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Chapter 2
Chemical Basis of Life
Anatomy & Physiology I (Dr. Rothschild)
2.1: Introduction
Why study chemistry in an
Anatomy and Physiology class?
- Body functions depend on cellular functions
- Cellular functions result from chemical changes
- Biochemistry helps to explain physiological processes
2
Matter
Properties
Mass, Volume
• Atoms smallest unit of matter
• Elements- one type of atom
3
Atomic Structure
Neutron
(n0)
Atoms - composed of subatomic particles:• Proton – carries a single positive charge
• Neutron – carries no electrical charge
• Electron – carries a single negative charge
Proton
(p+)
0
+
Nucleus
+
0
0
0
+
-
Electron
(e–)
• Central part of atom
• Composed of protons and neutrons
• Electrons move around the nucleus
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Lithium (Li)
Nucleus
4
Chemical Behavior of an Atom
1. Depends on electrons in
outermost shell
2. Valence electrons (valence
shell)
5. Orbitals describe the 3-D
space occupied (90% of the
time) by an electron as it
orbits a nucleus.
6. Reactivity of an atom arises
3. Atoms with the same
from the presence of
number of electrons in their
unpaired electrons in one or
valence shell exhibit similar
more orbitals of an atom’s
chemical behavior
valence shell
• Consider: F and Cl
– Both combine with Na 1:1
– NaF and NaCl
4. Completed valence shell
atoms are unreactive (inert)
7. Unpaired electrons of atoms
interact to complete their
valence shells
Elemental Isotopes
• Atoms have same number
of protons
• Isotopes have varying
numbers of neutrons in
their nucleus
• Isotopes behave similarly
in chemical reactions
despite different masses.
• Carbon (6C) Isotopes
– 12C (stable)
– 13C (stable)
– 14C (radioactive)
• Radioactive isotopes
decay spontaneously giving off particles and
energy
• Atomic mass number is
actually an average of
the atomic masses of all
the element’s isotopes
Bonding of Atoms
Bonds form when atoms combine with other atoms
Electrons occupy regions of space called orbitals (subshells)
Different energy levels (shells) circle the nucleus
Outermost (valence) electrons responsible for bonding
•Atoms may lose/gain electrons
•Atoms may share electrons
7
Bonding of Atoms: Ions
Ion
• An atom that gains or loses electrons to become stable
• An electrically charged atom
Cation
• A positively charged ion
• Formed when an atom loses electrons
11p+
12n0
17p+
18n0
Anion
• A negatively charged ion
• Formed when an atom gains
electrons
Sodium atom (Na)
Chlorine atom (Cl)
(a) Separate atoms
If a sodium atom loses an electron to a chlorine atom, the sodium
atom becomes a sodium ion (Na+), and the chlorine atom becomes
a chloride ion (Cl–).
8
Formula is a
ratio
NaCl is a compound, not a molecule
Ionic Compounds
Highly unequally electronegative atom
strips an electron from its partner’s
valence shell
Covalent Bonds
Formed when atoms share electrons
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H
-
H
-
H2
-
+
+
+
+
-
Hydrogen atom
+
Hydrogen atom
Hydrogen molecule
All organic (carbon) substances are formed by
covalent bonds, are molecules
10
Structural formulas show how atoms bond and are arranged in
various molecules
H
H
O
O C
O O
H H
H2
O2
O
CO2
H2O
Polar Molecules
Slightly negative end
Molecule with a slightly negative end and a
slightly positive end
Results when electrons are not shared equally in
covalent bonds
• Water is an important polar molecule
(a)
Slightly positive ends
11
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Elements and Compounds
Element: Cannot be broken down
• Bulk elements – required by the
body in large amounts
• Trace elements - required by the
body in small amounts
• Ultratrace elements – required by
the body in very minute amounts
Compound
• Two or more elements in a fixed
ratio
• Chemical bonds maintain ratio
• Example: Sodium Chloride
(NaCl)
Compound properties
different than elements that
form it
Molecules and Compounds
Compound – particle formed when two or more atoms
of different elements chemically combine
Molecule – particle formed when two or more atoms
chemically combine
Molecular formulas – depict the elements present
and the number of each atom present in the molecule
H2
C6H12O6
H2O
13
Hydrogen Bonds
A weak attraction between the positive end of
one polar molecule and the negative end of
another polar molecule
•Formed between water molecules
•Important for protein and nucleic acid
structure
H
H
O
H
Hydrogen bonds
O
H
H
O
H
O
H
H
O
H
H
14
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Chemical Reactions
Chemical reactions occur when chemical bonds form or
break among atoms, ions, or molecules
Reactants are the starting materials of the reaction - the
atoms, ions, or molecules
Products are substances formed at the end of the chemical
reaction
NaCl  Na+ + ClReactant
Products
15
Chemical Reactions
• Do not gain/lose atoms in a reaction
6 CO2 + 6 H2O  C6H12O6 + 6 O2
• Most reactions are reversible: products can change
back to the reactants
3 H2 + N2  2 NH3
• Chemical equilibrium: forward and reverse
reactions occur at the same rate
Types of Chemical Reactions
Synthesis Reaction – more complex chemical structure
is formed
A + B  AB
Decomposition Reaction – chemical bonds are broken to form
a simpler chemical structure
AB  A + B
Exchange Reaction – chemical bonds are broken and new
bonds are formed
AB + C  A + CB
AB + CD  AD + CB
17
Acids, Bases, and Salts
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Na+
Cl–
Salt crystal
Na+
Cl–
Ions in
solution
18
Acid and Base Concentration
pH scale - indicates the
concentration of hydrogen ions in
solution
Neutral – pH 7;
indicates equal
concentrations of H+
and OH-
Acidic – pH less than
Acidic
Relative
+
Amounts H
+
of H (red)
3.0
and OH–
2.0
apple
(blue)
gastric juice
juice
Each pH unit represents a 10
fold increase in hydrogen ion
concentration
5.3
4.2
cabbage
tomato
juice
8.4
7.4
6.6
Sodium
cow’s Human biocarbonate
blood
milk
6.0
corn
pH 0
1
Acidic
2
3
4
5
H+ concentration increases
7; indicates a greater
concentration of H+
6
8.0
7.0
Egg
Distilled white
water
7
Neutral
8
10.5
milk of
magnesia
11.5
Household
ammonia
Basic
OH–
9
10
11
12
13
14
OH– concentration increases
Basic (alkaline)
pH = -log [H+]
Power of hydrogen
Basic or alkaline – pH greater than 7;
indicates a greater concentration of OH19
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Acids, Bases, and Salts
Electrolytes – substances that release ions in water
NaCl  Na+ + Cl-
Salts –formed by the reaction between an acid & base
HCl + NaOH  H2O + NaCl
20
Changes in pH and Buffers
Blood pH
• Normal blood pH is 7.35 – 7.45
• Alkalosis occurs when blood pH rises to 7.5 – 7.8
• Acidosis occurs when blood pH drops to 7.0 – 7.3
• Homeostatic mechanisms help regulate pH
• Buffers are chemicals which act to resist pH changes
21
Buffers
• Minimize pH changes
• Accepts or donates hydrogen ions
• Most are a weak acid and its conjugate
base
• H2CO3  HCO3- + H+
Water
Hydrogen bonds
produce a
phenomenon
known as
cohesion
Water molecules
adhere to
substances
Water has a
greater surface
tension than
most other
liquids
Water and Energy Transfer
• Heat is the measure of the kinetic energy due
to molecular motion in a body of matter
• Temperature measures the the heat due to the
average kinetic energy
• Kinetic energy is transferred from a body with
a higher kinetic energy to a body with a lower
kinetic energy
• Temperature is measured using Celsius scale
• Calorie is a measure of heat
• Kilocalorie (kcal)
– Unit used in for cellular
reactions
Water: The Solvent of Life
•
•
•
•
•
Solutions
Solvents
Solutes
Aqueous Solutions
Water forms hydration
shells around
dissolved ions of an
ionic compound
• Water also surrounds
organic compounds if
they have ionic and
polar regions
Dissociation of Water
H2O  H+ + OH-
2.3: Chemical Constituents of Cells
Organic v. Inorganic Molecules
Organic molecules
• Contain C and H
• Usually larger than inorganic molecules
• Dissolve in water and organic liquids
• Carbohydrates, proteins, lipids, and nucleic acids
Inorganic molecules
• Generally do not contain C
• Usually smaller than organic molecules
• Usually dissociate in water, forming ions
• Water, oxygen, carbon dioxide, and inorganic salts
27
Inorganic Substances
Water
• Most abundant compound in living material
• Two-thirds of the weight of an adult human
• Major component of all body fluids
• Medium for most metabolic reactions
• Important role in transporting chemicals in the body
• Absorbs and transports heat
Oxygen (O2)
• Used by organelles to release energy from nutrients in
order to drive cell’s metabolic activities
• Necessary for survival
28
Inorganic Substances
Carbon dioxide (CO2)
• Waste product released during metabolic reactions
• Must be removed from the body
Inorganic salts
• Abundant in body fluids
• Sources of necessary ions (Na+, Cl-, K+, Ca2+, etc.)
• Play important roles in metabolism
29
Chemistry of Living Things
– C,H,O,N = 96%
– All biological compounds are based on
hydrocarbon chains
• C-C-C-C-C-C
• Chains are very long
– 4 Main types of biological compounds
•
•
•
•
Proteins
Carbohydrates
Lipids
Nucleic Acids
II.Proteins
– Composed of amino acid building
Protein
blocks
• COOH group
• NH2 Group
– Protein = Many amino acids hooked
together
• Special covalent bond = peptide bond
– Links C-N-C
• Only found in proteins
• Proteins = polypeptides
Four Levels of Protein Structure
Primary structure—Each
oblong shape in this
polypeptide chain represents
an amino acid molecule. The
whole chain represents a
portion of a protein molecule.
(a)
) Tertiary structure—
The pleated and coiled
polypeptide chain of a
protein molecule folds
into a unique threedimensional structure.
(c
Amino acids
H
) Secondary structure—
The polypeptide chain of a
protein molecule is often
either pleated or twisted to
form a coil. Dotted lines
represent hydrogen bonds.
R groups (see fig. 2.17)
are indicated in bold.
H
(b
C
H
C
H
N
C
O
C
R
N
O
C
H
H
H
H
H
R
R
H
H
H
N
O
C
R
N
C
Pleated
structure
N
H
H
N
C
H
R
C
C
O
O
N
C
H
C
H
C
O
C
H
H
H
C
N
C
O
R
O
Coiled
structure
N
C
H
C
N
O
HO
H
C
N
O
C
C
Three-dimensional
folding
H
C
H
N
R
H
R
R
R
C
H
C
N
O
C
H
R
C
H
N
R
H
N
N
HO
C
C
H O
H
C
O
N
R
C
R
R
C
H
H H
C
H
H
C
H
C
C
C
O
O
N
O
C
R
C
C
H
R
H
C
H
O
N
d) Quaternary structure—Two or
more polypeptide chains may be
connected to form a single
protein molecule.
(
32
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Animation: Protein Denaturation
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33
C.Functions of proteins
1) Enzymes
2) Muscles
3) Cell Membranes
4) Structure of cells
5) Some Hormones
a) insulin
III.Carbohydrates = sugars and starches
– Composed of monosaccharides
(single sugars)
• m.s.+m.s.  disaccharide + HOH
– Dehydration synthesis
– (m.s.+m.s.  polysaccharide+many HOH
(polysaccharide = starch)
• Examples of monosaccharides
– Glucose
– Fructose
– Galactose
• Examples of disaccharides
– Sucrose
– Lactose
– Maltose
Functions
• Provide energy to cells
• Supply materials to build cell structures
• Water-soluble
• Contain C, H, and O
• Ratio of H to O close to 2:1 (C6H12O6)
• Monosaccharides – glucose, fructose
• Disaccharides – sucrose, lactose
• Polysaccharides – glycogen, cellulose
36
Carbohydrate shapes
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H
O
C
H
H
C
O
O
C
H
H
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H
H
C
O
H
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H
C
O
H
H
C
O
H
H
C
O
H
H
(a) Some glucose molecules
(C6H12O6) have a straight
chain of carbon atoms.
O
C
H
C
H
O
O
H
H
H C
O
O
C
C
H
O
H
H
(b) More commonly, glucose
molecules form a ring structure.
(c) This shape symbolizes
the ring structure of a
glucose molecule.
37
Lipids
• Soluble in organic solvents; insoluble in water
• Fats (triglycerides)
• Used primarily for energy; most common lipid in the body
• Contain C, H, and O but less O than carbohydrates (C57H110O6)
• Building blocks are 1 glycerol and 3 fatty acids per molecule
• Saturated and unsaturated
H
H
H
H
C
C
C
O
O
O
H
Glycerol
portion
O
H
H
H
H
H
H
H
H
H
H
H
H
H
H
H
C
C
C
C
C
C
C
C
C
C
C
C
C
C
C
C
H
H
H
H
H
H
H
H
H
H
H
H
H
H
H
O
H
H
H
H
H
H
H
H
H
H
H
H
H
H
H
H
H
C
C
C
C
C
C
C
C
C
C
C
C
C
C
C
C
C
C
H
H
H
H
H
H
H
H
H
H
H
H
H
H
H
H
H
O
H
H
H
H
H
H
C
C
C
C
C
C
H
H
H
H
H
Fatty acid
portions
H
H
38
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Lipids
• Steroids
• Four connected rings of carbon
• Widely distributed in the body, various functions
• Component of cell membrane
• Used to synthesize hormones
• Cholesterol
H2
C
(a) General structure of a steroid
C
H
CH
CH2
CH
C
C
H2
CH
CH2
HC
C
H2C
HO
H2 C
CH3
CH3
H2 CH3 H
C
C
C
CH3
CH2
CH2
CH2
CH
CH3
CH2
C
H
(b) Cholesterol
39
Organic Substances
Lipids
• Phospholipids
• Building blocks are 1 glycerol, 2 fatty acids, and 1 phosphate per
molecule
• Hydrophilic and hydrophobic
• Major component of cell membranes
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H
Copyright © The McGraw-Hill Companies, Inc. Permission required for reproduction or display.
H
H
C
O
Fatty acid
H
C
O
Fatty acid
H
C
O
Fatty acid
H
Glycerol portion
(a) A fat molecule
Copyright © The McGraw-Hill Companies, Inc. Permission required for reproduction or display.
H
C
O
Fatty acid
H
C
O
Fatty acid
O
H
C
H
O
P
O–
O
Water-insoluble
(hydrophobic)
“tail”
H
H
C
C
H
H
H
N
H
Water-soluble
(hydrophilic)
“head”
Phosphate portion
(b) A phospholipid molecule
(the unshaded portion may vary)
(c) Schematic representation
of a phospholipid molecule
40
V.Nucleic Acids = DNA + RNA
• Made of 3 components
– 5-C sugar
– Phosphate
– Nitrogen Base
– Together these make 1 nucleotide
– Nucleotides = Building Blocks
• Functions
– Carries genetic code/blueprint
– Cell fuel (ATP)
– Important in cell cycles
Nucleic Acids
• Carry genes
• Encode amino acid sequences of proteins
• Building blocks are nucleotides
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P
B
S
• DNA (deoxyribonucleic acid) – double polynucleotide
• RNA (ribonucleic acid) – single polynucleotide
42
Nucleic Acids
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Copyright © The McGraw-Hill Companies, Inc. Permission required for reproduction or display.
P
B
S
P
B
B
B
B
B
B
B
B
P
P
S
B
S
P
S
P
S
B
S
P
S
P
S
B
S
P
S
(a)
B
S
P
S
P
B
P
S
B
P
B
S
P
S
P
B
S
B
P
S
P
S
(b)
P
43
44
Important Points in Chapter 2:
Outcomes to be Assessed
2.1: Introduction
 Give examples of how the study of living materials requires and
understanding of chemistry.
2.2: Structure of Matter
 Describe how atomic structure determines how atoms interact.
 Describe the relationships among matter, atoms, and molecules.
 Explain how molecular and structural formulas symbolize the
composition of compounds.
 Describe three types of chemical reactions.
 Explain what acids, bases, and buffers are.
 Define pH.
45
Important Points in Chapter 2:
Outcomes to be Assessed Continued
2.3: Chemical Constituents of Cells
 List the major groups of inorganic chemicals common in cells.
 Describe the general functions of the main classes of organic molecules
in cells.
46