Biology Lab (1005L)
Wolfson Campus
Laboratory Manual
Author: Arnold Fleisch
Lab 1.- Atoms and Molecules
Objectives
1.- Be able to define the following terms in writing:
a) atom
h) ionic bond
b) ion
i) element
c) isotope
j) acid
d) molecule
k) base
e) compound
i) covalent bond
f) electron
m) neutron
g) proton
2.- Be able to determine the number of protons,
neutrons, and electrons for any atom, given the
information on a periodic chart
3.- Be able to draw and label a diagram of any
atom with an atomic number less than 20,
given the information on a periodic chart.
4.- Be able to diagram a conceivable molecule
using all the atoms given and show the
shape of that molecule and the proper
number of bonds for each atom.
5.- Be able to describe in writing and / or by a
diagram the characteristics of ionic and
covalent bonds
6.- Be able to determine if a given solution is
an acid or a base by using any of following
indicators:
a) pHydrion paper
b) bromothymol blue
c) phenolphthalein
7.- Be able to interpret the pH number of a
solution
8.- Be able to interpret a chemical equation
and point out the reactants and the products
Atoms and Molecules
• All matter, including living matter, is made
up of small units know as atoms and
molecules.
• There are 92 different kinds of natural
atoms, known as elements.
• These atoms can be combined to form
millions of different molecules.
• The specific structure of an atom
determines the kinds of atoms that can
hold together to form larger molecules
• Each atom consist of protons, neutrons,
and electrons.
• Protons and neutrons in a central area
(nucleus) and
• The electron moving around some distance
from the nucleus.
• The protons are positively charged (+) and
the electrons are negatively charged (-)
Models of the Atom
Figure 2.1
• Since the electrons are light and are
moving very rapidly, there is a tendency
for these two forces-the mutual attraction
and the inertia of electron movement to be
equal. As a result, the electrons orbit
(circle) around the nucleus.
• The periodic table contains the different
kinds of elements that exist.
Composition of Matter
• Elements – unique substances that cannot
be broken down by ordinary chemical means
• Atoms – more-or-less identical building
blocks for each element
• Atomic symbol – one- or two-letter
chemical shorthand for each element
Properties of Elements
Each element has unique physical and
chemical properties
– Physical properties – those detected with our
senses
– Chemical properties – pertain to the way atoms
interact with one another
Identification of Elements
Figure 2.2
Identification of Elements
ISOTOPES
Figure 2.3
• The diagram below deals with the information
from a periodic table about a carbon atom.
6
← Atomic Number
(# of protons)
C
← Symbol
← Mass Number
12.1
The symbol for carbon is C . The number at the
top is the atomic number and tells you how
many protons or electrons are in the atom.
• In order to understand some of the important
biological concepts, it is necessary that you be
aware of information about atoms and
molecules.
Molecular Structure
• Specific atoms may be combined together
in certain ways to form a larger units called
molecules. The bonding together of atoms
is a very precise process.
• Some kinds of atoms are very reactive and
will combine with one or two other kinds of
atoms.
Chemical Bonds
• Electron shells, or energy levels, surround
the nucleus of an atom
• Bonds are formed using the electrons in
the outermost energy level
• Valence shell – outermost energy level
containing chemically active electrons
• Octet rule – except for the first shell which
is full with two electrons, atoms interact in
a manner to have eight electrons in their
valence shell
Chemically Inert Elements
• Inert elements have their outermost
energy level fully occupied by electrons
Figure 2.4a
Chemically Reactive Elements
• Reactive elements
do not have their
outermost energy
level fully
occupied by
electrons
Figure 2.4b
Types of Chemical Bonds
• Ionic
• Covalent
• Hydrogen
Ionic Bonds
Some kinds of atoms have such a strong
attraction for electrons that they will steal
from other atoms having electrons that are
rather loosely held to the atom. The specific
structure of an atom determines whether it
will gain or lose electrons to form an ion. All
ions are formed by either the gain or loss of
electrons. Atoms that lose electrons are
positively charged (+), and atoms that gain
electrons are negatively charged (-).
Ionic Bonds
• Ions are charged atoms resulting from the
gain or loss of electrons
• Anions have gained one or more
electrons
• Cations have lost one or more electrons
Formation of an Ionic Bond
• Ionic bonds form between atoms by the
transfer of one or more electrons
• Ionic compounds form crystals instead of
individual molecules
• Example: NaCl (sodium chloride)
Formation of an Ionic Bond
Figure 2.5a
Covalent Bond
• A second kind of bond that holds atoms
together to form molecules is known as a
covalent bond. In these bonds the
electrons are not actually transferred from
one atom to another as in the formation of
ions, but they may be shared by two or
more atoms. Each pair of electrons that is
shared is the equivalent of one covalent
bond.
Covalent Bonds
• Covalent bonds are formed by the sharing of
two or more electrons
• Electron sharing produces molecules
• It is possible to diagram molecules by allowing a
line to represent a single covalent bond.
H
l
H–C–H
l
H
Methane
Covalent bonding
• The diagram above indicates that a single
carbon atom (C) is sharing four electrons with
four different hydrogen atoms (H) and that each
of the four hydrogen atoms is sharing an
electron with the same carbon atom.
Single Covalent Bonds
Figure 2.6a
• If you know how many electrons each
atom will be able to share, you should be
able to diagram a variety of different kinds
of atoms.
• Sometimes two atoms may share more
than one pair of electrons, creating a
double bond.
• For example, 0=C=0
Double Covalent Bonds
Figure 2.6b
Triple Covalent Bonds
Figure 2.6c
Polar and Nonpolar Molecules
• Electrons shared equally between atoms
produce nonpolar molecules
• Unequal sharing of electrons produces
polar molecules
• Atoms with six or seven valence shell
electrons are electronegative
• Atoms with one or two valence shell
electrons are electropositive
Comparison of Ionic, Polar Covalent, and
Nonpolar Covalent Bonds
Figure 2.8
Hydrogen Bonds
•
•
•
•
Too weak to bind atoms together
Common in dipoles such as water
Responsible for surface tension in water
Important as intramolecular bonds, giving
the molecule a three-dimensional shape
PLAY
Water Transport
Hydrogen Bonds
The table below is a list of atoms and the
number of electrons they usually share.
Name of Atom Symbol of Element
Carbon
C
# of bond
Bonding capacity
4
C
Nitrogen
N
3
N
⁄
\
Oxygen
O
2
O
Hydrogen
H
1
H
Acids, Bases, and pH
• When some materials are dissolved in
water, they release hydrogen ions (H+).
Such solutions are known as acids.
• Other materials actually remove hydrogen
ions from solutions. These are known as
bases.
• It is frequently important to know if a
solution is a acid or a base , and a number
of different methods have been developed
to test solutions for their acidity or
alkalinity. All of these systems rely on a
scale known as the pH scale.
Many kind of material change color as
the pH of a solution change
Bromothymol Blue
Acid
Base
Neutral
Yellow
Blue
Green
Phenolphthalein Colorless Pink to red Colorless
Chemical Reaction
• A chemical reaction occurs when different
molecules react with one another in such a way
that bonds are broken and new molecular
combinations forms.
• The following exercise is an example of chemical
reaction
Exercise
1.- Place a small amount of sodium chloride solution in a test
tube. Add to it a few drops of silver nitrate solution. What
happens?
Sodium chloride + silver nitrate → sodium nitrate + silver chloride
NaCl
+ AgNO3
NaNO3 +
AgCl