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The Chemical Basis of Life

Atoms, elements, compounds, &

molecules
How molecules interact
Water is essential for life
Acids, bases and salts
Lectures by Tom Chen
ELEMENTS, ATOMS, AND MOLECULES 0

Chemicals play many more roles in life

– Making up our bodies, those of other
organisms, and the physical environment

2.1 Living organisms are composed of about 25

chemical elements
• About 25 different chemical elements
– Are essential to life

• Trace elements
– Are essential to life, but occur in minute
amounts
Atom: A unit of matter, the smallest unit of an element.
Element: A substance composed of atoms having an identical number
of protons in each nucleus. Elements cannot be reduced to simpler
substances by normal chemical means.
Carbon, hydrogen, oxygen, and nitrogen 0

Make up the bulk of living matter

Table 2.1
2.2: Trace elements are common additives to 0

food and water

• Dietary deficiencies in trace elements
– Can cause various physiological
conditions

Figure 2.2B

Figure 2.2A
2.3 Elements can combine to form compounds 0

• Chemical elements
– Combine in fixed ratios to form compounds

Sodium Chlorine Sodium Chloride

Figure 2.3
2.4 Atoms consist of protons, neutrons, and 0

electrons
• Atom: The smallest particle of matter that still
retains the properties of an element
Subatomic Particles
• An atom is made up of protons and neutrons
Located in a central nucleus
• The nucleus is surrounded by electrons
– – Electron
• Arranged in electron shells 2e – cloud
+ +
+
+

Nucleus

2 + Protons Mass
2 Neutrons number = 4
Figure 2.4A
2 – Electrons
Differences in Elements 0

• Atoms of each element

– Are distinguished by a specific
number of protons 0

Electron
cloud
6e–

++

Nucleus

6 + Protons
Mass
6 Neutrons number = 12

Figure 2.4B 6 – Electrons

Isotopes 0

The number of neutrons in an atom may vary

• Variant forms of an element are called isotopes
• Some isotopes are radioactive

Table 2.4

2.5 Radioactive isotopes can help or harm us

• Radioactive isotopes are useful as tracers
- For monitoring the fate of atoms in living
 Basic Research 0

• Biologists often use radioactive tracers

- To follow molecules as they undergo chemical
changes in an organism
Medical Diagnosis
• Radioactive tracers are often used for diagnosis
- In combination with sophisticated imaging instruments

Figure 2.5A Figure 2.5B

How brain function is studied now?
PET, CAT, MRI, etc.

Hearing, speaking, seeing, thinking about

words

Music
Appreciation
2.6 Electron arrangement determines the 0

chemical properties of an atom

• Electrons in an atom
– Are arranged in shells, which may
contain different numbers of
electrons
Outermost electron shell (can hold 8 electrons)
First electron shell (can hold 2 electrons)
Electron

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

Figure 2.6 Atomic number = 1 Atomic number = 6 Atomic number = 7 Atomic number = 8
Atoms whose shells are not full, tend to interact
with other atoms and gain, lose, or share
electrons. These interactions form chemical
bonds
Types of chemical bonds:
3. Ionic bond
4. Covalent bond
5. Hydrogen bond
 0
Ionic bonds are attractions between ions of
opposite charge
• When atoms gain or lose electrons
– Charged atoms called ions are created

+ –
– Transfer of
electron

–
Na Cl Na Cl

Na Cl
Sodium atom Chlorine atom Na+ Cl–
Sodium ion Chloride ion

Sodium chloride (NaCl)

• Sodium and chloride ions 0

– Bond to form sodium chloride, common table

salt
• An electrical attraction between ions with opposite
charges
– Results in an ionic bond

Na+

Cl–

Figure 2.7B
Covalent bonds join atoms into molecules through 0
electron sharing
• In covalent bonds, two atoms share one or more pairs of
outer shell electrons, forming molecules
Sharing of electrons may be EQUAL or UNEQUAL
0

• A molecule is nonpolar
– When its covalently bonded atoms share electrons
equally
• In a polar molecule 0

– Electrons are shared unequally

between atoms, creating a polar
covalent bond
(–) (–)

H H

Figure 2.9 (+) (+)

 0

Hydrogen bonds are weak bonds important in the

chemistry of life
• The charged regions on water molecules are
attracted to the oppositely charged regions on
nearby molecules

Hydrogen bonding occurs Hydrogen (–)

in other biologically bond (+)

H
important compounds such (–)
O
(+)
as proteins and DNA. (–)
H (+
)
(–)
(+)
 Surrounds
¾ of the
Can be used Used in food
Earth’s
for recreation preparation
surface

Supplies body Used for

with essential hygienic
minerals purposes

Helps in Source of
maintaining oxygen
homeostasis
Source of
Serves as energy e.g
Makes up
habitat for hydroelectric
almost 70%
aquatic power plants
of human’s
organisms
body
Essential Minerals
•are inorganic substances that exist naturally on and in
the earth
•14 minerals that have been shown by research to be
essential to human health are: calcium, chromium,
copper, fluorine, iodine, iron, magnesium,
manganese, molybdenum, phosphorus, potassium,
selenium, sodium and zinc
• “Essential” because they comprise human tissue
•Good sources of essential minerals include fruits,
vegetables, meats, nuts, beans and dairy products.
• Varying amounts of minerals can be obtained from
WATER
Importance of minerals in body
• crucial to the growth and production of bones, teeth,
hair, blood, nerves, skin, vitamins, enzymes and
hormones
•For healthy functioning of nerve transmission
• blood circulation
•cellular integrity
• energy production and muscle contraction
WATER’S LIFE-SUPPORTING PROPERTIES 0
Water is the solvent of life
• Polar or charged solutes dissolve when water
molecules surround them, forming aqueous
solutions
Na+
–
Na+
–
+
Cl–
+
– –
+
–
Cl– +
–
+
–
+ –
+
–
–
Ion in
solution Salt
crystal
WATER’S LIFE-SUPPORTING PROPERTIES 0
Hydrogen bonds make liquid water cohesive
• Due to hydrogen bonding
– Water molecules can move from a plant’s roots to its
leaves by adhesion
• Insects can walk on water due to surface tension
– Created by cohesive water molecules

Figure 2.11
WATER’S LIFE-SUPPORTING PROPERTIES 0
Water’s hydrogen bonds regulate temperature
• Water’s ability to store heat (high heat capacity)
– Moderates body temperature and climate
• It takes a lot of energy to disrupt hydrogen bonds
- So water is able to absorb a great deal of heat energy
without a large increase in temperature
• As water cools
- A slight drop in temperature releases a large amount
of heat
WATER’S LIFE-SUPPORTING PROPERTIES 0
Water has high heat of vaporization
A water molecule takes energy with it when
it evaporates
• Leading to evaporative cooling
Figure 2.12

Storm Turns Focus to Global Warming

Is the rash of powerful Atlantic storms in
recent years a symptom of global warming?
some scientists have maintained that the rise in mean global
temperatures over the last half a century — a well-documented
trend widely linked to human activities such as the burning of
fossil fuels — will inevitably have an effect on storms.
Ice is less dense than liquid water 0

• Hydrogen bonds hold molecules in ice farther apart than in

liquid water
• Ice is therefore less dense than liquid water which causes it
to float
• Floating ice protects lakes and oceans from freezing solid

Hydrogen bond

Ice Liquid water

Hydrogen bonds are stable Hydrogen bonds
constantly break and re-form
Living organisms are sensitive to acidic and basic conditions
Acid = An ionic compound that releases H+ ions in solution
Base = An ionic compound that accepts H+ ions or produces OH-
ions in solution
• Acidity is measured on the pH scale from 0 (most acidic) to 14
(most basic or alkaline)
 pH scale

The pH scale 0

1
0

H+

(Higher concentration of H+)

H +

H+ OH– H+

Increasingly ACIDIC
2 Lemon juice, gastric juice

• The pH of most cells OH–

H+ H+
H+ H+

3 Grapefruit juice, soft drink

Acidic solution

Is kept close to 7 4 Tomato juice

(neutral) by 5
buffers
6 Human urine

• Buffers are OH–

H+ H+
OH–
OH–
NEUTRAL
[H+]=[OH–] 7 Pure water

substances that OH– OH

H+ H+ H+
–

8
Human blood

resist pH change Neutral solution Seawater

(Lower concentration of H+)

9

Increasingly BASIC
10
Milk of magnesia

11
OH– Household ammonia
OH–
12
OH– H+ OH– Household bleach
OH– OH– –
OH 13
H+
Oven cleaner
Basic solution 14 Figure 2.15
 Acid precipitation threatens the environment 0

• Some ecosystems are threatened by acid

precipitation
• Acid precipitation is formed when air pollutants
from burning fossil fuels
– Combine with water vapor in the air to form
sulfuric and nitric acids
– Can kill trees and damage buildings

Figure B
Figure A
Salts
Are formed when an acid and a base react with one
another neutralizing the concentration of H+ ions
 the process is called neutralization

Acid Base Salt

Importance of acids, bases and salts in living
organisms

1. Life processes occur in neutral pH.

2. Acids, bases and salts when dissolved in water
serve as electrolytes.
3. Salts are abundant in our body in the form of
different body fluids like sweat and tears.
Electrolytes
•are the elements necessary for electrochemical
activity in our body.
•Water (H20) – and the three minerals sodium,
potassium and chloride are all necessary for the
transmission of electrical impulses between cells
 CHEMICAL REACTIONS 0

2.17 Chemical reactions change the composition of matter

• In a chemical reaction
- Reactants interact, atoms rearrange, and products result

2 H2 O2 2 H2O
Figure 2.17A
 0

This is the general equation for

photosynthesis—the process of capturing
sunlight energy and converting it to
chemical energy. Which of the following
are the reactants of this reaction?
• C6H12O6 and O2.
• CO2 and H2O.