This is the 2nd installment of my series about DNA & RNA! If you haven't read my first post yet, I will put the link right here! Last time, we talked about the structure of DNA, the complementary base-pairing, and how we can denature as well as reanneal DNA under different conditions. For this post, we will focus on the process of DNA replication and how we can repair DNA!
A. THE BASIS OF CHROMATIN ORGANIZATION
In our body, DNA is divided up into 46 chromosomes. About 200 base pairs of DNA wound themselves around histone proteins to form a nucleosome. The five histone proteins that are found in eukaryotic cells are H2A, H2B, H3, H4, and H1. The former four are part of the histone core that DNA wraps around. H1, on the other hand, is the last histone that helps seal off DNA and leaves the nucleosome to add stability to the structure.
In order to prevent DNA from losing information after it replicates, this process actually doesn't occur towards the end of a chromosome. Instead, a telomere - a simple repeating unit of TTAGGG - is formed and an enzyme called telomerase can help replace some of the sequences that are lost after each round of DNA replication. Telomeres are important because they can: 1) Help replace some of the sequences after each round of DNA replication; and 2) Their high G-C (triple bond) can prevent DNA from unraveling! Found in the center of chromosomes are a region of DNA called centromeres. They are composed of heterochromatin and contain high levels of G-C content. This is useful because two sister chromatids will not be separated until anaphase.
B. DNA REPLICATION
During replication, DNA serves as parental strands or "templates" for the new daughter strands. This process is considered to be semiconservative because the daughter strands still have one parental strand retained. The process of replication started when DNA unwinds at the origins of replication (specific locations on the DNA strand) and create replication forks on both sides. Note: The double stranded DNA in eukaryotic chromosome have multiple origins of replication.
Helicase, an enzyme that is responsible for unwinding DNA, is the first enzyme that arrives at the origin of replication. One it binds to the DNA strand, it will generate two single strands of DNA. Single-stranded DNA-binding proteins will bind to these strands to prevent the free purines and pyrimidines from binding to one another. After the strands are separated by helicase, however, the DNA helix is pushed further towards the telomeres and it starts to wrap onto itself - further straining the entire structure and cause the DNA strands to supercoil. To alleviate the stress and prevent it from breaking, DNA topoisomerases nick one or both strands - allowing the pressure to decrease - and reseal the cut strands.
Replisome helps assist DNA polymerases to read the parental strand that is oriented in the same direction, or "DNA template", to synthesize the new daughter strand. These enzymes read the template in a 3' to 5' direction and "continuously" synthesize the complementary/daughter strand in a 5' to 3' direction. The strand that is synthesized continuously is called the leading strand. DNA polymerases accomplish this by adding nucleotides to the growing DNA chain at the 3' end and create a complementary DNA strand to the parental strand (see figure 2). However, how do DNA polymerases add these nucleotides at the replication fork? The answer is lies in an enzyme called "primase". Primase helps synthesize a short RNA primer that is complementary to the template strand. Once the RNA primer binds to the DNA strand at the 3' end, DNA polymerase can then synthesize a new strand that is complementary to the template or "parental" strand.
As discussed above, we already know that DNA polymerases help synthesize the new strand from a 5' to 3' direction. However, what happens to the other strand, or the "lagging strand", that is antiparallel to the template strand? How do DNA polymerases read the lagging strand? In this case, the DNA polymerase has to come off the leading strand and latch itself onto the lagging strand to make a complementary strand for it. This means that the new "non-continuously" synthesized strand or "lagging strand" is consisted of small fragments called Okazaki fragments.
C. ONCOGENES AND ANTIONCOGENES
Contrary to what some might think, DNA can easily be damaged by radiation or chemicals. If it's not fixed, the damaged/mutated DNA can be replicated and passed onto daughter cells. There are genes in our body that when mutated, can lead to cancer. Genes that have been mutated and cause cancer are called oncogenes. Fun fact: When they haven't be mutated yet, we call them proto-oncogenes! These genes can be suppressed by tumor suppressor genes or antioncogenes (ie: p53 or Rb). If these genes are mutated, then they can't suppress tumor activity, promote cell cycle, and cause tumor growth.
D. DNA REPAIR
When a DNA strand is being synthesized, it will need to be inspected by DNA polymerase so that it can be proofread. If the newly synthesized strand have incorrectly paired bases, then that portion of the structure will be unstable. When DNA polymerase detects this instability, the incorrect base is excised and a correct one will take its place. The 3 different types of DNA repair are: Mismatch repair, nucleotide excision repair, and base excision repair.
In cases where there are mismatched repair, cells in the G2 phase have the necessary machinery to help fix this. Genes called MSH2 and MLH1 help detect and remove those errors. If DNA is exposed to ultraviolet light, it can induce the formation of thymine dimers. This can cause interferences in DNA replication and distort the shape of DNA helices. This can create a "bulging shape" in the middle of a strand. In this case, we can use nucleotide excision repair to remove the thymine dimers. An enzyme called excision endonuclease can then come in to nick the phosphodiester linkage in the backbone and remove the defective base pair. Once the incorrect based pair is replaced with the correct one, DNA polymerase can synthesize a new DNA and DNA ligase can then seal the nick in the strand (as seen in figure 3).
In cases where cytosine deamination (cytosine loses an amino group because DNA absorbs thermal energy) occurs, cytosine is converted to uracil. Because uracil is normally found in RNA and not DNA, we can use base excision repair to fix this error. The defected base is removed by glycosylase enzyme, AP endonuclease removes the damaged sequence at the apurinic/apyrimidinic (AP) site, DNA polymerase can fill in the gap, and DNA ligase can then seal the strand.
I'm Linh - a science geek who loves experimenting and tinkering with recipes! I hope that this blog brings more ideas into your kitchens! Happy eating folks! XOXO