How topoisomerases unknot knots that are formed in DNA
Introduction:
The study of properties of geometric objects under deformations is called topology; the subfield of topology that I will be discussing in this essay is called knot theory (Adams 6). Mathematical knots have two primary differences: one, they are infinitely thin, and two, they are always closed. Something very similar to the size and shape of mathematical knots is DNA. Not surprisingly, knots occur in DNA frequently on a normal basis.
DNA, short for Deoxyribonucleic Acid, is a molecule found in pairs in the shape of the double helix strands. The strands are composed of “sugars and phosphates,” and the pairs of bases are Adenine, Thyamine, Cytosine, and Guanine, or A, T, C, and G, respectively. Also, A is always paired with T while C is always paired with G. Knots in DNA make “biological functions” like replication, transcription, and recombination difficult to achieve (Adams 182). Fortunately there are enzymes called topoisomerases that find these knots and remove them from the DNA strand so that it is able to function easily (Adams 182). This is important because knots reduce the stability of DNA (Adams 182).
Mathematical Context:
The mathematical origins of knot theory traces back to the early nineteenth century works of Gauss, Listing, Helmholtz, Kelvin, Maxwell, and Talt (Sumners 39). In the beginning, Johann Frederich Carl Gauss, a German mathematician, who was interested in the idea of knots, contributed “analysis situs,” which describes the
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mathematical differences between simple and complex knots, to knot theory (Davis). Later on, more scientists became interested in knots. They believed that the universe was made up of an invisible and frictio...
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...lary that is easy to comprehend. Biochemists are experimenting and working hard to answer these difficult questions about how the different topoisomerases enzymes work to unknot knots in DNA.
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Resources
1. Adams, Colin. The Knot Book: An Elementary Introduction to the Mathematical Theory of Knots. Providence, Rhode Island: American Mathematical Society, 2004.
2. Sumners, De Witt. “Knot Theory and DNA.” Proceedings of Symposia in Applied Mathematics Volume 45 (1992): 39.
3. Knot Theory Online: The Web Site for Learning More about Mathematical Knot Theory. Payne, Bryson and Nardo. North Georgia College and State University. August 3, 2005.
4. Knot Theory History. Davis, Jim. August 3, 2005.
5. “Tangles in Biology.” pages 25-31.
Francis Crick (American) and James D. Watson (Englishman) had a problem with DNA (Deoxyribonucleic Acid) in 1950 because the individual pieces could not be seen. They could be seen with x-ray crystallography which could be done in Kings College, London. They were convinced that DNA was a double helix spiral ladder that contained chemical strands of two to four. It consisted of two strands that were interwoven.
The following is a review of the book, The Double Helix, by James D. Watson that was published in 1968. Here the Norton Critical Edition will be used for page numbering and insights for this review, which was edited by Gunter S. Stent and published in 1980. The Double Helix is a personal recollection of the period of time when the structure of DNA was discovered. James D. Watson (Watson) along with Francis Crick (Crick) were the two scientists who published a paper in 1953 which purposed a structure for DNA. For the most part their structure has stood the test of time, and since that time period many people have wanted to know details of how they discovered DNA’s structure (pp. 3). Therefore Watson’s purpose in writing the book was to describe his personal view of the events that lead to discovery of DNA’s three-dimensional structure, when they happened in 1952-53. He is well qualified to give an account of these things, for he was there in the middle of everything; he was one of the main players. In order to describe the events, apart from his sharp memory, Watson used letters he wrote to his family to help him remember dates and details, as well as suggestions from his associates who reviewed his manuscript. In the following paragraphs I will summarize the text, and follow that with my own review of
The molecule consisted of a double helix with phosphates, deoxyribose sugar molecules, and nitrogenous bases. If the spirals were split, the DNA could replicate, which explained why genes were transferred from parents to their children. Additionally, the order of compounds on the DNA indicated that there was a unique ‘code’ on each strand. Watson and Crick believed that this ‘code’ was translated into specific proteins. , ,
In April of 1953, James Watson and Francis Crick published a game changing paper. It would blow the mind of the scientific community and reshape the entire landscape of science. DNA, fully knows as Deoxyribonucleic Acid is the molecule that all genes are made of. Though it is a relatively new term with regard to the age of science, the story of DNA and the path to its discovery covers a much broader timeframe and had many more contributors than James Watson and Francis Crick. After reading the paper the audience should have a better understanding of what DNA is, the most important experiments that contributed to its ultimate discovery and the names and contributions of the lesser-known scientists that helped Watson and Crick turn their idea
The first and primary contribution to solving the DNA structure was the relationship of Crick and Watson. Without their teamwork and determination, another scientist would have discovered the structure before them. One of Crick’s bigger contributions was discovering the gene is self-replicating. After talking with John Griffith, Crick came up with the idea that the gene is self-replicating, meaning the gene has the ability “to be exactly copied when the chromosome number doubles during cell division”(126). With further discussion with Griffith, Francis believed that DNA replication involved specific attractive forces between the flat surfaces of the bases (128). One of Watson’s major contributions was after seeing the B form of DNA by Franklin, Watson knew that the structure of DNA was two-chained and that led to the building of the model of DNA (171). Also through research, Watson became aware that adenine and thymine pair together and are held by two hydrogen bonds that were identical in shape to the guanine and cytosine pair held together by at least two hydrogen bonds (194). This discovery showed that the two chains of DNA are complementary to each other. With these individual contributions coming together, Watson and Crick successfully were able to piece together the structure of DNA.
DNA is continuously evolving as it has developed various aspects of illicit cases, as well as playing vital roles in all cellular systems. The discovery of DNA has impacted and will trigger the fuel of new findings later in the future. DNA does not only significantly affect a cell’s function, but it aids the species to develop and reproduce, despite the altering conditions.
strands which make up the letters of a genetic code. In certain regions of a DNA strand
A predicament has occurred, in which you speak in the defense of a young female, considered to be guilty on the basis of hair color. Knowledge of the structure of DNA and its role in heredity, how DNA and RNA work together to produce proteins, and how brown hair can result from various gene combinations , will all be an important asset in determining if the young lady is guilty or not.
Most major discoveries have exciting stories to accompany them and account for said discovery. The discovery of DNA’s double helix by James Watson and Francis Crick is no exception.
DNA is a double-stranded helix, with the two strands connected by hydrogen bonds. A base are always paired with Ts, and Cs are always paired with Gs, which is consistent with and accounts for ...
DNA is the abbreviation for deoxyribonucleic acid. DNA is the genetic material found in cells of all living organisms. Human beings contain approximately one trillion cells (Aronson 9). DNA is a long strand in the shape of a double helix made up of small building blocks (Riley). There are four types of building blocks called bases connected with DNA: adenine, guanine, cytosine, and thymine. Each of the bases is represented by the letters A, G, C, and T. The bases are aligned in a specific order, adenine pairs with thymine and guanine pairs with cytosine; this determines a person’s genetic trait (DNA Initiative).
DNA supercoiling occurs in all cells that undergo genetic processing. This event blocks replicative and transcriptional machinery from binding to the DNA helix, which proves detrimental to the cell. However, current research is beginning to show that not all affects of supercoiling produce negative results. These studies prove that different coiling patterns increase the efficiency of epigenetic processes such as methylation and acetylation. Topoisomerase, a post-transcriptional monomeric enzyme, solves the winding problem of the double helix by implementing transient cuts in the genome. As these cuts build up, the genome is essentially fragmented by the enzyme and the cell is unable to express essential genes; this genomic degradation by topoisomerase serves as a viable pathway into cancer research. This review article synthesizes the many ideas surrounding topological cellular events, and presents a new direction for research on chromatin modification in cancerous cells. However, due to the time constraints of the project, this article will not thoroughly discuss the mechanistic process of the replication pathway.
The genetic information of an organism allows for the continuation of life. This genetic information is passed from parent to offspring via the molecule deoxyribonucleic acid (DNA). The structure of the DNA molecule provides a solution for the replication of the existing DNA molecule and furthermore the transmission of heritable information to the next generation. The scope of this essay will discuss how the molecular structure of DNA allows for DNA to replicate and transmit heritable information from one generation to the next.
DNA (deoxyribonucleic acid) is a self-replicating molecule or material present in nearly all living organisms as the main constituent in chromosomes. It encodes the genetic instructions used in the development and functioning of all known living organisms and many viruses. Simply put, DNA contains the instructions needed for an organism to develop, survive and reproduce. The discovery and use of DNA has seen many changes and made great progress over many years. James Watson was a pioneer molecular biologist who is credited, along with Francis Crick and Maurice Wilkins, with discovering the double helix structure of the DNA molecule. The three won the Nobel Prize in Medicine in 1962 for their work (Bagley, 2013). Scientist use the term “double helix” to describe DNA’s winding, two-stranded chemical structure. This shape looks much like a twisted ladder and gives the DNA the power to pass along biological instructions with great precision.
The Double Helix tells a tale of fierce competition, perseverance, and scientific innovation as we follow James Watson and his cohort Francis Crick on their quest to discover the secret to life, the structure of deoxyribonucleic acid. Although already fascinated with DNA, Watson struggled with finding chemistry exciting enough to learn it in depth. He had studied birds in college and thereby managed to avoid any formal chemistry or physics courses. As he later pursued a PhD in biochemistry, he realized he could put it off no longer and attempted to learn organic chemistry at Indiana University. However, after a mishap in the lab, he was encouraged instead to study nucleic acid chemistry with Herman Kalckar in Copenhagen. There, his mind strayed from his work and he began doing unauthorized research in the lab of Ole Maaløe, studying phages. Herman stopped teaching Watson after going through a divorce with his wife, and sent Watson off to a scientific conference in Naples. Although he was bored by many of the lectures, Maurice Wilkins’s talk about X-ray diffraction fascinated Watson. He was struck by an X-ray diffraction picture of DNA that Maurice presented and was determined to study the acid. He later got to know more about Maurice’s colleague, Rosalind Franklin, who was proud, stubborn, and very difficult to work with. Watson greatly admired the lecture given by the renowned Linus Pauling, who had discovered the structure of the alpha-helix and was thought of as the leader in DNA research in the scientific world.