Foundations in Microbiology

Seventh Edition

Chapter 2

The Chemistry of Biology

Lecture PowerPoint to accompany

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2.1 Atoms, Bonds, and Molecules

• Matter - all materials that occupy space and have mass

• Matter is composed of atoms• Atom - simplest form of matter not divisible into

simpler substances– Protons: (+) subatomic particles– Neutrons: neutral subatomic particles– Electrons: (-) subatomic particles

Figure 2.1a Three-dimensional model

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Figure 2.1b Simple model

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Different Types of Atoms

• All atoms share the same fundamental structure• Element - pure substances with a characteristic

number of protons, neutrons, and electrons and predictable chemical behaviors

Table 2.1 The Major Elements of Life

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Characteristics of Elements

Atomic number – number of protons

Mass number – number of protons and neutrons

Isotopes – variant forms of the same element that differ in the number of neutrons

Atomic weight – average mass numbers of all isotopic forms

Electron orbitals – volumes of space surrounding the atomic nucleus where electrons are likely to be found

Figure 2.1 Models of atomic structure

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Figure 2.2 Biologically important atoms

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Bonds and Molecules

• Molecule - a chemical substance that results from the combination of two or more atoms

• Compounds - molecules that are combinations of two or more different elements

• Formula/Mass weight - sum of all of the atomic masses of the atoms a molecule contains

• Chemical bonds - when 2 or more atoms share, donate, or accept electrons to form molecules and compounds– 3 types: covalent, ionic, and hydrogen

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3 Types of Chemical Bonds

1. Covalent bonds – electrons are shared among atoms

– Polar covalent bonds – unequal sharing– Nonpolar covalent bonds – equal sharing

2. Ionic bonds – electrons are transferred to one atom forming positively charged cations and negatively charged anions

3. Hydrogen bonds – weak bonds between hydrogen and other atoms

Figure 2.3 Three types of bonds

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Figure 2.4 Covalent bonds

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Figure 2.5 Polar molecule

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Figure 2.6 Ionic bonding

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Figure 2.7 Ionization

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Figure 2.8 Hydrogen bonding

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Electron Transfer and Oxidation-Reduction Reactions

Energy exchange in cells is a result of the

movement of electrons from one molecule to

another.

Oxidation – the loss of electrons

Reduction – the gaining of electrons

Redox reactions – essential to biochemical processes

Figure 2.9 Oxidation-reduction reaction

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Chemical Shorthand

• Reactants - molecules starting a reaction

• Products - substances left by a reaction

• Synthesis reaction - the reactants bond together in a manner that produces an entirely new molecule

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S O2 SO2+

Figure 2.10 Molecular and Structural Formulas

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Solutions: Mixtures of Molecules

Solutes – Na+ & Cl-

Solvent – H2O

Solution – a mixture of one or more substances called solutes, dispersed in a dissolving medium called a solvent

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• Most biological activities occur in aqueous (water-based) solutions

• Hydrophilic molecules - dissolve in water

• Hydrophobic molecules - repel water

• Amphipathic molecules - have both hydrophilic and hydrophobic properties

Figure 2.12 Hydration spheres formed around ions

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Acidity, Alkalinity, and the pH Scale

•Ionization of H2O releases hydrogen ions [H+] and hydroxyl ions [OH-]•pH scale – ranges from 0 to 14, expresses the concentration of H+ ions

•pH is the negative logarithm of the concentration of H+ ions.

•pH 2 = 0.01 moles/L H+ ions•pH 14 = 0.00000000000001 moles/L H+ ions

Figure 2.13 The pH scale

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Table 2.2

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The Chemistry of Carbon and Organic Compounds

• Organic chemicals – compounds containing carbon bonded to hydrogens

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• Carbon is the fundamental element of life– Contains 4 atoms in its outer orbital– Can form single, double, or triple covalent bonds– Can form linear, branched, or ringed molecules

Figure 2.14 The versatility of bonding in carbon

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Functional Groups of Organic Compounds

• Accessory molecules that bind to organic compounds

• Confer unique reactive properties on the whole molecule

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2.2 Macromolecules

• Biochemicals are organic compounds produced by living things

• Macromolecules: large compounds assembled from smaller subunits– Monomer: a repeating subunit– Polymer: a chain of monomers

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Macromolecules1. Carbohydrates – monosaccharides, disaccharides,

polysaccharides

2. Lipids – triglycerides (fats and oils), phospholipids, steroids

3. Proteins 4. Nucleic acids – DNA, RNA

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Carbohydrates

• Sugars and polysaccharides• General formula (CH2O)n

• Aldehydes and ketones

• Saccharide: simple carbohydrate– Monosaccharide: 3-7 carbons– Disaccharide: two monosaccharides– Polysaccharide: five or more monosaccharides

Figure 2.15a Common classes of carbohydrates

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Figure 2.15b Common classes of carbohydrates

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Carbohydrates• Subunits linked by glycosidic bonds• Dehydration synthesis: loss of water in a

polymerization reaction

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Carbohydrates• Functions – cell structure, adhesion, and metabolism

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Lipids• Long or complex, hydrophobic, C - H chains

• Triglycerides, phospholipids in membranes, steroids like cholesterol

• Functions– Triglycerides – energy storage– Phospholipid – major cell membrane component– Steroids – cell membrane component

Figure 2.18b Triglycerides

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Figure 2.19 Phospholipids - membrane molecules

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Figure 2.20 Membrane

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Proteins

• Predominant molecules in cells

• Monomer – amino acids – 20

• Polymer – peptide, polypeptide, protein

• Subunits linked by peptide bonds

• Fold into very specific 3-D shapes

• Functions – support, enzymes, transport, defense, movement

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Figure 2.21 Formation of a peptide bond

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Nucleic Acids• DNA and RNA• Monomer – nucleotide• DNA – deoxyribonucleic acid

– A,T,C,G – nitrogen bases– Double helix – Function – hereditary material

• RNA – ribonucleic acid– A,U,C,G – nitrogen bases– Function – organize protein synthesis

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Figure 2.24 Sugars and nitrogen bases of DNA and RNA

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Double Helix of DNA

• DNA is formed by two very long polynucleotide strands linked along their length by hydrogen bonds

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Passing on the Genetic Message

• Each strand is copied• Replication is guided by

base pairing• End result is two

separate double strands

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ATP: The Energy Molecule of Cells• Adenosine triphosphate

– Nucleotide - adenine, ribose, three phosphates

• Function - transfer and storage of energy

Insert figure 2.27 aATP molecule