Chapter 1

The Chemical Basis of

Life
 Matter: Elements and Compounds
– Matter is anything that occupies space and has
mass.
– Matter is composed of chemical elements.
• Elements are substances that cannot be broken down into
other simpler substances by ordinary chemical reactions.

• There are 92 naturally occurring elements on Earth.

– All of the elements are listed in the periodic table.

 Atoms
– Each element consists of one kind of atoms.
•An atom is the smallest unit of matter that
still retains the properties of an element.
 6

C
12

H He
Li Be B C N O F Ne
Na Mg Al Si P S Cl Ar
K Ca Sc Ti V Cr Mn Fe Co Ni Cu Zn Ga Ge As Se Br Kr
Rb Sr Y Zr Nb Mo Tc Ru Rh Pd Ag Cd In Sn Sb Te I Xe
Cs Ba La Hf Ta W Re Os Ir Pt Au Hg Tl Pb Bi Po At Rn
Fr Ra Ac Rf Db Sg Bh Hs Mt Uun Uuu Uub Uuq Uuh Uuo

Ce Pr Nd P S Eu Gd Tb Dy Ho Er T Yb Lu
m m m
Th Pa U Np Pu A C Bk Cf Es F Md No Lr
m m m
Figure 2.1
– Twenty-five elements are essential to life.

– Four elements make up about 96% of the weight of

the human body:
• Oxygen
• Carbon
• Hydrogen
• Nitrogen
 Carbon (C): 18.5%

Oxygen (O):
65.0%
Calcium (Ca): 1.5%
Phosphorus (P): 1.0%
Potassium (K): 0.4%
Sulfur (S): 0.3%
Sodium (Na): 0.2%
Chlorine (Cl): 0.2%
Magnesium (Mg):
Hydrogen (H):
0.1%
9.5% Trace elements: less than 0.01%
Boron (B) Manganese
Chromium (Mn)
Molybdenum (Mo)
Nitrogen (N):
(Cr)
Cobalt (Co) Selenium (Se)
3.3% Copper (Cu) Silicon (Si)
Fluorine (F) Tin (Sn)
Iodine (I) Vanadium (V)
Iron (Fe) Zinc (Zn)

Figure 2.2
Lack of iodine can cause goiter

Figure 2.3
 Atoms

– Atoms are composed of subatomic particles.

• A proton is positively charged.
• An electron is negatively charged.
• A neutron is electrically neutral.
Proton
• Positive charge Electron
• Determines atomic • Negative charge
number • Participates in
(element chemical chemical
properties)
reactions
• Outer-shell
electrons
determine chemical
behavior
Neutron
• No charge (neutral)
•Determines atomic Atom
mass
Elements differ in the number of subatomic particles in
their atoms.

• The number of protons, the atomic number,

determines the chemical properties of an element.

• An atom’s mass number is the sum of the number of

protons and neutrons.

• Isotopes: forms of the same element with different

mass numbers as a results of variation in number of
neutrons
 First electron shell Outer electron shell
(can hold 2 electrons) (can hold 8 electrons)
Electron

Hydrogen (H) Carbon (C) Nitrogen (N) Oxygen (O)

Atomic number = 1 Atomic number = 6 Atomic number = 7 Atomic number = 8
– Elements can combine to form compounds.
• Compounds are substances that contain two or
more elements in a fixed ratio.

• Combinations of atoms of different elements in a

fixed ratio produce molecules.

• E.g.
– NaCl (table salt)
– H2O (water)
 Chemical Bonding and Molecules

–Chemical reactions enable atoms

to give up or acquire electrons to
complete their outer shells.
 Covalent Bonds
– A covalent bond forms when two atoms share
one or more pairs of outer-shell electrons.

– Atoms held together by covalent bonds form a

molecule.

– The number of covalent bonds an atom can

form is equal to the number of additional
electrons needed to fill its outer shell.
 Polarity of covalent bonds
• Equal sharing of electrons
none polar covalent bonds
• Unequal sharing of electrons
polar covalent bonds
Name Electron configuration Structural formula Space-filling model Ball-and-stick model
(molecular formula)

Hydrogen gas (H2)

Single bond
(a pair of shared electrons)

Oxygen gas (O2)

Double bond
(two pairs of shared electrons)

Methane (CH4)
 Ionic bonds

–When an atom loses or gains

electrons, it becomes
electrically charged.
•Charged atoms are called ions.
•Ionic bonds are formed between
oppositely charged ions.
Outer shell The outer electron is stripped
has 1 electron from sodium and completes Complete
the chlorine atom’s outer shell outer shells
Outer shell
has 7 electrons

The attraction
Na Cl + − between the
Sodium atom Chlorine atom Na Cl ions—an ionic
Sodium ion Chlorine ion bond—holds
them together
Sodium chloride (NaCl)

Figure 2.6-2
Ionic bonding Hydration of an ionic compound

When the crystal of NaCl is added to water, the

sodium and chloride ions are pulled apart. When the
NaCl is dissolved, each Na+ and Cl- is surrounded by
water molecules electrically attracted to it.
 Hydrogen Bonds
– Formed between an atom that carries a partial
negative charge and an atom that carries a partial
positive charge.

– Water is a compound in which the electrons in its

covalent bonds are shared unequally.

• This causes water to be a polar molecule, one

with opposite charges on opposite ends.
Figure 2.16
δ– δ+

Water (H2O)

δ+
Hydrogen bond
δ–

Ammonia (NH3)

δ+ δ+

δ+
 δ+
δ+
(partial +ve
(partial +ve
)
)

H H

δ– (partial
-ve) Figure UN2-2
–The polarity of water results in weak
electrical attractions between
neighboring water molecules.

•These interactions are called

hydrogen bonds.
Hydrogen bond

Figure 2.8
 Water’s Life-Supporting Properties
– The polarity of water molecules and the
hydrogen bonding that results explain
most of water’s life-supporting
properties.
• Water molecules stick together.
• Water has a strong resistance to change in
temperature.
• Frozen water floats.
• Water is a common solvent for life.
Evaporation from the leaves

Microscopic tubes
Cohesion due to
hydrogen bonds
r
ate

between water
fw

molecules
wo
Flo

SEM

Figure 2.10
• Adhesion of the water to cell walls by hydrogen bonds helps resist the
downward pull of gravity.
• Cohesion due to hydrogen bonds between water molecules helps hold
together the column of water within the cells.

• Figure 3.3 Water transport in plants. Evaporation from leaves pulls water
upward from the roots through water-conducting cells. Because of the
properties of cohesion and adhesion, the tallest trees can transport water
more than 100 m.
 Hydrophilic and hydrophobic
molecules
• Hydrophilic: charged molecules, polar, loves
water (soluble in water)

• Hydrophobic: non-polar molecules, avoids

water or aqueous mediums/ fears water
(insoluble in water)
 Free reading
– Heat and temperature are related, but different.
• Heat is the amount of energy associated with the movement
of the atoms and molecules in a body of matter.
• Temperature measures the intensity of heat.
– Water can absorb and store large amounts of heat
while only changing a few degrees in
temperature.
– Water can moderate temperatures.
• Earth’s giant water supply causes temperatures to stay
within limits that permit life.
• Evaporative cooling removes heat from the Earth and from
organisms.
 Hydrogen bond

Liquid water Ice

 Water as the Solvent of Life
–A solution is a liquid consisting of a homogeneous
mixture of two or more substances.
• The dissolving agent is the solvent.
• The dissolved substance is the solute.
–When water is the solvent, the result is an aqueous
solution.
 Acids, Bases, and pH
– A chemical compound that releases H+ to solution is
an acid.
– A compound that accepts H+ and removes it from
solution is a base.
– Buffers are substances that resist pH change.
– Buffers
• Accept H+ ions when they are in excess
• Donate H+ ions when they are depleted

– To describe the acidity of a solution, chemists use

the pH scale.
 14
Oven cleaner
13

(lower H+ concentration)
Household
bleach

Increasingly basic
12
Household ammonia
11
Basic Milk of magnesia
solution
10

9
Seawater
8
Human blood
Neutral 7 Pure water
[H+] = [OH–]

6 Urine

(greater H+ concentration)
Neutral
solution
Increasingly acidic
5

4 Tomato juice

3 Grapefruit juice,
soft drink
2 Lemon juice,
gastric juice
1
Acidic
solution 0
pH scale
Figure 2.16
INTRODUCTION TO ORGANIC
COMPOUNDS
Life’s molecular diversity is based on the
properties of carbon

Diverse molecules found in cells are composed of

carbon bonded to other elements.

–Carbon-based molecules are called organic

compounds

–By sharing electrons, carbon can bond to four

other atoms

–By doing so, it can branch in up to four directions

Methane and other compounds
composed of only carbon and hydrogen
are called hydrocarbons

–Carbon, with attached hydrogen, can bond

together in chains of various lengths
 e.g. Methane

Structuralformula Ball-and-stickmodel Space-fillingmodel

The four single bonds of carbon point to the corners of a tetrahedron.

A chain of carbon atoms is called a carbon
skeleton.

–Carbon skeletons can be branched or unbranched.

–Therefore, different compounds with the same molecular

formula can be produced.

–These structures are called isomers

 Carbon skeletons vary in length.
Ethane Propane

Branching. Skeletons may be

unbranched or branched.

Butane IsobutanePropane

Double bonds.
2-ButeneSkeletons may have double
2-Butene
bonds, which can vary in location.
1-Butene

Skeletons may be arranged in rings.

Cyclohexane Benzene
 Isomers

• Isomers are compounds with the

same molecular formula but
different structures and properties
 Types of isomers
–Structural isomers* have different covalent
arrangements of their atoms.
–Geometric isomes*: have different spacial distribution
of atoms;
• Cis-trans isomers have the same covalent bonds but differ
in spatial arrangements
• Enantiomers are isomers that are mirror images of each
other
 have different covalent
arrangements of their atoms

Isomers are compounds

with the same molecular
formula but different
structures and properties have the same covalent bonds but
differ in spatial arrangements

are isomers that are mirror images of each other

• Enantiomers are important in

the pharmaceutical industry
• Two enantiomers of a drug
may have different effects
• Usually only one isomer is
biologically active
 Functional groups

A functional group Determines the chemical

characteristics of a hydrocarbon.
▪The functional groups are:

–Hydroxyl group—consists of a hydrogen bonded

to an oxygen.
–Carbonyl group—a carbon linked by a double
bond to an oxygen atom.
–Carboxyl group—consists of a carbon
double-bonded to both an oxygen and a hydroxyl
group.
–Amino group—composed of a nitrogen bonded to
two hydrogen atoms and the carbon skeleton.
–Phosphate group—consists of a phosphorus
atom bonded to four oxygen atoms.
Figure 4.9-a
CHEMICAL
GROUP Hydroxyl Carbonyl Carboxyl

STRUCTURE

(may be written HO—)

NAME OF Alcohols (Their specific names Ketones if the carbonyl group is Carboxylic acids, or organic acids
COMPOUND usually end in -ol.) within a carbon skeleton

Aldehydes if the carbonyl group

is at the end of the carbon skeleton

EXAMPLE

Ethanol Acetone Acetic acid

Propanal

FUNCTIONAL • Is polar as a result of the
PROPERTIES electrons spending more time
near the electronegative oxygen
atom.
• Can form hydrogen bonds with
water molecules, helping dissolve
organic compounds such as
sugars.
• A ketone and an aldehyde may be • Acts as an acid; can donate an
structural isomers with different H+ because the covalent bond
properties, as is the case for between oxygen and hydrogen
acetone and propanal. is so polar:
• Ketone and aldehyde groups are
also found in sugars, giving rise
to two major groups of sugars:
ketoses (containing ketone
groups) and aldoses (containing
aldehyde groups). Nonionized Ionized

• Found in cells in the ionized form

with a charge of 1− and called a
carboxylate ion.
Figure 4.9-b
Amino Sulfhydryl Phosphat Methyl
e

(may be
written HS—)

Amine Thiols Organic phosphates Methylated compounds

s

Glycine Cysteine Glycerol phosphate 5-Methyl cytidine

• Acts as a base; can • Two sulfhydryl groups can • Contributes negative charge to • Addition of a methyl group
pick up an H+ from the react, forming a covalent the molecule of which it is a part to DNA, or to molecules
surrounding solution bond. This “cross-linking” (2– when at the end of a molecule, bound to DNA, affects the
(water, in living helps stabilize protein as above; 1– when located expression of genes.
organisms): structure. internally in a chain of • Arrangement of methyl
phosphates). groups in male and female
• Cross-linking of cysteines • Molecules containing phosphate sex hormones affects their
in hair proteins maintains groups have the potential to react shape and function.
the curliness or straightness with water, releasing energy.
of hair. Straight hair can be
Nonionized Ionized “permanently” curled by
shaping it around curlers
and then breaking and
• Found in cells in the
re-forming the cross-linking
ionized form with a
bonds.
charge of 1+.
An example of similar compounds that
differ only in functional groups is sex
hormones:

–Male and female sex hormones differ only in

functional groups.

–The differences cause varied molecular actions.

–The result is distinguishable features of males and

females.
Estradiol

Female lion

Testosterone
Male lion