BIOL 203 Chapter 03 Cell Structure & Function PDF

CHAPTER 03 – CELL STRUCTURE AND FUNCTION CAPILANO UNIVERSITY - EUGENE CHU - BIOL 203 LEARNING OUTCOMES 3.1 Describe four major processes of living cells 3.2 Compare and contrast prokaryotic and eukaryotic cells 3.3 Describe the composition, function, and relevance to hum...

CHAPTER 03 – CELL STRUCTURE AND FUNCTION CAPILANO UNIVERSITY - EUGENE CHU - BIOL 203 LEARNING OUTCOMES 3.1 Describe four major processes of living cells 3.2 Compare and contrast prokaryotic and eukaryotic cells 3.3 Describe the composition, function, and relevance to human health of glycocalyces 3.4 Distinguish capsules from slime layers 3.5 Discuss the structure and function of bacterial flagella 3.6 List and describe different bacterial flagellar arrangements 3.7 Compare and contrast the structures and functions of fimbriae, pili, and flagella 3.8 Describe the common shapes and arrangements of bacterial cells 3.9 Describe the sugar and peptide portions of peptidoglycan CAPILANO UNIVERSITY - EUGENE CHU - BIOL 203 2 LEARNING OUTCOMES 3.10 Compare and contrast the cell walls of Gram-positive and Gram-negative bacteria in terms of structure and Gram staining 3.11 Compare and contrast the cell walls of acid-fast bacteria with typical Gram- positive cell walls 3.12 Describe the clinical implications of the structure of the Gram-negative cell wall 3.13 Diagram a phospholipid bilayer, and explain its significance in reference to a cytoplasmic membrane 3.14 Explain the fluid mosaic model of membrane structure 3.15 Describe the functions of a cytoplasmic membrane as they relate to permeability CAPILANO UNIVERSITY - EUGENE CHU - BIOL 203 3 LEARNING OUTCOMES 3.16 Compare and contrast the passive and active processes by which materials cross a cytoplasmic membrane 3.17 Define osmosis, and distinguish between isotonic, hypertonic, and hypotonic solutions 3.18 Define bacterial cytoplasm and its basic contents 3.19 Define inclusion 3.20 Describe the formation and function of endospores 3.21 Describe the structure and function of ribosomes and the cytoskeleton 3.22 Describe the structure and chemistry of archaeal and bacterial glycocalyces 3.23 Describe the structure and formation of archaeal flagella CAPILANO UNIVERSITY - EUGENE CHU - BIOL 203 4 LEARNING OUTCOMES 3.24 Compare and contrast archaeal and bacterial flagella 3.25 Compare the structure and function of archaal and bacterial fimbriae 3.26 Describe the structure and function of hami 3.27 Contrast the types of archaeal cell walls with each other and with bacterial cell walls 3.28 Contrast the archaeal cytoplasmic membrane with that of bacteria 3.29 Compare and contrast the cytoplasm of archaea with that of bacteria 3.30 Describe the composition, function, and importance of eukaryotic glycocalyces 3.31 Compare and contrast prokaryotic and eukaryotic cell walls and cytoplasmic membranes CAPILANO UNIVERSITY - EUGENE CHU - BIOL 203 5 LEARNING OUTCOMES 3.32 Contrast exocytosis and endocytosis 3.33 Describe the role of pseudopods in eukaryotic cells 3.34 Compare and contrast the cytoplasm of prokaryotes and eukaryotes 3.35 Identify nonmembranous and membranous organelles 3.36 Compare and contrast the structure and function of prokaryotic and eukaryotic flagella 3.37 Describe the structure and function of cilia 3.38 Compare and contrast eukaryotic cilia and flagella 3.39 Describe the structure and function of ribosomes, cytoskeletons, and centrioles CAPILANO UNIVERSITY - EUGENE CHU - BIOL 203 6 LEARNING OUTCOMES 3.40 Compare and contrast the ribosomes of prokaryotes and eukaryotes 3.41 List and describe the three main filaments of a eukaryotic cytoskeleton 3.42 Discuss the function of each of the following: nucleus, endoplasmic reticulum, Golgi body, lysosome, peroxisome, vesicle, vacuole, mitochondrion, and chloroplast 3.43 Label the structures associated with each of the membranous organelles 3.44 Describe the endosymbiotic theory of the origin of mitochondria, chloroplasts, and eukaryotic cells 3.45 List evidence for the endosymbiotic theory CAPILANO UNIVERSITY - EUGENE CHU - BIOL 203 7 PROCESSES OF LIFE (Organisms may not exhibit these processes at all times) CAPILANO UNIVERSITY - EUGENE CHU - BIOL 203 8 PROKARYOTIC CELLS Cells: living entities surrounded by a membrane, that are capable of growing, reproducing, responding and metabolizing. Prokaryotes: lack a nucleus (as well as other membranous organelles Typically small ~1.0 µm in diameter Prokaryotes include: Bacteria A typical prokaryotic cell Archaea CAPILANO UNIVERSITY - EUGENE CHU - BIOL 203 9 EUKARYOTIC CELLS Eukaryotes: possess a nucleus and other membranous organelles Typically larger ~10- 100 µm in diameter Typically more complex CAPILANO UNIVERSITY - EUGENE CHU - BIOL 203 10 EXTERNAL STRUCTURE OF BACTERIAL CELLS 1 Glycocalyces 2 Flagella 4 Pili 3 Fimbriae CAPILANO UNIVERSITY - EUGENE CHU - BIOL 203 11 BACTERIAL GLYCOCALYCES Glycocalyces: A gelatinous, sticky substance that surrounds the outside of the cell Composed of polysaccharides, polypeptides, or both Capsule: if composed of organized repeating units, firmly attached to the cell Slime layer: if it is loose and water-soluble CAPILANO UNIVERSITY - EUGENE CHU - BIOL 203 12 BACTERIAL GLYCOCALYX FUNCTIONS I’m harmful less Helps prevent against desiccation Helps to allow bacteria survive and attach to surfaces (more on this soon!) Prevent recognition by defense cells CAPILANO UNIVERSITY - EUGENE CHU - BIOL 203 13 DENTAL HYGIENE Dental plaque is caused by the formation of biofilm on teeth which allows other bacteria to adhere and multiply Bacteria can produce acids by fermentation of sugars, incite inflammation, break down bone. CAPILANO UNIVERSITY - EUGENE CHU - BIOL 203 14 BACTERIAL FLAGELLA Responsible for bacterial movement Similar structure in bacteria that have it Not all bacteria have one CAPILANO UNIVERSITY - EUGENE CHU - BIOL 203 15 BACTERIAL FLAGELLA https://www.youtube.com/watch?v=L-vprX2kpds&t=20s&ab_channel=JourneytotheMicrocosmos CAPILANO UNIVERSITY - EUGENE CHU - BIOL 203 16  BACTERIAL FLAGELLA - STRUCTURE 1 Three parts: 1. Filament: Hollow shaft. No membrane 2 (many), made of the protein flagellin. 2. Hook: Connects filament to the basal body. 3 3. Basal body: Anchors hook and filament to the cell wall and cytoplasmic membrane. Structure depends on if it is Gram + or - Grows from the tip of the flagella Each part has a different protein composition CAPILANO UNIVERSITY - EUGENE CHU - BIOL 203 17 BACTERIAL FLAGELLA - ARRANGEMENT Peritrichous: cover the surface Amphitrichous: both ends Monotrichous: one end Lophotrichous: several extending from CAPILANO UNIVERSITY - EUGENE CHU - BIOL 203 one or both ends 18 BACTERIAL FLAGELLA - ARRANGEMENT Endoflagella: spiral tightly around the cell A bundle of endoflagella can form an axial filament that wraps around the cell between the cytoplasmic membrane and the outer membrane Rotation causes corkscrew motion of the bacteria CAPILANO UNIVERSITY - EUGENE CHU - BIOL 203 19 BACTERIAL FLAGELLA - FUNCTION Flagella rotate 360o either clockwise or counterclockwise In peritrichous bacteria all flagella rotate in the same direction: Counterclockwise: flagella bundle together and causes the bacteria to move forwards (run) Clockwise: flagella unbundle and rotate independently causing the bacteria to change directions randomly (tumble) CAPILANO UNIVERSITY - EUGENE CHU - BIOL 203 20 FIMBRIAE Fimbriae: Sticky projections that adhere to one another and to other substances Typically shorter than flagella Can be used as a rope to pull bacteria towards objects CAPILANO UNIVERSITY - EUGENE CHU - BIOL 203 21 BIOFILMS http://hi-r-ed.com/Byram/CAUTI/(p4).htm Biofilms: 3D slimy masses of microbes adhering to a substrate and one another by means of fimbriae and glycocalyces Most bacteria in nature exist in biofilms Biofilms can form on many surfaces like pipes, catheters, drains, boats CAPILANO UNIVERSITY - EUGENE CHU - BIOL 203 22 PILUS Pilus (plural pili): a special fimbriae, that can transfer DNA from one cell to another Typically longer than other fimbriae, but shorter than flagella CAPILANO UNIVERSITY - EUGENE CHU - BIOL 203 23 BACTERIAL CELL WALLS Most (but not all) prokaryotes have a cell wall Provides structure and shape, protects from osmotic forces, aids in attaching to other cells, can help to resist antimicrobial drugs Bacteria are categorized as being Gram positive or negative CAPILANO UNIVERSITY - EUGENE CHU - BIOL 203 24 CELL WALL COMPOSITION Bacterial cell walls are made of peptidoglycan which has a protein (peptido-) and sugar (glycan) component The sugar component is a polymer with two regularly alternating molecules: N-acetylglucosamine (NAG) N-acetylmuramic acid (NAM) CAPILANO UNIVERSITY - EUGENE CHU - BIOL 203 25 CELL WALL COMPOSITION Chains of NAG and NAM are connected to other NAG and NAM chains by crossbridges of four amino acids (tetrapeptide) The tetrapeptides are held together by short connecting chains of amino acids CAPILANO UNIVERSITY - EUGENE CHU - BIOL 203 26 GRAM POSITIVE BACTERIAL CELL WALLS Gram + bacteria have a thick layer of peptidoglycan which contains teichoic acid Some teichoic acids are linked to lipids, forming lipoteichoic acids Lipoteichoic acids anchor peptidoglycan to the cytoplasmic membrane Note: Not found in Gram - bacteria CAPILANO UNIVERSITY - EUGENE CHU - BIOL 203 27 GRAM NEGATIVE BACTERIAL CELL WALLS Gram - bacteria have a thin peptidoglycan layer, but they have an outer membrane Note the absence of teichoic and lipoteichoic acids Braun lipoprotein: links the thin peptidoglycan layer with the outer membrane. CAPILANO UNIVERSITY - EUGENE CHU - BIOL 203 28 GRAM NEGATIVE BACTERIAL CELL WALLS Outer membrane: Inner leaflet: composed of phospholipids and proteins Outer leaflet: also contains lipopolysaccharide (LPS) Proteins called porins form channels and allow some solutes to enter and exit CAPILANO UNIVERSITY - EUGENE CHU - BIOL 203 29 GRAM NEGATIVE BACTERIAL CELL WALLS - LPS LPS has two sugar components Also has a lipid portion known as lipid A Can trigger fever, vasodilation, inflammation, shock, vomiting, diarrhea, and blood clotting in humans. Is released when gram negative bacteria die. CAPILANO UNIVERSITY - EUGENE CHU - BIOL 203 30 GRAM NEGATIVE BACTERIAL CELL WALLS - PERIPLASM Periplasmic space (periplasm): the space between the cytoplasmic membrane and the outer membrane Periplasm is composed of water, nutrients, enzymes, and substances secreted by the cell CAPILANO UNIVERSITY - EUGENE CHU - BIOL 203 31 PENICILLIN You are a doctor trying to treat a bacterial infection. The only antibiotic that you have available to you is penicillin which works by inhibiting the formation of peptidoglycan crosslinks. You know that bacteria with a cell wall need to constantly build and break down portions of their cell walls. Would penicillin be more effective against Gram + or – bacteria? Why? CAPILANO UNIVERSITY - EUGENE CHU - BIOL 203 32 BACTERIAL CYTOPLASMIC MEMBRANE A sterol Hopene – a hopanoid Also known as the cell membrane or the plasma membrane Phospholipid bilayer with integral and peripheral membrane proteins Separates the inside from the outside, is selectively permeable, and is a site for metabolic processes (like photosynthesis) Contains sterol-like molecules known as hopanoids to stabilize the membrane CAPILANO UNIVERSITY - EUGENE CHU - BIOL 203 33 MEMBRANE TRANSPORT The tendency for substances to diffuse across the membrane is dictated by: 1. Concentration gradient Substances tend to move from areas of high concentration to areas of low concentration 2. Electrical gradient (for charged substances) Oppositely charged substances are attracted to each other while substances of the charge tend to repel one another Collectively, these two are referred to as the electrochemical gradient CAPILANO UNIVERSITY - EUGENE CHU - BIOL 203 34 PASSIVE TRANSPORT Passive transport: transport that does not require the cell to expend energy. Includes: Diffusion Facilitated diffusion Osmosis CAPILANO UNIVERSITY - EUGENE CHU - BIOL 203 35 OSMOSIS Osmosis: Water behaves just like any solute and has the tendency to move from areas of high free water concentration, to areas of low free water concentration Solute concentrations can be described as being iso-, hyper-, or hypotonic if a solution has the same, greater, or lower solute concentration compared to another, respectively. CAPILANO UNIVERSITY - EUGENE CHU - BIOL 203 36 MEMBRANE TRANSPORT A bacterial toxin causes cells lining the digestive tract to secrete ions, causing the tract to become hypertonic. What effect would this have on a person’s water balance? CAPILANO UNIVERSITY - EUGENE CHU - BIOL 203 37 ACTIVE TRANSPORT Active transport requires an input of energy either directly, or indirectly Uniport: movement of one substance in one direction Symport: movement of two substances in the same direction Antiport: movement of two substances in opposite directions CAPILANO UNIVERSITY - EUGENE CHU - BIOL 203 38 ACTIVE TRANSPORT Coupled transport: when two solutes are transported simultaneously and their transport is coupled such that transport of either stops if the other is absent. Uses one chemical’s electrochemical gradient to provide the energy for the movement of the other CAPILANO UNIVERSITY - EUGENE CHU - BIOL 203 39 GROUP TRANSLOCATION Group translocation: the substance transported across the membrane is chemically changed during the process CAPILANO UNIVERSITY - EUGENE CHU - BIOL 203 40 CYTOPLASM OF BACTERIA Cytoplasm: gelatinous material in the cell Cytosol: liquid portion of the cytoplasm Nucleoid: DNA containing region Most bacteria have a single circular chromosome CAPILANO UNIVERSITY - EUGENE CHU - BIOL 203 41 INCLUSIONS (PHB) Inclusions: deposits of a substance stored in the cytosol of a cell Examples: lipids, starch, or nitrogen- phosphate- or sulfur- containing compounds Polyhydroxybutyrate (PHB): lipid polymer used to store energy CAPILANO UNIVERSITY - EUGENE CHU - BIOL 203 42 ENDOSPORES Endospores: environmentally resistant structures. Can be formed by the Gram + genera Bacillus or Clostridium Extremely resistant to drying, heat, radiation, and lethal chemicals 1 endospore is formed from 1 cell, thus not a reproductive structure CAPILANO UNIVERSITY - EUGENE CHU - BIOL 203 43 ENDOSPORES Clostridium botulinum can produce botulinum toxin causing weakness and paralysis Can form endospores which makes them very difficult to eliminate Can survive boiling water for several hours! Used in botox treatment Bacillus anthracis and Clostridium tetani can also form endospores CAPILANO UNIVERSITY - EUGENE CHU - BIOL 203 44 NONMEMBRANOUS ORGANELLES Ribosomes: molecular machines that synthesize proteins Composed of ribosomal RNA (rRNA) and proteins Have 70S ribosomes Cytoskeleton: internal scaffolding Involved in binary fission, orientation of NAG and NAM, segregation of DNA to certain parts of the bacterial cell Helical cytoskeleton CAPILANO UNIVERSITY - EUGENE CHU - BIOL 203 45 EXTERNAL STRUCTURES OF ARCHAEA - GLYCOCALYCES Archaeal glycocalyces are similar to bacterial ones Can function in the formation of biofilms No archaeon known to be pathogenic Staphylococcus aureus biofilm on an indwelling catheter CAPILANO UNIVERSITY - EUGENE CHU - BIOL 203 46 ARCHAEAL FLAGELLA Similar to bacterial flagella in some ways: Has a basal body, hook, and filament Extends outside of the cell Is not covered by a membrane Rotates like a propeller A bacterial flagella CAPILANO UNIVERSITY - EUGENE CHU - BIOL 203 47  BACTERIA FLAGELLA VS ARCHAEAL FLAGELLA Hollow, grows from tips Not hollow, grows from base Thick (~20 nm in diameter) Thin (~10-14 nm in diameter) Different amino acid composition Different amino acid composition Sugars rarely attached Sugars often attached Powered by proton movement Powered by ATP Jarrell and McBride (2008) The surprisingly diverse ways that prokaryotes move. Nature Reviews Microbiology 6: 466–676 Keiichi Namba et al. of the ERATO Protonic NanoMachine Project http://www.npn.jst.go.jp/index.html CAPILANO UNIVERSITY - EUGENE CHU - BIOL 203 48 ARCHAEAL FIMBRIAE AND HAMI Similar to bacterial fimbriae Hami: proteinaceous, fimbriae-like helical structures with prickles sticking out and a grappling hook-like end Allows attachment to surfaces CAPILANO UNIVERSITY - EUGENE CHU - BIOL 203 49 ARCHAEAL CELL WALLS Most archaea have a cell wall that lacks peptidoglycan Most are composed of polysaccharides, glycoproteins, or proteins Archaea typically spherical or rod shaped, but there are some exceptions CAPILANO UNIVERSITY - EUGENE CHU - BIOL 203 50 ARCHAEAL CELL CYTOPLASMIC MEMBRANES 1. Use branched hydrocarbon chains (sometimes as a monolayer!) 2. Use ether linkages rather than ester linkages to join hydrocarbons to glycerol Mechanically stronger, more stable at high temperatures and salt tolerant 3. Use L-glycerol instead of D-glycerol CAPILANO UNIVERSITY - EUGENE CHU - BIOL 203 51 https://www.khanacademy.org/science/biology/bacteria-archaea/prokaryote-structure/a/prokaryote-structure ARCHAEAL CYTOPLASM Have 70S ribosomes (like bacteria) However, the proteins are actually more similar to eukaryotic ones Have a fibrous cytoskeleton Have circular DNA like bacteria Genetic code is more similar to eukaryotes Lack membranous organelles CAPILANO UNIVERSITY - EUGENE CHU - BIOL 203 52 PROKARYOTIC COMPARISON CAPILANO UNIVERSITY - EUGENE CHU - BIOL 203 53 REVIEW Open up Kahoot (https://kahoot.it/) CAPILANO UNIVERSITY - EUGENE CHU - BIOL 203 54 EUKARYOTIC EXTERNAL STRUCTURE - GLYCOCALYCES Some animal and protozoan cells have one anchored to the cytoplasmic membrane Cell-cell recognition and adhesion Protection of the cell surface Permeability layer Not as organized as bacterial capsules Absent in eukaryotes with cell walls CAPILANO UNIVERSITY - EUGENE CHU - BIOL 203 55 EUKARYOTIC CELL WALLS Plants: Use cellulose Fungi: Use cellulose, chitin or glucomannan Algae: Use cellulose, proteins, agar, carrageenan, silicates, algin, calcium carbonate, or a combination of the above! CAPILANO UNIVERSITY - EUGENE CHU - BIOL 203 56 EUKARYOTIC CYTOPLASMIC MEMBRANES Differences with prokaryotes: Contain sterols (like cholesterol) to help maintain membrane fluidity Possess membrane rafts (lipid rafts) – distinct assemblages of lipids and proteins that remain together Often attach sugars to the outer surface of lipids and proteins. Rare in prokaryotes. Do not perform group translocation CAPILANO UNIVERSITY - EUGENE CHU - BIOL 203 57 ACTIVE TRANSPORT PROCESSES IN EUKARYOTES Endocytosis uptake of material forming vesicles at the plasma membrane Phagocytosis: uptake of large substances Involves the formation of pseudopods that surround substances Pinocytosis: indiscriminate uptake of fluid and dissolved solutes Exocytosis delivers lipids and proteins to the PM, but this is balanced by removal from endocytosis CAPILANO UNIVERSITY - EUGENE CHU - BIOL 203 EUKARYOTIC FLAGELLA Inside the cell, surrounded by the cytoplasmic membrane Composed of microtubules formed from the protein tubulin. Microtubules are in a 9+2 arrangement (9 microtubule doublets on the outside, 2 single microtubles in the middle) Anchored to a basal body in the cytoplasm in a 9+0 arrangement (9 microtubule triplets) Undulates rather than rotates CAPILANO UNIVERSITY - EUGENE CHU - BIOL 203 59 EUKARYOTIC CILIA Shorter and more numerous than flagella Surrounded by cytoplasmic membrane Same 9+2 arrangement anchored by a 9+0 basal body as flagella Not found in prokaryotes CAPILANO UNIVERSITY - EUGENE CHU - BIOL 203 60 EUKARYOTIC NONMEMBRANOUS ORGANELLES Ribosomes 80S, larger than prokaryotic ribosomes Cytoskeleton: Moves organelles within the cytosol, serves as an internal scaffold, maintains basic shape, helps move cytoplasmic membranes for locomotion Made of microtubules, intermediate filaments, and microfilaments CAPILANO UNIVERSITY - EUGENE CHU - BIOL 203 61 CENTRIOLES Centrioles: composed of nine microtubule triplets Found in some animal and fungal cells Two centrioles lie at right angles to one another are found in a region of the cytoplasm known as the centrosome Involved in mitosis and cytokinesis, formation of flagella and cilia CAPILANO UNIVERSITY - EUGENE CHU - BIOL 203 62 MEMBRANOUS ORGANELLES Contains the genetic material of the cell (multiple linear chromosomes) Surrounded by a double membrane called the nuclear envelope containing nuclear pores Nucleoplasm: the semiliquid matrix of the nucleus Nucleoli: specialized regions where RNA is synthesized CAPILANO UNIVERSITY - EUGENE CHU - BIOL 203 63 ENDOPLASMIC RETICULUM Categorized as smooth or rough depending on the presence of ribosomes studding the surface Rough: involved in protein synthesis and processing Smooth: lipid synthesis and transport, calcium storage, drug detoxification, and carbohydrate metabolism CAPILANO UNIVERSITY - EUGENE CHU - BIOL 203 64 GOLGI BODY Manufactures, receives, modifies and ships proteins throughout the cell Forms vesicles that bud off and fuse with other organelles or to the cytoplasmic membrane CAPILANO UNIVERSITY - EUGENE CHU - BIOL 203 65 LYSOSOMES, PEROXISOMES, VACUOLES, VESICLES Vesicle and vacuoles are sacs that store material (lipids, starch, water, ions, etc) Lysosomes: found in animal cells and contain hydrolytic enzymes to break down old cells, organelles, and phagocytosed material Peroxisomes: degrade metabolic wastes CAPILANO UNIVERSITY - EUGENE CHU - BIOL 203 66 MITOCHONDRIA The “powerhouse of the cell”, involved in ATP production Possess an inner membrane, outer membrane, and an intermembrane space Inner membrane contains folds called cristae The matrix lies within the inner membrane CAPILANO UNIVERSITY - EUGENE CHU - BIOL 203 67 CHLOROPLASTS Involved in photosynthesis Contains an inner and outer membrane Thylakoids: membranous sacs where photosynthesis is conducted Granum: stack of thylakoids Stroma: space outside of grana contained within the inner membrane CAPILANO UNIVERSITY - EUGENE CHU - BIOL 203 68 ENDOSYMBIOTIC THEORY Endosymbiont theory: an early ancestor of eukaryotic cells engulfed nonphotsynthetic prokaryotes and photosynthetic prokaryotes which ultimately became mitochondria and chloroplasts, respectively. Accounts for the two membranes, circular DNA, and presence of 70S ribosomes in both organelles Doesn’t explain: Why the nuclear envelop has two membranes Why most mitochondrial/chloroplast proteins come from nuclear DNA CAPILANO UNIVERSITY - EUGENE CHU - BIOL 203 69 BACTERIA VS EUKARYOTES Characteristic Bacteria Eukaryote Size Nucleus? Membrane-bound organelles? Structure and movement of flagella Cell wall composition Ribosome size Chromosome structure CAPILANO UNIVERSITY - EUGENE CHU - BIOL 203 70