MCB 250 Exam 2 Review (latest update)
questions with complete solutions
Explain why the cell generally keeps the DNA in a negatively supercoiled state -
correct answer ✔✔Negative supercoils favor local unwinding of the DNA
(transcription, DNA replication, and recombination)
Define Linking Number, Twist, and Writhe and their relationship - correct answer
✔✔Lk = total # of times DNA strands cross one another = Tw + Wr
Tw = twist bp/helical turn = number of helical turns
Used to describe the topological state of covalently closed, circular DNA
Invariant property of cccDNA (if no covalent bonds have been broken, Lk remains
constant)
Wr = writhe = number of times the helix crosses itself
Explain the mechanism of Type I topoisomerases - correct answer ✔✔TopoI and
TopoIII
RELAX DNA (fewer supercoils) WITHOUT ATP
Nick the DNA and pass one strand through the other and then ligate
Change Lk by 1
, Mechanism:
-Active site tyrosine attacks phosphodiester bond of one DNA strand, cleaving it
and creating covalent 5'-phosphotyrosyl protein-DNA linkage
-Enzyme changes to the open conformation
Unbroken DNA strand passes through the break in the first strand
-Enzyme in closed conformation; 3'OH (remaining from -Tyrosine attacking the
bond in step 1) attacks the 5'-phosphotyrosyl protein-DNA linkage to religate
cleaved DNA strand
Explain the mechanism of Type II topoisomerases - correct answer ✔✔TopoII and
TopoIV
RELAX supercoiling and are ATP dependent
Change Lk by 2
Covalent intermediate 5' phosphate to tyrosine
Pass both strands through another DNA double strand
What is the role of the active site tyrosine(s) in these mechanisms - correct
answer ✔✔Tyrosine attacks the phosphodiester bond in Type I and cleaves it to
form 5' phosphotyrosyl protein DNA linkage
Define why Gyrase is special - correct answer ✔✔Type II topoisomerase that ADDS
negative supercoils and relax positive supercoils
Change Lk by -2
Found ONLY IN PROKARYOTES
Negative coils introduced by gyrase are important for facilitating opening of the
double helix for replication and transcription
questions with complete solutions
Explain why the cell generally keeps the DNA in a negatively supercoiled state -
correct answer ✔✔Negative supercoils favor local unwinding of the DNA
(transcription, DNA replication, and recombination)
Define Linking Number, Twist, and Writhe and their relationship - correct answer
✔✔Lk = total # of times DNA strands cross one another = Tw + Wr
Tw = twist bp/helical turn = number of helical turns
Used to describe the topological state of covalently closed, circular DNA
Invariant property of cccDNA (if no covalent bonds have been broken, Lk remains
constant)
Wr = writhe = number of times the helix crosses itself
Explain the mechanism of Type I topoisomerases - correct answer ✔✔TopoI and
TopoIII
RELAX DNA (fewer supercoils) WITHOUT ATP
Nick the DNA and pass one strand through the other and then ligate
Change Lk by 1
, Mechanism:
-Active site tyrosine attacks phosphodiester bond of one DNA strand, cleaving it
and creating covalent 5'-phosphotyrosyl protein-DNA linkage
-Enzyme changes to the open conformation
Unbroken DNA strand passes through the break in the first strand
-Enzyme in closed conformation; 3'OH (remaining from -Tyrosine attacking the
bond in step 1) attacks the 5'-phosphotyrosyl protein-DNA linkage to religate
cleaved DNA strand
Explain the mechanism of Type II topoisomerases - correct answer ✔✔TopoII and
TopoIV
RELAX supercoiling and are ATP dependent
Change Lk by 2
Covalent intermediate 5' phosphate to tyrosine
Pass both strands through another DNA double strand
What is the role of the active site tyrosine(s) in these mechanisms - correct
answer ✔✔Tyrosine attacks the phosphodiester bond in Type I and cleaves it to
form 5' phosphotyrosyl protein DNA linkage
Define why Gyrase is special - correct answer ✔✔Type II topoisomerase that ADDS
negative supercoils and relax positive supercoils
Change Lk by -2
Found ONLY IN PROKARYOTES
Negative coils introduced by gyrase are important for facilitating opening of the
double helix for replication and transcription
