Problem 8 - Campbell Biology

Question

The spontaneous loss of amino groups from adenine in DNA results in hypoxanthine, an uncommon base, opposite thymine. What combination of proteins could repair such damage? \begin{equation}\begin{array}{l}{\text { (A) nuclease, DNA polymerase, DNA ligase }} \\ {\text { (B) telomerase, primase, DNA polymerase }} \\ {\text { (C) telomerase, helicase, single-strand binding }} \\ {\text { protein }} \\\ {\text { (D) DNA ligase, replication fork proteins, adenylyl }} \\ {\text { cyclase }}\end{array}\end{equation}

Step-by-Step Solution

Answer

Option A: nuclease, DNA polymerase, DNA ligase.

Step 1: Understanding the DNA damage

The loss of amino groups from adenine results in the formation of hypoxanthine, which pairs incorrectly with thymine. This type of damage can cause mutations if not repaired.

Step 2: Identifying the repair mechanism

The repair of such damage typically involves recognizing the altered base, removing it, and then filling in the gap with the correct base.

Step 3: Determining the enzymes required

To repair the site, the combination of enzymes needed would involve cutting out the damaged section, synthesizing the correct sequence, and sealing the new strand.

Step 4: Matching to the correct option

Evaluating the options provided: (A) nuclease, DNA polymerase, DNA ligase - These enzymes can excise the damaged base (nuclease), add the correct bases (DNA polymerase), and seal the strand (DNA ligase). (B) telomerase, primase, DNA polymerase - Not suitable as telomerase and primase are involved in different processes. (C) telomerase, helicase, single-strand binding protein - Not applicable to base repair. (D) DNA ligase, replication fork proteins, adenylyl cyclase - These are not the correct combination for base excision repair.

Step 5: Conclusion

The correct combination of proteins to repair the damage involves the enzymes in option A: nuclease, DNA polymerase, and DNA ligase.

Key Concepts

base excision repair

Base excision repair (BER) is a vital mechanism for correcting DNA mutations. It addresses small, non-helix-distorting base lesions caused by oxidation, alkylation, or deamination.

The BER process starts with the recognition of the abnormal base by specific DNA glycosylases. These enzymes scan the DNA for altered bases and then cleave the glycosidic bond, releasing the base and leaving an apurinic/apyrimidinic (AP) site.

Following this, an AP endonuclease cuts the backbone near the AP site to generate a break, which is critical for the subsequent repair steps.

nuclease function

Nucleases play a crucial role in the DNA repair process. They are enzymes that cleave the phosphodiester bonds between the nucleotides in nucleic acids.

In base excision repair, an AP endonuclease (a type of nuclease) is responsible for cutting the DNA strand at the site of damage. This incision is a necessary step to remove the wrong or damaged base and create a gap for the new base to be inserted.

Without the activity of nucleases, the damaged DNA strand would remain intact, leading to potential mutations and genomic instability.

DNA polymerase

DNA polymerase is essential in synthesizing new DNA strands during the repair process. Once the damaged section of DNA has been removed by nucleases, DNA polymerase comes into play.

It fills the gap left by the excised base, ensuring the correct complementary nucleotide is inserted based on the template strand's sequence. There are different types of DNA polymerases, but those involved in BER specifically add nucleotides to the 3' OH end of the cut strand.

By adding the correct nucleotides, DNA polymerase helps maintain the integrity and accuracy of the DNA sequence, preventing mutations.

DNA ligase

DNA ligase is an enzyme that plays a key role in sealing the nicks in the DNA backbone during repair. After DNA polymerase has added the correct base, a small gap or 'nick' still remains in the sugar-phosphate backbone.

DNA ligase catalyzes the formation of a phosphodiester bond between the adjacent nucleotides to close this nick. This action 'seals' the DNA strand, completing the repair process.

Without DNA ligase, the new DNA strand would remain discontinuous, which could lead to strand breaks and genome instability.

mutagenesis prevention

Preventing mutagenesis is a fundamental goal of DNA repair mechanisms like BER. Mutagenesis refers to changes in the DNA sequence, which can lead to mutations.

Such mutations can have various consequences, including the development of diseases like cancer. By correcting errors in the DNA promptly and accurately, repair mechanisms help maintain genomic stability.

In the specific scenario of deamination of adenine to hypoxanthine, efficient repair involving nucleases, DNA polymerase, and DNA ligase prevents the incorporation of incorrect bases, thereby avoiding potential mutagenesis. The enzymes ensure that the DNA sequence is restored to its original, correct state.