Chemical ans Molecular Composition of Microbes

Bacteriology at UW-Madison

The Microbial World

Lectures in Microbiology by Kenneth Todar PhD University of Wisconsin-Madison Department of Bacteriology

Chemical and Molecular Composition od Microbes

From atoms to elements to molecules to macromolecules to life

Chemistry is essential to the study of living things. Not to sound irreverent, but most of life is a series of chemical reactions. This lecture will review some principles of chemistry and biochemistry that are a driving force of all life.

All matter in the Universe is composed of elements. It is the elements that are identified and described in the Periodic Table of the Elements (Table 1), familiar to all beginning chemistry students. Elements are made up of atoms which consist of a variety of subatomic particles, the most important of which in biology are the negatively-charged electron (e^-) and the positively-charged proton (H⁺). Each element has distinct properties due to the distinct nature of its atom and the behavior of electrons, protons and other subatomic particles in its make-up.

The atom is the fundamental unit of an element and cannot be broken down further without changing the properties of the element. If an atom loses or gains one or more electrons, it will acquire an electrical charge. Such atoms are referred to as ions. Thus, if a sodium (Na) atom were to lose an electron it would acquire a positive charge and be symbolized Na⁺. If a chlorine (Cl) atom were to gain an electron it would symbolized Cl^-. Positively charged ions are called cations; negatively charged ions are anions.

Table 1. The Periodic Table of Elements. Given in the table are the distinct characteristics of the atom that comprises the element: 1. atomic number of the element (in the upper right corner of the element symbol) is the number of protons in the atom; atomic weight (below the symbol of the element) is derived from the combined weight of electrons, neutrons and protons which make up the atom. The atomic weight of an element must be known to calculate the molecular weight of a chemical compound that is formed when elements bond together together into molecules. The major elements of living systems are C, H, O, N, S, and P. Minor elements are Na, Mg, K, Ca, Mn, Fe, Co, Ni, Cu and Zn.

A cell, the fundamental unit of life on Earth, is composed of organic matter, the exact definition of which will be given below. Organic material is made up of a relatively small handful of elements,; cells are composed of over 97% carbon (C), oxygen (O), nitrogen (N), hydrogen (H), phosphorus (P) and sulfur (S).

Table 2. The major elements of bacteria

Carbon         C          50%
Oxygen                 O          20
Nitrogen               N          15
Hydrogen           H          8
Phosphorus        P            3
Sulfur                     S            1

When two or more elements interact with one another and achieve stability, a chemical compound is formed. The smallest part of the compound that retains the chemical properties of the compound is termed a molecule. The atoms in a molecule are joined to one another by some sort of chemical bond. Thus, two atoms of oxygen (O) joined together form O₂, or molecular oxygen while two atoms of nitrogen (N) joined together form N₂ (nitrogen gas) - the predominant gases in earth's atmosphere. Carbon (C) bonded with 2 atoms of O forms CO₂ (carbon dioxide) ; carbon bonded with 4 atoms of hydrogen is CH₄ (methane) - the two most prominent greenhouse gases. Two atoms of hydrogen (H) joined to an atom of oxygen form a molecule of H₂O or water, which is the predominant liquid on the planet.

Table 3. Major types of chemical bonds in biological molecules

Ionic bond: Force that hods ions together in a molecule

Covalent Bond: Force resulting from sharing electrons among the atoms of a molecule

Hydrogen Bond: The force from attractions between oppositely charged poles of adjacent molecules

When a covalent bond is formed between a carbon atom (C) and a hydrogen atom (H), an organic molecule is born. Natural organic compounds are a sign of present or past life. Since carbon atoms can bond to themselves in chains of great length, and since each carbon atom has four bonding sites to other atoms, elements or molecules, it makes sense to think that there are endless possibilities for the structure of different organic molecules. Hence, ultimately, the diversity of life.

Let's just look at some possibilities for "one-carbon" organic molecules.

CH₄ is methane, or natural gas
CH₃OH is methanol an alcohol that is an excellent fuel but causes blindness if you drink it
HCHO is formaldehyde, the stuff they will try to embalm you with
HCOOH is formic acid, put into insecticides and used in the dye industry
HCN is cyanide, a powerful respiratory poison
CO(NH₂)₂ is urea, a waste product in urine (Actually, urea doesn't contain a carbon to hydrogen bond (C-H), but it nonetheless should be considered an "organic" molecule.)

Some 1-Carbon organic molecules

As the number of carbon atoms in an organic molecule is increased, correspondingly-different organic compounds are created. Example are given in the table below.

Some C-2 and C-3 organic molecules

Depending on the occurrence of so-called "functional groups" on an organic molecule, it will have particular chemical properties and activities. Some important functional groups in biological molecules are listed and described below:

-CH₃ methyl group, the beginning group of fatty acids, many amino acids, some vitamins

-NH₃ amino group, seen in amino acids, peptides and proteins

-PO₄ phosphate group that occurs in phospholipids, nucleotides and some vitamins

-SH sulfhydryl group in certain amino acids, vitamins and proteins

-OH hydroxyl group seen in alcohols and sugars

-CHO aldehyde group as in acetaldehyde or formaldehyde

-C=O ketone group characteristic of key compounds in important metabolic pathways

-COOH carboxyl group, as in carboxylic acids and fatty acids

Some important functional groups in molecules encountered in microbiology

In any case, different arrangements of C, H, O, N, P and S atoms comprise the molecules that make up the structural and functional components of cells. But usually this requires that these monomeric "small" molecules be polymerized into polymeric "large" molecules called macromolecules. There are four fundamental types of macromolecules that occur in all forms of cells. Polysaccharides are composed of carbohydrate (sugar) molecules; lipids are composed of fatty acids; proteins are composed of amino acid molecules; and nucleic acids (DNA and RNA) are made up of molecules called nucleotides. These are the molecules of microbes and all other forms of life.

Table 4: Macromolecules that make up cell material

Macromolecule	Primary Subunits	Where found in a bacterial cell
Proteins	amino acids	Flagella, pili, cell walls, cytoplasmic membranes, ribosomes, cytoplasm (as enzymes)
Polysaccharides	sugars or other carbohydrate molecules	capsules, inclusions (storage), cell walls
Phospholipids	fatty acids	membranes
Nucleic Acids (DNA/RNA)	nucleotides	DNA: nucleus, nucleoid (chromosome), plasmids rRNA: ribosomes; mRNA, tRNA: cytoplasm

How macromolecules run living systems

All microbes have various structural and functional components composed of macromolecules that account for almost every aspect of their existence and behavior as cells. All cells have certain essential structural components such as DNA, ribosomes, a cell membrane, and some sort of cell wall or surface layer. Also, all cells have a self-replicating genome and hundreds of proteins that are responsible for the business reactions of life.

As discussed above, these macromolecules are made up of monomeric subunits such as carbohydrates, lipids, nucleotides or amino acids. The arrangement or sequence in which the subunits are put together, called the primary structure of the molecule, often determines the exact properties that the macromolecule will have. The diversity within primary structure of biological macromolecules accounts for the diversity that exists among life forms.

Carbohydrates

Carbohydrates are organic compounds of carbon, hydrogen and oxygen. Their empirical formula, (CH₂O)_n, is widely used as a symbol for an organic compound. Carbohydrates have a vital function as energy sources for many types of cells. They are also found in several bacterial structures including capsules and the cell wall. The common notion of a carbohydrate is a sugar such as glucose or sucrose, but certain alcohols and aldehydes also apply. Carbohydrate molecules, also called "saccharides", can be polymerized into polysaccharides which most often occur in microbial cells in the form of starch, glycogen and cellulose. Starch and glycogen are stored in microbial cells as reserves of energy; cellulose is a component of cell walls in the protista, and otherwise is the most abundant polymer on the planet because of its occurrence in the Plant Kingdom. Complex types of polysaccharides also occur in the cell surface structures of the bacteria (walls, capsules, etc.).

(above) Structure of two important carbohydrates, the sugars fructose and glucose. Glucose and fructose are isomers because they have identical molecular formulas (C₆H₁₂O₆) but different structural formulas. Glucose is shown in its chain form and in its more common ring form. Glucose and fructose are monosaccharides. Two other common sugars, sucrose and lactose, are disaccharides, because they consist of two sugar molecules bonded together. Sucrose is made up of glucose plus fructose, and lactose is composed of glucose and galactose. Polysaccharides such as starch, glycogen or cellulose are made up of hundreds of sugar molecules polymerized into a polysaccharide macromolecule.

(below) The structure for two disaccharides and one polysaccharide. During the synthesis of the dissaccharides, water is removed from the reactants. This is referred to as "dehydration synthesis". The polysaccharide pictured is a very complex arrangement of glucose molecules that have been joined together in a linear and branched fashion.

Lipids

Lipids are a broad group of organic molecules that dissolve in organic solvents such as benzene, ether or alcohol, but generally do not dissolve in water. Like carbohydrates, lipids are composed of C, H and O, but the proportion of O is much lower. The best known lipids are fats. Fats serve living organisms including some microbes as important energy sources. More importantly they are structural components of the cell membrane of most organisms. All cells have a membrane, one of the definitive characteristics of a cell because it retains the business molecules of life within a semipermeable boundary.

Fats are made up of a 3-carbon glycerol molecule attached to 2 (or 3) long-chain fatty acids. Each fatty acid usually has 16 or 18 carbon atoms in the chain. There are two major types of fatty acids. Saturated fatty acids contain the maximum number of carbon to hydrogen bonds (C-H), while the unsaturated fatty acids contain less than the maximum. An unsaturated fatty acid molecule reveals itself immediately by the occurrence of one or more double bonds between adjacent carbon atoms (C=C).

The molecular structures of fat components and synthesis of fat. Fats consist of glycerol (a 3-carbon alcohol) and fatty acids. The fatty acids may be saturated or unsaturated as shown. Unsaturated fats contain less hydrogen. Fat synthesis occurs when fatty acids are joined to glycerol during a dehydration reaction, as shown.

Proteins

Proteins are by far the most abundant organic components of microbes and other living things. They function as structural materials in cell walls, cell membranes and ribosomes, and they function as enzymes, a group of biological molecules that catalyze and regulate most chemical reactions in biological systems. Denaturation of proteins in an organism, as caused by heat or chemicals, usually leads to cell death.

Proteins are composed of amino acids that are linked to one another by a peptide (amide) bond. Each free amino acid has a carboxyl group (-COOH) and a free amino group (-NH2) as part of its molecular structure. During protein synthesis two amino acids can be joined together by a dehydration reaction that combines the carboxy group of one amino acid to the amino group of another amino acid via a peptide bond (CO:NH) as shown below. There are 20 amino acids used during protein synthesis. Since proteins are polypeptides (many amino acids joined together) consisting of up to hundreds of amino acid molecules, there is unlimited potential in their primary structure.

Structural formulas of several important amino acids. The so called "side groups" (highlighted blue) differ and determine the exact compound, but the "amino acid" portion of the molecule is the same in all molecules, consisting of an amino (NH₂) group and a carboxyl (COOH) group.

Amino acids are joined together to form peptides or polypeptides or proteins (depending on how many AA are joined together. This cartoon shows how one amino acid is joined to the next by a type of bond called a peptide bond. The -OH from the acid group of alanine combines with -H from the amino group of valine to form water (H₂O). The open bonds then link together to form a peptide bond between the two amino acids forming the dipeptide alanylvaline.

It is the exact sequence of amino acids in a protein, encoded by the genetic material (DNA), that determines the function of the protein in either its structural, enzymatic, or regulatory role in the cell. The chain of amino acids in the protein represents the primary structure of the protein. Proteins have a secondary structure that forms when the amino acid chain twists itself into a helical pattern. Hydrogen bonds and disulfide (S-S) bonds between nearby amino acids help maintain secondary structure and contribute to the tertiary structure that results from the coiled (secondary) structure folding back on itself. Hydrogen bonding maintains the protein in its tertiary structure. If subjected to heat or chemicals, the bonds break easily and the protein becomes denatured, thereby losing its activity.

The primary structure of the enzyme lysozyme is the exact sequence of the polypeptide chain of 129 amino acid. Secondary structure of the molecule forms when the amino acid chain twists itself into a helical pattern. Tertiary structure of the protein results from the coiled (secondary) structure folding back on itself. There are four pairs of cysteines that form disulfide bridges within the molecule. This, as well as hydrogen bonds between nearby amino acids, maintains the tertiary structure. Almost all proteins that are enzymes must maintain their tertiary structure in order to be active. Therefore, proteins are denatured by chemical or physical events that destroy their tertiary structure.

Nucleic Acids

The nucleic acids are among the largest macromolecules that occur in cells. There are two types of nucleic acids found in all cellular organisms: Deoxyribonucleic acid (DNA) and ribonucleic acid (RNA). DNA acts as the genetic material in the chromosome, while RNA mainly functions during the synthesis and construction of proteins.

Both DNA and RNA are composed of repeating subunits called nucleotides. A nucleotide has three molecular components, a carbohydrate molecule (deoxyribose or ribose), a phosphate group (PO₄), and a nitrogen-containing base, and is classified as either a purine or a pyrimidine. In DNA and RNA the purine bases are adenine (A) and guanine (G); in DNA the pyrimidine bases are thymine (T) and cytosine (C), but in RNA uracil (U) occurs in place of thymine.

DNA occurs in the chromosome of the cell and its function is to pass on genetic information to progeny cells and to direct (encode) the synthesis of proteins. To form the complete DNA molecule, two single strands of DNA oppose each other in a ladder-type arrangement where opposing bases hydrogen bond to one another. G and C line up opposite one another as do A and T. This forms the "complementary" double strand of DNA and ensures that one strand of DNA can encode precisely for the opposite strand of DNA, which is required for faithful DNA replication.

The molecular structure of nucleotide components. Nucleotides, the components of DNA and RNA, are composed of a carbohydrate (sugar), phosphate ions (PO₄), and a nitrogenous base. The carbohydrates in nucleotides are ribose and deoxyribose. Phosphate is formed from phosphoric acid. The nitrogenous bases include adenine and guanine, which are purine molecules, and thymine, cytosine and uracil which are pyrimidine molecules. Four bases occur in both DNA and RNA. However, DNA contains thymine and no uracil and RNA contains uracil and no thymine. At the bottom left in the drawing, a model DNA nucleotide and an RNA nucleotide are depicted.

Formation of a double-stranded molecule of deoxyribonucleic acid (DNA). (a) Two single-stranded DNA molecules line up next to each other to form a double-stranded molecule. Adenine (A) molecules always oppose Thymine (T) molecules, and Guanine (G) molecules always oppose Cytosine (C). (b) The double-stranded DNA molecule is is twisted as shown to form the "double helix" that is characteristic of chromosomal DNA in all living organisms.

RNA occurs as a single stranded molecule although there may be regions of the molecule where complementary base pairing can take place as in DNA. There are three primary classes of RNA, each of which has a role during the process of protein synthesis. Messenger RNA (mRNA) occurs in the cytoplasm of cells and functions as a carrier of the genetic message for protein synthesis from the DNA to the ribosomes, which are the sites of protein synthesis. The process is called transcription. Ribosomal RNA (rRNA) is associated with the ribosomes and stabilizes the protein synthesizing machinery during the process. Transfer RNAs (tRNA) are relatively small molecules of RNA that transfer specific amino acids from the cytoplasm to the ribosome and the growing polypeptide chain, during protein synthesis. This second step is called translation.

The ability of DNA replicate faithfully and to be transcribed into RNA that is translated into protein forms the basis for the "central dogma" of molecular biology.