Ch. 9 Topology Flashcards

1
Q

Describe viral chromosomes. (4)

A

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

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2
Q

Describe prokaryotic chromosomes. (4)

A

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

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3
Q

Describe eukaryotic chromosomes. (4)

A

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

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4
Q

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

A

size and structure

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5
Q

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

A

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

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6
Q

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

A

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

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7
Q

What is DNA topology?

A

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

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8
Q

What is supercoiling/supercoils?

A

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

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9
Q

What are the two kinds of supercoils?

A

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

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10
Q

Where does supercoiling occur (2) and why?

A

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

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11
Q

What is relaxed DNA?

A

DNA structure when there is NO supercoiling present.

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12
Q

What does separation of supercoiled DNA cause?

A

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

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13
Q

How is excessive coiling combated?

A

Specialized enzymes relieve excessive coiling and therefore prevent DNA breakage.

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14
Q

What do DNA topoisomerases do and how?

A

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

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15
Q

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

A

Negative SC: unwind
Positive SC: wind

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16
Q

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

A

Negative SC: wind
Positive SC: unwind

17
Q

What does over or underwinding of the DNA helix cause?

A

It causes bending of the helix which leads to supercoils

18
Q

What effect does bending have on DNA structure?

A

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

19
Q

How is the supercoil observed structurally?

A

Observed by the DNA twisting around its central axis.

20
Q

What is a linkage number?

A

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

21
Q

What does increasing Lk correlate to? Decreasing Lk?

A

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

22
Q

What do Type I topoisomerases do?

A

break one strand and change Lk by one

23
Q

What do Type II topoisomerases do?

A

break both strands and change Lk by two

24
Q

Do topoisomerases only add supercoils?

A

No. They can add or remove.

25
What do Bacterial Type I Topisomerases do and how do they do it? (2)
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.)
26
What do Bacterial Type II Topoisomerases do and how do they do it? (2)
It adds or removes two supercoils. It is ATP-dependent and cuts both DNA strands before passing the unbroken strands through.
27
What is a structural difference between bacterial topoisomerase I and II? (1)
Type II is composed of multiple subunits.
28
When is bacterial type II topoisomerase used?
Used during DNA replication to relieve coiling stress caused by helicase. (target of many antibiotics!)
29
What are the two main eukaryotic topoisomerases?
include type I and type II topoisomerases
30
What do eukaryotic topoisomerases do? What don't they do?
They relax positive and negative supercoiling, but NONE introduce negative supercoils
31
How can eukaryotic chromosomes be negatively supercoiled?
By wrapping DNA around histones (not done buy topoisomerases)
32
Why are eukaryotic topoisomerases important? (5)
Replication Transcription DNA repair Eukaryotic cell cycle Condensing chromosomes
33
What are SMC protiens?
Proteins that create contact between otherwise distant chromosome segments or different chromosomes facilitating chromosome condensation.
34
Where are SMC proteins found?
In all cells (but best studied in eukaryotes)
35
What are the two SMC proteins important in the cell cycle?
Cohesin and condensin
36
What is cohesin?
SMC protein that links sister chromatids after DNA replication through metaphase
37
What is condensin?
SMC protein that binds DNA to create positive supercoils to condense chromosomes