UNIVERSIDAD DE ZAMBOANGA

School of Allied Medicine

Department of Medical Technology

Human Anatomy and Physiology

With Pathophysiology

Basic Chemistry
Matter and Energy
• Matter—anything that occupies space and has mass (weight)
• Energy—the ability to do work
• Chemical
• Electrical
• Mechanical
• Radiant
Composition of Matter
• Elements—fundamental units of matter
• 96 percent of the body is made from four elements
• Carbon (C)
• Oxygen (O)
• Hydrogen (H)
• Nitrogen (N)
• Atoms—building blocks of elements
Subatomic Particles
• Nucleus
• Protons (p+)
• Neutrons (n0)
• Orbiting the nucleus
• Electrons (e–)
• Number of protons equals numbers of electrons in an atom
 Nucleus Nucleus

Helium atom Helium atom

2 protons (p+) 2 protons (p+)

2 neutrons (n0) 2 neutrons (n0)
2 electrons (e–) 2 electrons (e–)

(a) Planetary model (b) Orbital model

KEY:

= Proton = Electron
= Neutron = Electron cloud
Figure 2.1
Figure 2.2
Identifying Elements
• Atomic number—equal to the number of protons that the atom
contains
• Atomic mass number—sum of the protons and neutrons
Isotopes and Atomic Weight
• Isotopes
• Atoms of the same element with the same number of protons and the
same atomic number
• Vary in number of neutrons
Figure 2.3
Isotopes and Atomic Weight
• Atomic weight
• Close to mass number of most abundant isotope
• Atomic weight reflects natural isotope variation
Radioactivity
• Radioisotope
• Heavy isotope
• Tends to be unstable
• Decomposes to more stable isotope
• Radioactivity—process of spontaneous atomic decay
Molecules and Compounds
• Molecule—two or more atoms of the same elements
combined chemically
• Compound—two or more atoms of different elements
combined chemically
Figure 2.4
Chemical Reactions
• Atoms are united by chemical bonds
• Atoms dissociate from other atoms when chemical bonds are
broken
Electrons and Bonding
• Electrons occupy energy levels called electron shells
• Electrons closest to the nucleus are most strongly attracted
• Each shell has distinct properties
• The number of electrons has an upper limit
• Shells closest to the nucleus fill first
Electrons and Bonding
• Bonding involves interactions between electrons in the outer
shell (valence shell)
• Full valence shells do not form bonds
Inert Elements
• Atoms are stable (inert) when the outermost shell is complete
• How to fill the atom’s shells
• Shell 1 can hold a maximum of 2 electrons
• Shell 2 can hold a maximum of 8 electrons
• Shell 3 can hold a maximum of 18 electrons
Inert Elements
• Atoms will gain, lose, or share electrons to complete their
outermost orbitals and reach a stable state
• Rule of eights
• Atoms are considered stable when their outermost orbital has 8
electrons
• The exception to this rule of eights is Shell 1, which can only hold 2
electrons
Figure 2.5a
Reactive Elements
• Valence shells are not full and are unstable
• Tend to gain, lose, or share electrons
• Allow for bond formation, which produces stable valence
Figure 2.5b
Chemical Bonds
• Ionic bonds
• Atoms become stable through the transfer of electrons
• Form when electrons are completely transferred from
one atom to another
• Ions
• Result from the loss or gain of electrons
• Anions are negative due to gain of electron(s)
• Cations are positive due to loss of electron(s)
Figure 2.6
Figure 2.6, step 1
Figure 2.6, step 2
Figure 2.6, step 3
Chemical Bonds
• Covalent bonds
• Atoms become stable through shared electrons
• Electrons are shared in pairs
• Single covalent bonds share one pair of electrons
• Double covalent bonds share two pairs of electrons
Figure 2.7a
Figure 2.7b
Figure 2.7c
Covalent Bonds
• Covalent bonds are either nonpolar or polar
• Nonpolar
• Electrons are shared equally between the atoms of the molecule
• Electrically neutral as a molecule
Figure 2.8a
Covalent Bonds
• Covalent bonds are either nonpolar or polar
• Polar
• Electrons are not shared equally between the atoms of the molecule
• Have a positive and negative side or pole
Figure 2.8b
Chemical Bonds
• Hydrogen bonds
• Weak chemical bonds
• Hydrogen is attracted to the negative portion of polar molecule
• Provides attraction between molecules
 +
H H
O
–

Hydrogen bonds

+
H
O +
– H
– –
H
O +
+
H
H
+
O
– H

(a) (b)

Figure 2.9
Patterns of Chemical Reactions
• Synthesis reaction (A + B→AB)
• Atoms or molecules combine
• Energy is absorbed for bond formation
• Decomposition reaction (AB→A + B)
• Molecule is broken down
• Chemical energy is released
Figure 2.10a
Figure 2.10b
Patterns of Chemical Reactions
• Exchange reaction (AB + C→AC + B)
• Involves both synthesis and decomposition reactions
• Switch is made between molecule parts and different molecules are
made
Figure 2.10c
Biochemistry: Essentials
• Organic compounds
for Life
• Contain carbon
• Most are covalently bonded
• Includes carbohydrates, lipids, proteins, nucleic acids
• Inorganic compounds
• Lack carbon
• Tend to be simpler compounds
• Includes water, salts, and some acids and bases
Important Inorganic Compounds
• Water
• Most abundant inorganic compound in the body
• Vital properties
• High heat capacity
• Polarity/solvent properties
• Chemical reactivity
• Cushioning
Important Inorganic Compounds
• Salts
• Easily dissociate into ions in the presence of water
• Vital to many body functions
• Include electrolytes which conduct electrical currents
 +
H
– O
H
+
Water molecule

Na+

Na+

Cl–
Cl–

Salt Ions in
crystal solution Figure 2.11
Important
• Acids
Inorganic Compounds
• Release hydrogen ions (H+)
• Are proton donors
• Bases
• Release hydroxyl ions (OH–)
• Are proton acceptors
• Neutralization reaction
• Acids and bases react to form water and a salt
pH
• Measures relative concentration of hydrogen ions
• pH 7 = neutral
• pH below 7 = acidic
• pH above 7 = basic
• Buffers—chemicals that can regulate pH change
Figure 2.12
Chemical Reactions
• Dehydration synthesis—monomers or building blocks are
joined to form polymers through the removal of water
molecules
Figure 2.13a
Chemical Reactions
• Hydrolysis—polymers are broken down into monomers
through the addition of water molecules
Figure 2.13b
Important Organic Compounds
• Carbohydrates
• Contain carbon, hydrogen, and oxygen
• Include sugars and starches
• Classified according to size
• Monosaccharides—simple sugars
• Disaccharides—two simple sugars joined by dehydration
synthesis
• Polysaccharides—long-branching chains of linked simple
sugars
Figure 2.14a–b
Figure 2.14c
Figure 2.14d
Important Organic Compounds
• Lipids
• Contain carbon, hydrogen, and oxygen
• Carbon and hydrogen outnumber oxygen
• Insoluble in water
Lipids
• Common lipids in the human body
• Neutral fats (triglycerides)
• Found in fat deposits
• Source of stored energy
• Composed of three fatty acids and one glycerol molecule
• Saturated fatty acids contain only single covalent bonds
• Unsaturated fatty acids contain one or more double covalent
bonds
Glycerol 3 fatty acid chains Triglyceride, or neutral fat 3 water
molecules
(a) Formation of a triglyceride

Figure 2.15a
Figure 2.16a
Figure 2.16b
Lipids
• Common lipids in the human body (continued)
• Phospholipids
• Contain two fatty acids rather than three
• Form cell membranes
 Polar “head”

Nonpolar “tail”

Phosphorus-containing Glycerol 2 fatty acid chains

group (polar end) backbone (nonpolar end)
(b) Phospholipid molecule (phosphatidylcholine)

Figure 2.15b
Lipids
• Common lipids in the human body (continued)
• Steroids
• Include cholesterol, bile salts, vitamin D, and some hormones
• Cholesterol is the basis for all steroids made in the body
Figure 2.15c
Important Organic Compounds
• Proteins
• Account for over half of the body’s organic matter
• Provide for construction materials for body tissues
• Play a vital role in cell function
• Act as enzymes, hormones, and antibodies
• Contain carbon, oxygen, hydrogen, nitrogen, and
sometimes sulfur
• Built from amino acids
Proteins
• Amino acid structure
• Contain an amine group (NH2)
• Contain an acid group (COOH)
• Vary only by R groups
Amine Acid
group group

(a) Generalized (b) Glycine (c) Aspartic acid (d) Lysine (e) Cysteine
structure of all (the simplest (an acidic (a basic (a sulfur-
amino acids amino acid) amino acid) amino acid containing
amino acid)

Figure 2.17a-e
 (a) Primary structure. A
protein’s primary structure
is the unique sequence of
amino acids in the
Amino
acids polypeptide chain.

Hydrogen bonds
Amino
acids
(b) Secondary structure.
Two types of secondary
structure are named
alpha-helix and beta-
pleated sheet. Secondary
structure is reinforced by
hydrogen bonds. Dashed
lines represent the
hydrogen bonds in this
figure.
-pleated sheet
Alpha-
helix

Figure 2.18a-b
Figure 2.18c-d
Proteins
• Fibrous proteins
• Also known as structural proteins
• Appear in body structures
• Examples include collagen and keratin
• Stable
Figure 2.19a
Proteins
• Globular proteins
• Also known as functional proteins
• Function as antibodies or enzymes
• Can be denatured
 Heme group

Globin
protein

(b) Hemoglobin molecule composed of the

protein globin and attached heme groups.
(Globin is a globular or functional protein.)
Figure 2.19b
Enzymes
• Act as biological catalysts
• Increase the rate of chemical reactions
• Bind to substrates at an active site
 Product (P)
e.g., dipeptide
Substrates (S) Energy is Water is
e.g., amino acids absorbed; released. Peptide
bond is bond
+ H2O
formed.

Active site

Enzyme-substrate
complex (E-S)
Enzyme (E) 1 Substrates bind to active 2 Structural changes Enzyme (E)
site. Enzyme changes shape occur, resulting in the 3 Product is released.
to hold substrates in proper product. Enzyme returns to
position. original shape, ready
to catalyze another
reaction.

Figure 2.20
Important Organic
• Nucleic Acids
Compounds
• Built from nucleotides
• Pentose (5 carbon) sugar
• A phosphate group
• A nitrogenous base
• A = Adenine
• G = Guanine
• C = Cytosine
• T = Thymine
• U = Uracil.
 Deoxyribose
Phosphate sugar Adenine (A)

(a) Adenine nucleotide

(Chemical structure)

KEY:

Thymine (T) Cytosine (C)

Adenine (A) Guanine (G)

Figure 2.21a
Nucleic Acids
• Deoxyribonucleic acid (DNA)
• The genetic material found within the cell’s nucleus
• Provides instructions for every protein in the body
• Organized by complimentary bases to form a double-
stranded helix
• Contains the sugar deoxyribose and the bases adenine,
thymine, cytosine, and guanine
• Replicates before cell division
 Hydrogen bond

Deoxyribose
sugar
Phosphate

(d) Diagram of a DNA molecule

KEY:
Thymine (T) Cytosine (C)
Adenine (A) Guanine (G)
Figure 2.21c-d
Nucleic Acids
• Ribonucleic acid (RNA)
• Carries out DNA’s instructions for protein synthesis
• Created from a template of DNA
• Organized by complimentary bases to form a single-
stranded helix
• Contains the sugar ribose and the bases adenine,
uracil, cytosine, and guanine
• Three varieties are messenger, transfer, and ribosomal
RNA
Important Organic Compounds
• Adenosine triphosphate (ATP)
• Composed of a nucleotide built from ribose sugar, adenine base, and
three phosphate groups
• Chemical energy used by all cells
• Energy is released by breaking high energy phosphate bond
• ATP is replenished by oxidation of food fuels
 Adenine

High
energy
bonds

Ribose
Phosphates

(a) Adenosine triphosphate (ATP)

Adenosine diphosphate
(ADP)

(b) Hydrolysis of ATP

Figure 2.22a-b
(a) Chemical work. ATP provides the
energy needed to drive energy-
absorbing chemical reactions.

Solute

Membrane
protein
(b) Transport work. ATP drives the
transport of certain solutes (amino
acids, for example) across cell
membranes.

Relaxed Contracted
smooth smooth
muscle cell muscle cell
(c) Mechanical work. ATP activates
contractile proteins in muscle cells
so that the cells can shorten and
perform mechanical work.
Figure 2.23a-c