Cells: The Basic Units Of Life PDF

5 Cells: The Basic Units of Life  Biology I PHBLt 101 Lecture 5: Cellular organization of organisms Intended Learning Outcomes: A.2 Explain various experiments, list their applications, describe types of...

5 Cells: The Basic Units of Life  Biology I PHBLt 101 Lecture 5: Cellular organization of organisms Intended Learning Outcomes: A.2 Explain various experiments, list their applications, describe types of different microscopes, and recognize different techniques used in Biology and Biotechnology. A.3 Describe various diseases and relate them to lysosomal and genetic dysfunctions. A.4 Describe and correlate the data of various experiments. A.5 Recognize the cellular organization of life A.6 Describe structure and function of cell organelles and cytoskeleton B.1 Identify the proper scientific and medical terms, abbreviations & symbols related to Biology as a scientific discipline C.1 Illustrate and investigate experiments related to Biology. C.2 Analyze and determine biological based evidences in Biology practice. D.1 Communicate clearly by verbal means through discussing the assignments in the tutorials. D.2 Review information obtained from lecture slides as well as several text books to improve professional competencies. D.3 Use numeracy, calculation & statistical methods as well as information technology tools related to biological basics and experiments. 3 5 Cells: The Basic Units of Life The Cell: The Basic Unit of Life Prokaryotic Cells Eukaryotic Cells Organelles that Process Information The Endomembrane System Organelles that Process Energy Other Organelles 5-3 5 The Cell: The Basic Unit of Life Life requires a structural compartment separate from the external environment in which macromolecules can perform unique functions in a relatively constant internal environment. These “living compartments” are cells. The cell is the simplest collection of matter that can live. 5-4 5 The Cell: The Basic Unit of Life The Significance of being small Cell size is limited by the surface area-to-volume ratio. The surface of a cell is the area that interfaces with the cell’s environment. The volume of a cell is a measure of the space inside a cell. Surface area-to-volume ratio is defined as the surface area divided by the volume. For any given shape, increasing volume decreases the surface area-to-volume ratio. Smaller cells are more efficient in exchanging materials with their surroundings! 5-5 Figure 4.3 Why Cells are Small 5-6 5 How we study cells Because most cells are tiny, with diameters in the range of 1 to 100 m, microscopes are needed to visualize them. With normal human vision the smallest objects that can be resolved (i.e., distinguished from one another) are about 200 m (0.2 mm) in size. A sense of scale between living cells and atoms 5-7 5 The Cell: The Basic Unit of Life Light microscopes use glass lenses to focus visible light and typically have a resolving power of 0.2 m. Electron microscopes have magnets to focus an electron beam. The wavelength of the electron beam is far shorter than that of light, and the resulting image resolution is far greater (about 0.5 nm). Definitions:  Magnification: is the ratio of an object’s image size to its real size. Light microscopes can magnify effectively to about 1,000 times the actual size of the specimen; at greater magnifications, additional details cannot be seen clearly  Resolution: is a measure of the clarity of the image; it is the minimum distance two points can be separated and still be distinguished as two points. The light microscope cannot resolve detail finer than about 0.2 micrometer (μm), or 200 nanometers (nm), regardless of the magnification  Contrast: highlights differences in parts of the sample. 5-8  5 Fluorescence Microscopy Fluorescent dye: a molecule that absorbs light of one wavelength and then re-emits it at a longer wavelength Can be used alone or in combination with another molecule to gain specificity (antibodies) 5-13 Figure 9-13 Molecular Biology of the Cell (© Garland Science 2008) 5 Fluorescence Microscopy 5-14 5 5-15 5 The Cell: The Basic Unit of Life Cells show two organizational patterns: Prokaryotes have no nucleus or other membrane-enclosed compartments. They lack distinct organelles. Eukaryotes have a membrane-enclosed nucleus and other membrane-enclosed compartments or organelles as well. 5-16 5 The Cell: The Basic Unit of Life 5-17 5 Prokaryotic Cells Prokaryotes inhabit the widest range of environmental extremes. Prokaryotic cells are generally smaller than eukaryotic cells. Each prokaryote is a single cell, but many types can be found in chains or clusters. 5-18 Figure 5.5 Features shared by all prokaryotic cells:  All have a plasma membrane.  All have a region called the nucleoid where the DNA is concentrated.  The cytoplasm (the plasma- membrane enclosed region) consists of the nucleoid, ribosomes, and a liquid portion called the cytosol Supercoiled plasmid DNA Bacterial DNA Is Supercoiled 5-19  5 Prokaryotic Cells Prokaryotic Cells Specialized features of some prokaryotic cells:  A cell wall just outside the plasma membrane.  Some bacteria have another membrane outside the cell wall, a polysaccharide-rich phospholipid membrane.  Some bacteria have an outermost slimy layer made of polysaccharides and referred to as a capsule. Some bacteria have flagella, locomotory structures shaped like a corkscrew. Some bacteria have pili, threadlike structures that Pili help bacteria adhere to one another during mating or to other cells for food and protection. 5-20  5 Prokaryotic Cells Some bacteria, including cyanobacteria, can carry on photosynthesis. The plasma membrane is infolded and has chlorophyll. Pili Photosynthetic Membranes in Bacteria. The green stripes in this photosynthetic bacterium are membranes that contain the pigments and enzymes required for photosynthesis. This photo has been colorized to enhance the membranes. 5-21  5 Eukaryotic Cells Compartmentalization is the key to eukaryotic cell function. Each organelle or compartment has a specific role defined by chemical processes. Membranes surrounding these organelles keep away inappropriate molecules and also act as traffic regulators for raw materials into and out of the organelle. 5-22 5 Eukaryotic Cells Eukaryotes, animals, plants, fungi, and protists, have a membrane-enclosed nucleus in each of their cells. Eukaryotic cells:  Usually larger than prokaryotic cells.  have a variety of membrane-enclosed compartments called organelles (little organs).  have a protein scaffolding (network) called the cytoskeleton. 5-23 5 Figure 5.7 Eukaryotic Cells (Part 1) 5-24 5 Figure 5.7 Eukaryotic Cells (Part 2) 5-25 Figure 5.7 Eukaryotic Cells (Part 3) 5-26 Figure 5.7 Eukaryotic Cells (Part 4) 5-27 Figure 5.7 Eukaryotic Cells (Part 1) - lysosomes + Cellulosic cell wall - centrioles + Vacuole(s) + Plastid(s) + Glyoxysomes 5-28 5 Study of cell organells Cell organelles can be studied by light and electron microscopy. Stains are used to target specific macromolecules and determine chemical composition. Cell fractionation is used to separate organelles for biochemical analyses. Microscopy and cell fractionation can both be used to give a complete picture of the structure and function of each organelle. 5-29  5 Cell fractionation by centrifugation The centrifuge is used to fractionate cells into their component parts Figure 6.5 5-30  Centrifugation Differential centrifugation / sedimentation: A homogeneous (i.e. same concentration) medium is used. Particles sediment according to their sedimentation coefficients which in turn depend on their masses and shapes (radii) and the applied centrifugal force (compared to gravitational force expressed as × g; acceleration on earth = 981 cm/s2). The unit of the sedimentation coefficient is Svedberg (S). Particles having similar sedimentation rates are difficult to separate by “conventional” differential centrifugation procedure, and therefore, density gradient centrifugation would be used. 5-31 Figure 8-10 Molecular Biology of the Cell (© Garland Science 2008)  5 Cell fractionation The centrifuge  Is used to fractionate cells into their component parts Figure 6.5 5-32 5 RESULTS In early experiments, researchers used microscopy to identify the organelles in each pellet and biochemical methods to determine their metabolic functions. These identifications established a baseline for this methods, enabling today’s researchers to know which cell fraction they should collect in order to isolate and study particular organelles. 5-33 5 5-34 5 Organelles that Process Information The nucleus contains most of the cell’s DNA and is the site of DNA duplication to support cell reproduction. The nucleus also plays a role in DNA control of cell activities. Within the nucleus is a specialized region called the nucleolus, the RNA molecules found in ribosomes are manufactured and the large and small ribosomal subunits are assembled.. 5-35  5 Nuclear Envelope Two lipid bilayers form the nuclear envelope which is perforated with nuclear pores. The nuclear pores connect the interior of the nucleus with the rest of the cytoplasm. A pore complex, consisting of eight large protein granules, surrounds each pore. RNA and proteins must pass through these pores to enter or leave the nucleus. Nuclear proteins are synthesized by ribosomes in the cytosol and contain a “zip code”—a molecular address tag—that marks them for transport through the nuclear pore complex. This zip code allows the nuclear pore complex to open in some way that permits larger proteins and RNA molecules to pass through. This tag turned out to be a 17 amino acid sequence came to be called the nuclear localization signal (NLS). Proteins that leave the nucleus have a different signal, required for nuclear export. 5-36 Figure 5.9 The Nucleus is Enclosed by a Double Membrane 5-37  Chromatin and Chromosomes Figure 5.10 The chromatin consists of diffuse or very long, thin fibers in which DNA is bound to proteins. Prior to cell division these condense and organize into structures recognized as chromosomes. Chromosomes do not float freely inside the nucleus—instead, each chromosome occupies a distinct area, which may vary in different cell types and over the course of cell replication. 5-38 5 Nucleoplasm & nuclear lamina Surrounding the chromatin is the nucleoplasm. The nuclear lamina is a meshwork of proteins which maintains the shape of the nuclear envelope and the nucleus. Defects in a nuclear lamina can cause a rare class of premature aging disorders called Progeria. Children with progeria begin to show advanced features of aging around 18-24 months of age 5-39  5 Organelles that Process Information Ribosomes are the sites of Bottom of a centrifuge protein synthesis. tube In eukaryotes, functional ribosomes are found free in the cytoplasm, in mitochondria, bound to the endoplasmic reticulum, and in chloroplasts. They consist of a type of RNA called ribosomal RNA (rRNA), and more than 50 other proteins. Separation of the ribosomal subunits ( by density gradient centrifugation). The upper axis of the graph represents the centrifugal force, increasing from right to left, where the bottom of the centrifuge tube exists. At the end of the centrifugation cycle, the contents of the tube are distributed into 25 fractions. The sucrose gradient is then passed through a quartz cuvette and the absorbance of the UV light at 260 nm (A260) is continuously monitored. The numbers in the upper x-axis indicate the S-values of the particles that have migrated to the respective fraction. 5-37 5 Prokaryotic versus Eukaryotic ribosomes From Knippers “Molekulare Genetik”, 9th Ed. 2006; Thieme Verlag Elements of bacterial ribosomes. Under low Mg2+ concentrations, a ribosome dissociates into its two subunits. Under denaturing conditions each subunit can be dissociated into its components of rRNA and proteins. The proteins L7 and L12 are identical but L12 carries an acetyl group at its N-terminus. Proteins L26 and S20 are identical. Under suitable conditions the separated constituents can be reconstituted, i.e. back aggregate to the intact ribosome. 5-38 The Endomembrane System The endoplasmic reticulum (ER) is a network of interconnecting membranes distributed throughout the cytoplasm. The internal compartment, called the lumen, is a separate part of the cell with a distinct protein and ion composition. The ER’s folding generates a surface area much greater than that of the plasma membrane. At certain sites, the ER membrane is continuous with the outer nuclear envelope membrane. 5-42  The Endoplasmic Reticulum The rough ER (RER) has ribosomes attached. The smooth ER (SER) is a ribosome-free region of the ER. Cells that are specialized for synthesizing proteins for extracellular export have extensive ER membrane systems. 5-43 5 Functions of ER The smooth ER The rough ER  Synthesizes lipids  Has bound ribosomes  Metabolizes  Produces secretory carbohydrates proteins and  Stores calcium membranes, which  Detoxifies poison are distributed by transport vesicles 5-44 5 The Endomembrane System Cont. The Golgi apparatus The Golgi apparatus consists of flattened membranous sacs, called cisternae, and small membrane-enclosed transport vesicles. The Golgi apparatus has three roles:  Receive proteins from the ER and further modify them (often by glycosylation; attaching sugar).  Concentrate, package, and sort proteins before they are sent to their destinations.  Some polysaccharides for plant cell walls are synthesized. 5-45 Figure 5.12 The Golgi Apparatus Golgi apparatus receives, at its cis side, many of the transport vesicles produced in the rough ER. 5-46 5 The Endomembrane System Lysosomess Lysosomes are vesicles containing digestive enzymes that come in part from the Golgi. Lysosomes are sites for breakdown of food and foreign material brought into the cell by phagocytosis. Lysosomes are also the sites where digestion of spent cellular components occurs, a process called autophagy. 5-47 Figure 5.13 Lysosomes Isolate Digestive Enzymes from the Cytoplasm Malfunctioning lysosomes (due to a mutation in the HEXA gene) may result in a neuronal disorder called Tay-Sachs disease. 5-48  5 Organelles that Process Energy The Mitochondria The primary function of mitochondria is to convert the potential chemical energy of fuel molecules into a form that the cell can use (ATP). The production of ATP is called cellular respiration. Mitochondrial matrix contains ribosomes and several molecules of circular DNA. Thus, mitochondria possess their own genetic material and the machinery to manufacture their own RNAs and proteins. This non- chromosomal DNA is important because it encodes proteins (enzymes) needed for cellular respiration. 5-49 Figure 5.14 A Mitochondrion Converts Energy from Fuel Molecules into ATP (Part 1) Mitochondria have an outer lipid bilayer and a highly folded inner membrane. Folds of the inner membrane give rise to the cristae, which contain large protein molecules used in cellular respiration The region enclosed by the inner membrane is called the mitochondrial matrix. 5-50 5 Organelles that Process Energy Chloroplastss Plastids are organelles found only in plants and some protists. Chloroplasts, the sites where photosynthesis occurs, are one type of plastid. 5-51 5 Organelles that Process Energy Chloroplasts are surrounded by two layers, and have an internal membrane system. The internal membranes are arranged as thylakoids and grana. These membranes contain chlorophyll and other pigments. The fluid in which the grana are suspended is called the stroma. 5-52  5 Endosymbiotic theory & the origin of some organelles Endosymbiosis may explain the origin of mitochondria and chloroplasts. As both organelles are surrounded by double membranes, have their own genomes( circular like prokaryotic ones), have their own ribosomes(70S) According to the endosymbiosis theory, both organelles were formerly prokaryotic organisms that somehow became incorporated into a larger cell. Today, both mitochondria and chloroplasts have DNA and ribosomes (in the stroma), and are self-duplicating organelles, therefore referred to be semi-autonomous. 5-53 5 Other Organelles Chloroplast Peroxisomes, also Peroxisome called microbodies, are Mitochondrion small organelles that are specialized to compartmentalize toxic peroxides and break them down. Glyoxysomes are structurally similar organelles found in plant seeds. 1 µm 5-54  5 Other Organelles Vacuoles, found in plants and protists, are filled with an aqueous solution and are used to store wastes and pigments. Vacuoles may develop turgor pressure, a swelling that helps the plant cell maintain support and rigidity. Food vacuoles are formed in single-celled protists. Many freshwater protists have a contractile vacuole that helps eliminate excess water and restore proper salt balance. 5-55