The Chemistry of Microbiology

The Chemistry of Microbiology 2

Atoms • Matter – anything that takes up space and has mass • Atoms – the smallest chemical units of matter

Atoms • Atomic Structure • Electrons – negatively charged subatomic particles circling a nucleus • Nucleus – structure containing neutrons and protons • Neutrons – uncharged particles • Protons – positively charged particles

Figure 2.1 An example of a Bohr model of atomic structure. Electron shells Proton (p+) Nucleus Neutron (n0) Electron (e–)

Atoms • Atomic Structure • Element – composed of a single type of atom • Atomic number – equal to the number of protons in the nucleus • Atomic mass (atomic weight) – sum of masses of protons, neutrons, and electrons

Atoms • Isotopes • Atoms of a given element that differ in the number of neutrons in their nuclei • Stable isotopes • Unstable isotopes • Radioactive isotopes • Release energy during radioactive decay

Figure 2.2 Nuclei of the three naturally occurring isotopes of carbon. Additional neutron Proton Neutron Carbon-12 6 Protons 6 Neutrons Carbon-13 6 Protons 7 Neutrons Carbon-14 6 Protons 8 Neutrons

Atoms • Electron Configurations • Only the electrons of atoms interact, so they determine atom's chemical behavior • Electrons occupy electron shells • Valence electrons – electrons in outermost shell that interact with other atoms

Figure 2.3 Electron configurations. = + + First shell Second shell Electron shells of neon: three-dimensional view + = Second shell First shell Electron shells of neon: two-dimensional view

Figure 2.4 Bohr diagrams of the first 20 elements and their places within the chart known as the periodic table of the elements.

Atoms • Tell Me Why • Electrons zip around the nucleus at about 5 million miles per hour. Why don't some fly off?

Chemical Bonds • Valence – combining capacity of an atom • Positive if atom has electrons to give up • Negative if atom has spaces to fill • Stable when outer electron shells contain eight electrons • Chemical bonds – atoms combine by sharing or transferring valence electrons • Molecule – two or more atoms held together by chemical bonds • Compound – a molecule composed of more than one element

Chemical Bonds • Covalent bond – sharing of a pair of electrons by two atoms • Electronegativity – attraction of atom for electrons • The more electronegative an atom, the greater the pull its nucleus exerts on electrons

Figure 2.6 Electronegativity values of selected elements.

Chemical Bonds • Nonpolar Covalent Bonds • Shared electrons spend equal amounts of time around each nucleus • Atoms with similar electronegativities • No poles exist • Carbon atoms form four nonpolar covalent bonds with other atoms • Organic compounds contain carbon and hydrogen atoms

Figure 2.5a-b Four molecules formed by covalent bonds.

Figure 2.5c-d Four molecules formed by covalent bonds.

Chemical Bonds • Polar Covalent Bonds • Unequal sharing of electrons due to significantly different electronegativities • Most important polar covalent bonds involve hydrogen • Allow for hydrogen bonding

Figure 2.7 Polar covalent bonding in a water molecule.

Chemical Bonds • Ionic Bonds • Occur when two atoms with vastly different electronegativities come together • Atoms have either positive (cation) or negative (anion) charges • Cations and anions attract each other and form ionic bonds (no electrons shared) • Typically form crystalline ionic compounds known as salts

Figure 2.8 The interaction of sodium and chlorine to form an ionic bond.

Figure 2.9 Dissociation of NaCI in water.

Chemical Bonds • Hydrogen Bonds • Electrical attraction between partially charged H+ and full or partial negative charge on same or different molecule • Weaker than covalent bonds but essential for life • Help to stabilize 3-D shapes of large molecules

Figure 2.10 Hydrogen bonds.

Chemical Bonds • Tell Me Why • Chlorine and potassium atoms form ionic bonds, carbon atoms form nonpolar covalent bonds with nitrogen atoms, and oxygen forms polar covalent bonds with phosphorus. Explain why these bonds are the types they are.

Chemical Reactions • The making or breaking of chemical bonds • Involve reactants and products • Biochemistry involves chemical reactions of living things

Chemical Reactions • Synthesis Reactions • Involve the formation of larger, more complex molecules • Require energy (endothermic) • Common type is dehydration synthesis • Water molecule formed • All the synthesis reactions in an organism are called anabolism

Figure 2.11a Two types of chemical reactions in living things.

Chemical Reactions • Decomposition Reactions • Break bonds within larger molecules to form smaller atoms, ions, and molecules • Release energy (exothermic) • Common type is hydrolysis • Ionic components of water are added to products • All the decomposition reactions in an organism are called catabolism

Figure 2.11b Two types of chemical reactions in living things.

Chemical Reactions • Exchange Reactions • Involve breaking and forming covalent bonds • Have endothermic and exothermic steps • Atoms are moved from one molecule to another • Sum of all chemical reactions in an organism is called metabolism

Chemical Reactions • Tell Me Why • Why are decomposition reactions exothermic (release energy)?

Water, Acids, Bases, and Salts • Water • Most abundant substance in organisms • Many special characteristics due to two polar covalent bonds • Cohesive molecules – surface tension • Excellent solvent • Remains liquid across wide range of temperatures • Can absorb significant amounts of energy without changing temperature • Participates in many chemical reactions

Figure 2.12 The cohesiveness of liquid water. Hydrogen bonds Aquarius remigis, a water strider

Water, Acids, Bases, and Salts • Acids and Bases • Dissociated by water into component cations and anions • Acid – dissociates into one or more H+ and one or more anions • Base – binds with H+ when dissolved into water; some dissociate into cations and OH– • Concentration of H+ in solution expressed using the pH scale • Metabolism requires relatively constant balance of acids and bases • Buffers prevent drastic changes in internal pH • Microorganisms differ in their tolerance of various pH ranges • Some microbes can change the pH of their environment

Figure 2.13 Acids and bases.

Figure 2.14 The pH scale.

Water, Acids, Bases, and Salts • Salts • Compounds that dissociate in water into cations and anions other than H+ and OH– • Cations and anions of salts are electrolytes • Create electrical differences between inside and outside of cell • Transfer electrons from one location to another • Form important components of many enzymes

Water, Acids, Bases, and Salts • Tell Me Why • Why does the neutralization of an acid by a base often produce water?

Organic Macromolecules • Functional Groups • Contain carbon and hydrogen atoms • Atoms often appear in arrangements called functional groups • Macromolecules – large molecules used by all organisms • Lipids • Carbohydrates • Proteins • Nucleic acids • Monomers – basic building blocks of macromolecules

Organic Macromolecules • Lipids • Not composed of regular subunits • Are all hydrophobic • Four groups • Fats • Phospholipids • Waxes • Steroids

Figure 2.15 Fats (triglycerides). 3 Ester bond Dehydration synthesis Glycerol 3 fatty acids Fat (triglyceride) + Saturated fatty acid Monounsaturated fatty acid

Figure 2.16 Phospholipids. Organic group Cell Unsaturated fatty acid Hydrophilic (polar) head Phosphate group Glycerol Symbol Phospholipid bilayer Hydrophobic (nonpolar) tails Double bond Saturated fatty acid Unsaturated fatty acid Phospholipid

Organic Macromolecules • Lipids • Waxes • Contain one long-chain fatty acid covalently linked to long-chain alcohol by ester bond • Lack hydrophilic head • Completely insoluble in water

Figure 2.17 Steroids. Phospholipids Cholesterol Cell membrane

Organic Macromolecules • Monomers are the basic building blocks of macromolecules • Monomers join to form chains called polymers

The Chemistry of Microbiology