9 | DNA Topology

Question 0

The number, size and potential length of shortest human chromosome?

Answer 0

Chromosome #21 has 47 million base pairs and would be 16mm stretched out

Question 1

Human Cell Size

Answer 1

7-30 microns

Question 2

Centromere

Answer 2

Serve as attachment point to link chromosome(s) to mitotic spindle during metaphase

Question 3

Telomeres

Answer 3

Sequences at the ends of chromosomes that provide stability and protection from nucleases

Question 4

HAC

Answer 4

Human Artificial Chromosome

Question 5

Three Requirements for a Stable Artificial Chromosome

Answer 5

1) Centromere
2) Telomere
3) Appropriate number of replication origins

Question 6

Somatic Gene Therapy

Answer 6

Process of correcting disease causing gene errors in somatic cells

Question 7

Contour Length

Answer 7

Length along the axis of the double-helical DNA

or the circumference, in the event of circular chromosome

Question 8

Replicative Form

Answer 8

Specific types of viral DNA

dsRNA

Question 9

Plasmid

Answer 9

Small DNA free in the cytosol and capable of autonomous replication

Question 10

What is the primary structural compaction of DNA called?

Answer 10

Helical Coil

Question 11

DNA Supercoiling

Answer 11

Further coiling of double-helix in DNA

Question 12

Supercoiling is a manifestation of ________?

Answer 12

Structural strain

Question 13

Relaxed DNA

Answer 13

When there is no secondary bending or coiling of DNA upon itself

Question 14

DNA Topology

Answer 14

Conformational change due to thermal motion, stretching or interaction with other proteins or other molecules

Question 15

Discontinuous deformation results from ______?

Answer 15

DNA breakage

Question 16

DNA ligation

Answer 16

Joining of two DNA backbones

Question 17

Closed-circular DNA

Answer 17

Circular DNA with no breakage or discontinuity on either strand

Question 18

B-form DNA (turns/bp)

Answer 18

1 turn per 10.4 bp

Question 19

DNA underwinding

Answer 19

When a DNA molecule has fewer turns than would be expected in B-form DNA

Question 20

Deviation from the stability of B-form in DNA causes ______?

Answer 20

Thermodynamic strain

Question 21

Strand separation can be caused by ________.

Answer 21

DNA underwinding

Question 22

Linking Number (lk)

Answer 22

Topological feature of double-stranded DNA that cannot change when bent or deformed. Always an integer.

Question 23

My convention, if two strands of DNA are interwound in a _______ the “lk” is positive (+) and negative (-) if they are wound in a _______.

Answer 23

Right-handed helix; left-handed helix

Question 24

Linking number for DNA is undefined if _______.

Answer 24

Either strand is broken or discontinuous

Question 25

Linking number is equal to _______ / ________.

Answer 25

Base pairs; base pairs per turn

Question 26

A change in linkage number can be used to express ________.

Answer 26

Underwound DNA

Question 27

Superhelical Density (σ)

Answer 27

The change in number of turns divided by the number of turns in the relaxed DNA.

Question 28

General degree of DNA under-winding in cellular DNA falls between _____ and _____.

Answer 28

5% (σ= -0.05); 7% (σ= -0.07)

Question 29

Negative supercoiling

Answer 29

Supercoiling of underwound DNA

Question 30

Positive supercoiling

Answer 30

Supercoiling of overwound DNA

Question 31

Linkage number can be changed +/- 1 by breaking one-strand and rotating it 360° about the other strand than reattachment. This process is catalyzed in cells by _____.

Answer 31

Topoisomerases

Question 32

Topoisomers are _____.

Answer 32

Two forms of circular DNA who only differ topologically (i.e. linking number)

Question 33

Linking number can be broken down into two structural components _____ and _____.

Answer 33

Writhe (Wr); Twist (Tw) Lk = Wr + Tw

Question 34

Twist (Tw)

Answer 34

Local, spatial twisting relationship between base pairs

Question 35

Writhe (Wr)

Answer 35

The coiling of the helical axis

Question 36

Underwinding of right-handed helix can facilitate short regions of _____ or _____.

Answer 36

Left-handed helix; Z-DNA

Question 37

Plectonemic supercoiling

Answer 37

Whenever the helical structure exists in a simple or regular state. (Helical axis = ~40% of strand length)

Question 38

Solenoidal supercoiling

Answer 38

The addition of tight left-hand turns to further compaction beyond the plectonemic supercoiling alone.

Question 39

Plectonemic supercoiling provides stability in _____ while solenoidal supercoiling can be stabilized by ____ and provides a far greater degree of ____.

Answer 39

solution; protein binding; compaction

Question 40

____ is the primary mechanism by which underwinding contributes to compaction.

Answer 40

Solenoidal supercoiling

Question 41

DNA supercoiling (underwinding) is ____ regulated and effects many aspects of DNA ____.

Answer 41

precisely; metabolism

Question 42

The underwinding and/or relaxation of DNA is catalyzed by ____.

Answer 42

Topoisomerases

Question 43

There are two (2) classes of topoisomerases: ____ & ____.

Answer 43

Type I; Type II

Question 44

Type I Topoisomerases carry out the following four (4) tasks:

Answer 44

(1) Break one of the two DNA strands (2) Pass the unbroken strand through the break (3) Ligate the broken ends (4) Lk changed in increments of 1

Question 45

Type II Topoisomerases carry out the following two (2) tasks:

Answer 45

(1) Break both strands of DNA | (2) Lk changed in increments of 2

Question 46

How is uncontrolled relaxation during topological change avoided?

Answer 46

Topoisomerases never release the DNA while catalyzing the change.

Question 47

In bacteria, the following functions are carried out by Topoisomerase I, II(_____), III and IV; respectively:

Answer 47

``` (DNA gyrase) I: Supercoil relaxation II: Supercoil introduction III: Specializes in DNA repair and replication IV: Replicated chromosomal decatenation ```

Question 48

In eukaryotes, the following functions are carried out by Topoisomerase I, IIα, IIβ and III; respectively (in-particular):

Answer 48

I: (-) supercoil relaxation (DNA replication) IIα/IIβ: (+/-) supercoil relaxation (chromatin condensation, replication, transcription) III: Specializes in DNA repair and replication

Question 49

Topoisomerase activity can be observed via _____ because it will separate them based on _____ _____.

Answer 49

Gel electrophoresis; topoisomeric form

Question 50

``` SMC Proteins (Structural Maintenance of Chromosomes) ```

Answer 50

Class of enzymes facilitate the further condensation/compaction of cellular DNA by forming reversible loops that link DNA segments

Question 51

Bacterial, circular, daughter/sister chromosomes that are intertwined (while still continuous) are referred to as _____?

Answer 51

Catenanes

Question 52

Pairing of SMC1 and SMC3 form a functional unit called _____.

Answer 52

Cohesin

Question 53

Pairing of SMC2 and SMC4 form a functional unit called _____.

Answer 53

Condensin

Question 54

Cohesion _____ while Condensin_____.

Answer 54

link sister chromatids during mitosis immediately following replication; facilitate condensation as mitosis begin via positive supercoiling