Molecular Biology of the Cell by Bruce Alberts, Alexander Johnson, Julian Lewis, David Morgan, Martin Raff, Keith Roberts, Peter Walter by by Bruce Alberts, Alexander Johnson, Julian Lewis, David Morg

DNA REPAIR
269
Figure 5–39 The most common type of thymine dimer. This type of
damage occurs in the DNA of cells exposed to ultraviolet irradiation (as in
sunlight). A similar dimer will form between any two neighboring pyrimidine
bases (C or T residues) in DNA.
DNA Damage Can Be Removed by More Than One Pathway
Cells have multiple pathways to repair their DNA using different enzymes that act
upon different kinds of lesions. Figure 5–41 shows two of the most common pathways.
In both, the damage is excised, the original DNA sequence is restored by a
DNA polymerase that uses the undamaged strand as its template, and a remaining
break in the double helix is sealed by DNA ligase (see Figure 5–12).
The two pathways differ in the way in which they remove the damage from
DNA. The first pathway, called base excision repair, involves a battery of enzymes
called DNA glycosylases, each of which can recognize a specific type of altered
base in DNA and catalyze its hydrolytic removal. There are at least six types of
these enzymes, including those that remove deaminated Cs, deaminated As, different
types of alkylated or oxidized bases, bases with opened rings, and bases in
which a carbon–carbon double bond has been accidentally converted to a carbon–carbon
single bond. How is an altered base detected within the context of
the double helix? A key step is an enzyme-mediated “flipping-out” of the altered
nucleotide from the helix, which allows the DNA glycosylase to probe all faces of
the base for damage (Figure 5–42). It is thought that these enzymes travel along
DNA using base-flipping to evaluate the status of each base. Once an enzyme
finds the damaged base that it recognizes, it removes that base from its sugar.
The “missing tooth” created by DNA glycosylase action is recognized by an
enzyme called AP endonuclease (AP for apurinic or apyrimidinic, endo to signify
that the nuclease cleaves within the polynucleotide chain), which cuts the phosphodiester
backbone, after which the resulting gap is repaired (see Figure 5–41A).
Depurination, which is by far the most frequent type of damage suffered by DNA,
also leaves a deoxyribose sugar with a missing base. Depurinations are directly
repaired beginning with AP endonuclease, following the bottom half of the pathway
in Figure 5–41A.
P
P
P
P
P
O
O
C
N
C
H
O O
C
N
O
C
H
O
C
N
C
H
H
N
C
H
N
C
N H C
O
O
C
H
N
N
C C
H
MBoC6 m5.46/5.40
C O
CH 3
C O
CH 3
C O
CH 3
C O
CH 3
mutated
old strand
mutated
old strand
deaminated C
T
A
U
A
A
T
T
A
depurinated A
T
A
C
G
T
A
new strand
new strand
T
A
U
G
A
T
T
A
DNA
REPLICATION
a G has been
changed to an A
new strand
T
A
C
G
T
T
A
DNA
REPLICATION
an A-T nucleotide
pair has been deleted
new strand
T
A
C
G
A
T
T
A
T
A
C
G
A
T
T
A
old strand
old strand
(A)
unchanged
(B)
unchanged
Figure 5–40 How chemical modifications of nucleotides produce mutations. (A) Deamination of cytosine, if uncorrected, results in the
substitution of one base for another when the DNA is replicated. As shown in Figure 5–38, deamination of cytosine produces uracil. Uracil differs
from cytosine in its base-pairing properties and preferentially base-pairs with adenine. The DNA replication machinery therefore adds an adenine
when it encounters a uracil on the template strand. (B) Depurination can lead to the loss of a nucleotide pair. When the replication machinery
encounters a missing purine on the template strand, it may skip to the next complete nucleotide as illustrated here, thus producing a nucleotide
deletion in the newly synthesized strand. Many other types of DNA damage (see Figure 5–37), if left uncorrected, also produce mutations when the
DNA is replicated.