Lehninger Principles of Biochemistry 6th Ed 24.3 The Structure of Chromosome Chromatin Consists of DNA and Proteins Histones Are Small, Basic Proteins Nucleosomes Are the Fundamental Organizational Units of Chromatin Nucleosomes Are packed into Successively Higher-Order Structures Condensed Chromosome Structures Are Maintained by SMC proteins Bacterial DNA is Also Highly Organized Lehninger Principles of Biochemistry 6th Ed

Lehninger Principles of Biochemistry 6th Ed Summary 24.3 The structure of Chromosomes -The fundamental unit of organization in the chromatin of eukaryotic cells is the nucleosome, which consists of histone and a 200bp segment of DNA. A core protein particle containing eight histones (two copies each of histone H2A, H2B, H3, and H4) is encircled by a segment of DNA (about 146bp) in the form of a left-handed solenoidal supercoil -Nucleosomes are organized into 30nm fibers, and the fibers are extensively folded to provide the 10,000-fold compaction required to fit atypical eukaryotic chromosome into a cell nucleus. The higher-order folding involves attachment to a nuclear scaffold that contains histone H1, topoisomerase II, and SMC proteins. The SMC proteins, principally cohesion and condensin, play important roles in keeping the chromosomes organized during each stage of the cell cycles. -Bacterial chromosomes are extensively compacted into the nucleotide, but the chromosome seems to be much more dynamic and irregular in structure than eukaryotic chromatin, reflecting the shorter cell cycle and very active metabolism of bacterial cell. Lehninger Principles of Biochemistry 6th Ed

Lehninger Principles of Biochemistry 6th Ed Chromatin consists of fibers containing Protein and DNA The DNA in the chromatin is very tightly associated with proteins called histones, which pakage and order the DNA into structural units called nucleosomes + nonhistone proteins 1)maintain chromosome structure and 2)regulate the expression of specific gens) FIGURE 24-26 Nucleosomes. Regularly spaced nucleosomes consist of histone complexes bound to DNA. (a) Schematic illustration and (b) electron micrograph. Histones Are Small, Basic Proteins -MW : 11,000 ~21,000, rich in the basic AA arginine and lysine -5 major types (Table 24-4) Enzymatic modification: Methylation, acetylation, ADP-ribosylation, phosphorylation, glycosylation, sumoylation, or ubiquitination. =>affect the net electric charge, shape, and other properties of histones, structural and functional properties of the chromatin => play a role in the regulation of transcription. Lehninger Principles of Biochemistry 6th Ed

Lehninger Principles of Biochemistry 6th Ed Nucleosomes Are the Fundamental Organizational Units of Chromatin Compaction of a DNA molecule about 105uM long into a cell nucleus that is typically 5-10uM 2x(H2A+H2B+H3+H4) FIGURE 24-27a DNA wrapped around a nucleosome core. (a) Space-filling representation of a nucleosome protein core from the African frog Xenopus laevis, with different colors for the different histones (PDB ID 1AOI). (b) Top and (c) side views of the crystal structure of a nucleosome (gray surface contour) with 146 bp of bound DNA (blue). The DNA binds in a left-handed solenoidal supercoil that circumnavigates the histone complex 1.8 times. A schematic drawing is included in (c) for comparison with other figures depicting nucleosomes. Factors to affect the binding of DNA to histones in nucleosome cores -Topoisomerase have proved necessary for assembling chromatin from purified histones and closed-circular DNA in vitro -the sequence of the bound DNA histone cores donot bind randomly to DNA ex) depend on a local abundance of A=T bp in the DNA helix (figure 24-29) Lehninger Principles of Biochemistry 6th Ed

Nucleosomes Are the Fundamental Organizational Units of Chromatin But overall compaction in a chromosome-over 10,000 fold, Due to 30nm fiber >This packing requires 1 hisone H1 per nucleosome core. >The organization into 30nm fibers is punctuated by regions bound by seqeunce-specific (nonhistone) DNA-binding proteins. > Depends on the transcriptional activity of the particular region of DNA FIGURE 24-32 Loops of chromosomal DNA attached to a nuclear scaffold. The DNA in the loops is packaged as 30 nm fibers, so the loops are the next level of organization. Loops often contain groups of genes with related functions. Complete sets of histone-coding genes, as shown in this schematic illustration, seem to be clustered in loops of this kind. Unlike most genes, histone genes occur in multiple copies in many eukaryotic genomes. Scaffold itself may contain several proteins, notably large amounts of histone H1 (located in the interior of the fiber) and topoisomerase II. Additional layers of organizations in eukaryotic chromosomes (Figure 24-33) Principle: DNA compaction in eukaryotic chromosomes is likely to involve coils upon coils upon coils

Lehninger Principles of Biochemistry 6th Ed Condensed Chromosome Structures Are Maintained by SMC proteins -SMC ( structural maintenance of chromosomes) two major types, cohesions and condensin both of which are bound by regulatory and accessory proteins FIGURE 24-34 Structure of SMC proteins. (a) The five domains of the SMC primary structure. N and C denote the amino-terminal and carboxyl-terminal domains. (b) Each polypeptide is folded so that the two coiled-coil domains wrap around each other and the N and C domains come together to form a complete ATP-binding site. Two polypeptides are linked at the hinge region to form the dimeric V-shaped SMC molecule. (c) Electron micrograph of SMC proteins from Bacillus subtilis. (d) Cohesins are made up of pairs of Smc1 and Smc3 proteins, and condensins consist of Smc2-Smc4 pairs. These eukaryotic SMC proteins are bound by kleisin and some additional regulatory proteins (not shown). (e) ATP hydrolysis may serve to open and close the ATPase domain ends of the SMC protein dimer, which remain linked by kleisin (and other proteins not shown). FIGURE 24-35 Model for the roles of cohesins and condensins during the eukaryotic cell cycle. Cohesins are loaded onto the chromosomes during the G1 phase, tethering the sister chromatids together during replication. With the onset of mitosis, condensins bind and maintain the chromatids in a condensed state. During anaphase, an activity called separase removes the cohesin links. Once the chromatids separate, the condensins begin to unload and the daughter chromosomes return to an uncondensed state. Lehninger Principles of Biochemistry 6th Ed

Lehninger Principles of Biochemistry 6th Ed Bacterial DNA is Also Highly Organized -Bacterial chromosomes are extensively compacted into the nucleotide, but the chromosome seems to be much more dynamic and irregular in structure than eukaryotic chromatin, reflecting the shorter cell cycle and very active metabolism of bacterial cell. FIGURE 24-36 E. coli nucleoids. The DNA of these cells is stained with a dye that fluoresces when exposed to UV light. The light area defines the nucleoid. Note that some cells have replicated their DNA but have not yet undergone cell division and hence have multiple nucleoids. FIGURE 24-37 Looped domains of the E. coli chromosome. Each domain is about 10,000 bp in length. The domains are not static, but move along the DNA as replication proceeds. Barriers at the boundaries of the domains, of unknown composition, prevent the relaxation of DNA beyond the boundaries of the domain where a strand break occurs. The putative boundary complexes are shown as gray shaded ovoids. The arrows denote movement of DNA through the boundary complexes. Lehninger Principles of Biochemistry 6th Ed