Lecture 31 (add sequence portion)

Question 1

What are the three types of DNA coiling?

Answer 1

Negative, positive, and relaxed

Question 2

What type of coiling do prokaryotes and eukaryotes normally have?

Answer 2

Negative supercoiling

Question 3

What does negative supercoiling do to DNA? How does it prepare it?

Answer 3

Negative supercoil prepares the DNA for the replication process which requires separation of the DNA strands

Question 4

What is coiling in the opposite direction?

Answer 4

negative supercoiling

Question 5

What is DNA coiled in the same direction?

Answer 5

Positive coiling

Question 6

What type of coiling do bacterial genomes have?

Answer 6

Negative supercoiling

Question 7

At what bp does replication occur in E. Coli?

Answer 7

100,000 bp/min

Question 8

What is the enzyme that is responsible for unwinding the double helix strand of DNA?

Answer 8

Helicase but there are other enzymes ahead of helicase to remove positive supercoils. Helicase also generates supercoils ahead of the replication fork

Question 9

What other enzymes relieve positive supercoils that are NOT helicase?

Answer 9

Topoisomerase I and II

Question 10

What does topoisomerase do?

Answer 10

Unwind the double helix during DNA replication. These work ahead of the fork

Question 11

What does topoisomerase I do?

Answer 11

Can make single-stranded breaks to relax the helix. Uniwnds supercoils.

Question 12

What does topoisomerase II do?

Answer 12

It contains gyrase and is able to break and rejoin the double stranded DNA. Introduces supercoils

Question 13

How does topoisomerase I work? How does it bind?

Answer 13

It binds to one strand of DNA, cuts it, and the DNA can then swivel and relieve tension.The intact strand of DNA passes through the nick resulting in the relaxation of the torsional strain. Then, it forms a phosphodiester bind.

Question 14

What is true about topoisomerase I and energy?

Answer 14

It does not need ATP but instead transfers the phosphodiester bond from the DNA to the enzyme and back again. Does NOT hydrolyze

Question 15

What is true about topoisomerase II and energy use?

Answer 15

It requires ATP

Question 16

How does topoisomerase II work? How does it bind?

Answer 16

It uses ATP to cut both strands, passes the molecules through the cut section, and reseals the phosphodiester bond. It cleaves the strand and generates a negative coil. Relieves pos coil and introduces negative coiling

Question 17

What happens when coiling is too tight?

Answer 17

DNA can’t unwind for replication

Question 18

How do eukaryotes differ from prokaryotes during DNA replication?

Answer 18

Since they are linear, they do not rotate freely, also includes their binding to proteins.

Question 19

What relieves coiling in eukaryotes?

Answer 19

Topoisomerase I or II

Question 20

Why isn’t gyrase needed in eukaryotes?

Answer 20

Because gyrase introduced negative coils which is something that eukaryotes already have, they just need positive coils to be relieved

Question 21

What happens when topoisomerase is inhibited?

Answer 21

They are useful because they stop DNA replication, stop reading DNA for protein produc, and stop repair of DNA damage

Question 22

Why is topoisomerase inhibitors useful for cancer treatment?

Answer 22

It is useful because they stop replication in target cells that are replicative

Question 23

How do topoisomerase inhibitors work and benefit antibacterial drugs?

Answer 23

Inhibitors are helpful because they target prokaryotic topoisomerase and stop bacterial DNA replication and leaves eukaryotes topoisomerase untouched

Question 24

What are the antibacterials targeted by inhibitors?

Answer 24

nalixidic and ciprofloxacin

Question 25

What are the cancer treatments targeted by the inhibitors?

Answer 25

camptothecin, doxorubicin, and mitoxanthrone

Question 26

How many Pol does E. Coli have?

Answer 26

3 one in the leading strand, and two for the lagging strand

Question 27

What form does DNA need to be during DNA replication?

Answer 27

Negative coiling and chromatin must be dismantled prior to replication and reform daughter strands

Question 28

What controls replication?

Answer 28

Replication is based on DNA sequence on the Ori site and then binds to the initiator protein

Question 29

What does the initiator protein do?

Answer 29

regulate the replication of DNA

Question 30

Where does DNA synthesis begin?

Answer 30

At the origin which is adjacent to the replicator

Question 31

What are the roles of the initiator?

Answer 31

1.Initiator binds DNA 2. Initiator unwinds (a little) DNA at the origin 3. Initiator recruits other replication proteins: helicase, primase and the Pol III complex

Question 32

Where do eukaryotes initiate replication?

Answer 32

sites that have an AT-rich sequence and helicase unwinds because of hydrogen bonds

Question 33

What are some problems that arise in eukaryotes?

Answer 33

The needing to use a primer for DNA synthesis and then removing them causes replication to be complete in one stand. This causes for shortening in the strands over time after each round of replication.

Question 34

What enzyme do eukaryotes use to replicate ends completely?

Answer 34

telomerase

Question 35

What cells can extend their ends?

Answer 35

Germ(sperm and egg) and stem cells

Question 36

What are telomeres?

Answer 36

Repeat and non-coding

Question 37

How do telomeres work?

Answer 37

They work as chromosome caps and bind to proteins that protect the ends of chromosomes from end-joining and exonucleolytic digestion

Question 38

What is telomerase? How does it work?

Answer 38

It is a unique mechanism that synthesizes short DNA repeats

Question 39

What template does telomerase use?

Answer 39

RNA template for DNA synthesis(reverse transcriptase). Dependent on DNA polymerase

Question 40

What is true about telomerase and primers?

Answer 40

It has its own primer that allows extending. This first starts in the 3' end of DNA using the RNA primer

Question 41

What happens when telomerase has extended the 3'?

Answer 41

Primase and DNA polymerase can carry out replication using the new, longer end as a template

Question 42

What does DNA Pol III do?

Answer 42

adds the new bases

Question 43

What does DNA Pol I do?

Answer 43

DNA Pol I removes the RNA primer

Question 44

What does telomere binding proteins do? What type of protection does it have?

Answer 44

It protects from degradation by exonucleases, recombination, ligation

Question 45

What happens when telemore is lengthened?

Answer 45

more telomere binding proteins bind and inhibit telomerase

Question 46

What happens when telomere shortens?

Answer 46

reduced binding of telomere binding proteins allows telomerase to bind and lengthen telomere

Question 47

When is telomerase inactive?

Answer 47

somatic cells

Question 48

When is telomerase activated?

Answer 48

Immortalized (tumor) cells in cancer and activates multiple replication cycles