Chapter 6 The Biochemical Basis of Life

Burton’s Microbiology
for the Health Sciences
Section III.
Chemical and Genetic Aspects
of Microorganisms
Copyright © 2015 Wolters Kluwer • All Rights Reserved

Burton’s Microbiology
for the Health Sciences
Chapter 6. The Biochemical Basis of
Life

Chapter 6 Outline
• Introduction
• Organic Chemistry
– Carbon Bonds
– Cyclic Compounds
• Biochemistry
– Carbohydrates
– Lipids
– Proteins
– Nucleic Acids

Introduction
• A microorganism can be thought of as a “bag” of

chemicals that interact with each other in a variety of
ways; even the bag itself is composed of chemicals.
• Everything a microorganism is and does is related to
chemistry.
• Organic chemistry is the study of compounds that contain
carbon.
• Inorganic chemistry involves all other chemical reactions.
• Biochemistry is the chemistry of living cells⎯the
chemistry of life.

Organic Chemistry
• Organic compounds contain carbon.

• Organic chemistry is the branch of science that studies
organic compounds.
• Organic compounds are not necessarily related to living
organisms; although some organic compounds are
associated with living organisms, many are not.
• Organic chemistry involves fossil fuels, dyes, drugs,
paper, ink, paints, plastics, gasoline, rubber tires, food,
and clothing.

Organic Chemistry
Carbon Bonds
• Carbon atoms have a valence of 4, meaning that they

can bond to four other atoms.
• There are three ways in which carbon atoms can bond to
each other: single bond, double bond, and triple bond.
• A covalent bond is one in which a pair of electrons is
shared.
• When atoms of other elements attach to available carbon
bonds, compounds are formed.
• A series of carbon atoms bonded together is referred to
as a chain.

Organic Chemistry
Carbon Bonds (cont.)
• If only hydrogen atoms are bonded to the available carbon

bonds, hydrocarbons are formed.
• Therefore, a hydrocarbon is an organic molecule that contains
only carbon and hydrogen atoms; some examples of simple
hydrocarbons are shown here:

Organic Chemistry
Cyclic Compounds
• When carbon atoms link to

other carbon atoms to close
a chain, they form rings or
cyclic compounds.
• Benzene is a cyclic
compound with six carbons
and six hydrogens.
The benzene ring

Biochemistry
• Biochemistry is the study of biology at the molecular

level; it is the chemistry of living organisms.
• Biochemistry involves the study of biomolecules present
within living organisms; biomolecules in living organisms
are usually large molecules called macromolecules.
• Macromolecules include carbohydrates, lipids, proteins,
and nucleic acids.
– Other examples: vitamins, enzymes, hormones, and
energy-carrying molecules such as adenosine
triphosphate (ATP).

Biochemistry (cont.)
• Humans obtain their nutrients from the foods they eat.

– Carbohydrates, fats, nucleic acids, and proteins
contained in foods are digested; their components
are absorbed and carried to every cell in the body,
where they are broken down and rearranged.
• Microorganisms also absorb essential nutrients into the
cell by various means.
• The nutrients are then used in metabolic reactions as
sources of energy and as “building blocks” for enzymes,
structural macromolecules, and genetic materials.

Biochemistry
Carbohydrates
• Carbohydrates are biomolecules composed of carbon,
hydrogen, and oxygen (in the ratio 1:2:1).
• Examples include glucose, fructose, sucrose, lactose,
maltose, starch, cellulose, and glycogen.
• Categories of carbohydrates include monosaccharides,
disaccharides, and polysaccharides.

Carbohydrates
Monosaccharides
• Monosaccharides are the smallest and simplest of the

carbohydrates. Mono means one, referring to the number
of rings in the structure.
– Glucose (C6H12O6) is the most important
monosaccharide in nature; it may occur as a chain or
in alpha or beta ring configurations.
• Monosaccharides contain two to nine carbon atoms –
most contain five to six.
– A three-carbon monosaccharide is called a triose; a
four-carbon one is a tetrose; a five-carbon one is a
pentose; a six-carbon one is a hexose; a seven-
carbon is a heptose; and so on.

Carbohydrates
Monosaccharides (cont.)
• The main source of energy for body cells is glucose.

– The three forms of glucose are shown above.
– In humans, glucose is carried in the blood to cells where it
is oxidized to produce energy-carrying ATP. ATP is the
main energy source used to drive most metabolic
reactions.
Carbohydrates
Disaccharides
• “Di” means two; disaccharides are double-ringed sugars

that result from the combination of two monosaccharides
(following removal of a water molecule). This is known as
a dehydration synthesis reaction.
– Sucrose (table sugar), lactose, and maltose are
examples of disaccharides.
• Disaccharides react with water in a process called a
hydrolysis reaction, which causes them to break down
into two monosaccharides.

The Dehydration Synthesis
and Hydrolysis of Sucrose

Carbohydrates
Disaccharides (cont.)
• Recall that peptidoglycan is found in the cell walls of

all members of the Domain Bacteria; peptidoglycan is
a repeating disaccharide attached by proteins to form
a lattice that surrounds and protects the bacterial cell.
• Carbohydrates composed of three monosaccharides

are called trisaccharides; those composed of four are
called tetrasaccharides; those composed of five are
called pentasaccharides, and so on, until we come to
polysaccharides.

Carbohydrates
Polysaccharides
• The definition of a polysaccharide varies from one reference

book to another. In this book, polysaccharides are defined as
carbohydrates that are composed of many monosaccharides.
Most contain hundreds (e.g., starch and glycogen).
• Polysaccharides serve two main functions:
– Store of energy (e.g., glycogen in animal cells and starch
in plant cells)
– Provide a “tough” molecule for structural support and
protection (e.g., bacterial capsules)

Carbohydrates
Polysaccharides (cont.)
• Polysaccharides are examples of polymers⎯molecules that
consist of many similar subunits.
• In the presence of the proper enzymes or acids,
polysaccharides may be hydrolyzed or broken down into
disaccharides, and then into monosaccharides.

Carbohydrates
Polysaccharides (cont.)
• Some bacteria produce polysaccharide capsules for

protection from phagocytes.
• Plant and algal cells have cellulose (a polysaccharide) cell
walls to provide support.
• Some protozoa, fungi, and bacteria have enzymes that
can break down cellulose.
• When polysaccharides combine with other chemical
groups (amines, lipids, and amino acids), complex
macromolecules are formed.
– For example, chitin, the main component of the hard
outer covering of insects, spiders, and crabs, is found
in the cell walls of fungi.

Lipids
• An important class of biomolecules.

• Most lipids are insoluble in water, but soluble in fat
solvents, such as ether, chloroform, and benzene.
• Lipids are essential constituents of most living cells.
• Lipids can be classified into the following categories:
-Waxes -Glycolipids
-Fats and oils -Steroids
-Phospholipids -Prostaglandins and leukotrienes

The General Structure of Some Categories
of Lipids

Lipids
Fatty Acids
• Fatty acids are the building blocks of lipids; they are

long-chain carboxylic acids that are insoluble in water.
• Saturated fatty acids contain one single bond between
carbon atoms; they are solid at room temperature.
• Monounsaturated fatty acids have one double bond in the
carbon chain and are found in butter, olives, and
peanuts.
• Polyunsaturated fatty acids contain two or more double
bonds and are found in soybeans, safflowers, and corn.
• Essential fatty acids cannot be synthesized in the human
body and must be provided in the diet.

Lipids
Waxes
• A wax consists of a saturated fatty acid and a long-chain

alcohol.
– Examples: the wax coating on fruits, leaves, skin,
fur, and feathers of animals.
– The cell wall of Mycobacterium tuberculosis (the
causative agent of tuberculosis) contains waxes.
• These waxes protect M. tuberculosis from
digestion following phagocytosis by white blood
cells.
• These waxes make M. tuberculosis difficult to stain
and destain; this explains why M. tuberculosis is
acid-fast.

Lipids
Fats and Oils
• Fats and oils are the most common types of lipids. They are
also known as triglycerides because they are composed of
glycerol and three fatty acids.
• Most fats come from animal sources (e.g., beef); most oils
come from plant sources (e.g., olive oil).

Lipids
Phospholipids
• Phospholipids contain glycerol, fatty acids, a phosphate

group, and an alcohol. There are two types:
– Glycerophospholipids (also known as
phosphoglycerides)
– Sphingolipids
• Glycerophospholipids are the most abundant lipids in cell
membranes.
– A cell membrane is a lipid bilayer, consisting of two
rows of phospholipids, arranged tail-to-tail.

The Lipid Bilayer Structure
of Cell Membranes

Lipids
Phospholipids, cont.
• The outer membrane of Gram-negative bacterial cell

walls contains lipoproteins and lipopolysaccharide (LPS).
– LPS consists of a lipid and a polysaccharide portion.
• The cell walls of Gram-positive organisms do not contain
LPS.
• Lecithins and cephalins are glycerophospholipids found in
brain and nerve tissues, as well as egg yolks.
• Sphingolipids are phospholipids that contain sphingosine
rather than glycerol. Sphingolipids are found in brain and
nerve tissues. Sphingomyelin is one of the most
abundant sphingolipids, and makes up the myelin sheath
that coats nerve cells.

Lipids
Glycolipids, Steroids, Prostaglandins,and
Leukotrienes
• Glycolipids are abundant in the brain and in the myelin

sheath of nerves.
• Steroids are complex, four-ringed structures; examples
are cholesterol, bile salts, steroid hormones, and fat-
soluble vitamins (A, D, E, and K).
• Prostaglandins and leukotrienes are derived from a fatty
acid called arachidonic acid.
– Both have a wide variety of effects on body
chemistry such as controlling blood pressure or
hormones; leukotrienes can produce long-lasting
muscle contractions.

Proteins
• Proteins are the most essential chemicals in all living

cells; they are considered “the substance of life.”
• Some proteins are the structural components of
membranes, cells, and tissues; others are enzymes and
hormones.
• All proteins are polymers of amino acids.
• All proteins contain carbon, hydrogen, oxygen, and
nitrogen (and sometimes sulfur).

Proteins
Amino Acids
• Amino acids contain carbon, hydrogen, oxygen, and nitrogen;

some also have sulfur in the molecule.
• Humans can synthesize certain amino acids, but not others.
• The thousands of different proteins in the human body are
composed of a wide variety of amino acids in various quantities
and arrangements.
• The basic structure of an amino acid is shown here:

Proteins
Protein Structure
• Amino acids are linked together to form proteins via

covalent bonds referred to as peptide bonds; there are
dipeptides, tripeptides, and polypeptides.
• The linear sequence of amino acids is referred to as the
primary protein structure.
• The twisting or coiling of the chain of amino acids is
referred to as the secondary protein structure.
• The folding or entwining of the chain is the tertiary
protein structure.
• The bonding of two or more polypeptide chains is known
as the quaternary protein structure.

The Formation of a Dipeptide

Protein Structure
A.Primary structure
B.Secondary structure
C.Tertiary (globular)
structure
D.Quaternary structure

Proteins
Enzymes
• Enzymes are specialized protein molecules produced by

living cells. They are known as biological catalysts; that
is, they catalyze metabolic reactions.
– A catalyst is an agent that speeds up a chemical
reaction without being consumed in the reaction.
• Almost every chemical reaction in a cell requires a
specific enzyme.
• Some protein molecules function as enzymes by
themselves; other proteins, called apoenzymes, only
function when linked with a nonprotein cofactor (such as
Ca2+, Fe2+, Mg2+, Cu2+) or a coenzyme.

Proteins
Enzymes (cont.)
• Some apoenzymes require vitamin-type compounds

called coenzymes; examples are vitamin C, flavin-
adenine dinucleotide (FAD), and nicotinamide-adenine
dinucleotide (NAD).
• The combination of an apoenzyme plus a cofactor is
called a holoenzyme (i.e., a “whole” enzyme).
• Enzymes are usually named by adding the ending “-ase”
to the word. Hemolysins and lysozyme are examples of
enzymes not ending in “ase.”
• The specific molecule on which an enzyme acts is
referred to as that enzyme’s substrate.

Nucleic Acids
Function
• DNA and RNA form the fourth major group of

biomolecules in living cells.
• DNA and RNA are critical to proper functioning of a cell.
• DNA is the “hereditary molecule”⎯the molecule that
contains the genes and genetic code.
– Information in DNA must flow to the rest of the cell
for the cell to function properly⎯the flow is
accomplished by RNA.
• RNA molecules participate in the conversion of the
genetic code into proteins and other gene products.

Nucleic Acids
Structure
• In addition to the elements C, H, O, and N, DNA and RNA

also contain phosphorus, P.
• The building blocks of nucleic acid polymers are called
nucleotides.
– Nucleotides are more complex monomers than amino
acids.
• The building blocks of DNA are called DNA nucleotides.
• The building blocks of RNA are called RNA nucleotides.
• DNA contains dexoyribose as its pentose, whereas RNA
contains ribose as it pentose.

Two Nucleotides, Each Consisting of a
Nitrogenous Base (A or T), a Five-carbon Sugar
(S), and a Phosphate Group (P)

Nucleic Acids
Structure (cont.)
• There are three types of RNA, named for their function:

– Messenger RNA (mRNA)
– Ribosomal RNA (rRNA)
– Transfer RNA (tRNA)
• The five nitrogenous bases in nucleic acids are adenine
(A), guanine (G), thymine (T), cytosine (C), and uracil
(U). A and G are purines; T, C, and U are pyrimidines.
– Thymine is found in DNA but not in RNA. Uracil is
found in RNA, but not in DNA. The other three bases
are found in both.

The Pyrimidines and Purines
Found in DNA and RNA

DNA Structure
• For a double-stranded DNA molecule to form, the

nitrogenous bases on the two separate strands must
bond together.
– A always bonds with T via two hydrogen bonds.
– G always bonds with C via three hydrogen bonds.
– A–T and G–C are known as “base pairs.”
• The bonding forces of the double-stranded polymer cause
it to assume the shape of a double -helix, similar to a
right-handed spiral staircase.

A Section of a Nucleic Acid Polymer

Base Pairs That Occur in Double-stranded
DNA Molecules

Double-Stranded DNA Molecule, Also
Known as a Double Helix

DNA Replication
• When a cell is preparing to divide, all DNA molecules in

the chromosomes of the cell must duplicate, thereby
ensuring that the same genetic information is passed on
to both daughter cells. This is called DNA replication.
• DNA replication occurs by separation of the two DNA
strands and the building of complementary strands by
the addition of the correct DNA nucleotides.
• DNA polymerase (also known as DNA-dependent DNA
polymerase) is the most important enzyme required for
DNA replication.

DNA Replication

DNA Replication
Gene Expression
• A gene is a particular segment of a DNA molecule or

chromosome.
– A gene contains the blueprint that will enable a cell
to make what is known as a gene product.
• It is the sequence of the four nitrogenous bases of DNA
(i.e., A, G, C, and T) that spell out the instructions for a
particular gene product.
• Although most genes code for proteins, some code for
rRNA and tRNA.
• Some genes code for more than one gene product.

DNA Replication
Gene Expression (cont.)
• The Central Dogma explains the flow of genetic

information within a cell (proposed by Francis Crick in
1957).
– DNA mRNA protein.
– Also known as the “one gene–one protein
hypothesis.”
– One gene of a DNA molecule is used to make one
molecule of mRNA by a process known as
transcription.
– The genetic information in the mRNA is then used to
make one or more protein by a process known as
translation.

DNA Replication
• All genes on a chromosome are not being expressed at

any given time. It would not be logical for a cell to
produce a particular enzyme if it was not needed.
– Genes that are only expressed when the gene
products are needed are called inducible genes.
– Genes that are expressed at all times are called
constitutive genes.
• The process by which the genetic code within the DNA
molecule is transcribed to produce an mRNA molecule is
called transcription.
– The primary enzyme involved is RNA polymerase.

DNA Replication
• In eukaryotes, transcription occurs within the nucleus;

the newly formed mRNA molecules then travel out
through the pores of the nuclear membrane into the
cytoplasm, where they are used to produce proteins.
• In prokaryotes, transcription occurs in the cytoplasm;
ribosomes attach to the mRNA molecules as they are
being transcribed at the DNA; thus both transcription and
translation may occur simultaneously.

Transcription

DNA Replication
• The process of translating the message carried by mRNA,

whereby particular tRNAs carry amino acids to be bound
together in the proper sequence to make a protein, is
called translation.
• The base sequence of the mRNA molecule is read in
groups of three bases, called codons.
• The three-base sequence codon can be read by a
complementary three-base sequence (the anticodon) on
a tRNA molecule.

Chart to Illustrate the Sequence of Three Bases (GGC) in the DNA
Template That Codes for a Particular Codon (CCG) in mRNA,
Which in Turn Attracts a Particular Anticodon (GGC) on the tRNA
Carrying an Amino Acid (Proline in This Case)
DNA mRNA tRNA Amino

Template (Codon) (Anticodon) Acid
G C G
Proline
G C G
C G C

Translation (Protein Synthesis)

Chapter 6 The Biochemical Basis of Life

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Burton’s Microbiology

for the Health Sciences

Copyright © 2015 Wolters Kluwer • All Rights Reserved

Copyright © 2015 Wolters Kluwer • All Rights Reserved

Copyright © 2015 Wolters Kluwer • All Rights Reserved

• A microorganism can be thought of as a “bag” of

Copyright © 2015 Wolters Kluwer • All Rights Reserved

• Organic compounds contain carbon.

Copyright © 2015 Wolters Kluwer • All Rights Reserved

• Carbon atoms have a valence of 4, meaning that they

Copyright © 2015 Wolters Kluwer • All Rights Reserved

• If only hydrogen atoms are bonded to the available carbon

Copyright © 2015 Wolters Kluwer • All Rights Reserved

• When carbon atoms link to

The benzene ring

Copyright © 2015 Wolters Kluwer • All Rights Reserved

• Biochemistry is the study of biology at the molecular

Copyright © 2015 Wolters Kluwer • All Rights Reserved

• Humans obtain their nutrients from the foods they eat.

Copyright © 2015 Wolters Kluwer • All Rights Reserved

Copyright © 2015 Wolters Kluwer • All Rights Reserved

• Monosaccharides are the smallest and simplest of the

Copyright © 2015 Wolters Kluwer • All Rights Reserved

• The main source of energy for body cells is glucose.

• “Di” means two; disaccharides are double-ringed sugars

Copyright © 2015 Wolters Kluwer • All Rights Reserved

Copyright © 2015 Wolters Kluwer • All Rights Reserved

• Recall that peptidoglycan is found in the cell walls of

• Carbohydrates composed of three monosaccharides

Copyright © 2015 Wolters Kluwer • All Rights Reserved

• The definition of a polysaccharide varies from one reference

Copyright © 2015 Wolters Kluwer • All Rights Reserved

Copyright © 2015 Wolters Kluwer • All Rights Reserved

• Some bacteria produce polysaccharide capsules for

Copyright © 2015 Wolters Kluwer • All Rights Reserved

• An important class of biomolecules.

Copyright © 2015 Wolters Kluwer • All Rights Reserved

Copyright © 2015 Wolters Kluwer • All Rights Reserved

• Fatty acids are the building blocks of lipids; they are

Copyright © 2015 Wolters Kluwer • All Rights Reserved

• A wax consists of a saturated fatty acid and a long-chain

Copyright © 2015 Wolters Kluwer • All Rights Reserved

Copyright © 2015 Wolters Kluwer • All Rights Reserved

• Phospholipids contain glycerol, fatty acids, a phosphate

Copyright © 2015 Wolters Kluwer • All Rights Reserved

Copyright © 2015 Wolters Kluwer • All Rights Reserved

• The outer membrane of Gram-negative bacterial cell

Copyright © 2015 Wolters Kluwer • All Rights Reserved

• Glycolipids are abundant in the brain and in the myelin

Copyright © 2015 Wolters Kluwer • All Rights Reserved

• Proteins are the most essential chemicals in all living

Copyright © 2015 Wolters Kluwer • All Rights Reserved

• Amino acids contain carbon, hydrogen, oxygen, and nitrogen;

Copyright © 2015 Wolters Kluwer • All Rights Reserved

• Amino acids are linked together to form proteins via

Copyright © 2015 Wolters Kluwer • All Rights Reserved

Copyright © 2015 Wolters Kluwer • All Rights Reserved

Copyright © 2015 Wolters Kluwer • All Rights Reserved

• Enzymes are specialized protein molecules produced by

Copyright © 2015 Wolters Kluwer • All Rights Reserved

• Some apoenzymes require vitamin-type compounds

Copyright © 2015 Wolters Kluwer • All Rights Reserved

• DNA and RNA form the fourth major group of