Other Duties During DNA Replication

Question 1

List three additional problem addressed during replication.

Answer 1

1. Relieve DNA of physical strain of being opened by helicase
2. Ensure no mistakes are made when DNA pol III adds nucleotides to new DNA strand
3. Get ride of RNA-DNA hybrids caused by the RNA primers used in replication

Question 2

What is a method DNA uses itself to alleviate some tension?

Answer 2

Supercoiling

Question 3

Why does strain accumulate in DNA?

Answer 3

Double-phosphodiester backbone prevents the molecule from freely rotating

Question 4

How does DNA topoisomerase class I relieve DNA tension?

Answer 4

1. Intentionally breaks one of the phosphodiester bonds in DNA backbone
2. Uses tyrosine to form covalent bonds with 5’ phosphate group
3. DNA can freely rotate
4. Once strain is relieved, class I topoisomerase seals phosphodiester bond

Question 5

How does topoisomerase class II relieve DNA strain?

Answer 5

1. Breaks both phosphodiester bonds
2. Covalently binds to completely cut DNA strand
3. Allows interwound DNA molecules to pass over each other and helps relieve strain

Question 6

Give an example of a class II DNA topoisomerase

Answer 6

Gyrase

Question 7

How does DNA proofreading occur?

Answer 7

If an incorrect nucleotide is attached to DNA, it will not base-pair correctly with template.
DNA pol II cannot add more nucleotides when 3’ end of DNA is not correctly base-paired.
DNA pol III will use its 3’ to 5’ exonuclease activity (epsilon-subunit) to delete the incorrect base.

Question 8

What enzyme removes RNA primers?

Answer 8

DNA polymerase I

Question 9

How does DNA pol I remove RNA primers?

Answer 9

1. RNA primers removed by RNase such as RNase H or by exonuclease activity of DNA pol I
2. Gaps in dsDNA filled by polymerase activity of DNA pol I
3. DNA ligase joins adjacent bases via phosphodiester bonds