Describe the detailed structure of DNA and explain the manner in which this structure replicates itself in both prokaryotes and eukaryotes. 1. In living organisms, DNA exists as a pair of molecules that are held tightly together and form a double helix structure. Structurally DNA consists of two long polymers made from repeating units, which are called nucleotides. The backbone of the DNA strand is made by the alternating phosphate sugar residues. That sugar is 2-deoxyribose, which is five –carbon sugar called as pentose. Each sugar is joined together by phosphate group that forms the phosphodiester bond between third and fifth carbon atoms of adjacent sugar rings. In double helix structure, the nucleotide’s direction in one strand is opposite to their other stand direction (i.e. anti-parallel). The asymmetric ends of the DNA strands consist 5’ and 3’ ends where 5’ end has a terminal phosphate group, and the 3’ end has a terminal hydroxyl group. The DNA double helix is stabilized by hydrogen bonds between nucleotides and base-stacking interactions among the nucleobases. There are four bases found in DNA such as adenine (A) cytosine (C), guanine (G), and thymine (T). A and G are called purines and C and T are called pyrimidine. These four bases bind to the sugar or phosphate and form the complete nucleotide. Each nucleobase on one strand interacts with one type of nucleobase in the other strand. The purines form the hydrogen bonds to pyrimidine. Here, A bonds only to T by two hydrogen bonds, and C bonds only to G by three hydrogen bonds. 2. To explaine the manner in which this structure replicates itself in both prokaryotes and eukaryotes, let me first compare and contrast eukaryotes and prokaryotes. Prokaryotic organism and DNA Bacteria(like E.Coli) is the well known example for prokaryote. The organisms that lack nucleus or membrane bounded organelles are called prokaryotes.vEven though, most of the prokaryotes are unicellular, a few have multicellular stages in their life cycle. Generally, prokaryote’s cytoplasm contains ribosome and nucleoid with strands of irregular DNA. There is only a single loop of DNA present in the nucleoid. It does not have histone protein and occurs as a circular chromosome. In prokaryotes, many important genes are stored in satellite DNA, which is referred as plasmid. Prokaryotes contain only a single loop of chromosomal DNA. Replication mechamism: In prokaryotes the DNAs semi-conservative replication of the original helix is split in two strands forming a replication fork. In the division of the prokaryotic-circular DNA the (theta) model is used. From only one initiation site the replication fork moves in the opposite direction until they meet, serving the parental strands from one another (Module 9. DNA replication animation) In detail, the replication in prokaryotes starts from a sequence found on the chromosome called the origin of replication—the point at which the DNA opens up. Helicase opens up the DNA double helix, resulting in the formation of the replication fork. Single-strand binding proteins bind to the single-stranded DNA near the replication fork to keep the fork open. Primase synthesizes an RNA primer to initiate synthesis by DNA polymerase, which can add nucleotides only in the 5 to 3 direction. One strand is synthesized continuously in the direction of the replication fork; this is called the leading strand. The other strand is synthesized in a direction away from the replication fork, in short stretches of DNA known as Okazaki fragments. This strand is known as the lagging strand. Once replication is completed, the RNA primers are replaced by DNA nucleotides and the DNA is sealed with DNA ligase, which creates phosphodiester bonds between the 3-OH of one end and the 5 phosphate of the other strand. In prokaryotes, three main types of polymerases are known: DNA pol I, DNA pol II, and DNA pol III. It is now known that DNA pol III is the enzyme required for DNA synthesis; DNA pol I and DNA pol II are primarily required for repair. ingle-strand binding protein:during replication, protein that binds to the single-stranded DNA; this helps in keeping the two strands of DNA apart so that they may serve as templates. sliding clamp is utilized in prokaryotic DNA replication which is ring-shaped protein that holds the DNA pol on the DNA strand. Then, topoisomerase that further assists the replication mechanism, which is an enzyme that causes underwinding or overwinding of DNA when DNA replication is taking place. Eukaryotic organism and DNA All the animals, plants, and fungus are eukaryotic organisms; nuclear envelope is the most defining character for all eukaryotic organisms. Eukaryotes have ‘true’ nuclei that contain DNA and membrane bound organelles. In eukaryotes, mostly DNA is stored inside the cell nucleus, but some are found within the organelles such as chloroplasts and mitochondria. Histone protein and organized DNA are compacted inside the chromosome. Only some of the eukaryotes have the plasmid. Eukaryote DNA is found on tightly bound and organized chromosomes. The entire complex of a cellss DNA and associated protein called chromatin. Five major histomes are present in chromatin: four associated histones called H2A, H2B, H3, and H4, and the other called H1 (Tymoczko, p. 589). The repeating units of these histones form nucleosome, with nucleosome core particle and linker DNA. Amono-terminal tail is strickly lysine or arginine. Supercoiling and nucleosome formation compacts the DNA structure of eukaryotic DNA. Replication mechanism: In the linear-eukariotic DNA several initiation sites are used. These sites form replication bubbles, which grow and join as the fork moves (Module 9. DNA replication animation). Replication inveukaryotes are similar to prokaryotes, only more complexed. Eukaryotes have larger size of base paires as a first challange. Second challange is the fact that bacteria like E.Coli is contained on one chromosome and the eukaryotic human genome has 23 pairs of cromosomes that must be replicated. Linear chromosomes of eukaryotes are subject to shortenings and lagging stand complications. Replicons are employed to handle multiple origines of replication mechanism helped by licensing protein factors, that replicates only once and suspended after (Tymoczko, p. 608). Two distinct polymerases are needed to copy a eukaryotic replicon. An initiator polymerase alpha begins replication, that incude primase subunit used to synthesize RNA primer, as well as an active polymerase. After the polymerase has added a stretch of about 20 deoxyribonucleotides to the promer, it is replacded by DNA polymerase beta, assisting in process called polymerase switching, beacuase one polymerase switched another. Thertermore, the end of the replication of linear chtomosome isassisted by the telomerase which shortens the free ends, preventing the free tails from exonucleases digestion.
Posted on: Tue, 26 Nov 2013 08:06:13 +0000
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