Lesson 19: DNA Replication

Question 1

What is the central dogma?

Answer 1

A theory stating that genetic information flows only in one direction, from DNA, to RNA, to protein, or RNA directly to protein

Question 2

What does the structure of DNA suggest?

Answer 2

Structure of DNA suggests a method for replication. Structure determines function

Question 3

What was Menselson and Stahls experiment?

Answer 3

In 1958, Matthew menselson and Frank stahl devised an experiment to test the various models of DNA replication. Grew bacteria in a culture with a heavy isotope of nitrogen. Moved the bacteria into media with a lighter isotope of nitrogen. DNA made in this media will be less dense than DNA made in the first media. Separate the DNA based on density.

Question 4

What does the process of DNA replication require?

Answer 4

Many interacting proteins

Question 5

What are some facts of DNA replication?

Answer 5

DNA replication is amazingly fast (in humans 50 nucleotides/second and in bacteria 1000 nucleotides/second). DNA replication occurs without many errors, one error in 1 to 10 billion nucelotides

Question 6

What actually does the replication of DNA?

Answer 6

Enzymes and proteins DO replication. DNA is just a template.

Question 7

Where does DNA replication occur?

Answer 7

In the nucleus

Question 8

What gets copied?

Answer 8

The entire strand of DNA

Question 9

What is needed prior to cell division?

Answer 9

One DNA strand becomes two and each original strand acts as a template for base-pairing

Question 10

What is DNA replications process?

Answer 10

Semiconservative process: each new double helix contains one strand from the original DNA double helix and one new strand

Question 11

What are the origins of replication?

Answer 11

Replication begins at a specific site with a specific sequence of nucleotides, called an origin of replication. Proteins attach to the origin of replication and separate the two strands of DNA, forming a bubble. Replication proceeds in both directions, making the bubble bigger until the entire chromosome is copied

Question 12

What is the replication fork in DNA replication?

Answer 12

Each side of the bubble the DNA strands are being unwound and separated

Question 13

What are the origins of replication for eukaryotes?

Answer 13

Multiple chromosomes that are larger than bacterial chromosomes, linear chromosomes, and multiple sites where replication begins, instead of just one

Question 14

What is the helicase in the beginning of replication?

Answer 14

Process of replication begins when the helicase (enzyme) recognizes a specific area that starts replication. Helicase “unzips” the DNA double helix making two single strands

Question 15

What are the single stranded binding proteins (SSBPs)?

Answer 15

Bind to the newly separated DNA strands and prevent them from re-pairing

Question 16

What does the helicase do?

Answer 16

Protein that untwists the double helix at the replication fork

Question 17

What is the topoisomerase?

Answer 17

Protein that breaks, swivels, and rejoins the parental DNA ahead of the replication fork, relieving the strain caused by unwinding

Question 18

How does the starting of a new strand occur?

Answer 18

Once the DNA is unwound at an origin of replication the two parental strands serve as templates for the new strands that will be made. You need primer in order to start this process. New nucleotides are added to a free 3’ end

Question 19

What is primase?

Answer 19

An enzyme that creates an RNA molecule (primer) that is complementary to the template DNA strand.

The short RNA molecule is 5 to 10 nucleotides long and provides a 3’ end to which new DNA nucleotides are added

Question 20

What are DNA polymerases?

Answer 20

Enzymes that catalyses the synthesis of new DNA by adding nucleotides to a preexisting chain

Question 21

How many polymerases do prokaryotes and eukaryotes have?

Answer 21

Prokaryotes
Bacteria have two polymerases that are involved in DNA replication (pol III and polI)

Eukaryotes
Eukaryotes have a family of three polymerases that are primarily used for replication (pol alpha, s and e)

Question 22

What is DNA polymerase III?

Answer 22

Adds a nucleotide complementary to the template strand. Catalyses a covalent bond between the 3’ carbon of the existing DNA strand and the phosphate on the 5’ carbon of the new nucleotide

Question 23

What is the only way new nucleotides can be added to a DNA strand through DNA polymerase III?

Answer 23

DNA polymerase III can only add new nucleotides to the 3’ end of the DNA strand. It builds in 5’ to 3’ direction but reads from 3’ to 5’

Question 24

What is the leading strand?

Answer 24

On one template strand only on RNA primer is needed to initiate a long continuous complementary strand that forms as the replication fork progresses

Question 25

What is a problem that occurs on the lagging strand but not the leading strand?

Answer 25

DNA polymerase III on the leading strand follows helicase
DNA polymerase III on the lagging strand needs to build in the opposite direction

Question 26

What is the lagging strand?

Answer 26

To synthesize a new complementary strand on the other template strand, DNA polymerase III must move away from the replication fork in the 5’ to 3’ direction

Question 27

What are Okazaki fragments?

Answer 27

A series of short DNA segments on the lagging strand

Each Okazaki fragment needs a new RNA primer
100 to 200 nucleotides long in eukaryotes, 1000 to 2000 nucleotides long in bacteria

Question 28

What happens for each Okazaki fragment?

Answer 28

Primase makes an RNA primer

Question 29

What does DNA polymerase III do on the lagging strand?

Answer 29

Extends the complementary strand from the primer until it reaches the previously generated primer and Okazaki fragment and then falls off

Question 30

What happens after DNA polymerase III falls off of the lagging strand?

Answer 30

It is replaced by DNA polymerase I, which removes the RNA primer and replaces it with new DNA nucleotides

Question 31

What is DNA ligase on the lagging strand?

Answer 31

Catalyses the covalent bond between the two Okazaki fragments

Question 32

What is a replication machine?

Answer 32

DNA replication proteins work together to form a replication machine

Question 33

What does the replication machine do?

Answer 33

One complex of proteins at each replication fork works to synthesize new DNA on both the leading and lagging strand. The lagging strand loops back through the replication machine to generate Okazaki fragments. The replication machine is attached to the nuclear matrix. Primase, which is associated with the replication machine, controls the rate of replication

Question 34

How are mistakes repaired in DNA?

Answer 34

Cells have mechanisms to fix mistakes in DNA

only 1 in 10 billion nucleotides are mismatched at the end of replication (A to C or T to G). The replication machinery makes an error every 100000 nucleotides. DNA polymerases at the replication fork can “back up” and remove a nucleotide that is incorrectly paired (proofreading mechanism)

Question 35

How is mismatched DNA repaired?

Answer 35

Cells can repair mismatched DNA

Despite the proofreading mechanism of DNA polymerase, sometimes mismatches occur in Neely synthesized DNA

Other enzymes detect the mismatch, cut out the mismatched nucleotides and fill in the gap with the correct nucleotides called mismatch repair

Mismatch repair can also make repairs in DNA that occur through environmental damage in addition to mistakes that occur in replication