Inside the Cell
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Glossary - Cellbiology
1 Glossary - Cellbiology Blotting: (Blot Analysis) Widely used biochemical technique for detecting the presence of specific macromolecules (proteins, mRNAs, or DNA sequences) in a mixture. A sample first is separated on an agarose or polyacrylamide gel usually under denaturing conditions; the separated components are transferred (blotting) to a nitrocellulose sheet, which is exposed to a radiolabeled molecule that specifically binds to the macromolecule of interest, and then subjected to autoradiography. Northern B.: mRNAs are detected with a complementary DNA; Southern B.: DNA restriction fragments are detected with complementary nucleotide sequences; Western B.: Proteins are detected by specific antibodies. Cell: The fundamental unit of living organisms. Cells are bounded by a lipid-containing plasma membrane, containing the central nucleus, and the cytoplasm. Cells are generally capable of independent reproduction. More complex cells like Eukaryotes have various compartments (organelles) where special tasks essential for the survival of the cell take place. Cytoplasm: Viscous contents of a cell that are contained within the plasma membrane but, in eukaryotic cells, outside the nucleus. The part of the cytoplasm not contained in any organelle is called the Cytosol. Cytoskeleton: (Gk. ) Three dimensional network of fibrous elements, allowing precisely regulated movements of cell parts, transport organelles, and help to maintain a cell’s shape. • Actin filament: (Microfilaments) Ubiquitous eukaryotic cytoskeletal proteins (one end is attached to the cell-cortex) of two “twisted“ actin monomers; are important in the structural support and movement of cells. Each actin filament (F-actin) consists of two strands of globular subunits (G-Actin) wrapped around each other to form a polarized unit (high ionic cytoplasm lead to the formation of AF, whereas low ion-concentration disassembles AF). -
Bacterial Cell Membrane
BACTERIAL CELL MEMBRANE Dr. Rakesh Sharda Department of Veterinary Microbiology NDVSU College of Veterinary Sc. & A.H., MHOW CYTOPLASMIC MEMBRANE ➢The cytoplasmic membrane, also called a cell membrane or plasma membrane, is about 7 nanometers (nm; 1/1,000,000,000 m) thick. ➢It lies internal to the cell wall and encloses the cytoplasm of the bacterium. ➢It is the most dynamic structure of a prokaryotic cell. Structure of cell membrane ➢The structure of bacterial plasma membrane is that of unit membrane, i.e., a fluid phospholipid bilayer, composed of phospholipids (40%) and peripheral and integral proteins (60%) molecules. ➢The phospholipids of bacterial cell membranes do not contain sterols as in eukaryotes, but instead consist of saturated or monounsaturated fatty acids (rarely, polyunsaturated fatty acids). ➢Many bacteria contain sterol-like molecules called hopanoids. ➢The hopanoids most likely stabilize the bacterial cytoplasmic membrane. ➢The phospholipids are amphoteric molecules with a polar hydrophilic glycerol "head" attached via an ester bond to two non-polar hydrophobic fatty acid tails. ➢The phospholipid bilayer is arranged such that the polar ends of the molecules form the outermost and innermost surface of the membrane while the non-polar ends form the center of the membrane Fluid mosaic model ➢The plasma membrane contains proteins, sugars, and other lipids in addition to the phospholipids. ➢The model that describes the arrangement of these substances in lipid bilayer is called the fluid mosaic model ➢Dispersed within the bilayer are various structural and enzymatic proteins, which carry out most membrane functions. ➢Some membrane proteins are located and function on one side or another of the membrane (peripheral proteins). -
For the Safe Delivery of Essential Proteins
Dedicated ‘Bodyguards’ for the Safe Delivery of Essential Proteins Dr Brigitte Pertschy DEDICATED ‘BODYGUARDS’ FOR THE SAFE DELIVERY OF ESSENTIAL PROTEINS Ribosomes are undoubtedly one of the most essential cellular components in life. These macromolecules are responsible for the synthesis of proteins in all living cells. Dr Brigitte Pertschy, Dr Ingrid Rössler and Jutta Hafner at the Institute of Molecular Biosciences at the University of Graz, Austria, have discovered that the safe delivery of essential ribosomal proteins that make up the ribosomes is dependant on ‘private bodyguards’ or ‘chaperones’. Nascent Ribosomal Proteins Journey Ribosome synthesis is an important of their synthesis and proper folding Across the Cell to the Nucleus and continuous process. Dr Pertschy of the proteins. Importins have also describes that a growing cell requires been reported as aides in the import of The ribosome is the intricate nano- up to 1,000 ribosomes to be synthesised proteins to the cell nucleus as well as in machinery that translates messenger per minute. The r-proteins are protecting proteins from aggregation. RNA strands (mRNA) into protein. Our produced in the cell cytoplasm by the DNA holds the instructions for building ribosome itself (that way, the ribosome The team speculated that since every protein needed for our bodies to participates in its own reproduction). r-proteins are produced at extremely function. Initially, DNA is transcribed From there the r-proteins must travel high amounts and their correct into mRNA, which contains the amino to the cell nucleus where in a complex functioning is so critical for a cell, these acid sequence of a particular protein. -
Classification of Cell Death
Cell Death and Differentiation (2005) 12, 1463–1467 & 2005 Nature Publishing Group All rights reserved 1350-9047/05 $30.00 www.nature.com/cdd News and Commentary Classification of cell death: recommendations of the Nomenclature Committee on Cell Death G Kroemer*,1, WS El-Deiry2, P Golstein3, ME Peter4, D Vaux5, with or without, caspase activation and that ‘autophagic cell P Vandenabeele6, B Zhivotovsky7, MV Blagosklonny8, death’ represents a type of cell death with (but not necessarily W Malorni9, RA Knight10, M Piacentini11, S Nagata12 and through) autophagic vacuolization. This article details the G Melino10,13 2005 recommendations of NCCD. Over time, molecular definitions are expected to emerge for those forms of cell 1 CNRS-UMR8125, Institut Gustave Roussy, 39 rue Camille-Desmoulins, death that remain descriptive. F-94805 Villejuif, France 2 University of Pennsylvania School of Medicine, Philadelphia, PA 19104, USA Preface 3 Centre d’Immunologie INSERM/CNRS/Universite de la Mediterranee de Marseille-Luminy, Case 906, Avenue de Luminy, 13288 Marseille Cedex 9, It is obvious that clear definitions of objects that are only France shadows in Plato’s cage are difficult to be achieved. Cell death 4 The Ben May Institute for Cancer Research, University of Chicago, 924 E 57th and the different subroutines leading to cell death do not Street, Chicago, IL 60637, USA 5 escape this rule. Even worse, the notion of death is strongly Sir William Dunn School of Pathology, University of Oxford, Oxford OX1 3RE, influenced by religious and cultural beliefs, which may UK 6 Molecular Signalling and Cell Death Unit, Department for Molecular Biomedical subliminally influence the scientific view of cell death. -
Standard 2: CELL BIOLOGY – REVIEW of BASICS
Standard 2: CELL BIOLOGY – REVIEW OF BASICS CELL PART OR TYPE OF CELL WHERE FOUND WHAT DOES IT FUNCTION: MISCELLANEOUS ORGANELLE Prokaryotic cell Plant cell LOOK LIKE: Job it does in INFORMATION: things Eukaryotic cell Animal cell Describe or Draw the cell such as color, what it is Both Both made of, size, etc. plasma/cell See diagram Holds cell together Phospholipid bilayer with membrane both both Regulates what goes proteins in/out of cell Semipermeable cytoplasm both Clear thick jelly- Supports/protects both like material in cell cell organelles See diagram Control center nucleus eukaryotic both Contains DNA See diagram Where proteins are ribosome both both made See diagram Process proteins Golgi complex eukaryotic both that go to other /apparatus parts of cell Membrane-bound Digests materials lysosome eukaryotic animal sac of digestive within the cell enzymes Membrane-bound Stores water, food, One large one in plants vacuole eukaryotic both storage area waste and dissolved Many smaller ones in minerals animals endoplasmic Network of Transport materials Can be rough (with reticulum eukaryotic both membrane tubes throughout the cell ribosomes attached) or smooth (without ribosomes) See diagram Where cell respiration Called Powerhouse of cell mitochondria eukaryotic both occurs (releases Makes ATP from energy for cell to use) breaking down glucose See diagram Where photosynthesis Contains chlorophyll chloroplast eukaryotic plant takes place Converts light energy into chemical energy in glucose Some pro- and plant (also fungi Rigid structure -
Building the Interphase Nucleus: a Study on the Kinetics of 3D Chromosome Formation, Temporal Relation to Active Transcription, and the Role of Nuclear Rnas
University of Massachusetts Medical School eScholarship@UMMS GSBS Dissertations and Theses Graduate School of Biomedical Sciences 2020-07-28 Building the Interphase Nucleus: A study on the kinetics of 3D chromosome formation, temporal relation to active transcription, and the role of nuclear RNAs Kristin N. Abramo University of Massachusetts Medical School Let us know how access to this document benefits ou.y Follow this and additional works at: https://escholarship.umassmed.edu/gsbs_diss Part of the Bioinformatics Commons, Cell Biology Commons, Computational Biology Commons, Genomics Commons, Laboratory and Basic Science Research Commons, Molecular Biology Commons, Molecular Genetics Commons, and the Systems Biology Commons Repository Citation Abramo KN. (2020). Building the Interphase Nucleus: A study on the kinetics of 3D chromosome formation, temporal relation to active transcription, and the role of nuclear RNAs. GSBS Dissertations and Theses. https://doi.org/10.13028/a9gd-gw44. Retrieved from https://escholarship.umassmed.edu/ gsbs_diss/1099 Creative Commons License This work is licensed under a Creative Commons Attribution-Noncommercial 4.0 License This material is brought to you by eScholarship@UMMS. It has been accepted for inclusion in GSBS Dissertations and Theses by an authorized administrator of eScholarship@UMMS. For more information, please contact [email protected]. BUILDING THE INTERPHASE NUCLEUS: A STUDY ON THE KINETICS OF 3D CHROMOSOME FORMATION, TEMPORAL RELATION TO ACTIVE TRANSCRIPTION, AND THE ROLE OF NUCLEAR RNAS A Dissertation Presented By KRISTIN N. ABRAMO Submitted to the Faculty of the University of Massachusetts Graduate School of Biomedical Sciences, Worcester in partial fulfillment of the requirements for the degree of DOCTOR OF PHILOSPOPHY July 28, 2020 Program in Systems Biology, Interdisciplinary Graduate Program BUILDING THE INTERPHASE NUCLEUS: A STUDY ON THE KINETICS OF 3D CHROMOSOME FORMATION, TEMPORAL RELATION TO ACTIVE TRANSCRIPTION, AND THE ROLE OF NUCLEAR RNAS A Dissertation Presented By KRISTIN N. -
Introduction to the Cell Cell History Cell Structures and Functions
Introduction to the cell cell history cell structures and functions CK-12 Foundation December 16, 2009 CK-12 Foundation is a non-profit organization with a mission to reduce the cost of textbook materials for the K-12 market both in the U.S. and worldwide. Using an open-content, web-based collaborative model termed the “FlexBook,” CK-12 intends to pioneer the generation and distribution of high quality educational content that will serve both as core text as well as provide an adaptive environment for learning. Copyright ©2009 CK-12 Foundation This work is licensed under the Creative Commons Attribution-Share Alike 3.0 United States License. To view a copy of this license, visit http://creativecommons.org/licenses/by-sa/3.0/us/ or send a letter to Creative Commons, 171 Second Street, Suite 300, San Francisco, California, 94105, USA. Contents 1 Cell structure and function dec 16 5 1.1 Lesson 3.1: Introduction to Cells .................................. 5 3 www.ck12.org www.ck12.org 4 Chapter 1 Cell structure and function dec 16 1.1 Lesson 3.1: Introduction to Cells Lesson Objectives • Identify the scientists that first observed cells. • Outline the importance of microscopes in the discovery of cells. • Summarize what the cell theory proposes. • Identify the limitations on cell size. • Identify the four parts common to all cells. • Compare prokaryotic and eukaryotic cells. Introduction Knowing the make up of cells and how cells work is necessary to all of the biological sciences. Learning about the similarities and differences between cell types is particularly important to the fields of cell biology and molecular biology. -
SMC Complexes Orchestrate the Mitotic Chromatin Interaction Landscape
Curr Genet DOI 10.1007/s00294-017-0755-y REVIEW SMC complexes orchestrate the mitotic chromatin interaction landscape Yasutaka Kakui1 · Frank Uhlmann1 Received: 13 September 2017 / Revised: 14 September 2017 / Accepted: 16 September 2017 © The Author(s) 2017. This article is an open access publication Abstract Chromatin is a very long DNA–protein complex Keywords Chromosome condensation · SMC complex · that controls the expression and inheritance of the genetic Chromatin · Cell cycle · Hi-C information. Chromatin is stored within the nucleus in interphase and further compacted into chromosomes dur- ing mitosis. This process, known as chromosome condensa- Introduction tion, is essential for faithful segregation of genomic DNA into daughter cells. Condensin and cohesin, members of How chromatin is spatially organized within the cell nucleus the structural maintenance of chromosomes (SMC) fam- and within chromosomes is a fundamental question in cell ily, are fundamental for chromosome architecture, both biology. Centimeter-long DNA molecules change their spa- for establishment of chromatin structure in the interphase tial chromatin organization within micrometer-sized cells nucleus and for the formation of condensed chromosomes during cell cycle progression. In interphase, chromatin is in mitosis. These ring-shaped SMC complexes are thought distributed throughout the nucleus to express the genetic to regulate the interactions between DNA strands by topo- information. When cells enter mitosis, chromatin becomes logically entrapping DNA. How this activity shapes chro- compacted to form mitotic chromosomes. Chromosome mosomes is not yet understood. Recent high throughput condensation, the gross morphological change of spatial chromosome conformation capture studies revealed how chromatin organization in mitosis, is indispensable for chromatin is reorganized during the cell cycle and have the faithful inheritance of genetic information. -
The Biochemistry of Cell Death Cell Death: Apoptosis and Other Means to an End, Second Edition by Douglas R
Zampieri et al. Cell Death and Disease (2020) 11:259 https://doi.org/10.1038/s41419-020-2465-5 Cell Death & Disease BOOK REVIEW Open Access The biochemistry of cell death Cell Death: Apoptosis and Other Means to an End, Second Edition by Douglas R. Green, St. Jude Children’s Research Hospital, Cold Spring Harbor Laboratory Press, New York, 2018 Carlotta Zampieri 1, Carlo Ganini 1 and Gerry Melino 1 Can we impress you with a mind-blowing revelation? Douglas Green is one of the worldwide leading experts “Cells are not eternal in our bodies, but rather they on apoptosis and cell death. He has dealt with the role of encounter death!”1. cell death in the regulation of cancer and immune If someone pronounces this sentence at a biology class, response, studying the molecular events that drive the students will laugh. Why? Because cell death has been process, focusing on the induction-activation of apoptosis studied since the 60s of the last century. When we speak in T cells and the role of Myc, death receptors and Bcl-2 about apoptosis nowadays, we regard it as a well-known in this context. His deep understanding of the field truth. Anyway, this truth did not catch the attention of allowed him to write the first edition of this book in a scientists until the 1980s, where the interest in the field clear and straightforward manner, enriched by extremely exploded, leading to a dramatic increase of publications. informative figures. His talent as a biologist, as well as a Cell death passed “from neglect to hysteria” in only a few communicator, has been condensed in this second edi- years, citing Martin Raff2, one of the founders of the field. -
Plant & Animal Cells and Their Organelles
Cells and Their Organelles The cell is the basic unit of life. All cells are surrounded by a cell membrane (which is sometimes called a plasma membrane). The cell membrane is semipermeable, meaning it allows some substances to pass into the cell and blocks others out. Plant cells have an additional layer surrounding them called the cell wall. The cell wall is made of nonliving material called cellulose. The centriole (also called the "microtubule organizing center") is a small body located near the nucleus. The centriole is where microtubules are made. During cell division (mitosis), the centriole divides and the two parts move to opposite sides of the dividing cell. Only animal cells have centrosomes. Microtubules are shaped like soda straws and give the nucleus and cell its shape (like a skeleton gives you shape) Answer the questions after each reading section on your own paper, please! 1. What is the basic unit of living things? 2. What surrounds all cells? 3. What is meant by semipermeable? 4. What additional layer is found around the outside of plant cells? 5. Cell walls in plants are made up of C_ ___ ___ ___ ___ ___ ___ ___ ___. 6. Centrioles are found inside of what type of cell only? 7. Microtubules have what shape and do what jobs for the cell? __________________________________________________________________________________________ The nucleus (in the center of a cell) is a rounded body containing the nucleolus and a cell’s DNA. The nucleus controls most of the functions of the cell by controlling protein synthesis. The nucleus of plant and animal cells is surrounded by the nuclear membrane. -
DNA Damage Alters Nuclear Mechanics Through Chromatin Reorganisation
bioRxiv preprint doi: https://doi.org/10.1101/2020.07.10.197517; this version posted July 11, 2020. The copyright holder for this preprint (which was not certified by peer review) is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under aCC-BY-NC-ND 4.0 International license. DNA damage alters nuclear mechanics through chromatin reorganisation Ália dos Santos1, Alexander W. Cook1, Rosemarie E Gough1, Martin Schilling2, Nora Aleida Olszok2, Ian Brown3, Lin Wang4, Jesse Aaron5, Marisa L. Martin-Fernandez4, Florian Rehfeldt2,6* and Christopher P. Toseland1* 1Department of Oncology and Metabolism, University of Sheffield, Sheffield, S10 2RX, UK.2University of Göttingen, 3rd Institute of Physics – Biophysics, Göttingen, 37077, Germany. 3School of Biosciences, University of Kent, Canterbury, CT2 7NJ, UK. 4Central Laser Facility, Research Complex at Harwell, Science and Technology Facilities Council, Rutherford Appleton Laboratory, Harwell, Didcot, Oxford OX11 0QX, UK. 5Advanced Imaging Center, HHMI Janelia Research Campus, Ashburn, USA. 6University of Bayreuth, Experimental Physics 1, Bayreuth, 95440, Germany. *Corresponding Authors: Florian Rehfeldt [email protected] & Christopher P. Toseland [email protected] Key words: Mechanics, DNA damage, DNA organisation, Nucleus ABSTRACT Cisplatin, specifically, creates adducts within the DNA double-strand breaks (DSBs) drive genomic double helix, which then lead to double-strand instability. For efficient and accurate repair of breaks (DSBs) in the DNA during replication, these DNA lesions, the cell activates DNA through replication-fork collapse3. damage repair pathways. However, it remains DSBs can result in large genomic aberrations and unknown how these processes may affect the are, therefore, the most deleterious to the cell. -
Dual Effects of Thyroid Hormone on Neurons and Neurogenesis
Lin et al. Cell Death and Disease (2020) 11:671 https://doi.org/10.1038/s41419-020-02836-9 Cell Death & Disease ARTICLE Open Access Dual effects of thyroid hormone on neurons and neurogenesis in traumatic brain injury Chao Lin1,2, Nan Li3, Hanxiao Chang1,2,Yuqishen1,2,ZhengLi1,2,Wuwei1,2,HuaChen1,2,HuaLu1,2,JingJi 1,2 and Ning Liu1,2 Abstract Thyroid hormone (TH) plays a crucial role in neurodevelopment, but its function and specific mechanisms remain unclear after traumatic brain injury (TBI). Here we found that treatment with triiodothyronine (T3) ameliorated the progression of neurological deficits in mice subjected to TBI. The data showed that T3 reduced neural death and promoted the elimination of damaged mitochondria via mitophagy. However, T3 did not prevent TBI-induced cell death in phosphatase and tensin homolog (PTEN)-induced putative kinase 1 (Pink1) knockout mice suggesting the involvement of mitophagy. Moreover, we also found that T3 promoted neurogenesis via crosstalk between mature neurons and neural stem cells (NSCs) after TBI. In neuron cultures undergoing oxygen and glucose deprivation (OGD), conditioned neuron culture medium collected after T3 treatment enhanced the in vitro differentiation of NSCs into mature neurons, a process in which mitophagy was required. Taken together, these data suggested that T3 treatment could provide a therapeutic approach for TBI by preventing neuronal death via mitophagy and promoting neurogenesis via neuron–NSC crosstalk. 1234567890():,; 1234567890():,; 1234567890():,; 1234567890():,; Introduction treatments focus only on preventing complications or Traumatic brain injury (TBI) is considered to be a providing support in nature. leading cause of substantial mortality and long-term dis- Thyroid hormone (TH) is crucial for neural stem cell ability among young adults worldwide1.