Bettelheim / Brown / Campbell / Farrell / Torres

Introduction to General, Organic, and Biochemistry 11e

Chapter 25
Nucleotides, Nucleic
Acids, and Heredity

William H. Brown Beloit College www.cengage.com/chemistry/bettelheim

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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.
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.
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
• Figure 25-1 The five principal bases of DNA and RNA.

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Nucleosides
Nucleoside:
Nucleoside A compound that consists of D-ribose or
2-deoxy-D-ribose bonded to a purine or pyrimidine base
by a -N-glycosidic bond.

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Nucleotides
Nucleotide:
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.

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Nucleotides
Deoxythymidine 3’-monophosphate (3’-dTMP),

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Nucleotides
Adenosine 5’-triphosphate (ATP)
ATP serves as a common
currency into which energy gained from food is
converted and stored.

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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:
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:
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
Three-
dimensional
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 positively-
charged histones attract one another and form units
called nucleosomes.
Nucleosome:
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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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;
2-deoxy-D-ribose in RNA it is
D-ribose.
• DNA is always double stranded;
stranded there are several kinds
of RNA, all of which are single-stranded.

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Information Transfer-Figure 25-9

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RNA
Table 25-3 The roles of Different kinds of RNA

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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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Roles of Different kinds of RNA

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Genes, Exons, and Introns
Gene:
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:
Exon A section of DNA that, when transcribed, codes for a
protein or RNA.
Intron:
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 cells during transcription and translation.

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Genes, Exons, and Introns
• Figure 25-12 The properties of mRNA in eukaryotic cells
during transcription and translation

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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.
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.
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 acetylation-
deacetylation of lysine residues on histones. This
reaction eliminates some of the positive charges on
histones and weakens the strength of the DNA-histone
interaction.

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Replication of DNA
2. Relaxation of Higher-Order Structures of DNA.
Tropoisomerases (also called gyrases)
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. 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,
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 primase-
catalyzed 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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Replication of DNA
Figure 25-14 The addition of a nucleotide to the
growing DNA chain

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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?
• 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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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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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 heat-
resistant 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 Is DNA repaired?
• The viability of cells depends on DNA repair enzymes that
can detect, recognize, and remove mutations from DNA.
• Externally, UV radiation or highly reactive oxidizing
agents, such as superoxide, may damage a base.
• Errors in copying or internal chemical reactions, such as
deamination of a base, can create damage internally
Deamination of cytosine turns it into uracil, which creates
a mismatch. The former C-G base pair becomes a U-G
mispairing that must be removed.

• One of the most common base repair prepare means is

called BER, base excision repair (Figure 25-15).

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How Is DNA repaired?
• The BER pathway contains two parts:
• 1. A specific DNA glycolase (1) recognizes the damaged
base and catalyzes the hydrolysis of the -glycosidic
bond between that base and the deoxyribose, then
releases the damaged base completing the excision. The
sugar-phosphate backbone is still intact. At the AP site
(apurinic or apyrimidinic site) created in this way, (2) the
backbone is cleaved by a second enzyme, endonuclease.
A third enzyme, exonuclease (3), liberates the sugar-
phosphate unit of the damaged site.
• 2. In the synthesis step, the enzyme DNA polymerase (4)
inserts the correct nucleotide, cytidine, and the enzyme
DNA ligase seals (5) the backbone to complete the repair.

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Chapter 25 Nucleic Acids and Heredity

End
Chapter 25

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