Ch 9

Question 1

Centromere

Answer 1

Segment of each eukaryotic chromosome that functions during cell division as an attachment point for proteins that link the chromosome to the mitotic spindle

Question 2

Telomeres

Answer 2

Sequences at the ends of eukaryotic chromosomes that add stability by protecting the ends from nucleares and providing unique mechanisms for the faithful replication of linear DNA molecules

Question 3

Plasmids

Answer 3

Smaller circular DNA molecules that are few in the cytosol

Question 4

DNA supercooling

Answer 4

Coiling of DNA upon itself, generally as a result of bending, under winding, or over winding of the DNA helix

Question 5

Relaxed DNA

Answer 5

No net cooling of the DNA axis upon itself

Question 6

DNA topology

Answer 6

Continuous deformations include conformational changes due to stretching, thermal motion, or interaction with proteins or other molecules

Question 7

Closed circular DNA

Answer 7

Underwound circular DNA with no breaks in either strand

Question 8

Linking number(LK)

Answer 8

Number of times one closed circular DNA strand is wound about another, the number of topological links holding the circles together

Question 9

LK for right handed helix

Answer 9

Is +, stands inter wound in helix

Question 10

LK for left handed helix

Answer 10

(-)

Question 11

LK for relaxed DNA

Answer 11

LK = #of no/(# no/helical turn)

Question 12

Superhelical density

Answer 12

A measure of the # of turns removed relative to the number of turns present in relaxed DNA

Question 13

Negative supercoiling

Answer 13

The twisting of a helical(coiled) molecule on itself to form a right handed supercoil

Question 14

Positive supercoiling

Answer 14

The twisting of a helical(coiled) molecule on itself to form a led-handed supercoil

Question 15

Toposiomerases

Answer 15

Different forms of a covalently closed, circular DNA molecule that differ only in their linking number

Question 16

Plectonemic supercoiling

Answer 16

A structure in a molecular polymer that has a net twisting of strands about each other in some simple and regular way

Question 17

Solenodial supercoiling

Answer 17

A model for the arrangement of nucleosomes in the 30nm filament in which the nucleosome array assumes a spiral shape, w/the flat sides of adjacent nucleosomes next to each other

Question 18

Type I topoisomerase

Answer 18

Break one of the two DNA strands, pass the unbroken strand through the break, and lígate the broken ends (LK changes in increments of 1)

Question 19

Type II topoisomerase

Answer 19

Break both strands of DNA, change LK in increments of 2

Question 20

SMC proteins

Answer 20

Promote chromosome condensation by creating physical content between segments of DNA that may otherwise be distant from each other on the chromosome, or even in a different chromosome

Question 21

Cohesion

Answer 21

SMC proteins that link sister chromatids immediately after chromosomal replication & keep them together as the chromosomes condense to metaphase

Question 22

Condensins

Answer 22

SMC proteins that facilitate chromosomal condensation

Question 23

How does the length of a chromosome, either prokaryotic or eukaryotic, compare to the overall length of the cell?

Answer 23

Chromosomes are much longer than the biological packages-the cells, organelles, or viral particles
-the nucleus is about 1/3 the size of the cell

Question 24

How do centromeres differ between higher order and lower order eukaryotes?

Answer 24

The centromere sequences of higher eukaryotes are much longer and contain regions of simple sequence DNA consisting of tandem copies of one or a few 5-10 bp

Question 25

What happens at the centromere at mitosis?

Answer 25

Centromeres aren’t always in the middle of the chromosome However usually: proteins attach to the centromere as an attachment point to the mitotic spindle at metaphase; centromeres play a key role in stabilizing chromosome segregation during cell division

Question 26

What proteins attach to the centromere that aid in the separation of sister chromatids?

Answer 26

Kinetochore microtubules attach to the centromere to aid in separation during mitosis

Question 27

Key function of telomeres:

Answer 27

Solve end replication problem in linear DNA - telomeres are noncoding - telomerase has to complimentary base pair with telomere so if the sequence does not match the telomerase then it will not work

Question 28

How does telomerase elongate DNA strand?

Answer 28

Telomerase uses own RNA template to extend DNA molecule

Question 29

How does telomerase differ from DNA polymerase?

Answer 29

Telomerases allow replication in telomeres

Question 30

Is genetic information found in places other than the nucleus in eukaryotes?

Answer 30

Yes Mitochondria(functional RNA, tRNA, and rRNA) Chloroplast contain their own DNA -these are both circular

Question 31

What genes do we find on mitochondrial DNA, and how is that these genes offer supporting evidence to the endosymbiotic theory?

Answer 31

- 13 protein encoding genes - mitochondrial DNA codes for mitochondrial tRNAs, rRNAs and a few other mitochondrial proteins; more than 95% of mitochondrial proteins are encoded by nuclear DNA; mitochondria divides when the cells divide; their DNA is replicated before and during cell division - much smaller than nuclear DNA

Question 32

Is supercoiling necessary?

Answer 32

Yes, this is how DNA gets compacted

Question 33

DNA gyrase

Answer 33

Uses ATP to drive key conformational changes that counteract the thermodynamically unfavorable introduction of negative supercoils - only topoisomerase that introduces negative supercoils - cleaves both strands of DNA - only found in bacteria

Question 34

Underwound DNA gave how many base pairs per turn?

Answer 34

More than 10.5 bp/turn and it is negatively supercoiled(right handed helix) -more accessible to proteins

Question 35

Overwound DNA has how many base pairs per turn?

Answer 35

Fewer than 10.5 bp/turn and is positively supercoiled (left)

Question 36

Topoisomerase II in E.coli

Answer 36

DNA gyrase Function: works ahead of the helicase to relieve the strain of the supercoils

Question 37

Topoisomerase IV in E.coli

Answer 37

Unlinks chromosomes and then reconnects the chromosomes

Question 38

Which class of topoisomerase require ATP?

Answer 38

DNA gyrase

Question 39

What supercoiled state is DNA usually kept in in the cell and why?

Answer 39

DNA is maintained in a negatively supercoiled state because because cellular processes such as transcription and replication cause additional torsional strain -more accessible to proteins

Question 40

What is an example of an organism that does not have negatively supercoiled DNA?

Answer 40

Thermophiles -keep DNA positively supercoiled this

Question 41

Ciproflaxin

Answer 41

An antibiotic that prevents the resealing of strand breaks, broad spectrum

Question 42

What do antibiotics due?

Answer 42

Inhibit DNA gyrase and topoisomerase IV

Question 43

Which moves faster through gel, relaxed or supercoiled DNA?

Answer 43

Supercoiled

Question 44

What would a superhelical density of -0.03 indicate?

Answer 44

3% of the helical turns present in the DNA have been removed. The negative sign indicates that the change is due to underwinding

Question 45

Why are topoisomerases a target of chemotherapy?

Answer 45

Tumor cells generally contain elevated levels of topoisomerases -healthy cells can also be affected

Question 46

SMC proteins

Answer 46

Structural maintenance of chromosomes - promote chromosome condensation by creating physical contact between segments of DNA that are not in close proximity - found in all organisms - occur during mitosis and DNA repair - cohesion: forms loops between sister chromatids - condensin: interacts with the DNA and causes the DNA to become more condense - separase: cuts proteins

Question 47

Coding information:

Answer 47

Proteins and functional RNAs

Question 48

Sequence information:

Answer 48

- replication start and stop - protein attachment - chromosome maintenance