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The Chemical Level
of Organization
PowerPoint® Lecture Slide Presentation prepared by
Dr. Kathleen A. Ireland, Biology Instructor, Seabury Hall, Maui, Hawaii
Learning Objectives
• Describe an atom and compare the ways atoms
combine to form molecules.
• Distinguish among the types of chemical reactions
that are important to physiology.
• Describe the role of enzymes in metabolism.
• Distinguish between organic and inorganic
compounds.
• Explain the importance of water, pH and buffers to
living systems.
• Discuss the structures and functions of
carbohydrates, lipids, proteins, nucleic acids and
high energy compounds.
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SECTION 2-1
Atoms, Molecules and Bonds
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Atoms are the smallest stable units of matter
• Subatomic particles
• Protons = positive charge; weight of
approximately 1 Dalton
• Neutrons = no charge; weight similar to protons
• Electrons = negative charge; weigh 1/1836th
Dalton
• Protons and neutrons are found in the nucleus;
electrons occupy electron cloud
• Atomic number = proton number; atomic mass =
protons and neutrons
• Isotopes are elements with similar numbers of
protons but different numbers of neutron
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Figure 2.1 Hydrogen Atoms
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Figure 2.1
Electrons occupy a series of energy levels or
electron shells.
• The outermost electron shell determines the
reactivity of the element.
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Figure 2.2 Atoms and Energy Levels
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Figure 2.2
Atoms combine through chemical reactions
• Molecule = a chemical structure consisting of
molecules held together by covalent bonds
• Compound = a chemical substance composed of
atoms of two or more elements
• There are three types of bond: Ionic, covalent,
and hydrogen
• Ionic = attraction between positive cations and
negative anions
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Figure 2.3 Ionic Bonding
PLAY
Animation: Formation of Ions
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Figure 2.3
Covalent bonds exist between atoms that share
electrons to form a molecule
• Double covalent bond
• Non-polar covalent bond
• Polar covalent bond
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Figure 2.4a, b
Hydrogen bonds are weak forces that affect the
shape and properties of compounds
• Polar covalent bonds that occur when hydrogen
covalently bonds with another element
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Figure 2.5 Polar Covalent Bonds and the
Structure of Water
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Figure 2.5
Figure 2.6 Hydrogen Bonds
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Figure 2.6
Matter and chemical notation
• Matter can exist as a solid, liquid or gas
• Depends on the interaction of the component
atoms or molecules
• Molecular weight is the sum of the atomic
weights of the component atoms
• Chemical notation
• Short-hand that describes chemical
compounds and reactions
• See table 2.2 for examples of chemical notation
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SECTION 2-2
Chemical Reactions
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A chemical reaction occurs when reactants
combine to generate one or more products
• All chemical reactions in the body constitutes
metabolism
• Metabolism provides for the capture, storage and
release of energy
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Basic energy concepts
• Work = movement of an object or change in its
physical structure
• Energy = the capacity to perform work
• Kinetic energy is energy of motion
• Potential energy is stored energy resulting from
position or structure
• Conversions are not 100% efficient, resulting
in release of heat
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Metabolism
• Types of reaction
• Decomposition
• Synthesis
• Exchange
• Metabolism is the sum of all reactions
• Through catabolism cells gain energy (break
down of complex molecules)
• Anabolism uses energy (synthesis of new
molecules)
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Reversible reactions
• All reactions are theoretically reversible
• At equilibrium the rates of two opposing
reactions are in balance
• Anabolism = catabolism
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Enzymes, energy and chemical reactions
• Activation energy is the amount of energy needed
to begin a reaction
• Enzymes are catalysts
• Reduce energy of activation without being
permanently changed or used up
• Promote chemical reactions
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Figure 2.7 Enzymes and Activation Energy
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Figure 2.7
SECTION 2-3
Inorganic Compounds
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Nutrients and Metabolites
• Nutrients are essential chemical compounds
obtained from the diet
• Metabolites are molecules synthesized or broken
down inside the body
• These can be classified as organic or inorganic
compounds
• Organic compounds have carbon and hydrogen
as their primary structural component
• Inorganic compounds are not primarily carbon
and hydrogen
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Water and its properties
• Water is the most important constituent of the
body
• Solution is a uniform mixture of two or more
substances
• Solvent is the medium in which molecules of
solute are dispersed
• Water is the solvent in aqueous solutions
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Figure 2.8 Water molecules and solutions
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Figure 2.8
Electrolytes undergo ionization
• Compounds that interact readily with water are
hydrophilic
• Compounds that do not interact with water are
hydrophobic
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pH is a measure of the concentration of hydrogen
ions solution
• Neutral
• Acidic
• Basic
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Acids and Bases
• Acids release hydrogen ions into solution
• Bases remove hydrogen ions from solution
• Strong acids and strong bases ionize
completely
• Weak acids and weak bases do not ionize
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Figure 2.9 pH and Hydrogen Ion Concentration
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Figure 2.9
Salts and buffers
• Salt = an electrolyte whose cation is not hydrogen
and whose anion is not hydroxide
• Buffers remove or replace hydrogen ions in
solution
• Buffer systems maintain the pH of body fluids
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SECTION 2-4
Organic Compounds
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Organic compounds
• Organic compounds generally include
• Carbon
• Hydrogen
• and sometimes Oxygen
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Organic compounds
• Four major classes of organic compounds are
• Carbohydrates
• Lipids
• Proteins
• Nucleic acids
• High energy compounds are also organic
compounds
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Carbohydrates
• Important energy source for metabolism
• Monosaccharides, disaccharides and
polysaccharides
• Di- and polysaccharides formed from
monosaccharides by dehydration synthesis
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Figure 2.10c
Figure 2.11 The Formation and Breakdown of
Complex Sugars
PLAY
Animation: The formation and breakdown of complex sugars
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Figure 2.11
Figure 2.12 The Structure of a Polysaccharide
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Figure 2.12
Lipids include fats, oils, and waxes
• Five classes:
• Fatty acids
• Eicosanoids
• Glycerides
• Steroids
• Phospholipids
• Glycolipids
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Figure 2.13 Fatty acids
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Figure 2.13
Figure 2.15 Triglyceride Formation
• Triglycerides =
three fatty acids
attached by
dehydration
synthesis to one
molecule of
glycerol
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Figure 2.15
Steroids
• Are involved in cell membrane structure
• Include sex hormones and hormones regulating
metabolism
• Are important in lipid digestion
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Figure 2.16 Steroids
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Figure 2.16
Proteins perform many vital functions in the
body. The six important types are:
• Structural proteins
• Contractile proteins
• Transport proteins
• Enzymes
• Buffering proteins
• Antibodies
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Proteins are chains of amino acids
• Amino acids contain an amino group, a
carboxylic group and a radical group
• Polypeptides are linear sequences of amino acids
held together by peptide bonds
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Figure 2.18 Amino Acids
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Figure 2.18
Figure 2.19 Peptide Bonds
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Figure 2.19
The four levels of protein structure are:
• Primary structure (amino acids sequence)
• Secondary structure (amino acid interactions)
• Tertiary structure (complex folding)
• Quaternary structure (protein complexes)
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Figure 2.20 Protein Structure
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Figure 2.20
Enzyme reactions
• Reactants (substrate) interact to yield a product
by binding to the active site of the enzyme
• Cofactors must bond to the enzyme before
substrate binding can occur
• Coenzymes are organic cofactors commonly
derived from vitamins
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Figure 2.21 A simplified view of enzyme
structure and function
PLAY
Animation: Enzyme structure and function
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Figure 2.21
The shape of a protein determines its function
• Proteins pushed outside their optimal
temperature and pH range become temporarily
or permanently denatured and will cease to
function
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Nucleic acids
• Store and process information at the molecular
level
• Made of purines and pyrimidines
• DNA and RNA
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Figure 2.22 Purines and Pyrimidines
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Figure 2.22
Figure 2.23 Nucleic Acids: RNA and DNA
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Figure 2.23
Nucleic acids are chains of nucleotides
• Nucleotides are composed of a sugar, a phosphate
and a nitrogenous base
• Sugar = deoxyribose (DNA) or ribose (RNA)
• DNA Bases = adenine, thymine, cytosine,
guanine
• RNA bases = adenine, uracil, cytosine, guanine
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High energy compounds store cellular energy in
high energy bonds
• Adenosine triphosphate (ATP)
• Made by adding a phosphate group to
adenosine diphosphate (ADP)
• Process referred to as phosphorylation
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SECTION 2-5
Chemicals and Cells
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Biochemical compounds form functional units
called cells
• Metabolic turnover allows cells to change and to
adapt to changes in their environment
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You should now be familiar with:
• Atoms and how they combine to form
compounds.
• Chemical reactions and enzymes.
• Organic and inorganic compounds.
• Water, pH, and buffers.
• The structure and function of carbohydrates,
lipids, proteins, nucleic acids and high energy
compounds.
Copyright © 2004 Pearson Education, Inc., publishing as Benjamin Cummings