Module-2A - The Nucleus and DNA Organization PDF

Lecture 3: The Nucleus and DNA Organization July 6-7, 2023 Learning Objective - - - - Know the different components of the nucleus Know the composition and organization of nuclear membranes, pore and lamina Understand how proteins enter and leave the nucleus What happens to the nuclear membran...

Lecture 3: The Nucleus and DNA Organization July 6-7, 2023 Learning Objective - - - - Know the different components of the nucleus Know the composition and organization of nuclear membranes, pore and lamina Understand how proteins enter and leave the nucleus What happens to the nuclear membrane and lamina during cell division Understand how DNA compaction work, different levels of organization Understand the role(s) of histones and their organization Know the different types of chromatin Understand some of the experiments/ strategies used to make these discoveries Part I. The Nucleus Why did a nuclear envelope evolve? ● ● ● Compartmentalization It serves to establish an environment in which biochemical reactions are facilitated by high concentrations of both substrates and enzymes that act on them. It also prevents enzymes needed in one part of the cell from interfering with the orderly biochemical pathways in another. Other functions of the nucleus ● Serves for protection for the DNA ● It makes the cell more efficient What is contained within the Nucleus? ● ● ● ● The chromatin (highly extended nucleoprotein fibers in a non-mitotic cell) One or more nucleoli Nucleoplasm-the fluid in which the solutes of the nucleus are dissolved Nuclear matrix - protein containing fibrillar network Figure 4-9a Molecular Biology of the Cell (© Garland Science 2008) Different Components of the Nuclear Membrane A. Inner and Outer nuclear membrane B. Nuclear Lamina C. Nuclear Pore A. Nuclear Envelope ● ● Consists of two cellular membranes: ONM and INM Function: Serve as a barrier that keeps ions, solutes, and macromolecules from passing between the nucleus and the cytoplasm. A. Nuclear envelope ● ● ● The ONM is generally studded with ribosomes and is continuous with the ER The INM contains about 60 integral membrane proteins that binds the nuclear lamina These two membranes are fused at sites forming the nuclear pores that contain a complex assembly of proteins. Figure 12-8 Molecular Biology of the Cell (© Garland Science 2008) B. Nuclear Lamina Functions: ● ● current known functions Provides mechanical support to the nuclear envelope, Serves as a site of attachment for chromatin fibers - Potential role in gene expression? -> Chromatin lamins nuclear 4 to regulating 4 gene muscular have expression dystropy been linked Lamins ● The filaments of the NL are approximately 10 nm in diameter & composed of polypeptides called Lamins. ● ⑳ Cooper et al. The cell: a molecular approach ↓proteins Lamins are members of the same superfamily of polypeptides that assembly into the 10nm intermediate filaments (IFs) Lamin Structure and Organization Ask darfication this type posttranslational modification ↳ A Farnesly cysteine group. Farnesly 4 group is non is polar added and to the hydrophilic Cooper et al. The cell: a molecular approach of for process. lipid lipidation (adding of to protein) ~ integrated because of proteins The INM and Lamins ~ protein transmembrace I pro allow caming toue (NM anchor ↳ mutation cansing anchor INM. are It lamins, not to to properly related affects Emern, Lamins If Emern anchoring ↳ in 10 the not a laming to chromatin, gene complex expression. Cooper et al. The cell: a molecular approach ↳ also anchors nuclear anchors INm and envelope it ONM lamin to between the resultasitinBursatestine e a ↳ nuclear envelopes disinter prof Figure 12-20 Molecular Biology of the Cell (© Garland Science 2008) in the C. Nuclear Pore Complexes (NPCs) - ● ● INM, and ONMs merge Large elaborate nuclear structures known as NPCs perforate the nuclear envelope in all eukaryotes. Each NPC is composed of about 30 different Nucleoproteins or nucleoporins (NUPs) Figure 12-9d Molecular Biology of the Cell (© Garland Science 2008) nucleoporins under 48-fold symmetry cells dff. types of 4 the have election diff microscope numbers nucleoporins of nextpage ↳> Figure 12-9b Molecular Biology of the Cell (© Garland Science 2008) Number of NPCs ● ● Vary with the activity of the nucleus in transcription In inactive cells: eg. Nucleated erythrocyte; ● ● In active body cells: eg developing oocyte: ● ● hundreds/nucleus thousands /nucleus Highly active cells; developing oocyte: ● 50 million/nucleus NPCs A typical mammalian cell contains 30004000 NPCs Each NPC can transport up to 500 macromoleules per second and can transport in both directions at the same time. ● ● · a high mystery conjection of of how these can happen traffic. Cooper et al. The cell: a molecular approach all at once without I Cooper et al. The cell: a molecular approach nudeoporos G-Glycine Alanine FFenyl How are proteins transported into of the nucleus? 1. Nuclear Localization Signal (NLS) signaportedfound 2. Nuclear Transport Receptors (karyopherins) of cargo protein - Importin - Nuclear Transport Factor (NTF) 3. RAN-GTP or RAN-GDP -hydrolysis RAN-GDP) again 4. Ran-GAP GAP forming Exchanges 5. Ran-GEF in - protein to nucleus the carrier GTPase - Activating EDP GEF-Guanine GTP- GDP - Guanine Guarine protein to Exchange Factor Triphosphate Diphosphate (Converts Ran-GTP RAN Gip to Nuclear Localization Signal Nuclear xirus prosperusinlar ↳Suno hellcase todete and i ~assocation at the W Basic amino acids have -> nuclear proteins signals. localization sequence of -> encodes for that protein kinase pyruvate the found in 4phosphorylates ↳ -> NIs When Kinase, the 10 call22 -> NCS is piryate kinase vital in protein cytosol piruvate starts to to attached is nuclear transport Cooper et al. The cell: a molecular approach have proteins localization signals. How are proteins transported into of the nucleus? driving factor:diffusion -> the NIS +RAN is GPT resulting recognized by Importin binds the release to of Importin, resulting proteins. cargo the in confirmational change, d O e recognize by recognize 20 e the r elease morot ↑ GTP Nuctelt Nucell Nucleus ab firmation change cor exchanges C Cooper et al. The cell: a molecular approach ↑GDP - How are proteins transported out of the nucleus? 1. Nuclear Export Signal (NES) 2. Nuclear Transport Receptors (karyopherins) - Exportin -exports - NTF2 3. RAN-GTP or RAN-GDP 4. Ran-GAP 5. Ran-GEF How are proteins and RNAs transported out of the nucleus? recognized a by + hydrolyzes GDP - GTP to the releasing d protein cargo the release ↓ Freentercent of exportin ~recognitodateat the exchanges GDP to - GTP mGe - Cooper et al. The cell: a molecular approach How are proteins and RNAs transported out of the nucleus? Ab ↳ dissociates complex exporter mRN from 0 binds * To - Cooper et al. The cell: a molecular approach Nuclear Matrix composed ● ● ● · of: Network of thin protein-containing fibrils criss-crossing through the nuclear space. Maintains the shape of the nucleus. Serves to anchor the machinery for the various activities of the nucleus; transcription, RNA processing, and replication. Found everywhere in the nucleus Figure 12-19 Molecular Biology of the Cell (© Garland Science 2008)