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24
General, Organic, and
Biochemistry, 7e
Bettelheim,
Brown, and March
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24-1
24Chapter 24
Nucleotides, Nucleic
Acids, and Heredity
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24-2
24Introduction
• 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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24-3
24Introduction
• 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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24-4
24Nucleic 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
• a phosphate
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24-5
24Pyrimidine/Purine Bases
NH2
O
4
N
3
2
N
5
6
N
O
1
2
5
N
8
N
4
3
N
H
Purine
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N
H
Thymine (T)
(DN A and
so me RN A)
9
N
Uracil (U)
(i n RN A)
O
N
N
N
O
NH2
N
HN
H
Cytosine (C)
(D N A and
some RN A)
7
6
1
O
H
Pyrimidine
CH3
HN
N
O
N
H
A denine (A)
(DN A and RN A)
N
HN
H2 N
N
N
H
Guanine (G)
(DN A and RN A)
24-6
24Nucleosides
• 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
uracil
HN
-D -ribos ide
1
O
5'
HOCH 2
H
N
O
H
4'
3'
H
2'
HO
OH
Urid ine
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O
1'
H
a -N -glycosid ic
bon d
anomeric
carb on
24-7
24Nucleotides
• Nucleotide: a nucleoside in which a molecule of
phosphoric acid is esterified with an -OH of the
monosaccharide, most commonly either 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)
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N
24-8
24Nucleotides
• deoxythymidine 3’-monophosphate (3’-dTMP)
O
CH3
HN
5'
O
O
HOCH2
H
H
N
H
3'
O
H
1'
H
-
O P O
-
O
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24-9
24Nucleotides
• adenosine 5’-triphosphate (ATP) serves as a common
currency into which energy gained from food is
converted and stored
NH
2
N
O O O
O-P-O-P-O-P-O-CH2
N
O
O
O O
H
H
H
H
HO
OH
A denosin e 5'-trip hosph ate
(ATP)
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N
N
24-10
24Structure of DNA and RNA
• Primary Structure: the sequence of bases along
the pentose-phosphodiester backbone of a DNA
or RNA molecule
• base sequence is read from the 5’ end to the 3’ end
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24-11
24 Nucleic Acid - 1°
Structure
• A schematic diagram of a
nucleic acid
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24-12
24DNA - 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
molecules in which two antiparallel
polynucleotide strands are coiled in a righthanded manner about the same axis
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24
The DNA
Double
Helix
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24Base Pairing
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24-15
24Higher Structure of DNA
• DNA is coiled around proteins called histones
• histones are rich in the basic amine acids Lys and Arg,
whose side chains have a positive charge
• the negatively-charged DNA molecules and positivelycharged histones attract each other 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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24-16
24Chromosomes
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24Chromosomes
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24-18
24Chromosomes
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24-19
24Chromosomes
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24-20
24DNA 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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24-21
24RNA
• RNA molecules are classified according to their
structure and function
RN A type
S ize
Function
Mess enger
(mRN A )
750 bas e pairs
on average
directs amino acid
seq uence of protein s
Transfer
(tRN A)
from 73 to 93
bas e pairs
transp orts amino acids
to the site of p rotein
synth esis
Ribosomal
(rRN A )
very large;
MW up to 106
combines w ith proteins
to form ribosomes
Ribozymes
very large
(catalytic RN A)
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catalyze cleavage of part
of th eir ow n seq uences
in mRN A and tRN A
24-22
24Structure of tRNA
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24-23
24Genes, 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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24Genes, Exons, and Introns
• introns are cut out of mRNA before the protein is
synthesized
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24-25
24DNA Replication
• Replication involves separation of the two
original strands and synthesis of two new
daughter strands using the original strands as
templates
• DNA double helix unwinds at a specific point called an
origin of replication
• polynucleotide chains are synthesized in both
directions from the origin of replication; that is, DNA
replication is bidirectional
• at each origin of replication, there are two replication
forks, points at which new polynucleotide strands are
formed
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24-26
24DNA Replication
• DNA is synthesized from its 5’ -> 3’ end (from the 3’ -> 5’
direction of the template)
• the leading strand is synthesized continuously in the 5’
-> 3’ direction toward the replication fork
• the lagging strand is synthesized semidiscontinuously
as a series of Okazaki fragments, also in the 5’ -> 3’
direction, but away from the replication fork
• Okazaki fragments of the lagging strand are joined by
the enzyme DNA ligase
• replication is semiconservative: each daughter strand
contains one template strand and one newly
synthesized strand
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24DNA Replication
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24-28
24Replisomes
• Replisomes are assemblies of “enzyme factories”
Comp on ent
Fun ction
Helicases
Primase
Clamp protein
DN A polymerase
Ligas e
Unw ind s the D N A d ou ble helix
Syn thesizes primers
Thread s leadin g s trand
Joins as sembled nu cleotides
Joins Ok azaki fragmen ts
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24-29
24DNA Replication
• Opening up the superstructure
• during replication, the very condensed superstructure
of chromosomes is opened by a signal transduction
mechanism
• one step of this mechanism involves acetylation and
deacetylation of key lysine residues
Lys-CH2 CH2 CH2 CH2 NH3
Lysin e side ch ain
(has a pos itive charge)
+
acetylation
deacetylation
O
Lys-CH2 CH2 CH2 CH2 NH-CCH3
Acetylated lysine s ide chain
(has no charge)
• acetylation removes a positive charge and thus
weakens
the DNA-histone interactions
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24DNA Replication
• Relaxation of higher structures of DNA
• tropoisomerases (also called gyrases) facilitate the
relaxation of supercoiled DNA by introducing either
single strand or double strand breaks in the DNA
• once the supercoiling is relaxed by this break, the
broken ends are joined and the tropoisomerase
diffuses from the location of the replication fork
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24DNA Replication
• Unwinding the DNA double helix
• replication of DNA starts with unwinding of the double
helix
• unwinding can occur at either end or in the middle
• unwinding proteins called helicases attach themselves
to one DNA strand and cause separation of the double
helix
• the helicases catalyze the hydrolysis of ATP as the DNA
strand moves through; the energy of hydrolysis
promotes the movement
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24DNA Replication
• Primer/primases
• primers are short oligonucleotides of four to 15
nucleotides long
• they are required to start the synthesis of both
daughter strands
• primases are enzymes that catalyze the synthesis of
primers
• primases are placed at about every 50 nucleotides in
the lagging strand synthesis
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24DNA Replication
• DNA polymerases are key enzymes in replication
• once the two strands have separated at the replication
fork, the nucleotides must be lined up in proper order
for DNA synthesis
• in the absence of DNA polymerase, alignment is slow
• DNA polymerase provides the speed and specificity of
alignment
• along the lagging (3’ -> 5’) strand, the polymerases can
synthesize only short fragments, because these
enzymes only work from 5’ -> 3’
• these short fragments are called Okazaki fragments
• joining the Okazaki fragments and any remaining nicks
is catalyzed by DNA ligase
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24DNA Repair
• The viability of cells depends on DNA repair
enzymes that can detect, recognize, and repair
mutations in DNA
• Base excision repair (BER): one of the most
common repair mechanisms
• a specific DNA glycosylase recognizes the damaged
base
• it catalyzes the hydrolysis of the -N-glycosidic bond
between the incorrect base and its deoxyribose
• it then flips the damaged base, completing the excision
• the sugar-phosphate backbone remains intact
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24DNA Repair
• BER (cont’d)
• at the AP (apurinic or apyrimidinic) site thus created,
an endonuclease catalyzes the hydrolysis of the
backbone
• an exonuclease liberates the sugar-phosphate unit of
the damaged site
• DNA polymerase inserts the correct nucleotide
• DNA ligase seals the backbone to complete the repair
• NER (nucleotide excision repair) removes and
repairs up to 24-32 units by a similar mechanism
involving a number of repair enzymes
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24Cloning
• Clone: a genetically identical population
• Cloning: a process whereby DNA is amplified by
inserting it into a host and having the host
replicate it along with the host’s own DNA
• Polymerase chain reaction (PCR): an automated
technique for amplifying DNA using a heat-stable
DNA polymerase from a thermophilic bacterium
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24Cloning
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24Nucleic Acids
End
Chapter 24
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24-39