Download CHAPTER 1 THE MAIN THEMES OF MICROBIOLOGY

CHAPTER 2 THE CHEMISTRY OF BIOLOGY
Chemistry is introduced in this chapter. Matter, atoms, elements, and molecules are
defined. Chemical bonds are discussed in terms of their strength and formation, and the
concept of polar versus nonpolar compounds is highlighted. Chemical reactions, such as
oxidation-reduction and ionization, are examined in terms of their importance in cellular
metabolism. The structures of proteins, fats, carbohydrates, and lipids are elucidated.
Finally, the idea that the structure of macromolecules determines their properties is
discussed.
Learning Objectives
A student should learn the following concepts:
1. Materials that occupy space and have mass are called matter.
2. The organization of matter begins with the atom which is a combination of
protons (positive charge), neutrons (no charge), and electrons (negative charge).
3. An element is made up of only one kind of atom.
4. The properties of each element results from the numbers of protons, neutrons, and
electrons it contains.
5. The number of electrons in an element’s outermost orbital determines its chemical
properties and reactivity.
6. Most elements exist as molecules or compounds, which consist of atoms joined
by chemical bonds.
7. Chemical bonds result when two or more atoms share electrons (covalent bonds),
donate electrons (ionic bonds), or accept electrons (ionic bonds) between their
outer orbitals.
8. When electrons are not shared equally between atoms, an unequal distribution of
charges will result, and the molecule/compound is called polar (having a positive
pole and a negative pole).
9. When electrons are equally shared between atoms, an equal distribution of
charges will result, and the molecule/compound is called nonpolar (electrically
neutral).
10. Hydrogen bonding and Van der Waals forces are due to attractive forces between
nearby molecules and atoms.
11. Cells derive their energy from chemical reactions, by moving electrons from
molecule to molecule.
12. Substances entering a reaction are reactants, while substances left after a reaction
is complete are called products.
13. Reactions can involve the synthesis of substances, the decomposition of
substances, or the exchange of portions between substances.
14. Polar molecules that attract water to their surface are called hydrophilic, while
nonpolar molecules that repel water are called hydrophobic.
15. In pure water H+ and OH- are produced in equal amounts.
16. In an acidic solution the H+ ions outnumber the OH- ions.
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17. In a basic solution the OH- ions outnumber the H+ ions.
18. Inorganic chemicals do not contain both carbon and hydrogen.
19. Organic chemicals contain both carbon and hydrogen.
20. Carbohydrates, lipids, proteins, and nucleic acids consist of monomers bound
together in various lengths to form polymers.
21. Carbohydrates (made of monomers of monosaccharides) contain carbon,
hydrogen, and oxygen.
22. Lipids contain long carbon-hydrogen chains that are nonpolar or hydrophobic.
23. Phospholipids are unique in that they contain a polar region and a nonpolar
region.
24. The structure, behavior, and unique qualities of living things are a consequence of
their proteins (made of monomers of amino acids joined by peptide bonds).
25. Proteins contain up to four levels of structure, and the structure of a protein is
critical for its function.
26. Nucleic acids (DNA and RNA) consist of monomers of nucleotides.
27. DNA is the hereditary material in cells.
28. RNA is involved in protein synthesis.
Chapter Outline (also see Chapter Summary with Key Terms p. 53)
2.1
Atoms, Bonds, and Molecules: Fundamental Building Blocks
 Introduction
o Matter Is Made Up of Atoms
o Atoms Consist of:
 Protons
 Neutrons
 Electrons
 Different Types of Atoms: Elements and Their Properties
 The Major Elements of Life and Their Primary Characteristics
o Atomic Number, Mass Number, Isotopes, and Atomic Mass or Weight
o Electron Orbitals and Shells
o A Note About Mass, Weight, and Related Terms
 Bonds and Molecules
o Molecules, Compounds, and Valence
o Covalent Bonds: Molecules with Shared Electrons
 A Note about Diatomic Elements
 Polarity in Molecules
 Polar
 Nonpolar
o Ionic Bonds: Electron Transfer among Atoms
o Ionization: Formation of Charged Particles
o Hydrogen Bonding
o Electron Transfer and Oxidation-Reduction Reactions
o Chemical Shorthand: Formulas, Models, and Equations
 Reactants
Chapter 2 – The Chemistry of Biology
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2.2
 Products
 Chemical Equation
 Synthesis Reaction
 Decomposition Reactions
 Catalysts
Solutions: Homogeneous Mixtures of Molecules
o Solutes
o Solvents
o Concentration
o Hydrophilic
o Hydrophobic
o Amphipathic
o Molarity
Acidity, Alkalinity, and the pH Scale
o Acidic
o Basic
o pH Scale
o Neutralization Reactions
o Metabolism
The Chemistry of Carbon and Organic Compounds
o Inorganic Chemicals
o Organic Chemicals
Functional Groups of Organic Compounds
Macromolecules: Superstructures of Life
 Biochemistry: The Compounds of Life
o Macromolecules
o Monomers
o Polymers
 Carbohydrates: Sugars and Polysaccharides
o Introduction
 Aldehydes
 Ketones
 Saccharide
 Monosaccharide
 Disaccharide
 Polysaccharide
o The Nature of Carbohydrate Bonds
 Glycosidic Bonds
 Dehydration Synthesis
o The Functions of Carbohydrates in Cells
 Cellulose
 Agar
 Chitin
 Peptigolycan
 Lipopolysaccharide
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Chapter 2 – The Chemistry of Biology
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 Glycocalyx
 Starch
 Glycogen
Lipids: Fats, Phospholipids, and Waxes
o Storage Lipids
 Triglycerides
 Glycerol
 Fatty Acids
 Ester Bond
o Membrane Lipids
 Phospholipids
o A Note about Membranes
o Miscellaneous Lipids
 Steroids
 Cholesterol
 Ergosterol
 Prostaglandins
Proteins: Shapers of Life
o Proteins
 Amino Acids
 Peptide Bond
 Peptide
 Polypeptide
o Protein Structure and Diversity
 Primary Structure: Chain of Amino Acids
 Secondary Structure: Alpha Helix or Beta-Pleated Sheet
 Tertiary Structure: Bonds Between Functional Groups
 Quaternary Structure: Two or More Polypeptides
 Examples of Proteins:
 Enzymes
 Antibodies
 Receptors
The Nucleic Acids: A Cell Computer and Its Programs
o Deoxyribonucleic Acid (DNA)
o Ribonucleic Acid (RNA)
o Nucleic Acids Are Made of Nucleotides, Which Contain:
 A Nitrogen Base
 A Pentose Sugar
 A Phosphate
The Double Helix of DNA
o Making New DNA: Passing on the Genetic Message
 Replication
o RNA: Organizers of Protein Synthesis
 Messenger RNA
 Transfer RNA
 Ribosomal RNA
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Chapter 2 – The Chemistry of Biology
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o ATP: The Energy Molecule of Cells
Student Activities
1. After covering the section on Protein Structure and Diversity (p. 48), and
discussing the primary, secondary, tertiary, and quaternary structures of proteins,
have students research diseases which have been attributed to improperly folded
proteins. The list will vary but should include Alzheimer’s disease, cystic fibrosis,
cancer, Creutzfeldt-Jakob disease (CJD), and diabetes.
2. Visualizing molecules, compounds, and macromolecules is often difficult for
students, particularly when they always see the structures on a flat sheet of paper.
Use molecular model kits (most likely available in your chemistry department) to
build methane, a polysaccharide, and lipids. These kits can also be used to
demonstrate the formation of covalent bonds. To do this, first construct two
separate monosaccharides (monomers), then remove an OH group from one
monomer and an H group from the other monomer, join them together—thus
performing dehydration synthesis (see pp. 42-43).
3. Bring two see-through bottles with lids, water, salt, and cooking oil to class. Fill
both the bottles ¾ full with water, then add some oil to one bottle and some salt to
the other. Have students shake the bottles, then discuss the concept of hydrophilic
versus hydrophobic as the salt dissolves in the water and the oil coalesces into
droplets.
4. Bring some pH paper, small paper cups, and ammonia (any household cleaner
with a basic pH will work) to class. As students enter the classroom have them
pour small amounts of their beverages (cola, flavored water, coffee) into the cups.
Determine the pH of the beverages and ammonia using the pH paper. Then place
their beverages and the cleaner onto the pH scale in Figure 2.13. Have them
determine the concentration of hydrogen ions in the beverages and the
concentration of hydrogen ions in the cleaner.
5. After discussing Figure 2.26 on DNA replication, have students visit the site
http://www.pbs.org/wgbh/aso/tryit/dna/# and click on the link “DNA workshop
activity.” After selecting replication, students will be led through the steps in
DNA replication (unzipping and matching the base pairs).
Classroom Discussion
1. Ask students the following question: changing the number of which subatomic
particle (proton, neutron, or electron) changes the element? Through answering
this question students will define isotopes and ions.
2. Students may have a pre-formed opinion of the definition of organic. Spend time
discussing the definition of organic as it relates to chemistry as opposed to the
definition of organic in terms of agriculture.
3. As you cover the periodic table (Figure 2.2), explain that the table is arranged
vertically according to the number of electrons present in the outer shell (except
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for helium). With this knowledge it is easy for students to determine the reactivity
of the different atoms (without having to draw out all the shells). Also, it is a good
way for students to check their models to make sure they have the proper number
of electrons present in the outer shell.
4. When lecturing on the various types of chemical bonds, have students discuss
which bonds they think would be the strongest. List the order of strength of the
bonds (covalent, ionic, hydrogen, and Van der Waals) and discuss how the
strength of the bond correlates with the structure of the bond. This discussion will
allow you to focus on the difference between sharing electrons and donating or
accepting electrons as opposed to electrostatic forces.
5. Show Figure 2.15 and discuss the fact that glucose, fructose, and galactose all
have the same chemical formula (C6H12O6). Then look at the structures of
maltose, sucrose, and lactose that also have the same chemical formulas, but have
different structures. The difference in their structures becomes readily apparent in
lactose intolerant individuals, who can digest sucrose but not lactose. This
discussion can also highlight the specificity of enzymes and proteins, and how the
structure of compounds influences their function.
Applicable Online Quizzes
www.mhhe.com/talaro7
Chapter 2 Multiple Choice Quiz
Protein Denaturation Quiz
Key Terms and Phrases
matter
atom
protons
neutrons
electrons
nucleus
elements
atomic number (AN)
mass number (MN)
isotopes
atomic mass/weight
orbitals
molecule
compounds
formula mass
molecular weight
chemical bonds
valence
covalent bonds
polar
nonpolar
ionic bonds
ionization
ions
cations
anions
electrolytes
hydrogen bond
Van der Waals forces
oxidation reaction
reduction reaction
redox reaction
reducing agent
oxidizing agent
products
reactants
synthesis reaction
catalyst
solution
solute
solvent
hydrated
hydrophilic
hydrophobic
amphipathic
concentration
hydrogen ion
hydroxide ion
Chapter 2 – The Chemistry of Biology
acidic
basic
pH
neutralization
metabolism
inorganic chemicals
organic chemicals
functional groups
biochemistry
macromolecules
monomers
polymers
carbohydrate
aldehydes
ketones
monosaccharide
disaccharide
polysaccharide
hexose
pentose
fructose
lactose
maltose
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sucrose
glycosidic bonds
dehydration synthesis
cellulose
agar
chitin
peptidoglycan
lipopolysaccharide
glycocalyx
starch
glycogen
hydrolysis
lipid
triglycerides
fatty acids
glycerol
ester bond
membrane lipids
phospholipids
cholesterol
proteins
amino acids
peptide bond
peptide
polypeptide
primary structure
secondary structure
tertiary structure
cysteine
quaternary structure
enzymes
antibodies
deoxyribonucleic acid
(DNA)
ribonucleic acid (RNA)
nucleotides
nitrogen base
adenine (A)
guanine (G)
thymine (T)
cytosine (C)
uracil (U)
replication
adenine triphosphate
(ATP)
electronegativity
Instructors are encouraged to visit the Foundations in Microbiology ARIS (Assessment,
Review, Instruction System) site at www.mhhe.com/talaro7 for animations of key
processes, online quizzing, case presentations, and more.