Chapter 2

Chemistry
Instructor Jennifer Evens

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Atoms, Ions, and Molecules

A basic understanding of chemical concepts is
necessary to understand physiological processes
At its simplest level of organization, the human body
is composed of chemical structures:
atoms
ions
Molecules

Atoms, Ions, and Molecules: Matter, Atoms,

Elements, and the Periodic Table
Matter is anything that takes up space
Human body is composed of matter
Three forms:
solid (e.g., bone)
liquid (e.g., blood)
gas (e.g., oxygen)

Matter is composed of atoms

Atom, smallest particle that exhibits the chemical properties of
an element

Human Body and Chemistry

Chemical Elements
Element
Simplest form of matter i.e. H2O>Hydrogen and oxygen

> (unique)

Atom

smallest piece of an element .

Made up of Protons /Neutrons/Electrons >

(Not unique)

Identified by an atomic number (number of protons in nucleus)

arranged in periodic table by atomic number
Chemical Symbol Based on one or two letters, per Eng name some
Latin (Ferrum Fe, Kalium K, natrium NA)
91 naturally occurring, 24 pt of nl physiological roles in humans

Minerals
several elements classified here, extracted by soil (4% wt, =Ca & P)
P is a major component of nucleic acid , ATP and cell membranes

Atoms, Ions, and Molecules: Matter, Atoms,

Elements, and the Periodic Table
The components of an atom
Atoms composed of three subatomic particles:
protons
mass of one atomic mass unit (amu)
positive charge of one (+1)

neutrons
mass of one amu
no charge

electrons
1/1800th mass of a proton or neutron
negative charge of one (-1)
located at varying distance from the nucleus in regions called orbitals

Periodic
Table
Chemical
symbol Based
on one or two
letters of
Chemical name
Atomic
number
number of
protons in
nucleus
Atomic mass
equal to total
number of
protons and
neutrons

http://www.wpclipart.com/education/supplies/periodic_table_of_the_elements.png

Figure 2.1b
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Most Common Elements of the Human Body

Major elements
(collectively compose more than 98% of body weight)
Symbol

(b)

Lesser elements
(collectively compose less than 1% of body weight)

% Body weight

Symbol

% Body weight

Oxygen

65.0

Sulfur

0.25

Carbon

18.0

Potassium

0.20

Hydrogen

10.0

Na

Sodium

0.15

Nitrogen

3.0

Cl

Chlorine

0.15

Ca

Calcium

1.5

Mg

Magnesium

0.05

Phosphorus

1.0

Fe

Iron

0.006

Atoms, Ions, and Molecules: Matter, Atoms,

Elements, and the Periodic Table
Determining the number of subatomic particles
Proton number = atomic number
Neutron number = atomic mass atomic number
neutron number = (p + n) p
neutron number of Na = 23 11 = 12

Electrons number = proton number

Atoms, Ions, and Molecules: Matter, Atoms,

Elements, and the Periodic Table
Diagramming Atomic Structures
An atom has shells of electrons
surrounding the nucleus
Each shell with a given energy
level
Each shell holding a limited
number of electrons
Innermost shell two electrons,
second shell up to eight
Shells close to the nucleus: must
be filled first
Valence Electrons-outermost shell

Nucleus:

Figure 2.2b
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Shell model

Energy
shell
8 protons
8 neutrons
8 electrons

(b)
Proton (+)
Neutron (no charge)

Electron shells:

Electron ()

Atoms, Ions, and Molecules: Matter, Atoms,

Elements, and the Periodic Table
What subatomic particles determine the
mass of an atom? The charge of an atom?
Protons and neutrons determine the mass of an atom.
Protons and electrons determine the charge of an
atom.

Isotopes of Hydrogen
Isotopes
Same Element Copyright The McGraw-Hill Companies, Inc. Permission required for reproduction or display.
Variety of atoms
Differ from one
Carbon12
Carbon13
Carbon14
another in
protons
6 protons
6 protons
number neutrons 66 neutrons
7 neutrons
8 neutrons
6 electrons
Chemical
6 electrons
6 electrons
behavior the
same no matter
number of
neutrons
Reason for
variability in
atomic weight
Differ in physical
behavior
Many decay

Radioisotopes
Isotopes that
are unstable
and decay to
more stable
forms-Physical
Half Life
Radioactivity is
the decaying
process
During high
energy
radiation
electrons are
ejected from
atoms
converting
atoms to ions

Atoms, Ions, and Molecules: Chemical

Stability and the Octet Rule
Elements tend to lose, gain, or share electrons to
obtain complete outer shells with eight electrons
Known as the octet rule
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Number of valence electrons

1
IA

Figure 2.4

2
IIA

3
IIIA

4
IVA

5
VA

6
VIA

7
VIIA

8
VIIIA

He

Li

Be

Ne

Na

Mg

Al

Si

Cl

Ar

Ca

Atoms, Ions, and Molecules: Chemical

Stability and the Octet Rule
What is the relationship of the octet rule
and chemical stability?
A complete outer shell with eight electrons increases
chemical stability.

Molecules/Bonds
Molecules chemical particles
composed of 2 or more atoms united by a
chemical bond (same or different)
covalent bond - Atoms share electrons
ionic bond- Atoms give up and receive
electrons
Ionically bonded molecules separate to become ions in
water.
Ions in solution are electrolytes.

Compounds - molecules composed of

two or more elements

Common
Ions in the
Human body
and Their
Physiological
Significance
(Table 2.1a)

Common
Ions in the
Human body
and Their
Physiological
Significance
(Table 2.1b)

Ions and Ionic Compounds: Ions

Losing electrons and the formation of cations
Sodium can reach stability by donating an electron
Now satisfies the octet rule
Now has 11 protons and 10 electrons
Charge is +1

Ions with positive charge called cations

Ions and Ionic Compounds: Ions

Gaining electrons and the formation of anions
Chlorine can reach stability by gaining an electron
Now satisfies the octet rule
Now has 17 protons and 18 electrons
Charge is -1

Ions with negative charge called anions

Polyatomic ions are anions composed of more than
one atom
E.g., bicarbonate ion and phosphate ion

Ions and Ionic Compounds: Ions

General rules for assigning charges
Atoms with one, two, or three electrons in valence
shell become cations
E.g., calcium has two electrons in its outer shell
reaches stability by donating two electrons
develops a charge of +2

Atoms with five, six, or seven electrons become

anions
E.g., chlorine has seven electrons in its outer shell
reaches stability by gaining one electron
develops a charge of -1

Ions and Ionic Compounds: Ionic Bonds

Cations and anions may bind together in ionic bonds
Salts formed
For example, table salt (NaCl)
Each sodium atom donates one outer shell electron to a chlorine atom
Sodium and chlorine ions are held together by ionic bonds in a lattice
crystal structure
This is an ionic compound

Another example, magnesium chloride

Each magnesium atom donates one electron to two chlorine atoms

Figure 2.5

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Na
11p

(a) Sodium atom (Na)

Cl
17p

(b) Chlorine atom (Cl)

Na+

Cl

11p

17p

(c) Sodium ion (Na+)

Chloride ion (Cl)

Cl

Na+

Cl

Na+

Cl

Na+

Cl

Na+

Cl

(d) Lattice salt crystal of NaCl

Ions and Ionic Compounds: Ionic Bonds

Could an ionic bond form between two

cations?
No. Positively charged cations and negatively
charged anions may form ionic bonds. A cation and
another cation cannot form the electrostatic
interaction needed. Both want to lose electrons.

Covalent Bonding, Molecules, and Molecular

Compounds: Covalent Bonds
A covalent bond is formed when atoms share
electrons
Occurs when both atoms require electrons
Occurs with atoms that have four to seven electrons in their outer shell

Four elements of the human body form covalent

bonds most commonly:

oxygen (O)
carbon (C)
hydrogen (H)
nitrogen (N)

Covalent Bonding, Molecules, and Molecular

Compounds: Covalent Bonds
The number of bonds an atom can form
Simplest covalent bond formation occurs between
two hydrogen atoms
Each sharing its single electron

Oxygen needs two electrons to complete outer shell

Forms two covalent bonds

Nitrogen forms three bonds

Carbon forms four bonds

Covalent Bonding, Molecules, and Molecular

Compounds: Covalent Bonds
Single, double, and triple covalent bonds
Single covalent bond
One pair of electrons shared
e.g., between two hydrogen atoms

Double covalent bond

Two pairs of electrons shared
e.g., between two oxygen atoms

Triple covalent bond

Three pairs of electrons shared
e.g., between two nitrogen atoms

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Single covalent bond

Hydrogen gas (H2)

Single bond

(a)

Double covalent bond

Oxygen gas (O2)

Double bond

(b)

Triple covalent bond

Nitrogen gas (N2)

Triple bond

(c)

Figure 2.7

Covalent Bonding, Molecules, and Molecular

Compounds: Covalent Bonds
Carbon Skeleton Formation
Carbon can bond in straight chains, branched chains,
or rings
Carbon present where lines meet at an angle; additional atoms hydrogen
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Straight chain

Branched chain

Ring

Figure 2.9

C C

C C C

C C

C C
C

CH3
H3C

CH3
CH3

CH3
(a)

(b)

H3C

(c)

Covalent Bonding, Molecules, and Molecular

Compounds: Covalent Bonds
Nonpolar and polar covalent bonds (continued)
Atoms in a covalent bond may share electrons equally
or unequally
Atoms with different electronegativity share electrons unequally
This results in a polar covalent bond

Covalent Bonding, Molecules, and Molecular

Compounds: Intermolecular Attractions
Intermolecular attractions
Weak chemical attractions between molecules
Collectively important in maintaining the shape of complex molecules
such as DNA and protein
One type, the hydrogen bond
forms between polar molecules
attraction between partially positive hydrogen atom and a partially
negative atom
individually weak, collectively strong
influences how water molecules behave

Covalent Bonding, Molecules, and Molecular

Compounds: Intermolecular Attractions
Other intermolecular bonds:
van der Walls forces

nonpolar molecules
electrons orbiting nucleus briefly, unevenly distributed
induce unequal distribution of adjacent atom of another nonpolar molecule
individually weak

hydrophobic interactions
nonpolar molecules placed in a polar substance
if occurring between parts of large molecule, termed intramolecular
attractions

Molecular Structure of Water and the

Properties of Water: Molecular Structure
Water

Figure 2.12
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Water (H2O)
+

+
H

O
+

Hydrogen bonds form

between water molecules.

Water is a polar molecule due

to unequal sharing of electrons.
(a)

Hydrogen
bonds

+
+

(b)

Composes two-thirds of the

human body by weight
Polar molecule composed of
one oxygen atom bonded to
two hydrogen atoms
Oxygen atom with two
partial negative charges
Hydrogen with a single
positive charge
Can form four hydrogen
bonds with adjacent
molecules
central to waters properties

Water
Most chemicals in our body are chemicals that
are dissolved or suspended in water
50-75% of body = water
Key Functions
Solvency ability to dissolve other chemicals
separating ionic bonds into electrolytes
Hydrophilic substances that dissolve in water
Hydrophobic substances that dont dissolve in water

Lubricant- tears, joints

Transportation nutrients and waste
Chemical reactivity waters ability to participate
in chemical reactions, digestion
Chermal stability helps stabilize internal
temperature

Mixtures of other
substances
Solution consists of
Solute Particles of matter that are mixed with (salt)
Solvent a more abundant substance (water)
Solution is Defined by

Solute and solvent can not be distinguished from one another

Usually transparent
Solute will dissolve through most permeable membranes
Solute does not separate from solvent when allowed to stand
Concentration refers to the amount of solute relative to the
amount of solvent.
In comparing solutions, a hypertonic solution is more
concentrated, an isotonic solution is the same concentration,
and a hypotonic solution is less concentrated.

Tonicity
Refers t o solute/solvent
concentrations

Low solute

Equal concentration

High Solute

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Figure 2.14
CUSHIONS

Skull

Cerebrospinal
fluid

Brain

Fluid cushions
against sudden
movements.

REGULATES BODY TEMPERATURE

Water helps
regulate body
temperature
due to its high
specific heat
and high heat
of vaporization.

Heat

TRANSPORTS
Water is the fluid
medium to transport
substances in blood
and other body fluids
(e.g., blood, urine).

UNIVERSAL SOLVENT
LUBRICATES
Hydrophilic substance

Fluid serves as a
lubricant to
decrease friction.

CH2 OH
H C
H
HO C
HO C
H

O H
C
H
OH
C
OH

Nonelectrolytes
dissolve and
remain intact.

Pericardial sac
Pericardial fluid

Heart

HIGH SURFACE TENSION

Electrolytes
dissolve
and dissociate.

Na+

Water's high surface

tension causes
structures to adhere.
The moist alveoli in the
lungs are prevented
from collapsing and
adhering by surfactant.

Cl

Alveolus
Surfactant

Hydrophobic molecules
Water molecules
exclude nonpolar
molecules, thus
proteins are required
for their transport
within the body.

NEUTRAL pH

Amphipathic molecules

Polar portion
dissolves, nonpolar
portion excluded.
Amphipathic
molecules form
chemical barriers
(e.g., plasma
membranes, micelles).

Water has a neutral pH.

Body fluids are altered in
pH with the addition of
either an acid or a base.
Acidic

Alkaline

Molecular Structure of Water and the

Properties of Water: The Universal Solvent
How does the interaction of a nonelectrolyte
and water differ from the interaction of an
electrolyte and water?
Substances that dissolve in water but remain intact are
nonelectrolytes and cannot conduct an electric current
(e.g., glucose). Substances that both dissolve and
dissociate in water are electrolytes and can conduct an
electric current (e.g., NaCl).

Acidity
pH -acidity expession, measure derived from the
Molarity of [H]
Scale 0<7 acid
7neutral
7<14basic (alkaline)
Lower # the more H logatithmic of 10
Important to phys function to maintain pH, blood 7.35-7.45
acidosis < 7.35/alkalosis>7.45

Acid
is a proton donor molecule that releases a proton in water
H

Base
is a proton acceptor (OH, hydroxide ion; most bases tend
to be substances that accept H, but not necessarily NH
ammonium accepts)

Figure 2.15
Copyright The McGrawHill Companies, Inc. Permission required for reproduction or display.

H Concentration

pH Value

100

101

Hydrochloric acid (HCl): 1

102

Lemon juice, stomach acid: 23

103

10

105

Acidic

10

Neutral

107

Basic

108

H+ < OH

109

Decreasing
[H+]
Increasing
pH

1010

10

Antacid: 10.5

1011

11

Household ammonia: 10.511

1012

12

Household bleach: 12

1013

13

1014

14

H+ > OH
H+

H+

H+

H+

H+

H+

H+
H+

Increasing
Decreasing
pH

H+

H+

H+

H+
H+
H

[H+]

H+

H+

H+
+

H+

Examples

Wine: 2.43.5
Grapefruit juice: 3
Tomato juice: 4.7
Urine: 6
Milk, saliva: 6.36.6
Pure water: 7
Human blood: 7.4
Seawater: 8

Sodium hydroxide (NaOH): 14

Organic Compounds
Carbon
Organic chemistry is the study of compounds of
carbon
Versatile atom serving foundation for a wide variety of
structures
4 valence electrons, so binds with other atoms to
complete shell
Readily bonds to each other forming long chains,
branched molecules and rings
4 primary categories of the organic molecules of life:

Carbohydrates
lipids
Proteins
nucleic acids

Carbon bonds
Macromolecules long chains of carbons (starch
/DNA)
Polymers molecules made of repetitive series of
similar subunits called monomers
Polymerization joining of monomers
DNA - 4 different types (nucleotides)
Purine (Adenine and Guanine)
Pyrimidine (Thymine and Cytosine )

Proteins - 20 different types (Amino acids)

Polymerization is achieved through cells by

dehydration synthesis/condensation; joining two
monomers together by a covalent bond forming a
dimer
hydrolysis is the opposite, where covalent bond is
broken, this happens during digestion

Carbohydrates
Hydrophilic
Primary source of body's nutrient energy
General formula = (CH0) n=number of carbon
atoms -2 H for every O
Monosaccharide simplest; monomers; C6H12O6
Glucose/fructose/glactose

Disaccharides-Sugars composed of 2
monosaccharides
Sucrose/lactose/maltose

Polysaccharides long chains of glucose

Glycogen/starch/cellulose

All listed are sources of energy that can be quickly

mobilized and converted to glucose > into ATP

Lipids
Hydrophobic
Not composed of monomers
Consist of carbon, hydrogen, and oxygen atoms
C atoms form backbone of molecules
Many more H atoms then O atoms
Building blocks are often glycerol and fatty acids Less
oxidized then carbohydrates = higher caloric count

5 primary types
Fatty acid
Triglycerides
Phospholipids
Eicosanoids
Steroids

Proteins
Most versatile molecules in body
Polymer of amino acids
Amino acids are the building units of
proteins.
Composed of carbon, hydrogen, oxygen, and
nitrogen
Consist of an amine group, acid group, and R group
20 different types of amino acids, each different in
their R group

Long strings of amino acids called

polypeptides full to form functional proteins.

Protein
structure

Protein
structure
(concluded)

Protein Functions
Structure - keratin/collagen
Communication hormones and cell to cell signals
Membrane transport carriers of particles,
responsible for turning cell action on and off
Catalysis globular proteins (enzymes)are for
metabolic activity
Recognition and protection immune recognition
and clotting factors
Movement cell transport to muscle movement
Cell adhesion keep tissues together, immune
response , fertilization.

Protein
Functions
(Table 2.5)

Nucleic Acids
Two types in cells
Deoxyribonucleic acid (DNA)
Ribonucleic acid (RNA)

Building blocks are called

nucleotides.
Composed of 1 pentose sugar, 1
phosphate, 1 organic base

DNA Structure

Nucleotide basic unit composed

of
Phosphate
Deoxyribose sugar
Nitrogenous base

Sugar and Phosphate form

backbone (35 bonding order)
Nitrogenous bases
Two types of nitrogenous bases

Purine (Adenine and Guanine)

Pyrimidine (Thymine and Cytosine)

Join back bone by covalent bonds

Form rungs of ladder by paired
nitrogenous bases directed by hydrogen
bonding; purine to pyrimidine (not
random)

Adenine to Thyamine
Guanine to Cytosine

Hydrogen bonding allows for unzipping

of genetic material
Pairing allows for- Law of Complimentary
pairing

Maintains code (semi conservative replication)

Gives variety

ATP(nucleotide)>ADP
Most important energy transfer
molecule
Stores energy from exergonic
reactions (glucose oxide)
Releases energy within seconds for
physiological
like
polymerization
Adenosine
triphosphatase is an
enzyme
that hydrolyzes the third phosphate
bond to produce adenosine diphosphate
reactions
ATPase

Heat
Work

ATP + HO ADP + P + energy

Phosphorylation is the addition of the P carried out by enzymes called

i

Kinases; and is sometime the on/off switch

Organic Molecules

Type

Elements

Examples

Where found

Function

Monosaccharides

1. Glucose

blood

energy

1:2:1 ratio

(simple sugars)

2. Glycogen

liver &
muscle

stored energy

C H O(any
ratio)

Fatty acids & glycerol

1. Fats

adipose
tissue

stored energy,
insulation

2. Steroids
(sex hormones)

blood

regulate body

CARBOHYDRAT
E
CHO

LIPIDS

PROTEINS

CHON

Building Blocks

amino acids
(20 different amino acids)

NUCLEIC ACIDS C H O N P

nucleotides

3. Phospholipids cell membrane

structure

1. Structural

skin

strength

2. Contractile

muscle

movement

3.
Buffers

everywhere

stabilize pH

4. Antibodies

blood

attack foreign stuff

5. Transport

blood

transport stuff

6. Enzymes

everywhere

catalysts

7.Hormones

blood

regulate body

DNA

Nucleus

contains genetic info

nucleus &
cytoplasm

processes genetic info

RNA