Introduction to DNA Replication
The AP® Biology exam has a lot of content on DNA, and DNA replication will be a topic that you will be tested on so it is very critical to know it! In this AP® Biology Crash Course Review we will go over what you should know about DNA replication for the AP® Biology exam. DNA replication is a process that is constantly occurring. When cells replicate, they must pass their DNA to their daughter cells. During the development at conception, growth during the lifetime of the organism, and replacement of damaged or aged tissue there will be rapid cell division, and thus, we need a fast system. The DNA code must also be correct. If there is a difference in one base pair, it could be very problematic to the organism; thus the system must be precise and accurate. First, we will review the scientific history that lead to the modern understanding of how DNA is replicated. Next, we will review the actual mechanism for DNA replication. Finally, we will review the differences between eukaryotic and prokaryotic DNA replication.
History
The AP® Biology exam wants you to know and understand scientific theories. There were three major theories of how DNA could be replicated after the discovery of DNA by Watson and Crick. The three theories included: the semiconservative replication model, the conservative replication model, and the dispersive replication model. Semiconservative replication posited that the DNA strands were separated during DNA, and each single strand was used as a template for a new DNA strand. The theory of conservative replication hypothesized that during replication, the original DNA molecule would be used to form the new DNA molecule but after replication, it would become double stranded again creating the old molecule and a completely new molecule. Finally, dispersive replication supporters believed that the original DNA molecule was scattered into the new DNA and that the new DNA would contain both old and new pieces.
In order to figure out this controversy, a famous experiment was conducted. The experiment is after the scientists who conducted it; the Meselson-Stahl experiment. DNA is composed of sugar, phosphate, and a nitrogenous base. This experiment focused on the nitrogenous bases. The experiment added heavy nitrogen (15N) to bacteria and then transferred the DNA from the original bacteria to a tube with different bacteria which had been given regular nitrogen (14N). The first bacteria, treated with the heavy nitrogen, had DNA with heavy nitrogen in the bases while the second bacteria did not. The experimenters tracked where the nitrogen went in order to understand how the DNA was replicated. They found that the DNA was made up of one strand with heavy nitrogen and one with regular nitrogen supporting the semiconservative theory.
Now that we know how DNA is replicated we can delve into the detail of replication. There are three stages of replication which need to be addressed for the two strands of the parent DNA molecule.
Initiation
We will start first with our double stranded DNA parent molecule. When it is time for DNA to replicate, it first must be “unzipped”. The unzipping is done by an enzyme called DNA helicase. DNA helicase will cause the DNA to become single stranded. The single stranded DNA is not stable and wants to be double stranded again. Single stranded binding proteins (or SSBs for short) help to ensure that the DNA remains single stranded by stabilizing and covering the hydrophobic DNA strands.
When the two strands are separated, one strand will be 5 prime to 3 prime and one strand will be 3 prime to 5 prime. These strand orientations refer to where the phosphate and hydroxyl groups are. The 5 prime end is the end of the DNA with a phosphate group and the 3 prime end refers to the end of DNA with a hydroxyl group (on the sugar). The enzyme which carries out replication, DNA polymerase, can only move in the 5’ (‘ indicates prime) to 3’ direction. Because of this, there are two different ways that DNA is synthesized. We will start with the strand that is oriented in the 5’ to 3’ direction, and we will call it the leading strand.
Elongation: Leading Strand
After the strands have been separated (just a few base pairs will be exposed), DNA primase (another enzyme) attaches to the leading strand and puts down a short RNA or DNA primer. The primer will flag the DNA polymerase to attach to the primer and continue to synthesize the DNA by adding on matching nitrogenous bases. The base pairs match in the following ways: adenosine will pair with tyrosine and cytosine will match with guanine. The new strand will be given nitrogenous bases that pair with the template strand which will allow them to become a double stranded molecule at the end of replication. DNA polymerase will sit near the replication fork, as DNA helicase unzips the DNA, and then DNA polymerase will add the free nucleotides to the DNA strand. This type of replication is called continuous because DNA polymerase just moves down the strand adding the complimentary base pair to the DNA strand.
Elongation: Lagging Strand
The lagging strand is much more difficult to visualize and understand. The lagging strand is DNA which is oriented in the 3’ to 5’ direction; therefore DNA polymerase cannot just attach and run down the DNA strand. Replication of the lagging strand begins with DNA primase providing a short primer sequence on the template DNA, much like it does in the leading strand. Because it is not oriented 5’ to 3’, the lagging strand must replicate in fragments called Okazaki fragments. The fragments are synthesized away from the replication fork in fragments of about 100 to 200 base pairs long. DNA polymerase extends the primed sequence forming the fragments. The RNA fragments are removed by exonuclease activity (the DNA polymerase digests the RNA nucleotides) and the RNA is replaced by DNA. Finally, in order to put the Okazaki fragments together, another enzyme is needed. DNA ligase comes down the lagging strand and pushes the Okazaki fragments together to create a full strand of DNA. This type of DNA replication is considered discontinuous due to all of the fragments.
If you are having trouble visualizing this try to imagine DNA polymerase making a loop of the template DNA so that it can read it in the correct way (5’ to 3’) at the end of the loop it starts to read 3’ to 5’ again and must create a new loop. If this still seems difficult try checking out videos online like this one.
Because DNA is constantly being replicated, it is not unusual for mistakes in nucleotide placement to occur. To correct for this DNA polymerase has a subunit which proofreads the DNA as it moves down the strand. Any mutation in the DNA could cause a phenotypic change in the organism. It is essential for survival that mutations are limited.
Termination
After the DNA strands have been elongated they have been semi-conservatively replicated and there are two copies of the DNA. This will allow the DNA to be used in a new daughter cell.
Eukaryotic vs. Prokaryotic Replication
It is important to be able to distinguish DNA replication in prokaryotes and eukaryotes for the AP® Biology exam. Now that you understand replication, the differences between the two should be easier to understand.
Prokaryotes:
In prokaryotes, DNA replication occurs in the cytoplasm. The origin of replication (where replication begins) is a single spot in the DNA. Also, remember in prokaryotes the DNA is double stranded, but circular. Termination will occur when the circle has been completed. Additionally, in prokaryotes Okazaki fragments are much larger, usually about 1000-2000 base pairs.
Eukaryotes:
In eukaryotes, DNA replication occurs in the nucleus. There are many different origins of replication because DNA primase lays down primers at many different spots and because the DNA is much longer than in prokaryotes this helps optimize the time spent during replication. Even with multiple origins of replication, eukaryotic replication takes longer than prokaryotic replication due to the longer DNA.
Summary
In this AP® Biology crash course review, we went over DNA replication. We began with a review of the experiments done to understand DNA replication. We then reviewed all of the details of DNA replication. We finished up by contrasting eukaryotic and prokaryotic DNA replication. If you want to study DNA more, check out the other AP® Biology Crash Course Review articles that cover all other aspects of DNA that you need to know for the AP® Biology exam.
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