Fundamentals of Chemistry

Important words and concepts from Chapter 2, Black, 2002 (3/28/2003):

by Stephen T. Abedon (abedon.1@osu.edu) for Micro 509 at the Ohio State University

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(1) Chapter title: Fundamentals of Chemistry

(a) "All living and nonliving things, including microbes, are composed of matter…. All properties of microorganisms are determined by the properties of matter."

(b) The study of the properties of matter is called physics and chemistry. The study of the properties of matter associated with organisms is called biophysics and biochemistry. This chapter serves as a review of chemistry and biochemistry so that you will gain a more fundamental understanding of how the parts of organisms work, and therefore how microorganisms work.

(c) There exists a minimum of information that will be useful for you to understand about the chemistry of life, and these things include:

(i) The basic idea of what chemical bonds and chemical reactions are

(ii) The chemistry of water and water solutions

(iii) The properties of biomolecules such as carbohydrates, proteins, nucleic acids, and lipids

(d) This lecture will focus on these three areas

(e) For an introductory biology consideration of these topics see [the chemical context of life (MicroDude)] [water and the fitness of the environment (MicroDude)] [carbon and the molecular diversity of life (MicroDude)] [the structure and function of macromolecules (MicroDude)] [an introduction to metabolism (MicroDude)] [index]

(2) Chemical bonds

(a) When a chemical reaction occurs, what is happening is the making or breaking (or both) of chemical bonds (at least within aqueous solutions)

(b) Chemical bonds come in a variety of types

(i) Covalent bonds (strong)

(ii) Polar covalent bonds (strong)

(iii) Ionic bonds (weaker, at least within water solutions)

(iv) Hydrogen bonds (weak)

(d) [chemical bonds (MicroDude)] [index]

(3) Covalent bonds

(a) Covalent bonds are the strongest of bonds

(b) Covalent bonds involve a sharing of electrons between atoms

(d) [covalent bonds (MicroDude)] [index]

(4) Ionic bonds

(a) Ionic bonds involve less (often much less) sharing of electrons between atoms

(b) Ionic bonds result from one atom essentially giving an electron to another atom

(c) Especially when found within water solutions, ionic bonds are typically not as strong as covalent bonds—paticularly within water solutions as we find them in living things

(d) Example: Na-Cl (sodium-to-chlorine) bonds in table salt

(e) [ionic bonds (MicroDude)] [index]

(5) Polar covalent bond

(a) Polar covalent bonds are intermediate between ionic and covalent bonds

(b) Polar covalent bonds result when electrons are not shared equally between atoms

(d) Example: N-H (nitrogen-to-hydrogen) bonds found in nucleic acids and proteins

(e) [polar covalent bonds (MicroDude)] [index]

(6) Hydrogen bonds

(a) Hydrogen bonds are both covalent-like and ionic-like but are nevertheless very weak

(b) Hydrogen bonds are a consequence of one atom in one molecule (or different part of the same molecule) having too much charge (due to participation in a polar covalent bond) and a second atom having too little charge (ditto)

(c) Having too many or too few electrons gives these atoms partial charges and partial charges attract other partially charged atoms

(d) Example: O-H···O-H where the dotted line represents a hydrogen bond between a hydrogen (underlined) and an oxygen atom (also underlined)

(i) the former (H) has a partial positive charge—a partial loss of electron to the polar covalently bonded, not underlined oxygen to the left

(ii) the latter (O) has a partial negative charge—a partial gain of an electron from the polar covalently bonded, not underlined hydrogen to the right)

(e) [hydrogen bonds (MicroDude)] [index]

(7) Polar compound

(a) A polar compound is a molecule containing either ionic bonds or polar covalent bonds

(b) It is called polar because of its containing either partial or full charges on its atoms

(d) See Figure 2.4, Polar compounds and hydrogen bonding

(e) [polar compound (Google Search)] [water is a polar molecule (MicroDude)] [index]

(8) Metabolism [anabolism, catabolism]

(a) Metabolism is the sum-total of all of the chemical reactions that occur within your body

(b) Metabolism includes chemical reactions that require energy to proceed plus chemical reactions that give off energy when they occur

(c) The linkage between reactions that give off energy and the reactions that require energy in processes such as growth and reproduction is what life is all about

(d) In other words, you eat food at least in part to acquire molecules that you will break down to liberate energy, and you will use that energy to make more of the complex molecules that make up you

(e) Catabolism is the word that describes all of those metabolic reactions that give off energy (example: the reactions of glycolysis)

(f) Anabolism is the word that describes all of those metabolic reactions that require energy, e.g., synthesis (example: making proteins)

(g) [an introduction to metabolism (MicroDude)] [index]

(9) Water

(a) Water has numerous properties that make water a unique requirement for life

(b) All of these attributes ultimately result from water's propensity to form numerous hydrogen bonds with itself

(d) We will consider only three of those properties:

(i) The tendency of water to dissolve (i.e., associate closely with) polar compounds

(ii) The tendency of water to exclude (i.e., not associate with) not polar compounds (i.e., non-polar compounds)

(iii) pH

(e) [water and the fitness of the environment (MicroDude)] [index]

(10) Hydrophilicity (hydrophilic)

(a) A substance that readily dissolves in water is said to be hydrophilic (i.e., water-loving)

(b) Substances that contain ionic or polar covalent bonds can hydrogen bond with water molecules

(c) Water molecules like to be hydrogen bonded so any substance that can hydrogen bond with water will be able to replace water's hydrogen bonds with itself, and thereby become closely associated with, i.e. dissolved in water

(d) Examples of such substances include the sodium and chlorine ions from table salt (NaCl) and such biomolecules as carbohydrates and nucleic acids

(e) See Figure 2.5, Polarity and water molecules

(f) [hydrophilic (MicroDude)] [water as a solvent (MicroDude)] [hydrophilic functional groups (MicroDude)] [index]

(11) Hydrophobicity (hydrophobic)

(a) A substance that does not readily associate with water is said to hydrophobic (i.e., water-hating)

(b) Substances that contain numerous non-polar covalent bonds tend to be hydrophobic

(d) Hydrophobicity is extremely important to biological systems because it forms the basis of the structure of cell membranes and globular proteins (e.g., enzymes)

(e) [hydrophobic (MicroDude)] [hydrophobic exclusion (MicroDude)] [index]

(12) Hydrogen and hydroxyl ions

(a) Water molecules can disassociate into charged compounds (i.e., ions) called H⁺ (hydrogen ion) and OH^- (hydroxyl ion)

(b) There can only be so many of these ions in water (note: just accept this)

(i) The more hydroxyl ions there are around, the fewer hydrogen ions there can be (because excess hydroxyl ions will tend to combine with whatever hydrogen ions are around, forming water, significantly reducing the number of hydrogen ions around)

(ii) Similarly, excess hydrogen ions tend to mop up hydroxyl ions

(d) A solution containing an excess of hydroxyl ions is said to be basic and tastes bitter; note that an excess of hydroxyl ions has a corresponding dearth of hydrogen ions

(e) [hydrogen ion, hydroxyl ion (Google Search)] [index]

(13) pH

(a) To keep track of these relative concentrations of hydrogen and hydroxyl ions, one employs the pH scale

(b) Since you can figure out hydroxyl ion concentrations from hydrogen ion concentrations (the more hydrogen ion, the less hydroxyl ion, and vice versa), the scale only follows hydrogen-ion concentration

(d) Thus, a pH of 1 is very acidic while a pH of 12 is very basic (i.e., very not acidic)

(e) A pH that is neither acidic nor basic is pH 7; this is the pH of pure water as well as an approximation of the pH of many body fluids

(f) See Figure 2.7, The pH values of some common substances

(g) [pH (Google Search)] [pH (MicroDude)] [optimum pH (MicroDude)] [pH buffer (MicroDude)] [index]

(14) Biomolecules

(a) A large fraction of the molecules (biomolecules) found within organisms are organic molecules

(b) Organic molecules contain carbon-to-carbon (C-C) or carbon-to-hydrogen (C-H) bonds

(c) Oxygen is also very often found in the organic molecules that make up living things, as are Nitrogen and Phosphorus as well, etc.

(d) Organic biomolecules include carbohydrates, lipids, proteins, and nucleic acids

(e) [the structure and function of biomolecules (MicroDude)] [index]

(15) Oxidation and reduction

(a) Note that the more oxygen a biomolecule contains, roughly, the more oxidized it is said to be (conversely, the less oxygen, the more reduced)

(b) More-oxidized biomolecules tend to be more hydrophilic and tend to contain less energy, per carbon, than more-reduced biomolecules

(c) More-reduced biomolecules tend to be more hydrophobic and to contain more energy, per carbon, than more-oxidized biomolecules

(d) Another way of looking at this is that more C-C or C-H bonds a molecule has, the more reduced it is (i.e., the more reduced the carbons are) while the more C-O bonds a molecule has, the more oxidized it is (i.e., the more oxidized the carbons are)

(e) Reduced carbons tend to make up cell membranes as well as the interior of proteins and energy-dense (i.e., fatty) foods

(f) See Figure 2.8, Four classes of organic compound that incorporate oxygen

(g) [oxidation (MicroDude)] [reduction (MicroDude)] [index]

(16) Carbohydrates (sugars)

(a) Carbohydrates serve structural and energy-storage roles in organisms

(b) Carbohydrates are organic molecules that contain approximately one oxygen for every carbon (plus two hydrogens, hence the term carbo-hydrate)

(d) Sugars are either used as energy or are built up into polysaccharides

(e) Different polysaccharides serve either energy-storage or structural roles while sugars are involved either in energy storage or are combined with other substances (including other sugars) to produce polysaccharides as well as other biomolecules (e.g., nucleic acids)

(f) [carbohydrates (MicroDude)] [index]

(17) Monosaccharide

(a) A monosaccharide is a sugar that contains only a single unit of carbohydrate

(b) For example, glucose is a monosaccharide

(d) [monosaccharides (MicroDude)] [index]

(18) Disaccharide

(a) Disaccharides are sugars that consist of two monosaccharides linked together

(b) It is often preferable to move sugars around between cells within organisms as disaccharides rather than as monosaccharides,

(i) Sucrose is a disaccharide that represents how plants move sugars around

(ii) Lactose is a disaccharide that represents how mammals deliver sugars to babies

(c) See Figure 2.12a, Disaccharides

(d) [disaccharides (MicroDude)] [index]

(19) Polysaccharides

(a) Polysaccharides serve as either sugar-storage molecules (starches) or play structural roles (cellulose)

(b) See Figure 212b, Polysaccharides

(20) Lipids

(a) Lipids are a structurally diverse category of compounds that all display significant hydrophobicity

(b) This hydrophobicity stems from their containing a large number of C-H bonds (i.e., they are more reduced)

(d) Three common types of lipids are fatty acids, compounds containing fatty acids and the tri-alcohol glycerol, and cholesterol-like lipids called steroids

(e) [lipids (MicroDude)] [index]

(21) Fatty acids

(a) Fatty acids contain long reduced-carbon chains at one end and a hydrophilic carboxylic acid group at the other end

(b) See Figure 213b and c, the structure of fats

(c) Free fatty acids are not terribly common in organisms, though the sodium salts of free fatty acids are the very common man-made substance called soap

(d) [fatty acids (MicroDude)] [index]

(22) Glycerides (fat, oil)

(a) Fatty acids associated with glycerol (an alcohol) are very common

(b) A glycerol molecule that has been bound to three fatty acids is called a fat

(d) Fats serve as energy-storage molecules

(e) See Figure 213a, the structure of fats

(f) [triacylglyceride (Google Search)] [index]

(23) Phospholipids

(a) A fat that has one fatty acid removed and replaced with a phosphorous-containing compound is called a phospholipid

(b) Phospholipids are key components of cell membranes

(d) [phospholipids (MicroDude)] [index]

(24) Steroids

(a) Steroids serve as hormones in animals and play structural roles in mostly animal cell membranes

(b) In cell membranes, steroids such as cholesterol serve to stabilize the membrane

(25) Proteins

(a) Proteins are complex organic molecules that serve to define the complexity of life

(b) Proteins are built up, during a complicated process called translation, from individual protein-units called amino acids

(c) See Figure 2.18, Three levels of protein structure

(d) The chemical bonds linking amino acids are called peptide bonds and any time you see the word peptide you should think proteins and amino acids

(e) Proteins play structural roles

(f) Proteins also (indeed, perhaps more importantly) serve as enzymes, which are the catalysts that allow metabolic reactions to proceed

(g) [proteins (MicroDude)] [index]

(26) Denaturation

(a) The complex three-dimensional structure of a protein is vital for its proper functioning; these three-dimensional structures are not rigid but instead result from many covalent as well as non-covalent interactions between amino acid residues found within proteins

(b) See Figure 2.19, Quaternary protein structure

(d) Various processes important to microbiology involve protein denaturation including the killing of microorganisms outside of bodies (e.g., pasteurization)

(e) [denaturation (MicroDude)] [index]

(27) Nucleic acids

(a) DNA and RNA are nucleic acids

(b) Nucleic acids play information-storage, catalytic, and energy-storage roles

(c) In cellular organisms the DNA typically serves the permanent information-storage role while RNA serves a temporary information-storage role

(d) RNAs additionally play catalytic roles involved in the transfer of DNA-coded information to protein-coded information

(e) The energy-storage role typically occurs in the guise of ATP, an RNA nucleotide that serves as the primary energy-exchange molecule within cells

(f) [nucleic acids (MicroDude)] [index]

(28) Nucleotides

(a) Nucleotides consist of

(i) A five-carbon sugar (e.g., ribose or deoxyribose)

(ii) A nitrogenous base

(iii) One or more phosphates

(b) Nucleotides are the building blocks of nucleic acid polymers (such as DNA)

(d) See Figure 2.20, Nucleotides

(e) [nucleotides (MicroDude)] [index]

(29) Complementary base pairing and the double helix

(a) The key to information storage by nucleotides is complementary base pairing with a double helical structure

(b) The double helix consists of alternating sugar (ribose or deoxyribose) and phosphate residues that have nitrogenous bases projecting into the middle

(c) These nitrogenous bases interact specifically (through hydrogen bonding) with one another (in a process called base pairing) such that the nitrogenous base called adenine (A) can only interact with the nitrogenous base called thymine (T); similarly cytosine (C) can only interact with guanine (G)

(d) These specific interacts mean two things:

(i) Each strand within a double helix can specify the other strand

(ii) Each strand can potentially serve as a template for the polymerization of an additional, complementary strand

(e) This template-directed polymerization occurs during both DNA replication and RNA transcription

(f) See Figure 2.21, Nucleic and [sic] structure

(g) [complementary base pairing (Google Search)] [double helix (MicroDude)] [index]

(30) Vocabulary [index]

(a) Biomolecules

(b) Carbohydrates