Overview: A Chemical Connection to Biology

• Biology is a multidisciplinary science

• Living organisms are subject to basic laws of
physics and chemistry
• One example is the use of formic acid by ants to
maintain “devil’s gardens,” stands of Duroia trees

Copyright © 2008 Pearson Education, Inc., publishing as Benjamin Cummings

Fig. 2-2
EXPERIMENT

Cedrela Insect
sapling barrier

Duroia Outside,
tree Inside, protected
unprotected Inside,
protected

Devil’s Outside,
garden unprotected

RESULTS
Dead leaf tissue (cm2)

16
after one day

12

0
Inside, Inside, Outside, Outside,
unprotected protected unprotected protected
Cedrela saplings, inside and outside devil’s gardens
Concept 2.1: Matter consists of chemical elements in
pure form and in combinations called compounds
• Organisms are composed of matter
• Matter is anything that takes up space and has
mass
Fig. 2-3

• Matter is made up of elements

• An element is a substance that cannot be broken
down to other substances by chemical reactions
• A compound is a substance consisting of two or
more elements in a fixed ratio
• A compound has characteristics different from those
of its elements

Sodium
chloride

Sodium Chlorine
Essential Elements of Life

• About 25 of the 92 elements are essential to life

• Four are the most important to life, they make up 96%
of living matter
– Carbon
– Hydrogen
– Oxygen
– Nitrogen
• Most of the remaining 4% consists of calcium,
phosphorus, potassium, and sulfur
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Fig. 2-4

Trace elements are those required by an organism in

minute quantities

(a) Nitrogen deficiency (b) Iodine deficiency

Concept 2.2: An element’s properties
depend on the structure of its atoms

• Each element consists of unique atoms

• An atom is the smallest unit of matter that still
retains the properties of an element
• Atoms are composed of subatomic particles
• Subatomic Particles include:
– Neutrons (no electrical charge)
– Protons (positive charge)
– Electrons (negative charge)
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Atomic Number and Atomic Mass

• Atoms of the various elements differ in number

of subatomic particles
• An element’s atomic number is the number of
protons in its nucleus
• An element’s mass number is the sum of
protons plus neutrons in the nucleus
• Atomic mass, the atom’s total mass, can be
approximated by the mass number

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Isotopes

• All atoms of an element have the same number

of protons but may differ in number of neutrons
• Isotopes are two atoms of an element that
differ in number of neutrons
• Radioactive isotopes decay spontaneously,
giving off particles and energy

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 Applications of radioactive isotopes

– Dating fossils
– Tracing atoms through metabolic processes
– Diagnosing medical disorders

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The Energy Levels of Electrons

• Energy is the capacity to cause change

• Potential energy is the energy that matter has
because of its location or structure
• The electrons of an atom differ in their amounts
of potential energy
• An electron’s state of potential energy is called
its energy level, or electron shell

Copyright © 2008 Pearson Education, Inc., publishing as Benjamin Cummings

Fig. 2-8
(a) A ball bouncing down a flight
of stairs provides an analogy
for energy levels of electrons

Third shell (highest energy

level)

Second shell (higher Energy

energy level) absorbed

First shell (lowest energy

level)
Energy
lost
Atomic
nucleus
(b)
Electron Distribution and Chemical Properties

• The chemical behavior of an atom is

determined by the distribution of electrons in
electron shells
• The periodic table of the elements shows the
electron distribution for each element

Periodic Table

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Fig. 2-9

Hydrogen 2 Atomic number Helium

1H He 2He
Atomic mass 4.00 Element symbol
First
shell Electron-
distribution
diagram

Lithium Beryllium Boron Carbon Nitrogen Oxygen Fluorine Neon

3Li 4Be 5B 6C 7N 8O 9F 10Ne
Second
shell

Sodium Magnesium Aluminum Silicon Phosphorus Sulfur Chlorine Argon

11Na 12Mg 13Al 14Si 15P 16S 17Cl 18Ar
Third
shell

Valence electrons are those in the outermost shell, or

valence shell
Concept 2.3: The formation and function of
molecules depend on chemical bonding between
atoms

• Atoms with incomplete valence shells can

share or transfer valence electrons with
certain other atoms
• These interactions usually result in atoms
staying close together, held by attractions
called chemical bonds

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Covalent Bonds Hydrogen
atoms (2 H)

• A covalent bond is the

sharing of a pair of
valence electrons by two
atoms
• In a covalent bond, the
shared electrons count as
part of each atom’s
valence shell

Hydrogen
molecule (H2)
Fig. 2-12
Name and Electron- Lewis Dot Space-
Molecular distribution Structure and filling
Formula Diagram Structural Model
Formula

(a) Hydrogen (H2)

(b) Oxygen (O2)

(c) Water (H2O)

(d) Methane (CH4)

• Nonpolar covalent bond - the atoms share
the electron equally
• Polar covalent bond -atoms do not share
the electron equally
• Unequal sharing of electrons causes a partial
–
charge for each atom or molecule
• Water!
O

H H
+ +
H2O
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Weak Chemical Bonds

• Most of the strongest bonds in organisms

are covalent bonds that form a cell’s
molecules
• Weak chemical bonds, such as ionic
bonds and hydrogen bonds, are also
important
• Weak chemical bonds reinforce shapes of
large molecules and help molecules
adhere to each other

Copyright © 2008 Pearson Education, Inc., publishing as Benjamin Cummings

Ionic Bonds

• Atoms sometimes strip electrons from their

bonding partners
• An example is the transfer of an electron
from sodium to chlorine
• After the transfer of an electron, both
atoms have charges
• A charged atom (or molecule) is called an
ion

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Fig. 2-14-2

• A cation is a positively charged ion

• An anion is a negatively charged ion
• An ionic bond is an attraction between an
anion and a cation

Na Cl Na Cl

Na Cl Na+ Cl–
Sodium atom Chlorine atom Sodium ion Chloride ion
(a cation) (an anion)

Sodium chloride (NaCl)

• Compounds formed by ionic bonds are called
ionic compounds, or salts
• Salts, such as sodium chloride (table salt), are
often found in nature as crystals

Na+
Cl–
Van der Waals Interactions

• If electrons are distributed asymmetrically in

molecules or atoms, they can result in “hot
spots” of positive or negative charge
• Van der Waals interactions are attractions
between molecules that are close together as a
result of these charges

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• Collectively, such
interactions can be
strong, as between
molecules of a gecko’s
toe hairs and a wall
surface

Fig. 2-UN1
Molecular Shape and Function

• A molecule’s shape is usually very important to

its function
• A molecule’s shape is determined by the
positions of its atoms’ valence orbitals
• In a covalent bond, the s and p orbitals may
hybridize, creating specific molecular shapes

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Fig. 2-17b

Space-filling Ball-and-stick Hybrid-orbital Model

Model Model (with ball-and-stick
model superimposed)

Unbonded
electron
pair

104.5º

Water (H2O)

Methane (CH4)
(b) Molecular-shape models
• Biological molecules recognize and interact
with each other with a specificity based on
molecular shape
• Molecules with similar shapes can have similar
biological effects

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Fig. 2-18
Key
Carbon Nitrogen
Hydrogen Sulfur
Natural endorphin Oxygen
Morphine

(a) Structures of endorphin and morphine

Natural
endorphin Morphine

Endorphin
Brain cell receptors
(b) Binding to endorphin receptors
Concept 2.4: Chemical reactions make and break
chemical bonds
• Chemical reactions are the making and
breaking of chemical bonds
• The starting molecules of a chemical
reaction are called reactants
• The final molecules of a chemical reaction
are called products

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 6 CO2 + 6 H20 → C6H12O6 + 6 O2

• Photosynthesis is an
important chemical
reaction
• Sunlight powers the
conversion of
carbon dioxide and
water to glucose
and oxygen
Fig. 2-19

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• Some chemical reactions go to completion:
all reactants are converted to products
• All chemical reactions are reversible:
products of the forward reaction become
reactants for the reverse reaction
• Chemical equilibrium is reached when the
forward and reverse reaction rates are equal

Copyright © 2008 Pearson Education, Inc., publishing as Benjamin Cummings

You should now be able to:

1. Identify the four major elements

2. Distinguish between the following pairs of
terms: neutron and proton, atomic number
and mass number, atomic weight and
mass number
3. Distinguish between and discuss the
biological importance of the following:
nonpolar covalent bonds, polar covalent
bonds, ionic bonds and Van der Walls
reactions.

Copyright © 2008 Pearson Education, Inc., publishing as Benjamin Cummings

Lab 2: Measurements and Pipetting
Do Exercises 4 & 5
• You may work with
your lab team.
• Exercise 5 part 6 –
leaf collection – I will
provide leaves

• When you are done with your leaves, please

place them in a paper bag and label them with
your group number.