Wednesday, April 27, 2011

The Eureka Enzyme!

DNA polymerase hard at work in the cell!
Photo from
   Imagine this: it is 12 AM, and you are just starting the ten page research paper you’ve known about for weeks merely eight hours before it is due. Sweat drops on the keyboard as your fingers glide across the keyboard, there is no time to waste, but can you guarantee you will not make any grammatical errors along the way? Is there such thing as an organism/molecule that can work at a speedy pace AND make minimal, if any, errors? DNA polymerase I can! The enzyme works at adding 16-20 nucleotides/s to a new DNA strand in E.coli, which is slow for a polymerase. Its fellow isozyme, DNA polymerase III, can add 250-1,000 nucleotides/s in E. coli!
View down the double helix
   The accuracy of DNA polymerase enzyme is remarkable, research has shown it inserts an incorrect base pair every 104-105 bases in eukaryotes. Not impressed? DNA polymerase is also its own editor! It has proofreading capabilities and inhibits the addition of a nucleotide following a mismatch, increasing the accuracy of DNA polymerase 102-103 fold. Spell check cannot compare. If one factors in the enzyme’s proofreading capabilities, the enzyme makes an error every 106 to 108 base pairs!
   Textbook version of DNA polymerase activity
Photo from
   Still not convinced DNA polymerase is the shizz? Think you could live without it? Think again. If a nucleotide mismatch goes unrepaired, known as a mutation, it can go unnoticed in the organism, dubbed a silent mutation, or it can be deleterious to the organism. This single nucleotide change alters only one amino acid in the protein chain, but the results are devastating. One of the most well known example of a point mutation is sickle-cell anemia, and without daily treatment the average life expectancy of the patient is 20-40 years.
Double helix in stick display in rainbow coloring
   There has also been strong evidence linking cancer and the amount of mutations in mammals. You know how you are always told to wear sunscreen while basking in the sunshine? This is why; UV light induces the formation of dimers within DNA and contributes to the 10 percent of all DNA damages caused by environmental factors. Dimers cause kinks and bends in DNA, which results in permanent damage. This can ultimately lead to skin cancer, the number one form of cancer in the United States. DNA polymerase is also an important target for anti-viral drugs, as DNA viruses program their own DNA polymerases. This has been used to combat viruses such as herpes, which infects 16.2 percent of the U.S. population, or about one out of six, people 14-49 years of age.
     DNA polymerase was destined for great things since its discovery in 1956. It was coined the “eureka” enzyme before all of its fundamental roles in life were revealed. Without this enzyme, life as we know it would cease to exist. As the late John Calvin once said, “DNA is life, the rest is just details.”

Genital Herpes. CDC, Dec. 2007. Web. 25 Apr. 2011.
Goodshell, David S. RCSB Protein Data Bank. N.p., Mar. 2000. Web. 17 Mar. 2000.
Nelson, David L., and Michael M. Cox. Principles of Biochemistry. 5th ed. New York:
W.H. Freeman and Company, 2008. 979-982. Print.
Nelson, David L., and Michael M. Cox. Principles of Biochemistry. 5th ed. New York:
W.H. Freeman and Company, 2008. 289-290. Print.
Sickle cell anemia. Ed. Linda Vorvick, Yi-Bin Chen, and David Zieve. A.D.A.M., 31 Jan. 2010.
Web. 25 Apr. 2011. <>.
Skin Cancer. CDC, 23 March 2010. Web. 25 Apr. 2011.

Thursday, March 17, 2011

The Secret of Life

DNA polymerase was first discovered in 1956 by Arthur Kornberg and his colleagues and was the first enzyme in DNA synthesis to be revealed. It was immediately coined the “eureka enzyme” and rightfully so. Now know to perform various roles in DNA replication, including synthesis of new strand, DNA repair, and proofreading, DNA polymerase’s discovery has allowed for tools such as PCR to exist and made our current understanding of DNA synthesis possible. Prior to its discovery, scientists thought DNA synthesis was too complicated of a process to understand.1
DNA polymerase in action! Image obtained from
DNA polymerase is notorious for its astounding accuracy in DNA replication. Its base selectivity and proofreading capability results in less than one mutation per genome duplication. There are currently three known DNA polymerases responsible for dividing up the work of eukaryotic nuclear genome replication. It has recently been found when DNA polymerase ϵ in humans loses its capability to correct its errors in replication the fidelity of the replicated strand is still maintained.2 This was the first piece of evidence that human DNA polymerase is more accurate than polymerase in yeast cells and is being further researched.

Not only is DNA polymerase faithful to its host, it can also repair damages in DNA. Specifically DNA polymerase III in E. coli is crucial for repairing damages caused by hydrogen peroxide, a byproduct of oxidative metabolism, and methyl methanesulfonate (MMS), an alkylating agent.3 Experiments has also shown that DNA polymerase is important in repairing DNA induced by UV damage.

Because DNA polymerase plays an essential role in DNA synthesis, mutations of the enzyme can lead to cancerous cells. Studies have been found that 30% of tumors in humans contained a mutated DNA polymerase β. When the enzyme is altered, more base substitution errors in occur in DNA replication, which may lead to cancerous cells.4 Overexpression the enzyme has also been linked to tumors. The connection between certain cancers and altered DNA polymerase β opens the door for new therapeutic treatments to be looked into.

You may be asking yourself, how is DNA polymerase capable of multiple roles in DNA synthesis? As my high school AP biology teacher drilled: structure dictates function. The structure of the enzyme resembles a hand with three distinct catalytic sites. A site for adding nucleotides to the new DNA strand, proofreading, and removal of primer all exist on this single protein. The synthesized DNA strand rests in the “palm” of the enzyme while DNA polymerase is hard at work.5 It is safe to say that life as we know it would cease to exist without DNA polymerase.

Two "versions" of DNA polymerase in E. coli (left) and Thermus aquaticus (right). Photo obtained from RCSB Protein Data Bank.

1Lehman, I. R. "Discovery of DNA Polymerase." The Journal of Biological Chemistry 5 June (2003). Web. 17 Mar. 2011. <>.

2Korona, Dagmara A., Kimberly G. LeCompte, and Zachary F. Pursell. "The high fidelity and unique error signature of human DNA polymerase ε." Nucleic Acids Research 29 Oct. (2010). PubMed. Web. 17 Mar. 2011. <>.

3Hagensee, M. E., S. K. Bryan, and R. E. Moses. "DNA polymerase III requirement for repair of DNA damage caused by methyl methanesulfonate and hydrogen peroxide." Journal of Bacteriology Oct. (1987). PubMed. Web. 17 Mar. 2011. <>.

4Starcevic, D., S. Dalal, and J. B. Sweasy. "Is There a Link Between DNA Polymerase Beta and Cancer?" Cell Cycle Aug. (2004). PubMed. Web. 17 Mar. 2011. <>.

5Goodshell, David S. RCSB Protein Data Bank. N.p., Mar. 2000. Web. 17 Mar. 2000. <>.

Wednesday, March 2, 2011

DNA is life, the rest is just details

My personal favorite image. Please note the beautiful double helix. 
It's the organic residues' time to shine!
All that DNA duplication and proofreading keeps the enzyme in lean shape!
The paparazzi (aka PyMol) took another colorful shot of the enzyme.

So. Many. Atoms.