Nucleus & Chromatin Structure PDF

NUCLEUS & CHROMATIN STRUCTURE Dr. S.V.Mullegama By the end of this session you will be able to: 1. Describe the structural organization of genetic information in human cells, all the way from individual nucleotides to entire chromosomes. 2. Outline the major structural and regulatory elements o...

NUCLEUS & CHROMATIN STRUCTURE Dr. S.V.Mullegama By the end of this session you will be able to: 1. Describe the structural organization of genetic information in human cells, all the way from individual nucleotides to entire chromosomes. 2. Outline the major structural and regulatory elements of human protein- coding genes. 3. Describe the structural features of DNA, its physical properties, and the enzymes that influence the topology of DNA. 4. Explain how the genetic code is used to specify the positions of amino acids in proteins and the significance of the term “reading frame.” Nucleus Nucleus Nucleus The largest organelle of the cell. Shapes: spherical, lobulated, elongated All eukaryotic cells but NOT mature erythrocytes (red blood cells) contain a nucleus. Some cells have more nuclei: 1. Skeletal muscle cells 2. Osteoclasts 3. Hepatocytes Function: Houses the genetic material encoded in the DNA of the chromatin and directs protein synthesis in the cytoplasm via rRNA, mRNA and tRNA. These RNAs are synthesized in the nucleus. Let’s make a mini concept map… Structure of the Nucleus Nuclear Envelope Double-layered membrane that encloses the contents of the nucleus during most of the cell's lifecycle Consists of two concentric membranes: outer nuclear membrane inner nuclear membrane Outer nuclear membrane contains numerous ribosomes Inner nuclear membrane covered by the nuclear lamina, a network of intermediate filaments (lamins) that stabilizes the membrane Nuclear lamins provide mechanical support and are involved in various processes of the cell cycle (e.g., transcription, signal transduction, chromatin organization) A mutation in the gene encoding for lamin A results in Hutchinson-Gilford progeria syndrome The membranes are separated from each other by: perinuclear cisterna  Genetic condition characterized by the dramatic, rapid appearance of aging beginning Clinical Correlation: in childhood. Affected children typically look normal at birth Hutchinson-Gilford and in early infancy, but then grow more slowly than other children and do not gain weight at progeria syndrome the expected rate (failure to thrive). They develop a characteristic facial appearance including prominent eyes, a thin nose with a beaked tip, thin lips, a small chin, and protruding ears. The LMNA gene provides instructions for making a protein called lamin A. This protein plays an important role in determining the shape of the nucleus within cells. It is an essential scaffolding (supporting) component of the nuclear envelope, which is the membrane that surrounds the nucleus Nuclear Pores Nuclear envelope is perforated with holes Regulate passage of molecules between the nucleus and cytoplasm: permitting some to pass through the membrane but not others. Molecules allowed into nucleus: DNA RNA Molecules that provide the energy for constructing genetic material. Nuclear Pore Complex The NPC is composed of nearly 100 proteins some of which are arranged in eightfold symmetry around the margin of the pore. Function: Permits passive movement across the nuclear envelope via open channel for simple diffusion. Most proteins regardless of size pass in either direction only by receptor- mediated transport. These proteins have clusters of certain amino acids known as nuclear localization segments that act as signals for transport. Nucleolus Dense non-membrane bound structure Some cells may have more than one nucleolus Contains rDNA → transcribed into rRNA Assembles ribosomal subunits. EUKARYOTIC GENOME Overview nucleated eukaryotic somatic cell contains the same blueprint—a set of genetic information collectively known as the genome. human genome is contained within two distinct compartments. : the nucleus and the mitochondria The bulk of the genome, containing about 20,000 to 25,000 genes encoded by DNA, is contained within a set of linear chromosomes within the cell nucleus and contains genetic material of both maternal and paternal origin. DNA Building Blocks DNA contains a structural blueprint for all genetic instructions. Long double-stranded helical linear molecule composed of multiple nucleotide sequences. Acts as a template for the synthesis of RNA. The complete nucleotide sequence of a human is in the 46 chromosomes of each cells. If stretched out and placed end to end would measure about 6 feet length!!! DNA Building Blocks Nucleotide composed of: Base (Purine or Pyrimidine) Deoxyribose sugar Phosphate group Two of the bases are heterocyclic compounds or purines adenine (A) and guanine (G) Two are six-member rings known as pyrimidines cytosine (C) and thymidine (T).  Double Helix the two chains are coiled around a common axis called the helical axis. the chains are paired in an antiparallel manner (i.e., the 5′ end of one strand is paired with the 3′ end of the other strand the hydrophilic deoxyribose-phosphate backbone of each chain is on the outside of the molecule, whereas the hydrophobic bases are stacked inside. The overall structure resembles a twisted ladder. spatial relationship between the two strands in the helix creates a major (wide) groove and a minor (narrow) groove. grooves provide access for the binding of regulatory proteins to their specific recognition sequences along the DNA chain.  Base Pairing The bases of one strand of DNA are paired with the bases of the second strand adenine (A) is always paired with a thymine (T) cytosine (C) is always paired with a guanine (G) Therefore, one polynucleotide chain of the DNA double helix is always the complement of the other. Given the sequence of bases on one chain, the sequence of bases on the complementary chain can be determined The base pairs are held together by hydrogen bonds: two between A and T and three between G and C The base pairs are also stacked along the axis so that the planes of their rings are parallel. The hydrogen bonds of the base pairs, plus the hydrophobic interactions between the stacked bases, stabilize the structure of the double helix.  Thermodynamic Properties of DNA Since higher GC-content DNA involves more hydrogen bonds, more energy is needed to break the bonds and to denature it When the temperature reaches >95° C, nearly all the DNA molecules will have been denatured into single strands. As we cool the DNA to 20° C (about room temperature), the DNA will start to renature, or “zip” back together and assume its original double- stranded helix. Summary: DNA always read in 5’ 3’direction Major groove, minor groove 3 H-bonds for G-C pairs, 2 for A-T pairs higher GC-content DNA → more energy is needed to break the bonds and to denature it Plays an important role in thermodynamics of DNA B-Form of DNA is the ”normal’ form  Chromatin Chromatin consist of 1. Very long double-stranded DNA molecules 2. Equal mass of small basic proteins: Histones 3. Small quantity of ribonucleic acid (RNA) Histones heterogeneous group of closely related arginine- and lysine-rich basic proteins, which together make up one- fourth of amino acid residues. these positively charged amino acids help histones to bind tightly to the negatively charged sugar phosphate backbone of DNA. Functionally, histones provide for the compaction of chromatin. DNA Packaging  Nucleosomes Nucleosomes are the fundamental organization upon which the higher-order packing of chromatin is built. Nucleosome core consists of a complex of eight histone proteins (two molecules each of histone H2A, H2B, H3, and H4) (octamer) with double- stranded DNA wound around it. 146 base pairs (bp) of DNA are associated with the nucleosome particle, and a 50- to 70-bp span of linker DNA bound by a linker histone H1 separates each nucleosome Minor histone variants exist in the eukaryotic genome. H2AX is sometimes present in place of H2A and is known to participate in the chromosome repair process Nucleosomes also regulate gene expression, or activity, by determining whether the DNA sequences can be accessed by transcription factors Histones are a locus for Epigenetic Modifications Covalent modification of histones changes its physical properties, including altering its affinity for DNA Acetylation generally leads to reduced affinity for DNA and loosens packing  Increased transcription (of specific genes) Methylation generally leads to increased affinity for DNA and tighter packing Decreased transcription (of specific genes) Chromatin remodeling complexes Chromatin Euchromatin Heterochromatin Extended chromatin Highly condensed Less condensed Contains an additional histone, H1, which wraps around groups of Formed by adjacent nucleosomes nucleosomes, thus forming 30nm where the nucleosome core diameter filaments of helical coils consisted of two copies each of of six nucleosomes per turn histones H2A, H2B, H3 and H54. Gene-poor Gene-rich Transcriptionally silent Easily transcribed Chromosome Consist of chromatin extensively folded into loops that maintained by DNA binding proteins Single, long DNA molecular, histones that are assembles into nucleosomes. More in the Genetics Session of the Course!! Gene More about genes and mutations in genetics part of the course! Summarize QUESTIONS TO THINK ABOUT All eukaryotic cells have a nucleus except which type of cells? mature erythrocytes (red blood cells) Which part of the nucleus assembles ribosomal subunits? Nucleolus Dense non-membrane bound structure Some cells may have more than one nucleolus Contains rDNA → transcribed into rRNA Assembles ribosomal subunits. The Nucleotide structure consists of what three parts?  Nucleotide composed of: Base (Purine or Pyrimidine) Deoxyribose sugar Phosphate group What are the function of the nuclear lamins and what disorder is caused by a mutation in a nuclear lamin?  covered by the nuclear lamina, a network of intermediate filaments (lamins) that stabilizes the membrane Nuclear lamins provide mechanical support and are involved in various processes of the cell cycle (e.g., transcription, signal transduction, chromatin organization) Which bases are purines? Adenine pairs with what pyrimidine? DISCUSSION ON HOW TO STUDY AND PREPARE FOR THE EXAM Questions?