Life and Chemistry:
Small Molecules
2
Life and Chemistry: Small Molecules
• The Mechanistic View of Life
• Atoms: The Constituents of Matter
• Chemical Bonds: Linking Atoms Together
-------------------------------------------------------• Chemical Reactions: Atoms Change Partners
• Water: Structure and Properties
• Acids, Bases, and the pH Scale
• Properties of Molecules
2
Mechanistic View of Life
The mechanistic view of life:
Life is chemically based, and it
obeys universal laws of
chemistry & physics.
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
2
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)
Figure 2.3 The Periodic Table (Part 2)
2
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 1)
2
Atoms: The Constituents of Matter
• All atoms of an element have the same number of
protons, but not necessarily the same number of
neutrons.
• Atoms of the same element that have different
atomic weights are called isotopes.
Figure 2.4 Isotopes Have Different Numbers of Neutrons
2
Atoms: The Constituents of Matter
• Some isotopes are radioisotopes, which emit
energy as alpha, beta, and gamma radiation from
their nuclei.
• Radioactive decay transforms the original atom
into another atom, usually of another element.
2
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
• The first shell is the innermost shell and has just
one orbital, called the s orbital.
• The s orbital fills first and its electrons have the
lowest energy.
• The second shell is next closest to the nucleus
and has one s and three p orbitals.
• The second shell can accommodate eight
electrons, two per orbital.
Figure 2.6 Electron Orbitals
2
Atoms: The Constituents of Matter
• The outermost shell of an atom determines how it
reacts with other atoms.
• Generally, if eight electrons are in the outer shell,
the atom is stable and does not tend to react.
• Atoms which do not have eight electrons in the
outermost shell will share, gain, or lose electrons
to arrive at a stable state.
2
Atoms: The Constituents of Matter
• The tendency of atoms to be stable when they
have eight electrons in their outermost shells is
called the rule of eight, or the octet rule.
• Hydrogen and phosphorus are exceptions to the
octet rule.
Figure 2.3 The Periodic Table (Part 1)
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.
2
Chemical Bonds: Linking Atoms Together
• Covalent bonds are very strong.
• Each covalent bond has a predictable length, angle,
and direction, which makes it possible to predict the
three-dimensional structures of molecules.
• A double covalent bond occurs when atoms share
two pairs of electrons; in triple covalent bonds
atoms share three electron pairs.
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
2
Chemical Bonds: Linking Atoms Together
• Ionic bonds are formed by the electrical
attraction between ions with opposite charges.
• 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.
Figure 2.14 Water Molecules Surround Ions
Properties of Molecules
2
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
End of Part A
2
Announcements
• Survey Form Due Today
• Deadline for Online Quiz #1
(Chapter 2) is midnight,
September 6 (next
Wednesday); handout & demo
2
Life and Chemistry: Small Molecules
• The Mechanistic View of Life
• Atoms: The Constituents of Matter
• Chemical Bonds: Linking Atoms Together
--------------------------------------------------------
• Review: Animation – Electron Shells & Reactivity
• Chemical Reactions: Atoms Change Partners
• Water: Structure and Properties
• Acids, Bases, and the pH Scale
• Properties of Molecules
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.
2
Structure of Propane
Source: http://kjd.edu-ctr.pref.kanagawa.jp/edb2/chem/models/3d/Propane.jpg
Figure 2.15 Bonding Partners and Energy May Change in a Chemical Reaction
Properties of Molecules
2
What’s to Come? Metabolic Pathways
Source: http://www.humboldt.edu/~rap1/BiochSupp/PathwayDiagrams/FolMetPath.gif
2
Chemical Reactions: Atoms Change Partners
• Changes in energy usually accompany chemical
reactions. For example, heat and light are
released in the propane reaction.
• In living cells, it is unusual to have reactions that
release light (exceptions: e.g., firefly)
• However, heat is a common product in cellular
reactions. Why does a corpse have a much lower
body temperature than someone who is living?
• Also common are changes in potential energy!
2
Potential Energy
• Stored energy, such as that in chemical bonds, is
called potential energy and is available for future
use. For example, the potential energy in glucose
can be used to make ATP.
• We can measure the potential energy of
molecules and express it in units of heat called
calories.
• A calorie is the amount of heat required to raise
the temperature of one gram of pure water from
14.5°C to 15.5°C.
Figure 2.16 Hydrogen Bonds Hold Water Molecules Together (Part 2)
Properties of Molecules
2
Water: Structure and Properties
Due to its shape, polarity, and ability to form
hydrogen bonds, water has some unusual
properties.
• Ice floats in liquid water; normally the solid form of
a substance is more dense than the liquid form.
• Water has a high specific heat.
• Water has a high heat of vaporization.
Figure 2.16 Hydrogen Bonds Hold Water Molecules Together (Part 1)
Properties of Molecules
2
Water: Specific Heat
• A great deal of heat energy is required to change
the temperature of liquid water because the
hydrogen bonds must be broken.
• Specific heat is the number of calories needed to
raise one gram of a substance 1oC. The specific
heat of liquid water is 1.
• Liquid water has a higher specific heat than most
other small molecules in liquid form.
2
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. (Role of sweating and panting.)
• Condensing has the opposite effect, releasing
heat.
2
Cohesion and Surface Tension
• Source: http://www.npl.co.uk/acoustics/techguides/wetting/images/insect.jpg
2
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.
2
Water as a Solvent
• Source: http://www.uccs.edu/~rmelamed/MicroFall2002/Chapter%202/water%20solvent.jpg
2
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).
2
Water: Structure and Properties
• The mole concept is fundamental to quantitative
analysis, which deals with concentrations or the
amount of a substance in a solution.
• A mole is the amount of a substance in grams
whose weight is equal to its molecular weight.
For example, methane (CH4) has a mw = 16.04
• One mole of any given compound contains
approximately 6.02 x 1023 molecules of that
compound (Avogadro’s number).
2
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.
2
Acids & Bases
Source: http://dbhs.wvusd.k12.ca.us/webdocs/AcidBase/Lab-AcidBaseTitration/BottleHCl&NaOH.JPG
2
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+.
2
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 (e.g., amino acids). It
functions as an acid because
 —COOH  —COO– + H+
2
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)+
2
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
2
Acids, Bases, and the pH Scale
• A buffer is a mixture of a weak acid and its
corresponding base.
• Because buffers can react with both added bases
and acids, they make the overall solution resistant
to pH change.
• Buffers illustrate the law of mass action:
 Addition of reactants to one side of a reaction
drives the reaction in the direction that uses
that component.
Figure 2.19 Buffers Minimize Changes in pH
Properties of Molecules
2
Properties of Molecules
• Chemists use the characteristics of composition,
structure, reactivity, and solubility to help classify
molecules.
• Two other properties that influence the behavior of
molecules are the presence of recognizable
functional groups, and the existence of isomers of
molecules.
2
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
2
Properties of Molecules
• Isomers are molecules that have the same
chemical formula but different arrangements of
the atoms.
• Structural isomers differ in terms of how atoms
are joined together.
• Optical isomers are mirror images of each other.
• Optical isomers can occur whenever a carbon has
four different atoms or groups attached to it.
Figure 2.21 Optical Isomers
Properties of Molecules