Lecture 2/10/25 Flashcards
Central Dogma & Cells
What is topoisomerase?
An enzyme that alters DNA topology by cutting and rejoining strands.
Why is topoisomerase needed?
It relieves supercoiling tension during DNA replication and packaging.
What does it mean when DNA is nicked?
A nick is a single-strand break in the DNA backbone.
What is a double-strand break (DSB)?
A break in both strands of DNA that can lead to severe genomic damage.
How does topoisomerase I differ from II?
Topo I cuts one strand (changing linking number by 1, no ATP) while Topo II cuts both strands (changing linking number by 2, requires ATP).
What is DNA gyrase?
A bacterial type II topoisomerase that introduces negative supercoils.
How does DNA gyrase affect the linking number?
It decreases the linking number by introducing negative supercoils.
What does the term ‘linking number’ mean?
The total number of times one DNA strand winds around the other.
Why is managing supercoiling important?
Excess supercoiling can block replication and transcription.
What is the nascent strand?
The newly synthesized DNA strand during replication.
In which direction is DNA synthesized?
In the 5’ to 3’ direction.
What is meant by DNA polymerase processivity?
The number of nucleotides added per binding event by the polymerase.
What increases polymerase processivity in bacteria?
The sliding clamp (B clamp) tethers the polymerase to DNA.
What is the role of a primer in replication?
It provides a free 3’ hydroxyl group to begin DNA synthesis.
What does helicase do?
It unwinds the DNA double helix using ATP.
What is the function of DNA ligase?
It seals nicks by joining DNA fragments, such as Okazaki fragments.
What is the difference between the primer and template strand?
The primer strand provides the free 3-OH group for extension, the template strand is a guide for complementary base pairing
How does polymerase help with DNA Replication? What does it need?
Binds to the template strand and synthesizes the new DNA strand.
How does helicase help with DNA Replication? What does it need?
Unwinds DNA.
How does ligase help with DNA Replication? What does it need?
Seals nicks in the backbone of DNA and joins okazaki fragments
How do bacteria use toposiomerase II? How is it inhibited??
It resolves knots and catenones by passing a duplex through a transient double bond in another duplex. Certain inhibitors inhibit topoisomerase to treat infections and cancers. (stops bacterial cell duplication)
