Q1) What secondary structures make up the large C-terminal domain of the Klenow fragment?
Answer: The large C-terminal domain contains a six-stranded antiparallel β-sheet at the bottom of the cleft region and contains three α-helices on one side and four α-helices on the other side of the cleft region.
Q2) Describe the three-dimensional structure of the large C-terminal domain of the Klenow fragment?
Answer: The large C-terminal domain contains a significantly deep cleft, with a considerable area to enable the binding of the B-DNA. The overall domain itself is shaped almost like a cupped right hand where, in this case, α-helices on either side of the cleft form the thumb and fingers, while the β sheet forms the palm of the hand.
Q3) What secondary structures make up the …show more content…
Why?
Answer: The phosphate group of the DNA backbone that the enzyme interacts with contains several negatively charged oxygen groups. Therefore, it makes sense that positively charged residues such as the R group of lysine would be expected to interact with the oxygen groups of phosphate. Furthermore, these oxygen groups can form strong and stable hydrogen bonds and thus, they would be likely to form hydrogen bonds with the R groups of amino acids such as asparagine.
Q9) Give examples of amino acids residues found in the catalytic site of the DNA polymerase that interact with DNA?
Answers: Some of the positively charged amino acids that interact with DNA include Lys-635, while examples of amino acids that can hydrogen bond with the oxygen in the phosphate backbone of the DNA include Asn-675 and Asn-678.
Q10) What structural properties of the large domain make it suitable to bind DNA?
Answer: The cleft of the large domain contains several positively charged residues in a helical pattern along the cleft in a complementary fashion to the phosphate groups in the backbone of the
Answer: The large C-terminal domain contains a six-stranded antiparallel β-sheet at the bottom of the cleft region and contains three α-helices on one side and four α-helices on the other side of the cleft region.
Q2) Describe the three-dimensional structure of the large C-terminal domain of the Klenow fragment?
Answer: The large C-terminal domain contains a significantly deep cleft, with a considerable area to enable the binding of the B-DNA. The overall domain itself is shaped almost like a cupped right hand where, in this case, α-helices on either side of the cleft form the thumb and fingers, while the β sheet forms the palm of the hand.
Q3) What secondary structures make up the …show more content…
Why?
Answer: The phosphate group of the DNA backbone that the enzyme interacts with contains several negatively charged oxygen groups. Therefore, it makes sense that positively charged residues such as the R group of lysine would be expected to interact with the oxygen groups of phosphate. Furthermore, these oxygen groups can form strong and stable hydrogen bonds and thus, they would be likely to form hydrogen bonds with the R groups of amino acids such as asparagine.
Q9) Give examples of amino acids residues found in the catalytic site of the DNA polymerase that interact with DNA?
Answers: Some of the positively charged amino acids that interact with DNA include Lys-635, while examples of amino acids that can hydrogen bond with the oxygen in the phosphate backbone of the DNA include Asn-675 and Asn-678.
Q10) What structural properties of the large domain make it suitable to bind DNA?
Answer: The cleft of the large domain contains several positively charged residues in a helical pattern along the cleft in a complementary fashion to the phosphate groups in the backbone of the