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Living Organisms Living systems are separated from other chemical systems by; • The capacity for replication; • The presence of enzymes and other complex molecules; • A membrane that separates the internal chemicals from the external chemical environment. Terms applied to cells • Heterotrophs (other-feeder): an organism that obtains its energy from another organism. Animals, fungi, bacteria, and many protistans are heterotrophs. • Autotrophs (self-feeder): an organism that makes its own food, it converts energy from an inorganic source in one of two ways • Photosynthesis is the conversion of sunlight energy into C-C covalent bonds of a carbohydrates. This led to the oxidative metabolism • Chemosynthesis is the capture of energy released by certain inorganic chemical reactions. Time scale of Evolution • Life emerged at least 3.8 billion years ago. • Simple organic molecules could form and spontaneously polymerize into macromolecules. • No free oxygen but consists CO2 and N2.. Also small amount of H2, H2S and CO. • RNA world-self replicating RNA molecules. Evolution of cells From the Cell, A Molecular Approach 2nd edition; Cooper; ASM Press & Snauer 4.2 Cell sizes vary with their function • Below is a list of the most common units of length biologists use (metric) Table 4.2 • Cell size and shape relate to function Figure 4.2 Why cell size vary? • Smallest cells: – Mycoplasmas; they have the smallest genome • Bulkiest cells: – Bird eggs, young need a lot of food • Longest cells: – Nerve cells, can transmit signals over long ranges What limits cell size? • Lower limits – What does the cell need to contain? • Must house DNA, proteins, and organelles (in eukaryotes). • Upper limits – It must have enough surface area, why? • Must be able to obtain enough nutrients from the environment. Prokaryotic Cells • Archaebacteria • Eubacteria • They have plasma membrane • They have nucleoid • They have cytoplasm with ribosomes Prokaryote (pro=before, karyo=nucleus) From Life: The Science of Biology, 4th Edition Sinauer & WH Freeman Prokaryotic cells • • • • Very diverse in their metabolic capabilities. Some archae are found in hot springs Some of them are photosynthetic. Some are able to oxidize inorganic ions to obtain energy • prokaryotes are asexual, meaning their offspring nearly always bear the exact characterisics of the parent cell. Division is by binary fission. Prokaryotic cells • Prokaryotic DNA is organized as a circular chromosome. • DNA is supercoiled • Most of DNA is protein coding Prokaryotes • In Greek pro means before and karyon refers to nucleus. • Nucleoid(=nucleus like), coiled DNA of a prokaryote. • No organelles in prokaryotes. • Ribosomes (that assemble amino acids) are free in cytoplasm. • Cell membrane surrounds the cell; cell wall protects the cell. In some, there is a sticky coat called a capsule (works like a glu). • Pili and flagella are for attachment and movement. Procaryote sizes and structures From Molecular Biology of the Cell Third edition; Alberts; Garland Schematic diagram of a typical prokaryotic cell. Specialized features of some prokaryotes-1 • Cell wall: Outside the PM. Supports the cell and determines the shape. • It contains peptidoglycan. • It is not a barrier and some toxins can cause disease From Life: The Science of Biology, 4th Edition Sinauer & WH Freeman Specialized features of some prokaryotes-2 • Capsule: • It encloses cell wall and outer membrane. • It may protect from WBC • It is not necessary for living Specialized features of some prokaryotes-3 • Mesosome: • It is formed by infolding of the PM • It may aid the movement in & out of the cell of materials. It may also aid the replication of DNA and cell division. Specialized features of some prokaryotes-4 • Flagella • Bacterium moves with its help • It is anchored to the PM and cell wall Specialized features of some prokaryotes-5 • Pili • projected from the surface • helps to adhere to another bacteria • shorter than flagella From the Cell, A Molecular Approach 2nd edition; Cooper; ASM Press & Snauer Structures of animal cells From the Cell, A Molecular Approach 2nd edition; Cooper; ASM Press & Snauer Eukaryotic Cells: • Plasma membrane: to define its boundary and retain its content • Membranous subcompartments (organelles): various cellular functions are localized • Nucleus: to house the DNA • Cytoplasm: • Plant cells also have a cell wall outside the PM • Animal cells are usually surrounded by an extracellular matrix. Membranes in eukaryotic cells • It consists of phospholipids and proteins organized into two layers (Phospholipid bilayer) • It has a polar (hydrophilic) head and two nonpolar (hydrophobic) tails. Diagram of a phospholipid bilayer From: Life 4th Edition, by Sinauer Associates MEMBRANE STRUCTURE AND FUNCTION 5.10 Membranes organize the chemical activities of cells • Membranes organize the chemical reactions making up metabolism Cytoplasm Figure 5.10 Biological membranes: • To regulate molecular traffic from one side to another • To restrict the passage of materials, especially polar ones, since its hydrophobicity of its interior. • To allow interactions amongst the cells. (i.e. recognition of WBC). • To provide energy (mitochondria and choloroplast) 5.11 Membrane phospholipids form a bilayer • Phospholipids are the main structural components of membranes • They each have a hydrophilic head and two hydrophobic tails Head Symbol Tails Figure 5.11A • In water, phospholipids form a stable bilayer – The heads face outward and the tails face inward Water Hydrophilic heads Hydrophobic tails Water Figure 5.11B • The plasma membrane of an animal cell Glycoprotein Carbohydrate (of glycoprotein) Fibers of the extracellular matrix Glycolipid Phospholipid Cholesterol Microfilaments of the cytoskeleton Figure 5.12 Proteins CYTOPLASM Biological membranes: From http://www.biosci.uga.edu/almanac/bio_103/notes/may_15.html. Structure of an animal cell From http://www.biosci.uga.edu/almanac/bio_103/notes/may_15.html. Nucleus • Nuclear envelope: Inner and outer nuclear membranes • Nuclear pores • Nucleolus From: Life 4th Edition, by Sinauer Associates Liver Cell Nucleus From: www.DennisKunkel.com Nuclear envelope and nuclear pores From: Life 4th Edition, by Sinauer Associates From: www.DennisKunkel.com Nucleus • Chromatin: DNA associated with proteins, forms long fibers. • Each fiber constitutes a chromosome. • Chromosomes condense during mitosis/meiosis. • Chromosomes are enclosed within a nuclear envelope, a double membrane with pores. • Nucleolus consists of parts of the chromatin DNA combined with RNA and proteins (components of ribosomes are made). Cytoplasm • Organelles • cytoskeleton: maintain the shape of the cell as well as anchoring organelles, moving the cell and controlling internal movement of structures • Microtubules • Actin • Intermediate filaments Many cell organelles are related through the endomembrane system • The endomembrane system is a collection of membranous organelles – These organelles manufacture and distribute cell products – The endomembrane system divides the cell into compartments – Endoplasmic reticulum (ER) is part of the endomembrane system Endomembrane System • Contains • Rough ER (makes membrane and proteins) • Smooth ER (makes lipids, destroys toxins, stores calcium • Golgi • Lysosomes • Vacuoles • Nuclear envelope Rough ER • Contains ribosomes. • It makes membrane when necessary. • Some proteins made by RE are inserted into the ER membrane. • Phospholipids are made by ER enzymes. • ER membrane enlarges. • Makes proteins secreted by the cell. – Secretory proteins, e.g., antibody, a defensive molecule. Ribosomes synthesize the proteins of the antibody, they are assembled in the ER. Short chains of sugars are linked (glycoprotein), are transported in the transport vesicle, that buds off. 4.8 Rough endoplasmic reticulum makes membrane and proteins • The rough ER manufactures membranes • Ribosomes on its surface produce proteins Transport vesicle buds off 4 Ribosome Sugar chain 1 Figure 4.8 Polypeptide 3 Secretory (glyco-) protein inside transport vesicle Glycoprotein 2 ROUGH ER Ribosomes From: Life 4th Edition, by Sinauer Associates From: www.DennisKunkel.com Smooth ER • Continuous with RE, and lack ribosomes. • It has enzymes within the membrane. • Synthesize lipids (fatty acids, phospholipids, steroids) depending on the type of the cell. • Regulate the amount of sugar released from liver cells into the bloodstream. • Other enzymes break drugs, detoxify. • SER increase by exposure to drugs and produce tolerance. Sometimes it can not distinguish between drugs, so tolerance to a wide range of drugs occurs. (Barbiturate, a sedative, may decrease the effectiveness of antibiotics. 4.9 Smooth endoplasmic reticulum has a variety of functions • Smooth ER synthesizes lipids • In some cells, it regulates carbohydrate metabolism and breaks down toxins and drugs SMOOTH ER ROUGH ER Nuclear envelope Ribosomes SMOOTH ER Figure 4.9 ROUGH ER Endoplasmic Reticulum From: Life 4th Edition, by Sinauer Associates From: www.DennisKunkel.com 4.10 The Golgi apparatus finishes, sorts, and ships cell products • The Golgi apparatus consists of stacks of membranous sacs – These receive and modify ER products, then send them on to other organelles or to the cell membrane Golgi Apparatus • Flattened sacs looking like a stack of pitabread. • Sacs are not interconnected. • A cell may contain a few or a lot of them, depending on its activity. • It serves as a molecular warehouse and finishing factory through modification of substances manufactured by ER. Golgi Apparatus • One side of the Golgi receives the molecule within the transport vesicle for modification. • It marks and sorts the molecules into different batches for different destinations. • Molecules move from sac to sac in transport vesicles (they are shipped). • At the shipping site, they are stored, the finished products are exported (to membrane, lysosome, etc.) Golgi Apparatus From: Life 4th Edition, by Sinauer Associates Golgi Apparatus From: www.DennisKunkel.com • The Golgi apparatus Golgi apparatus Golgi apparatus “Receiving” side of Golgi apparatus Transport vesicle from ER New vesicle forming “Shipping” side of Golgi apparatus Transport vesicle from the Golgi Figure 4.10 Lysosomes digest the cell’s food and wastes • Lysosomes are sacs of digestive enzymes budded off the Golgi LYSOSOME Nucleus Figure 4.11A Lysosomes • Is produced by the RER and Golgi. • Lysosome means breakdown body, so they contain digestive enzymes in a membrane. • RER puts the enzymes and membranes together, then Golgi chemically modifies them, and releases mature lysosomes. Lysosomes • Food vacuoles engulf nutrients, lysosomes fuse with the food vacuoles to digest them. Upon digestion, amino acids are released and reused. • Lysosomes destroy harmful bacteria, such that white blood cells ingest bacteria, later to be emptied into lysosome. • Recycling centers for damaged organelles. Lysosomes From: Life 4th Edition, by Sinauer Associates • Lysosomal enzymes – – – – digest food destroy bacteria recycle damaged organelles function in embryonic development in animals Rough ER Transport vesicle (containing inactive hydrolytic enzymes) Plasma membrane Golgi apparatus Engulfment of particle Lysosome engulfing damaged organelle “Food” LYSOSOMES Food vacuole Figure 4.11B Digestion Abnormal lysosomes can cause fatal diseases • Lysosomal storage diseases are hereditary – They interfere with other cellular functions – Examples: Pompe’s disease, Tay-Sachs disease Lysosomal Diseases • Lysosomal storage diseases in which a person lacks a hydrolytic enzyme of the lysosome. Lysosomes become fat with indigestable substances. • They are fatal in childhood. – Pompe’s disease, harmful amounts of glycogen accumulate in liver cells (lack lysosomal alpha glucosidase). – Tay-Sachs disease affects the nervous system because lysosomes lack a lipid digesting enzyme, nerve cells accumulate excessive lipid molecules. Vacuoles function in the general maintenance of the cell • Plant cells contain a large central vacuole – The vacuole has lysosomal and storage functions Central vacuole Nucleus Figure 4.13A Vacuoles • Different types • Food vacuoles work with lysosomes. • Plant cells have vacuoles that can serve as a large lysosome, absorbs water allowing cell to grow. • Pigment vacuoles in the petals of a flower. • Contractile vacuoles, wheels with spikes. Spikes collect water, and hubs expel it. • Protists may have contractile vacuoles – These pump out excess water Nucleus Contractile vacuoles Figure 4.13B A review of the endomembrane system • The various organelles of the endomembrane system are interconnected structurally and functionally Rough ER Transport vesicle from Golgi Transport vesicle from ER Plasma membrane Vacuole Nucleus Lysosome Smooth ER Nuclear envelope Golgi apparatus Figure 4.14 4.16 Mitochondria harvest chemical energy from food • Mitochondria carry out cellular respiration – This process uses the chemical energy in food to make ATP for cellular work Mitochondria • Mitochondria contain their own DNA (termed mDNA) • They function as the sites of energy release (following glycolysis in the cytoplasm) and ATP formation (by chemiosmosis). • Mitochondria are bounded by two membranes. The inner membrane folds into a series of cristae, which are the surfaces on which ATP is generated. Mitochondria From: Life 4th Edition, by Sinauer Associates From: www.DennisKunkel.com Chloroplasts convert solar energy to chemical energy • Chloroplasts are found in plants and some protists • Chloroplasts convert solar energy to chemical energy in sugars Chloroplast Stroma Inner and outer membranes Granum Figure 4.15 Intermembrane space Chloroplast • Photosynthesizing organelles of plants and protists. • Internal membranes partition the chloroplast into three major components. – Intermembrane space between outer and inner membranes. – Stroma and network of tubules, and interconnected hollow discs (grana). – The space inside the tubules and discs. Mitochondria • Convert energy from one chemical form to another, making ATP. • Two compartments – Intermembrane space, a liquid filled compartment. – In the intermembrane the mitochondrial matrix, in which cellular respiration takes place. • Highly folded, enzymes that make ATP are embedded, folds are called cristae (increase membrane surface area). MITOCHONDRION Outer membrane Intermembrane space Inner membrane Cristae Figure 4.16 Matrix • When the bond joining a phosphate group to the rest of an ATP molecule is broken by hydrolysis, the reaction supplies energy for cellular work Phosphate groups Adenine Hydrolysis Energy Ribose Adenosine triphosphate Adenosine diphosphate (ADP) Figure 5.4A Potential energy of molecules • How ATP powers cellular work Reactants Protein Products Work Figure 5.4B What happens to old, worn-out mitochondria? Mitochondrial numbers are controlled by autophagy. This is a process by which lysosomes are involved in controlling cell constituents. This Figure shows the process; it is taken from Fawcett, A Textbook of Histology, Chapman and Hall, 12th edition, 1994. THE CYTOSKELETON AND RELATED STRUCTURES • A network of protein fibers makes up the cytoskeleton Figure 4.17A • Microfilaments of actin enable cells to change shape and move • Intermediate filaments reinforce the cell and anchor certain organelles • Microtubules – give the cell rigidity – provide anchors for organelles – act as tracks for organelle movement Microfilaments (e.g., actin) • provides mechanical strength to the cell • links transmembrane proteins (e.g., cell surface receptors) to cytoplasmic proteins • Used in mitosis • interact with myosin ("thick") filaments in skeletal muscle fibers to provide the force of muscular contraction Intermediate filaments • These cytoplasmic fibers average 10 nm in diameter (and thus are "intermediate" in size between actin filaments (8 nm) and microtubules (25 nm). • Examples: – keratins are found in epithelial cells and also form hair and nails; – nuclear lamins form a meshwork that stabilizes the inner membrane of the nuclear envelope; Microtubules • Microtubules are straight, hollow cylinders have a diameter of about 25 nm • are variable in length but can grow 1000 times as long as they are thick • are built by the assembly of dimers of alpha tubulin and beta tubulin. • are found in both animal and plant cells Microtubule motors • There are two major groups of microtubule motors: – kinesins – dyneins cytoskeleton From: Life 4th Edition, by Sinauer Associates Actin subunit Tubulin subunit Fibrous subunits 25 nm 7 nm MICROFILAMENT Figure 4.17B 10 nm INTERMEDIATE FILAMENT MICROTUBULE Cytoskeleton • Meshwork of fine fibers for structural support and cell movement, and transmitting signals. – Microfilaments: made of actin (globular), a twisted double chain of actin molecules (change shape). – Intermediate filaments: fibrous proteins with a ropelike structure, work for reinforcement and hold tension. – Microtubules: straight, hollow tubes composed of tubulins, elongate by adding subunits of tubulin pairs, disassembled. Cilia and flagella move when microtubules bend • Eukaryotic cilia and flagella are locomotor appendages that protrude from certain cells • A cilia or flagellum is composed of a core of microtubules wrapped in an extension of the plasma membrane Cilia and Flagella • Used for locomotion. • Core of microtubules wrapped in an extension of the plasma membrane. • A ring of nine microtubule doublets surrounds a central pair of microtubules. • Dynein arms (motors) bends the microtubules. FLAGELLUM Electron micrograph of sections: Outer microtubule doublet Plasma membrane Flagellum Central microtubules Outer microtubule doublet Plasma membrane Figure 4.18A Basal body Basal body (structurally identical to centriole) • Clusters of microtubules drive the whipping action of these organelles Microtubule doublet Dynein arm Figure 4.18B Sliding force EUKARYOTIC CELL SURFACES AND JUNCTIONS • Cells interact with their environments and each other via their surfaces • Plant cells are supported by rigid cell walls made largely of cellulose – They connect by plasmodesmata, channels that allow them to share water, food, and chemical messages Walls of two adjacent plant cells Vacuole PLASMODESMATA Layers of one plant cell wall Cytoplasm Plasma membrane Figure 4.19A • Animal cells are embedded in an extracellular matrix – It is a sticky layer of glycoproteins – It binds cells together in tissues – It can also have protective and supportive functions • Tight junctions can bind cells together into leakproof sheets • Anchoring junctions link animal cells • Communicating junctions allow substances to flow from cell to cell TIGHT JUNCTION ANCHORING JUNCTION COMMUNICATING JUNCTION Plasma membranes of adjacent cells Figure 4.19B Extracellular matrix Epithelial cells • Epithelia are sheets of cells that provide the interface between masses of cells and a cavity or space (a lumen). • The portion of the cell exposed to the lumen is called its apical surface. • The rest of the cell (i.e., its sides and base) make up the basolateral surface. Tight Junctions • They seal epithelial cells • They prevent the passage of molecules and ions through the space between cells. • They block the movement of integral membrane proteins (red and green ovals) between the apical and basolateral surfaces of the cell. Human Lung Epithelia • The epithelial cells of the human lung express a growth stimulant, called heregulin, on their apical surface and heregulin receptors, called erbB, on the basolateral surface. • As long as the sheet of cells is intact, there is no stimulation of erbB by heregulin thanks to the seal provided by tight junctions. • However, if the sheet of cells becomes broken, heregulin can reach its receptors. The result is an autocrine stimulation of mitosis leading to healing of the wound. Anchoring (Adherence) junctions • provide strong mechanical attachments between adjacent cells. – They hold cardiac muscle cells tightly together as the heart expands and contracts. Adherence junctions • They are built from: – cadherins — transmembrane proteins (shown in red) whose extracellular segments bind to each other and whose intracellular segments bind to catenins (yellow). Catenins are connected to actin filaments Gap Junctions • are intercellular channels some 1.5 - 2 nm in diameter. These permit the free passage between the cells of ions and small molecules (up to a molecular weight of about 1000 daltons). • They are constructed from 4 (sometimes 6) copies of one of a family of a transmembrane proteins called connexins. Desmosomes • Desmosomes are localized patches that hold two cells tightly together. They are common in epithelia (e.g., the skin). Desmosomes are attached to intermediate filaments of keratin in the cytoplasm. 4.20 Eukaryotic organelles comprise four functional categories • Eukaryotic organelles fall into four functional groups Table 4.20 Table 4.20 (continued)