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OH
OH
Base
O
O
O—
O—
O—
O—
—O—P--—O—P—O—P—O—H
2
C
5'
1'
4'
2'
3'
—
— —
O
—
— —
O
—
— —
Nucleoside
Nucleoside monophosphate
Nucleoside diphosphate
Nucleoside triphosphate
Nucleotides
A
B
C
Base
Nucleotide
(Base+sugar)
Nucleotide
(Base+sugar+phosphate)
Nucleic Acid
Purines
Adenine
Guanine
Cytosine
Thymine
Uracil
Pyrimidines
Adenosine
Deoxyadenosine
Guanosine
Deoxyguanosine
Cytidine
Deoxycytidine
Thymidine
Deoxythymidine
Uridine
Deoxyuridine
AMP
dAMP
GMP
dGMP
CMP
dCMP
TMP
dTMP
UMP
dUMP
ADP
dADP
GDP
dGDP
CDP
dCDP
TDP
dTDP
UDP
dUDP
ATP
dATP
GTP
dGTP
CTP
dCTP
TTP
dTTP
UTP
dUTP
RNA
DNA
RNA
DNA
RNA
DNA
RNA
DNA
RNA
DNA
Monophosphate
Diphosphate
Triphosphate
D
FIGURE 2-1. Biochemistry of DNA. (A)
Structure of the biochemical components of DNA and RNA (purines, pyrimidines,
sugars, and phosphate). (B) Diagram depicting the chemical structure of the various components of DNA. (C) Diagram of
a DNA polynucleotide chain. The biochemical components (purines, pyrimidines, sugar, and phosphate) form a polynu-
cleotide chain through a 3
,5-phosphodiester bond. (D) Nomenclature of nucleosides and nucleotides in RNA and DNA.
AMP
adenylate or adenosine 5-monophosphate dAMP 2-deoxyadenosine 5-monophosphate ADP adenosine
5
-diphosphate dADP 2-deoxyadenosine 5-diphosphate ATP adenosine 5-triphosphate dATP 2-deoxyadeno-
sine 5
-triphosphate GMP guanylate or guanosine 5-monophosphate dGMP 2-deoxyguanosine 5-monophosphate
GDP
guanosine 5-diphosphate dGDP 2-deoxyguanosine 5-diphosphate GTP guanosine 5-triphosphate dGTP
2
-deoxyguanosine 5-triphosphate CMP cytidylate or cytidine 5-monophosphate dCMP 2-deoxycytidine 5-
monophosphate CDP
cytidine 5-diphosphate dCDP 2-deoxycytidine 5-diphosphate CTP cytidine 5-triphosphate
dCTP
2-deoxycytidine 5-triphosphate TMP thymidylate or thymidine 5-monophosphate dTMP 2-deoxythymi-
dine 5
-monophosphate TDP thymidine 5-diphosphate dTDP 2-deoxythymidine 5-diphosphate TTP- thymidine 5-
triphosphate dTTP
2-deoxythymidine 5-triphosphate UMP uridylate or uridine 5-monophosphate dUMP 2-
deoxyuridine 5
-monophosphate UDP uridine 5-diphosphate dUDP 2-deoxyuridine 5-diphosphate UTP uridine
5
-triphosphate dUTP 2-deoxyuridine 5-triphosphate.
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16
BRS Genetics
1
1
2
B
A
C
μ
m
8,800-fold
Double helix DNA
30-nm fiber
μ
m
μ
m
FIGURE 2-2. DNA packaging. (A)
Diagram depicting the various levels of packaging of double helix DNA found within a
metaphase chromosome. Double helix DNA is wound around a histone octamer of H2A, H2B, H3, and H4 to form a nucle-
osome. Nucleosomes are pulled together by histone H1 to form a 30 nm diameter fiber. The 30 nm fiber exists either as
extended chromatin or as secondary loops within a condensed metaphase chromosome. (B) Electron micrograph of DNA
isolated and subjected to treatments that unfold DNA to a nucleosome. The “beads on a string” appearance is the basic
unit of chromatin packaging called a nucleosome. The globular structure (“bead”) (arrow 1) is a histone octamer. The lin-
ear structure (“string”) (arrow 2) is DNA. (C) Compaction of DNA in a chromosome. The double helix DNA of a chromo-
some is shown unraveled and stretched out measuring 88,000 um in length. During metaphase of mitosis, chromatin can
become highly compacted. For example, human chromosome 1 contains about 260,000,000 bp. The distance between
each base pair is 0.34 nm. So that, the physical length of the DNA comprising chromosome 1 is 88,000,000 nm or 88,000 um
(260,000,000 X 0.34nm
88,000,000 nm). During metaphase, all the chromosomes condense such that the physical length
of chromosome 1 is about 10 um. Consequently, the 88,000 um of DNA comprising chromosome 1 is reduced to 10 um,
resulting in an 8,800-fold compaction.
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1.
In humans, the female is functionally
hemizygous due to X chromosome inactiva-
tion. The inactivated chromosome is thus
composed of which of the following?
(A)
satellite 1 DNA
(B)
beta-satellite DNA
(C)
facultative heterochromatin
(D)
constitutive heterochromatin
(E)
euchromatin
2.
The levels of DNA packaging are depicted
in which of the following sequences?
(A)
alpha satellite DNA, heterochromatin,
centromere, euchromatin, metaphase
chromosome
(B)
constitutive heterochromatin, euchro-
matin, facultative heterochromatin,
metaphase chromosome
(C)
purines, pyrimidines, phosphates, nucle-
osome, 30 nm chromatin fiber,
metaphase chromosome
(D)
double helix DNA, nucleosome, 30 nm
chromatin fiber, extended chromatin,
metaphase chromosome
(E)
double helix DNA, histones, nucleo-
somes, extended chromatin, metaphase
chromosome
3.
The nitrogenous bases that make up the
nucleotides of DNA are listed in which one of
the following?
(A)
deoxyribose and ribose
(B)
deoxyribose, ribose, and phosphate
(C)
adenine, thymine, cytosine, uracil
(D)
adenine, thymine, cytosine, guanine
4.
Which one of the following is a major
component of centromeric DNA?
(A)
the Barr body
(B)
the XY body
(C)
alpha satellite DNA
(D)
Z-DNA
5.
Which one of the following is the way
bases are paired in a double helix of DNA?
(A)
A-T, G-C
(B)
A-U, G-C
(C)
A-G, C-T
(D)
A-C, G-T
17
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18
1. The answer is (C).
Both copies of the X chromosome in females are active only for a short
time early in development.
2. The answer is (E).
Double helix DNA is coiled around histones that are organized into
nucleosomes, which form the extended chromatin that compacts into a metaphase chro-
mosome.
3. The answer is (D).
A DNA nucleotide consists of one of the nitrogenous bases adenine,
thymine, cytosine or guanine, the sugar deoxyribose, and a phosphate group. Uracil and the
sugar ribose are components of RNA nucleotides.
4. The answer is (C).
The 171 base pair repeat unit of alpha satellite DNA makes up much of
the centromeric DNA.
5. The answer is (A).
In DNA, adenine (A) pairs with thymine (T) and guanine (G) pairs with
cytosine (C). In RNA, adenine pairs with uracil (U).
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19
A.
Chromosome replication occurs during
S phase
of the cell cycle and involves both DNA syn-
thesis and histone synthesis to form chromatin.
B.
The timing of replication is related to the chromatin structure. An
inactive gene
packaged as
het-
erochromatin
is replicated
late in S phase
(e.g., in a female mammalian cell, the inactive X chro-
mosome called the
Barr body
is packaged as heterochromatin and is replicated late in S phase).
C.
An
active gene
packaged as
euchromatin
is replicated early in S phase (e.g., in the pancreatic
beta cell, the insulin gene will be replicated early in S phase. However, in other cell types (e.g.,
hepatocytes) where the insulin gene is inactive, it will be replicated late in S phase.
D.
DNA polymerases absolutely require the
3
-OH end
of a based paired primer strand as a sub-
strate for strand extension. Therefore, a
RNA primer
(synthesized by a
primase
) is required to
provide the free 3
-OH group needed to start DNA synthesis.
E.
DNA polymerases copy a DNA template in the
3
S
S
5
direction,
which produces a new DNA
strand in the
5
S
S
3
direction
.
F. Deoxyribonucleoside 5
-triphosphates (dATP, dTTP, dGTP, dCTP)
pair with the corresponding
base (A-T, G-C) on the template strand and form a
3
,5-phosphodiester bond
with the
3
-OH
group on the deoxyribose sugar,
which releases a
pyrophosphate
.
G.
Replication is described as
semiconservative
which means that a molecule of double helix
DNA contains one intact parental DNA strand and one newly synthesized DNA strand.
A.
The process starts when
topoisomerase
nicks (or breaks) a single strand of DNA, which
causes DNA unwinding.
B.
Chromosome replication begins at specific nucleotide sequences located throughout the
chromosome called
replication origins
.
Eukaryotic DNA contains
multiple replication origins
to ensure rapid DNA synthesis. Normally, the S phase of the mammalian cell cycle is
8 hours
.
C. DNA helicase
recognizes the replication origin and opens up the double helix at that site,
forming a
replication bubble
with a
replication fork
at each end. The stability of the replication
fork is maintained by
single-stranded binding proteins
.
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