Foundations in Microbiology Seventh Edition Lecture PowerPoint to accompany Foundations in Microbiology Seventh Edition Talaro Chapter 2 The Chemistry of Biology Copyright © The McGraw-Hill Companies, Inc. Permission required for reproduction or display.

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

Figure 2.1b Simple model

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

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

Figure 2.2 Biologically important atoms

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

3 Types of Chemical Bonds Covalent bonds – electrons are shared among atoms Polar covalent bonds – unequal sharing Nonpolar covalent bonds – equal sharing Ionic bonds – electrons are transferred to one atom forming positively charged cations and negatively charged anions Hydrogen bonds – weak bonds between hydrogen and other atoms

Figure 2.3 Three types of bonds

Figure 2.4 Covalent bonds

Figure 2.5 Polar molecule

Figure 2.6 Ionic bonding

Figure 2.7 Ionization

Figure 2.8 Hydrogen bonding

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

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 S + O2 SO2

Figure 2.10 Molecular and Structural Formulas

Solutions: Mixtures of Molecules Solution – a mixture of one or more substances called solutes, dispersed in a dissolving medium called a solvent Solutes – Na+ & Cl- Solvent – H2O

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

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

Table 2.2

The Chemistry of Carbon and Organic Compounds Organic chemicals – compounds containing carbon bonded to hydrogens

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

Functional Groups of Organic Compounds Accessory molecules that bind to organic compounds Confer unique reactive properties on the whole molecule

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

Macromolecules Carbohydrates – monosaccharides, disaccharides, polysaccharides Lipids – triglycerides (fats and oils), phospholipids, steroids Proteins Nucleic acids – DNA, RNA

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

Figure 2.15b Common classes of carbohydrates

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

Carbohydrates Functions – cell structure, adhesion, and metabolism

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

Figure 2.19 Phospholipids - membrane molecules

Figure 2.20 Membrane

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

Figure 2.21 Formation of a peptide bond

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

Figure 2.24 Sugars and nitrogen bases of DNA and RNA

Double Helix of DNA DNA is formed by two very long polynucleotide strands linked along their length by hydrogen bonds

Passing on the Genetic Message Each strand is copied Replication is guided by base pairing End result is two separate double strands

ATP: The Energy Molecule of Cells Adenosine triphosphate Nucleotide - adenine, ribose, three phosphates Function - transfer and storage of energy Insert figure 2.27 a ATP molecule