Cell Theory and Cellular structures.pdf

Dunman High School Organelles and Cellular Structures DUNMAN HIGH SCHOOL DHP YR 5 BIOLOGY CORE IDEA 1: ORGANELLES AND...

Dunman High School Organelles and Cellular Structures DUNMAN HIGH SCHOOL DHP YR 5 BIOLOGY CORE IDEA 1: ORGANELLES AND CELLULAR STRUCTURES LEARNING OBJECTIVES (a) Outline the cell theory with the understanding that cells are the smallest unit of life, all cells come from pre-existing cells; and living organisms are composed of cells. (b) interpret and recognise drawings, photomicrographs and electronmicrographs of the following membrane systems and organelles: rough and smooth endoplasmic reticulum, Golgi body, mitochondria, ribosomes, lysosomes, chloroplasts, cell surface membrane, nuclear envelope, centrioles, nucleus and nucleolus (for practical assessment, candidates may be required to operate a light microscope, mount slides and use an eyepiece graticule and a stage micrometer) (c) Outline the functions of the membrane systems and organelles listed in (b). (d) Describe the structure of a typical bacterial cell (small and unicellular, peptidoglycan cell wall, circular DNA, 70S ribosomes and lack of membrane bound organelles). (e) Describe the structural components of viruses, including enveloped viruses and bacteriophages, and interpret drawing and photographs of them. (f) Discuss how viruses challenge the cell theory and concepts of what is considered living. OVERVIEW OF TOPIC: 1. Cell theory 2. Range of Sizes of Cells and Their Units of Measurements 3. Structure of typical cell A. Eukaryotes B. Prokaryotes 4. Virus REFERENCES Campbell,N.A. and Reece,J.B. (2011). Biology 9th Edition. Clegg,C.J. and Mackean, D.G. (2000). Biology: Principles and Applications. Karp, G. (2002). Cell and Molecular Biology. R. Soper, Taylor,D.J.,Green,N.P.O. and Stout,G.W. (2002). Biological Science. 3rd Edition. Voet,D. and Voet, J.G. (2004). Biochemistry.R 1 Dunman High School Organelles and Cellular Structures Monitor Your Own Learning (Test your knowledge) Instructions: Please attempt the questions by filling in your answers only on the left column before the lecture. Do not refer to any sources or notes for answers. True or Statements True or False False 1 One principle of the cell theory states that all cells have F a nucleus. 2 Another strand of the cell theory states that all living T organisms are comprised of one or more cells. 3 Most cells are small so that they have a large T surface-area-to-volume ratio. 4 The nucleolus is the site of synthesis of mRNA. F 5 The endoplasmic reticulum is continuous with the T nuclear envelope. 6 All cells that synthesize proteins have ribosomes. T 7 A secretory protein is synthesized on free ribosomes in F the cytosol. 8 Chloroplasts and mitochondria contain 80S ribosomes. F 9 Viruses are obligate intracellular parasites. T 10 All viruses have an outer membrane / envelope. F 2 Dunman High School Organelles and Cellular Structures 1. CELL THEORY MODERN CELL THEORY The Cell Theory (Cell Concept) put forward by Schleiden and Schwann in 1938 embodies our current understanding of the cell, based on discoveries of the previously mentioned individuals and others. The cell theory states that: 1. Cells are the smallest unit of life.  basic structural and functional units in living things  smallest living structures able to carry out all processes needed for life E.g. ATP and protein synthesis 2. Living cells arise from pre-existing living cells (biogenesis).  Mitosis / meiosis + cytokinesis in eukaryotes  Binary fission in prokaryotes 3. All living things are made up of one or more cells. All chemical reactions necessary to maintain life and reproduce take place within the cell. Living cells typically have:  membranes which regulate movement of substances in and out  organelles in the cytoplasm for different functions  hereditary information (DNA) (which codes for specific characteristics) which is passed from parent to daughter cells Learn more about the development of Cell theory by watching this video: The w acky history ofcelltheory - Lauren Royal-W oods https://youtu.be/4OpBylwH9DU?si=MxiJqnynGYt61FvB 3 Dunman High School Organelles and Cellular Structures 2. RANGE OF SIZES OF CELLS AND THEIR UNITS OF MEASUREMENTS  Most cells are between 1 and 100 μM in diameter and thus can be viewed with the aid of a light microscope (LM).  The light microscope however cannot resolve details finer than about 200 nm. And hence, most subcellular structures i.e. organelles can only be observed through electron microscopy (EM). Units of measurement: 1 centimeter (cm) = 10-2 m 1 millimeter (mm) = 10-3 m 1 micrometer (µm) = 10-3 mm = 10-6 m 1 nanometer (nm) = 10-3 µm = 10-6 mm = 10-9 m 1 angstrom (Å) = 10-10 m (usually used to measure thickness of cell membranes or certain macromolecules) Note:  The micrometer is used in describing whole cells or large cell structures.  The nanometer is used in describing cell ultrastructures and large organic molecules.  Comparatively, a light microscope only has a resolution* of up to 200 nm (the size of a small bacterium). Why it is important for cells to be small The surface area to volume ratio (SA:V) plays a significant role in defining the size a cell can be.  As a cell grows, metabolic activity increases. However, the SA:V ratio decreases. Which implies a comparatively smaller surface area for the cell to transport substances in and out to support the higher metabolic rate.  When a cell is unable to absorb nutrients or eliminate waste products efficiently enough to support the increased volume, the cell experiences cellular distress which may lead to cell death. Diffusion Distance: The increased size also means that the distance from the centre of the cell to the cell membrane increases, making it more difficult for molecules to diffuse from the cell membrane to the interior of the cell and vice versa. This increased distance can impede the cell's metabolic activities, limiting its functionality and potentially its survival. 4 Dunman High School Organelles and Cellular Structures Upper and lower limit of cell sizes Lowest limit of cell size Probably determined by the smallest volume into which the minimum number and size of essential cellular components may be fitted in order for independent cellular existence to be possible. Upper limit of cell size is determined by – (a) Surface area to volume ratio (b) Diffusion distance (c) Nucleo-cytoplasmic ratio 5 Dunman High School Organelles and Cellular Structures 3. STRUCTURE OF A TYPICAL CELL Cells come in a huge variety of sizes and shapes, and carry out a wide range of activities. Yet they all share certain common features. All cells have a cell surface membrane (plasma membrane). Within this membrane the cell can be divided into 2 main areas: an area containing the cell’s genetic material (DNA) and the cytoplasm, which contains everything else (organelles / enzymes) the cell needs to carry out its functions. At the most basic level, cells can be divided into 2 types: eukaryotes prokaryotes (‘Eu’ = True; ‘Karyote’ = Nut = Nucleus (‘Pro’ = Before; ‘Karyote’ = Nut = Nucleus (Greek)) (Greek)) cells with a true nucleus and other cells without a true nucleus and other membrane bound organelles membrane bound organelles e.g. plant and animal cells e.g.bacteria and archaebacteria In the following sections we will look the typical structures / organelles found in both eukaryotes and prokaryotes. A. EUKARYOTES Eukaryotes contain various membrane bound organelles, as well as non-membrane bond organelles suspended within a jelly-like material called cytosol. The position and movement of these organelles are controlled by the cytoskeleton. Some eukaryotic cells also possess a cell wall (plants/fungi). A1. MEMBRANE BOUND ORGANELLES A1.1 NUCLEUS  Largest organelle  Size = ~10-20 m in diameter  Shape = Typically spherical, may be ovoid or lobed  Found in all eukaryotic cells except mature phloem sieve tube elements and red blood cells (erythrocytes).  Usually one nucleus per cell (uninucleated) but some cells can be binucleated (eg. Paramecium) or multinucleated (eg. skeletal muscle fibres)  Capable of dividing (mitosis /meiosis) prior to cell division such that daughter cells will each get a nucleus. Functions  Site of DNA replication  Site of RNA synthesis via transcription 6 Dunman High School Organelles and Cellular Structures Structure of Nucleus 1. Nuclear envelope (or nuclear membrane)  Composed of two membranes (an outer membrane and an inner membrane) separated by a fluid-filled space of 25 nm.  The outer membrane of the nuclear envelope is continuous with another organelle, the endoplasmic reticulum.  The nuclear envelope is perforated by nuclear pores lined by a protein octet, which permit the passage of large molecules such as RNA (mRNA, tRNA), proteins and ribosomal subunits. 2. Nucleoplasm  The gel-like matrix of the nucleus.  Contain ground substances such as chromatin, enzymes, chemical substances (ions, proteins / enzymes) and nucleotides.  It serves as a medium for diffusion of metabolites and large macromolecules. 3. Chromatin  DNA is organized along with histone proteins into chromatin.  Double stranded DNA coils 1.65x around histone octamer to form nucleosomes, with linker DNA between each nucleosomes. This results in chromatin described as beads-on-a-string.  During cell division, the chromatin coiled up into a highly condensed form and becomes visible as chromosomes (packing of DNA into chromosomes will be covered in core idea 2)  The number of chromosomes in a cell varies according to the individual species. 7 Dunman High School Organelles and Cellular Structures  Chromatin is found in two varieties: i. Euchromatin (transcriptionally active)  Loosely coiled form of chromatin that is rich in gene concentration.  Too disperse to be visible under light microscopy without staining. Appears as light-colored when stained and observed under a light microscope. In contrast, heterochromatin stains darkly.  Loosely coiled structure allows RNA polymerase and transcription factors to bind, initiating transcription. ii. Heterochromatin (transcriptionally inactive)  Modifications to DNA and histone proteins (covered in core idea 2) results in a more tightly coiled chromatin structure.  Regions that are non-coding (eg. Centromere, telomere) or contain genes that are transcriptionally inactive (due to spatial and temporal regulations) are usually heterochromatic (covered in core idea 2). 4. Nucleolus  Observed as one or more, large, dense and roughly spherical bodies in the nucleus of non-dividing cells, not surrounded by a membrane  Function = site of rRNA synthesis and assembly of ribosomal subunits (refer to A2.1 Ribosomes) 8 Dunman High School Organelles and Cellular Structures A1.2 ENDOPLASMIC RETICULUM (ER) ‘Endo’ = within; ‘Plasmic’ = cytoplasm; ‘Reticulum’ = a complex network  Consist of an extensive 3-D network of membranous tubules and sacs known as cisternae (singular: cisterna).  ER membrane separates the internal compartment of the ER called the cisternae space, from the cytosol.  Originates from the outer membrane of the nuclear envelope. The space between the membranes of the nuclear envelope is continuous with the cisternal space.  The ER can be differentiated into the rough ER and the smooth ER. Smooth ER Rough ER Structure  Appears smooth due to lack  Appears “rough” under electron of ribosomes on its surface microscope because of the presence of ribosomes on its surface  Consists of a meshwork of  a system of flattened fine tubules membrane-bound sacs called cisternae  Continuous with the outer  Continuous with the outer membrane membrane of the nuclear of the nuclear envelope envelope Functions  Site of lipid synthesis (e.g.  Site of protein synthesis where phospholipids, steroids, polypeptides fold into its native 3D cholesterol) conformation after being synthesized  Storage and release of Ca2+. at the bound ribosomes.  In the adrenal gland, sER produces steroid hormones.  Detoxification of drugs and poisons in the liver. SER may contain enzymes that catalyse reactions for detoxifying harmful drugs, alcohol, barbiturates (sedatives) and waste metabolic products.  sER of some stomach cells secrete hydrochloric acid, necessary for protein digestion. 9 Dunman High School Organelles and Cellular Structures Rough ER 1. Smooth ER 2. Mitochondrion 3. Free ribosome 10 Dunman High School Organelles and Cellular Structures A1.3 GOLGI APPARATUS (GA)  Consists of a stack of smooth surfaced, flattened membrane-bound sacs called cisternae and a system of associated vesicles called Golgi vesicles.  The cis face (convex ‘forming face’), which is closely associated with the rough and smooth ER, receives products by accepting transport vesicles from the ER.  The products in ER are packaged into transport vesicles which travel along microtubule tracks to fuse with Golgi at the cis face.  In the GA’s cisternal space, the proteins / lipids undergo chemical modification, eg. Glycosylation, during cis-trans maturation.  At the trans face (concave ‘maturing face’), vesicles pinches off from the GA forming Golgi vesicles.  Vesicles containing hydrolytic enzymes are known as lysosomes.  Vesicles containing proteins bound for secretion or proteins that function on the cell surface membrane are known as secretory vesicles. Functions 1. Site of proteins and lipids chemical modification, E.g. glycosylation. 2. Sorts and packages proteins into vesicles and targets them to various cellular locations.  Hydrolytic enzymes packaged into lysosomes (refer to A1.4).  Secretory proteins or proteins targeted to the cell surface membrane are packaged into secretory vesicles. The contents of secretory vesicles are released after exocytosis (covered in core idea 1: Transport across membrane).  Vesicles that contain non-cellulosic complex polysaccharides fuses to form the cell plate during cytokinesis of plant cells’ cell division. Diagram showing fusion of Golgi vesicles in the formation of cell plate for new cell wall synthesis 11 Dunman High School Organelles and Cellular Structures THE ENDOMEMBRANE SYSTEM The eukaryotic cell's endomembrane system is a network of organelles involved in manufacturing and material transport, allowing the cell to make, move and break down cellular products. The endomembrane system consists of the nuclear envelope, rough and smooth endoplasmic reticulum (ER), the Golgi apparatus as well as the cell's plasma membrane, and includes the vesicles that bud off these membranes for intracellular transport exocytosis and endocytosis. Movement of vesicles occurs along microtubule tracks. 12  Dunman High School Organelles and Cellular Structures A1.4 LYSOSOME ‘Lyse’ = to break apart, ‘soma’ = body  Small, spherical vesicles that is surrounded by a single membrane  Appear as darkly staining spherical bodies under electron microscope.  Contain hydrolytic enzymes such as lipases, proteases and nucleases.  Contents of lysosomes are acidic as the enzymes have a low optimum pH of 5. breaking down damaged organelles Functions of lysosome containing hydrolytic enzymes 1. Digestion of pathogens / materials ingested by phagocytosis / endocytosis. Refer to   After the cell carries out phagocytosis / endocytosis, the pathogen / materials in figure are contained within a phagosome / endosome. Fusion of the lysosome with (next page) the phagosome / endosome results in the formation of secondary lysosomes where ingested materials are digested.  Eg. Digestion of pathogen in macrophages after phagocytosis (covered in infectious diseases topic) 2. Degradation of worn-out organelles during Autophagy Refer to   worn-out organelles within a cell are fused with lysosomes, forming in figure autophagosomes. (next page)  Enzymes in the lysosomes break down the organelles.  The soluble products are absorbed into the surrounding cytoplasm where they may be used in the construction of new organelles. Note usage of terms  Primary lysosomes – lysosomes arising from Golgi apparatus  Secondary lysosomes – formed by fusion of primary lysosomes and small endocytic vesicles (e.g. food vacuoles)  Autophagosomes – small membranous vesicles enclosing worn-out organelles 3. Autolysis  Upon injury or infection, hydrolytic enzymes in lysosomes are released, leading to self-destruction of the cell. Note: Autolysis and apoptosis are not the same. Apoptosis refers to programmed cell death, during which lysosomes are not involved. 13 Dunman High School Organelles and Cellular Structures 4. For the breakdown of extracellular content  e.g. the sperm releases its hydrolytic enzymes by exocytosis to digest the sheath of nutrient cells surrounding the ovum, in order to facilitate fertilization. 14 Dunman High School Organelles and Cellular Structures A1.5 MITOCHONDRIA (singular: mitochondrion) Structure  Appear under EM mostly as rod-shaped or cylindrical (but may be dumbbell or spherical)  Vary in size, diameter within the range 0.5-1.5 µm and length about 2.5-10 µm  Consists of a double membrane separated by an extremely narrow fluid-filled space:  Smooth outer membrane: Highly permeable to small solutes but blocks passage of proteins and other macromolecules  Highly convoluted inner membrane which forms cristae (singular: crista): Irregular series of partitions to increase the surface area for enzyme (ATP synthase) and protein (of electron transport chain) attachment needed for cellular respiration (oxidative phosphorylation)  Intermembrane space: Temporary storage of protons to generate a proton gradient for electron transport chain  The membranes enclose the mitochondrial matrix which is semi-fluid and finely granular. It is the site of Krebs cycle during aerobic respiration and site of fatty acid oxidation.  The matrix contains circular mitochondrial DNA (mtDNA) and 70S ribosomes, which are characteristic of prokaryotes (refer to B. Prokaryotes). These enable mitochondria to be semi-autonomous whereby they can grow and divide independently of the cell. Function  Site of aerobic respiration for ATP synthesis. (covered in Respiration topic) 15 Dunman High School Organelles and Cellular Structures A1.6 CHLOROPLASTS ‘Chloro’= green, ‘Plast’ = plastids  Move through the cell by cytoplasmic streaming in order to absorb as much light as possible Cytoplasmic Streaming https://youtu.be/H4kkQvKsNzw ?si=HNZaE2fE1o9bUXFx Structure of chloroplasts  Biconvex discs / lens-shaped  Enclosed by a double membrane collectively known as the chloroplast envelope  The outer and inner membranes are separated by a very narrow fluid-filled intermembrane space.  Outer membrane – smooth and continuous  Inner membrane – extend inwards as a system of membranes called thylakoids, a type of lamellae (singular: lamella).  Thylakoid is a system of flattened membranous sacs which contains electron transport chains and photosynthetic pigments.  Thylakoids form stacks known as grana (singular: granum), and the thylakoid connecting the grana is known as the inter-granal thylakoid / lamellae.  The fluid surrounding the thylakoid membrane is the stroma, which contains the chloroplast circular DNA, 70S ribosomes, starch grains and enzymes. 16 Dunman High School Organelles and Cellular Structures Structure of chloroplast Function  Site of photosynthesis  Light-dependent reactions of photosynthesis occur on the thylakoid membrane  light-independent reactions occur in the stroma How eukaryotic cells get mitochondria and chloroplast – The Endosymbiosis Theory During the 1980s, Lynn Margulis proposed the theory of endosymbiosis to explain the origin of mitochondria and chloroplasts from permanent resident prokaryotes. According to this idea, a larger prokaryote (or perhaps early eukaryote) engulfed or surrounded a smaller prokaryote some 1.5 billion to 700 million years ago. H ow w e think com plex cells evolved - Adam Jacobson https://youtu.be/9i7kAt97XYU?s i=Q7PqfKMNUUd9_wCx 17 Dunman High School Organelles and Cellular Structures Maternal inheritance of mitochondria (and chloroplast) DNA During sexual reproduction, the fusion of sperm and ovum results in the formation of zygote. The nuclear DNA of zygote contains 50% maternal and 50% paternal origin. However, mitochondrial DNA is usually inherited from the mother. A1.7 VACUOLES  Fluid-filled sac bound by a single membrane. PLANT VACUOLES Structure  Filled with cell sap, an aqueous solution of dissolved food materials, ions, waste products and pigments  Enclosed by single membrane known as tonoplast. 18 Dunman High School Organelles and Cellular Structures Functions 1. Stores reserves of important organic compounds (eg. protein storage in seeds) 2. Stores inorganic ions. Eg. K+ and Cl- 3. Disposal sites for metabolic by-products (e.g. calcium oxalate crystals / latex) that would endanger the cell if they accumulated in the cytosol 4. May contain pigments that colour the cells. Eg red and blue pigments of petals that help attract pollinating insects to flowers, red onion. 5. May help protect the plant against predators by containing compounds that are poisonous or unpalatable to animals such as alkaloids. 6. Plays a role in plant growth by absorbing water and elongating the cell ANIMAL VACUOLES Structure  Usually very much smaller and less permanent than plant vacuole  Small vacuoles are often called vesicles and may contain engulfed solids or liquids Functions 1. Food vacuoles: Formed by phagocytosis  E.g. in the case of intracellular digestion by some protozoa and macrophages 2. Contractile vacuoles: Found in many freshwater protists to pump excess water from the cell (osmoregulation)  E.g. Paramecium had contractile vacuoles that pump excess water out of the cell. A2. NON-MEMBRANE BOUND ORGANELLES A2.1 RIBOSOMES  Found in all cells  May occur as free ribosomes or as bound ribosomes in eukaryotes.  Free ribosomes are suspended in the cytosol, while bound ribosomes are attached to rough endoplasmic reticulum. 19 Dunman High School Organelles and Cellular Structures Structure  Consists of 2 subunits – a small subunit and a large subunit.  Ribosomes are composed of proteins and rRNA.  rRNA is synthesized in the nucleolus of eukaryotic cells. This is also the site where ribosomal RNA and proteins assemble into ribosomal subunits.  There are 2 types of ribosomes – 80S and 70S ribosomes. [S is the sedimentation coefficient of a particle during centrifugation determined by its molecular size and geometrical shape.] Eukaryotic ribosome Prokaryotic ribosome Type 80S 70S Small subunit 40 30 Large subunit 60 50 Function  Site of polypeptide synthesis during translation  In eukaryotes, proteins that functions within the cytosol are synthesized at the free ribosomes. Proteins that are membrane-bound, enclosed within membrane or destined for secretion are synthesized at the bound ribosomes on rough ER. 20 Dunman High School Organelles and Cellular Structures Synthesis of ribosomes in eukaryotes  rRNA genes transcribed to give rRNA in the nucleolus.  Ribosomal protein genes are transcribed in the nucleus to give mRNA in the nucleus. mRNA is translated at free ribosomes in the cytoplasm. Ribosomal proteins are transported into the nucleolus via nuclear pores.  Ribosomal proteins and rRNA assemble in the nucleolus to form separate small and large subunits.  The subunits assemble on mRNA during translation. 21 Dunman High School Organelles and Cellular Structures A2.2 CENTRIOLES  Found in animal cells and lower plant cells (e.g. algae and mosses) but absent in higher plant cells.  Located next to the nucleus.  Found within a region known as the centrosome during nuclear division. Structure  Exist as a pair of rod-like structures, positioned with their longitudinal axis at right angles to each other  Cylinder is made up of 9 triplets of microtubules arranged in a ring. Function  Organise spindle fibres during cell division of animal cells. 22 Dunman High School Organelles and Cellular Structures A3. CYTOSOL  Cytoplasmic matrix contains water (90%), organic molecules, inorganic ions and waste products (CO2) as well as many enzymes. Function  Store vital chemicals  Site of certain metabolic pathways  E.g. glycolysis, fatty acid synthesis, translation A4. CYTOSKELETON  The cytoskeleton is the network of fibres throughout the cytoplasm that forms a dynamic framework for support and movement of a cell.  It consists of microtubules, intermediate fibers, and microfilaments, which together maintain cell shape, anchor organelles, and cause cell movement.  The microtubules and microfilaments are frequently assembled and disassembled according to cellular needs for movement and maintaining cell shape. Intermediate filaments are more permanent than microtubules and microfilaments. 23 Dunman High School Organelles and Cellular Structures Microtubules Microfilaments Intermediate fibres  Made of globular protein  Made of globular protein Made of diverse tubulin (α-tubulin and actin proteins within the β-tubulin) keratin family  Tubulin tube may elongate by adding tubulin units to one end  Straight, hollow fibres  Solid structures (not  Solid structure Structure about 25 nm in diameter tubular) with diameter  with diameter of about 5-7 nm which about 10 nm appears as a helix of two intertwining actin chains  May occur singly or in  May occur as bundles in  May occur as bundles bundles the cytoplasm in the cytoplasm  May dissociate or  May dissociate or  More stable than reassemble to build reassemble to build microtubules and microtubules elsewhere microfilaments elsewhere microfilaments to in the cell in the cell enforce cells and organize tissue  Cellular support  Cellular support  Structural role:  Tracks for organelle  Localised contraction of provides mechanical movement (involves cells, such as the pinching strength to cells and protein known as kinesin of cell into two during cell tissues and dyenin) division  Fixes the location of Functions  Cellular movement –  Muscle contraction certain organelles formation of cilia and e.g. nucleus sits  Cytoplasmic streaming - within a cage of flagella for motility important in moving intermediate  Separation of organelles such as filaments. chromosomes during mitochondria and nuclear division chloroplast  Deposition of cellulose A5. CELLULOSE CELL WALL (ONLY IN PLANTS) Structure  External to plasma membrane  Consists of cellulose fibres embedded in an amorphous polysaccharide matrix of pectin/lignin  Permeable to water and solutes Function  To provide mechanical support for plant cell and to the plant (especially herbaceous plants)  As water enters the cell osmotically, the cell wall resists expansion and an internal pressure is created which provides turgidity for the cell and the plant.  The strength may be increased by the presence of lignin in the matrix between the cellulose fibres. 24 Dunman High School Organelles and Cellular Structures Structure of cellulose cell wall B. PROKARYOTES  Prokaryotic cells (bacteria) lack membrane bound organelles and are among the smallest of all organisms.  Size: most range in diameter from 0.5-2µm.  Shape: 3 basic shapes o spherical (singular: coccus, plural: cocci) o rod-like (singular: bacillus, plural: bacilli) o spiral shaped (comma-shaped: vibrio; wavy-shaped: spirillum; corkscrew-shaped: spirochete)  Arrangement: many bacteria are also found in distinctive arrangements of groups of cells. 25 Dunman High School Organelles and Cellular Structures Ultrastructure of prokaryotic cells 1. PEPTIDOGLYCAN CELL WALL Structure Peptidoglycan consists of parallel polysaccharide chains made of alternating units of N-acetylglucosamine (NAG) and Nacetylmuramic acid (NAM), cross-linked in regular fashion by short peptide chains. 26 Dunman High School Organelles and Cellular Structures  Bacteria can be classified as gram positive or gram negative based on the structure of their cell walls.  Gram staining is a method of staining to classify bacteria based on their cell wall structure. A bacteria sample is first smeared on a glass microscopic slide and crystal violet (primary stain) is applied. After which, iodine is added as a mordant. Alcohol is added to destain and finally safranin added to counterstain. Gram positive Have a thick layer of peptidoglycan and no outer bacteria membrane Stained blue-purple by gram stain Gram negative Have a thin layer of peptidoglycan and an outer bacteria membrane / envelope. (Role of the outer membrane in the survival of bacteria will be covered in Infectious diseases topic) Stained red by gram stain Function  Confers the cell rigidity and shape.  Prevents the cell from lysis when it absorbs water via osmosis. 27 Dunman High School Organelles and Cellular Structures 2. PLASMA MEMBRANE  Partially permeable membrane.  Structures and functions similar to that of the eukaryotic cells. Other membranal structures  Mesosome: infoldings of the cell membrane which are formed in some bacteria during binary fission  facilitate the separation of the two daughter molecules of DNA after replication.  increase the surface area for enzymatic reactions that are associated with respiration.  Photosynthetic membranes  Present only in photosynthetic bacteria.  Contain photosynthetic pigments i.e. chlorophyll.  Similar membranes may also be associated with nitrogen fixation. 3. GENETIC MATERIAL  Bacteria have only 1 chromosome, which is a single circular double-stranded DNA containing only several thousand genes.  Found in nucleoid region (not membrane bound).  Associated with histone-like proteins  Transcriptionally active genes are found in loosely coiled regions  Transcriptionally inactive genes found in supercoiled regions 28 Dunman High School Organelles and Cellular Structures 4. 70S RIBOSOMES (refer to A2.1 Ribosomes) Other structures that are not always present 5. PLASMIDS  small, self-replicating circular DNA (contains its own origin of replication) occurring in addition to the chromosomal DNA  possesses only a few genes, which generally give extra survival advantage E.g. genes which confer resistance to antibiotics E.g. F plasmid contains fertility factor gene which confers sex pili 6. CAPSULE  slimy secretions of certain bacteria.  Usually consist of polysaccharides.  Can serve to unite bacteria into colonies.  Also enable bacteria to stick to surfaces such as teeth, mud and rocks, and offer useful additional protection to the bacteria. 7. FLAGELLA  Many bacteria are motile due to one or more flagella.  Each flagellum is rigid and wave-shaped.  Cork screw motion of flagella facilitates movement of bacteria. 8. PILI (SINGULAR = PILUS)  Surface appendages / fine protein rods projecting from the walls of some bacteria.  Shorter and thinner than flagella.  Aid in the attachment to specific cells or surfaces.  E.g. Sex pili are involved in bridging two bacteria, thus allowing the donor bacteria to transfer DNA to the recipient bacteria. This results in conjugation, a form of horizontal gene Pilli on E. coli transfer. 29 Dunman High School Organelles and Cellular Structures 4. Virus STRUCTURAL COMPONENTS OF VIRUSES  The structures of virions are quite diverse, varying widely in size, shape and chemical composition.  A virion consists of: A. Viral genome B. Capsid protein C. Envelope (present only in some viruses) A. Viral genome (a genome is a complete set of genes)  The viral genome is a molecule of nucleic acid (either DNA or RNA) that functions as the genetic material of the virus. It can be: o single or segmented o circular or linear o single-stranded or double-stranded  The genes present on the viral genome are relatively few in number, ranging from 3-1000 depending on species.  The genome codes for the synthesis of the viral components and viral enzymes required for replication. (Refer to annex for the six forms of viral nucleic acid and how they give viral proteins) 30 Dunman High School Organelles and Cellular Structures B. Capsid  The capsid is the protective protein coat enclosing the viral genome. Together, the structure is known as nucleocapsid.  Capsids are formed from structural subunits called capsomeres, arranged in a precise and highly repetitive pattern around the nucleic acid.  The information for proper assembly of proteins into capsomeres is contained within the structure of the proteins themselves, and the overall process of assembly is thus called self-assembly.  The capsid serves to protect and introduce the genome into the host cells.  Some viruses consist of no more than a genome surrounded by a capsid and are called naked viruses (viruses without envelope). Viral Structure Viral Structure (Polyhedral Virus) (Helical Virus) 31 Dunman High School Organelles and Cellular Structures (c) Envelope  Many viruses have complex membranous structures surrounding the polyhedral or helical nucleocapsid. They are called the enveloped viruses.  Enveloped viruses are common in the animal world (for example, influenza virus), but some enveloped bacterial viruses are also known.  The envelope is composed of phospholipids and glycoproteins and for most viruses, is derived from host cell membranes by a process called budding.  The envelope comes from the host cell’s nuclear membrane, ER, vacuolar membranes, or cell membrane.  Although the envelope is usually of host origin, the virus does incorporate proteins of its own, often appearing as glycoprotein spikes, into the envelope.  These glycoprotein spikes function in attaching the virus to receptors on susceptible host cells (recognition).  As such viral envelopes contain a combination of viral and host cell molecules. 32  Dunman High School Organelles and Cellular Structures STRUCTURE OF A BACTERIOPHAGE  Bacteriophages are viruses that only infect bacteria.  Some bacteriophages are structurally more complex than typical nucleocapsid or enveloped viruses and may possess a unique tail structure composed of a base plate, tail fibers, and a contractile sheath.  Other Bacteriophages, however, are simple icosahedrals or helical. Typical structure 1. Genome : dsDNA Capsid / icosahedral head 2. Capsid : Capsomeres Sheath Tail fibers Base plate Tail / Sheath Tail fibers 3. No envelope / Naked Base plate (a) (b) Fig (a) A T-even bacteriophage consisting of a head, sheath and tail. (b) Bacteriophages come in a variety of different sizes and shapes. 33 Dunman High School Organelles and Cellular Structures Is virus a cell? Is virus living?  Viruses are obligate intracellular parasites.  Viruses must invade a cell (host) in order replicate and multiply.  Viruses require the host’s machinery, e.g. ribosomes and enzymes, to synthesize their own genetic materials and proteins.  Viruses, like cells, o carry genetic information encoded in their nucleic acid o can undergo mutations o can reproduce  Viruses, unlike cells, o cannot carry out metabolism on their own o cannot produce energy / ATP o cannot reproduce on their own o do not possess the characteristics of living things e.g. movement, feeding, excretion, growth and sensitivity o do not grow in size or undergo division  Virus particles (virions) are produced from the assembly of pre-formed components, whereas other organisms grow in size from an increase in the integrated sum of their components and reproduce by division.  Viruses are infectious agents with both living and non-living characteristics. Living characteristics of viruses (a) They can grow in numbers and reproduce at a fantastic rate, but only in living host cells. (b) They can mutate. Non-living characteristics of viruses (a) They are acellular, that is, they contain no cytoplasm or cellular organelles. (b) They do not carry out metabolism on their own and must replicate using the host cell’s metabolic machinery. In other words, viruses do not grow and divide outside their hosts. Instead new viral components are synthesized and assembled within the infected host cell. (c) They possess DNA or RNA but never both (except Cytomegalovirus which possesses both DNA core and several mRNA segments). An isolated virus is biologically inert, unable to replicate its genes or regenerate its own supply of ATP.  Viruses are characterized by also having an extracellular state  enables them to be easily transmitted from one host to another  each virus has a host range, a limited number of host cells that it can infect  This extracellular form has enabled some viruses to replicate themselves in a host in a way that is destructive to the host cell. This destructive replication accounts for the fact that some viruses are agents of disease. 34