Chapter 2: The Cell - An Overview (PDF)

Image Source: https://www.behance.net/gallery/15570899/Cell-Collage The Cell: An Overview Chapter 2  The endomembrane system Divides eukaryotic cells into functional and structural compartments Membranes connected directly (physically) OR indirectly by vesicles Vesicles are sm...

Image Source: https://www.behance.net/gallery/15570899/Cell-Collage The Cell: An Overview Chapter 2  The endomembrane system Divides eukaryotic cells into functional and structural compartments Membranes connected directly (physically) OR indirectly by vesicles Vesicles are small membrane- bound sacs that transfer substances between parts of system Image Source: https://byjus.com/biology/endomembrane-system/  Endoplasmic Reticulum (ER) More than half the total membrane in many eukaryotic cells Extensive interconnected network (reticulum) of membranous channels and cisternae (pockets) Cisterna surrounds an enclosed space (ER lumen)  Smooth ER No ribosomes attached to membrane surfaces Tubular cisternae Synthesizes lipids that become part of cell membranes Convert drugs, poisons, and toxins in liver into tolerable or easily removed substances  Rough ER Many ribosomes on outer surface Flattened cisternae Proteins made on ribosomes attached to the ER enter ER lumen, where they fold into their final form  Rough ER Chemical modifications, such as addition of carbohydrate groups to produce glycoproteins, occur in lumen Can remain in ER or sent to other destinations Proteins are delivered to other regions of cell (e.g., Golgi complex) within small vesicles that pinch off from ER Image Source: https://www.slideshare.net/slideshow/biology-cells-1011/6090664#17  Proportions of ER More Smooth ER More Rough ER More lipids, toxic substance breakdown More proteins that are secreted outside of cell Image Source: https://www.chegg.com/homework-help/questions-and-answers/look-micrographs-google-search-find- major-function-leydig-cell-pancreatic-endocrine-cell-s-q66559975#question-transcript  Golgi complex Stack of flattened, membranous sacs (cisternae) ER proteins enter on cis face (facing nucleus) via transport vesicles that fuse with membrane Proteins chemically modified / tagged by removing segments or adding functional groups, or lipid or carbohydrate units Modified proteins exit from trans face (facing plasma membrane) in vesicles that bud off from membrane  Exocytosis Proteins to be secreted from cell Transported to membrane in secretory vesicles Contents released to exterior by exocytosis Membrane of vesicle fuses with plasma membrane Signaling molecules (hormones, neurotransmitters), waste products, toxic substances, enzymes  Endocytosis Vesicles also form by reverse process, endocytosis Brings molecules into cell from exterior Plasma membrane pinches off into cytoplasm as endocytic vesicle Carry materials to Golgi complex or other destinations such as lysosomes in animal cells  Lysosomes Small, membrane-bound vesicles Hydrolytic enzymes - digest complex molecules Cells recycle subunits of these molecules Found in animals, but not in plants In plants function done by central vacuole  Lysosomes Formed by budding from Golgi complex Hydrolytic enzymes synthesized in rough ER Image Source: https://www.slideshare.net/slideshow/biology-cells-1011/6090664#19  Lysosomes pH within lysosomes is acidic (pH = 5) Significantly lower than the pH of cytosol (pH = 7.2) Lysosomal enzymes digest contents endocytic vesicles, worn out organelles (autophagy), and materials engulfed by phagocytes (cells of immune system or “food”) Image source: https://www.chegg.com/homework-help/questions-and-answers/nucleus-1-um-vesicle- containing-two-damaged-organelles-1-um-mitochondrion-fragment-peroxis-q55902407 Vesicle traffic in the cytoplasm Fig. 2.17, p. 44  Mitochondria 5 Membrane-bound organelles Cellular respiration Energy-rich food molecules broken down into water (H20) + carbon dioxide (CO2) by mitochondrial reactions in presence of oxygen Energy captured in ATP Image Source: https://commons.wikimedia.org/wiki/File:Cellular_Respiration_Simple.png  Mitochondria 5 Two membranes surrounding an inner compartment Mitochondrial matrix Outer mitochondrial membrane covers the organelle Inner mitochondrial membrane expanded by folds - cristae ATP-generating reactions occur in cristae / folds and matrix  The cytoskeleton Interconnected system of protein fibers and tubes that extends throughout cytoplasm Maintains cell’s characteristic shape and internal organization Functions in movement  The cytoskeleton Image Source: https://www.macmillanhighered.com/BrainHoney/Resource/6716/digital_first_content/trunk/test/morris2e/morris2e_ch10_5.html  Microtubules Assembled from tubulin proteins Microtubule wall - 13 protein filaments (linear polymers of tubulin dimers) arranged side by side Dimers organized head-to-tail in each filament - polarity (+ and – ends) Dynamic structures Changing lengths by addition or removal of tubulin dimers Add or detach more rapidly at + end  Microtubules 7 Anchor – endomembrane system (ER, Golgi, lysosomes, secretory vesicles), some mitochondria Provide tracks – vesicles move between cell interior and plasma membrane Separate and move chromosomes during cell division Maintain animal cell shape Cell motility – cilia and flagella Image source: https://www.docsity.com/en/electron-micrograph-of-cytoskeleton-fundamentals- of-biology-lecture-slides/241298/  Intermediate filaments Assembled from large and varied group of intermediate filament proteins Occur singly, in parallel bundles, and in interlinked networks Either alone or in combination with microtubules, microfilaments, or both Provide mechanical strength in many cells and tissues Tissue-specific in protein composition (unlike microtubules and microfilaments)  Microfilaments 7 Thin protein fibers assembled from actin subunits Polarity (+ and – ends) Structural and movement functions Contractile elements in muscle fibers Cytoplasmic streaming Transport nutrients, proteins, and organelles in animal and plant cells Responsible for amoeboid movement Divide cytoplasm when animal cells divide Image Source: https://apbiologyctd.wordpress.com/cytoskeleton/  Motor proteins Eukaryotic cell movements generated by “motor” proteins Walk along cytoskeletal filaments carrying vesicles and other organelles Bind filament on one end, bind cargo on other end Energy for walking comes from ATP Walk unidirectionally, either toward + https://organismalbio.biosci.gatech.edu/chemical-and-electrical-signals/effectors-and-movement/ or – end, depending on motor protein  Motor proteins Myosin – walk along microfilaments Kinesin – walk along microtubules Dynein – walk along microtubules Make attachment, forcefully swivel a short distance, and then release Tail domain – carries cargo Motor domain – walks on cytoskeleton Image Source: https://www.nature.com/articles/35036069  Centrosome Microtubules formed and radiate outward from cell center, or centrosome Centrosome is a “microtubule-organizing center” (MTOC) Midpoint are centrioles Two short, microtubule rings  Flagella and Cilia Elongated, motile structures Extend from cell surface Cilia are shorter Cilia occur in greater numbers Flagella propel cell through watery medium Cilia move fluids over cell surface Image Source: https://www.sciencefacts.net/cilia-and-flagella.html Flagella and Cilia Circle of double microtubules surrounds central pair of single microtubules (9 + 2 complex) Dynein motor proteins slide microtubules over each other Produce movements of flagellum and cilium Specialized structures of plant cells Image Source: https://milliemakesbiologyeasy.blogspot.com/2016/03/24-compare-structures-of-plant-and.html  Plastids 6 Chloroplasts yellow-green plastids Contain green pigment (chlorophyll) Sites of photosynthesis in plant cells Absorbs light energy and converts to chemical energy Image Source: https://www.khanacademy.org/science/ap-biology/cellular-energetics/photosynthesis/a/intro-to-photosynthesis  Plastids Chromoplasts – makes and stores pigments in fruits and flowers Contains carotenoids (red, orange and yellow pigments) Many types plastids are colorless Leucoplasts - storage molecules (including starch, lipids, proteins) in Image Source: https://mmegias.webs.uvigo.es/02-english/5-celulas/6-plastos.php non-photosynthetic organs Amyloplast – starch storage organ  Plastids All plastids contain DNA genomes and molecular machinery for transcription and translation Some of the proteins within plastids are encoded by their own genomes Others encoded by nuclear genes and imported into organelles Image Source: https://search.library.wisc.edu/digital/ARUK3QI434C5BX8J  Chloroplasts 6 Surrounded by an outer boundary membrane Inner boundary membrane Completely encloses inner compartment – stroma Within stroma – third membrane system Flattened, closed sacs (thylakoids) If thylakoids are stacked – grana Thylakoid membranes contain chlorophyll  Central vacuoles Large vesicles Specialized functions unique to plants 90% or more of cell’s volume One or more large central vacuoles Pressure supports cell Forces cell content to membrane Membrane that surrounds central vacuole = Tonoplast Contains transport proteins that move substances into and out of vacuole Image Source: https://socratic.org/questions/how-do-you- identify-vacuole-from-a-microscopic-image-of-plant-cells  Central vacuoles Functions Storage (useful substances or waste products) Maintain internal turgor pressure Maintains acidic internal pH Pigments concentrated in vacuoles produce colors of many flowers Enzymes that break down biological molecules Molecules that provide chemical defenses Image Source: against pathogenic organisms https://www.labxchange.org/library/items/lb:LabXchange:fb8910d2:l x_image:1?source=%2Flibrary%2Fclusters%2Flx- cluster%3AChemistryResources%3Fsource%3D%2Flibrary%2Fclu sters%2Flx-cluster%3Alxc-fox  Cell walls Extracellular Separates interior contents of cell from exterior environment Image Source: https://stileapp.com/au/library/publishers/stile/compilations/science-ngss/6065632a-b968-41c5-8ed2- bc6eb466b0a7/preview/33-cells-under-the-microscope/LBk7 Provides shape Support individual cells Contain pressure produced in central vacuole Protect cells against invading bacteria and fungi  Cell walls Cell wall consist of plants – mostly cellulose fungi – mostly chitin bacteria – mostly peptidoglycans Provide tensile strength Embedded in network of carbohydrates (hemicellulose, pectin) Image Source: https://www.sciencefacts.net/cell-wall.html  Cell walls Plant cell walls may have multiple layers: Primary cell wall Relatively thin and flexible Found in all cells Secondary cell wall (in some cells) Located between plasma membrane and primary cell wall Impregnated with f.e. lignin Very rigid and hydrophobic Found in cells involved in support, protection, or nutrient transport Image Source https://apbiologyctd.wordpress.com/extracellular-matrix-and-cell-junctions/  Cell walls Pectin-rich middle lamella Thin layer between primary walls of adjacent cells Perforated by plasmodesmata Plasma membrane-lined channels that connect cytosol of adjacent cells Allow ions and small molecules to move directly from one cell to another through cytosol Middle lamella Image Source https://apbiologyctd.wordpress.com/extracellular-matrix-and-cell-junctions/  The animal cell surface Cell adhesion Cell junctions - reinforces Extracellular matrix molecules (CAMs) - adhesion, seal spaces and (ECM) - supports and bind cells together provide direct communication protects cells and between cells provides mechanical linkages between tissues Image Source: https://www.researchgate.net/figure/Cell-cell-and-cell-substrate- junction-types-in-epithelial-cells-Tight-junction-seals_fig4_275027480  Cell adhesion Plasma membrane glycoproteins that bind to specific molecules on other cells Image Source: https://bscb.org/learning-resources/softcell-e- learning/extracellular-matrix-and-cell-adhesion-molecules/ Maintain body form and structure CAMs help cells stick to each other and to their surroundings Cancer cells typically lose adhesions Break loose and migrate to new locations Some bacteria and viruses target CAMs Some role in recognition of self Image of human epithelial cells with cadherin stained green and nucleus blue. Cell junctions  Cell junctions: Anchoring junctions Anchoring junctions Form buttonlike spots, or belts, run entirely around cells “welding” adjacent cells together Desmosomes junctions Intermediate filaments anchor junction in underlying cytoplasm Adherens junctions Microfilaments anchor cytoskeletal component  Cell junctions: Tight junctions Tight connections between membranes of adjacent cells Seal spaces between cells in cell layers that cover internal organs, outer surfaces of body, or layers that line internal cavities and ducts Direct fusion of proteins on outer surfaces of plasma membranes of adjacent cells  Cell junctions: Gap junctions Allow ions and small molecules to pass through direct channels from one cell to another Hollow protein cylinders embedded in plasma membranes of adjacent cells line up Form a pipeline - connects cytoplasm of one cell with cytoplasm of next Allows communication between cells within a tissue Organ operates as coordinated unit  Connections between cells Plant cells Image Source: https://bio.libretexts.org/Bookshelves/Introductory_and_General_Biology/Principles_of_Biology/01%3A_Chapter_1/05%3A_Cell_Stru cture_and_Function/5.14%3A_Extracellular_matrix_and_intercellular_junctions  Extracellular Matrix (ECM) Many animal cells are embedded in ECM Proteins and polysaccharides secreted by cells themselves Connected to cytoskeletal elements and transmembrane proteins  ECM Glycoproteins main component of ECM Most abundant ECM glycoprotein - collagen Consistency of matrix depends on network of proteoglycans surrounding collagen fibers Image Source: https://febs.onlinelibrary.wiley.com/doi/10.1111/febs.15776  How do we know what different cell parts do?? Cell fractionation Cells are broken up and the different organelles they contain separate out Used to help us study cell structures and functions Cell fractionation is a two-stage process: homogenization and centrifugation Image Source: https://namrataheda.blogspot.com/2013/01/isolation-of-cell-organelles.html  Homogenization Breaking cells and tissues Without destroying the inside contents Image Source: https://www.open.edu/openlearn/science-maths-technology/a- tour-the-cell/content-section-2.2.1 Image Source: https://www.researchgate.net/profile/Amirul- Islam/publication/337608966/figure/fig6/AS:830403099258890@1574994935314/Diff erent-types-of-cell-disruption-techniques.png  Centrifugation In broken-cell homogenate all the pieces are still mixed together Separated using centrifugation Separates fragments based on size and density Image Source: https://www.iqsdirectory.com/articles/centrifuge.html  Centrifugation Particles in solution pulled downward by Earth gravitational force Sedimentation principle Centrifugal acceleration causes denser substances and particles to move outward in radial direction Mass or density higher than solvent – sink Mass or density lower than solvent – float Image Source: https://www.geeksforgeeks.org/separation-by-centrifugation/  Differential centrifugation Difference in sedimentation rate Difference in size and densities Centrifugation at progressively higher speeds Separate particles according to size and density Image Source: https://www.open.edu/openlearn/science-maths-technology/a-tour-the-cell/content-section-2.2.1  Density gradient centrifugation Variation of differential centrifugation Separation not complete Pellets contain mixture of cellular components Sample centrifuged in medium that gradually increases in density from top to bottom Image Source: https://www.open.edu/openlearn/science-maths-technology/a-tour-the-cell/content-section-2.2.1  Density gradient centrifugation Movement through density gradient Optimizes separation of particles of different density and size into different levels or bands in gradient Can be removed as separate 'fractions' Image Source: https://www.open.edu/openlearn/science-maths-technology/a-tour-the-cell/content-section-2.2.1 Density gradient centrifugation Image Source: https://www.frontiersin.org/journals/plant-science/articles/10.3389/fpls.2022.1014532/full Image Source: https://smartclass4kids.com/animal-cell-diagram/ Image Source: https://www.expii.com/t/cell-organelle-types-functions-10333