Chapter 2: Chemistry
The study of matter, anything that has mass.
I. Elements
Pure substances. Atoms are the “building blocks”. They contain three types of subatomic
particles: neutrons and protons (+) in the nucleus, electrons (-) “orbit” in shells. Closest shell to
the nucleus holds two electrons, second and thirds shells can hold eight each.
Elements are arranged in the Periodic Table based on atomic number: the number of protons.
Initially, an atom has equal number of protons and electrons (electrically neutral).
Some elements, e.g. O & C, have atoms with variable numbers of neutrons- these are isotopes.
Isotopes are radioactive when extra neutrons release measurable energy as they degrade. They
are potentially dangerous and used medically in PET imaging (nuclear medicine).
II. Molecules
Formed by bonds between atoms. Bonds represent potential energy which is released as kinetic
energy when bonds are broken. Electrons provide the motivation for bonding; only atoms with
filled outermost electron shells are unreactive. Free radicals are disruptive, unstabile charged
groups of atoms- involved in aging.
(A) Ionic Bonds – formed between ions: electrically charged atoms or groups of atoms.
Electrons are exchanged to satisfy valence requirements: number of electrons needed to transfer to
maintain filled outermost shell. These bonds are weak and not very important biologically.
e.g. in NaCl (table salt).
(B) Covalent Bonds – Electrons are shared. These bonds are much stronger and more
biologically important, most common in organisms.
(C) Hydrogen Bonds – Weak electrical attractions between H+ and a negative end of
another molecule. e.g. between water molecules.
III. Water
Most important inorganic substance. Inorganic chemicals are common outside of living things and
do not contain carbon. Hydrogen bonds between molecules create cohesion, which is responsible
for the following unique properties:
(A) Water is the universal polar solvent – almost all biologically important chemicals,
which are also polar, dissolve in it. “Like dissolves in like”.
(B) Water is liquid at room temperature – this makes it an especially stabile fluid to base
living tissues on.
(C) Water resists temperature changes – therefore, living things can better maintain
constant body temperature just by being largely composed of water.
(D) Capillary action draws water and aqueous solutions through narrow tubes, such as
blood vessels.
(E) Water and aqueous solutions exhibit surface tension.
IV. pH
A reference to this balance: H2O -------------- H+ and OH-.
Acids increase the relative number of H+s; bases do the opposite.
The pH scale is from 0-14. 7 = neutral (#H+s = # OH-s).
Low pHs are acidic; low pHs are alkaline.
Buffers maintain pH homeostasis. e.g. carbonic acid.
V. Organic Molecules
Associated with living things, contain carbon, formed by covalent bonding, large and complex
molecules. Two opposite types of reactions:
Anabolic (bonds forms), dehydration syntheses, energy needed, vs.
Catabolic (bonds break), hydrolysis decompositions, energy released.
These reactions occur simultaneously due to the transfer of energy from the catabolic to the
anabolic.
(A) Carbohydrates – contain carbon, oxygen and hydrogen in the following proportions:
C(H2O)n. These molecules function primarily as “fuel”.
-1- monosaccharides – e.g. glucose, fructose, ribose. Most with 5-6 carbons.
-2- disaccharides – e.g. sucrose, lactose.
-3- oligosaccharides
-4- polysaccharides: most made of glucoses. e.g. starch (glucose storage in plants), cellulose
(undigested), and glycogen (glucose storage in animals).
(B) Lipids – uniquely nonpolar, hydrophobic. Carbon, hydrogen and oxygen in no particular
ratio.
-1- triglycerides – most common. Oils, energy storage.
Each molecule = glycerol + three fatty acids. Characteristics determined by fatty acids included.
e.g. saturated are solid at room temperature.
-2- phospholipids – glycerol, phosphate group, two fatty acids. Important for membrane structure.
-3- steroids: four hydrocarbon rings. Cholesterol, hormones (estrogens, testosterone, cortisol….).
(C) Proteins – carbon, hydrogen, oxygen and nitrogen. Made of amino acids: twenty
types, nine are essential (needed in diet). Each has an amino (N containing) group. Linked via
peptide bonds to form polypeptides. Called proteins when a minimum of 100 amino acids. Many
are large and complex, with 3D shape.
Many are enzymes: catalysts for all biochemical reactions. Specific for substrates, quickly
recycled. Create product(s). Their destruction is called denaturation: loss of 3D shape.
(D) Nucleic Acids: DNA and RNA.
Each composed of nucleotides: formed by phosphate groupd, sugar and nitrogenous base.
-1- RNA: ribonucleic acid. Sugar = ribose, bases = A, U, C, G.
A single strand of nucleotides.
-2- DNA: deoxyribonucleic acid. Sugar = deoxyribose, bases = A, T, C, G.
Genetic code = order of the bases, equivalent to letters o an alphabet.
Double strand of nucleotides connected by complementary bases.
(E) ATP – a unique nucleotide for energy storage and provision.
Adenosine triphosphate.
ATP yields ADP + phosphate group + energy.
Its catabolism fuels most energy-requiring activities in all living organisms.
The production of ATP from ADP requires a phosphate group, energy (usually provided by the
bonds of glucose), and almost always oxygen. This process is cellular respiration.