Chapter 4: Inside the Cell PDF

1 Chapter 4: Inside the Cell 2 Outline: Cells Under the Microscope The Plasma Membrane The Two Main Types of Cells Objectives: Recognize the key components of the cell plasma membrane. Distinguish among the types of membrane proteins by function. Identify the characteristics common to all cells. Dis...

1 Chapter 4: Inside the Cell 2 Outline: Cells Under the Microscope The Plasma Membrane The Two Main Types of Cells Objectives: Recognize the key components of the cell plasma membrane. Distinguish among the types of membrane proteins by function. Identify the characteristics common to all cells. Distinguish between prokaryotic and eukaryotic cells. Identify the structures of a prokaryotic cell. Cells and the Cell Theory Cells are the smallest unit of organization that can perform all activities required for life The cell theory states that: o All living organisms are composed of one or more cells. o A cell is the basic structural and functional unit of living organisms. o All cells arise from pre-existing cells. https://www.dreamstime.com/cell-theory-evolution-pre-existing-cells-development-outline-diagram-celltheory-evolution-pre-existing-cells-image236890068 4 Cells Under the Microscope Cells are extremely diverse Each type in our body is specialized for a particular function. Nearly, all require a microscope to be seen. Light microscope Invented in the seventeenth century Electron microscope Invented in 1930s 5 Relative Sizes of Some Living Things and Their Components Biologists use microscopes and biochemistry to study cells Cells are usually too small to be seen by the naked eye It is helpful to understand how cells are studied Types of Microscopes Light microscopes (LMs) Light microscopes can magnify effectively to about 1,000 times the size of the actual specimen Too low to study organelles, the membrane-enclosed structures in eukaryotic cells Electron microscopes (EMs) are used to study subcellular structures magnification (up to 2 million times) Scanning electron microscopes (SEMs) Transmission electron microscopes (TEMs) Three important parameters of microscopy: Magnification, the ratio of an object’s image size to its real size Resolution, the measure of the clarity of the image, or the minimum distance of two distinguishable points Contrast, visible differences in brightness between parts of the sample 9 The Limit to Cell Size: Why are cells so small? Cell need surface areas large enough for entry and exit of materials Surface-area-to-volume ratio Small cells have more surface area for exchange. Adaptations to increase surface area Microvilli in the small intestine increase surface area for absorption of nutrients 10 Basic features of all cells: All cells have: A plasma membrane to regulate movement of material Cytoplasm where chemical reactions occur Contain ribosomes to make proteins Genetic material for growth and reproduction 1 Chapter 4: Inside the Cell Prokaryotes 1 Chapter 4: Inside the Cell 2 Outline Eukaryotic Cells Organelles and their functions Outside the Eukaryotic Cell Objectives Identify the general function of the organelles in a eukaryotic cell. State the components of the endomembrane system, and list their functions. Relate the specific components of the cytoskeleton to their diverse roles within the cell. 3 Tour of the Eukaryotic Cell 4 Structure of a Typical Animal Cell 5 Structure of a Typical Plant Cell ku.ac.ae Structure of a Typical Plant Cell 6 A Tour inside the Eukaryotic cell The main constituents of a eukaryotic cell: o Nucleus o Ribosomes (also found in prokaryotes) o Endomembrane system § Nuclear membrane § Endoplasmic reticulum § Golgi apparatus § Transport vesicles § lysosomes o Vacuoles o Energy-related organelles § Chloroplasts (in plants) § Mitochondria (in both plants and animals) o Cytoskeleton o Cilia and Flagella ku.ac.ae Nucleus Stores genetic information DNA organized into genes, which specify a polypeptide Relayed to ribosome using messenger RNA (mRNA) Nucleolus—region where RNA and ribosomal RNA (rRNA) are made Nuclear envelope has double membrane It permit passage in and out of the nucleus through the nuclear pores 8 The Nucleus: Information Central In the nucleus, DNA is organized into discrete units called chromosomes Each chromosome contains one DNA molecule associated with proteins, called chromatin Chromatin condenses to form discrete chromosomes as a cell prepares to divide 10 Ribosomes: Protein Factories Carry out protein synthesis in the cytoplasm Found in both prokaryotes and eukaryotes Ribosomes are composed of two subunits Receive mRNA as instructions sequence of amino acids in a polypeptide ku.ac.ae Ribosomes In eukaryotes ribosomes build proteins in two locations: oIn the cytosol (free ribosomes) oOn the outside of the endoplasmic reticulum or the nuclear envelope (bound ribosomes) 12 The Nucleus, Ribosomes, and Endoplasmic Reticulum (ER) 13 Endomembrane System 14 Endomembrane System Consists of nuclear envelope, membranes of endoplasmic reticulum, Golgi apparatus, and numerous vesicles Helps compartmentalize cell Restricts certain reactions to specific regions Transport vesicles: carry molecules from one part of the system to another. 15 Endomembrane System: Endoplasmic Reticulum Accounts for more than half of the total membrane in many eukaryotic cells. Physically continuous with outer membrane of nuclear envelope There are two distinct regions of ER: Rough ER Studded with ribosomes Modifies proteins Forms transport vesicles to Golgi apparatus Smooth ER Continuous with rough ER No ribosomes Synthesizes lipids (phospholipids and steroids Function depends on cell Produces testosterone, detoxifies drugs Endomembrane System: Golgi apparatus Stack of flattened saccules Transfer station Receives vesicles from ER Modifies molecules within the vesicles Sorts and repackages for new destination Some are lysosomes. Lysosomes Vesicles that digest molecules or portions of the cell Digestive enzymes 16 Lysosomes: Digestive Compartments A lysosome is a membranous sac of hydrolytic enzymes that can digest macromolecules or portions of the cell Lysosomal enzymes work best in the acidic environment inside the lysosome Hydrolytic enzymes and lysosomal membranes are made by rough ER and then transferred to the Golgi apparatus for further processing Tay-Sachs disease: lysosomes in nerve cells are missing an enzyme for a particular lipid molecule 18 Vacuoles Membranous sacs that are larger than vesicles Vacuoles perform a variety of functions in different kinds of cells: In plants: store nutrients, plant pigment and maintain water balance In Animal: They are very small in animal cells and store and keep away waste products 19 Energy-Related Organelles: Mitochondria Found in both plants and animals Usually only visible under an electron microscope Break down carbohydrates to produce adenosine triphosphate (ATP) Location of Cellular respiration—needs oxygen, produces carbon dioxide. ku.ac.ae Mitochondrion Structure Bounded by double membrane Inner membrane folds called cristae Increase surface area Inner membrane encloses matrix Mixture of enzymes assisting in carbohydrate breakdown Matrix also contains its own DNA and ribosomes.?? Access the text alternative for slide images. 20 21 Energy-Related Organelles: Chloroplasts Use solar energy to synthesize carbohydrates through the process of photosynthesis Found in plants and algae Chloroplasts have their own DNA and ribosomes?? Three-membrane system Double membrane enclosing stroma Thylakoids formed from third membrane stacked to form a granum Thylakoid membrane contains pigments that capture solar energy The Evolutionary Origins of Mitochondria and Chloroplasts Mitochondria and chloroplasts have similarities with bacteria Enveloped by a double membrane Contain free ribosomes and circular DNA molecules Grow and reproduce somewhat independently in cells These similarities led to the endosymbiont theory It suggests that an early ancestor of eukaryotes engulfed an oxygen-using nonphotosynthetic prokaryotic cell 23 The Cytoskeleton The Cytoskeleton is a network of interconnected protein filaments and tubules Extends from the nucleus to the plasma membrane extending throughout the cytoplasm It is only found in eukaryotes Maintains cell shape: It organizes the cellʼs structures and activities, anchoring many organelles 24 Components of the Cytoskeleton 1. Microtubules are : Hollow cylinders thickest of the three components of the cytoskeleton Help maintain cell shape and act as track for organelles and other materials to move 2. Intermediate filaments are: Ropelike assembly that run from nuclear envelope to plasma membrane (Intermediate in size) 25 Components of the Cytoskeleton 3. Microfilaments (Actin filaments): Two chains of monomers twisted in a helix Forms a dense web to support the cell are the thinnest components 26 The Cytoskeleton and Motor Proteins Motor proteins allow cell and organelles to move along tracks provided by the cytoskeleton. Myosin, kinesin, and dynein Instrumental in allowing cellular movements Myosin Interacts with actin Muscle contraction Kinesin and dynein Move along microtubules Transport vesicles from Golgi apparatus to final destination 27 Components of the Cytoskeleton- Centrioles The centrosome has a pair of centrioles, each with nine triplets of microtubules arranged in a ring Only found in animal cells; not present in plant cells In cell division, microtubules grow out from a centrosome near the nucleus 28 Cilia and Flagella For movement of the cell or fluids past the cell Similar construction in both Cilia shorter and more numerous than flagella 29 Outside the Eukaryotic Cell: Extracellular components Cell wall provides support in plants, Fungi and Protists cells Plant cell walls has: Primary cell walls Cellulose fibrils and noncellulose substances Wall stretches when cell is growing Secondary cell walls (some plant cells) Forms inside primary cell wall e,g Woody plants Lignin: complex organic polymers adds strength Plasmodesmata Plant cells connected by numerous channels that pass through cell walls 30 Exterior Cell Surfaces in Animals No cell wall Extracellular matrix (ECM) Is made up of glycoproteins such as collagen, proteoglycans, and fibronectin Matrix varies—flexible in cartilage, hard in bone 31 Cell Junctions: Neighboring cells in tissues, organs, or organ systems often adhere, interact, and communicate through direct physical contact Intercellular junctions help integrate cells into higher levels of structure and function. Junctions Between Cells of the Intestinal Wall 32 Adhesion Junctions Adhesion junctions between cells fasten cells together into strong sheets Internal cytoplasmic plaques joined by intercellular filaments Sturdy but flexible sheet of cells 33 Tight Junctions Tight junctions (anchoring junctions) Adjacent plasma proteins joined Impermeable barrier: preventing leakage of extracellular fluid 34 Gap Junctions Allow communication between two cells Adjacent plasma membrane channels joined provide cytoplasmic channels between adjacent cells Revision Questions Which structure is common to all three domains of life? a) b) c) d) e) nucleus endoplasmic reticulum mitochondria phospholipid bilayer cell membrane endocytotic vesicles Where are enzymes responsible for biosynthesis of membrane lipids located? a) b) c) d) e) endoplasmic reticulum nucleus lysosomes Golgi apparatus plasma membrane What is the correct order of the exocytosis or secretion pathway? a) b) c) d) e) rough ER, endosome, Golgi apparatus, smooth ER rough ER, Golgi apparatus, smooth ER, plasma membrane smooth ER, rough ER, exocytosis, Golgi apparatus rough ER, Golgi apparatus, transport vesicle, plasma membrane rough ER, Golgi apparatus, endosome, plasma membrane, transport vesicle Which image shows the best resolution? d) e) Which of the following correctly lists the objects in order from largest to smallest? a) b) c) d) human body, mitochondrion, lipid, frog egg frog egg, mitochondrion, lipid, human body human body, frog egg, mitochondrion, lipid mitochondrion, frog egg, lipid, human body What kind of cell would you be examining if you identified fimbriae? a) b) c) d) e) plant animal fungal bacterial All of the above are possible. If you were studying mutant cells and found that many proteins are going to the wrong compartments in these cells, where is the mutation having the greatest effect? a) b) c) d) e) nuclear envelope endoplasmic reticulum Golgi apparatus peroxisome mitochondrion 43 Thank You ku.ac.ae 2 Prokaryotes are single-celled organisms that make up domains Bacteria and Archaea Nucleoid Ribosomes Plasma membrane Bacterial chromosome Cell wall Capsule 0.5 µm (a) A typical rod-shaped bacterium (b) A thin section through the bacterium Bacillus coagulans (TEM) 3 Prokaryotic Cells Generally smaller and simpler in structure than eukaryotic cells Allows them to reproduce very quickly and effectively Extremely successful group of organisms Bacteria Well known because some cause disease Others have roles in the environment Some are used to manufacture chemicals, food, drugs, and so on. ku.ac.ae Adapted to diverse and extreme environments, they are the most abundant organisms on Earth Halophiles—require high salt concentrations to grow Thermoacidophiles—extremely hot, acidic environments like hot springs and submarine thermal vents (80°C ) Why is this lake’s water pink? ku.ac.ae Archaea in the genus Halobacterium 6 The Prokaryotes The prokaryotic genome has less DNA than the eukaryotic genome Most of the genome consists of a circular chromosome No nucleus—single circular chromosome found in nucleoid (region of cell) No membrane-bounded organelles Cytoplasm surrounded by plasma membrane and cell wall Sometimes a capsule—protective layer Cell wall maintains the shape of a cell Far greater metabolic capabilities than more complex organisms Structural and functional adaptations contribute to prokaryotic success 7 Prokaryotic Cell Structure Access the text alternative for slide images. 8 Origin of the First Cells First living cells were prokaryotes. Found in rocks 3.5 billion years old May have existed before that but no fossils found yet Conditions on early Earth very different from today. Temperatures high, little free oxygen Abiotic (without life) synthesis of organic molecules with input from energy sources Lightning, sunlight, meteorite impact, volcanic activity 9 Origin of the First Cells Protocells Cell-like structures complete with outer membrane. May have resulted from self-assembly of macromolecules Gave rise to cellular life Some researchers think the first hereditary molecule was RNA. Over time, the more stable DNA became the long-term solution. 10 Prokaryotes Bacteria Most diverse and prevalent organisms on Earth Tens of thousands of different bacteria identified Likely many more exist but not yet identified What are the 5 criterion to identify a bacteria ? 1. 2. 3. 4. 5. Shape Membrane Type Oxygen Needs Energy and Carbon Sources Nitrogen Metabolism 1. Shape Some form chains or bunches. Most are unicellular, but some species form colonies Most common three shapes—rods (bacilli), spheres (cocci), and spirals (spirilla or spirochetes) Most prokaryotic cells are 0.5–5 µm, much smaller than the 10–100 µm of many eukaryotic cells Plasmids—extrachromosomal DNA in some Bacteria have ribosomes but no membrane-bounded organelles. Motile bacteria generally have flagella but never cilia—not like eukaryotic flagella. 1. Shape Streptococci E. coli Treponema palladium 2. Membrane Type (Gram-Staining) Outer cell wall is strengthened by peptidoglycan. Prevents bursting or collapsing Some have additional capsule outside the cell wall Note: Archea don’t have peptidoglycan 2. Membrane Type (Gram-Staining) Eukaryote cell walls are made of cellulose or chitin Most bacterial cell walls instead contain peptidoglycan, a network of sugar polymers cross-linked by polypeptides Archaeal walls contain a variety of polysaccharides and proteins, but lack peptidoglycan 2. Membrane Type (Gram-Staining) Scientists use the Gram stain to classify bacteria by cell wall composition Gram-positive bacteria have simpler walls with a large amount of peptidoglycan The walls of gram-negative bacteria have less peptidoglycan and are more complex with an outer membrane that contains lipopolysaccharides 3. Oxygen Needs Obligate aerobes : must use oxygen Obligate anaerobe: are poisoned by oxygen, uses fermentation or anaerobic respiration Facultative anaerobe: uses oxygen when available and fermentation or anaerobic respiration if not 4-Bacterial Nutrition Autotrophs require CO2 as a carbon source (e.g. plants) Heterotrophs require an organic nutrient to make organic compounds (e.g. animals) Phototrophs obtain energy from light (plants) Chemotrophs obtain energy from chemicals 19 4- Bacterial Nutrition (autotrophs) Photoautotrophs (Like plants) Cyanobacteria (Photosynthetic bacteria) Use solar energy and carbon dioxide to make food Chemoautotrophs Don’t use solar energy to reduce carbon dioxide Like deep sea vent bacteria living inside tube worms Chemoheterotrophs (Like animals) Most bacteria are chemoheterotrophs Take in organic molecules as a source of energy and carbon 5. Nitrogen Metabolism Nitrogen is essential for the production of amino acids and nucleic acids in all organisms Nitrogen fixation Plants are unable to fix atmospheric nitrogen (N₂ gas). Bacteria converts N₂ into a form that plants use ammonia (NH3) N2 N2 ATMOSPHERE SOIL Nitrogen-fixing bacteria Denitrifying bacteria H+ (from soil) NH3 NH4+ Ammonifying (ammonia) (ammonium) bacteria Organic material (humus) Nitrate and nitrogenous organic compounds exported in xylem to shoot system NH4+ Nitrifying bacteria NO3(nitrate) Root 21 Nitrogen fixation: Nodules of a Legume Mutualistic bacteria live inside root nodules. Appendeges in prokayotes: Fimbriae Stick to substrates Flagellum Motility Flagella—propulsion Fimbriae—attachment to surfaces Conjugation pili—DNA transfer Pilus To exchange DNA Internal Organization and DNA 1 µm 0.2 µm Lack of complex compartmentalization but specialized membranes (metabolic functions) Respiratory membrane Circular chromosome (nucleoid) Sometimes some small DNA molecules called plasmids DNA replication, transcription and Translation similar to eukaryotes (smaller ribosomes, protein complex involved …) Thylakoid membranes (a) Aerobic prokaryote (b) Photosynthetic prokaryote Chromosome Plasmids 1 µm Endospores Bacteria can produce a “sleeping” structure able to survive to harsh conditions Dehydrate and collapse inside three heavy spore coats Can survive harshest environments Survive for very long periods of time Coat Endospore 0.3 µm 25 Bacteria Reproduce Asexually Bacteria (and archaea) reproduce asexually by binary fission. Rapid reproduction, mutation, and genetic recombination promote genetic diversity in prokaryotes Key features of prokaryotic reproduction: 1. They are small 2. They reproduce by binary fission (every 1–3 hours) 3. They have short generation times https://simple.wikipedia.org/wiki/Binary_fission Genetic recombination Genetic diversity is due to Genetic recombination through three processes. Transformation: taking up and incorporating foreign DNA from the surrounding environment. Transduction: the movement of genes between bacteria by phages (from “bacteriophages,” viruses that infect bacteria) Conjugation: the process where genetic material is transferred between prokaryotic cells Genetic recombination Transformation Transduction Conjugation Phage 1 µm A+ B+ Donor cell Sex pilus A+ B+ A+ Recombination A+ A- B- A+ B- Recipient cell Recombinant cell 29 Prokaryotes play crucial roles in the biosphere Why prokaryotes are important ? Primary producers (base of food chain) Frees oxygen from carbon dioxide Chemoheterotrophic prokaryotes function as decomposers, digest dead organic remains to return inorganic nutrients to producers. Life would halt without decomposers Prokaryotes can increase the availability of nitrogen, phosphorus, and potassium for plant growth Prokaryotes are the principal agents in bioremediation, the use of organisms to remove pollutants from the environment Ecological interactions of Prokaryotes Symbiosis is an ecological relationship in which two species live in close contact: a larger host and smaller symbiont - Mutualism, both symbiotic organisms benefit - Commensalism, one organism benefits while neither harming nor helping the other in any significant way - Parasitism, an organism called a parasite harms but does not kill its host Parasites that cause disease are called pathogens Prokaryotes have both beneficial and harmful impacts on humans Some prokaryotes are human pathogens, but many others have positive interactions with humans Beneficial bacteria Bacteria that break down food that is undigested by our intestines Pathogenic bacteria Bacteria cause about half of all human diseases e.g more than 1.5 million people die each year of tuberculosis (Mycobacterium tuberculosis) Salmonella Cholera … Bacteria in Food Science and Biotechnology Wide variety of foods use bacteria. Fermentation produces lactic acid. Pickles cucumbers, curdles milk into cheese, and gives tangy flavor Experiments using prokaryotes have led to important advances in DNA technology For example, E. coli is used in gene (to produce vitamins, antibiotics, and hormones) Insulin, human growth hormone, and vaccines Most antibiotics are discovered in soil bacteria. 34 Applications using bacteria Bacteria can also be used in bioremediation, the use of organisms to remove pollutants from the environment Ability of bacteria to break down pollutants is exploited Some bioengineered Damage from human impact can be lessened if conditions are right (nutrients, such as nitrogen and phosphates). (example Deep Water Horizon spill). 35 Bacterial Diseases in Humans Pathogens are able to produce a toxin and/or adhere to surfaces and sometimes invade organs or cells. Toxins are small organic molecules or pieces of bacteria released when bacteria die. Often, toxins cause more problems than the growth of the microbe itself. Clostridium tetani causes tetanus (lock jaw). Antibiotics generally either inhibit protein synthesis or inhibit cell wall production. Thank You ku.ac.ae 11 The Plasma Membrane Marks boundary between outside and inside of a cell Is a selective barrier that allows sufficient passage of oxygen, nutrients, and waste to service the volume of every cell Phospholipid bilayer with embedded proteins Polar heads (hydrophilic) of phospholipids face into watery medium Nonpolar tails (hydrophobic) face each other The structure of the plasma membrane is also known as the Fluid mosaic model 12 A Model of the Plasma Membrane: Fluid mosaic model ku.ac.ae Membrane Protein Diversity a. Channel proteins :Form tunnel for specific molecules b. Transport proteins: Involved in passage of molecules through the membrane, sometimes requiring input of energy c. Cell recognition proteins: Enable our body to distinguish between our own cells and cells of other organisms d. Receptor proteins: Allow signal molecules to bind, causing a cellular response e. Enzymatic proteins: participate in metabolic reactions f. Junction proteins:Form junctions between cells and Cell-to-cell adhesion and communication 13 Basic Features of all cells: Cytoplasm, Ribosomes and Genetic material Cytoplasm: is the gelatinous liquid that fills the inside of a cell. o composed of water (80%), salts, and various organic molecules. o Medium for chemical reactions within the cell cytoplasm Ribosome is an intercellular structure made of both RNA and protein Ribosome o the site of protein synthesis in the cell Genetic material is the hereditary substance in the cell. o carries all information specific to an organism. DNA 15 There are Two Main Types of Cells Two main types of cells based on organization of genetic material Prokaryotic cells—lack membrane-bounded nucleus Eukaryotic cells—have nucleus housing DNA 16 A Prokaryotic Cell 17 Eukaryotic cell: Typical Animal Cell The Two Main Cell Types Prokaryotes Eukaryotes Small (~5µm) Simple Relatively Large (~40µm) No Nucleus 70s ribosomes Circular DNA in cytoplasm One “un-true” chromosome Unicellular organisms No membrane-bound organelles Cell division by binary fission Plasma Membrane Cytoplasm Ribosomes Genetic material Relatively complex Nucleus present 80s ribosomes DNA packed inside the nucleus More than one chromosome Usually multicellular (some are unicellular) Membrane bound organelles are present Somatic cell division by mitosis, germ cell division by meiosis The Two Main Cell Types Only organisms of the domains Bacteria and Archaea consist of prokaryotic cells Protists, fungi, animals, and plants all consist of eukaryotic cells Thank You ku.ac.ae