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Chapter 2
The Chemical Basis of Life I:
Atoms, Molecules, and Water
Lecture Outline
BIOLOGY
Sixth Edition
Robert J. Brooker, Eric P. Widmaier,
Linda E. Graham, Peter D. Stiling
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No reproduction or further distribution permitted without the prior written consent of McGraw Hill, LLC.
Introduction
• Living organisms are made of chemicals, which are
altered via chemical reactions.
• These reactions occur between atoms and molecules and
may require or release energy.
• Inorganic chemistry- the nature of atoms and molecules,
with the exception of those that contain rings or chains of
carbon.
• Organic chemistry- the study of carbon containing
molecules.
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Review
1. Everything that contains mass and occupies space is called ________.
2. Which of the following describes the smallest functional unit of matter?
a. Electrons
b. Elements
c. Molecules
d. Compounds
e. Atoms
3. Matter is composed of functional units called _______, two or more of which, when
bonded together, form a(n) ______.
4. A pure substance made up of only one kind of atom is called an _____.
5. Name examples of elements
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Review
Which of the following letters are electrons, protons and neutrons?
+
+
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How many protons, neutrons and electrons does
each this atoms have?
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Table 2.2
Table 2.2 Chemical Elements Essential for Life in Many Organisms*
Most abundant in living organisms (approximately 95% of total mass)
Element Symbol % Human body mass % All atoms in human body
Oxygen O 65 25.5
Carbon C 18 9.5
Hydrogen H 9 63.0
Nitrogen N 3 1.4
Mineral elements
(less than 1% of total mass)
Calcium Ca Potassium K
Chlorine Cl Sodium Na
Magnesium Mg Sulfur S
Phosphorus P
Trace elements
(less than 0.01% of total mass)
Boron B Manganese Mn
Chromium Cr Molybdenum Mo
Cobalt Co Selenium Se
Copper Cu Silicon Si
Fluorine F Tin Sn
Iodine I Vanadium V
Iron Fe Zinc Zn
*Although these are the most common elements in living organisms, many other trace and mineral elements have reported functions. For example,
aluminum is believed to be a cofactor for certain chemical reactions in animals, but it is generally toxic to plants.
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Hydrogen, oxygen, carbon, & nitrogen
Make up about 95% of the mass in living organisms
• Hydrogen and oxygen occur primarily in water
• Nitrogen is found in proteins
• Carbon is the building block of all living matter
Mineral elements (chemical elements other than O, H, C and N that are
required for life) - make up less than 1% of the total mass of the organism
Trace elements - less than 0.01%
• Present in small quantities but are essential for normal growth and
function.
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Chemical Bonds and Molecules
Molecule
• Two or more atoms bonded together
• O2
Compound
• Any molecule composed of two or more elements
• H2O; C6H12O6
• Properties of a compound can be drastically different than
the properties of the individual elements in the compound
▪ Na is soft silvery metal
▪ NaCl is white relatively hard crystal that dissolved in water.
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Covalent Bonds Puentes de Hidrógeno Iónicos
How do they occur?
Between which types of atoms
do they occur?
Relative force of bond
Example
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Covalent bonds
Atoms share a pair of electrons
Occurs between atoms with unfilled outer electron shells
Covalent bonds are strong chemical bonds, because the
shared electrons behave as if they belong to each atom
Structural formula, a covalent bond between atoms is
represented by a line indicating a pair of shared electrons.
Can share …
• 1 pair of electrons – single bond, example
• 2 pair of electrons – double bond, example
• 3 pairs of electrons – triple bond, example
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Octet rule
• Atoms are stable when their outer shell is full
• For many atoms, the outer shell is filled with 8 electrons
(“the octet rule”)
• An exception is hydrogen, which fills its outer shell with
just 2 electrons
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Figure 2.7
Hydrogen forming 1 covalent bond with fluorine
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Figure 2.9
Double bond between two oxygen atoms.
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Figure 2.8
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Covalent bonds
• Some atoms attract shared electrons more strongly than
do other atoms.
• The electronegativity of an atom is a measure of its
ability to attract electrons in a bond with another atom.
Atoms with higher values attract electrons more strongly than
do those with lower values.
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Nonpolar covalent bonds
• Covalent bonds between atoms with similar
electronegativities are called non polar covalent bonds.
• Atoms that form nonpolar covalent bonds differ in
electronegativity by less than 0.4.
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Polar covalent bonds
• When two atoms with an electronegativity difference from
0.4 to 1.8 form a covalent bond, the shared electrons are
more likely to be closer to the nucleus of the atom with
higher electronegativity.
• Such bonds are polar covalent bonds.
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Figure 2.10
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Identify polar and nonpolar covalent bonds
Which of the following covalent bonds are polar?
___ C-C
___ O-H
___ C-H
___ H-H
___ N-H
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How many covalent bonds can these atom form?
Nitrogen has 3 electrons in its outermost electron shell. A
nitrogen atom can form how many covalent bonds with
another nitrogen atom?
A) 1
B) 2
C) 3
D) 4
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Hydrogen bonds
One molecule can loosely associate with another molecule
through a hydrogen bond.
Hydrogen atom of one molecules becomes electrically
attracted to an electronegative atom in another polar
molecule.
Represented as dashed or dotted lines
Individually, these are weak bonds that can form and break
easily
Collectively, many H bonds can be strong overall
• Holds DNA strands together
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How many water molecules can interact with one water
molecule?
Draw this interaction
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Figure 2.11
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Hydrogen bonds
The weakness of individual bonds is also important.
The reversible nature of hydrogen bonds allows molecules to
interact and then become separated again.
Small molecules may bind to proteins called enzymes via
hydrogen bonds.
Enzymes are molecules that catalyze biologically important
chemical reactions
• Small molecules may bind to enzymes via hydrogen
bonds
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van der Waals dispersion forces
• Another type of weak molecular attraction
• Arise because electrons are located within orbitals in a
random way
• At any moment in time, the electrons in the outer shells of
the atoms may be evenly or unevenly distributed.
• A fleeting electrical attraction to other nearby molecules
may arise
• Collective strength can be quite strong
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Ionic bonds
An ion is an atom or molecule that has gained or lost one or
more electrons
• Cations – have a net positive charge (+)
• Anions – have a net negative charge (−)
Ionic bond occurs when a cation binds to an anion.
Example is NaCl, table salt
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Figure 2.12
b: Charles D. Winters/Science Source
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Table 2.3
Table 2.3 Ionic Forms of Some Common Elements in Living
Organisms
Atom Chemical Ion Ion Electrons
symbol symbol gained or lost
Calcium Ca Calcium ion Ca2+ 2 lost
Chlorine Cl Chloride ion Cl− 1 gained
Hydrogen H Hydrogen ion H+ 1 lost
Magnesium Mg Magnesium ion Mg2+ 2 lost
Potassium K Potassium ion K+ 1 lost
Sodium Na Sodium ion Na + 1 lost
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Covalent Bonds Hydrogen bonds Ionic
How do they occur?
Between which types of atoms
do they occur?
Relative force of bond
Example
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Covalent Bonds Puentes de Hidrógeno Iónicos
When a hydrogen atom in one polar
molecule becomes electrically
How do they occur? Share a pair of electrons When a cation binds to an anion
attracted to an electronegative atom
in another polar molecule
Hydrogen atom of onem olecule and
Between which types of atoms Between atoms whose outer Occur between atoms that differ
electronegative atom of another.
do they occur? shell is not full greaty in their electronegativity
Both polar molecules.
Strong because the shared
Relative force of bond electrons behave as if they Weak interaction Strongest bonds
belong to each atom.
Hydrogen bonds
Example H-F NaCl
between water molecules
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Properties of Water 1
• Bodies of all organisms largely composed of water
• Up to 95% of the weight of certain plants comes from
water.
• 60 to 70% of human body weight comes from water
• Water is an important liquid in the surrounding
environments of many organisms
• Most chemical reactions in nature involve molecules that
are dissolved in water, including reactions inside cells
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Figure 2.15
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Properties of Water 2
Solution = solutes in a solvent
• Solutes are dissolved substances
• Solvent is the liquid
In an aqueous solution, water is the solvent
Ions and molecules with polar covalent bonds will dissolve in
water
These are hydrophilic
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Why do salts dissolve in water?
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Why do salts dissolve in water?
• The covalent bonds linking the two hydrogen atoms to oxygen are
polar.
• The oxygen is slightly negatively charged and the hydrogen slightly
positive.
• To dissolve in water, a substance must be electrically attracted to
water molecules.
• Example: NaCL
o Na+ is attracted to the partial negative oxygen.
o Cl- is attracted to the partial positive hydrogen.
Clusters of water molecules surround the ions, allowing Na+ and Cl- to
separate from each other and enter the water- dissolve.
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Figure 2.16
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Solutes
Hydrophilic – “water-loving”
• Readily dissolve in water
• Molecules with ionic and/or polar covalent bonds
Hydrophobic – “water-fearing”
• Do not dissolve in water
• Nonpolar molecules like hydrocarbons, oils
Amphipathic – “both loves”
• Have both polar/ionized and nonpolar regions
• May form micelles in water
• Detergent is an amphipathic molecule
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Figure 2.17
• Polar (hydrophilic)
regions at the surface of
the micelle
• Nonpolar (hydrophobic)
ends are oriented toward
the interior of the micelle
(top right): Dr Jeremy Burgess/Science Source
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H20 exists in 3 states
• Water exists on Earth in 3 states- solid, liquid and gas.
• Predominantly, water exists as a liquid, where hydrogen
bonds constantly form and break.
• If the temperatures rise, the rate at which hydrogen bonds
break increases, and molecules of water escape into
gaseous state.
• If temperatures fall, hydrogen bonds are broken less
frequently, and water becomes crystallized.
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Why does ice float on liquid water?
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H20 Exists in 3 States
H20 molecules in ice tend to lie
in a more orderly and open
arrangement, with greater
intermolecular distances,
making it less dense
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Properties of Water
• The heat required to vaporize 1 mole of any substance at
its boiling point is called the substance heat of
vaporation.
• Heat of fusion is the amount of heat that must
be withdrawn or released from a substance to cause it
to change from liquid to solid.
• For water, both are high.
• This is due to the collective force of hydrogen bonds
between water molecules.
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Not just a solvent
Water has many important functions in living organisms:
• Water can vaporize in its gaseous state even at normal
temperatures!!
• Evaporative cooling- in any volume of water at any
temperature, some vibrating water molecules have higher
energy than others. Those with the highest energy break
their hydrogen bonds and escape into the gaseous state.
During this process, energy is released in the form of
heat.
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Figure 2.19
b: Aaron Haupt/Science Source; d: Chris McGrath/Getty Images; e: Dana Tezarr/Getty Images; f: Gallo Images-Anthony Bannister/Getty Images; g: Sergei Mironenko/Shutterstock
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Not just a solvent
Water has many important functions in living organisms:
• Cohesion (molecules of the same type attract each other).
Water molecules are attracted to each other due to
hydrogen bonds.
• Adhesion (unlike molecules attract each other). Water
tend to cling to surface where it can hydrogen bond.
• The adhesive properties of water allow it to coat the
surfaces of the digestive track, serving as a lubricant.
• Surface tension– measure of attraction between
molecules at the surface of a liquid
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Figure 2.19
b: Aaron Haupt/Science Source; d: Chris McGrath/Getty Images; e: Dana Tezarr/Getty Images; f: Gallo Images-Anthony Bannister/Getty Images; g: Sergei Mironenko/Shutterstock
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Acids and Bases 1
• Pure water dissosiates to a very small extent into
+ −
hydrogen ions (H ) and hydroxide ions (OH )
• A property of water is that the product of the concentration
of H+ and OH- is:
H+ OH− = 10 −7 M 10 −7 M = 10 −14 M
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Acids and Bases 2
When certain substances are dissolved in water they may
release or absorb H or OH-
Acids are molecules that release hydrogen ions in solution
+
• A strong acid releases more H than a weak acid
Bases lower the concentration
• Some release OH−
• Others bind H+
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The pH scale
The addition of acids or bases to water may alter the pH
concentration, thus scientists have use a log scale to
describe the concentration of these ions.
• pH = −log
10 Η+
• Acidic solutions are pH 6 or below
• pH 7 is neutral
• Alkaline solutions are pH 8 or above
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Figure 2.20
[H+]
pH
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Effects of pH
The pH of a solution can affect
• The shapes and functions of molecules
• The rates of many chemical reactions
• The ability of two molecules to bind to each other
• The ability of ions or molecules to dissolve in water
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Buffers
• Organisms usually tolerate only small changes in pH
• Buffers help to maintain a constant pH
• An acid-base buffer system can shift to remove or
release H+ to adjust for changes in pH
CO2 + H2O H2CO3 H+ + HCO3-
(carbonic acid) (bicarbonate)
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