Ch. 9 Topology

Question 1

Describe viral chromosomes. (4)

Answer 1

ss or ds
DNA or RNA
Contained in a capsid
Circular, Linear, or Segmented

Question 2

Describe prokaryotic chromosomes. (4)

Answer 2

dsDNA (cells!)
NOT contained in a nucleus
Usually single
Usually circular

Question 3

Describe eukaryotic chromosomes. (4)

Answer 3

dsDNA (cells!)
Contained in a nucleus
Usually linear
Often in pairs (homologs)

Question 4

How do viral, prokaryotic, and eukaryotic chromosomes differ? (2)

Answer 4

size and structure

Question 5

What is a feature ALL chromosomes have regardless of the type?

Answer 5

ALL are larger (longer) than the cells or viruses that carry them and MUST be packaged. (long but thin)

Question 6

How is packaging generically performed; aka what do packaging methods avoid doing to DNA?

Answer 6

Packaging is performed in different ways that alter DNA structure WITHOUT breaking the DNA.

Question 7

What is DNA topology?

Answer 7

The size and structure of DNA and how it is packaged.

Question 8

What is supercoiling/supercoils?

Answer 8

DNA supercoiling is further coiling the DNA double helix. Supercoils are additional coils introduced into DNA double helix.

Question 9

What are the two kinds of supercoils?

Answer 9

Overwinding (positive) of the double helix
Underwinding (negative) of the double helix

Question 10

Where does supercoiling occur (2) and why?

Answer 10

It occurs in cells and viruses to create a reduced DNA footprint in the cell/capsid

Question 11

What is relaxed DNA?

Answer 11

DNA structure when there is NO supercoiling present.

Question 12

What does separation of supercoiled DNA cause?

Answer 12

Processes that separate DNA strands (replication, transcription, etc.) can cause excessive strain on the DNA that could cause breakage of DNA.

Question 13

How is excessive coiling combated?

Answer 13

Specialized enzymes relieve excessive coiling and therefore prevent DNA breakage.

Question 14

What do DNA topoisomerases do and how?

Answer 14

They produce supercoiling by breaking, winding, or unwinding the DNA helix and re-ligating the DNA strands.

Question 15

How do you ADD a supercoil to a negative supercoil? Positive supercoil?

Answer 15

Negative SC: unwind
Positive SC: wind

Question 16

How do REMOVE a supercoil from a negative supercoil? Positive supercoil?

Answer 16

Negative SC: wind
Positive SC: unwind

Question 17

What does over or underwinding of the DNA helix cause?

Answer 17

It causes bending of the helix which leads to supercoils

Question 18

What effect does bending have on DNA structure?

Answer 18

Puts strain on base pairs, which makes them easier to separate by enzymes like polymerases.

Question 19

How is the supercoil observed structurally?

Answer 19

Observed by the DNA twisting around its central axis.

Question 20

What is a linkage number?

Answer 20

Lk: how often one strand wraps around another; how supercoiling is quantified

Question 21

What does increasing Lk correlate to? Decreasing Lk?

Answer 21

increasing Lk = positive supercoiling (200→202)
decreasing Lk = negative supercoiling (200→198)

Question 22

What do Type I topoisomerases do?

Answer 22

break one strand and change Lk by one

Question 23

What do Type II topoisomerases do?

Answer 23

break both strands and change Lk by two

Question 24

Do topoisomerases only add supercoils?

Answer 24

No. They can add or remove.

Question 25

What do Bacterial Type I Topisomerases do and how do they do it? (2)

Answer 25

It adds or removes one supercoil. NOT ATP-dependent; one high energy bond is replaced by another at each step. (Tyr-OH interacts with phosphodiester bond and nucleophilic attack occurs breaking one strand. The other is passed through.)

Question 26

What do Bacterial Type II Topoisomerases do and how do they do it? (2)

Answer 26

It adds or removes two supercoils. It is ATP-dependent and cuts both DNA strands before passing the unbroken strands through.

Question 27

What is a structural difference between bacterial topoisomerase I and II? (1)

Answer 27

Type II is composed of multiple subunits.

Question 28

When is bacterial type II topoisomerase used?

Answer 28

Used during DNA replication to relieve coiling stress caused by helicase. (target of many antibiotics!)

Question 29

What are the two main eukaryotic topoisomerases?

Answer 29

include type I and type II topoisomerases

Question 30

What do eukaryotic topoisomerases do? What don't they do?

Answer 30

They relax positive and negative supercoiling, but NONE introduce negative supercoils

Question 31

How can eukaryotic chromosomes be negatively supercoiled?

Answer 31

By wrapping DNA around histones (not done buy topoisomerases)

Question 32

Why are eukaryotic topoisomerases important? (5)

Answer 32

Replication Transcription DNA repair Eukaryotic cell cycle Condensing chromosomes

Question 33

What are SMC protiens?

Answer 33

Proteins that create contact between otherwise distant chromosome segments or different chromosomes facilitating chromosome condensation.

Question 34

Where are SMC proteins found?

Answer 34

In all cells (but best studied in eukaryotes)

Question 35

What are the two SMC proteins important in the cell cycle?

Answer 35

Cohesin and condensin

Question 36

What is cohesin?

Answer 36

SMC protein that links sister chromatids after DNA replication through metaphase

Question 37

What is condensin?

Answer 37

SMC protein that binds DNA to create positive supercoils to condense chromosomes