Atoms and Molecules: Why Study Chemistry in A Biology Course?

10/11/2010
Copyright 2002 by Harcourt College Publishers, a division of Thomson Learning
Biology, Sixth Edition
Atoms and Molecules

BL201

Chapter 2, Atoms and Molecules
Why study chemistry in a biology course?

The processes of life are chemistry!
The structural substance of living material can
be understood through chemistry
The information system of life (based on DNA)
can be understood through chemistry
SO, to understand living systems, you must
understand the molecular and chemical nature
of life.
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Elements
Elements are substances that cannot be
broken down into simpler substances by
chemical reactions (i.e., non-nuclear
reactions)
O, C, H, N, Ca, and P account for >98 % of
mass of living organisms
Other elements are important too but are
present in small quantities
Atoms
Atoms are the smallest forms of matter that
retain the chemical characteristics of a given
element
Atoms have a nucleus , which:
Contains protons (p)
May contain neutrons (n)
Clouds of electrons (e) surround the nucleus
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Protons, Electrons, & Neutrons

Protons have +1 charge and have a mass of
1 atomic unit (AU)
Neutrons have no charge but have a mass of
1.005 AU
Electrons have a -1 charge and a mass of
1/1800 AU
The Periodic Table

Elements are grouped and described in the
Periodic Table
Columns refer to the number of valence

electrons (electrons in the outer shell).
Rows refer to the specific orbitals used for

the ground state of that atom (i.e., the rows
tell where the electrons are located).
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The Periodic Table

Column 1 elements have only one electron in
their valence shell.
These elements easily give up that electron.
Column 5, 6, & 7 elements need 3, 2, or 1
electron(s), respectively, to fill their outer shells
and are electronegative: they pull electrons from
other elements.
Column 8 elements have full outer shells and are
inert, because they need not react to fill their
valence shells.
Chemical symbol
Atomic number
1
Chemical name
O
OXYGEN
HYDROGEN
N
NITROGEN
Number
of e in
each
energy
level
Na
12
Mg
26
MAGNESIUM
AT. MASS 16.00 amu
CARBON
1
AT. MASS 1.01 amu
25
He
AT. MASS 14.01 amu
10
Ne
11
NEON
SODIUM
Li
Be
28 2
Na Mg
K
24
AT. MASS 24.31 amu
AT. MASS 12.01 amu
Ca Sc Ti
Cr Mn Fe Co Ni
Ne
Ai
Si
Cl Ar
Cu Zn Ga Ge As Se Br Kr
28
28 1
AT. MASS 20.18 amu
AT. MASS 22.99 amu
Rb Sr
19
POTASSIUM
AT. MASS 39.10 amu
Zr
Cs Ba (L) Hf
Fr
28 8 1
Ra (A)
(L)
(A)
Nb Mo Tc Ru Rh Pd Ag Cd In
Ta W Re Os Ir
Ca
Sn Sb Te I
15
Pt PHOSPHORUS
17
Cl
Bi
CHLORINE
Po At Rn
16
SULFUR
20
CALCIUM
La
Sm Eu Gd
28 8 2
Pu
Am Cm Bk Cf
28 7
Tm Y
28 5
AT. MASS 35.45 amu
AT. MASS 30.97 amu
Ac
Xe
Es Fm Md N
28 6
AT. MASS 32.07 amu
AT. MASS 40.08 amu
Periodic Table
Fig. 2.01
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Atomic Number & Atomic

Weight
The number of protons is called the
atomic number Z
The atomic number defines the element if
the number of protons changes, the element
changes
The number of protons + the number of
neutrons = the atomic weight A
In an uncharged atom, the number of protons
equals the number of electrons

Isotopes
Atoms that vary in Atomic Weight are called isotopes

Isotopes vary in the number of neutrons
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Practical Uses of Isotopes
Molecules containing different isotopes are not

metabolized differently from each other
Thus, molecules containing radioactive
isotopes can be made and used to trace
movement of those molecules in an organism,
or in its cells
Radioactive isotopes are used to diagnose and
treat disease;
Radioactive isotopes can be used to date
fossils
Ions: Bohr Model

Hydrogen: 1 p, 1 e
Hydrogen ion: 1p
No net charge
Charge +1
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Orbitals
Orbitals are the location actually the space
or volume - occupied by electrons.
Orbitals are therefore probability density
functions of the position of the electrons.
Each individual orbital has 2 spaces for

electrons.

Orbitals
2 electrons each
1s
2s
p orbitals
s and p orbitals
can combine
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Electrons and Energy
The energy levels of the electrons are called shells.

Shells can have one or more orbitals within them.
The outermost shell is the valence shell.
The farther away the electron is from the nucleus,
the greater its potential energy.
-
Lower energy

Higher energy
Combinations of Atoms:
Molecules and Compounds
Atoms may stick together and form molecules,
which are combinations of atoms.
If a molecule is formed from more than one
element (i.e., from different atoms), we call the
resulting molecule a compound.
The molecular weights are merely the sum of
the atomic weights. Thus, NaCl has a
molecular weight of 58, because it contains one
sodium (Na) and one chloride (Cl) atom.
10/11/2010
Covalent Bonds
In covalent bonds, two electrons are shared per bond

The outer shells of both atoms become filled
More than one bond can occur between two atoms
Thinking About Covalent

Bonds
The Lewis structure uses

dots to indicate the
number of electrons in
the valence shells of
atoms:
methane
In contrast, a structural
model uses a line to
represent the shared
pair of electrons:
10/11/2010
Ionic Bonds
In ionic bonds, electrons are donated by
one atom to another
An electronegative atom steals an electron
from another atom to fill its valence shell
That is, one or more electrons LEAVE one
atomic center to live with another
Ionic Bonds in Salt
10
10/11/2010
Dissolution of salt
Water easily dissolves salts, because it forms
hydration shells around the ions.
Water is the solvent; the salt is the solute.
To be able to dissolve in water, solutes must
be polar or ionic.
Polar Covalent
Bonds
Electronegative O pulls
e- from H in water
This causes a partial (+)
charge on the H, and a
partial (-) charge on the
O
Partial charges are
indicated by lower case
deltas (d)
The bonds between O
and H are polar covalent
bonds
d+
d-
d+
11
10/11/2010
Hydrogen Bonds
H is needed (hence the name).
An electronegative atom must be covalently bonded
to the H.
The electronegative atom incompletely pulls electrons
away from the H nucleus they become displaced,
but not removed from the H.
Examples of such electronegative atoms are O,
N, S.
Note that all of these elements need electrons to fill
their valence shells see the Periodic Table.
Van der Waals

Short-lived charges on the surface of molecules
induce opposite charges in adjacent molecules: Van
der Waals bonds
+ +
-
+
- +
+
+ -
12
10/11/2010
Reduction and Oxidation

Reduction is the gain of an electron.
Oxidation is the loss of an electron.
Reduction/oxidation (redox) reactions are
reactions where there is transfer of electrons;
there is always a simultaneous reduction AND
oxidation.
Water (H2O)
Earth is a water planet
H2O covers 70% of the earths surface
H2O governs energetic processes over the
planet
H2O is essential for life
H2O is a major constituent of organisms
composition: 50-90% for terrestrials, up to
98% for marine
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10/11/2010
Water is Polar
Water is a dipole
O pulls electrons
from H
O end is partially (-),
H ends are (+)

Water Forms
Hydrogen Bonds
Partial charges
interact
Hs attracted to Os
Causes water to
self-associate
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10/11/2010
Hydrogen
Bonding
Gaseous water molecules

interact very little
Liquid water molecules are

hydrogen bonded, but can
slip past each other
As water freezes, it forms a
crystalline lattice because H
bonding lasts longer
Fewer water molecules per
unit volume in ice, compared
to liquid water: ice floats

Thermodynamic Properties of Water

Temperature measures molecular movement.
The higher the temperature, the greater the movement
Water has high specific heat. It takes 1 calorie / g
water to raise the temperature 1O Celsius
because water molecules are constrained by H-bonding
Water has high heat of vaporization. It requires

540 calories to change 1 g of liquid water to 1 g of
water vapor
H bonds must be broken
Thus, when water changes from liquid to gas, it carries off
much heat, resulting in evaporative cooling
15
10/11/2010
Water Protects the Planet

Thus, water resists temperature changes
Without water, temperatures would fluctuate
greatly from day to night, and season to
season
Noticeable in maritime environments mild,
while deserts undergo very harsh changes in
temperature

Water is
Sticky
Water is sticky because of H
bonding
Cohesive sticks to itself
Adhesive sticks to other things
Meniscus
Creeps into (imbibes) small polar
spaces (moves up fine capillaries
because it sticks to glass, which is
charged)
16
10/11/2010
Water has High Surface Tension

Water sticks to itself strongly and so has high
surface tension
Forms meniscus
Forms droplets
Small animals can skate on surface

Other Water Interactions

Water is involved in making and breaking
large molecules
Hydrolysis (breaking by adding water)
Condensation or dehydration synthesis
(building by removing water)
17
10/11/2010
Water is a
Superb Solvent
Masks ions to cause
them to come apart
Makes hydration
shells of water
around an ion
Solvates ionic and

polar compounds
readily

Acids, Bases, and Buffers

Acids release protons (proton donors)
Bases absorb protons (proton acceptors)
Example:
HCl (acid actually a gas, dissolves in water)
H+ + Cl NaOH (base - solid dissolves in water)
Na+ + OH-
18
10/11/2010
pH
pH is a measure of the free hydrogen ion concentration
pH = - log10 [H+]
Pure water has only 10-7 M free hydrogen ion; thus it is
pH 7
The sum of the exponents of the free H+ and OH- is
always 14, which is to say that the product of the
concentrations is always 1 X 10-14
Given the [OH-] you can easily calculate [H+], and vice
versa
Acid and Base

When water is neutral, pH=7, pOH=7
neither acid nor base
But when water has an excess of protons (hydrogen

ions) then it is acid and pH < 7
Similarly, when water has a reduced number of
protons, it is basic, and pH > 7
Hydrogen ions do not exist in water as such; instead,
they combine with water to make H3O+, or hydronium
ion. For simplicity, we just work with H.+
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10/11/2010
pH is Very Important
Cell function is greatly dependent on pH
Normal physiological pH is usually close to pH 7.4
Minor deviations from physiological pH can be very

devastating to biochemical reactions (and therefore,
to life processes)
pH of
Common
Solutions
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10/11/2010
Buffers Minimize Changes in pH

Buffers are molecules that act as acids or
bases or both
They are weakly (i.e., incompletely) ionizing
Many buffers are both acid and base at the
same time
Bicarbonate is an important buffer in
vertebrate blood:
CO2 + H2O
Carbon dioxide
H2CO3
Carbonic acid

H+ + HCO3Bicarbonate ion
Salts
Acids and bases combine to form salts and
water
When salts are dissolved in water, their
components separate as ions, which in turn are
referred to as electrolytes, because they can
carry current polar substances are NOT
electrolytes
HCl + NaOH
H2O
+ NaCl
21

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10/11/2010

Copyright 2002 by Harcourt College Publishers, a division of Thomson Learning

Biology, Sixth Edition