Life and Chemistry:
Small Molecules
2
Atoms: The Constituents of Matter
• All matter is composed of atoms.
• Each atom consists of at least one proton and
one electron.
• Atoms have mass. The mass comes mostly from
the proton and a neutrally charged body called a
neutron.
Figure 2.2 The Helium Atom
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Atoms: The Constituents of Matter
• Each element contains only one type of atom.
• Information on elements is arranged in logical
order in a table called the periodic table.
• The periodic table arranges elements left to right
based on their atomic number, and in columns
based on similarities in their properties.
Figure 2.3 The Periodic Table (Part 1)
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Atoms: The Constituents of Matter
• Each element has a unique atomic number
which is the number of protons found in an atom
of the element.
• The mass number is the number of protons plus
the number of neutrons.
• The mass number is used as the weight of the
atom, in units called daltons.
• Each element has a unique symbol: H is
hydrogen, C is carbon, Na is sodium, and Fe is
iron.
Figure 2.3 The Periodic Table (Part 2)
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Atoms: The Constituents of Matter
• The region in which an electron travels is called the
electron’s orbital.
• The orbitals constitute a series of electron shells, or
energy levels, around the nucleus.
• Two electrons at most can occupy each orbital.
2
Atoms: The Constituents of Matter
2
Chemical Bonds: Linking Atoms Together
• A molecule is two or more atoms bonded
together.
• A chemical bond is an attractive force that links
two atoms together.
2
Chemical Bonds: Linking Atoms Together
• A covalent bond is formed by sharing of a pair of
electrons between two atoms.
• In hydrogen molecules (H2), a pair of electrons
share a common orbital and spend equal amounts
of time around each of the two nuclei.
• The nuclei stay some distance from each other
due to mutually repelling positive charges.
Figure 2.8 Electrons Are Shared in Covalent Bonds
Properties of Molecules
2
Chemical Bonds: Linking Atoms Together
• Molecules made up of more than one type of
atoms are called compounds.
• Every compound has a molecular weight that is
the sum of all atoms in the molecule.
Figure 2.10 Covalent Bonding With Carbon
Properties of Molecules
2
Chemical Bonds: Linking Atoms Together
• Electrons are not always shared equally between
covalently bonded atoms.
• The attractive force that an atom exerts on
electrons is called electronegativity.
• When a molecule has nuclei with different
electronegativities, an electron spends most of its
time around the nucleus with the greater
electronegativity.
2
Chemical Bonds: Linking Atoms Together
• Unequal sharing of electrons causes a partial
negative charge around the more electronegative
atom, and a partial positive charge around the
less electronegative atom, resulting in a polar
covalent bond.
• Molecules that have polar covalent bonds are
called polar molecules.
Figure 2.11 The Polar Covalent Bond in the Water Molecule
Properties of Molecules
2
Chemical Bonds: Linking Atoms Together
• Hydrogen bonds may form within or between
atoms with polar covalent bonds.
• The d– portion of one molecule has a weak
attraction to the d+ portion of another molecule.
Each of these attractions is called a hydrogen bond.
• Hydrogen bonds do not share electrons.
• Although hydrogen bonds are weak, they tend to be
additive, and they are of profound biological
importance.
Figure 2.12 Hydrogen Bonds Can Form between or within Molecules
Properties of Molecules
2
Chemical Bonds: Linking Atoms Together
• Ionic bonds involve a complete transfer of one or
more electrons.
• Ions are formed when an atom loses or gains
electrons.
• Positively charged ions are called cations.
• Negatively charged ions are called anions.
Figure 2.13 Formation of Sodium and Chloride Ions
Properties of Molecules
Figure 2.14 Water Molecules Surround Ions
• Ionic bonds are formed
by the electrical attraction
between ions with
opposite charges.
Properties of Molecules
• Table salt has chloride
and sodium ions, held
together by ionic bonds.
• When salt is introduced
into water, the partial
charges of the water
molecules can easily
interfere with the ionic
bonds.
2
Figure 2.3 The Periodic Table (Part 1)
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Chemical Bonds: Linking Atoms Together
• Polar molecules tend to be hydrophilic.
Substances that are ionic or polar often dissolve
in water due to hydrogen bonds.
• Nonpolar molecules are called hydrophobic
because they tend to aggregate with other
nonpolar molecules.
• Nonpolar molecules are also attracted to each
other via relatively weak attractions called van
der Waals forces.
2
Chemical Reactions: Atoms Change Partners
• Chemical reactions occur when atoms combine or
change partners.
• In a chemical reaction, reactants are converted to
products.
• A chemical reaction can be written as an
equation. The equation must balance because
matter is neither created nor destroyed.
Figure 2.15 Bonding Partners and Energy May Change in a Chemical Reaction
Properties of Molecules
2
Water: Structure and Properties
• Ice is held in a crystalline
structure by the orientation of
water molecules’ hydrogen
bonds.
• Each molecule forms
hydrogen bonds with four
other molecules.
• These four hydrogen bonds
increase the space the water
molecules take up, so water
expands as it freezes, and ice
is less dense than liquid water.
• For these reasons, ice floats in
liquid water.
Figure 2.16 Hydrogen Bonds Hold Water Molecules Together (Part 1)
Properties of Molecules
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Water: Structure and Properties
• Compared to other nonmetallic substances, ice
requires a lot of heat to melt because hydrogen
bonds must be broken.
• The opposite process, freezing, requires water to
lose a great deal of heat.
• A great deal of heat energy is required to change
the temperature of liquid water because the
hydrogen bonds must be broken.
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Water: Structure and Properties
• The heat of vaporization is the amount of heat
needed to change a substance from its liquid
state to its gaseous state.
• A lot of heat is required to change water to a
gaseous state because the hydrogen bonds of the
liquid water must be broken.
• Evaporation has a cooling effect by absorbing
calories.
• Condensing has the opposite effect, releasing
heat.
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Water: Structure and Properties
• Water has a cohesive
strength because of
hydrogen bonds.
• The cohesive strength
of water molecules
allows the transport of
water from the roots to
the tops of trees.
• Water has high
surface tension, which
means that the surface
of liquid water is
relatively difficult to
puncture.
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Water: Structure and Properties
• Water is the solvent of life.
• Living organisms are over 70 percent water by
weight and many reactions take place in this
watery environment.
• A solution is a substance (the solute) dissolved
in a liquid (the solvent).
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Water: Structure and Properties
• The mole concept is fundamental to quantitative
analysis. A mole is the amount of a substance in
grams whose weight is equal to its molecular
weight.
• One mole of any given compound contains
approximately 6.03 x 1023 molecules of that
compound (Avogadro’s number).
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Water: Structure and Properties
• A 1 molar (1 M) solution is one mole of a
compound dissolved in water to make one liter.
• Example: One mole of NaCl is the atomic weight
of Na (23) plus the atomic weight of Cl (35.5), or
58.5, in grams. When 58.5 grams of NaCl are
dissolved in water to make one liter, the solution is
1 molar.
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Acids, Bases, and the pH Scale
• Some substances dissolve in water and release
hydrogen ions (H+); these are called acids. Their
release is called ionization.
• Other substances dissolve in water and release
hydroxide ions (OH–); these are called bases.
• Acids donate H+; bases accept H+.
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Acids, Bases, and the pH Scale
• Acids release H+ ions in solution.
• If the reaction is complete, it is a strong acid, such
as HCl.
• The carboxyl group (—COOH) is common in
biological compounds. It functions as an acid
because
 —COOH  —COO– + H+
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Acids, Bases, and the pH Scale
• Bases accept H+ in solution.
• NaOH ionizes completely to Na+ and OH–. The
OH– absorbs H+ to form water. It is a strong
base.
• The amino group (—NH2) is an important part of
many biological compounds; it functions as a
weak base by accepting H+:
 —NH2 + H+  —(NH3)+
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Acids, Bases, and the pH Scale
• Many large molecules in biological systems
contain weak acid or base groups.
• Water is really a weak acid and has a slight
tendency to ionize into H+ and OH–.
• This ionization is very important for living
creatures and the chemical reactions they must
perform because the H+ ion is so reactive.
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Acids, Bases, and the pH Scale
• pH is the measure of hydrogen ion concentration.
• It is defined as the negative logarithm of the
hydrogen ion concentration in moles per liter.
• The pH scale indicates the strength of a solution
of an acid or base. The scale values range from 1
through 14.
• A pH 7 means the concentration of hydrogen ions
is 1 x 10–7 moles per liter of water.
Figure 2.18 pH Values of Some Familiar Substances
Properties of Molecules
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Properties of Molecules
• Functional groups give specific properties to
molecules.
• Functional groups are covalently bonded to
organic molecules.
• Amino acids are biological molecules that contain
both a carboxyl group and an amino group.
Figure 2.20 Some Functional Groups Important to Living Systems (Part 1)
Properties of Molecules
Figure 2.20 Some Functional Groups Important to Living Systems (Part 2)
Properties of Molecules
Figure 2.20 Some Functional Groups Important to Living Systems (Part 3)
Properties of Molecules