General Biology Bio 110 - Chapter 4 PDF

General Biology Bio 110 Chapter 4  CONTENTS Part 1 Life on Earth: An Overview Chapter 1 PART II Chemistry of Life a. Basic Chemistry Chapter 2 b. Chemistry of Organic Molecules...

General Biology Bio 110 Chapter 4  CONTENTS Part 1 Life on Earth: An Overview Chapter 1 PART II Chemistry of Life a. Basic Chemistry Chapter 2 b. Chemistry of Organic Molecules Chapter 3 PART III The Cell a. Cell Structure and Function Chapter 4 b. Membrane Structure and Function Chapter 5  Part IIIa THE CELL a. Cell Structure and Function  4.1 Cellular Level of Organization a. Cell Theory: Organisms are composed of cells. Cells are the basic units of structure and function in organisms. Cells come only from pre-existing cells because cells are self- reproducing. b. Cell Shape: Cells are quite small; mostly less than 1 mm; some are even as small as 1 μm. Figure 4.1 outlines the visual range of the eye, light microscope and electron microscope Figure 4.1 The sizes of living things and their components. b. Cell Shape (cont.): I. Why are Cells so Small ? Small cells are likely to have an adequate surface area for exchanging wastes for nutrients. For example, cutting a large cube into smaller cubes provides a lot more surface area per volume. The calculations show that a 4-cm cube has a surface-area-to- volume ratio of only 1.5:1, whereas a 1-cm cube has a ratio of 6:1 (Figure 4.2). Figure 4.2 Surface-area-to-volume relationships.  Part IIIa 4.2 Prokaryotic Cells  4.2 Prokaryotic Cells Fundamentally, two different types of cells exist: Prokaryotic cells: are so named because they lack a membrane- bound nucleus. They present in great numbers in the air and soil and live in and on other organisms. Eukaryotic cell: cell with a nucleus. Based on DNA and RNA base sequences, prokaryotic cells (Figure 4.3) are divided into two separate types or domains called Bacteria and Archaea. Bacteria are well known because they cause some serious diseases, such as tuberculosis and decompose the remains of dead organisms and, hence, contribute to ecological cycles. Bacteria also assist humans in manufacturing all sorts of products, from industrial chemicals to foodstuffs and drugs (ex., human insulin). Figure 4.3 Prokaryotic cell. 4.2 Prokaryotic cells: a. The Structure of Prokaryotes Prokaryotes are quite small; size is 1.1–1.5 μm wide and 2.0–6.0 μm long. The three common shapes are: A rod-shaped bacterium called a bacillus, occur as pairs or chains. Spherical-shaped bacterium is a coccus, occur as pairs. Bacteria shapes. Some long rods are twisted into spirals. Spirillum (long rod) if it is rigid or spirochete if it is flexible. b. Organization of Bacteria: 1. Cell Envelope : I. Plasma membrane, a phospholipid bilayer with embedded proteins with important function of regulating the entrance/exit of substances into/out of the cytoplasm. II. Cell wall, to maintain cell’s shape. A plant cell has cellulose, while peptidoglycan (amino disaccharide and peptide fragments) in bacterium. III. Glycocalyx A layer of polysaccharides lying outside the cell wall, sometimes called a capsule (See Figure 4.3). It aids against drying out and helps bacteria resist a host’s immune system and attach almost to any Figure 4.3 Prokaryotic cell. surface.  2. Cytoplasm: Cytoplasm is a semi-fluid solution composed of water and inorganic and organic molecules encased by a plasma membrane. DNA is found in a chromosome that coils up and is located in a region called the nucleoid. Many bacteria also have an extra- chromosomal piece of circular super-coiled DNA called a plasmid. Bacterial plasmid. Plasmids are routinely used in biotechnology laboratories as vectors to transport DNA into a bacterium. 2. Cytoplasm( continued) A bacterial cell contains thousands of protein-synthesizing ribosomes with RNA and protein in two subunits (large and small). Motile bacteria can move in water by the means of flagella (a protein) (see Figure 4.3). The number and location of flagella can be used to help distinguish Figure 4.3 Prokaryotic cell. different types of bacteria.  Part IIIa 4.3 Eukaryotic Cells  Eukaryotic cell Eukaryotic cell, also, has a plasma membrane to separates the contents of the cell from the environment and regulates the passage of molecules into/out of the cytoplasm. a. Origin of Eukaryotic Cell: While Figure 4.4 suggests that nucleus is evolved as a result of plasma membrane invagination, the endosymbiotic theory says that mitochondria and chloroplasts, the two energy-related organelles, arose when a large eukaryotic cell engulfed independent prokaryotes. This explains why they are bound by a double membrane and contain Figure 4.4 Origin of organelles by their own genetic material separate endosymbiosis. from that of the nucleus. b. Structure of Eukaryotic Cell: Figures 4.5 and 4.6 represent the generalized animal and plant cell. Some eukaryotic cells, notably plant cells, have a cell wall in addition to a plasma membrane. Cell wall contains cellulose fibrils and has a different composition from the bacterial cell wall. The compartments of a eukaryotic cell, typically called organelles, are membranous. The nucleus is an organelle that houses the genetic material within eukaryotic chromosomes. The nucleus communicates with ribosomes in the cytoplasm, while organelles of the endomembrane system—notably the endoplasmic reticulum and the Golgi apparatus—communicate with one another by means of transport vesicles. b. Structure of Eukaryotic Cell (continued): Communication with the energy-related organelles—mitochondria and chloroplasts—is less obvious. An animal cell has only mitochondria, while a plant cell has both mitochondria and chloroplasts. The cytoskeleton is composed of protein fibers that maintains the shape of the cell and assists in the movement of organelles. The protein fibers serve as tracks for the transport vesicles that take molecules from one organelle to another. Cells can become specialized by the presence or absence of particular organelles. The final result has been the complexity by which different tissues arrange in organs, each with a particular structure and function.  Animal Cell and Plant Cell Figure 4.5 animal cell. Figure 4.6 Plant cell anatomy...  Part III a 4.4 The Nucleus and Ribosomes  4.4 The Nucleus and Ribosomes The nucleus is essential to the life of a cell. It contains the genetic information passed from cell to cell and from generation to generation. The ribosomes use this information to carry out protein synthesis. a. The Nucleus: The nucleus appears as an oval structure located near the center of most eukaryotic cells (Figure 4.7). The nucleus contains chromatin; a network of strands that undergoes coiling into rod-like structures called Figure 4.7 Anatomy of the nucleus. chromosomes. 4.4 The Nucleus and Ribosomes a. The Nucleus: All the cells of an individual contain the same number of chromosomes and cell division ensures that daughter cells receive the same number of chromosomes (2n), except for the egg and sperm, which usually have half this number (n). The chromosomes are the carriers of genetic information containing DNA, protein and some RNA (ribonucleic acid). Genes, composed of DNA, are units of heredity located on the chromosomes. Figure 4.7 Anatomy of the nucleus.  4.4 The Nucleus and Ribosomes a. The Nucleus (cont.): The nucleus is separated from the cytoplasm by a double membrane known as the nuclear envelope with nuclear pores to permit the passage of mRNA out of the nucleus to the cytoplasm and the passage of proteins from the cytoplasm to the nucleus. Three types of RNA are produced in the nucleus: ribosomal RNA (rRNA), joins with proteins to form subunits of ribosomes. messenger RNA (mRNA), specifies the sequence of amino acids in a protein. transfer RNA (tRNA), participates in the assembly of amino acids during protein synthesis. 4.4 The Nucleus and Ribosomes b. Ribosomes: Ribosomes are particles where protein synthesis occurs. They are composed of two subunits, one large and one small; represent a mix of proteins and rRNA. In eukaryotic cells, some ribosomes occur freely within the cytoplasm, either singly or in groups called polyribosomes and others are attached to the endoplasmic reticulum (ER). Ribosomes receive mRNA from the nucleus and this mRNA represents the genetic code indicating the needed sequence of amino acids in a particular protein  Part III a 4.5 The Endomembrane System  The Endomembrane System a. Endoplasmic Reticulum: The endoplasmic reticulum (ER) is membranous flattened small sacs physically continuous with the nuclear envelope (Figure 4.8). ER consists of rough ER and smooth ER forming vesicles that transport molecules to other parts of the cell, ex., the Golgi apparatus. Rough ER contains ribosomes, hence, has the capacity to produce proteins. Figure 4.8 Endoplasmic reticulum (ER). The Endomembrane System( cont.) Rough ER contains enzymes that can add carbohydrate (sugar) chains to proteins, eg., glycoproteins. Smooth ER is associated with the production of lipids and testosterone and with the detoxification of drugs. Figure 4.8 Endoplasmic reticulum (ER). The Endomembrane System( cont.) b. The Golgi Apparatus: The Golgi apparatus consists of a stack of three to twenty curved, flattened membranes (Figure 4.9). It contains enzymes that change one sugar for the other. It can modify the carbohydrate chains first attached to proteins in the rough ER to a signal molecule that determines the protein’s final destination in the cell. It, also, sorts the modified molecules and packages them into vesicles that depart from the outer face; secretion or exocytosis Figure 4.9 Golgi apparatus.  The Endomembrane System( cont.) c. Lysosomes: Lysosomes are membrane-bounded vesicles produced by the Golgi apparatus. They store powerful digestive enzymes to assist in digesting material taken into the cell and destroy nonfunctional organelles and portions of cytoplasm (Figure 4.10). Some white blood cells defend the body by engulfing bacteria that are enclosed within vacuoles. When lysosomes fuse with these vacuoles, the bacteria are digested. Figure 4.10 Lysosomes.  Part IIIa 4.6 The Energy-Related Organelles The Energy-Related Organelles: Chloroplasts and mitochondria are the two eukaryotic (plant and algae) membranous organelles that specialize in converting energy to a form that can be used by the cell. During photosynthesis, chloroplasts, use solar energy through photosynthesis to synthesize carbohydrates; an organic nutrient molecule for plants and all living things, by this equation: solar energy + carbon dioxide + water → carbohydrate + oxygen Cellular respiration is the process by which carbohydrates are broken down in mitochondria to produce ATP by this equation: carbohydrate + oxygen → carbon dioxide + water + energy The energy is used for active transport and energy-requiring processes in cells.  The Energy-Related Organelles a. Chloroplasts: Some algal cells have only one chloroplast, while some plant cells have as many as a hundred. Chloroplasts have a three-membrane system (Figure 4.11). They are bounded by a double membrane enclosing the semi-fluid stroma, which contains enzymes and thylakoids, disk-like sacs formed from a third chloroplast membrane Figure 4.11 Chloroplast structure. The Energy-Related Organelles a. Chloroplasts (cont.): Photosynthesis consists of two separate sets of reaction (Figure 4.12); the light reactions and the Calvin cycle reactions. Steps of light reactions are: solar energy is absorbed. water is split so that oxygen is released. ATP and NADPH are produced. Figure 4.12 The process of photosynthesis. The Energy-Related Organelles a. Chloroplasts (cont.): Steps of the Calvin cycle reactions are: CO2 is absorbed. CO2 is reduced to a carbohydrate (CH2O) by utilizing ATP and NADPH from the light reaction. Then, ADP and NADP+ go back to light reactions, where they become ATP and NADPH once more so that carbohydrate production can continue. Figure 4.12 The process of photosynthesis. - Figure 4.12.b The process of photosynthesis.  The Energy-Related Organelles b. Mitochondria: Nearly all eukaryotic cells contain mitochondria (Figure 4.13). The number of mitochondria varies in cells depending on their activities; liver cells have as many as 1000 mitochondria, while fat cells contain few mitochondria It has two membranes; the inner is highly twisted to increase the surface area into cristae that flew into a semi- fluid matrix. Figure 4.13 Mitochondrion structure. The Energy-Related Organelles: b. Mitochondria: The matrix contains mitochondrial DNA and ribosomes and a highly concentrated mixture of enzymes that break down carbohydrates and other nutrient molecules. Mitochondria produce most of the ATP utilized by the cell to supply the chemical energy through a process called cellular respiration (Figure 4.14). Figure 4.14 Cellular respiration.  The Energy-Related Organelles: b. Mitochondria( cont.) Respiration is the process by which cells acquire energy by breaking down nutrient molecules produced by photosynthesis through the use of oxygen (O2) and the breakdown of glucose to release carbon dioxide, water (H2O) and energy (enough to produce 36-38 ATP molecules). Figure 4.14 Cellular respiration.  The Energy-Related Organelles: b. Mitochondria (cont.) Cellular respiration involves four phases: 1. Glycolysis. 2. Preparatory reaction, 3. The citric acid cycle. 4. The electron transport chain. (Figure 4.15). Figure 4.15 Phases of glucose breakdown.  The Energy-Related Organelles: The four faces are the following: 1. Glycolysis takes place outside the mitochondria and does not require the presence of oxygen; anaerobic, while other phases take place inside the mitochondria, where oxygen is required, aerobic. Glycolysis; breakdown of glucose to two molecules of pyruvate. Oxidation results in NADH and provides energy for the net gain of two ATP molecules. Figure 4.15 Phases of glucose breakdown.  The Energy-Related Organelles:- 2. The preparatory (prep) reaction; where pyruvate is broken down to two acetyl groups and CO2 is released. Figure 4.15 Phases of glucose breakdown. The Energy-Related Organelles:- 3. The citric acid cycle; where oxidation occurs, NADH results, and more CO2 is released. The citric acid cycle is able to produce one ATP per turn. Because two acetyl groups enter the cycle per glucose molecule, the cycle turns twice Figure 4.15 Phases of glucose breakdown. The Energy-Related Organelles. 4. The electron transport chain (ETC); where NADH and energy are used to produce ATP. Figure 4.15 Phases of glucose breakdown.  - Figure 4.15 Phases of glucose breakdown.  The Energy-Related Organelles. c. Flow of Energy: The equation for photosynthesis in a chloroplast is opposite to that of cellular respiration in a mitochondrion (Figure 4.16). The ultimate source of energy for producing a carbohydrate in chloroplasts is the sun. Figure 4.16 Photosynthesis (chloroplast) versus cellular respiration (mitochondrion).  The Energy-Related Organelles. c. Flow of Energy: The ultimate goal of cellular respiration in a mitochondrion is the conversion of carbohydrate energy into that of ATP molecules. Therefore, there is a flow of energy through chloroplasts to carbohydrates and then through mitochondria to ATP molecules. Figure 4.16 Photosynthesis (chloroplast) versus cellular respiration (mitochondrion). The Energy-Related Organelles: d. Cycling of Chemicals: During cellular respiration, living things utilize carbohydrate and oxygen produced by chloroplasts during photosynthesis and the carbon dioxide produced by mitochondria return back to chloroplasts. Therefore, chloroplasts and mitochondria allow a flow of energy through living things and permit a cycling of chemicals.  Part III a 4.7 Other Vesicles and Vacuoles 4.7 Other Vesicles and Vacuoles a. Peroxisomes: Peroxisomes are membrane-bounded vesicles that found in the cytoplasm of virtually all eukaryote cells. Peroxisome owe their name to hydrogen peroxide generating and scavenging activates. Peroxisomes contain oxidative enzymes. Certain enzymes within peroxisome( by using molecular oxygen) remove hydrogen atoms from specific organic substrate( labeled as R) in an oxidative reaction, producing hydrogen peroxide (H2O2): RH2 + O2 → R + H2O2 Hydrogen peroxide, a toxic molecule, is immediately broken down to water and oxygen by another peroxisomal enzyme called catalase. In germinating seeds, peroxisomes oxidize fatty acids into molecules that can be converted to sugars needed by the growing plant. 4.7 Other Vesicles and Vacuoles b. Vacuoles: Vacuoles are membranous sacs specialized for storing excess water, substances and digestive enzymes for breaking down nutrients in the cell (Figure 4.17). Few animal cells contain vacuoles. Typically, plant cells have a large central vacuole that may take up to 90% of the volume of the cell. Plant vacuoles contain cell sap of water, sugars, salts, water- soluble pigments and toxic molecules. Figure 4.17 Plant vacuole. 4.7 Other Vesicles and Vacuoles b. Vacuoles: The pigments are responsible for many of the red, blue, or purple colors of flowers and some leaves. Toxic substances help protect a plant from herbivorous animals. A plant cell can rapidly increase in size by enlarging its vacuole. As organelles age and become nonfunctional, they fuse with the vacuole, where digestive enzymes break them down. This is a function carried out by lysosomes in animal cells. Figure 4.17 Plant vacuole. Thank you General Biology Bio 110 Chapter 5 Contents Part 1 Life on Earth: An Overview Chapter 1 PART II Chemistry of Life a. Basic Chemistry Chapter 2 b. Chemistry of Organic Molecules Chapter 3 PART III The Cell a. Cell Structure and Function Chapter 4 b. Membrane Structure and Function Chapter 5  Part III b THE CELL b. Plasma Membrane Structure and Function  5.1 Plasma Membrane Structure and Function Plasma membrane is a phospholipid bilayer (Figure 5.1) in which transmembrane protein molecules are either partially (peripheral) or wholly embedded (integral). A phospholipid is an amphipathic molecule; has both a hydrophilic (water- loving) region and a hydrophobic (water-fearing) region. The hydrophilic polar heads of the phospholipid molecules naturally face the outside and inside of the cell, where water is found. The hydrophobic non- polar tails face each other. Cholesterol is another lipid found in the animal plasma membrane; and steroids are found in the plasma membrane of plants. Figure 5.1 General structure of plasma membrane. 5.1 Plasma Membrane Structure and Function a. Fluid-Mosaic Model: The fluidity of the membrane is due to its lipid component. The latter prevents the membrane from solidifying as external temperatures drop. At higher temperatures, lipid makes the membrane less fluid. The mosaic nature of the plasma membrane is due to its protein content, which is able to move sideways in the membrane. b. Carbohydrate Chains: Both lipids and proteins can have attached carbohydrate (sugar) chains. If so, these molecules are called glycolipids and glycoproteins, respectively. In animal cells, the carbohydrate chains of proteins facilitate adhesion between cells, reception of signaling molecules and cell-to-cell recognition. In humans, carbohydrate chains are also the basis for the A, B and O blood groups. 5.1 Plasma Membrane Structure and Function c. Functions of the Proteins: Channel protein; allows hydrogen ions to flow across the inner mitochondrial membrane (Figure 5.2a). Carrier protein; transports sodium and potassium ions across the plasma membrane of a nerve cell (Figure 5.2b). Figure 5.2 Membrane protein diversity. 5.1 Plasma Membrane Structure and Function c. Functions of the Proteins (continued): Cell recognition protein; helps the body recognizes when it is being invaded by pathogens so that an immune response can occur (Figure 5.2c). Receptor protein; has a particular shape that allows a specific molecule to bind to it (Figure 5.2d) causing the protein to change its shape and initiate a response. Figure 5.2 Membrane protein diversity. 5.1 Plasma Membrane Structure and Function d. Permeability of the Plasma Membrane: Plasma membrane regulates the passage of molecules into/out of the cell. The plasma membrane can carry out this function because it is differentially (selectively) permeable; eg., certain substances can move across the membrane while others cannot (Figure 5.3). Small non-charged molecules, such as carbon dioxide, oxygen and alcohol, can freely cross the membrane. These molecules are said to follow their concentration gradient as they move from an area where their concentration is high to an area where their concentration is low. Figure 5.3 How molecules cross plasma membrane? 5.1 Plasma Membrane Structure and Function d. Permeability of the Plasma Membrane (continued): For example, carbon dioxide is produced when a cell carries on cellular respiration. Therefore, carbon dioxide is also following a concentration gradient when it moves from inside the cell to outside the cell. Water passively moves through a membrane channel protein called aquaporin; eg., accounts for why water can cross a membrane more quickly than expected. Ions and polar molecules, such as glucose and amino acids, can slowly cross a membrane. Therefore, they are often assisted across the plasma membrane by carrier proteins. Figure 5.3 How molecules cross plasma membrane?  Part III b 5.2 Types of Transport Across Cell Membrane Passive Transport: Passive transport is a diffusion across the plasma membrane with no energy investment. Passive transport could be : a. Simple diffusion: Diffusion net movement of a substance down its concentration gradient means from a high concentration region to a low concentration region. b. Osmosis: is the special form of diffusion of water across differentially ( selectively) permeable membrane due to concentration difference. c. Facilitated diffusion: Uses transport protein to move high to low concentration without the use of energy. Example: glucose or amino acids moving from blood into a cell 5.2 Passive Transport Across Membrane a. Diffusion: Diffusion is the movement of molecules from a higher to a lower concentration until equilibrium is achieved; distributed equally (Figure 5.4). Ex., when a crystal of dye is placed in water, the dye and water molecules move in various directions, but their net movement is toward the region of lower concentration. Figure 5.4 Diffusion process. 5.2 Passive Transport Across Membrane: a. Diffusion (continued): Eventually, the dye is dissolved in water, resulting in equilibrium and a colored solution. A solution contains a solute (the dye); usually a solid, and a solvent (water); usually a liquid. Figure 5.4 Diffusion process. 5.2 Passive Transport Across Membrane. b. Osmosis: Osmosis is the diffusion of water across a differentially (selectively) permeable membrane due to concentration difference. To illustrate this, a tube containing a 10% solute solution is covered at one end by a differentially permeable membrane and then placed in a beaker containing a 5% solute solution (Figure 5.5a). Figure 5.5 Osmosis process. 5.2 Passive Transport Across Membrane. b. Osmosis (continued): Diffusion always occurs from higher to lower concentration. Therefore, a net movement of water takes place across the membrane from the beaker to the inside of the thistle tube (Figure 5.5b). The solute does not diffuse out of the thistle tube because the membrane is not permeable to the solute. Figure 5.5 Osmosis process. 5.2 Passive Transport Across Membrane b. Osmosis (continued): As water enters and the solute does not exit, the level of the solution within the thistle tube rises (Figure 5.5c). In the end, the concentration of solute in the thistle tube is less than 10% and the concentration of solute in the beaker is greater than 5%. Figure 5.5 Osmosis process. 5.2 Passive Transport Across Membrane b. Osmosis (continued): Water enters the thistle tube due to the osmotic pressure of the solution within the thistle tube. In other words, water will diffuse in the direction of higher osmotic pressure. This explains why water is absorbed by the kidneys and taken up by capillaries in the tissues. Figure 5.5 Osmosis process. 5.2 Passive Transport Across Membrane Water balance between cells and their surrounding is crucial to organism: - Tonicity: is a term that describes the ability of a solution to cause a cell to gain or lose water. - Isotonic: indicates that the concentration of a solute is the same on both sides.( outside and inside the cell). - Hypotonic: indicates that the concentration of solute is higher inside the cell. - Hypertonic: indicates that the concentration of the solute is higher outside the cell. 5.2 Passive Transport Across Membrane 1. Isotonic Solution Solution where the solute and the water concentrations inside and outside the cell are equal 5.2 Passive Transport Across Membrane: 2. Hypotonic Solution Solution that causes cells to swell, or even to burst (cytolysis), due to intake of water due to the higher concentration of solute inside the cell. The swelling of a plant cell in a hypotonic solution creates turgor pressure and expansion of the cytoplasm because the vacuole gains water. Organisms that live in fresh water, ex., protozoans, have to prevent the uptake of too much water. Freshwater fishes have well-developed kidneys that excrete a large volume of diluted urine. Animal cell Plant cell 5.2 Passive Transport Across Membrane 3. Hypertonic Solution: Solution that causes cells to shrink due to loss of water (plasmolysis) from their vacuoles due to the higher concentration of solute outside the cell and water will leave the cell, Meats are sometimes preserved by salting them, but the bacteria are not killed by the salt but by the lack of facilitated water in the meat. Marine animals cope with their hypertonic environment in various ways: Sharks increase/decrease urea in their Animal blood until their blood is isotonic with the cell environment. Marine fishes drink large amount of water and excrete salts across their gills. Plant Have you ever seen a marine turtle cry? cell It is ridding its body of salt by means of glands near the eye. Hypotonic vs Hypertonic 5.2 Passive Transport Across Membrane : c. Facilitated Transport: Biologically useful molecules are able to enter and exit the cell at a rapid rate either by: Ways of a channel protein; water transport. Because of membrane carrier proteins; glucose and amino acids transport. These transport proteins are specific; each can transport with only a certain type of molecule or ion (Figure 5.6), Ex., glucose can cross the membrane hundreds of times faster than the other sugars. Figure 5.6 Facilitated transport. 5.2 Passive Transport Across Membrane: c. Facilitated Transport (continued): The carrier is believed to undergo a change in shape that moves the molecule across the membrane. Facilitated transport explains the rapid passage of water and other molecules across the plasma membrane. Neither diffusion nor facilitated transport requires an expenditure of energy because the molecules are moving down their concentration gradient in the same direction they tend to move anyway. Figure 5.6 Facilitated transport.  Part IIIb 5.3 Active Transport Across Membrane 5.3 Active Transport Across Membrane a. Active Transport: In active transport, molecules or ions move through the plasma membrane, exactly opposite to the process of diffusion. Both carrier proteins and an expenditure of energy are needed to transport molecules against the concentration gradient. In this case, chemical energy (ATP molecules usually) is required for the carrier to combine with the substance to be transported. Therefore, cells involved in active transport, such as kidney cells, have a large number of mitochondria near membranes where active transport is occurring. Proteins involved in active transport often are called pumps. 5.3 Active Transport Across Membrane a. Active Transport: One type of pump in animal cells, but is especially associated with nerve and muscle cells, moves sodium ions (Na+) to the outside of the cell and potassium ions (K+) to the inside of the cell; sodium-potassium pump (Figure 5.7). Figure 5.7 Sodium-potassium pump. , 5.3 Active Transport Across Membrane b. Bulk Transport: Because macromolecules (polypeptides or polysaccharides) are too large to be transported by carrier proteins, they are transported into and out of the cell by vesicle formation; membrane-assisted transport that requires an expenditure of energy. The vesicle membrane keeps the contained macromolecules from mixing with molecules within the cytoplasm. 1. Exocytosis: Exocytosis is a way substances can exit a cell and endocytosis is a way substances can enter a cell. During exocytosis, a vesicle - often produced by Golgi-fuses with the plasma membrane as Figure 5.8 Exocytosis. secretion occurs (Figure 5.8) for insulin, hormones and digestive enzymes. 5.3 Active Transport Across Membrane 2. Endocytosis: During endocytosis, cells take in substances by vesicle formation. Portion of the plasma membrane invaginates to envelop the substance and then the membrane forms an intracellular vesicle. Endocytosis occurs in one of three ways (Figure 5.9): Phagocytosis; to transport large substances, ex., a virus, food particle or another cell. Pinocytosis; to transport small substances, such as a macromolecule, into the cell. Receptor-mediated endocytosis; a special form of pinocytosis. Figure 5.9 Methods of endocytosis. 5.3 Active Transport Across Membrane 2. Endocytosis (cont.) Phagocytosis is common in unicellular organisms such as amoebas. It also occurs in humans. Certain types of human white blood cells are mobile like an amoeba. This process is necessary towards the development of immunity to bacterial diseases. Pinocytosis occurs when vesicles form around a liquid or very small particles. The intestinal wall and plant root cells use pinocytosis to ingest substances. Pinocytosis involves a significant amount of the plasma membrane because it occurs continuously. Figure 5.9 Methods of endocytosis. 5.3 Active Transport Across Membrane 2. Endocytosis(cont.)  Loss of plasma membrane due to pinocytosis is balanced by the occurrence of exocytosis. Receptor-mediated endocytosis uses a receptor protein shaped in such a way that a specific molecule such as a vitamin or lipoprotein can bind to it. Receptor-mediated endocytosis is involved in the transfer and exchange of substances between cells. Such an exchange takes place when substances move from maternal blood into fetal blood at the placenta. Figure 5.9 Methods of endocytosis. Thank you General Biology Bio 110 Chapter 6 Contents: PART V Microbiology Chapter 6 PART VI Plant Chapter 7 PART VII Animal Chapter 8 PART IX Genetic Basis of Life a. Cell Cycle and Genetic Disorders Chapter 9 b. Classical Genetics and Modern Chapter 10 Biotechnology Part V: Microbiology 6.1 General Biology of Viruses a. Viral Structure b. Viral Replication 1. Lytic Reproductive Cycles Destroy Host Cells 2. In Lysogenic Cycles, Viruses Integrate into the Host DNA 6.2 General Biology of Prokaryotes a. Structure of Prokaryotes (bacteria and archaea) b. Reproduction in Prokaryotes 1. Characteristics of Bacterial Cells 2. Characteristics of Archaea 6.3 General Biology of Protists 6.4 General Biology of fungi a. Structure of Fungi b. Reproduction of Fungi  Part V 6.1 General Biology of Viruses  6.1 General Biology of Viruses ◌A ِ virus is a submicroscopic infectious agent that replicates only inside living cells of an organism. Viruses infect all types of life forms, from, animal and plants to microorganisms including bacteria and archaea. (see Table 6.1). Viral diseases are of concern to everyone; as it is estimated that the average person catches a cold two or three times a year. Viruses have a DNA or RNA genome, but they can reproduce only by using the metabolic machinery of a host cell. Table 6.1 a. Viral Structure: The size of a virus is comparable to that of a large protein molecule and ranges in size from 10-400 nm, though, they are best studied through electron microscopy. Viruses can be purified and crystallized and become infectious, e.g., invade host cell.  6.1 General Biology of Viruses a. Viral Structure (continued) Viruses are categorized by: size and shape type of nucleic acid, including whether it is single-stranded or double-stranded Figure 6.1a Structure of a bacteria- the presence or absence of an infecting virus. outer envelope. Viruses vary in shape from polyhedral (Figure 6.1a) to thread-like or rod-like (Figure 6.1b,c). Figure 6.1c Structure of a human-infecting Figure 6.1b Structure of a plant-infecting virus. virus. 6.1 General Biology of Viruses a. Viral Structure (continued): However, all viruses possess the same basic anatomy: An outer capsid composed of protein subunits and an inner core of nucleic acid—either DNA or RNA, but not both. The viral capsid may be surrounded by an outer membranous envelope with glycoprotein spikes (Figure 6.1c); if not, the virus is said to be naked (Figure 6.1a,b). Some viruses infect bacteria (Figure 6.1a), plant (Figure 6.1b), animal or human (Figure 6.1c). A viral genome has as little as three and as many as 100 genes. A viral particle may also contain various proteins, especially enzymes such as the polymerases, needed to produce viral DNA and/or RNA. 6.1 General Biology of Viruses b. Viral Reproduction: Viruses infect bacterial, plant, animal and human cells in similar ways. Focus will be given to phage infection of bacteria because this process is best understood. Two types of viral reproductive cycles are lytic and lysogenic: 1- Lytic Reproductive Cycles Destroy Host Cells 2- Lysogenic Cycles, where Virus Integrates into Host DNA In the lytic cycle, the virus lyses (destroys) the host cell. When the virus infects a susceptible host cell, it forces the host to use its metabolic machinery to replicate viral particles. Five steps are typical in lytic viral reproduction (Figure 6.2a-e): 1- Attachment 2- Penetration. 3- Biosynthesis 4- Assembly or or maturation. 5- Release  6.1 General Biology of Viruses I. Attachment: The virus attaches to specific receptors on the host cell. This process ensures that the virus infects only its specific host. The reproductive cycle of viruses begins with a virus attaches to the host cell in a lock-and-key manner- with a receptor on the host cell’s outer surface. The attachment is responsible for the specificity between viruses and their host cells.  Ex., tobacco mosaic virus (TMV) cannot infect human cells because its capsid cannot attach to the receptors on the surfaces of human cells. Figure: 6.2a Lytic cycle. 6.1 General Biology of Viruses: II. Penetration: The virus penetrates the host plasma membrane and moves into the cytoplasm. Some phages inject only their nucleic acid into the cytoplasm of the host cell; the capsid remains on the outside. Figure: 6.2b Lytic cycle.  6.1 General Biology of Viruses:- III. Biosynthesis: The viral genome contains all the information necessary to produce new viruses. Once inside, the virus degrades the host-cell nucleic acid and uses the molecular machinery of the host cell to replicate its own nucleic acid and to produce viral proteins. Many antiviral drugs interfere with replication of viral nucleic acid. IV. Assembly or maturation: The newly synthesized viral components are assembled into new viruses. Figure 6.2c Lytic cycle. Figure 6.2d Lytic cycle.  6.1 General Biology of Viruses:- V. Release: Assembled viruses are released from the cell. Generally, lytic enzymes, produced by the phage late in the replication process, destroy the host plasma membrane. The time required for viral reproduction, from attachment to the release of new viruses, varies from 1 hour. Once released, the viruses infect other cells and process is repeated. How do bacteria protect themselves from phage infection? bacteria produce restriction enzymes, that cut up the foreign DNA of the phage; to prevent the phage DNA from duplication. The bacterial cell protects its own DNA by slightly modifying its DNA after replication by methylation of a given base so that the Figure: 6.2e Lytic cycle. restriction enzyme does not recognize the sites it would cut.  6.1 General Biology of Viruses:- b. Viral Reproduction (continued): 2. lysogenic Cycles, where Virus Integrates into Host DNA Viruses do not always destroy their hosts. In a lysogenic cycle, the viral genome usually becomes integrated into the host bacterial DNA. The integrated virus is called a prophage or provirus. When the bacterial DNA replicates, the prophage also replicates (Figure 6.2f). Certain external conditions (such as ultraviolet light or X-rays) cause viruses to revert to a lytic cycle and then destroy their host. Sometimes non-lytic viruses become lytic spontaneously. Figure: 6.2f Lysogenic cycle.  6.1 General Biology of Viruses:- b. Viral Reproduction (continued); Figure 6.2 Lytic and lysogenic cycles.  Part V 6.2 General Biology of Prokaryotes  6.2 General Biology of Prokaryotes a. Structure of Prokaryotes (bacteria and archaea) Prokaryotes generally range in size (1-10 μm length and 0.7-1.5 μm width) with a cell wall situated outside the plasma membrane to prevent it from collapsing due to osmotic changes. In many bacteria, the cell wall is surrounded by a layer of polysaccharides called a glycocalyx or capsule. Many bacteria and archaea have a layer comprised of protein, or glycoprotein, instead of a glycocalyx; such a layer is called an S-layer. In parasitic forms of bacteria, these outer coverings help protect the cell from host defenses. Some prokaryotes move by means of flagella (Figure 6.3). Figure: 6.3 Flagella.  6.2 General Biology of Prokaryotes: a. Structure of Prokaryotes (continued): A bacterial flagellum has a filament composed of strands of the protein flagellin. The archaeal flagellum is similar to bacteria but lacking a basal body. A prokaryotic cell lacks the membranous organelles of an eukaryotic cell. Although prokaryotes do not have a nucleus, they have a single chromosome of a circular strand of DNA. Many prokaryotes also have accessory rings of DNA called plasmids. Protein synthesis in prokaryotic cell is carried out by smaller ribosomes than eukaryotic ribosomes. Figure: 6.3 Flagella.  6.2 General Biology of Prokaryotes: b. Reproduction of Prokaryotes: Mitosis does not occur in prokaryotes. Instead, prokaryotes reproduce asexually by means of binary fission (Figure 6.4). The single circular chromosome replicates and then two copies separate as the cell enlarges. Newly formed plasma membrane and cell wall separate the cell into two cells. Prokaryotes have a generation time as short as 12 minutes. As prokaryotes are haploid (1n), sexual reproduction does not occur, but the following three means of genetic recombination have been observed in prokaryotes: Conjugation Transformation Transduction Figure 6.4 Binary fission.  6.2 General Biology of Prokaryotes: b. Reproduction of Prokaryotes (continued): Conjugation Two bacteria are temporarily linked together (Figure 6.5a,b) by a filament called pilus, where the donor cell passes DNA to a recipient cell. pilus Figure 6.5a Conjugation. Figure 6.5bConjugation.  6.2 General Biology of Prokaryotes: b. Reproduction of Prokaryotes (continued): Transformation a cell picks up (from the surroundings) free pieces of DNA secreted by live prokaryotes or released by dead prokaryotes (Figure 6.6). Transduction bacteriophages carry portions of DNA from one bacterial cell to another (Figure 6.7). Figure 6.7 Transduction. Figure 6.6 Transformation.  6.2 General Biology of Prokaryotes: 1. Characteristics of Bacterial Cells Bacteria are the more common type of prokaryote (over 2,000 known different bacteria). Most bacterial cells are protected by a cell wall that contains the unique molecule peptidoglycan; a complex of polysaccharides linked by amino acids. Groups of bacteria are commonly differentiated from one another by using the Gram stain procedure: Gram-positive bacteria appear purple under light microscope. Gram-negative bacteria appear pink. This difference is dependent on the construction of the cell wall; the Gram-positive bacteria have a thick layer, whereas Gram-negative bacteria have a thin layer.  6.2 General Biology of Prokaryotes: 1. Characteristics of Bacterial Cells (continued): Bacteria (and archaea) can also be described in terms of their three basic cell shapes (Figure 7.8): Spirilli (spirillum) or spiral-shaped bacilli (bacillus) or rod-shaped cocci (coccus) or spherical Figure 6.8 Bacterial basic cell shapes.  6.2 General Biology of Prokaryotes: 2. Characteristics of Archaea: Archaea are considered to be a unique group of bacteria. Archaea have a different rRNA sequence of bases than that of bacteria. The eukarya are more closely related to the archaea than to the bacteria because they share the same ribosomal proteins (not found in bacteria) and have similar types of tRNA. The plasma membranes of archaea contain unusual lipids that allow many of them to function at high temperatures; lipids of archaea contain glycerol linked to hydrocarbons, while linked to fatty acids in bacteria. The cell walls of archaea do not contain peptidoglycan, but largely composed of polysaccharides.  Part V 6.3 General Biology of Protists  6.3 General Biology of Protists The word protist reflects the idea that protists were the first existed eukaryotes. They are a group of primary aquatic (marine) eukaryotic organisms with diverse body forms, types of reproduction, modes of nutrition and lifestyles. Protists include algae, diatoms, water molds, slime molds and protozoa with unicellular, colonial or simple multicellular organisms (Figure 6.9). Diatoms have an orange-yellow color because they contain a carotenoid pigment in addition to chlorophyll. Protists have eukaryotic cells characterized by membranous organelles; mitochondria and chloroplasts. Protist vary in size from microscopic algae Figure 6.9 Multicellular Diatom. and protozoans to multicellular brown or green alga that can exceed 200 m in length.  6.3 General Biology of Protists Protists acquire nutrients in a number of different ways. Ex., algae are photosynthetic and gather energy from sunlight. Many protozoans ingest food by endocytosis, thereby forming food vacuoles. Endocytosis is a process by which substances are moved into the cell from the environment. A slime mold ingests decaying plant material in the same manner. Asexual reproduction by mitosis is the norm in protists. Sexual reproduction involving meiosis and spore formation generally occurs only under stressed environment. Spores are resistant to adverse conditions and can survive until favorable conditions return once more. While the protists have great medical importance because several cause diseases in humans, they also are of enormous ecological importance.  6.3 General Biology of Protists Being aquatic, the photosynthesizers give off oxygen and function as producers in water. Protists can be characterized according to modes of nutrition. Algae are autotrophic, as are land plants, while protozoans and slime molds tend to be heterotrophic by ingestion, as are animals. Green algae Slime molds Slime molds spores  Part V 6.4 General Biology of fungi 6.4 General Biology of fungi a. Structure of Fungi:  Fungi ( singular: fungus are a kingdom of usually multicellular eukaryotic organisms that are heterotrophs ( cannot make their own food) and have important roles in nutrient cycling in an ecosystem.  There are over 80.000 species of fungi known so far.  Animals ingest food, while fungi absorb food, where they send out digestive enzymes into immediate environment and then, when organic matter is broken down, the cells absorb the resulting nutrient molecules.  6.4 General Biology of fungi a. Structure of Fungi : Therefore, animals and fungi are more closely related to each other than either is to plants. Some fungi, including the yeasts, are unicellular; however, the vast majority of species have a multicellular structure known as a mycelium (Figure 6.11a). A mycelium is a network of filaments called hyphae (Figure 6.11b). Hyphae give the mycelium quite a large surface area to facilitate absorption of nutrients into the body of a fungus. c. Monokaryotic hypha d. Dikaryotic hypha a. Mycelium b. Hyphae e. Polykaryotic hypha Figure 6.11 Fungi body plan.  6.4 General Biology of fungi a. Structure of Fungi (continued) In most fungi, hyphae are divided by cross walls, called septa, into individual cells containing one (monokaryotic) or two (dicaryotic) nuclei (Figure 6.11c,d). The septa of many fungi have pores that permit organelles to flow from cell to cell. Some fungi are polykaryotic; lack septa. In these species, nuclear division is not followed by cytoplasmic division to result in multinucleated, giant cell (Figure 6.11e). c. Monokaryotic hypha d. Dikaryotic hypha a. Mycelium b. Hyphae e. Polykaryotic hypha Figure 6.11 Fungi body plan.  6.4 General Biology of fungi a. Structure of Fungi (continued): Fungal cells are quite different from plant cells, not only by lacking chloroplasts but also by having a cell wall that contains chitin and not cellulose. Chitin, like cellulose, is a polymer of glucose, but with a nitrogen- containing amino group attached to it. Chitin is also found in insects. The energy reserve of fungi is not starch but glycogen, as in animals. Except for the aquatic species, fungi lack motility in which they move toward a food source by growing toward it. Hyphae can cover as much as a kilometer a day !!!  6.4 General Biology of fungi b. Reproduction of Fungi: Both sexual and asexual reproduction occur in fungi. Fungal sexual reproduction involves these stages: During sexual reproduction (Figure 6.12), hyphae from two different mating types make contact and fuse. In some species, nuclei from the two mating types fuse immediately, while in others, the nuclei do not fuse. A hypha that contains paired haploid nuclei is said to be n+n or dikaryotic. When nuclei fuse (2n), zygote undergoes meiosis prior to spore formation. Figure 6.12 Sexual reproduction.  6.4 General Biology of fungi b. Reproduction of Fungi (continued): Fungal spores germinate directly into haploid hyphae. As an adaptation to life, fungi produce non-mobile, wind-blown spores during both sexual and asexual reproduction. When a spore lands upon an appropriate food source, it germinates and begins to grow. Asexual reproduction usually involves the production of spores by a specialized part of a single mycelium. Alternately, asexual reproduction can occur by fragmentation—a portion of a mycelium begins a life of its own. Also, unicellular yeasts reproduce asexually by budding; a small cell forms and gets Figure 6.13 Asexual pinched off as it grows to full size (Figure reproduction. 6.13). Thank you