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Chapter 25:
Nucleotides, Nucleic Acids, and Heredity
DNA Replication, Transcription
and Translation
Overview
DNA
Replication
A
Transcription
A
Translation
A
A
DNA
A
mRNA
α
Protein
Francis Crick (1958): Central Dogma of Molecular
Biology
DNA Structure
• Deoxyribonucleic acid (DNA)
• Structure: Double Helix
(Two strands)
• Function: long-term storage
of information
DNA Replication
Enzymes:
1-Helicase
A
A
2-DNA Polymerase 3-Topoisomerase 4-DNA primase 5-DNA Ligase
RNA Structure
• Ribonucleic acid (RNA)
• Structure: Single strand
• Functions:
o
mRNA: information carrier
o
rRNA: Ribosomes Constituent
o
tRNA: amino acid transporter
• Four bases :
(adenine, cytosine, guanine and uracil)
Transcription
A
A
Protein Structure
• Polypeptide:
amino acids arranged in a linear chain
• Structure:
multiple linear and 3D structures
• Functions:
o
Enzymes
o
Cell signaling (insulin)
o
Ligand binding (antibodies)
o
Transport
o
Structural
Translation
A
α
• Initiation:
the small subunit of the ribosome
binds to 5' end of the mRNA with the
help of initiation factors
• Elongation:
additional amino acid is added to the
growing polypeptide chain
• Termination:
one of the three termination codons
moves into the A site
Video
The Molecules of Heredity
• Each cell of our bodies contains thousands of different
proteins.
• How do cells know which proteins to synthesize out of
the extremely large number of possible amino acid
sequences?
• From the end of the 19th century, biologists suspected
that the transmission of hereditary information took
place in the nucleus, more specifically in structures
called chromosomes.
• The hereditary information was thought to reside in
genes within the chromosomes.
• Chemical analysis of nuclei showed chromosomes are
made up largely of proteins called histones and nucleic
acids.
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The Molecules of Heredity
• By the 1940s, it became clear that deoxyribonucleic
acids (DNA) carry the hereditary information.
• Other work in the 1940s demonstrated that each gene
controls the manufacture of one protein.
• Thus the expression of a gene in terms of an enzyme
protein led to the study of protein synthesis and its
control.
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Nucleic Acids
There are two kinds of nucleic acids in cells:
• Ribonucleic acids (RNA).
• Deoxyribonucleic acids (DNA).
Both RNA and DNA are polymers built from monomers
called nucleotides. A nucleotide is composed of:
• A base, a monosaccharide, and a phosphate.
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Purine/Pyrimidine Bases
N H2
O
4
N
3
2
N
5
6
N
O
1
2
5
N
8
N
3
N9
4
H
Puri ne
N
H
Thymine (T)
(DNA onl y)
N
Uraci l (U)
(in RNA only)
O
N
N
N
O
N H2
N
HN
H
Cytosine (C)
(DNA and
some RNA)
7
6
1
O
H
Pyri mi dine
CH3
HN
N
O
N
H
Adenine (A)
(DNA and RNA)
N
HN
H 2N
N
N
H
Guani ne (G)
(DNA and RNA)
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Nucleosides
Nucleoside: A compound that consists of D-ribose or 2deoxy-D-ribose bonded to a purine or pyrimidine base by
a -N-glycosidic bond.
uracil
HN
-D -ribos ide
1
O
5'
HOCH 2
H
N
O
H
4'
3'
O
H
2'
HO
OH
Urid ine
1'
H
a -N -glycosid ic
bon d
anomeric
carb on
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Nucleotides
Nucleotide: A nucleoside in which a molecule of phosphoric
acid is esterified with an -OH of the monosaccharide,
most commonly either at the 3’ or the 5’-OH.
NH2
N
O
5'
N
O-P-O-CH2
O
N
H
H
1'
O
H 3'
H
HO
OH
Aden os in e 5'-monophosp hate
(5'-A MP)
N
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Nucleotides
Adenosine 5’-triphosphate (ATP) serves as a common
currency into which energy gained from food is
converted and stored.
anhydride
N H2
ester
N
O
O
O
O- P-O- P-O- P-O-CH 2
N
O
O
O
O
H
H
H
H
OH
HO
N
N
AMP
ADP
Adenos ine 5'-triphosphate
(ATP)
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DNA—Primary (1°) Structure
For nucleic acids, primary structure is the sequence of
nucleotides, beginning with the nucleotide that has the
free 5’ terminus.
• The strand is read from the 5’end to the 3’end.
• Thus, the sequence AGT means that adenine (A) is the
base at the 5’ terminus and thymine (T) is the base at
the 3’ terminus.
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Structure of DNA and RNA
Figure 25.2
Schematic
diagram of a
nucleic acid
molecule. The
four bases of
each nucleic acid
are arranged in
various specific
sequences. The
base sequence is
read from the 5’
end to the 3’ end.
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DNA—2° Structure
Secondary structure: The ordered arrangement of nucleic
acid strands.
• The double helix model of DNA 2° structure was
proposed by James Watson and Francis Crick in 1953.
Double helix: A type of 2° structure of DNA in which two
polynucleotide strands are coiled around each other in a
screw-like fashion.
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THE DNA Double Helix
Figure 25.4
Threedimensional
structure of
the DNA
double helix.
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Base Pairing
Figure 25.5 A and
T pair by forming
two hydrogen
bonds. G and C
pair by forming
three hydrogen
bonds.
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Superstructure of Chromosomes
DNA is coiled around proteins called histones.
• Histones are rich in the basic amino acids Lys and Arg,
whose side chains have a positive charge.
• The negatively-charged DNA molecules and positivelycharged histones attract one another and form units
called nucleosomes.
Nucleosome: A core of eight histone molecules around
which the DNA helix is wrapped.
• Nucleosomes are further condensed into chromatin.
• Chromatin fibers are organized into loops, and the
loops into the bands that provide the superstructure of
chromosomes.
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Superstructure of Chromosomes
• Figure 25.8
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Superstructure of Chromosomes
• Figure 25.8 cont’d
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Superstructure of Chromosomes
• Figure 25.8 cont’d
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DNA and RNA
The three differences in structure between DNA and RNA
are:
• DNA bases are A, G, C, and T; the RNA bases are A, G,
C, and U.
• the sugar in DNA is 2-deoxy-D-ribose; in RNA it is Dribose.
• DNA is always double stranded; there are several kinds
of RNA, all of which are single-stranded.
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Information Transfer
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RNA
Table 25.3 The roles of Different kinds of RNA
RN A type
Size
Fun ction
Tran sfer RN A
(tRN A)
Small
Trans ports amin o acid s
to site of protein s yn thesis
Ribosomal RN A
(rRN A )
Several kin ds;
variable in s ize
Mes senger RN A
(mRN A )
Variab le
Comb ines w ith p roteins to
form ribosomes ,
th e site of p rotein synth esis.
Directs amin o seq uence of
proteins .
Small n uclear
RN A (s nRN A
Small
Proces ses in titial mRN A to its
mature form in euk aryotes .
Micro RN A
(miRN A)
Small
Affects gen e expressions;
important in grow th an d
development
Small in tefering
RN A(s iRN A )
Small
Affects gen e expression ; us ed
by s cientis ts to k nock out gene
being stud ied.
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Structure of tRNA
Figure 2.10 Structure of tRNA.
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Structure of rRNA
• Figure 25.11 The structure of a typical
prokaryotic ribosome.
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Ribosome
• Figure 25.11 cont’d
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Genes, Exons, and Introns
Gene: A segment of DNA that carries a base sequence that
directs the synthesis of a particular protein, tRNA, or
mRNA.
• There are many genes in one DNA molecule.
• In bacteria, the gene is continuous.
• In higher organisms, the gene is discontinuous.
Exon: A section of DNA that, when transcribed, codes for a
protein or RNA.
Intron: A section of DNA that does not code for anything
functional.
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Genes, Exons, and Introns
• Figure 25.12 The properties of mRNA molecules in
prokaryotes versus eukaryotic cells during transcription
and translation.
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Genes, Exons, and Introns
• Figure 2.12 cont’d
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Replication of DNA
The DNA in the chromosomes carries out two functions:
• (1) It reproduces itself. This process is called
replication.
• (2) It supplies the information necessary to make all the
RNA and proteins in the body, including enzymes.
Replication begins at a point in the DNA called the origin
of replication or a replication fork.
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Replication of DNA
Figure 25.13 General features of the replication of DNA.
The two strands of the DNA double helix are shown
separating at the replication fork.
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Replication of DNA
The replication of DNA occurs in number of distinct steps.
1. Opening up of the superstructure of the chromosomes.
One key step is this process is acetylationdeacetylation of lysine residues on histones. This
reaction eliminates some of the positive charges on
histones and weakens the strength of the DNA-histone
interaction.
Histone-(CH2 ) -NH3
+
-
+ CH3 COO
acetylat ion
deacet ylation
HO
Histone-(CH2 ) -N-C-CH3 + H2 O
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Replication of DNA
2. Relaxation of Higher-Order Structures of DNA.
Tropoisomerases (also called gyrases) temporarily
introduce either single-or double strand breaks in
DNA.
Once the supercoiling is relaxed, the broken strands
are joined together and the tropoisomerase diffuses
from the location of the replication fork.
3. Unwinding the DNA Double Helix.
Replication of DNA molecules starts with the
unwinding of the double helix which can occur at
either end or in the middle. Special unwinding
proteins called helicases, attach themselves to one
DNA strand and cause the separation of the double
helix.
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Replication of DNA
4. Primers/Primases
Primers are short—4 to 15 nucleotides long—RNA
oligonucloetides synthesized from ribonucleoside
triphosphates. They are needed to initiate the primasecatalyzed synthesis of both daughter strands.
5. DNA Polymerase
Once the two strands are separated at the replication
fork, the DNA nucleotides must be lined up. In the
absence of DNA polymerases, this alignment is
extremely slow. The enzyme enables complementary
base pairing with high specificity. While bases are
being hydrogen bonded to their partners, polymerases
join the nucleotide backbones.
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Replication of DNA
Along the lagging strand 3’—>5”, the enzymes can
synthesize only short fragments, because the only
way they can work is from 5’ to 3’. These resulting
short fragments consist of about 200 nucleotides
each, named Okazaki fragments after their
discoverer.
6. Ligation
The Okazaki fragments and any nicks remaining are
eventually joined by DNA ligase.
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DNA Repair
The viability of cells depends on DNA repair enzymes that
can detect, recognize, and remove mutations from DNA.
The most common repair mechanism is called base
excision repair (BER). This pathway contains two parts.
1. A specific DNA glycosylase recognizes the damaged
base. It hydrolyzes the N-C’ -glycosidic bond between
the damaged base and the deoxyribose, then releases the
damaged base. The sugar-phosphate backbone is still
intact.
2. The backbone is cleaved by a second enzyme, an
endonuclease. A third enzyme, an exonuclease, then
liberates the sugar-phosphate unit of the damaged site.
3. In the synthesis step, DNA polymerase inserts the correct
nucleotide and the enzyme DNA ligase seals the
backbone to compete the repair.
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How Do We Amplify DNA?
• To study DNA for basic and applied scientific purposes,
we must have enough of it to work with.
• Millions of copies of selected DNA fragments can be made
within a few hours with high precision by a technique
called polymerase chain reaction (PCR).
• To use PCR, the sequence of a gene to be copied or at
least a sequenced segment bordering the desired DNA
must be known.
• In such a case, two primers that are complementary to
the ends of the gene or to the bordering DNA can be
synthesized. The primers are polynucleotides
consisting of 12 to 16 nucleotides. When added to the
target DNA segment, they hybridize with the end of
each strand of the gene.
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How Do We Amplify DNA
A polymerase extends the primers in each direction as
individual nucleotides are assembled and connected on the
template DNA. In this way two copies are created.
The two-step process is repeated (cycle 2) when the primers
are hybridized with new strands and the primers extended
again. At this point, four new copies have been created. The
process is continued, and in 25 cycles, 225 or some 33 million
copies can be made.
This process is practical because of the discovery of heatresistant polymerases isolated from bacteria that live in hot
thermal vents on the sea floor. A temperature of 95°C is
required to unwind the double helix to hybridize the primer to
the target DNA.
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How Do We Amplify DNA?
• Figure 25.16 Polymerase chain reaction (PCR).
Oligonucleotides complementary to a given DNA
sequence prime the synthesis of only that sequence.
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