DNA Replication and

chapter
17 Transcription

I. NUCLEIC ACID STRUCTURE

A. The structure of DNA
1. Chemical components of DNA
a. Each polynucleotide chain of DNA contains nucleotides, which consist of a nitrogenous
base (A, G, C, or T), deoxyribose, and phosphate.
b. The bases are the purines adenine (A) and guanine (G) and the pyrimidines cytosine
(C) and thymine (T).
c. Phosphodiester bonds join the 30 -carbon of one sugar to the 50 -carbon of the next sugar
(Figure 17-1).
2. DNA double helix
a. Each DNA molecule is composed of two polynucleotide chains joined by hydrogen
bonds between the bases (Figure 17-2).
(1) Adenine on one chain forms a base pair with thymine on the other chain.
(2) Guanine base pairs with cytosine.
(3) The base sequences of the two strands are complementary. Adenine on one strand is
matched by thymine on the other, and guanine is matched by cytosine.
b. The chains are antiparallel. One chain runs in a 50 to 30 direction; the other chain runs
30 to 50 (Figure 17-3).
c. The double-stranded molecule is twisted to form a helix with major and minor grooves
(Figure 17-4).
(1) The base pairs that join the two strands are stacked like a spiral staircase in the interior
of the molecule.
(2) The phosphate groups are on the outside of the double helix. Two hydroxyl groups
of each phosphate are involved in phosphodiester bonds. The third is free and
dissociates its proton at physiologic pH, giving the molecule a negative charge
(Figure 17-1).
(3) The B form of DNA, first described by Watson and Crick, is right-handed and contains 10
base pairs per turn.
(4) Other forms of DNA include the A form, which is similar to the B form but more com-
pact, and the Z form, which is left-handed and has its bases positioned more toward the
periphery of the helix.
3. Denaturation, renaturation, and hybridization
a. Denaturation: Alkali or heat causes the strands of DNA to separate but does not break
phosphodiester bonds.
b. Renaturation: If strands of DNA are separated by heat and then the temperature is slowly
decreased under the appropriate conditions, base pairs reform, and complementary
strands of DNA come back together.
c. Hybridization: A single strand of DNA or RNA pairs with complementary base sequen-
ces on another strand of DNA or RNA.

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252 Biochemistry, Molecular Biology, and Genetics

5' end NH2

N
N
H Adenine
O
N N H
O P O CH2
– O
O
NH2
H N
Cytosine
O H O
N
O P O CH2
– O
O

O
N
N H
H Guanine
O
N N NH2
O P O CH2
– O
O
Phosphate
backbone O
H3C N H
Thymine
O H O
N
O P O CH2
– O
O

Phosphodiester
bond
O

3' end
FIGURE 17-1 A segment of a polynucleotide strand. This strand contains thymine and deoxyribose, so it is a segment of DNA.

Thymine Cytosine
H H H
H Adenine Guanine
C H H
O H N H
C N C O
5 C N C N
4 H
H C6 C 7 H C C H
3N 6
C 8
C N C C
1 H 5 H N
2 N1
ain ain
N 9 N
C 4C N C C N
2
3 ch ch
ain
C N To ain O
C N To
O H N
ch H ch
To To H
11.1 A 10.8 A
FIGURE 17-2 The base pairs of DNA.
 Chapter 17 DNA Replication and Transcription 253

T A

C G
5' 3'

G C
3' 5'

A T

FIGURE 17-3 Antiparallel strands of DNA. Note that the strands

run in opposite directions. A, adenine; C, cytosine; G, guanine; T, Deoxyribose Phosphate
thymine.

4. DNA molecules are extremely large

a. The entire chromosome of the bacterium Escherichia coli is circular and contains more
than 4 3 106 base pairs.
b. The DNA molecule in the longest human chromosome is linear and is over 7.2 cm long.
5. Packing of DNA in the nucleus
a. The chromatin of eukaryotic cells consists of DNA complexed with histones in nucleo-
somes (Figure 17-5).
(1) Histones are relatively small, basic proteins with a high content of arginine and lysine.
(Prokaryotes do not have histones.)
(2) Eight histone molecules form an octamer, around which about 140 base pairs of DNA
are wound to form a nucleosome core.
(3) The DNA that joins one nucleosome core to the next is complexed with histone H1.
b. The ‘‘beads-on-a-string’’ nucleosomal structure of chromatin is further compacted to
form solenoid structures (helical, tubular coils).
6. Mitochondrial DNA
a. The mitochondrial genome is a double-stranded circular DNA molecule found within
the mitochondrial matrix.
(1) The genetic code for the mitochondria is slightly different than that of genomic DNA.
(2) The genome codes for 13 protein subunits of the electron transport chain, a large and
small ribosomal RNA (rRNA), and 22 transfer RNAs (tRNAs).

Minor
groove Stacked bases

Major
groove

FIGURE 17-4 The DNA double helix.

254 Biochemistry, Molecular Biology, and Genetics

Histone
Nucleosome H1
core

Linker
DNA
Core
histones
DNA (H2A, H2B,
The H3, and H4)
FIGURE 17-5 A polynucleosome.
solenoid (Adapted from Olins DE, Olins AL:
Nucleosomes: The structural quan-
tum in chromosomes. American
Scientist 66:708, 1978.)

b. Mitochondrial DNA is maternally inherited.

(1) Mitochondria from the egg contribute exclusively to the zygote.
(2) The mitochondria autonomously reproduce, and therefore, all the mitochondria are of
maternal origin.
c. Mitochondrial DNA has a high mutation rate (about 5 to 10 times greater than the nuclear
genome).

B. The structure of RNA

1. RNA differs from DNA
a. The polynucleotide structure of RNA is similar to DNA except that RNA contains the
sugar ribose rather than deoxyribose and uracil (U) rather than thymine. (A small
amount of thymine is present in tRNA.)
b. RNA is generally single stranded (in contrast to DNA, which is double stranded).
(1) When strands loop back on themselves, the bases on opposite sides can pair: adenine
with uracil (A to U) and guanine with cytosine (G to C).
(2) RNA molecules have extensive base pairing, which produces secondary and tertiary
structures that are important for RNA function.
(3) RNA molecules recognize DNA and other RNA molecules by base pairing.
c. Some RNA molecules act as catalysts of reactions; thus, RNA, as well as protein, can
have enzymatic activity.
(1) Ribozymes, usually precursors of rRNA, remove internal segments of themselves, splic-
ing the ends together.
(2) RNAs also act as ribonucleases, cleaving other RNA molecules (e.g., RNase P cleaves
tRNA precursors).
(3) Peptidyl transferase, an enzyme in protein synthesis, consists of RNA.
2. Messenger RNA (mRNA) contains a cap structure and a poly(A) tail.
a. The cap consists of methylated guanine triphosphate (GTP) attached to the hydroxyl
group on the ribose at the 50 end of the mRNA.
(1) The N7 in the guanine is methylated.
(2) The 20 -hydroxyl groups of the first and second ribose moieties of the mRNA also may be
methylated (Figure 17-6).

CLINICAL Many viruses, such as the influenza virus, transfer the 7-methyl G cap from host
CORRELATES cell mRNAs to viral mRNA, which functions to increase mRNA stability and
increase translation of the mRNA.