MCAT Biochemistry Review

Chapter 6: DNA and Biotechnology

6.4 DNA Repair

The structure of DNA can be damaged in a number of ways such as exposure to chemicals or radiation. DNA is very susceptible to damage and if the damage is not corrected, it will subsequently be copied and passed on to daughter cells. Damage can include breaking of the DNA backbone, structural or spontaneous alterations of bases, or incorporation of the incorrect base during replication. Any defect in the genetic code can cause an increased risk of cancer, so the cell has multiple processes in place to catch and correct genetic errors. This helps maintain the integrity and stability of the genome from cell to cell, and from generation to generation.


Certain genes, when mutated, can lead to cancer. Cancer cells proliferate excessively because they are able to divide without stimulation from other cells and are no longer subject to the normal controls on cell proliferation. By definition, cancer cells are able to migrate by local invasion ormetastasis, a migration to distant tissues by the bloodstream or lymphatic system. Over time, cancer cells tend to accumulate mutations.

Mutated genes that cause cancer are termed oncogenes. Oncogenes primarily encode cell cycle-related proteins. Before these genes are mutated, they are often referred to as proto-oncogenes. The first gene in this category to be discovered was src (named after sarcoma, a category of connective tissue cancers). The abnormal alleles encode proteins that are more active than normal proteins, promoting rapid cell cycle advancement. Typically, a mutation in only one copy is sufficient to promote tumor growth and is therefore considered dominant.

Tumor suppressor genes, like p53 or Rb (retinoblastoma), encode proteins that inhibit the cell cycle or participate in DNA repair processes. They normally function to stop tumor progression, and are sometimes called antioncogenes. Mutations of these genes result in the loss of tumor suppression activity, and therefore promote cancer. Inactivation of both alleles is necessary for the loss of function because, in most cases, even one copy of the normal protein can function to inhibit tumor formation. In this example, multiple mutations or “hits” are required.


While the outcome of oncogenes and mutated tumor suppressor genes is the same (cancer), the actual cause is different. Oncogenes promote the cell cycle while mutated tumor suppressors can no longer slow the cell cycle. Oncogenes are like stepping on the gas pedal; mutated tumor suppressors are like losing the brakes.


DNA polymerase moves along a single strand of DNA, building the complementary strand as it goes. While DNA polymerase is almost 100 percent accurate, it does occasionally make errors.


During synthesis, the two double-stranded DNA molecules will pass through a part of the DNA polymerase enzyme for proofreading. When the complementary strands have incorrectly paired bases, the hydrogen bonds between the strands can be unstable, and this lack of stability is detected as the DNA passes through this part of the polymerase. The incorrect base is excised and can be replaced with the correct one, as shown in Figure 6.16. If both the parent and daughter strands are simply DNA, how does the enzyme discriminate which is the template strand, and which is the incorrectly paired daughter strand? It looks at the level of methylation: the template strand has existed in the cell for a longer period of time, and therefore is more heavily methylated. Methylation also plays a role in the transcriptional activity of DNA, as described in Chapter 7 of MCAT Biochemistry Review. This system is very efficient, correcting most of the errors put into the sequence during replication. DNA ligase, which closes the gaps between Okazaki fragments, lacks proofreading ability. Thus, the likelihood of mutations in the lagging strand is considerably higher than the leading strand.

Figure 6.16. Proofreading by DNA Polymerase

Mismatch Repair

Cells also have machinery in the G2 phase of the cell cycle for mismatch repair; these enzymes are encoded by genes MSH2 and MLH1, which detect and remove errors introduced in replication that were missed during the S phase of the cell cycle. These enzymes are homologues of MutSand MutL in prokaryotes, which serve a similar function.


Most of the repair mechanisms involve proteins that recognize damage or a lesion, remove the damage, and then use the complementary strand as a template to fill in the gap. Our cell machinery recognizes two specific types of DNA damage in the G1 and G2 cell cycle phases and fixes them through nucleotide excision repair or base excision repair.

Nucleotide Excision Repair

Ultraviolet light induces the formation of dimers between adjacent thymine residues in DNA. The formation of thymine dimers interferes with DNA replication and normal gene expression, and distorts the shape of the double helix. Thymine dimers are eliminated from DNA by a nucleotide excision repair (NER) mechanism, which is a cut-and-patch process, as shown in Figure 6.17. First, specific proteins scan the DNA molecule and recognize the lesion because of a bulge in the strand. An excision endonuclease then makes nicks in the phosphodiester backbone of the damaged strand on both sides of the thymine dimer and removes the defective oligonucleotide. DNA polymerase can then fill in the gap by synthesizing DNA in the 5′ to 3′ direction, using the undamaged strand as a template. Finally, the nick in the strand is sealed by DNA ligase.

Figure 6.17. Thymine Dimer Formation and Nucleotide Excision Repair

Base Excision Repair

Alterations to bases can occur with other cellular insults. For example, thermal energy can be absorbed by DNA and may lead to cytosine deamination. This is the loss of an amino group from cytosine and results in the conversion of cytosine to uracil. Uracil should not be found in a DNA molecule and is thus easily detected as an error; however, detection systems exist for small, non-helix-distorting mutations in other bases as well. These are repaired by base excision repair. First, the affected base is recognized and removed by a glycosylase enzyme, leaving behind anapurinic/apyrimidinic (AP) site, also called an abasic site. The AP site is recognized by an AP endonuclease that removes the damaged sequence from the DNA. DNA polymerase and DNA ligase can then fill in the gap and seal the strand, as described above.

MCAT Concept Check 6.4:

Before you move on, assess your understanding of the material with these questions.

1.    What is the difference between an oncogene and a tumor suppressor gene?

2.    How does DNA polymerase recognize which strand is the template strand once the daughter strand is synthesized?

3.    For each of the repair mechanisms below, in which phase of the cell cycle does the repair mechanism function? What are the key enzymes or genes specifically associated with each mechanism?

Repair mechanism

Phase of Cell Cycle

Key Enzymes/Genes

DNA polymerase (proofreading)


Mismatch repair


Nucleotide excision repair


Base excision repair


4.    What is the key structural difference in the types of lesions corrected by nucleotide excision repair vs. those corrected by base excision repair?