BIOLOGY 113 - MICROBIOLOGY Lecture 2: Chemical Principles - Bond types, reactions, organic compounds The discipline of microbiology addresses

the biology of a diverse group of organisms - All of these share the feature of lacking tissue organization (Tortora et al., Figure 1.1) = The bacteria are prokaryotes; that is, their genetic material is not enclosed in a nucleus; most bacteria possess a cell wall containing peptidoglycan = The archaea are a second group of prokaryotes; none of these are parasites of humans = Fungi are simple eukaryotes that obtain nutrition by absorption of dissolved nutrients from their environment = Protozoans are unicellular eukaryotes classified according to their means of locomotion = Algae are photosynthetic eukaryotic microorganisms = Viruses are unique in being noncellular; structurally, they consist of a nucleic acid genome encased in a capsid consisting of protein and (sometimes) lipid. Viral reproduction depends on the metabolism of an infected cell. Thus, all viruses are parasites - Note that size is not the common feature; there are many macroscopic fungi and certain marine algae (e.g., kelps) are among the largest known organisms. - Because of their medical importance as agents of infection, certain multicellular helminthes e.g., flatworms, roundworms) are included in the study of microbiology. These organisms are not microorganisms in the strict sense, since they do possess organized tissues. Fundamental properties of matter - Organization of atoms (Tortora et al. Fig 2.1) = Protons, neutrons, electrons = In uncharged atoms, electrons balance protons = Electrons are organized into orbitals; the reactivity of an atom often depends on distribution of electrons in "outer shells" - Elements = All atoms of an element contain the same number of protons, which gives the atomic number = The atomic weight depends on number of protons plus neutrons; the term isotope refers to atoms of the same element with different numbers of neutrons and hence atomic weight (e.g., 12 C and 14 C) - Ions = Atoms acquire charge when they gain or lose electrons = Cations have a deficiency of electrons (relative to protons) and are positively charged; anions have a surplus of electrons (again, relative to protons) and are negatively charged. = The tendency to become ionized varies among the elements - Molecules = Molecules are formed from atoms joined together by bonds = A compound is a substance consisting of single type of molecule; organic compounds contain carbon Appreciation for the biology of microorganisms requires a sense for molecular biology, the chemical basis of living processes. - Like all molecules, those involved in living processes are formed from atoms linked together by chemical bonds = Ionic bonds form between charged atoms, whether alone or part of a larger molecule; salts are examples of compounds formed by ionic bonding (Tortora et al., Figure 2.2) = Covalent bonds result from the sharing of one or more electron pairs between atoms (Tortora et al., Figure 2.3) = The sharing of electron pairs in covalent bonds is not always equal; this results in a bond that is said to be polar, that is "sort of negative" at one end and "sort of positive" at the other

 Especially important in biological systems are covalent bonds between hydrogen and oxygen or nitrogen Molecules possessing such polar covalent bonds can form both intermolecular and intramolecular hydrogen bonds, of which an excellent example is the bonding that accounts for some of the properties of water (Tortora et al., Figure 2.4) - Life depends on the control of chemical reactions, especially on appropriately channeling the chemical energy involved in the formation and breakage of chemical bonds = One way that chemical reactions can be classified is according to the whether the reaction requires or releases energy Chemical reactions that require an input of energy are called endergonic reactions; in living systems, most of the reactions involved in building macromolecules are endergonic A chemical reaction that releases energy is called exergonic; examples of exergonic reactions are those involved in breakdown of nutrients = Reactions can also be understood in terms of the fate of the molecules involved When two or more atoms, ions, or molecules combine to form a new and larger molecule, the reaction is a synthesis reaction; synthesis reactions are typically endergonic Decomposition reactions split large molecules into smaller molecules or atoms; decomposition reactions are typically exergonic Exchange reactions combine both synthesis and decomposition reactions = Note that all chemical reactions, in theory, are reversible - A clue to how living systems control chemical reactions comes from a consideration of factors determining reaction rates = Collision theory suggests that reactions occur when reactants collide in a configuration that favors the reaction = Reaction rate is said to depend on the proportion of reactant molecules at or above the activation energy for the reaction (Tortora et al., Figure 2.5(a)) = The importance of enzymes in living systems centers on their ability to influence reaction rates by forming enzyme-substrate complexes that favor a reactive configuration, thus "lowering" the activation energy of a reaction (Tortora et al., Figure 2.5(b)). Aqueous solubility - Ionic compounds are often dissociated in water (Tortora et al. Fig 2.6) - Polar organic compounds also interact with water molecules through hydrogen bonding - Nonpolar organic compounds tend to be hydophobic, and do not readily dissolve in water - Amphipathic compounds may disperse to allow polar (or charged) groups to interact with water while burying hydrophobic groups - Solute concentration is usually expressed as molarity, the weight of solute in grams per litre solution, expressed relative to the solute's molecular weight. Acids, Bases, and pH (Tortora et al. Figs 2.7, 2.8) - Acids generate protons (hydrogen ions, H+) when dissociated into water = A strong acid (e.g., HCl) is an acid that dissociates almost completely in solution = a weak acid (e.g., acetic acid) is only partially dissociated in water - Bases consume protons when dissociated into water. - pH measures the concentration of protons in aqueous solution = pH = -log10 [H+]; pure water, with a [H+] of 10-7 M, has a pH of 7 = Addition of acids decreases pH by contributing protons to the solution = Addition of bases increases pH by removing protons from solution - Buffers are combinations of weak acids and their conjugate bases that tend to minimize the impact of addition or consumption of protons from aqueous solution.

Many of the characteristic chemical and physical properties of organic molecules result from the properties of their functional groups (Tortora et al. Table 2.3; in that table, note the use of "R" to refer to the "remainder" of a molecule) - Some of these groups have ionic forms = Carboxyl groups may be be anionic at high pH = Amino gorups may be cationic at low pH - Hydroxy and carbonyl groups participate in extensive hydrogen bonding, both between and within molecules - Sulfhydryl groups are especially in formation of covalent bonds within and between polypeptide chains