Introduction to the Cell Cell History Cell Structures and Functions
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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). -
Chloroplast Transit Peptides: Structure, Function and Evolution
reviews Chloroplast transit Although the first demonstration of precursor trans- port into chloroplasts was shown over two decades peptides: structure, ago3,4, only now is this area of cell biology becom- ing well understood. Many excellent reviews have been published recently on the evolution of plas- function and tids5, the evolution of organelle genomes6, the mechanism of gene transfer from organelles to the nucleus7 and the mechanism of protein import into evolution chloroplasts8,9. Proteins destined to plastids and other organ- elles share in common the requirement for ‘new’ Barry D. Bruce sequence information to facilitate their correct trafficking within the cell. Although in most cases this information resides in a cleavable, N-terminal sequence often collectively referred to as signal It is thought that two to three thousand different proteins are sequence, the different organelle-targeting se- targeted to the chloroplast, and the ‘transit peptides’ that act as quences have distinct properties and names: ‘signal peptides’ for the endoplasmic reticulum, chloroplast targeting sequences are probably the largest class of ‘presequences’ for the mitochondria and ‘transit peptides’ for chloroplasts and other plastids. This targeting sequences in plants. At a primary structural level, transit review focuses on recent progress in dissecting peptide sequences are highly divergent in length, composition and the role of the stromal-targeting domain of chloro- plast transit peptides. I will consider briefly the organization. An emerging concept suggests that transit peptides multitude of distinct functions that transit peptides contain multiple domains that provide either distinct or overlapping perform, provide an update on the limited struc- tural information of a number of transit peptides functions. -
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). -
Intelligent Design, Abiogenesis, and Learning from History: Dennis R
Author Exchange Intelligent Design, Abiogenesis, and Learning from History: Dennis R. Venema A Reply to Meyer Dennis R. Venema Weizsäcker’s book The World View of Physics is still keeping me very busy. It has again brought home to me quite clearly how wrong it is to use God as a stop-gap for the incompleteness of our knowledge. If in fact the frontiers of knowledge are being pushed back (and that is bound to be the case), then God is being pushed back with them, and is therefore continually in retreat. We are to find God in what we know, not in what we don’t know; God wants us to realize his presence, not in unsolved problems but in those that are solved. Dietrich Bonhoeffer1 am thankful for this opportunity to nature, is the result of intelligence. More- reply to Stephen Meyer’s criticisms over, this assertion is proffered as the I 2 of my review of his book Signature logical basis for inferring design for the in the Cell (hereafter Signature). Meyer’s origin of biological information: if infor- critiques of my review fall into two gen- mation only ever arises from intelli- eral categories. First, he claims I mistook gence, then the mere presence of Signature for an argument against bio- information demonstrates design. A few logical evolution, rendering several of examples from Signature make the point my arguments superfluous. Secondly, easily: Meyer asserts that I have failed to refute … historical scientists can show that his thesis by not providing a “causally a presently acting cause must have adequate alternative explanation” for the been present in the past because the origin of life in that the few relevant cri- proposed candidate is the only known tiques I do provide are “deeply flawed.” cause of the effect in question. -
Centrosome-Nuclear Envelope Tethering and Microtubule Motor
bioRxiv preprint doi: https://doi.org/10.1101/442368; this version posted October 12, 2018. 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. Centrosome-nuclear envelope tethering and microtubule motor-based pulling forces collaborate in centrosome positioning during mitotic entry Vincent Boudreau1, Richard Chen1, Alan Edwards1, Muhammad Sulaimain1, Paul S. Maddox1* 1 Department of Biology, University of North Carolina at Chapel Hill * Direct all correspondence to this author at [email protected]. Centrosome positioning relative to the nucleus and cell nuclear envelope and at the cortex to ensure proper centrosome shape is highly regulated across cell types, during cell migration positioning (De Simone et al., 2016). Dynein regulators including and during spindle formation in cell division. Across most sexual- LIS-1 are also required for centrosome separation in the embryo ly reproducing animals, centrosomes are provided to the oocyte (Cockell et al., 2004), although their spatio-temporal contributions through fertilization and must be positioned properly to establish remain elusive. Despite our understanding of microtubule cyto- the zygotic mitotic spindle. How centrosomes are positioned in skeleton-based pulling forces, the contribution of key mitotic kinas- space and time through the concerted action of key mitotic en- es and phosphatases to centrosome positioning remains unclear. try biochemical regulators including Protein Phosphatase 2A The net effect of molecular regulators is a biophysical (PP2A-B55/SUR-6), biophysical regulators including Dynein mechanism required for positioning centrosomes during mitotic and the nuclear lamina is unclear. -
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. -
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 -
Volvox Barberi Flocks, Forming Near-Optimal, Two
bioRxiv preprint doi: https://doi.org/10.1101/279059; this version posted March 8, 2018. 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. Volvox barberi flocks, forming near-optimal, two-dimensional, polydisperse lattice packings Ravi Nicholas Balasubramanian1 1Harriton High School, 600 North Ithan Avenue, Bryn Mawr, PA 19010, USA Volvox barberi is a multicellular green alga forming spherical colonies of 10000-50000 differentiated somatic and germ cells. Here, I show that these colonies actively self-organize over minutes into “flocks" that can contain more than 100 colonies moving and rotating collectively for hours. The colonies in flocks form two-dimensional, irregular, \active crystals", with lattice angles and colony diameters both following log-normal distributions. Comparison with a dynamical simulation of soft spheres with diameters matched to the Volvox samples, and a weak long-range attractive force, show that the Volvox flocks achieve optimal random close-packing. A dye tracer in the Volvox medium revealed large hydrodynamic vortices generated by colony and flock rotations, providing a likely source of the forces leading to flocking and optimal packing. INTRODUCTION behavior (see, e.g., [8, 9] and references therein) but their interactions are often dominated by viscous forces (e.g. fluid drag) unlike larger organisms which are The remarkable multicellular green alga Volvox barberi dominated by inertial forces. Here, I show that V. [1] forms spherical colonies of 10,000 to 50,000 cells barberi colonies, which are themselves composed of many embedded in a glycol-protein based extra cellular matrix individual cells acting together, show collective behavior (ECM) and connected by cytoplasmic bridges that may at a higher level of organization. -
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. -
Living Cell Cytosol Stability to Segregation and Freezing-Out: Thermodynamic Aspect
1 Living Cell Cytosol Stability to Segregation and Freezing-Out: Thermodynamic aspect Viktor I. Laptev Russian New University, Moscow, Russian Federation The cytosol state in living cell is treated as homogeneous phase equilibrium with a special feature: the pressure of one phase is positive and the pressure of the other is negative. From this point of view the cytosol is neither solution nor gel (or sol as a whole) regardless its components (water and dissolved substances). This is its unique capability for selecting, sorting and transporting reagents to the proper place of the living cell without a so-called “pipeline”. To base this statement the theoretical investigation of the conditions of equilibrium and stability of the medium with alternative-sign pressure is carried out under using the thermodynamic laws and the Gibbs” equilibrium criterium. Keywords: living cellular processes; cytosol; intracellular fluid; cytoplasmic matrix; hyaloplasm matrix; segregation; freezing-out; zero isobare; negative pressure; homogeneous phase equilibrium. I. INTRODUCTION A. Inertial Motion in U,S,V-Space A full description of the thermodynamic state of a medium Cytosol in a living cell (intracellular fluid or cytoplasmic without chemical interactions is given by a relationship matrix, hyaloplasm matrix, aqueous cytoplasm) is a between the internal energy U, entropy S and volume V [5]. combination of the water dissolved substances. It places in the The mathematical procedure for a negative pressure supposes cell between the plasma membrane, the nucleus and a vacuole; using absolute values of the internal energy U and entropy S. it is a medium keeping granular-like and whisker-like The surface φ(U,S,V) = 0 corresponds to the all structures. -
Algae of the Genus Volvox (Chlorophyta) in Sub-Extreme Habitats T A.G
Short Communication T REPRO N DU The International Journal of Plant Reproductive Biology 12(2) July, 2020, pp.156-158 LA C P T I F V O E B Y T I DOI 10.14787/ijprb.2020 12.2. O E I L O C G O S I S T E S H Algae of the genus Volvox (Chlorophyta) in sub-extreme habitats T A.G. Desnitskiy Department of Embryology, Saint-Petersburg State University, Saint-Petersburg, 199034, Universitetskaya nab. 7/9, Russia e-mail: [email protected]; [email protected] Received: 18. 05. 2020; Revised: 08. 06. 2020; Accepted and Published online: 15. 06. 2020 ABSTRACT Literature data on the life of green colonial algae of the genus Volvox (Chlorophyta) in sub-extreme habitats (polar, sub-polar and mountain regions) are critically considered. Very few species (primarily homothallic Volvox aureus) are able to thrive in such conditions. Keywords : Geographical distribution, reproduction, sub-extreme habitats, Volvox. The genus Volvox Linnaeus (Volvocaceae, Chlorophyta) Peru (South America) at the elevation of more than five includes more than 20 species of freshwater flagellate algae thousand meters above sea level seems to be doubtful. The (Nozaki et al. 2015), providing an opportunity to study the illustration from this article (which focuses mainly on developmental mechanisms in a relatively simple system diatoms) shows a spherical colony with a diameter of about 14 consisting of two cellular types (somatic and reproductive). μm, consisting of several hundred very small cells (Fritz et al. Volvox carteri f. nagariensis Iyengar is a valuable model of 2015, p. -
Cell Growth-Regulated Expression of Mammalian MCM5 and MCM6 Genes Mediated by the Transcription Factor E2F
Oncogene (1999) 18, 2299 ± 2309 ã 1999 Stockton Press All rights reserved 0950 ± 9232/99 $12.00 http://www.stockton-press.co.uk/onc Cell growth-regulated expression of mammalian MCM5 and MCM6 genes mediated by the transcription factor E2F Kiyoshi Ohtani1, Ritsuko Iwanaga1, Masataka Nakamura*,1, Masa-aki Ikeda2, Norikazu Yabuta3, Hiromichi Tsuruga3 and Hiroshi Nojima3 1Human Gene Sciences Center, Tokyo Medical and Dental University, Tokyo 113-8510, Japan 2Department of Developmental Biology, Graduate School of Dentistry, Tokyo Medical and Dental University, Tokyo 113-8549, Japan; 3Department of Molecular Genetics, Research Institute for Microbial Diseases, Osaka University, Suita 565-0871, Japan Initiation of DNA replication requires the function of family (MCM2-7) that have been identi®ed in yeast, MCM gene products, which participate in ensuring that Xenopus, and human. Mcm proteins seem to regulate DNA replication occurs only once in the cell cycle. the initiation at the replication origin where the loading Expression of all mammalian genes of the MCM family of the proteins onto the origin recognition complex is induced by growth stimulation, unlike yeast, and the (ORC) is regulated by Cdc6 and cyclin-dependent mRNA levels peak at G1/S boundary. In this study, we kinases (Donovan et al., 1997; Tanaka et al., 1997). examined the transcriptional activities of isolated human However, the mechanism(s) by which Mcm proteins MCM gene promoters. Human MCM5 and MCM6 control the initiation of DNA replication remains promoters with mutation in the E2F sites failed in unclear. promoter regulation following serum stimulation and Xenopus Mcm proteins seem to be able to access exogenous E2F expression.