02_Handout_2.pdf

SH1909 The Cell Theory postulated by Schleiden, Schwann, and Virchow CELL is compose...

SH1909 The Cell Theory postulated by Schleiden, Schwann, and Virchow CELL is composed of three (3) tenets: 1. Cells are the smallest and most basic unit of structure and function of organisms Prokaryotic Eukaryotic 2. All organisms are composed of cells 3. Cells arise from pre-existing cells Archaea Bacteria Eukarya H. walsbyi E. coli H. sapiens Cells – Identification and Classification Figure 1.0 Classification of Organisms Based on Cell Structure First record of seeing a cell and identifying it Pro= before, Eu= true, karyon= kernel. The main difference between prokaryotes and eukaryotes, therefore, is the presence belongs to Robert Hooke of an enclosed structure to separate the genetic material of the All cells share common structural features: cell, known as the Nucleus. 1. Cell/plasma membrane Prokaryotic Cells -the outer boundary of the cell Earliest and most primitive cells which separates its contents from the environment. Contains only simple structures with very little It varies in composition. differentiation Size varies from 0.1-5 µm (with few exceptions) 2. Cytoplasm Consists of organisms from the Domain -a gel-like substance that Archaea and Bacteria constitutes the cells internal environment and holds all of the structural components of the cell. For Structure Capsule The outermost layer that encases the 3. Genetic material entire cell for additional protection. -Deoxyribose nucleic acid (DNA) is Usually composed of polysaccharides the genetic material which holds information for cell Cell wall A rigid case that encloses the entire cell activities and function and gives it shape. For Bacteria: Peptidoglycans are present, 4. Ribosomes while for Archaea: No peptidoglycans -structures that manufacture are present. proteins which are needed for cell function Plasma A semipermeable membrane that membrane encloses the internal structures of the Cells can differ in number, size, components, cell that regulates the passage of and composition molecules into and out of the cell. For Based on structural differences, cells can be Bacteria: Fatty acids are what classified as either Prokaryotic or Eukaryotic composes this membrane, while for 02 Handout 2 *Property of STI  [email protected] Page 1 of 13  SH1909 Archaea: Non-fatty acid lipids are its For Genetic Material composition. Nucleoid Region of the cell where DNA is present. Mesosome Folds of the plasma membrane that Prokaryotes do not have an enclosed enter the area of the cytoplasm. This is structure for its genetic material such as a where the electron transport system for nucleus. Ribosomes and enzymes are the creation of cell energy is located. seen near this region Cytoplasm The gel-like substance that fills the Plasmid Small independent loops of DNA which & Cytosol interior of the cell. It holds the other are separate from the chromosomal DNA components of the cell. The cytosol is found in the nucleoid. This is important for the liquid portion of the cytoplasm the genetic advantages of prokaryotes. Table 1.2 Components of a Prokaryotic Cell used for Table 1.0 Components of a Prokaryotic Cell used for Structural Integrity Genetic Function For Activities and Function Ribosome Small structures that are scattered throughout the cytoplasm for the process of protein synthesis. Prokaryotes have a 50s and 30s subunit, forming a 70s ribosome. Pili Tubular structures present in the cell surface for cell-to-cell communication and passing of genetic material. Flagellum A tail-like appendage anchored to the Image 1.0 A Labeled diagram of a Prokaryotic Cell cell membrane and wall that allows a Source: https://owlcation.com/stem/Biolog-101-Cells prokaryote locomotion through a circular motion. This can either be seen at the end of the cell or scattered randomly. Fimbriae Additional small and bristle-like fibers scattered throughout the cell surface. They are used for attachment, navigation, and propelling certain molecules or objects toward the cell. Table 1.1 Components of a Prokaryotic Cell used for Cell Activities and Motor Function Image 1.1 A Labeled micrograph of a E. coli Source: http://ibbiology.wikifoundry.com/ 02 Handout 2 *Property of STI  [email protected] Page 2 of 13  SH1909 Eukaryotic Cells ▪ Three carbon glycerol molecule Highly evolved, complex structures, and larger ▪ Two fatty acid tails size compared to prokaryotes Size varies from 10-100 µm (with few o The charged phosphate group and the exceptions) glycerol molecule form the Exhibits heavy Compartmentalization of phospholipids polar head internal structures known as Organelles o The two (2) fatty acids makeup the non- Divided into Protista, Fungi, Plantae, and polar hydrophobic tail Animalia o The hydrophobic tails move away from Derivations vary per classification, but all have the environment and cluster together the general components of a typical eukaryotic forming the middle portion of the lipid cell bilayer of the plasma membrane, while Cell structures can be categorized as either for: the hydrophilic heads are faced toward 1. Structures for protection the environment. 2. Genetic control organelles o Because the middle portion of the 3. Manufacturing, Storing, Distributing, and membrane is non-polar, this causes it Breakdown organelles to have selective permeability, 4. Energy processing organelles meaning non-polar molecules such as 5.Organelles for structural support, glucose cannot pass freely through the movement, and communication between cells cell I. STRUCTURES FOR PROTECTION Membrane Proteins Cell Membrane The cell membrane is also composed of Functions as a barrier to separate the proteins and other molecules which are environment and the internal structures of the randomly scattered cell The presence of membrane proteins and other molecules is why the cell membrane is termed Also regulates the passage of molecules to and as Fluid Mosaic (coined by Nicolson and from the cell Singer). Composed of two (2) sheets of phospholipids, hence the name Phospholipid bilayer o Phospholipids are organic molecules that exhibit both polar (hydrophilic) and non-polar (hydrophobic) ends. o The cause of its bipolar nature is due to the three (3) key structures it Image 2.0 A Fluid Mosaic Model Showing the possesses: Structures of the Cell Membrane ▪ Charged Phosphate group Source: https://biofoundations.org/repairing-the-cell- membrane/ 02 Handout 2 *Property of STI  [email protected] Page 3 of 13  SH1909 Only found in plant cells (but also present Structures Embedded in Cell Membrane in prokaryotic bacteria) Create passageways for ions Composition varies per classification. Transport and non-polar molecules to Some examples would be: Proteins pass freely through the cell membrane 1. Plants and algae: Polysaccharide Channel Form tunnels for the import cellulose Proteins and export of materials and Because cellulose is rigid and does wastes not allow free passage of molecules, plants Cell Enable cells to distinguish own and algae have openings which allow water Recognition cells from that of other and molecules to diffuse Proteins organisms Junction Assist in cell-to-cell adhesion 2. Fungi: Chitin Proteins and communication between cells Cytoplasm Receptor Facilitate exchange of signals It is the jellylike substance contained within the Proteins between cells by changing its cell membrane. Generally composed of the cell shape to allow specific organelles (not including the nucleus) and molecules (ligands) to bind to cytosol it Cytosol is the liquid component of the Enzymatic Participate in metabolic cytoplasm and is largely composed of water Proteins reactions such as degradation Organelles are compartmentalized structures and synthesis to sustain life in which offer efficiency and provides the cell the the cell ability to do different complex metabolic Carbohydrate Serve as identification tags for reactions in localized areas Chains the cell recognition proteins 1. Membranous organelles (single Cholesterol Strengthens the cell membrane) membrane by making it more Golgi body, lysosomes, smooth flexible but less fluid. It also and rough endoplasmic reticulum, vesicle, makes the membrane less vacuole permeable to water-soluble substances 2. Membranous organelles (double Table 2.0 Structures Embedded in the Cell Membrane and their Functions membrane) Nucleus, mitochondria, plastids Cell Wall An additional boundary between the cell 3. Non-membranous organelles membrane and the environment for added Ribosome, centriole structural support and protection 02 Handout 2 *Property of STI  [email protected] Page 4 of 13  SH1909 II. GENETIC CONTROL ORGANELLES DNA Nucleus The long-chain molecule of inheritance made of The storehouse of genetic information (DNA). It segmented portions called genes which functions to prevent damage to the DNA and contains the information needed for cell direct all cell activity. activities (such as protein synthesis) Numerous proteins are needed for genetic The molecule is compacted by proteins called function, so the nucleus has specialized histones which form a condense structure structures to facilitate their entry: called chromatin and condenses further into 1. Nuclear envelope chromosomes when cell division is occurring. A two (2) membrane structure that There are two types of chromatin seen in the encloses the nucleus and separates it from nucleus: the cytoplasm 1. Euchromatin Contains active DNA, stains lightly 2. Perinuclear space when viewed under the microscope The space between the two (2) membranes of the nuclear envelope 2. Heterochromatin Contains inactive DNA, stains 3. Nucleoplasm deeply when viewed under the microscope The semifluid substance inside the nucleus 4. Nuclear pores Perforations in the nuclear envelope that regulate the passage of materials (usually proteins, ribosomes, and RNA) 3. Nucleolus Condensed region of the nucleus where synthesis of ribosomal RNA (or rRNA) and ribosomal subunits are Image 2.1 A Micrograph of a Nucleus Showing its centralized Specialized Structures Source: https://www.histology.leeds.ac.uk /cell/nucleus.php rRNA is combined with imported proteins to form the large and small ribosomal subunits. These subunits exit through the nuclear pores and combine once within the cytoplasm 02 Handout 2 *Property of STI  [email protected] Page 5 of 13  SH1909 III. MANUFACTURING, STORING, Secretory proteins made from the DISTRIBUTING, AND BREAKDOWN RER are typically used by specialized cells ORGANELLES (i.e. pituitary glands: hormones), or can even be secreted outside the cell (i.e. Endoplasmic Reticulum (ER) mammary glands: milk proteins) An extensive folded membrane that occupies a large space in the cytoplasm. 2. Smooth ER (SER) Due to its large size, the ER is folded like a Region adjacent to the RER where maze where the membranous tubules and no ribosomes are present and whose flattened sacs are called cisternae, while the cisternae are membranous tubules spaces between them are the cisternal space Its main functions are mostly o The cisterna (singular) is continuous involving metabolic processes such as with the nuclear envelope, and so the synthesis and transport of lipids, perinuclear space is also continuous metabolism of carbohydrates, and with the cisternal space detoxification of drugs and poisons. A specialized form of SER in o This connection allows the synthesized muscle cells is the sarcoplasmic reticulum ribosomes from the nucleolus to be where calcium ions are stored and transported directly to the ER released. When a nerve signal stimulates the muscle the release of ions triggers a The presence of ribosomes in the ER allows it to be contraction classified into two (2) regions: 1. Rough ER (RER) Region closest to the nucleus whose cisternae are flattened sacs, and are studded with ribosomes, giving it a rough appearance when viewed from the microscope Proteins are formed and temporarily stored in the cisternal space A short carbohydrate attaches to the formed protein (converting it into a Image 2.2 Diagram of an Endoplasmic Reticulum Showing glycoprotein, a secretory protein) thereby its Specialized Regions Source: https://cellsorganelles.weebly.com/packaging-shipping- making it ready for cell use and-producing.html Secretory proteins are moved to the specialized transitional ER, where transport vesicles take them to the Golgi body for further packaging 02 Handout 2 *Property of STI  [email protected] Page 6 of 13  SH1909 Golgi Apparatus/Body o Stacks of cisternae which acts as a processing system that sorts, modifies, and packages products from the ER o Proteins finish their folding here to become functional o Enzymes in the Golgi body manufacture and attach carbohydrates that serve as name tags for the cell o The Golgi has specialized regions that interact with the ER, the rest of the cell, and with each Image 2.3 Micrograph of an Endoplasmic Reticulum other through vesicles budding off from the Showing its Specialized Regions Source: http://ibbio.pbworks.com/w/page/59800989/Prokaryotic Golgi cisternae %20and%20Eukaryotic%20Cells o These regions are arranged from the closest to the ER up to the ones near the plasma Ribosomes membrane: Sites of protein synthesis 1, Cis-face Spherical granules composed of two subunits, The receiving end of the Golgi. the large subunit and small subunit, Where transport vesicles from the ER are synthesized in the nucleolus. These subunits fused with the cisterna of the Golgi. Also exit to the cytoplasm and combine to form responsible for the returning incorrectly ribosomes sent proteins back to the ER Each ribosome consists of ~70 proteins and several ribosomal RNA (rRNA) 2. Dictyosome/medial-face Found as either bound ribosomes attached to Bulk or main stacks of cisternae. the RER and nuclear membrane, or free Responsible for processing proteins and ribosomes suspended in the cytosol lipids and directing them to their o They are structurally identical and can destinations. alternate roles depending on the needs of the cell 3. Trans-face Proteins synthesized by free ribosomes The shipping end of the Golgi. function as enzymes or structural proteins Sorts and directs the modified proteins to Proteins synthesized by bound ribosomes their destination by budding off secretory function as secretory proteins or hormones vesicles 02 Handout 2 *Property of STI  [email protected] Page 7 of 13  SH1909 packaged by the Golgi body where it fuses with transport vesicles carrying cell debris o The main function of lysosomes is intracellular digestion by means of autophagy Peroxisome o Structurally identical to lysosomes however, the enzymes present are from the Golgi body and have much higher concentrations than lysosomes o Mainly function to dispose of toxic substances Image 2.4 Diagram of Golgi Body and lipids Source: http://animalia-life.club/other/golgi-apparatus-labeled- diagram.html IV. ENERGY PROCESSING ORGANELLES Mitochondria o Double membranous structures that supply energy to the cell by means of cellular respiration medial o Consists of their own ribosomes and DNA, which is the basis of the endosymbiotic theory o The space between the double membranes is cis called the intermembrane space Vesicles trans o The two membranes of the mitochondria allow vacoules it perform functions for cellular respiration: lysosomes 1, Outer Membrane peroxisome Smooth continuous boundary that Image 2.5 Micrograph of Golgi Body encapsulates all the contents of the Source: https://www.thinglink.com/scene/ 698921523674611713 mitochondria Lysosomes 2. Inner Membrane o Free floating organelles that contain enzymes Has intricately folded structures that dismantle and recycle food particles, called cristae where enzymes responsible captured bacteria, worn-out organelles, and for cellular respiration are located. The debris number of cristae is proportional to the o The enzymes, known as lysozyme, originates energy requirements of the cell In between from the RER, is recognized, refined, and these folds is the mitochondrial matrix 02 Handout 2 *Property of STI  [email protected] Page 8 of 13  SH1909 This region also contains DNA and ribosomes for the genetic function of the mitochondria o Mitochondria are the sites of energy production where adenosine triphosphate (ATP), the cell’s source of chemical energy, is synthesized o The process of converting energy-rich molecules (e.g. pyruvate) is known as the Kreb’s Cycle which makes use of pyruvate oxidation and produces carbon dioxide as a waste product Image 2.7 Micrograph of Mitochondria o Mitochondria are considered semi-autonomous Source: https://www.thestudentroom.co.uk/show organelles because they can grow and divide thread.php?t=1422067 on their own Plastids o A group of large organelles only found in plant cells and not animal cells. Can be divided into 3 groups: 1. Chloroplasts Green colored plastids due to the green pigments: chlorophyll a and bChloroplasts are the sites of energy production in plants because this is where photosynthesis occurs. This process makes use of solar energy and transforms Image 2.6 Diagram of Mitochondria Source: https://biology.tutorvista.com/animal-and-plant- it into energy-rich molecules cells/mitochondria.html Chloroplasts are parallel to mitochondrion due to their double membrane features and the presence of their own DNA. It has other specialized structures such as: a. Outer Membrane b. Inner Membrane c. Thylakoid 02 Handout 2 *Property of STI  [email protected] Page 9 of 13  SH1909 The third membrane system folded 3. Leucoplasts into flattened sacs. Photosynthetic Non-colored plastids that do not pigments such as chlorophyll a and b are contain pigments. They function mainly as found here, which is why this is where light- storage for nutrients dependent reactions occur here Starch filled leucoplasts are called The thylakoid membrane Amyloplasts. Those that store oil are called separates the stroma and the grana Elaioplsts, and those that store proteins are called Aleuroplasts d. Granum Stacks of thylakoids that increase the surface area for the attachment of chlorophyll Each chloroplast has around 50 grana, and each granum is made of around 50 thylakoids Each granum is connected to the other by an intergranal lamellae Image 2.8 Micrograph of Chloroplast S: Stroma, EM: Envelope Membrane, GT: Granular Thylakoid, e. Stroma ST: Stroma thylakoid Source: https://www.researchgate.net/figure/Thin-section- An enzyme-rich gel-like matrix electron-micrograph-of-a-young-tobacco-chloroplast-Two- found inside the chloroplast. It contains envelope-membranes_fig2_7536996 DNA, ribosomes, photosynthetic enzymes, lipid droplets, and starch. This is where light-independent reactions occur via the enzymes present V. ORGANELLES FOR STRUCTURAL 2. Chromoplasts SUPPORT, MOVEMENT, AND Colored plastids rich in pigments COMMUNICATION BETWEEN CELLS such as carotenoids instead of chlorophyll Cytoskeleton which give fruits, flowers, and leaves their o A flexible network of protein threads and fibers orange, yellow, and red colors that provide mechanical and structural Chromoplasts can arise from framework of support throughout the cell. chloroplasts that have lost their chlorophyll Additionally, it helps in directing cell movement, (i.e. ripening of fruits) transport, and responses o There are three (3) major protein components of the cytoskeleton: 02 Handout 2 *Property of STI  [email protected] Page 10 of 13  SH1909 1. Microtubule o Centrosome division is crucial in preceding and The thickest and longest filament stimulating cell division: composed of tubulin assembled into hollow 1. Division of Centriole tubes that can rapidly add or remove tubulin Each centriole will divide into two molecules (2), and each of the two (2) pairs will move It can function as a trackway where into opposite poles of the cell specialized proteins use it as a path to carry cargo such as vesicles 2. Formation of asters and spindle fibers From the pair of centrioles, asters 2. Intermediate Filament will form and will be the source of a system Smaller than microtubules and of microtubules called spindle fibers where appears ropelike. Provides the cell tensile chromosomes can attach and be pulled strength, thus allowing it to stretch without toward the respective poles. Plant cells do breaking. It is composed of multiple protein not form asters when dividing subunits Centrioles can also divide to form basal bodies where cilia and flagella are 3. Microfilament formed: The thinnest filament composed of actin which is present in nearly all cell types a. Cilia of eukaryotes. It can provide strength to Both cilia and flagella have a 9+2 resist stretching, compression, and assists pattern regarding the microtubules that in anchorage compose them Actin filaments are especially Short, numerous extensions that notable in muscle cells, where it works move in a coordinated to propel the cell together with myosin to produce muscle contractions b. Flagella Longer extensions which occur Centrosomes and Centrioles singly or in pairs. Movement is done by o A small dense region in the cytoplasm where means of a propeller motion. microtubules are assembled and arranged, thus termed the Microtubule Organizing Center (MTOC) o Inside the centrosome are two hollow cylinders made of filaments (which are microtubule triplets) called the centriole o The centriole is composed of 9 filaments arranged in a circular pattern 02 Handout 2 *Property of STI  [email protected] Page 11 of 13  SH1909 Cell Surface and Junctions o Cells are joined to each other by structures A called junctions. In plants, the plasma B membrane and cytoplasmic fluid extend specialized structures between cells called C plasmodesmata to communicate and pass D molecules effectively o Animal cells have different types of junctions E depending on their location and function: F 1. Tight Junctions Fuses cells together to form an G H impassable barrier using actin fibers attaching to membrane-anchored Image 2.9 Micrograph of Animal Cell proteins, forming cell sheets A: Plasma membrane, B: Golgi body, C: Centrosome, D: Important in controlling Mitochondria, E: Lysosome, F: Nucleus, G: Endoplasmic Reticulum, H: Cytoplasm biochemical movement (e.g. stomach Source: https://quizlet.com/219495003/aice-biology-chapter-1- animal-cell-electron-micrograph-labeling-diagram/ fluids should not seep into the surrounding tissue) 2. Adhesion Junctions Connects two (2) neighboring cells References together or a cell to the extracellular References matrix. Acts like screws using Hofnagels, M. (2016). General Biology Books I and cytoskeletal fibers to form strong II. Quezon City: McGraw-Hill Education. Morales-Ramos, A., & Ramos, J. A. (2017). sheets with spaces between them Exploring Life Through Science: General Biology 1. Quezon City: Phoenix Publishing House, Inc. 3. Gap Junctions Similar to plasmodesmata, wherein a channel protein links with the cytoplasm of an adjacent cell to allow exchange of ions and nutrients 02 Handout 2 *Property of STI  [email protected] Page 12 of 13  SH1909 DEFINITIONS BOX Cell membrane DNA Cytoplasm RNA Cytosol Genes Ribosomes Histones Prokaryote Ribosomal subunits Eukaryote Secretory protein Electron transport system Glycoprotein Compartmentalization Transitional ER Organelles Transport vesicles Hydrophilic Enzymes Hydrophobic Hormones Phospholipids rRNA Fluid Mosaic Model Endosymbiotic Theory Chlorophyll Photosynthesis Krebs Cycle Tubulin Actin and Myosin Centrosomes Centrioles Cilia Flagella Asters and Spindle Fibers 02 Handout 2 *Property of STI  [email protected] Page 13 of 13