Chemistry Basics for
Anatomy & Physiology
1
Why study chemistry in A&P?
- Body functions depend on cellular functions
- Cellular functions result from chemical changes
- Biochemistry helps to explain physiological
processes
- Because we all are just “giant
bags of ……”
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
3
Elements
4
Some Particles of Matter
5
Atomic Structure
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Atoms - composed of
subatomic particles:
• Proton – carries a
single positive charge
• 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
Neutron
(n0)
-
Proton
(p+)
0
+
+
0
0
0
+
Lithium (Li)
-
Electron
(e–)
Nucleus
6
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
• The number of
protons plus the
number of neutrons
in one atom
• Electrons do not
contribute to the weight of
the atom
7
Isotopes
Isotopes
• Atoms with the same atomic numbers but with
different atomic weights
• Atoms with the same number of protons and
electrons but a different number of neutrons
• Oxygen often forms isotopes (O16, O17, and O18)
• Unstable isotopes are radioactive; they emit
energy or atomic fragments
9
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
H 2O
10
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
11
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)
-
12
Bonding of Atoms
• force that holds atoms together
• depends on the number of electrons in the
valence shell
– 8 electrons is chemically stable
– Octet rule (most prevalent in elements with
atomic number <20)
13
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
Anion
• A negatively charged ion
• Formed when an atom gains
electrons
11p+
12n0
Sodium atom (Na)
17p+
18n0
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–).
14
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
Sodium ion (Na+)
17p+
18n0
–
Chloride ion (Cl–)
Sodium chloride
(b) Bonded ions
These oppositely charged particles attract electrically and join by
an ionic bond.
Cl–
(c) Salt crystal
Ionically bonded substances form arrays such as a crystal of NaCl.
15
Covalent Bonds
• Formed when atoms share electrons
• Most common bond in the body
• Strongest
16
Covalent Bonds
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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
17
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
H 2O
O
C
O
CO2
18
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 (if shared equally – nonpolar)
• Water is an important polar molecule
Slightly negative end
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(a)
Slightly positive ends
19
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
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H
O
H
O
H
O
H
H
O
(b)
Hydrogen bonds
H
H
H
20
Chemical Reactions
Chemical reactions occur when chemical bonds form or
break among atoms, ions, or molecules. Based on
valence electrons
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
21
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
A + B  AB
22
Types of Chemical Reactions
Redox Reaction – Reactions involving the transfer
of electrons (oxidation state changed)
Oxidation is the loss of electrons
Reduction is the gain of electrons
Many biological processes are redox reactions
Cellular respiration is the oxidation of
glucose and the reduction of oxygen to water
Also reduction of NAD+ to NADH and
oxidation of NADH to NAD+
23
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
24
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
25
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
26
Acids, Bases, and Salts
Electrolytes – substances that release ions in water
NaCl  Na+ + Cl-
Acids – electrolytes that dissociate to release hydrogen
ions in water (proton donor)
HCl  H+ + Cl-
Bases – substances that release ions that can
combine with hydrogen ions (proton acceptor)
NaOH  Na+ + OH-
Salts – electrolytes formed by the reaction between
an acid and a base
HCl + NaOH  H2O + NaCl
27
Acid and Base Concentration
pH scale - indicates the
concentration of hydrogen ions in
solution
Neutral – pH 7;
indicates equal
concentrations of H+
and OHAcidic – pH less than
7; indicates a greater
concentration of H+
Acidic
Relative
Amounts H+
of H+ (red)
3.0
and OH–
2.0
apple
(blue)
gastric juice
juice
pH 0
1
Acidic
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5.3
4.2
cabbage
tomato
juice
2
3
4
5
H+ concentration increases
8.4
7.4
6.6
Sodium
cow’s Human biocarbonate
blood
milk
6.0
corn
6
8.0
Egg
7.0
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 OH28
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
29
Organic Substances
Carbohydrates
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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.
C
O
O
C
H
H
O
H
O
H
H C
C
C
H
O
O
H
H
(b) More commonly, glucose
molecules form a ring structure.
(c) This shape symbolizes
the ring structure of a
glucose molecule.
30
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
31
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 and unsaturated
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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
H
H
H
H
H
C
C
C
C
C
C
C
H
C
H
C
C
C
C
H
H
H
H
H
C
C
H
H
H
H
H
H
Fatty acid
portions
H
H
H
32
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
33
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.
H2C
HO
(a) General structure of a steroid
C
H
H2
C
H2 C
CH3
C
HC
C
C
H2
(b) Cholesterol
C
H
CH3
H2 CH3 H
C
C
C
CH
CH2
CH
CH2
CH
CH3
CH2
CH2
CH2
CH
CH3
CH2
34
Organic Substances
Proteins
• Structural material
• Energy source
• Hormones
• Receptors
• Enzymes
• Antibodies
• Protein building blocks
are amino acids
• Amino acids held
together with peptide bonds
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H
S
R
H
N
C
C
H
H
O
OH
(a) General structure of an amino
acid. The portion common to all
amino acids is within the oval.
It includes the amino group
(—NH2) and the carboxyl group
(—COOH). The "R" group,
or the "rest of the molecule,“
is what makes each amino
acid unique.
H
H
H
C
H
C
C
C
H
C
H
C
H
C
H
N
C
C
H
H
O
OH
(b) Cysteine. Cysteine has an
R group that contains sulfur.
H
H
C
H
N
C
C
H
H
O
OH
Phenylalanine. Phenylalanine
has a complex R group.
Improper metabolism of
phenylalanine occurs in the
disease phenylketonuria.
35
Organic Substances
Proteins
Four Levels of Protein Structure
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Amino acids
H
(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.
H
(c) Tertiary structure—
The pleated and coiled
polypeptide chain of a
protein molecule folds
into a unique threedimensional structure.
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.
H
N
H
C
O
C
R
N
O
C
C
H
N
R
H
C
N
C
H
Pleated
structure
N
R
H
O
C
O
H
H
H
O
H
R
C
R
N
H
C
N
C
O
N
O
H
R
C
N
R
H
C
N
C
C
O
HO
O
Coiled
structure
N
C
H
H
O
H
H
C
H
R
C
N
N
R
C
O
C
N
C
C
H
C
C
R
N
N
C
R
C
H
N
C
C
HO
C
C
H O
H
C
C
R
Three-dimensional
folding
H
C
H
C
R
H
C
C
H
H H
H
R
N
O
H
O
C
H
H
R
R
C
H
H
C
O
H
O
H
R
H
(d) Quaternary structure—Two or
more polypeptide chains may be
connected to form a
single
protein molecule.
H
C
N
O
36
Organic Substances
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
37
Organic Substances
Nucleic Acids
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Copyright © The McGraw-Hill Companies, Inc. Permission required for reproduction or display.
P
B
P
S
P
P
S
P
S
P
S
P
S
B
B
B
B
B
B
B
P
S
P
S
P
S
P
S
B
P
S
(a)
B
S
S
B
P
B
P
S
B
P
B
S
S
B
P
B
S
B
P
B
S
(b)
S
P
38