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1
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2
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
3
2.2: Structure of Matter
Matter – anything that takes up space and has mass (weight).
It is composed of elements.
Elements – composed of chemically identical atoms:
• 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
Atoms – smallest particle of an element
4
Table 2.1 Some Particles of Matter
5
Elements and Atoms
• All matter is composed of elements
•Elements are:
• Bulk elements
• Trace elements
• Ultratrace elements
• Elements are composed of atoms of the same type
• Compounds are composed of atoms of different types
that are chemically bonded
6
Atomic Structure
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Atoms - composed of
subatomic particles:
Neutron
(n0)
-
• Proton – carries a single
positive charge
Proton
(p+)
• Neutron – carries no
electrical charge
• Electron – carries a single
negative charge
Nucleus
• Central part of atom
• Composed of protons and
neutrons
• Electrons move around the
nucleus
0
+
+
0
0
0
+
Lithium (Li)
-
Electron
(e–)
Nucleus
7
Atomic Number
and
Atomic Weight
Atomic Number
• Number of protons in the nucleus of one atom
• Each element has a unique atomic number
• Equals the number of electrons in the atom
Atomic Weight
• Approximated by the number of protons plus the number of
neutrons in one atom (since a proton and a neutron each have an
approximate atomic weight of one)
• Electrons do not contribute to the weight of the atom
8
Isotopes
Isotopes
• Atoms with the same atomic numbers but with
different atomic weights
• Different numbers of neutrons
• Oxygen often forms isotopes (O16, O17, and O18)
• Radioactive isotopes are unstable, releasing energy or
pieces of themselves (atomic radiation)
For an element, the atomic weight is often considered the
average of the atomic weights of its isotopes.
9
2.1 From Science to Technology
Radioactive Isotopes Reveal Physiology
10
2.2 From Science to Technology
Ionizing Radiation:
From the Cold War to Yucca Mountain
11
Molecules and Compounds
Molecule – particle formed when two or more atoms
chemically combine
Compound – particle formed when two or more atoms of
different elements chemically combine
Molecular formulas – depict the elements present and
the number of each atom present in the molecule
H2
C6H12O6
H2O
12
Molecules and Compounds
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H
H
O
13
Bonding of Atoms
• Bonds form when atoms combine with other atoms
• Electrons of an atom occupy regions of space called
electron shells which circle the nucleus
• For atoms with atomic numbers of 18 or less, the following
rules apply:
• The first shell can hold up to 2 electrons
• The second shell can hold up to 8 electrons
• The third shell can hold up to 8 electrons
14
Bonding of Atoms
• Lower shells are filled first
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• If the outermost shell is full, the atom is stable
-
+
Hydrogen (H)
0
-
-
+
+ 0
+
0
0
0
+
+
0
-
-
Helium (He)
Lithium (Li)
-
15
Ionic Bonds
Ionic Bonds
• An attraction between a cation and an anion
• Formed when electrons are transferred from one atom to
another atom
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Copyright © The McGraw-Hill Companies, Inc. Permission required for reproduction or display.
Na+
+
11p+
12n0
17p+
18n0
Sodium ion (Na+)
–
Cl–
Chloride ion (Cl–)
Sodium chloride
16
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)
17
Covalent Bonds
• Formed when atoms share electrons
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H
-
H
-
H2
-
+
+
+
+
-
Hydrogen atom
+
Hydrogen atom
• Hydrogen atoms form single bonds
• Oxygen atoms form two bonds
• Nitrogen atoms form three bonds
• Carbon atoms form four bonds
Hydrogen molecule
H―H
O=O
N≡N
O=C=O
18
Bonding of Atoms:
Structural Formula
• Structural formulas show how atoms bond and are arranged in
various molecules
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H
H
H
H2
O
O
O2
H
O
H2O
O
C
CO2
19
O
Bonding of Atoms:
Polar Molecules
Polar Molecules
• 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
Slightly negative ends
20
(a)
Slightly positive ends
Hydrogen Bonds
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
O
H
O
H
O
H
H
O
(b)
Hydrogen bonds
H
H
21
H
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
22
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 + CD  AD + CB
Reversible Reaction – the products can change back to the
reactants
23
A + B n AB
Acids, Bases, and Salts
Electrolytes – substances that release ions in water
NaCl  Na+ + Cl-
Acids – electrolytes that dissociate to release hydrogen ions
in water
HCl  H+ + Cl-
Bases – substances that release ions that can combine with
hydrogen ions
NaOH  Na+ + OH-
Salts – electrolytes formed by the reaction between an acid
and a base
HCl + NaOH  H2O + NaCl
24
Acids, Bases, and Salts
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Na+
Cl–
Salt crystal
Na+
Cl–
Ions in
solution
25
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
7; indicates a greater
concentration of H+
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Acidic
Relative
+
Amounts H
+
of H (red)
3.0
and OH–
2.0
apple
(blue)
gastric juice
juice
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
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)
Basic or alkaline – pH greater than 7;
indicates a greater concentration of OH26
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
27
2.3: Chemical Constituents
of Cells
Organic vs. 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 and H
• Usually smaller than organic molecules
• Usually dissociate in water, forming ions
• Water, oxygen, carbon dioxide, and inorganic salts
28
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
29
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+, Ca+2, etc.)
• Play important roles in metabolism
30
Organic Substances
Carbohydrates
• 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
31
Organic Substances
Carbohydrates
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H
O
C
H
H
C
O
O
C
H
H
Copyright © The McGraw-Hill Companies, Inc. Permission required for reproduction or display.
H
H
C
O
H
Copyright © The McGraw-Hill Companies, Inc. Permission required for reproduction or display.
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.
32
Organic Substances
Carbohydrates
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Copyright © The McGraw-Hill Companies, Inc. Permission required for reproduction or display.
O
O
O
O
(b) Disaccharide
(a) Monosaccharide
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O
O
O
(c) Polysaccharide
33
Organic Substances
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 fatty acids have only single carbon to carbon bonds
• Unsaturated fatty acids have one or more carbon to carbon
double bond
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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
H H H
(a) Saturated fatty acid
H
H
H
H
H
H
H
H
H
H
H
H
O
H
O
C
H
H
H
H
H
H
H
H
C
C
C
C
C
C
C
C
H H H
(b) Unsaturated fatty acid
H
H
H
H
O
H
O
C
H
34
Organic Substances
Lipids
• Fats (triglycerides)
• Saturated fats contain three saturated fatty acids
• Mostly solid and come from animals
•
Unsaturated fats contain at least one unsaturated fatty acid
• Mostly liquid and come from plants
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H
H
H
H
C
C
C
H
Glycerol
portion
O
O
O
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
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
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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
36
Organic Substances
Lipids
• Steroids
• Four connected rings of carbon
• Widely distributed in the body, various functions
• Component of cell membrane
• Used to synthesize hormones
• Cholesterol
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Copyright © The McGraw-Hill Companies, Inc. Permission required for reproduction or display.
H2
C
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
37
(a) General structure of a steroid
(b) Cholesterol
Organic Substances
Proteins
• Structural material
• Energy source
• Hormones
• Receptors
• Enzymes
• Antibodies
• Protein building blocks are
amino acids
• Amino acids held
together with peptide bonds
H
C
H
C
H
C
C
H
C
H
H
S
R
H
N
C
C
H
H
O
OH
H
C
H
C
H
N
C
C
H
H
O
OH
H
H
C
H
N
C
C
H
H
O
OH
38
Organic Substances
Proteins
Four Levels of Protein Structure
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Amino acids
(a) Primary structure—Each
oblong shape in this
polypeptide chain represents
an amino acid molecule. The
whole chain represents a
portion of a protein molecule.
C
H
C
H
N
C
(b) 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.
C
R
N
O
C
H
N
H
O
H H
H
R
C
N
C
N
C
H
O
H
H H
H
O
R
R
H
H
C
Pleated
structure
H
R
H
C
O
C
O
C
H
H
H
H O
H
C
N
O
R
R
N
H
C
O
C
O
Coiled
structure
H
O
R
H
C
N
H OR
N
C
R
C
HO
H
N C
C
C
H
C
N
C
N
R
C
C
N
H
C
R
C
N
H
H
C
C
HO
C
C
N
C
C
R
N
R
N
C
R
H
C
H
C
R
H
C
O
H
O
N
O
C
R
C
H
H
O
H
C
N
H
O
(c) Tertiary structure—
The pleated and coiled
polypeptide chain of a
protein molecule folds
into a unique three-dimensional
structure.
Three-dimensional
folding
(d) Quaternary structure—Two or more
polypeptide chains may be connected
to form a single protein molecule.
39
Animation: Protein Denaturation
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40
Organic Substances
Nucleic Acids
• 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
41
Organic Substances
Nucleic Acids
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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
42
2.3 From Science to Technology
CT Scanning and PET Imaging
43
Important Points in Chapter 2:
Outcomes to be Assessed
2.1: Introduction
 Give examples of how the study of living materials requires an
understanding of chemistry.
2.2: Structure of Matter
 Describe the relationships among matter, atoms, and molecules.
 Describe how atomic structure determines how atoms interact.
 Explain how molecular and structural formulas symbolize the
composition of compounds.
 Describe three types of chemical reactions.
 Describe the differences among acids, bases, and buffers.
 Explain the pH scale.
44
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 and
explain the function(s) of each group.
 Describe the general functions of the main classes of organic molecules
in cells.
45
Quiz 2
Complete Quiz 2 now!
Read Chapter 3.
46