3. What is Genetics??
Genetics is the study of the inheritance, or heredity, of living things.
It is a wide-ranging science that explores
1. the transmission of biological properties (traits) from parent to offspring;
2. the expression and variation of those traits;
3. the structure and function of the genetic material; and
4. how this material changes.
4. The study of genetics takes place on several levels.
Organismal genetics observes the heredity of the whole organism or cell;
chromosomal genetics examines the characteristics and actions of chromosomes;
and molecular genetics deals with the biochemistry of the genes.
All of these levels are useful areas of exploration, but in order to understand the
expressions of microbial structure, physiology, mutations, and pathogenicity, we
need to examine the operation of genes at the cellular and molecular levels.
5. The study of microbial genetics provides a greater understanding of human genetics
and an increased appreciation for the astounding advances in genetic engineering we
are currently witnessing.
6. The Nature of the Genetic Material
For a species to survive, it must have the capacity of selfreplication.
In single-celled microorganisms, reproduction involves the division of the cell by means
of binary ﬁssion or budding, but these forms of reproduction involve a more signiﬁcant
activity than just simple cleavage of the cell mass.
Because the genetic material is responsible for inheritance, it must be accurately
duplicated and separated into each daughter cell to ensure normal function.
This genetic material itself is a long molecule of DNA that can be studied on several
7. The Levels of Structure and Function of the Genome
The genome is the sum total of genetic material of a cell. Although most of the
genome exists in the form of chromosomes, genetic material can appear in
nonchromosomal sites as well.
For example, bacteria and some fungi contain tiny extra pieces of DNA(plasmids),
and certain organelles of eucaryotes (the mitochondria and chloroplasts) are
equipped with their own genetic programs.
Genomes of cells are composed exclusively of DNA, but viruses contain either DNA
or RNA as the principal genetic material.
9. In general, a chromosome is a discrete cellular structure composed of
a neatly packaged elongate DNA molecule.
The chromosomes of eucaryotes and bacterial cells differ in several
The structure of eucaryotic chromosomes consists of a DNA molecule
tightly wound around histone proteins, whereas a bacterial
chromosome (chromatin body) is condensed and secured into a
packet by means of histone-like proteins.
10. Eucaryotic chromosomes are located in the nucleus; they
vary in number from a few to hundreds; they can occur in
pairs (diploid) or singles (haploid); and they appear elongate.
In contrast, most bacteria have a single, circular chromosome,
although many bacteria have multiple circular chromosomes
and some have linear chromosomes.
12. The gene
A gene can be deﬁned from more than one perspective.
In classical genetics, the term refers to the fundamental unit of heredity
responsible for a given trait in an organism.
In the molecular and biochemical sense, it is a site on the chromosome that
provides information for a certain cell function.
More speciﬁcally still, it is a certain segment of DNA that contains the
necessary code to make a protein or RNA molecule.
13. Genes fall into three basic categories: structural genes that code for proteins, genes that
code for RNA, and regulatory genes that control gene expression.
The sum of all of these types of genes constitutes an organism’s distinctive genetic
makeup, or genotype.
The expression of the genotype creates traits (certain structures or functions) referred to
as the phenotype.
All organisms contain more genes in their genotypes than are manifested as a phenotype
at any given time.
In other words, the phenotype can change depending on which genes are “turned on”
14. The Size and Packaging of Genomes
Genomes vary greatly in size.
The smallest viruses have four or ﬁve genes; the bacterium Escherichia
coli has a single chromosome containing 4,288 genes, and a human cell
packs about ten times that many into 46 chromosomes.
The chromosome of E. coli would measure about 1 mm if unwound
and stretched out linearly, and yet this ﬁts within a cell that measures
just over 1 mm across, making the stretched-out DNA 1,000 times
longer than the cell.
16. Still, the bacterial chromosome takes up only about one-third to one half
of the cell’s volume.
Likewise, if the sum of all DNA contained in the 46 human chromosomes
were unraveled and laid end to end, it would measure about 6 feet.
How can such elongated genomes ﬁt into the minuscule volume of a cell,
and in the case of eucaryotes, into an even smaller compartment, the
* The answer lies in the regular coiling of the DNA chain (Insight 9.1). “Next slide”
17. Packing the mass of DNAinto the cell involves
several levels of DNAstructure called supercoils or
In the simpler system of procaryotes, the circular
chromosome is packaged by the action of a special
enzyme called a topoisomerase(specifically, DNA
This enzyme coils the chromosome into a tight
bundle by introducing a reversible series of twists
into the DNA molecule.
The system in eucaryotes is more complex, with
three or more levels of coiling.
First, the DNA molecule of a chromosome, which is
linear, is wound twice around the histone proteins,
creating a chain of nucleosomes.
18. The nucleosomes fold in a spiral formation upon one another.
An even greater supercoiling occurs when this spiral arrangement further twists
on its radius into a giant spiral with loops radiating from the outside.
This extreme degree of compactness is what makes the eucaryotic chromosome
visible during mitosis.
In addition to reducing the volume occupied by DNA, supercoiling solves the
problem of keeping the chromosomes from getting tangled during cell division,
and it protects the code from massive disruptions due to breakage.
20. The DNA Code: A Simple Yet Profound Message
Examining the function of DNA at the molecular level requires an even closer look at
To do this we will imagine being able to magnify a small piece of a gene about 5
What such ﬁne scrutiny will disclose is one of the great marvels of biology.
21. James Watson and Francis Crick put the
pieces of the puzzle together in 1953 to
discover that DNA is a gigantic molecule, a
type of nucleic acid, with two strands
combined into a double helix.
The general structure of DNA is universal,
except in some viruses that contain single-
22. The basic unit of DNA structure is a nucleotide, and a chromosome in a typical
bacterium consists of several million nucleotides linked end to end.
Each nucleotide is composed of;
23. The nucleotides covalently bond to form a sugar-phosphate linkage that
becomes the backbone of each strand. Each sugar attaches in a repetitive pattern
to two phosphates.
One of the bonds is to the number 5 prime carbon on deoxyribose, and the other
is to the 3 prime carbon, which confers a certain order and direction on each
24. The nitrogenous bases, purines and pyrimidines, attach by covalent bonds at the
1prime position of the sugar.
They span the center of the molecule and pair with appropriate complementary
bases from the other strand.
The paired bases are so aligned as to be joined by hydrogen bonds. Such weak
bonds are easily broken, allowing the molecule to be “unzipped” into its
This feature is of great importance in gaining access to the information encoded in
the nitrogenous base sequence.
25. Pairing of purines and pyrimidines is not random; it is dictated by the formation of
hydrogen bonds between certain bases.
Thus, in DNA, the purine adenine (A) always pairs with the pyrimidine thymine
(T), and the purine guanine (G) always pairs with the pyrimidine cytosine (C).
New research also indicates that the bases are attracted to each other in this
pattern because each has a complementary three-dimensional shape that matches
Although the base-pairing partners generally do not vary, the sequence of base
pairs along the DNA molecule can assume any order, resulting in an inﬁnite
number of possible nucleotide sequences.
26. Other important considerations of DNA structure concern the nature of the double helix
The halves are not oriented in the same direction.
One side of the helix runs in the opposite direction of the other, in what is called an
The order of the bond between the carbon on deoxyribose and the phosphates is used to
keep track of the direction of the two sides of the helix.
Thus, one helix runs from the 5 prime to 3 prime direction, and the other runs from the 3
prime to 5 prime direction.
27. This characteristic is a signiﬁcant factor in DNA synthesis and translation.
As apparently perfect and regular as the DNA molecule may seem, it is not exactly
The torsion in the helix and the stepwise stacking of the nitrogen bases produce
two different-sized surface features, the major and minor grooves.
29. The Signiﬁcance of DNA Structure
The arrangement of nitrogenous bases in DNA has two essential effects.
1. Maintenance of the code during reproduction
The constancy of base-pairing guarantees that the code will be retained during cell
growth and division.
When the two strands are separated, each one provides a template (pattern or model)
for the replication (exact copying) of a new molecule.
Because the sequence of one strand automatically gives the sequence of its partner,
the code can be duplicated with ﬁdelity.
31. 2. Providing variety
The order of bases along the length of the DNA strand constitutes the genetic
program, or the language, of the DNA code.
The message present in a gene is a precise sequence of these bases, and the
genome is the collection of all DNA bases that, in an ordered combination, are
responsible for the unique qualities of each organism.
32. It is tempting to ask how such a seemingly simple code can account for the extreme
differences among forms as diverse as a virus, E. coli, and a human.
The English language, based on 26 letters, can create an inﬁnite variety of words, but
how can an apparently complex genetic language such as DNA be based on just four
nitrogen base “letters”? A mathematical example can explain the possibilities.
For a segment of DNA that is 1,000 nucleotides long, there are 41,000 different sequences
Carried out, this number would approximate 1.5 x 10602, a number so huge that it
provides nearly endless degrees of variation.
33. DNA Replication: Preserving the Code and Passing It On
The sequence of bases along the length of a gene constitutes the language of DNA.
For this language to be preserved for hundreds of generations, it will be necessary
for the genetic program to be duplicated and passed on to each offspring.
This process of duplication is called DNA replication.
34. In the following example, we will show replication in bacteria, but
with some exceptions, it also applies to the process as it works in
eucaryotes and some viruses.
Early in binary ﬁssion, the metabolic machinery of a bacterium
responds to a message and initiates the duplication of the
This DNA replication must be completed during a single generation
time (around 20 minutes in E. coli).
35. The Overall Replication Process
What features allow the DNA molecule to be exactly duplicated, and how is its integrity retained?
DNA replication requires a careful orchestration of the actions of 30 different enzymes, which
separate the strands of the existing DNA molecule, copy its template, and produce two complete
36. A simpliﬁed version of replication includes the following:
1. uncoiling the parent DNA molecule,
2. unzipping the hydrogen bonds between the base pairs, thus separating the two strands
and exposing the nucleotide sequence of each strand (which is normally buried in the
center of the helix) to serve as templates, and
3. synthesizing two new strands by attachment of the correct complementary nucleotides
to each single-stranded template.
Acritical feature of DNA replication is that each daughter molecule will be identical to
the parent in composition, but neither one is completely new; the strand that serves as a
template is an original parental DNA strand.
The preservation of the parent molecule in this way, termed semiconservative
replication , helps explain the reliability and ﬁdelity of replication.
38. Reﬁnements and Details of Replication
The origin of replication is a short sequence rich in adenine and thymine that, you will
recall, are held together by only two hydrogen bonds rather than three.
Because the origin of replication is AT-rich, less energy is required to separate the two
strands than would be required if the origin were rich in guanine and cytosine.
Prior to the start of replication, enzymes called helicases (unzipping enzymes) bind to
the DNA at the origin.
These enzymes untwist the helix and break the hydrogen bonds holding the two
strands together, resulting in two separate strands, each of which will be used as a
template for the synthesis of a new strand.
39. The process of synthesizing a new daughter strand of DNA using the parental
strand as a template is carried out by the enzyme DNA polymerase III.
The entire process of replication does, however, depend on several enzymes and
can be most easily understood by keeping in mind a few points concerning both
the structure of the DNA molecule and the limitations of DNA polymerase III.
These points include:
40. 1. The nucleotides that need to be read by DNA polymerase III are buried deep within
the double helix. Accessing these nucleotides requires both that the DNA molecule be
unwound and that the two strands of the helix be separated from one another.
2. DNA polymerase III is unable to begin synthesizing a chain of nucleotides but can only
continue to add nucleotides to an already existing chain.
3. DNA polymerase III can only add nucleotides in one direction, so a new strand is
always synthesized 5 prime to 3 prime.
With these constraints in mind, the details of replication can be more easily
41. Replication begins when an RNA primer is synthesized and enters at the origin of
DNA polymerase III cannot begin synthesis unless it has this short strand of RNA to
serve as a starting point for adding nucleotides.
Because the bacterial DNA molecule is circular, opening of the circle forms two
replication forks, each containing its own set of replication enzymes.
The DNA polymerase III is a huge enzyme complex that encircles the replication fork
and adds nucleotides in accordance with the template pattern.
As synthesis proceeds, the forks continually open up to expose the template for
42. Because DNA polymerase is correctly oriented for synthesis only in
the 5 prime to 3 prime direction of the new molecule (red) strand, only
one strand, called the leading strand, can be synthesized as a
continuous, complete strand.
The strand with the opposite orientation (3 prime to 5 prime) is termed
the lagging strand.
Because it cannot be synthesized continuously, the polymerase adds
nucleotides a few at a time in the direction away from the fork (5
prime to 3 prime).
43. As the fork opens up a bit, the next segment is synthesized backward to the point
of the previous segment, a process repeated at both forks until synthesis is
In this way, the DNA polymerase is able to synthesize the two new strands
This manner of synthesis produces one strand containing short fragments of DNA
(100 to 1,000 bases long) called Okazaki fragments.
These fragments are attached to the growing end of the lagging strand by another
enzyme called DNA ligase.
44. Elongation and Termination of the Daughter Molecules
The addition of nucleotides proceeds at an astonishing pace, estimated in some bacteria
to be 750 bases per second at each fork! As replication proceeds, one new double
strand loops down.
The DNA polymerase I removes the RNA primers used to initiate DNA synthesis and
replaces them with DNA.
When the forks come full circle and meet, ligases move along the lagging strand to
begin the initial linking of the fragments and to complete synthesis and separation of
the two circular daughter molecules.
45. Like any language, DNA is occasionally “misspelled” when an incorrect base is added to
the growing chain.
Studies have shown that such mistakes are made once in approximately 108 to 109 bases,
but most of these are corrected.
If not corrected, they are referred to as mutations and can lead to serious cell dysfunction
and even death.
Because continued cellular integrity is very dependent on accurate replication, cells have
evolved their own proofreading function for DNA.
DNA polymerase III, the enzyme that elongates the molecule, can also detect incorrect,
unmatching bases, excise them, and replace them with the correct base.
DNA polymerase I can also proofread the molecule and repair damaged DNA.
46. Replication in Other Biological Systems
The replication pattern of eucaryotes is similar to that of procaryotes.
It also uses a variety of DNA polymerases, and replication proceeds in both directions
from the point of origin.
A novel form of DNA synthesis called rolling circle occurs in circular genetic material
found in plasmids and some bacterial viruses.
In general, it involves the replication of one strand of the parent DNA, forming a single
strand that rolls off the circle.
This strand is then replicated, thus converting it to a double-stranded duplicate of the
original DNA molecule.