Cell – Structure and Function MODULE - 1 Diversity and Evolution of Life
Total Page:16
File Type:pdf, Size:1020Kb
Load more
Recommended publications
-
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). -
Physical and Chemical Basis of Cytoplasmic Streaming
Annual Reviews www.annualreviews.org/aronline .4n~t Rev. Plant Physiol 1981. 32:205-36 Copyright© 1981by AnnualReviews In~ All rights reserved PHYSICAL AND CHEMICAL BASIS OF CYTOPLASMIC ~7710 STREAMING Nobur6 Kamiya Department of Cell Biology, National Institute for Basic Biology, Okazaki, 444 Japan CONTENTS INTRODUCTION........................................................................................................ 206 SHUTI’LE STREAMINGIN THE MYXOMYCETEPLASMODIUM ................ 207 General...................................................................................................................... 207 ContractileProperties of the PlasmodialStrand ...................................................... 208 Activationcaused by stretching .................................................................................. 208 Activationcaused by loading .................................................................................... 209 Synchronizationof local ,hythms .............................................................................. 209 ContractileProteins .................................................................................................. 210 Plasmodiumactomyosin .......................................................................................... 210 Plusmodiummyosin ................................................................................................ 210 Plusmodiumactin.................................................................................................... 211 -
Overview of the Cytoskeleton from an Evolutionary Perspective
Downloaded from http://cshperspectives.cshlp.org/ on October 1, 2021 - Published by Cold Spring Harbor Laboratory Press Overview of the Cytoskeleton from an Evolutionary Perspective Thomas D. Pollard1 and Robert D. Goldman2 1Departments of Molecular Cellular and Developmental Biology, Molecular Biophysics and Biochemistry, and Cell Biology ,Yale University, New Haven, Connecticut 06520-8103 2Department of Cell and Molecular Biology, Northwestern University Feinberg School of Medicine, Chicago, Illinois 60611 Correspondence: [email protected] SUMMARY Organisms in the three domains of life depend on protein polymers to form a cytoskeleton that helps to establish their shapes, maintain their mechanical integrity, divide, and, in many cases, move. Eukaryotes have the most complex cytoskeletons, comprising three cytoskeletal poly- mers—actin filaments, intermediate filaments, and microtubules—acted on by three families of motor proteins (myosin, kinesin, and dynein). Prokaryotes have polymers of proteins ho- mologous to actin and tubulin but no motors, and a few bacteria have a protein related to intermediate filament proteins. Outline 1 Introduction—Overview of cellular 4 Overview of the evolution of the cytoskeleton functions 5 Conclusion 2 Structures of the cytoskeletal polymers References 3 Assembly of cytoskeletal polymers Editors: Thomas D. Pollard and Robert D. Goldman Additional Perspectives on The Cytoskeleton available at www.cshperspectives.org Copyright # 2018 Cold Spring Harbor Laboratory Press; all rights reserved; doi: 10.1101/cshperspect.a030288 Cite this article as Cold Spring Harb Perspect Biol 2018;10:a030288 1 Downloaded from http://cshperspectives.cshlp.org/ on October 1, 2021 - Published by Cold Spring Harbor Laboratory Press T.D. Pollard and R.D. Goldman 1 INTRODUCTION—OVERVIEW OF CELLULAR contrast, intermediate filaments do not serve as tracks for FUNCTIONS molecular motors (reviewed by Herrmann and Aebi 2016) but, rather, are transported by these motors. -
Unit 2 Cell Biology Page 1 Sub-Topics Include
Sub-Topics Include: 2.1 Cell structure 2.2 Transport across cell membranes 2.3 Producing new cells 2.4 DNA and the production of proteins 2.5 Proteins and enzymes 2.6 Genetic Engineering 2.7 Respiration 2.8 Photosynthesis Unit 2 Cell Biology Page 1 UNIT 2 TOPIC 1 1. Cell Structure 1. Types of organism Animals and plants are made up of many cells and so are described as multicellular organisms. Similar cells doing the same job are grouped together to form tissues. Animals and plants have systems made up of a number of organs, each doing a particular job. For example, the circulatory system is made up of the heart, blood and vessels such as arteries, veins and capillaries. Some fungi such as yeast are single celled while others such as mushrooms and moulds are larger. Cells of animals plants and fungi have contain a number of specialised structures inside their cells. These specialised structures are called organelles. Bacteria are unicellular (exist as single cells) and do not have organelles in the same way as other cells. 2. Looking at Organelles Some organelles can be observed by staining cells and viewing them using a light microscope. Other organelles are so small that they cannot be seen using a light microscope. Instead, they are viewed using an electron microscope, which provides a far higher magnification than a light microscope. Most organelles inside cells are surrounded by a membrane which is similar in composition (make-up) to the cell membrane. Unit 2 Cell Biology Page 2 3. A Typical Cell ribosome 4. -
IB DIPLOMA PROGRAMME Debora M
OXFORD IB PREPARED BIOLOGY IB DIPLOMA PROGRAMME Debora M. Primrose Contents Introduction iv 9 Plant biology (AHL) 1 Cell biology 9.1 Transport in the xylem of plants 103 9.2 Transport in the phloem of plants 107 1.1 Introduction to cells 2 9.3 Growth in plants 110 1.2 Ultrastructure of cells 4 9.4 Reproduction in plants 113 1.3 Membrane structure 6 1.4 Membrane transport 7 10 Genetics and evolution (AHL) 1.5 The origin of cells 9 10.1 Meiosis 117 1.6 Cell division 11 10.2 Inheritance 121 2 Molecular biology 10.3 Gene pools and speciation 125 2.1 Molecules to metabolism 14 11 Animal physiology (AHL) 2.2 Water 15 11.1 Antibody production and vaccination 128 2.3 Carbohydrates and lipids 16 11.2 Movement 133 2.4 Proteins 20 11.3 The kidney and osmoregulation 137 2.5 Enzymes 21 11.4 Sexual reproduction 141 2.6 Structure of DNA and RNA 23 2.7 DNA replication, transcription and translation 24 12 Data-based and practical questions 147 2.8 Cell respiration 26 2.9 Photosynthesis 28 A Neurobiology and behaviour 3 Genetics A.1 Neural development 157 A.2 The human brain 159 3.1 Genes 30 A.3 Perception of stimuli 161 3.2 Chromosomes 32 A.4 Innate and learned behaviour (AHL) 165 3.3 Meiosis 33 A.5 Neuropharmacology (AHL) 167 3.4 Inheritance 35 A.6 Ethology (AHL) 169 3.5 Genetic modification and biotechnology 37 B Biotechnology and bioinformatics 4 Ecology B.1 Microbiology: organisms in industry 172 4.1 Species, communities and ecosystems 40 B.2 Biotechnology in agriculture 174 4.2 Energy flow 43 B.3 Environmental protection 178 4.3 Carbon cycling 45 -
Chapter 13 Protein Structure Learning Objectives
Chapter 13 Protein structure Learning objectives Upon completing this material you should be able to: ■ understand the principles of protein primary, secondary, tertiary, and quaternary structure; ■use the NCBI tool CN3D to view a protein structure; ■use the NCBI tool VAST to align two structures; ■explain the role of PDB including its purpose, contents, and tools; ■explain the role of structure annotation databases such as SCOP and CATH; and ■describe approaches to modeling the three-dimensional structure of proteins. Outline Overview of protein structure Principles of protein structure Protein Data Bank Protein structure prediction Intrinsically disordered proteins Protein structure and disease Overview: protein structure The three-dimensional structure of a protein determines its capacity to function. Christian Anfinsen and others denatured ribonuclease, observed rapid refolding, and demonstrated that the primary amino acid sequence determines its three-dimensional structure. We can study protein structure to understand problems such as the consequence of disease-causing mutations; the properties of ligand-binding sites; and the functions of homologs. Outline Overview of protein structure Principles of protein structure Protein Data Bank Protein structure prediction Intrinsically disordered proteins Protein structure and disease Protein primary and secondary structure Results from three secondary structure programs are shown, with their consensus. h: alpha helix; c: random coil; e: extended strand Protein tertiary and quaternary structure Quarternary structure: the four subunits of hemoglobin are shown (with an α 2β2 composition and one beta globin chain high- lighted) as well as four noncovalently attached heme groups. The peptide bond; phi and psi angles The peptide bond; phi and psi angles in DeepView Protein secondary structure Protein secondary structure is determined by the amino acid side chains. -
Phragmoplast Microtubule Dynamics – a Game of Zones Andrei Smertenko1,2,‡, Seanna L
© 2018. Published by The Company of Biologists Ltd | Journal of Cell Science (2018) 131, jcs203331. doi:10.1242/jcs.203331 REVIEW SPECIAL ISSUE: PLANT CELL BIOLOGY Phragmoplast microtubule dynamics – a game of zones Andrei Smertenko1,2,‡, Seanna L. Hewitt2,3, Caitlin N. Jacques2,4, Rafal Kacprzyk1, Yan Liu2,5, Matthew J. Marcec2,6, Lindani Moyo2,6, Aaron Ogden1,2, Hui Min Oung1,2, Sharol Schmidt1,2 and Erika A. Serrano-Romero2,5 ABSTRACT during anaphase from the remnants of the central spindle (Segui- Plant morphogenesis relies on the accurate positioning of the partition Simarro et al., 2004). It consists of microtubules, actin, membrane (cell plate) between dividing cells during cytokinesis. The cell plate is compartments and proteins that associate with or regulate the above synthetized by a specialized structure called the phragmoplast, which (Boruc and Van Damme, 2015; Lipka et al., 2015). The microtubule consists of microtubules, actin filaments, membrane compartments component of the phragmoplast consists of two aligned arrays that and associated proteins. The phragmoplast forms between daughter flank the so-called phragmoplast midzone, where cell plate assembly nuclei during the transition from anaphase to telophase. As cells are takes place (Fig. 1). The initial phragmoplast has a disk shape with a commonly larger than the originally formed phragmoplast, the diameter that approximately equals that of the daughter nuclei construction of the cell plate requires phragmoplast expansion. (Fig. 1); however, the parental cell is generally wider. For example, This expansion depends on microtubule polymerization at the the length of a cambium cell exceeds the diameter of the disk-shaped phragmoplast forefront (leading zone) and loss at the back (lagging phragmoplast during late anaphase by up to 100 fold (Larson, 1994). -
PEX5 Regulates Autophagy Via the Mtorc1-TFEB Axis During Starvation
Eun et al. Experimental & Molecular Medicine (2018) 50:4 DOI 10.1038/s12276-017-0007-8 Experimental & Molecular Medicine ARTICLE Open Access PEX5 regulates autophagy via the mTORC1-TFEB axis during starvation So Young Eun1,JoonNoLee2,In-KooNam2, Zhi-qiang Liu1,Hong-SeobSo 1, Seong-Kyu Choe1 and RaeKil Park2 Abstract Defects in the PEX5 gene impair the import of peroxisomal matrix proteins, leading to nonfunctional peroxisomes and other associated pathological defects such as Zellweger syndrome. Although PEX5 regulates autophagy process in a stress condition, the mechanisms controlling autophagy by PEX5 under nutrient deprivation are largely unknown. Herein, we show a novel function of PEX5 in the regulation of autophagy via Transcription Factor EB (TFEB). Under serum-starved conditions, when PEX5 is depleted, the mammalian target of rapamycin (mTORC1) inhibitor TSC2 is downregulated, which results in increased phosphorylation of the mTORC1 substrates, including 70S6K, S6K, and 4E- BP-1. mTORC1 activation further suppresses the nuclear localization of TFEB, as indicated by decreased mRNA levels of TFEB, LIPA, and LAMP1. Interestingly, peroxisomal mRNA and protein levels are also reduced by TFEB inactivation, indicating that TFEB might control peroxisome biogenesis at a transcriptional level. Conversely, pharmacological inhibition of mTOR resulting from PEX5 depletion during nutrient starvation activates TFEB by promoting nuclear localization of the protein. In addition, mTORC1 inhibition recovers the damaged-peroxisome biogenesis. These data suggest that PEX5 may be a critical regulator of lysosomal gene expression and autophagy through the mTOR-TFEB- autophagy axis under nutrient deprivation. 1234567890():,; 1234567890():,; Introduction Mitochondrial antiviral-signaling protein (MAVS) func- Peroxisome is an essential cellular organelle for per- tions as an antiviral signaling platform to induce the forming various metabolic activities, including oxidation interferon-independent signaling pathways4. -
Role of the BUB3 Protein in Phragmoplast Microtubule Reorganization During Cytokinesis
UC Davis UC Davis Previously Published Works Title Publisher Correction: Role of the BUB3 protein in phragmoplast microtubule reorganization during cytokinesis. Permalink https://escholarship.org/uc/item/1gw1799k Journal Nature plants, 4(9) ISSN 2055-0278 Authors Zhang, Hongchang Deng, Xingguang Sun, Baojuan et al. Publication Date 2018-09-01 DOI 10.1038/s41477-018-0215-9 Peer reviewed eScholarship.org Powered by the California Digital Library University of California ARTICLES https://doi.org/10.1038/s41477-018-0192-z Corrected: Publisher Correction Role of the BUB3 protein in phragmoplast microtubule reorganization during cytokinesis Hongchang Zhang1,2,6, Xingguang Deng2,3,6, Baojuan Sun2,4, Sonny Lee Van2, Zhensheng Kang5, Honghui Lin3, Yuh-Ru Julie Lee 2* and Bo Liu 2* The evolutionarily conserved WD40 protein budding uninhibited by benzimidazole 3 (BUB3) is known for its function in spindle assembly checkpoint control. In the model plant Arabidopsis thaliana, nearly identical BUB3;1 and BUB3;2 proteins decorated the phragmoplast midline through interaction with the microtubule-associated protein MAP65-3 during cytokinesis. BUB3;1 and BUB3;2 interacted with the carboxy-terminal segment of MAP65-3 (but not MAP65-1), which harbours its microtubule- binding domain for its post-mitotic localization. Reciprocally, BUB3;1 and BUB3;2 also regulated MAP65-3 localization in the phragmoplast by enhancing its microtubule association. In the bub3;1 bub3;2 double mutant, MAP65-3 localization was often dissipated away from the phragmoplast midline and abolished upon treatment of low doses of the cytokinesis inhibitory drug caffeine that were tolerated by the control plant. The phragmoplast microtubule array exhibited uncoordinated expansion pat- tern in the double mutant cells as the phragmoplast edge reached the parental plasma membrane at different times in differ- ent areas. -
The Mechanics of Motility in Dissociated Cytoplasm
THE MECHANICS OF MOTILITY IN DISSOCIATED CYTOPLASM MICAH DEMBO Theoretical Biophysics, Theoretical Division, Los Alamos National Laboratory, Group T-10, Mail Stop K710, Los Alamos, New Mexico 87545 ABSTRACT We stimulate the dynamical behavior of dissociated cytoplasm using the Reactive Flow Model (Dembo, M., and F. Harlow, 1986, Biophys. J., 50:109-121). We find that for the most part the predicted dynamical behavior of the cytoplasm is governed by three nondimensional numbers. Several other nondimensional parameters, the initial conditions, and boundary conditions are found to have lesser effects. Of the three major nondimensional parameters, one (D#) controls the percentage of ectoplasm, the second (CO) controls the sharpness of the endoplasm-ectoplasm boundary, and the third (R#) controls the topological complexity of the endoplasm-ectoplasm distribution. If R# is very small, then the cytoplasm contracts into a single uniform mass, and there is no bulk streaming. If R# is very large, then the cytoplasmic mass breaks up into a number of clumps scattered throughout the available volume. Between these clumps the solution undergoes turbulent or chaotic patterns of streaming. Intermediate values of R# can be found such that the mass of cytoplasm remains connected and yet undergoes coherent modes of motility similar to flares (Taylor, D.L., J.S. Condeelis, P.L. Moore, and R.D. Allen, 1973, J. Cell Biol., 59:378-394) and rosettes (Kuroda, K., 1979, Cell Motility: Molecules and Organization, 347-362). INTRODUCTION (Dembo et al., 1986). Here we will consider two experi- in which chemical reaction is an essential The reactive flow model is a putative description of motile mental systems fluid part of the dynamics. -
The Association of Peroxisomes with the Developing Cell Plate in Dividing Onion Root Cells Depends on Actin Microfilaments and Myosin
Planta (2003) 218: 204–216 DOI 10.1007/s00425-003-1096-2 ORIGINAL ARTICLE David A. Collings Æ John D. I. Harper Æ Kevin C. Vaughn The association of peroxisomes with the developing cell plate in dividing onion root cells depends on actin microfilaments and myosin Received: 5 April 2003 / Accepted: 23 June 2003 / Published online: 21 August 2003 Ó Springer-Verlag 2003 Abstract We have investigated changes in the distribu- cling of excess membranes from secretory vesicles via the tion of peroxisomes through the cell cycle in onion b-oxidation pathway. Differences in aggregation, a (Allium cepa L.) root meristem cells with immunofluo- phenomenon which occurs in onion, some other mono- rescence and electron microscopy, and in leek (Allium cots and to a lesser extent in tobacco BY-2 suspension porrum L.) epidermal cells with immunofluorescence and cells, but which is not obvious in the roots of Arabidopsis peroxisomal-targeted green fluorescent protein. During thaliana (L.) Heynh., may reflect differences within the interphase and mitosis, peroxisomes distribute randomly primary cell walls of these plants. throughout the cytoplasm, but beginning late in ana- phase, they accumulate at the division plane. Initially, Keywords Actin microfilaments Æ Allium Æ peroxisomes occur within the microtubule phragmoplast Microtubule Æ Cell plate Æ Peroxisome Æ Phragmoplast in two zones on either side of the developing cell plate. However, as the phragmoplast expands outwards to Abbreviations BDM: 2,3-butanedione monoxime Æ DAPI: form an annulus, peroxisomes redistribute into a ring 4¢,6-diamidino-2-phenylindole Æ ER: endoplasmic reti- immediately inside the location of the microtubules. -
The Revised Classification of Eukaryotes
See discussions, stats, and author profiles for this publication at: https://www.researchgate.net/publication/231610049 The Revised Classification of Eukaryotes Article in Journal of Eukaryotic Microbiology · September 2012 DOI: 10.1111/j.1550-7408.2012.00644.x · Source: PubMed CITATIONS READS 961 2,825 25 authors, including: Sina M Adl Alastair Simpson University of Saskatchewan Dalhousie University 118 PUBLICATIONS 8,522 CITATIONS 264 PUBLICATIONS 10,739 CITATIONS SEE PROFILE SEE PROFILE Christopher E Lane David Bass University of Rhode Island Natural History Museum, London 82 PUBLICATIONS 6,233 CITATIONS 464 PUBLICATIONS 7,765 CITATIONS SEE PROFILE SEE PROFILE Some of the authors of this publication are also working on these related projects: Biodiversity and ecology of soil taste amoeba View project Predator control of diversity View project All content following this page was uploaded by Smirnov Alexey on 25 October 2017. The user has requested enhancement of the downloaded file. The Journal of Published by the International Society of Eukaryotic Microbiology Protistologists J. Eukaryot. Microbiol., 59(5), 2012 pp. 429–493 © 2012 The Author(s) Journal of Eukaryotic Microbiology © 2012 International Society of Protistologists DOI: 10.1111/j.1550-7408.2012.00644.x The Revised Classification of Eukaryotes SINA M. ADL,a,b ALASTAIR G. B. SIMPSON,b CHRISTOPHER E. LANE,c JULIUS LUKESˇ,d DAVID BASS,e SAMUEL S. BOWSER,f MATTHEW W. BROWN,g FABIEN BURKI,h MICAH DUNTHORN,i VLADIMIR HAMPL,j AARON HEISS,b MONA HOPPENRATH,k ENRIQUE LARA,l LINE LE GALL,m DENIS H. LYNN,n,1 HILARY MCMANUS,o EDWARD A. D.