Module-2b-DNA-compaction.pdf

Module 2 – Part 2: Packaging the Genome Outline 1. DNA 2. Chromatin (30-nm and 300 nm) 3. Chromosome (700 nm and 1400 nm) Deoxyribose Nucleic Acid (DNA) § Watson and Crick reported that DNA consisted of two polynucleotide strands wrapped into a double helix. • The sugar-phosphate backbone is on...

Module 2 – Part 2: Packaging the Genome Outline 1. DNA 2. Chromatin (30-nm and 300 nm) 3. Chromosome (700 nm and 1400 nm) Deoxyribose Nucleic Acid (DNA) § Watson and Crick reported that DNA consisted of two polynucleotide strands wrapped into a double helix. • The sugar-phosphate backbone is on the outside. • The strands are antiparallel. • The nitrogenous bases are perpendicular to the backbone in the interior. • Specific pairs of bases give the helix a uniform shape. • • A pairs with T, forming two hydrogen bonds, and G pairs with C, forming three hydrogen bonds. 1 Deoxyribose Nucleic Acid (DNA) Sugar Cytosine (C) Thymine (T) Pyrimidines One circular Adenine (A) Sugar Thymine (T) component Sugar Sugar Guanine (G) Adenine (A) Purines Two circular component Guanine (G) Cytosine (C) 1 Deoxyribose Nucleic Acid (DNA) SCIENTIFIC DISCOVERY: DNA is a double-stranded helix ↳ In between 18 Rum these strands Purine + purine: too wide Pyrimidine + pyrimidine: too narrow Purine + pyrimidine: width consistent with X-ray data fulfills the distance of 2-Bum 1 Deoxyribose Nucleic Acid (DNA) DNA and RNA are polymers of nucleotides § A nucleotide is composed of a • nitrogenous base, • five-carbon sugar, and • phosphate group. 1 DNA T A C T G Sugar-phosphate backbone A C G T A C G A G T Covalent bond joining nucleotides T C A C A C A A G T structure Phosphate group Nitrogenous base Sugar Nitrogenous base (can be A, G, C, or T) C G T A A DNA double helix DNA nucleotide T Thymine (T) T Phosphate group G G G G Sugar (deoxyribose) DNA nucleotide Two representations of a DNA polynucleotide 1 Figure 10.3D -> & moleforce cular ter in is about 2m DNA * how does DNA fit in long a small Hydrogen bond Answer: DNA Base pair Ribbon model purine IS very compact pyrimidine Partial chemical structure nucleus? Computer model 1 Chromatin Uncompacted form of DNA associated with proteins present in the nucleus. “beads-on-a-string” structure Nucleosomes + linker DNA Figure 4-23 (part 1 of 2) Molecular Biology of the Cell (© Garland Science 2008) 2 Nucleosome -combination ● ● histone d DNA The beads in the “bead-on-a-string” structure of the chromatin. DNA wrapped around the the histone. ● ● of Histones are responsible for the first and most basic level of chromatin packing Each nucleosome core particle consist of 8 histone proteins 2 H2A-H2B dimer and 2 H3-H4 dimer; histone octamer and a DS DNA that is 147 base pairs long 2 Histones ● ● ● Small proteins that possess an unusually high content of the amino acid lysine and arginine Highly conserved 5 classes of histones ● ● ● ● ● H1 H2A H2B H3 H4 2 Chromatin carboxyl C-terminal Figure 4-25 Molecular Biology of the Cell (© Garland Science 2008) 2 Chromatin - tetramerize Figure 4-26 (part 1 of 2) Molecular Biology of the Cell (© Garland Science 2008) dimerize 2 How are Nucleosomes formed? Hyd Hy dimerizes, dimers with will tetramence a H3 d Hy, creating tetramer. H2A and the H2B dimers H3- Hy dimerizes. bind to the tetramer. 2 dimers and 2 creates Figure 4-26 Molecular Biology of the Cell (© Garland Science 2008) H3-H4 of dimers a of H2A-HIB histone octamer 2 Diagram of Histones and Nucleosomes around the DNAwill wrap The 2nd loop does not fully histone times, 1.7 close. Cell Biology by Thomas D. Pollard 2 The Nucleus as an organized Organelle DNA:2-3UM beads 2nd on a string:linm level of compaction Figure 4-72 Molecular Biology of the Cell (© Garland Science 2008) 2 30 nm-Fiber Zig-Zag Model An Alternating Figure 4-31 Molecular Biology of the Cell (© Garland Science 2008) Two Potential Models Solenoid pattern. Intercolated pattern 2 30 nm-fiber How is the 30 nm-fiber stacked so closely? Histone Tails (H4) ~ N-terminal Histone (H1) 2 2 Types of Chromatins ● Euchromatin: dispersed or extended form of chromatin -less packed, genes easily accessible that contains are more actively expressed ● Chromatin that remains compacted during interphase is called heterochromatin. more packed, genes ● are less accessible less expressed Typically found at the nuclear periphery 2 2 Classes of Heterochromatins - always compact intosomefor females net are gene Constitutive heterochromatin : remains in the compacted state in all cells at all times and thus is permanently silenced. -> ● centromer, ↳> Facultative heterochromatin: chromatin that has been specifically inactivated during certain phases of an organism's life or in certain types of differentiated cells. ● ↳ genes but that were are not once expressed anymore. 2 The Nucleus as an organized Organelle Genes · each ● ● ● associated with each other typically in close proximity other. Chromatin fibers are concentrated into a distinct territory Genes that reside on different chromosomes but are engaged in the same process can come together within the nucleus where they can be transcribed simultaneously (genes that encode rRNA synthesis) Proteins involved in pre-mRNA processing are localized to discrete sites called speckles. with Chromosomal Territories: Speckles: protein involved: SP35 (splicing factor) 2 Does chromatin compact further? 4When cell not - cell a division, undergoes genes typically expressed. Chromatin becomes and compact no are there more is access 4further Figure 4-72 Molecular Biology of the Cell (© Garland Science 2008) compaction When do we see further compaction? 300 nm-fiber smc each a proteins dimerizes dimer other, this with will have head. Condensins: Dimerized smc proteins 2 condensins: interacts through - Tail : hinge the hinge - Head: DNA-binding W 3 Chromosome -Condensing to will allow chromatin, LOOP Appears during metaphase Condensin hinges come together to form the core of the chromosome Figure 4-20 Molecular Biology of the Cell (© Garland Science 2008) Figure 4-20 Molecular Biology of the Cell (© Garland Science 2008)