![]() This linear form of DNA with 12.5 bp per turn is an unstable structure that does not naturally occur in cells. For example, a linear 50 base pair (bp) DNA molecule with five turns in the double helix (10 bp per turn) would have 12.5 bp per turn if it is underwound by one turn (50 bp/4 turns = 12.5 bp/turn) (see the left-hand side of Figure 2.2). Underwinding of the DNA double helix produces fewer turns in the helix. In both cases, the DNA double helix is stabilized by supercoiling - Image created by SL ![]() Underwinding by one turn produces an unstable structure with four turns, while overwinding by one turn produces an unstable structure with six turns. Figure 2.2 Negative and Positive Supercoiling – The molecule in the center of the image contains five turns, with each turn containing 10 base pairs (bp). Introducing counterclockwise twists into a right-handed helix produces underwinding of the helix. DNA is naturally a right-handed helix, meaning that the two DNA strands interact by hydrogen bonding to produce a helix that rotates clockwise. Also suppose that the bottom support is held firmly in place, while the top support is twisted in the left-handed or counterclockwise direction. Suppose a piece of linear double-stranded DNA is connected to two supports, one on each end of the molecule. What are the three levels of chromosome compaction in prokaryotic cells?.Prokaryote Cell pictured left adapted from OpenStax (access for free at ) - Image created by SL For the sake of simplicity, macrodomains are not included in this diagram. Figure 2.1 Bacterial Chromosome Compaction - Bacterial chromosome compaction involves the formation of microdomains (middle), followed by supercoiling (right). Topoisomerases (see below) direct the supercoiling of E. To compact the bacterial chromosome even further, the microdomains are supercoiled (i.e., twists are introduced into the microdomains see Figure 2.1). Some examples of NAPs include histone-like nucleoid structuring (H-NS) proteins and structural maintenance of chromosomes (SMC) proteins. Microdomains and macrodomains are formed when the repetitive DNA sequences (see Part 1) within bacterial DNA bind to proteins called nucleoid-associated proteins (NAPs). Each macrodomain contains 80–100 bundled microdomains. Adjacent microdomains are further bundled together to create regions called macrodomains (not shown in Figure 2.1). coli chromosome forms 400 to 500 microdomains, each of which contains approximately 10,000 base pairs (bp) of DNA. Each microdomain is a loop connected to a centralized core structure composed of DNA binding proteins. To compact the DNA tenfold, the bacterial cell forms microdomains within the chromosome (see Figure 2.1). The bacterial chromosome must be compacted approximately 500–1000 times to fit into the nucleoid region within a bacterial cell. Chromosome Compaction Strategies in Prokaryotes and Eukaryotes Bacterial Chromosome Compaction This compaction of the X chromosome effectively silences one copy of every X-linked gene in the cell. X chromosome inactivation involves compacting one of the two X chromosomes found in the cells of female mammals to produce a condensed structure called a Barr body. The second section within Part 2 will explore the process of X chromosome inactivation (XCI). Human cells package a genome that is 200,000 times longer than the diameter of the nucleus! coli can package a chromosome 1.2 millimeters (mm) in length in a cell that is only 0.002 mm long (~1000 times compaction). For example, a virus called bacteriophage lambda can package a 17 micrometer (µm) long nucleic acid molecule into a virus particle less than 0.1 µm in diameter (~200 times compaction) the intestinal bacterium E. Chromosome compaction is a significant problem for all organisms. This process of packaging DNA inside cells is called chromosome compaction. The first section will discuss how large DNA molecules are compacted to fit inside virus particles, prokaryotic cells, and eukaryotic cells. The Part 2 reading assignment is divided into two sections.
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