BioChem 7.1 DNA structure and replication

Question 1

How does the discovery of the DNA structure give insight into the mechanism of DNA replication?

Answer 1

As we know that DNA has a double stranded structure, and is defined by their sequence in order to store genetic information, we can deduct that a replication of a strand can be created through the information of the complementary strand.

Question 2

Outline the protocol of the Hershey and Chase experiment.

Answer 2

1. Phages were attached to a bacterial cell.
2. The DNA is transferred through injection into the bacterial cell.
3. Phage had normal DNA but was covered in radioactive protein coat
4. Phages were attached to bacterial cell, and DNA was transferred and reproduced. Next generation was not radioactive.
5. Phage had radioactive DNA covered in normal protein coat.
6. Next generation was radioactive.

Question 3

What is a phage?

Answer 3

A phage is a type of virus that infects bacteria. Phages are made from DNA covered with a coat of protein.

Question 4

From the Hershey and Chase experiment, what can we deduce?

Answer 4

From the experiment we can deduce that protein does not pass on genetic information or even contain such.
From the experiment we can also deduce that DNA is inherited by the next generation. Therefore, DNA stores genetic material that is information needed for the next generation

Question 5

What can we deduce from the X-ray crystallography?

Answer 5

From the crystallography we can find that strands over lap like intersections and therefore DNA should be a double stranded helix.

Question 6

What does the DNA Helicase do?

Answer 6

In DNA replication, DNA Helicase unzips the double stranded DNA helix by breaking apart the hydrogen bonds.

Question 7

What does DNA gyrase do?

Answer 7

DNA gyrase releases tension from the DNA double helix. It does this by breaking both strands and unwinding the strand by 2 coils and then fusing the DNA strands back together.

Question 8

What does DNA polymerase I do?

Answer 8

DNA polymerase I replaces the RNA strand with a DNA strand.

Question 9

What does DNA polymerase III do?

Answer 9

DNA polymerase builds complementary DNA strands (sugar phosphate backbone)

Question 10

What do single stranded binding proteins do?

Answer 10

Single stranded binding proteins prevent the single DNA strands from sticking back together.

Question 11

What does DNA primase do?

Answer 11

DNA primase inserts a piece of RNA to the single strand

Question 12

What are Okazaki fragments?

Answer 12

Are the sections of DNA on the lagging strand that need to be connected

Question 13

What does dNTP do?

Answer 13

DNA polymerase II uses dNTP (Deoxynucleotide triphosphate) to build a new complementary strand of DNA (connecting the Okazaki fragments). Two phosphate groups are removed

Question 14

What does DNA ligase do?

Answer 14

DNA ligase is responsible for joining the Okazaki fragments to create a continuous strand.

Question 15

Name at least 5 functions in DNA replication.

Answer 15

○ Helicase
		○ DNA gyrase 
		○ single strand binding proteins 
		○ DNA primase
		○ DNA polymerases I 
		○ DNA polymerases III
		○ Okazaki fragments 
		○ deoxynucleoside triphosphates (dNTPs) - also known as 'free nucleotides'

Question 16

In which direction does DNA replication occur?

Answer 16

DNA replication occurs in a 5’ to 3’ direction because DNA polymerase 3 only adds nucleotides to the 3’ end of the primer.

Question 17

Outline the process of DNA replication (on the leading strand)

Answer 17

1. DNA helicase unzips the double stranded DNA helix by breaking the hydrogen bonds
2. The single stranded binding proteins attach themselves to each strand to prevent them from sticking back together.
3. DNA Primase adds a new RNA strand to the single strand.
4. DNA polymerase III builds a new complementary DNA strand. The existing strand is used as a template using the complementary base pairing rules
5. DNA polymerase I replaces the RNA primer with a short DNA strand.
   On the leading strand DNA polymerase III can build a complementary DNA strand continuously.

Question 18

Outline the process of DNA replication (on the lagging strand)

Answer 18

1. On lagging strand the new complementary DNA strand must be built in sections called Okazaki fragments due to the fact that the DNA polymerase III only goes in one direction, 5’ to 3’
2. DNA ligase is required to join together the Okazaki fragments.
   On the lagging strand DNA polymerase III has to work discontinuously because it only works in one direction from 5’ to 3’

Question 19

When does DNA replication occur in eukaryotic chromosomes?

Answer 19

DNA replication initiates at many points in eukaryotic chromosomes.
This is because eukaryotic genomes are usually larger than prokaryotic genomes. So DNA is replicated at many points simultaneously in order to limit the time required for DNA replication to occur.

Question 20

What are the sites called where DNA unwinding and initiation of replication occurs?

Answer 20

These sites are called origins of replication and form replication bubbles.
As replication bubbles expand they eventually fuse together. Two generate two separate semi conservative double strands of DNA

Question 21

How can DNA be sequenced?

Answer 21

1. DNA fragments made from PCR
2. Fragments are denatured (heat)
3. single strands are placed into tubes (4 dif) that contain primers, polymerase, nucleotides (to replicate DNA)
4. also contains special nucleotides called dideoxynucleotides (from ddNTP) labelled with flourescent
5. This nucleotide prevents further addition of nucleotides
6. there is a dideoxynucleotide for each nitrogenous base (one in each tube)
7. Fragments separated by gel electrophoresis
8. compare colour of florescence and length