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CHAPTER 2: THE
CHEMICAL LEVEL OF
ORGANIZATION
Bio 137 Anatomy & Physiology I
Why study Chemistry in A & P?
• Cellular functions are due to chemical changes in
the body
• Metabolism of nutrients
• Changes in the amount of water and salt in the body’s
fluids
How Matter is Organized
• All forms of matter are composed of chemical elements
which are substances that cannot be split into simpler
substances by ordinary chemical means.
• Elements are given letter abbreviations called chemical symbols.
Elements
• Bulk elements – required by the body in large amounts
• O, C, H, N make up 95% of body weight
• Trace elements – required by the body in small amounts
• Hormone production, enzyme activity, protein production, found in
vitamins
Atomic Structure
• Elements are composed of atoms
• Atom – smallest unit of matter that retains the properties
of an element
• C = 1 atom of the element Carbon
• H2 = ______________________
Subatomic Particles
• Atoms are composed of
subatomic particles
• Protons and neutrons are
located in the atomic
nucleus
• Electrons revolve around
this nucleus
Subatomic Particles
• Protons have a +1 charge and a mass of 1
• Neutrons have no charge and a mass of 1
• Electrons have a negative charge, negligible mass
Isotopes
• All atoms of a particular element have the same atomic number
(proton number) but may have different neutron numbers and
atomic weights
• These are called Isotopes
• Oxygen
• Atomic number = 8
• Atomic weight = 15.99
• Isotopes of oxygen include O16, O17 and O18
• Atomic weight in periodic table is an average of the weight of the
isotopes of an element
• Elements in nature exist as a mixture of isotopes!!
Radioactive Isotopes
• Isotopes whose nucleus decays spontaneously,
releasing subatomic particles and energy
(radioactive decay)
• Includes O, I, Fe, P and Co
• Uses:
• To detect and treat disease
• Metabolic labeling of structures in a cell
• Dating of fossils
• Determining rate of DNA synthesis
Rules of Atomic Structure
• Proton number is always equal to the electron number in
an atom
• Therefore, the charge of an atom is zero
• ATOMS ARE NEUTRAL IN CHARGE
Atomic Number
• Equal to the proton number
• All atoms of an element have the same atomic
number
• What is the atomic # of He?
• P?
• C?
• Ar?
• How many electrons does each have?
Periodic Table Problems
• Locate nitrogen on the periodic table.
• What is its atomic number?
• What is its atomic weight?
• Proton #?
• Electron #?
Periodic Table Problems
• Locate chlorine on the periodic table.
• What is its atomic number?
• What is its atomic weight?
• Proton #?
• Electron #?
Molecules
• Particle formed when 2 or more atoms combine
• H2 → H-H
• O2 → O=O
• Molecular formula depicts #’s and kinds of atoms in a
molecule
• H 2O
• C6H12O6
Energy Levels of Electrons
• Electrons revolve around the atomic nucleus in shells
• Each shell can hold a limited number of electrons
• 1st shell holds only 2 electrons
• 2nd and 3rd shells hold up to 8 electrons
Electrons
• What is the electron shell diagram for oxygen?
• First determine proton number.
• Then determine electron number.
• Next, draw electron shell diagram.
What is the electron shell diagram for
neon?
Electrons
• If the outermost electron shell is full, the atom is stable and will
not react with other atoms
• Inert
• If the outer shell is NOT full, the atom can react with other atoms
• *Can gain or lose electrons to have a full shell*
• Valence Electrons - Electrons found in the outer shell that
determine an atom’s chemical behavior
• Unpaired valence electrons are involved in chemical bonding
• Electrons can be transferred or shared
Chemical Bonds
• Forces that hold together atoms
• Occurs due to the interaction of unpaired valence
electrons
• Atoms can gain or lose electrons to obtain a full shell
• Electrons can be transferred or shared
• The goal is to have a filled outer shells and no overall
charge
• Ex: If have 7 valence electrons, easier to gain 1
electron than give up 7
Unpaired Valence Electrons
• How many unpaired valence electrons does an
atom of carbon have? ________
• How many unpaired valence electrons does an
atom of chlorine have? _________
• Valence electrons determine how an atom can
bond to another atom
Types of Chemical Bonds
1.
Ionic Bond
2.
Hydrogen Bond
3.
Covalent Bond
1.
Polar Covalent
2.
Non-Polar Covalent
Formation of Ions
• Atoms are electrically neutral, no charge
• Proton # = electron #
• If an atom gains or loses an electron to form a chemical
bond:
• Becomes electrically charged
• Is called an ion
• Electron # > proton # = ______ charge
• Electron # < proton # = ______ charge
Ions
• The atomic number of sodium is 11.
• Draw an electron shell diagram for sodium.
• Sodium tends to lose/gain an electron?
• Draw an atom of chlorine.
• How do you think it will react with another atom?
Ions
• Anion
• Negatively charged ion
• More _________ than __________
• Cation
• Positively charged ion
• More _________ than __________
Ionic Bond
• Ions of opposite charge attract to form Ionic Bonds
• Weak bonds that are easily broken
• Forms salts: NaCl, KCl
2
1
+
Na
Na
Sodium atom
(an uncharged
atom)
Cl
Cl
Chlorine atom
(an uncharged
atom)
Na
Na+
Sodium on
(a cation)
–
Cl
Cl–
Chloride ion
(an anion)
Sodium chloride (NaCl)
Hydrogen Bond
• Bond between a hydrogen atom of one compound
and a more electronegative atom (usually O or N)
• Electronegativity - Attraction of one atom of a molecule for
the electrons in a covalent bond
• Easily broken and reformed
• Very important biologically
• Holds Water molecules together
• Strands of the DNA double helix
• Protein folding
Water
• 1 water molecule binds to
another through a
hydrogen bond
Covalent Bond
• Bond formed when atoms SHARE valence electrons
• Very strong, not readily broken
• These bonds hold the human body together
Nonpolar Covalent Bonds
• If the attraction for electrons is equal, it is a non-polar
covalent bond and electrons are shared equally
•
H-H
•
O=O
Polar Covalent Bonds
• If the attraction for electrons is unequal, a polar covalent
bond is formed and electrons are not shared equally
• Results in an unequal distribution of charge
•
H-O-H
d–
O
d+
H
H
H2O
d+
Chemical Bonds Review
• 1 single water molecule?
• Bathtub full of water?
• Equal share of electrons?
• Unequal share of electrons?
• Ions of opposite charge?
• Hydrogen atom of one compound and an electronegative
atom?
Chemical Reactions
• Chemical reactions form or break chemical bonds
between atoms, ions, or molecules
• Reactants are starting materials changed by the chemical
reaction
• Products are atoms, ions or molecules formed at the end
of the chemical reaction
NaCl → Na+ + Cl-
Reactant
Products
Chemical Reactions
• An exergonic reaction releases energy (usually in the form
of heat during catabolism of food) by breaking a bond with
more energy than the one being formed.
• An endergonic reaction requires that energy be added,
usually from a molecule called ATP, to form a bond.
Types of Chemical Reactions
• Synthesis - Anabolism
• Chemical bonds are formed between 2 or more atoms, ions or
molecules
• Endergonic
• Decomposition - Catabolism
• Bonds are broken to form simpler molecules, atoms or ions
• Exergonic
Chemical Reactions
• Types of chemical reactions can be broadly classified as:
• Synthesis reactions – Anabolism
• A + B ➙ AB
• Building a protein from amino acids
• Decomposition reactions – Catabolism
• AB ➙ A + B
• Breakdown of glycogen into glucose molecules
• Exchange reactions
• AB + CD ➙ AD + CB
• Reversible reactions
• AC ↔ A + C
Types of Compounds in Living Matter
Organic molecules
• contain C and H
• usually larger than inorganic molecules
• carbohydrates, proteins, lipids, and nucleic acids
Inorganic molecules
• generally do not contain C (except CO2)
• usually smaller than organic molecules
• usually dissolve in water or react with water to release
ions (electrolytes)
• water, carbon dioxide, oxygen, inorganic salts
Inorganic Substances: Salts
• Electrolytes
• Substances that release ions when dissolved in water
• Includes molecules held together by ionic bonds
• Salts are electrolytes
• NaCl, HCl
• NaCl → Na+ + Cl-
Inorganic Salts: Electrolytes
• Abundant in body fluids
• sources of necessary ions (Na+, Cl- , K+, Ca++, etc.) that
play important roles in metabolic processes
• Maintain fluid balance, pH, muscle contraction, nerve impulse
conduction
• Electrolyte concentrations must be maintained within
relatively narrow limits
• Electrolyte balance
Beneficial Properties of Water
• Polar covalent molecule
• Major component of all body cells (70%)
• Excellent solvent (important role in transporting chemicals)
• Provides medium site for most metabolic reactions
(dehydration vs. hydrolysis)
• Excellent temperature buffer
• Provides an excellent cooling mechanism
• Major component of mucus and other lubricating fluids
Water Dissociation
• Dissociation of water molecules leads to acidic and
basic conditions that affect living organisms and
chemical reactions
• Dissociates into a hydroxide ion and a hydrogen ion
H2O ↔ H+ + OHHydrogen Hydroxide
ion
ion
• Hydrogen and hydroxide ions are very reactive
Acids and Bases
• Acid
• Electrolytes that release hydrogen ions into water
• HCl → H+ + Cl-
• Base
• Any substance that reduces the hydrogen ion
concentration of a solution
• Donates hydroxide ions in water or accepts H+
• NaOH → Na+ + OH• HCO3- + H+ → H2CO3
The pH Scale
• pH of a solution is determined by the relative
concentration of hydrogen ions
• [H+] denotes concentration in molarity (M)
• Acidic – pH less than 7
• Greater concentration of H+ ions
• Basic – pH greater than 7
• More concentration of OH- ions and less concentration
of H+ ions
• Neutral – pH of 7
• Equal concentrations of H+ and OH-
pH Values
Buffering Systems
• Buffer
• Substance that minimizes a change in pH
• Function by donating H+ when needed and accepting H+
when in excess
Carbonic Acid Buffering System
• Maintains blood pH around 7.4
• CO2 + H2O ↔ H2CO3 ↔ HCO3- + H+
• We will discuss this extensively in the Respiratory
System!!
Inorganic Molecules
• Carbon Dioxide
• Waste product of metabolism
• Reacts with water to form carbonic acid
• Is removed from the body via respiration
• Oxygen
• Necessary for efficient breakdown of nutrients (cellular respiration)
Organic Molecules
• Contain C, H and O
• Includes the macromolecules:
• Carbohydrates
• Lipids
• Proteins
• Nucleic acids
• Very important in biology
• Used for energy, structural material, basis of hereditary
information
Carbohydrates
• Composed of C, H & O in a defined relationship
• (CH2O) – some multiple of this
• Monosaccharides - Simple sugars
• Disaccharides - 2 monosaccharides joined through
dehydration synthesis
• Polysaccharides
• Hundreds to thousands of monosaccharides joined together
• *Serve as a source of energy and as structural
materials
Monosaccharides

Simple sugars
 Can be used for fuel
 Can be converted into other organic molecules

Includes Ribose, deoxyribose, glucose, fructose &
galactose
Glucose
• Serves as the energy molecule for eukaryotes
• Breakdown produces ATP through cellular respiration
• C6H12O6 + 6O2 → 6CO2 + 6H2O + 38 ATP
• ATP is used as the energy molecule to drive other reactions in a
cell
Disaccharides
• 2 monosaccharides joined together through
dehydration
• Sucrose (table sugar), lactose (milk sugar),
maltose
Polysaccharides
• Hundreds to thousands of monosaccharides joined
together
• Starch, glycogen, cellulose
Polysaccharides
• Glycogen – sugar
storage form in humans
• Liver and skeletal muscle
• Polymer of glucose
• Glycogen stores can be
depleted in one day
• Glycogenolysis
Lipids
• Long hydrocarbon (C-H) chains
• Insoluble in water
• Non-Polar (Hydrophobic)
• Includes Fats, phospholipids and steroids
• Important as energy stores, constituent of cell
membranes
Triglycerides: Fats
• Composed of a glycerol (polar) head and 3 fatty acid
tails
• Fatty acid (FA)– large C chain ending in a carboxyl
group
• Vary in # of C’s and presence of double bonds
• Glycerol – 3 Carbon alcohol, FA attached to each C
• FA attached to glycerol can vary
Fats
• Saturated fat
• long hydrocarbon chain with no double bonds in the fatty acid
• Animal fats, molecules pack tight together
• Unsaturated fat
• 1 or more double bonds between C atoms in the fatty acid chain
• Plant and fish oils, can not pack tight together
• What is a Hydrogenated fat?
Phospholipids

Main component of eukaryotic cell
membranes
• Composed of a glycerol
head and 2 fatty acid tails
• 3rd C attached to a phosphate
group
Phospholipid Structure
• Consists of a hydrophilic “head” and 2 hydrophobic “tails”

Forms a Phospholipid bilayer that excludes water

Main component of eukaryotic cell membranes
Steroids
• C skeleton of 4 fused
rings
• Are derived from
cholesterol
• Also present in cell
membranes
• Sex hormones
• Adrenal hormones
Nucleic Acids
• Store hereditary information that is used to direct
protein synthesis
• Includes DNA and RNA
• Building blocks are nucleotides
• Sugar, phosphate and nitrogenous base
DNA
• Deoxyribonucleic Acid
• Deoxyribose (5C) sugar
• Sugar phosphate backbone with bases attached to the sugar
• Forms a double helix
• 4 nitrogenous bases
• Adenine
Thymine
• Guanine
Cytosine
DNA
• A binds T on the opposite strand
• C binds G on the opposite strand
• Hydrogen bonds between bases of the strands
• Stores hereditary information to direct protein synthesis
• Found in our chromosomes
DNA
5 end
O
OH
Hydrogen bond
P
–O
3 end
OH
O
O
A
T
O
–O
O
O
P
O
O
H2C
O
G
O
C
O
O
CH2
O
O
O–
P
H2C
O
O
C
O
G
O
O
O
CH2
P
O
O
H2C
O
O
A
O
O
CH2
O
O
(b) Partial chemical structure
O–
P
T
OH
3 end
Figure 16.7b
O–
P
O
O
P
–O
–O
CH2
O–
P
O
5 end
2-30
DNA Double Helix
5’ end
3’ end
Sugar-phosphate
backbone
Base pair (joined by
hydrogen bonding)
Old strands
A 3’ end
Nucleotide
about to be
added to a
new strand
5’ end
3’ end
Figure 5.27
5’ end
New
strands
3’ end
Gene
• A gene is a sequence of DNA nucleotides that contains
the information to make a protein
• DNA
RNA
Protein
RNA
• Ribonucleic acid
• Ribose sugar, nitrogenous base, phosphate
• Single stranded
• RNA sequence is read from DNA sequence
• Bases:
• Adenine
• Guanine
Uracil
Cytosine
• RNA sequence contains information to build amino acid
sequence
Proteins
• Account for >50% of the dry mass of most cells
• Have numerous functions important to cells
• Are composed of amino acids joined by a peptide bond
• 20 different amino acids
exist
Four Levels of Protein Structure
• Primary
• Secondary
• Tertiary
• Quaternary
• Structural levels result in a protein’s conformation (3-dimensional
shape), which determines how it functions
Protein Functions
• Enzymes
• Structural molecules
• Defense molecules (antibodies)
• Storage (ovalbumin)
• Transport (hemoglobin)
• Communication (receptor molecules)
• Movement (actin and myosin)
• Hormone gene product (insulin)
Protein Denaturation
• Extreme conditions can cause proteins to denature
• Loss of 3-dimensional shape
• Extreme pH values
• Extreme temperatures
• Harsh chemicals
• High Salt concentrations
• Perms, cooked egg white