Chapter 22.

Nucleic Acids
22.1 Types of Nucleic Acids
22.2 Nucleotides: Building Blocks of Nucleic Acids
22.3 Primary Nucleic Acid Structure
22.4 The DNA Double Helix
22.5 Replication of DNA Molecules
22.6 Overview of Protein Synthesis
22.7 Ribonucleic Acids
Chemistry at a Glance: DNA Replication
22.8 Transcription: RNA Synthesis
22.9 The Genetic Code
22.10 Anticodons and tRNA Molecules
22.11 Translation: Protein Synthesis
22.12 Mutations
Chemistry at a Glance: Protein Synthesis
22.13 Nucleic Acids and Viruses
22.14 Recombinant DNA and Genetic Engineering
22.15 The Polymerase Chain Reaction
22.16 DNA Sequencing
Students should be able to:
1. Relate DNA to genes and chromosomes.
2. Describe the structure of a molecule of DNA including the base-pairing
pattern.
3. Describe the structure of a nucleotide of RNA.
4. Describe the structure of a molecule of RNA.
5. Describe the three kinds of RNA and construct a pictorial representation.
6. Summarize the physiology of DNA in terms of replication and protein
synthesis.
7. List the sequence of events in DNA replication and explain why it is referred
to as semiconservative.
8. Evaluate the process of transcription.
9. Evaluate the process of translation.
10. Given a DNA coding strand and the genetic code , determine the
complementary messenger RNA strand, the codons that would be involved in
peptide formation from the messenger RNA sequence, and the amino acid
sequence that would be translated.
11. Define mutation.
12. Differentiate between base substitutions and base insertions and/or
deletions.
13. Discuss sickle-cell anemia.
14. Describe how viruses are referenced and categorized.
15. Define bacteriophage.
16. Describe the structure and reproductive cycle(s) of viruses.
17. Analyze the HIV virus as an example of a retrovirus.
18. Evaluate the dangers associated with emerging viruses.

1
22.6 Overview of Protein Synthesis
22.7 Ribonucleic Acids
Chemistry at a Glance: DNA Replication
22.8 Transcription: RNA Synthesis
22.9 The Genetic Code
22.10 Anticodons and tRNA Molecules
22.11 Translation: Protein Synthesis
22.12 Mutations
Chemistry at a Glance: Protein Synthesis
22.13 Nucleic Acids and Viruses
22.14 Recombinant DNA and Genetic Engineering
22.15 The Polymerase Chain Reaction
22.16 DNA Sequencing

Introduction
A most remarkable property of living cells is their ability to produce exact
replicas of themselves. This is due to the cells containing fact that all the
instructions needed for making the complete organism of which they are a
part. Nucleic acids are the molecules within a cell that are responsible for
these amazing capabilities.

The first isolation of nucleic acid we now refer to as DNA was accomplished
by Swiss physiologist Johann Friedrich Miescher circa 1870 while studying
the nuclei of white blood cells. In the 1920's nucleic acids were found to be
major components of chromosomes, small gene-carrying bodies in the nuclei
of complex cells. Elemental analysis of nucleic acids showed the presence of
phosphorus, in addition to the usual C, H, N & O. We now know that nucleic
acids are found throughout a cell, not just in the nucleus, the name nucleic
acid is still used for such materials.
A nucleic acid is a polymer in which the monomer units are nucleotides.
There are two Types of Nucleic Acids:
DNA: Deoxyribonucleic Acid: Found within cell nucleus for storing and
transfering of genetic information that are passed from one cell to other
during cell division
RNA: Ribonucleic Acid: Occurs in all parts of cell serving the primary
function is to synthesize the proteins needed for cell functions.

22.1 Types of Nucleic Acids

The nucleic acids are very large molecules that have two main parts. The
backbone of a nucleic acid is made of alternating sugar and phosphate
molecules bonded together in a long chain, represented below:

2
 sugar phosphate sugar phosphate ...

Each of the sugar groups in the backbone is attached (via the bond shown in
red) to a third type of molecule called a nucleotide base. There are only four
different nucleotide bases can occur in a nucleic acid and are classified as
pyrimidine or purine bases:

Though only four different nucleotide bases can occur in a nucleic acid, each
nucleic acid contains millions of bases bonded to it. The order in which these
nucleotide bases appear in the nucleic acid is the coding for the information
carried in the molecule. In other words, the nucleotide bases serve as a sort
of genetic alphabet on which the structure of each protein in our bodies is
encoded.

3
DNA
In most living organisms (except for viruses), genetic information is stored
in the molecule deoxyribonucleic acid, or DNA. DNA is made and resides in
the nucleus of living cells. DNA gets its name from the sugar molecule
contained in its backbone(deoxyribose); however, it gets its significance
from its unique structure. Four different nucleotide bases occur in DNA:
adenine (A), cytosine (C), guanine (G), and thymine (T).

22.2 Nucleotides: Building Blocks of Nucleic Acids

Names of DNA Nucleotide

Name Base Nucleoside 5'-Nucleotide

DAMP Adenine 2'-Deoxyadenosine 2'-Deoxyadenosine-5'-monophosphate

DCMP Cytosine 2'-Deoxycytidine 2'-Deoxycytidine-5'-monophosphate

DGMP Guanine 2'-Deoxyguanosine 2'-Deoxyguanosine-5'-monophosphate

DTMP Thymine 2'-Deoxythymidine 2'-Deoxythymidine-5'-monophosphate

RNA has the same nucleotide srtuctiure except the thymine base is replaces
by uracil.

22.3 Primary Nucleic Acid Structure

Polynucleotides
In polynucleotides, nucleotides are joined to one another by covalent bonds
between the phosphate of one and the sugar of another. These linkages are
called phosphodiester linkages. This nucleic acids found in the cell have
primary structures that arise from the end-to-endl polymerization of single
nucleotide units. The links between each nucleotide are formed by
esterification reactions between the sugar's C3′ hydroxyl group and the -
phosphate of an incoming nucleoside triphosphate (NTP) to form a
phosphoester linkage.

The sugar is ribose in the case of RNA, deoxyribose in DNA. This

polymerization process leaves a free hydroxyl on the incoming nucleotide (on
the 3′ C of the sugar) to serve for the next reaction in chain elongation.

22.4 The DNA Double Helix

4
The 1962 Nobel Prize in Physiology or Medicine was awarded to Crick,
Watson and Wilkins for the discovery of the molecular structure of DNA –
the double helix.
Chemical Structure of the DNA double strands
DNA (deoxyribonucleic acid) is a double-stranded molecule that is twisted
into a helix like a spiral staircase. Each strand is comprised of a sugar-
phosphate backbone and numerous base chemicals attached in pairs.

The four bases that make up the stairs in the spiraling staircase are adenine
(A), thymine (T), cytosine (C) and guanine (G). These stairs act as the
"letters" in the genetic alphabet, combining into complex sequences to form
the words, sentences and paragraphs that act as instructions to guide the
formation and functioning of the host cell. Maybe even more appropriately,
the A, T, C and G in the genetic code of the DNA molecule can be compared
to the "0" and "1" in the binary code of computer software. Like software to
a computer, the DNA code is a genetic language that communicates
information to the organic cell.

Genetic code
The DNA code, like a floppy disk of binary code, is quite simple in its basic
paired structure. However, it's the sequencing and functioning of that code
that's enormously complex. Through recent technologies like x-ray
crystallography, we now know that the cell is not a "blob of protoplasm", but

5
rather a microscopic marvel that is more complex than the space shuttle.
The cell is very complicated, using vast numbers of phenomenally precise
DNA instructions to control its every function.

22.5 Replication of DNA Molecules

Before a cell divides, its DNA is replicated (duplicated.) Because the
two strands of a DNA molecule have complementary base pairs, the
nucleotide sequence of each strand automatically supplies the information
needed to produce its partner. If the two strands of a DNA molecule are
separated, each can be used as a pattern or template to produce a
complementary strand. Each template and its new complement together
then form a new DNA double helix, identical to the original.
Before replication can occur, the length of the DNA double helix about
to be copied must be unwound. In addition, the two strands must be
separated, much like the two sides of a zipper, by breaking the weak
hydrogen bonds that link the paired bases. Once the DNA strands have
been unwound, they must be held apart to expose the bases so that new
nucleotide partners can hydrogen-bond to them.
The enzyme DNA polymerase then moves along the exposed DNA
strand, joining newly arrived nucleotides into a new DNA strand that is
complementary to the template.
Each cell contains a family of more than thirty enzymes to insure the
accurate replication of DNA.

6
22.6 Overview of Protein Synthesis

DNA code: containing specific base code is used to create a specific

polypepetide-the protein containing a certain sequence of amino acids.

The genetic code present in the DNA and later transcribed into mRNA
consists of 64 triplets of nucleotides. These triplets are called
codons.With three exceptions, each codon encodes for one of the 20 amino
acids used in the synthesis of proteins. That produces some redundancy in
the code: most of the amino acids being encoded by more than one codon.

RNA polymerase: RNA polymerases are enzyme complexes that synthesize

mRNA molecules using DNA as a template, in the process known as
transcription.

Protein snthesis can be divided into two parts:

1. Transcription
Before the synthesis of a protein begins, the corresponding RNA molecule is
produced by RNA transcription. One strand of the DNA double helix is used
as a template by the RNA polymerase to synthesize a messenger RNA
(mRNA). This mRNA migrates from the nucleus to the cytoplasm. During
this step, mRNA goes through different types of maturation including one

7
called splicing when the non-coding sequences are eliminated. The coding
mRNA sequence can be described as a unit of three nucleotides called a
codon.
2. Translation
The ribosome binds to the mRNA at the start codon (AUG) that is
recognized only by the initiator tRNA. The ribosome proceeds to the
elongation phase of protein synthesis. During this stage, complexes,
composed of an amino acid linked to tRNA, sequentially bind to the
appropriate codon in mRNA by forming complementary base pairs with the
tRNA anticodon. The ribosome moves from codon to codon along the
mRNA. Amino acids are added one by one, translated into polypeptidic
sequences dictated by DNA and represented by mRNA. At the end, a release
factor binds to the stop codon, terminating translation and releasing the
complete polypeptide from the ribosome.

One specific amino acid can correspond to more than one codon. The genetic
code is said to be degenerate.

22.7 Ribonucleic Acids

One of the two main types of nucleic acid (the other being DNA), which
functions in cellular protein synthesis in all living cells. Like DNA, it consists
of strands of repeating nucleotides joined in chainlike fashion, but the
strands are single and it has the nucleotide uracil (U) where DNA has
thymine (T).

Messenger RNA
Whereas most types of RNA are the final products of their genes, mRNA is
an intermediate in information transfer. It carries information from DNA to
the ribosome in a genetic code that the protein-synthesizing machinery
translates into protein. Specifically, mRNA sequence is recognized in a

8
sequential fashion as a series of nucleotide triplets by tRNAs via base pairing
to the three-nucleotide anticodons in the tRNAs. There are specific triplet
codons that specify the beginning and end of the protein-coding sequence.
Thus, the function of mRNA involves the reading of its primary nucleotide
sequence, rather than the activity of its overall structure. Messenger RNAs
are typically shorter-lived than the more stable structural RNAs, such as
tRNA and rRNA. See Genetic code
Small nuclear RNA
Small RNAs, generally less than 300 nucleotides long and rich in uridine (U),
are localized in the nucleoplasm (snRNAs) and nucleolus (snoRNAs) of
eukaryotic cells. There they take part in RNA processing, such as intron
removal during eukaryotic mRNA splicing and posttranscriptional
modification that occurs during production of mature rRNA. See Intron
Catalytic RNA
RNA enzymes, or ribozymes, are able to catalyze specific cleavage or joining
reactions either in themselves or in other molecules of nucleic acid. See
Catalysis, Ribozyme

22.8 Transcription: RNA Synthesis

Transcription is the process of creating an equivalent RNA copy of a

sequence of DNA in double helix. Both RNA and DNA have base pairs of
nucleotides as a complementary language that can be converted back and
forth from DNA to RNA in the presence of the correct enzymes, RNA
polymerase. During transcription, a DNA sequence is read by RNA
polymerase, which produces a complementary, antiparallel RNA strand. As
opposed to DNA replication, transcription results in an RNA complement that
includes uracil (U) in all instances where thymine (T) would have occurred in
a DNA complement.
Transcription is the first step leading to gene expression. The stretch
of DNA transcribed into an RNA molecule is called a transcription unit and
encodes at least one gene. If the gene transcribed encodes for a protein, the
result of transcription is messenger RNA (mRNA), which will then be used to
create that protein via the process of translation. Alternatively, the
transcribed gene may encode for either ribosomal RNA (rRNA) or transfer
RNA (tRNA), other components of the protein-assembly process, or other
ribozymes.
A DNA transcription unit encoding for a protein contains not only the
sequence that will eventually be directly translated into the protein (the
coding sequence) but also regulatory sequences that direct and regulate the
synthesis of that protein. The regulatory sequence before (upstream from)
the coding sequence is called the five prime untranslated region (5'UTR),
and the sequence following (downstream from) the coding sequence is called
the three prime untranslated region (3'UTR).

9
Transcription has some proofreading mechanisms, but they are fewer and
less effective than the controls for copying DNA; therefore, transcription has
a lower copying fidelity than DNA replication.
As in DNA replication, DNA is read from 3' → 5' during transcription.
Meanwhile, the complementary RNA is created from the 5' → 3' direction.
Although DNA is arranged as two antiparallel strands in a double helix, only
one of the two DNA strands, called the template strand, is used for
transcription. This is because RNA is only single-stranded, as opposed to
double-stranded DNA. The other DNA strand is called the coding strand,
because its sequence is the same as the newly created RNA transcript
(except for the substitution of uracil for thymine). The use of only the 3' →
5' strand eliminates the need for the Okazaki fragments seen in DNA
replication.Transcription is divided into 5 stages: pre-initiation, initiation,
promoter clearance, elongation and termination.

Splicing of mRNA: Splicing is a modification of an RNA after transcription,

in which introns (nonessential part opf the code)are removed and
exons(essential part opf the code) are joined. Also tThe UTRs, non-coding
parts of exons at the ends of the mRNA is also removed.

Codon: The code is defined as a mapping of three-nucleotide base

sequences and the amino acids. A triplet codon in a nucleic acid sequence
usually specifies a single amino acid (though in some cases the same codon
triplet in different locations can code unambiguously for two different amino
acids.

10
22.9 The Genetic Code

DNA code: containing specific base code to create a specific polypepetide-

the protein containing a certain sequence of amino acids.

The genetic code consists of 64 triplets of nucleotides. These triplets are

called codons.With three exceptions, each codon encodes for one of the 20
amino acids used in the synthesis of proteins. That produces some
redundancy in the code: most of the amino acids being encoded by more
than one codon.

One codon, AUG serves two related functions:

 it signals the start of translation

 it codes for the incorporation of the amino acid methionine (Met) into
the growing polypeptide chain

The genetic code can be expressed as either RNA codons or DNA codons.
RNA codons occur in messenger RNA (mRNA) and are the codons that are
actually "read" during the synthesis of polypeptides during translation. But
each mRNA molecule acquires its sequence of nucleotides by transcription
from the corresponding gene. Because DNA sequencing has become so rapid
and because most genes are now being discovered at the level of DNA
before they are discovered as mRNA or as a protein product, it is extremely
useful to have a table of codons expressed as DNA. So here are both.

Note that for each table, the left-hand column gives the first nucleotide of
the codon, the 4 middle columns give the second nucleotide, and the last
column gives the third nucleotide.

The RNA Codons

Second nucleotide
U C A G
UUU Phenylalanine UCU Serine UAU Tyrosine UGU Cysteine
U
(Phe) (Ser) (Tyr) (Cys)
UUC Phe UCC Ser UAC Tyr UGC Cys C
U UUA Leucine (Leu) UCA Ser UAA STOP UGA STOP A
UGG
UUG Leu UCG Ser UAG STOP Tryptophan G
(Trp)
CCU Proline CAU Histidine CGU Arginine
C CUU Leucine (Leu) U
(Pro) (His) (Arg)

11
 CUC Leu CCC Pro CAC His CGC Arg C
CAA Glutamine
CUA Leu CCA Pro CGA Arg A
(Gln)
CUG Leu CCG Pro CAG Gln CGG Arg G
ACU AAU
AGU Serine
AUU Isoleucine (Ile) Threonine Asparagine U
(Ser)
(Thr) (Asn)
AUC Ile ACC Thr AAC Asn AGC Ser C
A
AAA Lysine AGA Arginine
AUA Ile ACA Thr A
(Lys) (Arg)
AUG Methionine
ACG Thr AAG Lys AGG Arg G
(Met) or START
GCU Alanine GAU Aspartic GGU Glycine
GUU Valine Val U
(Ala) acid (Asp) (Gly)
GUC (Val) GCC Ala GAC Asp GGC Gly C
G
GAA Glutamic
GUA Val GCA Ala GGA Gly A
acid (Glu)
GUG Val GCG Ala GAG Glu GGG Gly G
Genome:
the genome is the entirety of an organism's hereditary information. It is
encoded either in DNA or, for many types of virus, in RNA.

The Human Genome Project - the entire human genome is currently

being decoded by labs around the world. The project, which started in 1990,
aims to have the complete 3.2 billion base pair genome completed is a high
quality form in 2003, at a final cost of over 3 billion dollars. Recently (1998)
a private company, Celera Genomics, has amassed enough high speed
automated DNA sequencers and computing power (second only to the
Pentagon)

22.10 Anticodons and tRNA Molecules

These small RNAs (70–90 nucleotides) that act as adapters to translate the
nucleotide sequence of mRNA into protein sequence. They do this by
carrying the appropriate amino acid to the ribosome during the process of
protein synthesis. Each cell contains at least one type of tRNA specific for
each of the 20 amino acids, and usually several types. The base sequence in
the mRNA directs the appropriate amino acid-carrying tRNAs to the ribosome
to ensure that the correct protein sequence is made.

12
tRNA Secondary Structure

The translation process is fundamentally straightforward.

The mRNA strand bearing the transcribed code for
synthesis of a protein interacts with relatively small RNA
molecules (about 70-nucleotides) to which individual
amino acids have been attached by an ester bond at the
3'-end. These transfer RNA's (tRNA) have distinctive
three-dimensional structures cosisting of loops of single-
stranded RNA connected by double stranded segments.
This cloverleaf secondary structure is further wrapped into
an "L-shaped" assembly, having the amino acid at the end
of one arm, and a characteristic anti-codon region at the
other end. The anti-codon consists of a nucleotide triplet that is the
complement of the amino acid's codon(s). Models of two such tRNA
molecules are shown to the right. When read from the top to the bottom, the
anti-codons depicted here should complement a codon in the previous
table.

22.11 Translation: Protein Synthesis

This process involves following components:

mRNA: Messenger RNA which is a single stranded copy of a DNA double

helix base par sequence with uracil in the places where thyamine was.

13
Ribosome

Ribosomes are the components of cells that make proteins from amino acids.
Ribosomes then read the information in the mRNA and use the codond to
produce proteins.

tRNA: The genetic code is read during translation using transfer-RNA,

tRNAs that have 3-base anticodons complementary to codons in mRNA.

The Steps of Translation

1. Initiation

 The small subunit of the ribosome binds to a site "upstream" (on the
5' side) of the start of the message.
 It proceeds downstream (5' -> 3') until it encounters the start codon
AUG. (The region between the cap and the AUG is known as the 5'-
untranslated region [5'-UTR].)
 Here it is joined by the large subunit and a special initiator tRNA.
 The initiator tRNA binds to the P site (shown in pink) on the ribosome.

14
  In eukaryotes, initiator tRNA carries methionine (Met). (Bacteria use
a modified methionine designated fMet.)

2. Elongation

 An aminoacyl-tRNA (a tRNA
covalently bound to its amino acid)
able to base pair with the next codon
on the mRNA arrives at the A site
(green) associated with:
o an elongation factor (called
EF-Tu in bacteria)
o GTP (the source of the needed
energy)
 The preceding amino acid (Met at the
start of translation) is covalently
linked to the incoming amino acid
with a peptide bond (shown in red).
 The initiator tRNA is released from
the P site.
 The ribosome moves one codon
downstream.
 This shifts the more recently-arrived
tRNA, with its attached peptide, to
the P site and opens the A site for
the arrival of a new aminoacyl-tRNA.
 This last step is promoted by another
protein elongation factor (called
EF-G in bacteria) and the energy of another molecule of GTP.

Note: the initiator tRNA is the only member of the tRNA family that can bind
directly to the P site. The P site is so-named because, with the exception of
initiator tRNA, it binds only to a peptidyl-tRNA molecule; that is, a tRNA with
the growing peptide attached.

The A site is so-named because it binds only to the incoming aminoacyl-

tRNA; that is the tRNA bringing the next amino acid. So, for example, the
tRNA that brings Met into the interior of the polypeptide can bind only to the
A site.

15
3. Termination

 The end of translation occurs when the ribosome reaches one or more
STOP codons (UAA, UAG, UGA). (The nucleotides from this point to
the poly(A) tail make up the 3'-untranslated region [3'-UTR] of the
mRNA.)
 There are no tRNA molecules with anticodons for STOP codons.
 However, protein release factors recognize these codons when they
arrive at the A site.
 Binding of these proteins —along with a molecule of GTP — releases
the polypeptide from the ribosome.
 The ribosome splits into its subunits, which can later be reassembled
for another round of protein synthesis.

22.12 Mutations

A mutation is a permanent change in the DNA sequence of a gene or the

genetic code. Mutations in a gene's DNA sequence can alter the amino acid
sequence of the protein encoded by the gene.

How does this happen? Like words in a sentence, the DNA sequence of each
gene determines the amino acid sequence for the protein it encodes. The
DNA sequence is interpreted in groups of three nucleotide bases, called
codons. Each codon specifies a single amino acid in a protein.

Mutations can lead to changes in the structure of an encoded protein or to a

decrease or complete loss in its expression. Because a change in the DNA
sequence affects all copies of the encoded protein, mutations can be
particularly damaging to a cell or organism. In contrast, any alterations in
the sequences of RNA or protein molecules that occur during their synthesis
are less serious because many copies of each RNA and protein are
synthesized.

Geneticists often distinguish between the genotype and phenotype of an

organism. Strictly speaking, the entire set of genes carried by an individual
is its genotype, whereas the function and physical appearance of an
individual is referred to as its phenotype.

Chemistry at a Glance: Protein Synthesis

22.13 Nucleic Acids and Viruses

All viruses have genes made from either DNA or RNA, long molecules that
carry genetic information; all have a protein coat that protects these genes;

16
and some have an envelope of fat that surrounds them when they are
outside a cell. Viroids do not have a protein coat and prions contain no
RNA or DNA. Viruses vary from simple helical and icosahedral shapes, to
more complex structures. Most viruses are about one hundred times smaller
than an average bacterium. The origins of viruses in the evolutionary history
of life are unclear: some may have evolved from plasmids—pieces of DNA
that can move between cells—while others may have evolved from bacteria.
In evolution, viruses are an important means of horizontal gene transfer,
which increases genetic diversity.

22.14 Recombinant DNA and Genetic Engineering

1. Isolate Gene of Interest
The gene for producing a protein is isolated from a cell. The gene is on the
DNA in a chromosome. Special DNA cutting proteins are used to cut out
certain sections of DNA. The gene can be isolated and then copied so that
many genes are available to work with.
2. Prepare Target DNA
In 1973, two scientists named Boyer and Cohen developed a way to put DNA
from one organism into the DNA of bacteria. This process is called
recombinant DNA technology. First, a circular piece of DNA called a plasmid
is removed from a bacterial cell. Special proteins are used to cut the plasmid
ring to open it up.

3. Insert
DNA into Plasmid
The host DNA that produces the wanted protein is inserted into the opened
plasmid DNA ring. Then special cell proteins help close the plasmid ring.

17
4. Insert Plasmid back into cell
The circular plasmid DNA that now contains the host gene is inserted back
into a bacteria cell. The plasmid is a natural part of the bacteria cell. The
bacteria cell now has a gene in it that is from a different organism, even
from a human. This is what is called recombinant DNA technology
5. Plasmid multiplies
The plasmid that was inserted into the bacteria cell can multiply to make
several copies of the wanted gene. Now the gene can be turned on in the
cell to make proteins.
6. Target Cells Reproduce
Many recombined plasmids are inserted into many bacteria cells. While they
live, the bacteria's cell processes turn on the inserted gene and the protein
is produced in the cell. When the bacterial cells reproduce by dividing, the
inserted gene is also reproduced in the newly created cells.
7. Cells Produce Proteins
The protein that is produced can be purified and used for a medicine,
industrial, agricultural, or other uses. Check out the Uses section to see how
GE is used.

22.15 The Polymerase Chain Reaction

The polymerase chain reaction is a technique for quickly "cloning" a

particular piece of DNA in the test tube (rather than in living cells like E.
coli). Thanks to this procedure, one can make virtually unlimited copies of a
single DNA molecule even though it is initially present in a mixture
containing many different DNA molecules.

The technique was made possible by the discovery of Taq polymerase, the
DNA polymerase that is used by the bacterium Thermus auquaticus that
was discovered in hot springs. This DNA polymerase is stable at the high
temperatures need to perform the amplification, whereas other DNA
polymerases become denatured.

Since this technique involves amplification of DNA, the most obvious

application of the method is in the detection of minuscule amounts of
specific DNAs. This important in the detection of low level bacterial
infections or rapid changes in transcription at the single cell level, as well
as the detection of a specific individual's DNA in forensic science (like
in the O.J. trial). It can also be used in DNA sequencing, screening for
genetic disorders, site specific mutation of DNA, or cloning or
subcloning of cDNAs.

There are three basic steps in PCR. First, the target genetic material must be
denatured-that is, the strands of its helix must be unwound and separated-

18
by heating to 90-96°C. The second step is hybridization or annealing, in
which the primers bind to their complementary bases on the now single-
stranded DNA. The third is DNA synthesis by a polymerase. Starting from
the primer, the polymerase can read a template strand and match it with
complementary nucleotides very quickly. The result is two new helixes in
place of the first, each composed of one of the original strands plus its newly
assembled complementary strand.

All PCR really requires in the way of equipment is a reaction tube, reagents,
and a source of heat. But different temperatures are optimal for each of the
three steps, so machines now control these temperature variations
automatically.

22.16 DNA Sequencing

DNA sequencing is the determination of the precise sequence of nucleotides

in a sample of DNA.

19
The most popular method for doing this is called the dideoxy method or
Sanger method (named after its inventor, Frederick Sanger, who was
awarded the 1980 Nobel prize in chemistry [his second] for this
achievment).

Replicating a DNA strand in the presence of dideoxy-T

MOST of the time when a 'T' is required to make the new strand, the enzyme
will get a good one and there's no problem. MOST of the time after adding a
T, the enzyme will go ahead and add more nucleotides. However, 5% of the
time, the enzyme will get a dideoxy-T, and that strand can never again be
elongated. It eventually breaks away from the enzyme, a dead end product.

Sooner or later ALL of the copies will get terminated by a T, but each time
the enzyme makes a new strand, the place it gets stopped will be random.
In millions of starts, there will be strands stopping at every possible T along
the way.

ALL of the strands we make started at one exact position. ALL of them end
with a T. There are billions of them ... many millions at each possible T
position. To find out where all the T's are in our newly synthesized strand, all
we have to do is find out the sizes of all the terminated products!

20