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Organization of Dna in a Chromosome Objectives TOPIC: ORGANIZATION OF DNA IN A CHROMOSOME OBJECTIVES: To learn about the components of a chromosome To know about different models proposed to explain organization of DNA in a chromosome CHROMOSOMAL COMPONENTS: Chromosomes contain chromatin material. Chromatin material is made up of 30-40% DNA , 50-60% Proteins and 01-10% RNA. The composition may vary from species to species. DNA: Direct DNA: These are the specific regions of chromatin material arranged linearly in a haploid set of chromosomes called genome. All the structural genes are made up of these DNA. Recombinant DNA: It is made ou only few hundreds of nitrogenous bases. Each genome containsabout thousands to million copies of this DNA. In humans- 70% Direct DNA and 30% recombinant DNA is observed. In Rye- 08% Direct DNA and 92% recombinant DNA is observed Proteins: Two types of proteins are found in a chromosome 1. Histones or Basic Proteins 2. Non-histones or Acidic proteins 1.Histones or Basic Proteins: these proteins contain more amounts of Arginine and lysine amino acids. They are cationic and strongly bind to anionic nucleic acids by electrostatic attractions at a particular pH. In Eukaryotic cells, Histones are of 5 types. ULTRA STUCTURE OF CHROMOSOME: Chromatin fibres are the basic units of chromosome structure. Chromosome model refers to organization of chromatin fibres in a chromosome. The arrangement of DNA in a chromosome and their mode of binding with histones is explained by various models by many scientists of which the following models are dicscussed in this chapter. Two models were widely accepted to explain the folding of DNA. 1. Folded Fibril Model 2. Nucleosome model 1.Folded Fibril model: This model was originally proposed by DuPraw in 1965. According to this model, folding of a very long chromatin fibre leads to formation of chromatin structure visible at metaphase. 1. Chromatin fibres are basic units of chromosome which are about 230 Å in diameter. 2. A single chromatin fibre is found in each chromatid which consists of a single coiled double DNA helix. 3. The folding of chromatin fibre in different ways results in the development of chromatin structure which is observed at metaphase. 4. Two copies of chromatin fibre are formed from a single chromatin as result of DNA replication during interphase. 5. The replication of chromatin is initially restricted to the chromosome arms so that both the sister chromatins are held together. 6. The replication of chromatin in the centromere region takes place where two chromatins have to separate out. 7. Extensive folding of chromatin fibres leads to significant reduction in their length and increase in thickness and stainability 8. This folded structure further undergoes super coiling, which leads to further reduction in the length and increase in the thickness of chromosomes. Electron micrographs of metaphase chromosome support this model. Hence this model is widely accepted. 2. Nucleosome-Solenoid Model: This model of chromatin organisation was put forth Kornberg and Thomas in 1974. Chromatin is composed of DNA, RNA, histones and other proteins. Chromatin fibres are 300 Å in diameter. Nucleosome: 1. Nucleosomes are the fundamental packing unit particles of the chromatin. They appear as “beads-on-a-string”. 2. Nucleosome is the smallest structural component of chromatin and is produced through interactions between DNA and histone proteins. 3. Each nucleosome is a disc-shaped particle with a diameter of about 11 nm and 5.7 nm in height containing 2 copies of each 4 nucleosome histones–H2A, H2B, H3, and H4. 4. Each nucleosome is composed of a histone octamer and 146 base pairs (bp) of DNA. 5. Each nucleosome consists of (a) a core particle and (b) linker or spacer DNA . a. The core particle has two copies each of H2B, H3 and H4 histone molecules. Thus it has a histone octamer. The core particle is about 100 Å in diameter and 60 Å in height. b. A duplex DNA strand is tightly wound around this core particle making two circles. Spacer or linker DNA has four base pairs. One molecule of histone H1 is connected with linker DNA. The super coiled nucleosome fibre is known as solenoid. Steps involved in solenoid model: 1. DNA is condensed into an 11 nm fiber that represents an approximate 6-fold level of compaction. This is achieved through nucleosome assembly. 2. Each nucleosome consists of histone octamer core, assembled from the histones H2A, H2B, H3 and H4 (or other histone variants in some cases) and a segment of DNA that wraps around the histone core. Adjacent nucleosomes are connected via “linker DNA”. 3. Histone octamer forms a protein core [(i.e., a core of histone tetramer (H3, H4)2 and the apolar regions of 2 (H2A and H2B)] around which the double- stranded DNA helix is wound about one three fourth time(1¾) time containing 146 base pairs. 4. In chromatin, the linker DNA extends as a continuous thread from nucleosome to nucleosome. 5. Each nucleosome bead is separated from the next by a region of linker DNA which is generally 54 base pair long and contains single H1 histone protein molecule. 6. Generally, DNA makes two complete turns around the histone octamers and these two turns (200 bp long) are sealed off by H1 molecules. 7. On average, nucleosomes repeat at intervals of about 200 nucleotides or base pairs. For example, a eukaryotic gene of 10,000 nucleotide pairs will be associated with 50 nucleosomes and each human cell with 6 x 109 DNA nucleotide pairs contains 3 x 107 Folding of DNA: Solenoid model: 1. The first step involved in folding of DNA is the assembly of the DNA with a newly synthesized tetramer (H3-H4), are specifically modified (e.g. H4 is acetylated at Lys5 and Lysl2 (H3-H4)), to form a sub-nucleosomal particle, which is followed by the addition of two H2A-H2B dimers. 2. The next step is the maturation step that requires ATP to establish regular spacing of the nucleosome cores to form the nucleo-filament. 3. During this step the newly incorporated histones are de-acetylated. 4. Next, the incorporation of linker histones is accompanied by folding of the nucleo- filament into the 30 nm fiber, the structure of which remains to be explained. From DNA to Chromosome: 2nm DNA-----11nm filament (beaded nucleosome chain)----30nm filament- ----- pleat as loop chain ------bind to the sites on nuclear skeleton where is AT enriched ------ assembly of chromosome Bibliography: 1. McGinty, R. K., & Tan, S. (2014). Nucleosome structure and function. Chemical reviews, 115(6), 2255– doi:10.1021/cr500373h 2. https://www.easybiologyclass.com/nucleosome-model-of-chromosomes-in- eukaryotes-short-notes/ 3. http://www.biologydiscussion.com/cell-biology/nucleosome-model/nucleosome- model-of-chromatin-assembly-cell-nucleus-biology/78886 4. https://www.mechanobio.info/genome-regulation/what-are-nucleosomes/ 5. https://www.ncbi.nlm.nih.gov/pubmed/958895 6. https://youtu.be/gbSIBhFwQ4s .
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