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
© 2008 Kenneth Todar PhD
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
A cell, the
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
relatively small handful of elements,; cells are composed of over 97%
carbon (C), oxygen (O), nitrogen (N), hydrogen (H), phosphorus (P) and
Table 2. The major
elements of bacteria
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
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
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"
CH4 is methane, or
CH3OH is methanol
an alcohol that is an excellent fuel but causes blindness if you drink
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
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
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.
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
-COOH carboxyl group, as in carboxylic acids and fatty acids
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
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.
Macromolecules that make up cell material
found in a bacterial cell
|Flagella, pili, cell walls,
cytoplasmic membranes, ribosomes, cytoplasm (as enzymes)
|sugars or other carbohydrate
|capsules, inclusions (storage),
|DNA: nucleus, nucleoid
rRNA: ribosomes; mRNA, tRNA: cytoplasm
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
have certain essential structural components such as DNA, ribosomes,
membrane, and some sort of cell wall or surface layer.
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
structure of biological macromolecules accounts for the diversity
among life forms.
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.).
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.
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 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
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 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
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
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.
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
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.
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.
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
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
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
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
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
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.
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
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
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.
Written and Edited by Kenneth Todar. All rights
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