various cellular
activities.
When the bond to ATPs terminal phosphate group is
hydrolyzed, energy is released.
The energy from decomposition reactions is used to
regenerate ATP from ADP and inorganic phosphate.
