BIO: DNA Replication

Question 1

DNA Replication is:

Answer 1

• semiconservative, meaning that each strand in the DNA double helix acts as a template for the synthesis of a new, complementary strand.
• 1 template & 1 new (daughter)

Question 2

Where does replication begin?

Answer 2

at the origin

Question 3

Which enzyme unwinds the DNA?

Answer 3

• helicase unwinds the DNA ahead of the replication, by breaking the hydrogen bonds between the nitrogenous base pairs.
• this is to form a replication fork at the origin of replication where DNA replication begins.

Question 4

When Helicase unwinds the DNA strands, what is required?

Answer 4

ATP HYDROLYSIS

The release of chemical energy, stored in a high-energy phosphoanhydride bond in ATP, by breaking the bond.

Question 5

In which direction does the replication forks extends, as replication continues?

Answer 5

bi-directionally

The directionality of DNA polymerase and the fact that the DNA double helix is always anti-parallel means that the two DNA strands are copied in different ways.

Question 6

Other than helicase, which key enzyme is involed in DNA replication?

Answer 6

DNA polymerase

Question 7

DNA polymerase functions

Answer 7

• responsible for the synthesis of DNA
• Add nucleotides only in 5′ to 3′ direction
• requires a template to incorprate complementary nucleotides
• can only add a new nucleotide where a free 3′-OH group is available. This ensures the selective coupling of free nucleotides.

Question 8

Nucleotides Image

Answer 8

Question 9

Where does the phosphodiester bond form?

Answer 9

• phosphodiester bond forms between the 3′-OH and the 5′ phosphate of the next nucleotide.

Question 10

RNA Primase

Answer 10

• An enzyme that synthesizes RNA primers complementary to the DNA strand.
• This primer provides the free 3′-OH end to start replication

Question 11

Which strand is considered the continous strand?

Answer 11

• Leading strand/the template strand
• replicated continuously in the 3′ to 5′ direction and is oriented in the same direction as the replication fork.

Question 12

which strand is made in fragments?

Answer 12

• Lagging strand
• synthesized in the opposite direction from the replication fork
  
  • runs 5′ to 3′ away from the fork
• as the fork moves forward, the DNA polymerase (which is moving away from the fork) must come off and reattach on the newly exposed DNA.

Question 13

What are the fragments called?

Answer 13

• Okazaki fragments
• The leading strand can be extended from one primer alone, whereas the lagging strand needs a new primer for each of the short Okazaki fragments.

Question 14

In total, DNA replication requires all of these enzymes:

Answer 14

• DNA polymerase, DNA primase, DNA helicase, DNA ligase, and topoisomerase.

Question 15

DNA Ligase

Answer 15

An enzyme that seals gaps between Okazaki fragments on the lagging strand

Question 16

Topoisomerase:

Answer 16

• An enzyme that functions ahead of the replication fork to prevent supercoiling of the DNA by introducing breaks and then sealing them.

Question 17

What is the difference of origin replication between eukaryotes & prokaryotes?

Answer 17

• circular prokaryotic genomes only have one origin of replication
• linear, multiple origins are present in eukaryotic genome to allow for faster replication.

Question 18

single-strand binding proteins (SSBP):

Answer 18

Proteins that bind to the separated DNA strands during replication, preventing the strands from reforming the DNA helix

Question 19

Telomers

Answer 19

Repetitive nucleotide sequences at eukaryotic chromosome ends that protect genes from being lost over multiple replication cycles

Question 20

Telomerase:

Answer 20

• in eukaryotic cells
• with RNA-dependent DNA polymerase activity (an enzyme that can make DNA using RNA as a template)
• extends telomeres to protect chromosome ends
• active in somatic cells, but is active in germ cells.
• (somatic): body cells of an organism
• (germ): reproduction cells of an organism (egg/sperm)

Question 21

Prokaryotic & Eukaryotic DNA replication similarities & difference:

Answer 21

• The enzymes involved in the replication of prokaryotic DNA: DNA polymerase I to III, helicase, ligase, primase, sliding clamp, topoisomerase, and single-strand binding proteins (SSBs).
• The basics of DNA replication are similar in prokaryotes and eukaryotes, but eukaryotes have many more enzymes involved.

Question 22

Prokaryotic DNA replication

Answer 22

Question 23

sliding clamp

Answer 23

helps to hold the DNA polymerase in place when nucleotides are being added

Question 24

DNA polymerase III

Answer 24

that extends the RNA primers by adding nucleotides in the 5′ to 3′ direction; the main factor that synthesizes new DNA

Question 25

how are the RNA primers removed?

Answer 25

• by exonuclease activity
• removes nucleotides from the end of a DNA or RNA molecule

Question 26

DNA Polymerase I

Answer 26

• removes the RNA primers and replaces them with newly synthesized DNA
• proofreads DNA and normally has exonuclease activity in the 5′-3′ as well as the 3′-5′ direction that allows it to remove primers and damaged or incorrect bases at the ends of the strand

Question 27

Exonucleases

Answer 27

• It cannot fix mistakes in the middle of a strand, only at the ends

Question 28

which enzymes can fix mistakes in the middle of the strand?

Answer 28

• through endonucleases
• base excision repair and nucleotide excision enzymes have endonuclease activity to remove damaged bases and mismatched nucleotides from the middle of a DNA strand, respectively.

Question 29

What if an enzyme doesn’t have a 5’-3’ exonuclease activity? How is the DNA proofread?

Answer 29

Can only be proofread in the 3’-5’ direction on the template strand, so only errors at the 3’ end of the growing strand can be repaired!