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Chapter 02
Lecture Outline
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2.1: The Importance of Chemistry in
Anatomy and Physiology
Why study chemistry in Anatomy & Physiology?
• Chemistry is concerned with composition of substances
and how they change in chemical reactions
• Human body, food, and medications are all composed of
• All anatomical structures are chemicals, and all
physiological processes are based on chemical reactions
• Biochemistry helps explain physiological and disease
2.2: Structure of Matter
• Matter: Anything that takes up space and has mass.
Matter is composed of elements. Solids, liquids, and
gases are matter.
• Elements: Simplest types of matter with certain
chemical properties. 98 naturally occurring elements.
• Atoms: Smallest particles of an element that have
properties of that element
Structure of Matter
Different elements are required by the body in different
• Bulk elements: required by the body in large amounts
(C, O, H)
• Trace elements: required by the body in small
amounts (Fe, I)
• Ultratrace elements: required by the body in very
minute amounts (As)
Structure of Matter
Table of major and
trace elements in the
human body
Atomic Structure
Atoms: Composed of
subatomic particles:
• Proton: Carries a single
positive charge
• Neutron: Carries no electrical
• Electron: Carries a single
negative charge
• Central part of atom
• Composed of protons and
• Electrons move around the
Atomic Structure
Atomic Number & Atomic Weight
• Atomic Number:
• Number of protons in the nucleus of an atom of a
specific element
• Each element has a unique atomic number
• Number of protons is equal to the number of
electrons in the atom; atoms are electrically neutral
• Atomic Weight:
• The number of protons plus the number of neutrons
in one atom
• Electrons do not contribute to the weight of the atom
• All atoms of a certain element have same atomic number
• Isotopes are atoms with the same atomic numbers but
with different atomic weights
• Isotopes contain different numbers of neutrons, but same
number of protons & electrons
• Oxygen often forms isotopes (O16, O17, and O18, with
representing atomic weights)
• Radioactive isotopes are unstable, releasing energy or
atomic fragments (atomic radiation) until they gain
stability; some are used to detect and treat disease.
For any element, the atomic weight is often considered the
average of the atomic weights of all of its isotopes.
From Science to Technology 2.1
Radioactive Isotopes Reveal Physiology
Radioactive iodine-131 can be used to destroy cancerous
thyroid gland tissue. This is very effective, because the
thyroid gland is the only part of the body that actively
transports and metabolizes iodine.
Radioactive isotopes have many medical uses: detecting
coronary blood vessel disorders, evaluating kidney function,
measuring hormone concentrations in body fluids, and
assessing changes in bone density.
From Science to Technology 2.2
Ionizing Radiation:
From the Cold War to Yucca Mountain
Radiation (alpha, beta, and gamma) is called ionizing
radiation, because its energy can remove electrons from
atoms, resulting in the formation of ions. The free
electrons can damage nearby atoms.
Ionizing radiation sources include X rays, naturally
occurring radioactive elements in the crust of the earth,
and nuclear weapons.
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 = a molecule of hydrogen
• C6H12O6 = a molecule of glucose
• H2O = a molecule of water
Molecules and Compounds
Molecules of hydrogen or
oxygen form when 2 identical
atoms combine chemically.
When 2 atoms of hydrogen
combine with 1 atom of oxygen,
the compound water is formed.
Bonding of Atoms
• Chemical bonds form when atoms combine with other
atoms. They result from interactions between the
electrons of the atoms.
• Electrons of an atom occupy regions of space called
electron shells (energy 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
• Lower energy shells / inner orbits are filled first, and are
stable with a certain number of electrons in the outermost
shell (2, 8 or 18—in larger atoms)
Bonding of Atoms
Bonding of Atoms: Ions
• An atom that gains or loses electrons to become stable
• An electrically charged atom
• A positively charged
• Formed when an
atom loses electrons
• A negatively charged
• Formed when an atom
gains electrons
Bonding of Atoms: Ionic Bonds
Ionic Bonds:
• Formed when electrons are transferred from one atom to
another atom
• The attraction between a cation and an anion forms a
very strong bond between the ions, called an ionic bond.
Bonding of Atoms: Covalent Bonds
Covalent Bonds: Strong chemical bonds, formed between
atoms that share electrons
Two atoms of hydrogen (H) have combined to form a
hydrogen molecule (H2). Both atoms in the molecule
become stable.
Bonding of Atoms: Covalent Bonds
Hydrogen molecules (H2) often combine with oxygen (O2)
molecules to form water molecules (H2O).
Bonding of Atoms:
Structural Formulas
Structural formulas show how atoms bond and are arranged
in various molecules.
One line between atoms means that 1 pair of electrons are
being shared (forming single bonds), while two lines
indicate that 2 pairs are being shared (forming double
Bonding of Atoms: Polar Molecules
Polar Molecules:
• Molecules with a slightly negative end & a slightly positive end
• Results from unequal sharing of electrons in covalent bonds
• Water is an important polar molecule
In this water molecule, the
O nucleus pulls the
electrons more strongly
than the H nuclei, since
it contains more positively
charged protons.
Bonding of Atoms: Hydrogen Bonds
Hydrogen Bond:
• A weak attraction between
the slightly positive (H) end
of one polar molecule and
the slightly negative (N or
O) end of another polar
• Formed between adjacent
water molecules
• Important for protein and
nucleic acid structure
Chemical Reactions
Chemical reactions occur when chemical bonds form or
break between atoms, ions, or molecules.
Reactants are the starting materials of a chemical reaction:
the atoms, ions, or molecules.
Products are substances formed at the end of the chemical
Na+ + Cl(Products)
The above reaction involves the dissociation of NaCl in
water to form Na+ and Cl- ions.
Types of Chemical Reactions
Synthesis Reaction: more complex chemical structure is formed
Decomposition Reaction: chemical bonds are broken to form a
simpler chemical structure
Exchange Reaction: chemical bonds are broken and new bonds
are formed
Reversible Reaction: the products can change back to the
Acids, Bases, and Salts
Electrolytes: Substances that release ions in water. The
solution can conduct an electric current, so it is called an
NaCl  Na+ + ClAcids: Electrolytes that dissociate to release hydrogen ions in
HCl  H+ + ClBases: Substances that release ions that can combine with
hydrogen ions
NaOH  Na+ + OHSalts: Electrolytes formed by the reaction between an
acid and a base
HCl + NaOH  H2O + NaCl
Acids, Bases, and Salts
When an ionically bonded
substance is put into water,
the charged ions are attracted
to the slightly charged ends
of the polar water molecules.
This dissociates the
substance, and the ions
become surrounded by water
molecules. The substance is
now called an electrolyte,
since it can now carry an
electric current.
Acid and Base Concentrations
• Concentrations of acids and bases affect chemical
reactions in living organisms.
• H+ ion concentration is measured in g/L of body fluid
• pH scale is used as shorthand for H+ ion concentration; it
is based on the number of decimal places in the
• If H+ ion concentration = 0.01 g/L, the pH = 2
• If H+ ion concentration = 0.000000001 g/L, the pH =9
• pH scale runs from 0 – 14; each number represents a
tenfold difference in H+ ion concentration
• Acids have a pH <7, and bases have a pH >7
• A pH of 7 is neutral
Acid and Base Concentrations
The higher the H+
concentration, the
lower the pH, and
the higher the
The lower the H+
concentration, the
higher the pH, and
the lower the acidity
(which corresponds
to higher alkalinity).
Acid and Base Concentrations
• pH Scale: Indicates the concentration of hydrogen ions in a
• Neutral: A pH of 7 indicates equal concentrations of H+ and
OH-. This is the pH of water.
• Acidic: A pH of <7 indicates a greater concentration of H+
than OH• Basic (alkaline): A pH >7 indicates a higher concentration of
OH- than H+
Acid and Base Concentrations
Normal range of blood pH is 7.35 – 7.45
Acidosis occurs when blood pH drops to 7.0 – 7.3
• Makes a person feel disoriented, fatigued
• Caused by vomiting of alkaline intestinal contents,
diabetes, lung disease with impaired CO2 exhalation
Alkalosis occurs when blood pH rises to 7.5 – 7.8
• Makes a person feel dizzy and agitated
• Caused by high altitude breathing, vomiting of acidic
stomach contents, high fever, taking excess antacids
• Homeostatic mechanisms help regulate pH
• Buffers are chemical systems which act to resist pH
changes; bind and release H+ ions to regulate pH
2.3: Chemical Constituents of Cells
Organic vs. Inorganic Molecules
• Organic molecules:
• Contain C and H
• Dissolve in water and organic liquids
• Water-soluble organic compounds do not release ions,
and are non-electrolytes
• Carbohydrates, proteins, lipids, and nucleic acids
• Inorganic molecules:
• Generally do not contain C and H
• Usually dissolve in water and dissociate, forming
ions, and are electrolytes
• Water, oxygen, carbon dioxide, and inorganic salts
Inorganic Substances
• 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
• Water balance exists when gains equal losses
Oxygen (O2):
• Used by organelles to release energy from nutrients
in order to drive cell’s metabolic activities
• Necessary for survival
Inorganic Substances
Carbon dioxide (CO2):
• Waste product released during metabolic reactions
• Must be removed from the body through exhaling
Inorganic salts:
• Abundant in body fluids
• Sources of necessary ions (Na+, Cl-, K+, Ca+2, etc.)
• Play important roles in metabolism
• Help control H2O concentration, pH, blood clotting,
nerve and muscle processes
• Electrolyte balance exists when gains equal losses
Organic Substances:
Main source of cellular energy
Supply materials to build cell structures
Contain C, H, and O
Ratio of H to O close to 2:1 (C6H12O6 = glucose)
Size classification of carbohydrates:
• Monosaccharides (single sugars): glucose, fructose
• Disaccharides (double sugars): sucrose, lactose
• Polysaccharides (complex carbohydrates: starch,
glycogen, cellulose)
Organic Substances:
Organic Substances:
Organic Substances: Lipids
• Insoluble in water, but soluble in organic solvents
• Include triglycerides (fats), phospholipids, steroids
• Important component of cell membranes, and have several
functions in cells
• Most abundant lipids are triglycerides (fats):
a. Used for cellular energy
b. Contain more energy per gram than carbohydrates
c. Contain C, H, and O, but less O than carbohydrates
d. Consist of 1 molecule of glycerol and 3 fatty acids
Organic Substances: Lipids
• Saturated fatty acids have only single carbon-carbon bonds.
Most are solid at room temperature, and of animal origin.
• Unsaturated fatty acids have one or more carbon-carbon
double bond. Most are liquid at room temperature, and are
of plant origin.
Organic Substances: Lipids
A triglyceride is composed of 1 glycerol molecule and 3 fatty
Organic Substances: Lipids
• Consist of 1 glycerol, 2 fatty acids, and 1 phosphate
• Have hydrophilic and hydrophobic ends
• Major component of cell membranes
Organic Substances: Lipids
• 4 connected rings of carbon
• Widely distributed in the body, various functions
• Component of cell membranes
• Used to synthesize adrenal and sex hormones
• Cholesterol is the main steroid in the body
Organic Substances: Proteins
• Proteins are used as structural materials, energy source,
hormones, receptors, enzymes, antibodies
• Consist of building blocks called amino acids
• An amino acid contains an amino (-NH2) group, a carboxyl
(COOH) group, and a unique R (side chain) group
Organic Substances: Proteins
Amino acids are bound to each other by peptide bonds:
Peptide bonds form between the amino group of one amino
acid, and the carboxyl group of the adjacent amino acid.
Organic Substances: Proteins
4 Levels of Protein Structure:
• Primary: Amino acid sequence
• Secondary: Pleated or twisted
structure formed by hydrogen
bonding between nonadjacent
amino acids
• Tertiary: Unique 3-dimensional
folded shape of the protein
• Quaternary: Structure formed by
some proteins, when 2 or more
polypeptide chains are connected
to become 1 protein.
Organic Substances: Nucleic Acids
• Carry genetic code (DNA) or aid in protein synthesis (RNA)
• Encode amino acid sequences of proteins
• Building blocks are called nucleotides, which consist of a
sugar (S), a phosphate group (P), and an organic base (B).
• DNA (Deoxyribonucleic acid): a double chain of nucleotides
• RNA (Ribonucleic acid): a single chain of nucleotides
Organic Substances: Nucleic Acids
Organic Substances: Nucleic Acids
Two major types of nucleic acids: DNA and RNA
• Stores the genetic code
• Contains the sugar deoxyribose
• Structure—double helix
• Composed of nucleotides
• Interacts with DNA to conduct protein synthesis
• Contains the sugar ribose
• Structure—single strand
• Composed of nucleotides
From Science to Technology 2.3
CT Scanning and PET Imaging
Computerized Tomography (CT) imaging:
• Used to visualize internal anatomy
• Uses X-ray emitting device to create 3-dimensional image of soft
• Differentiates tissues with slightly different densities, tumors
Positron Emission Tomography (PET) imaging:
• Uses radioactive isotopes that emit positrons (unusual positively
charge electrons) to detect biochemical activity
• Used to detect various brain disorders, blood flow, normal brain
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