DNA Replication

Template A single stranded DNA sequence that acts as the guiding pattern for producing a complementary DNA strand.

Semi conservative replication Process of replication in which each DNA molecule is composed of one parent strand and one newly synthesized strand.

DNA Helicase The enzyme that unwinds double helical DNA by disrupting hydrogen bonds.

Anneal The pairing of complementary strands of DNA through hydrogen bonding.

Single-stranded binding proteins A protein that keeps separate strands of DNA apart.

DNA gyrase The bacterial enzyme that relieves the tension produced by the unwinding of DNA during replication.

Replication Fork The region where the enzymes replicating a DNA molecule are bound to untwisted, single stranded DNA.

Replication Bubble The region where two replication forks are I close proximity to each other, producing a bubble in the replicating DNA.

DNA polymerase lll The enzyme responsible for synthesizing complementary strands of DNA during DNA replication

Deoxyribonucleoside triphosphates Molecules composed of a deoxyribose bonded to three phosphate groups and a nitrogenous base.

RNA Primer A sequence of 10 to 60 RNA bases that is annealed to a region of single stranded DNA for the purpose of initiating DNA replication.

Primase The enzyme that builds RNA primers

Leading strand The new strand of DNA that is synthesized continuously during replication

Lagging strand The new strand of DNA that is synthesized in short fragments which are later joined together.

Okazaki fragments Short fragments of DNA that are a result of synthesis of the lagging strand during DNA replication

DNA polymerase l An enzyme that removes RNA primers and replaces them with the appropriate deoxyribonucleotides during DNA replication

DNA ligase The enzyme that joins DNA fragments together by catalyzing the formation of a bond between the 3’ hydroxyl group and a 5’ phosphate group on the sugar-phosphate backbones

Exonuclease An enzyme that cuts out nucleotides at he end of a DNA strand.

1. What does it mean when DNA replication is referred to as semi-conservative? DNA replication is referred to as semi-conservative because when the parent strand unzips and acts as a template for the newly replicated DNA, each new daughter strand produced contains one new DNA strand and half of the parent strand.

2. What begins the process of DNA replication? The process of DNA replication begins when proteins bind to the DNA strand at the site called the replication origin.

3. What is the function of DNA helicase? DNA helicase is one of several enzymes that work to unwind and expose the DNA template. Helicase unwinds the DNA helical by breaking the hydrogen bonds between the base pairs.

4. What keeps the complementary bases apart during DNA replication? The complementary bases have a natural tendency to anneal, that is to join by hydrogen bonding. The single-stranded binding proteins (SSBp) bind to the exposed single strands of DNA and block or prevent the hydrogen bonding between the nitrogen bases.

5. What is the function of DNA gyrase? The unwinding of the DNA strand produces tension so the bacterial enzyme DNA gyrase functions to relieve the tension. It does this by cutting the DNA strands and allowing them to swirl around and resealing them when the process is completed.

6. Can DNA be fully unwound? Explain. DNA cannot be fully unwound because its size is too large in comparison with the rest of the cell.

7. Explain the role of replication forks and replication bubbles in DNA replication. Replication forks are the junctions on the DNA strand where they are still joined after it has been unwound. A replication bubble will form when two replication forks are in close proximity of one another. The area between the two forks is the replication bubble.

8. Explain the steps taken by DNA polymerase lll to synthesize the complementary strand during the replication process. You may use point form. The following steps outline the role of DNA polymerase lll as it synthesizes a complementary strand of DNA: DNA polymerase lll can only function under certain conditions. It synthesizes DNA in the 5’ to 3’ direction adding free deoxyribonucleoside triphosphates to the 3’ end, and it also requires an initial starting 3’ end to begin elongation. An RNA primer of 10 to 60 base pairs of DNA is annealed to the template strand and it marks the initiation sequences as temporary for ease of removal later on. Now in place the DNA polymerase lll can start the elongation process by adding free deoxyribonucleoside triphosphates to the growing complementary strand.

Deoxyribonucleoside triphosphates are free bases in the nucleoplasm used to build the new complementary strands of DNA The DNA polymerase lll breaks the bond between the first and second phosphate and uses the energy produced to drive the dehydration synthesis reaction that is bonding the free nucleotide to the elongating strand. The remaining 2 phosphates are recycled by the cell. Synthesis of DNA happens in the 5’ to 3’ direction which means that only one complementary strand can be continuously built. The leading strand which uses the 3’ to 5’ template as its guide is built continuously towards the replication fork. The lagging strand is synthesized in short fragments discontinuously in the opposite direction of the replication fork.

The short fragments built by DNA polymerase lll along the lagging strand are known as Okazaki fragments, named after the scientist who discovered them. DNA polymerase l removes the RNA primers from the leading and lagging strands and replaces them with the appropriate nucleotide. The Okazaki fragments of the lagging strand are joined by the enzyme DNA ligase through the formation of a bond between the 3’ hydroxyl group and the 5’ phosphate group. Once the two strands are synthesized the DNA molecules will automatically twist into the double helix shape.

9. After replication is completed DNA polymerase lll and polymerase l proofread the new strand to look for mistakes. Explain how mistakes can be corrected. DNA polymerase lll and polymerase l act as proofreaders to check and make sure there have no been any mistakes in the replication process. Either enzyme acts as cutting enzyme of exonuclease. If a mistake is found the incorrectly paired nucleotide is removed or excised and the correct one is added.