CHAPTER 2

2.1 The Organization of Matter: Elements and Atoms

 Element – a pure substance that cannot be broken down into simpler
substances (92 on earth)
 Matter – anything that occupies space and ahs mass
 Living organisms are composed of about 25 key elements
o Carbon, Hydrogen, Oxygen, Nitrogen make up 96%
o Trace elements = several elements that occur in quantities so small
they cannot be calculated
 Elements are composed of atoms, which combine to form molecules
o Atoms – the smallest units that retain the chemical and physical
properties of an element
o Molecules – atoms combined chemically in fixed numbers and
ratios
o Formula – the name of a molecule written in chemical shorthand
o Compounds – molecules whose component atoms are different
(such as carbon dioxide)
2.2 Atomic Structure
 Each element consist of one type of atom
 Structure of an atom
o Atomic nucleus makes up 99.9% of its mass and is surrounded by
one of more electrons
 The atomic nucleus contains protons and neutrons
o Protons = positive; Nucleus = uncharged; Electrons = negative
o Atomic number – the number of protons in the nucleus of each kin
of atom
o Isotopes – distinct forms of the atoms of an element, all with the
same number of protons but different numbers of neutrons
 Differ in mass and other physical characteristics but have the
same chemical properties
o Dalton – unit of measurement (1.66 x 10-24)
o Mass number – based off the total number of protons and neutrons
in the nucleus
 The nuclei of some atoms are unstable and tend to break down to form
simpler atoms
o The nuclei of some isotopes are unstable and break down, or
decay, giving off particles of matter and energy that can be
detected as radioactivity
o The decay transforms the unstable, radioactive isotope
(radioisotope) into an atom of another element
o EX: carbon isotope
 The electrons of an atom occupy orbitals in the nucleus
o Number of electrons surrounding the nucleus is equal to the
number of protons in the nucleus
 o Electrons are in a constant motion and moves so fast that it almost
occupies all the locations at the same time
o Orbital – the locations where an electron occurs most frequently
around the atomic nucleus
 Orbitals occur in discrete layers around an atomic nucleus
o Within an atom, electrons are found in regions of space called
energy levels (or shells)
o 1s22s22p63s23p64s23d104p65s24d105p6 ect.
o Larger atoms have more energy levels
 The number of electrons in the outermost energy level of an atom
determines its chemical activity
o The electrons in an atom’s outermost energy level are known as
valence electrons
o Those whose orbitals aren’t full are chemically reactive
o If the energy level is filled it is nonreactive
o Those with 8 electrons completely filling the four orbitals of the
outer energy level, such as neon and argon, are stable (Fig. 2.6)
o Atoms that differ from the stable configuration by more than one or
two electrons tend to attain stability by sharing electrons with other
atoms
2.3 Chemical Bonds
 The four chemical linkages that are important in biological molecules are:
o Ionic bonds: resulting from electrical attractions between atoms that
have lost or gained electrons
o Covalent bonds: formed by electron sharing between atoms
o Hydrogen bonds: noncovalent bonds formed by unequal electron
sharing between hydrogen atoms and oxygen nitrogen or sulfur
atoms
o Der Waals forces: weak molecular attractions over short distances
 Ionic bonds are multidirectional and vary in strength
o EX: in NaCl the sodium atom readily loses a single electron to
achieve a stable outer energy level
o Cation = positively charged ion
o Anion = negatively charged ion
 Ionic bonds are common among the forces that hold ions, atoms and
molecules together in living organisms because these bonds have three
key features:
o They exert an attractive force over greater distances than any other
chemical bond
o Their attractive force extends in all directions
o They vary in strength depending on the presence of other charged
substances
 Ions set up strong and stable attractions that are not usually disturbed
 Covalent bonds are formed by electrons in shared orbitals
 o Covalent bonds form when atoms share a pair of valence electrons
rather than gaining or losing them
o Represented by ----- or :
 H:H H----H
o Carbon typically forms covalent bonds as well as oxygen,
hydrogen, nitrogen and sulfur
 Unequal electron sharing results in polarity
o Electronegativity is the measure of an atom’s attraction for the
electrons it shares in a chemical bond with another atom
o The more electronegative, the stronger the attraction
o Depending on the difference in electronegativity, a bond can be
classified as nonpolar covalent or polar covalent
o In nonpolar covalent bonds, electrons are shared equally
o In polar covalent bonds they are shared unequally
o EX: water’s molecule is arranged in an unequal charge distribution
o The presence of –OH, --NH, or –SH groups tends to make regions
in biological molecules containing them molar
 Polar molecules tend to associate with each other and exclude nonpolar
molecules
o Polar molecules attract and align themselves with other polar
molecules and with charge ions and molecules. These polar
associations crease environments that tend to exclude nonpolar
molecules
 Reduce surface area exposed to the surrounding polar
environment
o Polar molecules are hydrophilic (water lovers) and non polar
substances are classified as hydrophobic
 EX: water and vegetable oil
 Hydrogen bonds also involve unequal electron sharing
o When hydrogen atoms are made partially positive by sharing
electrons unequally with oxygen, nitrogen or sulfur, they may be
attracted to nearby oxygen, nitrogen or sulfur atoms made partially
negative by unequal electron sharing in a different covalent bond
o Individual hydrogen bonds are weak compared with ionic and
covalent bonds
o The weak attractive force of hydrogen bonds makes them much
easier to break than covalent and ionic bonds, particularly when
elevated temperature increases the movements of molecules
 Van der Waals forces are weak attractions over very short distances
o Even weaker than hydrogen bonds
o These forces develop between nonpolar molecules or regions of
molecules when, through their constant motion, electrons
accumulate by chance in one part of a molecule or another. This
process leads to ones of positive and negative charge, making the
molecule polar
 o Found on the pads of geckos
 Bonds form and break in chemical reactions
o Chemical reactions occur when atoms or molecules interact to form
new chemical bonds or break old ones
o As a result of bond formation or breakage, atoms are added to or
removed from molecules, or the linkages of atoms in molecules are
rearranged
o VOCAB: reactants, products, chemical equations
2.4 Hydrogen Bonds and the Properties of Water
 A lattice of hydrogen bonds gives water unusual properties
o Hydrogen bonds form readily between water molecules in both
liquid water and ice
o Water lattice – each water molecule in liquid water forms an
arrangement
o Ice lattice – spaces the water molecules farther apart than the
water lattice
 EX: ice cubes are larger than water volume poured into the
tray
o Ice floats because it is less dense than water
 The hydrogen-bond lattice of water contributes to polar and nonpolar
environments in and around cells
o If present, the competing attractions open the water lattice, creating
a cavity into which the polar or charged molecule can move. By
contrast, nonpolar molecules are unable to disturb the ater lattice.
The lattice thus excludes nonpolar substances, forcing them to form
the nonpolar associations that expose the least surface area to the
surrounding water
o The polar and nonpolar environments created by water are critical
to the organization of cells (EX: biological membranes)
o Exclusion by the water molecules forces the lipid molecules to
associate into a double layer, a bilayer, in which only the polar ends
of the surface molecules are exposed to the water. The nonpolar
ends of the molecules associate in the interior of the bilayer, where
they are not exposed to the water. Exclusion of their nonpolar
regions by water is all that holds membranes together.
 The small size and polarity of its molecules makes water a good solvent
o Because water molecules are small and strongly polar, they readily
penetrate or coat the surfaces of other polar and charged
molecules and ions.
o The surface coat, called a hydration layer, reduces the attraction
between the molecules or ions and promotes their separation and
entry into a solution
o VOCAB: solute, solvent, concentration, Avogadro’s number,
molecular weight, mole, molarity
  The hydrogen-bond lattice gives water other life-sustaining properties as
well
o Water has an unusual ability to resist changes in temperature by
absorbing or releasing heat, plus an unusually high boiling point
o Water has an unusually high internal cohesion and surface tension
 The boiling point and temperature-stabilizing effects of water
o The hydrogen-bond lattice of liquid water retards the escape of
individual water molecules as the water is heated. As a result,
relatively high temperatures and the addition of considerable heat
are required to break enough hydrogen bonds to make water boil
(and makes water have a high specific heat—measured In calories)
o Heat of vaporization – the large amount of heat that must be added
to give water molecules enough energy of motion to break loose
from liquid water and form a gas
 Cohesion and surface tension
o Internal cohesion – the high resistance of water molecules to
separation, provided by the hydrogen-bond lattice (EX: roots in
plants holding water)
o Maintenance of the long columns of water in the tubes is aided by
adhesion, in which molecules “stick” to the walls of the tubes by
forming hydrogen bonds with charged and polar groups in
molecules that form the walls of the tubes
o Surface tension – the force that denies the formation of hydrogen
bonds on the side of water that faces air

2.5 Water Ionization and Acids, Bases and Buffers

 The most critical property of water that is unrelated to its hydrogen-bond
lattice is its ability to separate, or dissociate, to produce positively charged
hydrogen ions (H+, or protons) and hydroxide ions (OH-)
 Substances act as acids or bases by altering the concentrations of H = and
OH- ions in water
o Acids – proton donors that release H= and anions when they are
dissolved in water
o Bases – proton acceptors that reduce the H+ concentration of a
solution
o The concentration of H+ ions in a water solution, as compared with
the concentration of OH- ions, determines the acidity of the solution.
This is measured on a pH scale.
 pH = -log10[H+]
 Each whole number on the pH scale represents a value 10
times greater or less than the next number.
 Buffers keep pH under control
o Living organisms control the internal pH of their cells with buffers,
substances that compensate for pH changes by absorbing or
 releasing H+. Most buffers are weak acids or bases (or
combinations of both).
o Hyperventilation is what happens when the carbonic acid buffer is
no longer able to maintain pH at normal levels
**Self-Test and Review on pgs. 39, 40**