Download (DNA).

Puria Rafsanjani
Mehrshad Nourani
Ashkan Novin
Nucleotides, Nucleic
acids, and Heredity
While these dogs might appear to be a normal
mother and puppy, the latter is really the first
cloned dog, Snuppy. The larger dog is a male
Afghan whose DNA was used to create the
clone.
History of Genes discovery
 From
about the end of the nineteenth century, biologists
suspected that the transmission of hereditary information from
one generation to another took place in the nucleus of the
cell. More precisely, they believed that structures within the
nucleus, called chromosomes, have something to do with
heredity.
 Different
species have different numbers of chromosomes in
the nucleus. The information that determines external
characteristics (red hair, blue eyes) and internal characteristics
(blood group, hereditary diseases) was thought to reside in
genes located inside the chromosomes.
What does DNA do?
 The
information that tells the cell which proteins to
manufacture is carried in the molecules of DNA. We now
know that not all genes lead to the production of protein,
but all genes do lead to the production of another type of
nucleic acid, called ribonucleic acid (RNA).
What Are Nucleic Acids Made Of?
 Two
kinds of nucleic acids are found in cells: ribonucleic
acid (RNA) and deoxyribonucleic acid (DNA). Each has its
own role in the transmission of hereditary information.

As we just saw, DNA is present in the chromosomes of the
nuclei of eukaryotic cells. RNA is not found in the
chromosomes, but rather is located elsewhere in the
nucleus and even outside the nucleus, in the cytoplasm.
Nucleic Acids => A. Bases
 The
bases found in DNA and RNA are chiefly those shown
in Figure. All of them are basic because they are
heterocyclic aromatic amines.
Purines
Pyrimidines
The five principal bases of DNA and RNA. The hydrogens shown in blue
are lost when the bases bond to monosaccharides.
What the hell are purines and Pyrimidines 
 Pyrimidine
is a heterocyclic aromatic organic
compound similar to benzene and pyridine,
containing two nitrogen atoms at positions 1
and 3 of the six-member ring.
What the hell are purines and Pyrimidines 
A
purine is a heterocyclic aromatic organic
compound. It consists of a pyrimidine ring fused
to an imidazole ring.
 Purines
are the most widely occurring nitrogencontaining heterocycle in nature.
 Imidazole
is an organic compound with the
formula (CH)2N(NH)CH.
Nucleic Acids => A. Bases
 adenine
(A) and guanine (G)—are purines
 the
other three—cytosine (C), thymine (T), and uracil (U)—
are pyrimidines.
Purines
Pyrimidines
The five principal bases of DNA and RNA. The hydrogens shown in blue
are lost when the bases bond to monosaccharides.
 The
two purines (A and G) and one of the pyrimidines (C) are
found in both DNA and RNA,
 but
uracil (U) is found only in RNA, and thymine (T) is found
only in DNA. Note that thymine differs from uracil only in the
methyl group in the 5 position.
Nucleic Acids => B. Sugars
 The
sugar component of RNA is D-ribose. In DNA, it is
2-deoxy-D-ribose (hence the name deoxyribonucleic
acid).
Nucleoside:
 The
combination of sugar and base is known as a
nucleoside.

The purine bases are linked to C-1 of the monosaccharide
through N-9 (the nitrogen at position 9 of the fivemembered ring) by a b-N-glycosidic bond:
Nucleoside:
 The
pyrimidine bases are linked to C-1 of the
monosaccharide through their N-1 by a b-N-glycosidic
bond.
Nucleic Acids => C. Phosphate
 The
third component of nucleic acids is phosphoric acid.
When this group forms a phosphate ester bond with a
nucleoside, the result is a compound known as a nucleotide.
For example, adenosine combines with phosphate to form the
nucleotide adenosine 5’ -monophosphate (AMP):
The ‘ sign in adenosine
5’-monophosphate is used to
distinguish which molecules the
phosphate is bound to. Numbers
without primes refer to positions
on the purine or pyrimidine
base. Numbers on the sugar are
denoted with primes.
14
 we
will see how DNA and RNA are chains of
nucleotides.
In summary:
A
nucleoside : Base 1 Sugar
A
nucleotide : Base 1 Sugar 1 Phosphate
A
nucleic acid : A chain of nucleotides
What Is the Structure of DNA and RNA?
A. Primary Structure
 Nucleic
acids are polymers of nucleotides. Their
primary structure is the sequence of nucleotides.
Note that it can be divided into two parts:
 (1)
the backbone of the molecule and

(2) the bases that are the side-chain groups. The
backbone in DNA consists of alternating
deoxyribose and phosphate groups.

Each phosphate group is linked to the 3’ carbon
of one deoxyribose unit and simultaneously to the
5’ carbon of the next deoxyribose unit.
 The
primary structure of RNA is the same
except that each sugar is ribose (so an -OH
group appears in the 2’ position) rather
than deoxyribose

and U is present instead of T.
What Is the Structure of DNA and RNA?
B. Secondary Structure of DNA
 DNA
is composed of two strands entwined around each
other in a double helix.
 The
sugar–phosphate backbone is on the outside,
exposed to the aqueous environment, and the bases
point inward. The bases are hydrophobic, so they try to
avoid contact with water. Through their hydrophobic
interactions, they stabilize the double helix.
 The
bases so paired form hydrogen
bonds with each other, two for A-T and
three for G-C, thereby stabilizing the
double helix. A-T and G-C are
complementary base pairs.
 The
bases of DNA cannot stack properly
in the double helix if a purine is opposite
a purine or if a pyrimidine is opposite a
pyrimidine.
 Only
one hydrogen bond is possible for
TG or CA. These combinations are not
found in DNA.
 The
form of the DNA double helix shown
in Figure is called B-DNA.
 It
is the most common and most stable
form. Other forms become possible
where the helix is wound more tightly or
more loosely, or is wound in the opposite
direction.

With B-DNA, a distinguishing feature is
the presence of a major groove and a
minor groove, which arise because the
two strands are not equally spaced
around the helix.
 Interactions
of proteins and drugs with
the major and minor grooves of DNA
serve as an active area of research.
What Is the Structure of DNA and RNA?
C. Higher-Order Structures of DNA
 If
a human DNA molecule were fully stretched out, its
length would be perhaps 1 m. However, the DNA
molecules in the nuclei are not stretched out, but rather
coiled around basic protein molecules called histones.
 The
acidic DNA and the basic histones attract each other
by electrostatic (ionic) forces, combining to form units
called nucleosomes.
 In
a nucleosome, eight histone
molecules form a core, around which a
147-base-pair DNA double helix is
wound.
 Nucleosomes
are further condensed
into chromatin when a 30-nm-wide fiber
forms in which nucleosomes are wound
in a solenoid fashion, with six
nucleosomes forming a repeating unit.

Chromatin fibers are organized still
further into loops, and loops are
arranged into bands to provide the
superstructure of chromosomes.
let us summarize the three differences in
structure between DNA and RNA:
 1.
DNA has four bases: A, G, C, and T. RNA has three of
these bases—A,G, and C—but its fourth base is U, not T.
 2.
In DNA, the sugar is 2-deoxy-D-ribose. In RNA, it is Dribose.
 3.
DNA is almost always double-stranded, with the helical
structure shown.
 There
are several kinds of RNA, None of them has a
repetitive double-stranded structure like DNA, although
base-pairing can occur within a chain. When it does,
adenine pairs with uracil because thymine is not present.
 Other
combinations of hydrogenbonded bases are also possible
outside the confines of a double
helix.
17.4 What Are the Different Classes
of RNA? =>1. Messenger RNA (mRNA)
 mRNA
molecules are produced in the process called
transcription, and they carry the genetic information from
the DNA in the nucleus directly to the cytoplasm, where
most of the protein is synthesized.

Messenger RNA consists of a chain of nucleotides whose
sequence is exactly complementary to that of one of the
strands of the DNA.
 This
type of RNA is not long-lived, however. It is synthesized
as needed and then degraded, so its concentration at
any given time is rather low. The size of mRNA varies
widely, with the average unit containing perhaps 750
nucleotides.
central dogma of molecular
biology:
 The
fundamental process of
information transfer in cells.
 (1)
Information encoded in the
nucleotide sequence of DNA
is transcribed through synthesis
of an RNA molecule whose
sequence is dictated by the
DNA sequence.
 (2)
As the sequence of this
RNA is read (as groups of three
consecutive nucleotides) by
the protein synthesis
machinery, it is translated into
the sequence of amino acids
in a protein.
17.4 What Are the Different Classes
of RNA? =>2. Transfer RNA (tRNA)
 Containing
from 73 to 93
nucleotides per chain, tRNAs are
relatively small molecules. There is at
least one different tRNA molecule
for each of the 20 amino acids from
which the body makes its proteins.
 Transfer
RNA molecules contain not
only cytosine, guanine, adenine,
and uracil, but also several other
modified nucleotides, such as 1methylguanosine.
17.4 What Are the Different Classes
of RNA? =>2. Transfer RNA (tRNA)
17.4 What Are the Different Classes
of RNA? =>3.Ribosomal RNA (rRNA)
 Ribosomes,
which are small spherical bodies located in the cells
but outside the nuclei, contain rRNA. They consist of about 35%
protein and 65% ribosomal RNA (rRNA). These large molecules
have molecular weights up to 1 million. As you already know,
protein synthesis takes place on the ribosomes.
 Ribosomes
consist of two subunits, one larger than the other. In
turn, the smaller subunit consists of one large RNA molecule and
about 20 different proteins; the larger subunit consists of two RNA
molecules in prokaryotes (three in eukaryotes) and about 35
different proteins in prokaryotes (about 50 in eukaryotes).
17.4 What Are the Different Classes
of RNA? =>4. Small Nuclear RNA (snRNA)
A
recently discovered RNA molecule is sn- RNA, which is found,
as the name implies, in the nucleus of eukaryotic cells. This type
of RNA is small, about 100 to 200 nucleotides long, but it is
neither a tRNA molecule nor a small subunit of rRNA.
 In
the cell, it is complexed with proteins to form small nuclear
ribonucleoprotein particles, sn- RNPs, pronounced “snurps.”
Their function is to help with the processing of the initial mRNA
transcribed from DNA into a mature form that is ready for export
out of the nucleus. This process is often referred to as splicing,
and it is an active area of research.
17.4 What Are the Different Classes
of RNA? =>5. Micro RNA (miRNA)
A
very recent discovery is another type of small RNA, miRNA. These
RNAs are only 20–22 nucleotides long but are important in the timing
of an organism’s development.
 They
inhibit translation of mRNA into protein and promote the
degradation of mRNA. It was recently discovered, however, that
these versatile RNAs can also stimulate protein production in cells
when the cell cycle has been arrested.
 They
play important roles in cancer, stress respsonses, and viral
infections.
17.4 What Are the Different Classes
of RNA? =>6. Small Interfering RNA (siRNA)
 Short
stretches of RNA (20–30 nucleotides long), called small
interfering RNA, have been found to have an enormous control over
gene expression.
 This
process serves as a protective mechanism in many species, with
the siRNAs being used to eliminate expression of an undesirable gene.

siRNAs lead to the degradation of specific mRNA molecules.
 In
what has become an explosion of new biotechnology, many
companies have been created to produce and market designer
siRNAs to knock out hundreds of known genes. This technology also
has medical applications, as siRNA has been used to protect mouse
liver from hepatitis and to help clear infected liver cells of the disease.
17.5 What Are Genes?

A gene is a stretch of DNA, containing a few hundred
nucleotides, that carries one particular message—for example,
“make a globin molecule” or “make a tRNA molecule.” One
DNA molecule may have between 1 million and 100 million
bases. Therefore, many genes are present in one DNA
molecule.

In bacteria, this message is continuous; in higher organisms, it is
not. That is, stretches of DNA that spell out (encode) the amino
acid sequence to be assembled are interrupted by long
stretches that seemingly do not code for anything. The coding
sequences are called exons, short for “expressed sequences,”
and the noncoding sequences are called introns, short for
“intervening sequences.”
 In
other words, the
introns function as
spacers and, in rare
instances, as enzymes,
catalyzing the splicing
of exons into mature
mRNA.
 Figure
shows the
difference between
prokaryotic and
eukaryotic production
of proteins.
 In
humans, only 3% of the DNA codes for proteins or
RNA with clear functions. Introns are not the only
noncoding DNA sequences, however.
 Satellites
are DNA molecules in which short nucleotide
sequences are repeated hundreds or thousands of
times. Large satellite stretches appear at the ends and
centers of chromosomes and provide stability for the
chromosomes.
 Smaller
repetitive sequences, called mini-satellites or
microsatellites, are associated with cancer when they
mutate.
17.6 How Is DNA Replicated?
Introduction
 In
a human cell, some 3 billion base pairs must be
duplicated at each cell cycle, and a fully grown human
being may contain more than 1 trillion cells.
 Each
cell contains the same amount of DNA as the
original single cell.
17.6 How Is DNA Replicated?
Introduction
 Replication
begins at a point in the DNA called an origin
of replication.
 In
human cells, the average chromosome has several
hundred origins of replication where the copying occurs
simultaneously.

The DNA double helix has two strands running in opposite
directions.
 The
point on the DNA where replication is proceeding is
called the replication fork.
17.6 How Is DNA Replicated?
 Replication
is bidirectional and takes place at the same
speed in both directions. An interesting detail of DNA
replication is that the two daughter strands are synthesized
in different ways.
 One
of the syntheses is continuous along the 3’→5’ strand.
It is called the leading strand. Along the other strand that
runs in the 5’→3’ direction, the synthesis is discontinuous. It
is called the lagging strand.
 Replication
always proceeds from the 5’ to the 3’ direction
from the perspective of the chain that is being synthesized.
 General
features of the replication of DNA. The two
strands of the DNA double helix are shown separating at
the replication fork.

The actual reaction occurring is a nucleophilic
attack by the 3’ hydroxyl of the deoxyribose of
one nucleotide against the first phosphate on
the 5’ carbon of the incoming nucleoside
triphosphate.

One of the more interesting aspects of DNA
replication is that the basic reaction of
synthesis always requires an existing chain with
a nucleotide that has a free 3’-hydroxyl to do
the nucleophilic attack. DNA replication
cannot begin without this preexisting chain to
latch onto. We call this chain a primer. In all
known forms of replication, the primer is made
out of RNA, not DNA.
 Replication
is a very complex process involving a number of
enzymes and binding proteins. A growing body of evidence
indicates that these enzymes assemble their products in
“factories” through which the DNA moves. Such factories
may be bound to membranes in bacteria. In higher
organisms, the replication factories are not permanent
structures.
 Instead,
they may be disassembled and their parts
reassembled in ever-larger factories. These assemblies of
enzyme “factories” go by the name of replisomes, and they
contain key enzymes such as polymerases, helicases, and
primases.
Steps of DNA Replication :
1. Opening up the superstructure
 During
replication, the very condensed superstructure of
chromosomes must be opened so that it becomes
accessible to enzymes and other proteins.
A
complicated signal transduction mechanism
accomplishes this feat. One notable step of the signal
transduction is the acetylation and deacetylation of key
lysine residues of histones.

When histone acetylase, an enzyme, puts acetyl groups
on key lysine residues, some positive charges are
eliminated and the strength of the DNA–histone
interaction is weakened
Steps of DNA Replication :
1. Opening up the superstructure
 Histone
 This
Acetylation :
process allows the opening up of key regions on the
DNA molecule. When another enzyme, histone
deacetylase, removes these acetyl groups, the positive
charges are reestablished. That, in turn, facilitates
regaining the highly condensed structure of chromatin.
Steps of DNA Replication :
2. Relaxation of Higher-Order Structures of DNA
 Topoisomerases
(also called gyrases) are enzymes that
facilitate the relaxation of supercoiling in DNA. They do so
during replication by temporarily introducing either singleor double-strand breaks in DNA.
 The
transient break forms a phosphodiester linkage
between a tyrosyl residue of the enzyme and either the 5’
or 3’ end of a phosphate on the DNA.
 Once
the supercoiling is relaxed, the broken strands are
joined together, and the topoisomerase diffuses from the
location of the replicating fork. Topoisomerases are also
involved in the untangling of the replicated chromosomes,
before cell division can occur.
Steps of DNA Replication :
3. Unwinding the DNA Double Helix
 The
replication of DNA molecules starts with the unwinding
of the double helix, which can occur at either end or in
the middle.
 Special
unwinding protein molecules, called helicases,
attach themselves to one DNA strand and cause the
separation of the double helix.
 Helicases
of eukaryotes are made of six different protein
subunits. The subunits form a ring with a hollow core, where
the single-stranded DNA sits. The helicases hydrolyze ATP
as the DNA strand moves through.
 The
energy of the hydrolysis promotes this movement.
Steps of DNA Replication :
4. Primers/Primases
 Primers
are short—4 to 15 nucleotides long—RNA
oligonucleotides synthesized from ribonucleoside
triphosphates.
 They
are needed to initiate the synthesis of both daughter
strands. The enzyme catalyzing this synthesis is called
primase.
 Primases
form complexes with DNA polymerase in
eukaryotes.
 Primers
are placed about every 50 nucleotides in the
lagging-strand synthesis.
Steps of DNA Replication :
5. DNA Polymerase
 Once
the two strands are separated at the replication
fork, the DNA nucleotides must be lined up.
 All
four kinds of free DNA nucleotide molecules are present
in the vicinity of the replication fork. These nucleotides
constantly move into the area and try to fit themselves into
new chains.
 Wherever
a cytosine, for example, is present on one of the
strands of an unwound portion of the helix, all four
nucleotides may approach, but three of them will be
turned away because they do not fit. Only the nucleotide
of guanine fits.
Steps of DNA Replication :
5. DNA Polymerase

In the absence of an enzyme, this alignment is extremely slow.
The speed and specificity are provided by DNA polymerase. It
surrounds the end of the DNA template– primer complex,
creating a specifically shaped pocket for the incoming
nucleotide. With such a close contact, the activation energy is
lowered and the polymerase enables complementary base
pairing with high specificity at a rate of 100 times per second.

While the bases of the newly arrived nucleotides are being
hydrogen-bonded to their partners, polymerases join the
nucleotide backbones.

Along the lagging strand 3’ to 5’, the enzymes can synthesize
only short fragments because the only way they can work is
from 5’ to 3’. These short fragments consist of about 200
nucleotides each, named Okazaki fragments after their
discoverer.
And Again :
Steps of DNA Replication :
6. Ligation
 The
Okazaki fragments and any nicks remaining are
eventually joined together by another enzyme, DNA
ligase.
 At
the end of the process, there are two double-stranded
DNA molecules, each exactly the same as the original
molecule.
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