Basic Concepts of DNA Replication

Question 1

DNA replication is

Answer 1

Semiconservative

Question 2

one strand of the parent double helix is

Answer 2

conserved in each new

DNA molecule.

Question 3

Initiation process

Answer 3

1- unwinded of DNA

2- breaking the hydrogen bonds

Question 4

Proteins/enzymes involved in DNA replication

Answer 4

• DnaA
• Helicase
• Single strand binding proteins
• Topoisomerase l
• Topoisomerase lol
• Primase

Question 5

Elongation (Proteins / Enzymes involved in DNA replication)

Answer 5

DNA polymerase lll

3’-5’ exonuclease

Question 6

RNA primers removal & the gap filling with DNA

Answer 6

• DNA polymerase l
• 5’-3’ exonuclease
• 3’-5’ exonuclease
• Ligase

Question 7

Chromosome end replication problem & process in Eukaryotes

Answer 7

• telomerase

Question 8

In prokaryotes, DNA replication begins at a site called

Answer 8

The origin of replication (ori)

Question 9

The ori contains specific

Answer 9

A/T rich sequences

Question 10

Why ones the ori contain specific A/T rich sequences?

Answer 10

The double bonded A/T-rich regions are relatively weaker to break than the triple bonded G/C-rich region.

Question 11

1st DnaA rote in binds onto the Ori site

WHYY??

Answer 11

stretches the double strand DNA each other.

Question 12

When the two strands unwindthey create a a Y-shaped structure in both sides called

Answer 12

Replication fork

Question 13

Replication fork allows to start the replication

Answer 13

Bi-directionally

Question 14

Helicase binds to the replication fork and unwinds the duplex DNA by

Answer 14

breaking the hydrogen bonds and using ATP as energy source.

Question 15

Single stranded binding proteins

Answer 15

SSB helps to keep the two strands of DNA separated so that the DNA polymerase can bind and start replication.

Question 16

SSB

Answer 16

Protect the DNA from uncleared the might degrade single stranded DNA

Question 17

Supercoiled DNA will be unwound by

Answer 17

DNA Topoisomerase

Question 18

DNA Topoisomerase

Answer 18

Cuts the DNA strand,
Unwinds the super coil,
And reseals the cut.

Question 19

To initiate replication

Answer 19

DNA polymerase requires a RNA primer

Question 20

RNA primer is synthesized by

Answer 20

primase

Question 21

Primase, a RNA polymerase enzyme

Answer 21

synthesizesa short stretch of RNA (~10 nts long) that are complementary and antiparallel to the DNA template.

Question 22

What starts synthesizing the complementary DNA strand after putting small RNA primer?

Answer 22

DNA polymerase III

Question 23

DNA polymerase III is a

Answer 23

Holoenzyme

Question 24

DNA polymerase enzyme activities are

Answer 24

5’-3’ DNA polymerase

3’-5’ exonuclease

Question 25

DNApolymeraseIIIholoenzymeencirclesthe DNA strand forming like a

Answer 25

sliding clamp and moves along the template strand.

Question 26

The strand synthesized in the 5'→3' direction towards the replication fork

Answer 26

leading strand

Question 27

The strand synthesized in the 5'→3‘ direction opposite to the replication fork

Answer 27

is known as lagging strand

Question 28

In leading strand

Answer 28

Use not one RNA primer

Question 29

On the lagging strand template, primase continuously synthesizes many RNA primers...Why ?

Answer 29

Because, in lagging strand, primase waits for the helicase breaking the replication fork

Question 30

DNA polymerase III extends each RNA primer as a short DNA fragment of ~ 1000 nts.

Answer 30

These fragments are called Okazaki fragments

Question 31

DNA replication is

Answer 31

Semi-discontinuous

Question 32

DNA polymerase III can naturally make an error every

Answer 32

10^7 nucleotide pairs

Question 33

The 3'→5' exonuclease activity of DNA polymerase III

Answer 33

will remove the incorrect nucleotide.

Question 34

Then the 5’-3’ polymerase subunit of DNA polymerase III

Answer 34

Replaces is with the correct nucleotide

Question 35

all the RNA primers synthesized by primase should be removed from the DNA.

Answer 35

This creates many gaps in the newly synthesized DNA including in between Okazaki fragments

Question 36

The gap will be filled by the

Answer 36

DNA polymerase I

Question 37

Major three activities of DNA polymerase I

Answer 37

5’-3’ polymerase 5’-3’ exonuclease 3’-5’ exonuclease

Question 38

5’-3’ exonuclease

Answer 38

Removes RNA primer from 5’ to 3’ direction

Question 39

5’-3’ polymerase of DNA polymerase I

Answer 39

Fills the gap

Question 40

3’-5’ exonuclease

Answer 40

Proofreads if an roar occurs during synthesis

Question 41

The 3’-5’ exonuclease

Answer 41

remove only one nucleotide at the 3’ end

Question 42

The 5’-3’ exonuclease

Answer 42

remove many nucleotides from the 5’ to 3’ direction

Question 43

the newly synthesized all DNA fragments will be linked with phosphodiester bonds by

Answer 43

The enzyme DNA ligase

Question 44

Ori of replication for prokaryotes

Answer 44

Single

Question 45

Ori of replication for eukaryotes

Answer 45

Multiple sites

Question 46

RNA primer synthesis for prokaryotes

Answer 46

By primase

Question 47

RNA primer synthesis for eukaryotes

Answer 47

Polymerase α (alpha) | This also initiates DNA synthesis

Question 48

Leading strand synthesis & proof reading for prokaryotes

Answer 48

DNA polymerase III | 3’-5’ exonuclease

Question 49

Leading strand synthesis & proof reading for eukaryotes

Answer 49

Polymerase ε (pol ε) | 3’-5’ exonuclease

Question 50

RNA primer removal for prokaryotes

Answer 50

5’-3’ exonuclease activity of DNA polymerase I

Question 51

RNA primer removal for eukaryotes

Answer 51

RNase H & flap endonuclease

Question 52

RNA primer gap is filled by DNA for prokaryotes

Answer 52

DNA polymerase I

Question 53

RNA primer gap is filled by DNA for eukaryotes

Answer 53

Polymerase ε

Question 54

Lagging strand synthesis & proof reading in eukaryotes

Answer 54

Polymerase γ

Question 55

tandem repetitive nucleotides

Answer 55

Is a telomere

Question 56

Telomere is located at

Answer 56

At end of each eukaryotic chromosome

Question 57

In humans, average telomere length decrease from

Answer 57

11 kb ——> 4 kb

Question 58

Telomere will not be shortened in

Answer 58

Germ cells Stem cells Cancer cells Because of the telomerase enzyme

Question 59

Telomerase activity

Answer 59

``` RNA nucleotides (UCCCAA) template Reverse transcriptase activity ```

Question 60

Telomerase activity is naturally inhibited in

Answer 60

Normal somatic cells

Question 61

telomerase synthesizes complementary telomere repeat (AGGGTT) at the 3’ end of the full length leading strand (5’-3’ direction) by using its

Answer 61

reverse transcriptase activity & RNA template (UCCCAA)

Question 62

Inhibition of Viral DNA replication in the host cells by

Answer 62

nucleoside analogs

Question 63

Didanosine

Answer 63

Used to treat HIV patients | Anti-retro viral medacation

Question 64

Didanosine

Answer 64

2’,3’ dideoxyinosine | ANALOG OF ADENOSINE

Question 65

In didanosine

Answer 65

3'-OH group on the deoxyribose sugar moiety has been replaced by hydrogen.

Question 66

Azidothymidine = zidovudine = (AZT)

Answer 66

Analog of thymidine | Antiretroviral medication

Question 67

In AZT the 3’OH group

Answer 67

replaced by an azido group

Question 68

Camptothecin (CPT)

Answer 68

Is Topoisomerase I inhibitor

Question 69

CPT binds to the DNA at the topoisomerase I | cleavage site

Answer 69

And it prevents DNA uncoiling and thus inhibiting the replication of cancer cells.

Question 70

Etoposide

Answer 70

topoisomerase II inhibitor.