DNA Structure and Replication in Eukaryotes and Prokaryotes

Question 1

[6-minute video]: The Structure of DNA

Answer 1

🧬

Question 2

[8-minute video]: DNA Replication - Amoeba Sisters

Answer 2

🧬

Question 3

Define DNA replication.

Answer 3

This is the biological process of producing two identical replicas of DNa from one original DNA molecule.

Question 4

What are the three major steps in DNA replication.

Answer 4

◾ Initiation
◾ Elongation
◾ Termination

Question 5

DNA replication: Initiation

Can DNA replication initiate randomly at any point in DNA?

Answer 5

No

Question 6

DNA replication: Initiation

Where does DNA replication begin?

Answer 6

DNA replication begins at a specific site termed as the origin of replication, which is a specific sequence that can be recognized by initiator proteins called DnaA.

Question 7

DNA replication: Initiation

What role does DnaA play in DNA replication?

Answer 7

It binds to the DNA molecule at the origin sites, flagging it for the docking of other proteins and enzymes essential for DNA replication.

Question 8

DNA replication: Initiation

What enzyme is recruited to unwind the DNA double helix into single strands, and how does it function?

Answer 8

The enzyme helicase is recruited to unwind the DNA double helix into single strands. Helicases break the hydrogen bonds between base pairs in an energy-dependent manner (ATP hydrolysis is required).

Question 9

DNA replication: Initiation

What is the replication fork, and what role do single-strand binding proteins (SSB) play in DNA replication?

Answer 9

The replication fork is the region of DNA where the hydrogen bonds are broken, and DNA is unwound. Single-strand binding proteins (SSB) bind to the unwound regions** to prevent them from annealing**, allowing the replication process to proceed in two opposite directions along the DNA molecule.

Question 10

DNA replication: Initiation

What enzyme is responsible for the synthesis of a new, complementary strand of DNA, and what additional roles does it play?

Answer 10

DNA polymerases are responsible for the synthesis of a new, complementary strand of DNA using the existing strand as a template. In addition to replication, they also play an important role in DNA repair and recombination.

Question 11

DNA replication: Initiation

Why can’t DNA polymerases start DNA synthesis independently, and what enzyme provides the necessary 3′ hydroxyl group?

Answer 11

DNA polymerases cannot start DNA synthesis independently because they require a 3′ hydroxyl group to start the addition of complementary nucleotides. This is provided by an enzyme called DNA primase, which synthesizes a short stretch of RNA (a primer) complementary to the existing DNA strands.

Question 12

DNA replication: Initiation

What is a primer in DNA replication, and what role does it play?

Answer 12

A primer is a short segment comprising 9-12 nucleotides. It provides DNA polymerase the required platform to begin copying a DNA strand. Once the primers are formed on both strands, DNA polymerases extend these primers into new DNA strands.

Question 13

DNA replication: Initiation

What causes supercoiling during DNA replication, and how is it resolved?

Answer 13

The unwinding of DNA during replication may cause supercoiling in the regions following the fork. These DNA supercoils are relaxed by a specialized enzyme called topoisomerase, which binds to the DNA stretch ahead of the replication fork.

Question 14

DNA replication: Elongation

What role does DNA polymerase III play during the elongation phase of DNA replication?

Answer 14

DNA polymerase III starts synthesizing a complementary sequence in each of the separated strands, using the parental strands as templates for the newly synthesizing daughter strands.

Question 15

DNA replication: Elongation

How does the directionality of DNA polymerization affect the replication process?

Answer 15

Elongation is unidirectional, meaning DNA is always polymerized in the 5′ to 3′ direction. This results in continuous replication on the template strand that runs 3′ to 5′, and discontinuous replication on the template strand that runs 5′ to 3′.

Question 16

DNA replication: Elongation

What is the leading strand in DNA replication?

Answer 16

The leading strand is the DNA strand that is synthesized continuously in the 5′ to 3′ direction, using the template strand that runs in the 3′ to 5′ direction.

Question 17

DNA replication: Elongation

How does DNA polymerase III contribute to the synthesis of the leading strand?

Answer 17

DNA polymerase III recognizes the 3′ OH end of the RNA primer and adds new complementary nucleotides, continuously generating the new leading strand as the replication fork progresses.

Question 18

DNA replication: Elongation

How is the lagging strand synthesized during DNA replication?

Answer 18

The lagging strand is synthesized in a discontinuous manner by generating a series of small fragments of new DNA in the 5′ to 3′ direction. These fragments are called Okazaki fragments. [Diagram 1] [Diagram 2]

Question 19

How does DNA ligase contribute to the completion of DNA replication?

Answer 19

After primer removal, the lagging strand still contains gaps or nicks between the adjacent Okazaki fragments. DNA ligase identifies and seals these nicks by creating a phosphodiester bond between the 5′ phosphate and 3′ hydroxyl groups of adjacent fragments, ensuring the newly synthesized DNA strand is continuous and complete.

Question 20

How does DNA polymerase III synthesize the lagging strand during DNA replication?

Answer 20

DNA polymerase III extends the RNA primer by adding new nucleotides in the 5′ to 3′ direction, creating short Okazaki fragments. When it encounters a previously formed fragment, it falls off, releases the DNA strand, and slides upstream to start the extension of another RNA primer. A sliding clamp holds the DNA pol III in place during this process, resulting in the synthesis of the lagging strand.

Question 21

How are RNA primers removed and replaced during DNA replication?

Answer 21

RNA primers are removed by the enzyme DNA polymerase I (DNA pol I) via its 5′ ⇒ 3′ exonuclease activity. DNA pol I then replaces the RNA primers with new deoxyribonucleotides using its 5′ ⇒ 3′ DNA polymerase activity, ensuring the newly synthesized DNA strands are continuous and free of RNA.