DNA synthesis

Question 1

Name features of the DNA helix?

Answer 1

It consist of two antiparallel polynucleotide chains from a right hand helix, in which the bases are on the inside of the helix but the phosphates and the sugars are on the outside.

Question 2

How are the polynucleotide chains linked together ?

Answer 2

the polynucleotide chains are linked together by hydrogen bonds between the bases A & T and C & G

Question 3

Why is DNA replication conservative ?

Answer 3

DNA replication is conservative as the two

Question 4

how many turns for ever 10 base-pairs in B-form DNA?

Answer 4

1 turn

Question 5

what does the two daughter duplex composed off?

Answer 5

the two daughter duplex are composed of 1 new DNA and 1 paternal DNA

Question 6

How is DNA replication initiated?

Answer 6

DNA replication is initiated at specific site on DNA called replication origins.
DNA at the origin sites unwinds to form a replication bubble and allow access to the replication machinery.

Question 7

at which stage does DNA synthesis occur?

Answer 7

DNA synthesis occurs at the S phases of the cell cycle and involves complete unwinding of the parental strand.

Question 8

what is the time span of the cell cycle in bacteria?

Answer 8

the cell cycle has a time span of 30 mins.

Question 9

what is the span of the cell cycle on mammal cells?

Answer 9

16-24 hours

Question 10

how long does DNA synthesis take place?

Answer 10

DNA synthesis takes 8 hours.

Question 11

discuss replication in bacteria ?

Answer 11

Bacterial DNA is circular and supercoiled and it has a single origin of replication.
Proteins can bind at this origin of replication and unwind the two parental strand = allows separation of the parental strand to begin.

Question 12

what is a replication bubble?

Answer 12

it is when the parental strand have been unwound in the region and we’er beginning to copy them.

Question 13

what is the replication fork?

Answer 13

parental DNA is undergoing unwinding to make the separated strands

Question 14

in what direction is the replication in bacteria?

Answer 14

the direction of the bacteria is Bi- directional as it occurs in both directions.

Question 15

what was the first polymerase to be discovered?

Question 15

what was the first polymerase to be discovered?

Question 16

what are the four building blocks used in the synthesis of DNA?

Question 17

how the addition of a base to the template strand mage an irreversible reaction?

Question 18

why must one strand be made discontinuously?

Answer 18

One strand must be made discontinuously due to the directionality of DNA polymerase as it only works in a 5’ to 3’ end.

Question 19

which polymerase is responsible for circular DNA synthesis ?

Answer 19

polymerase gamma.

Question 20

the use of DNA helicase

Answer 20

DNA helicase is present in both eukaryotic and prokaryotic cells.
DNA helicase as the replication fork which is uses ATP to break the base pairs between the two strand of parental DNA. This allows the DNA to be opened up and copied by the replicative DNA polymerase.

Question 21

how does DNA prevent being digested by nucleases?

Answer 21

DNA prevents being digested by nucleases as it’s usually coated DNA binding protein (single strand binding protein).

Question 22

DNA synthesis in bacteria

Answer 22

in bacteria theres is a single replicative polymerase = Pol3 that is able to replicates both leading and lagging strand.
In order to initiate replication on the lagging strand Pol3 needs a primer.

E coli has an enzyme =. primase which lays down a turn of abut 11 nucleotides of RNA. this provides Pol3 with a 3’ end to being replication which leads to formation of Okazaki fragments.
Each Okazaki fragments begins with a bit of RNA and rest in DNA.
The RNA is removed by a repair DNA polymerase in E coil named polymerase 1.

Question 23

DNA replication in Eukaryotic

Answer 23

DNA replications beings with the unwinding of the replication strand by DNA helicase at the start of the replication fork.
Following on there are different types of DNA polymerase. One being the delta DNA polymerase which acts on the lagging strand. On the lagging strand there is till the need for a primer thus polymerase alpha in complex with primase lays down the primer which puts a small amount RNA followed by the alpha polymerase which puts a small out DNA = RNA-DNA primer. The other being DNA epsilon which acts on the leading strand.
when processing the Okazaki fragments the Polymerase delta can displace the RNA copying DNA then a nuclease comes in the trims off the RNA.
The ligase comes and joins up the fragments.

Question 24

what is a nuclease?

Question 25

1 intertwining evert 10 base pairs = problem ?

Answer 25

As the two strands are pulled apart to make the parental strands available for copying the intertwining is pushes ahead on the replication fork to form positive super-coils. This acts as a counterforce against unwinding.

Question 26

How does DNA overcome “DNA winding problem”

Answer 26

DNA overcomes DNA winding problem by using Topoisomerase (enzyme which can break and rejoin DNA)
Topoisomerase removes the positive supercoils ahead of DNA replication fork.

Question 27

How does DNA synthesis occur with high DNA fidelity?

Answer 27

Human cells must replicate 3 x 109 basepairs of DNA
Error rate in DNA replication is ~1 in 1010. Why so low?

1. DNA polymerase- error rate ~ 1 in 108- low due to base pairing and proof-reading/editing function of the enzyme
2. Mismatch repair system- corrects most of the polymerase
   errors. Multienzyme system highly conserved across species

Question 28

Why is the mismatch repair system important?

Answer 28

The mismatch repair system is important as patients who have an inherited defects in mismatch repair genes have a predisposition to colon cancer.

Question 29

Name DNA replication inbitors in Antitumour & Antiviral-AIDS& Antibacterial

Answer 29

DNA replication inhibitors are important antibacterial, antitumour and antiviral agents:

  Antibacterial           Antitumour            Antiviral-AIDS

  Ciprofloxacin		Etoposide		AZT and
   Levofloxacin		Doxorubicin		others
Novobiocin		Mitoxantrone

(Gyrase			(Topo II 			(Reverse
    inhibitors)		inhibitors)		transcriptase)

Question 30

what is the Polymerase Chain Reaction (PCR)?
Why is it such a useful technique in biochemistry and medicine?