Lesson 2: Cell and Its Organelles Notes PDF

 LESSON 2: CELL ITS ORGANELLES 100 micrometers (μm). 5 micrometers (μm) CELL  All Cells Exhibit Basic Structural Similarities 1. Centrally located GENETIC MATERIAL ✓ Every cell contains DNA, the hereditary molecule. ✓ In PROKARYOTES, t...

 LESSON 2: CELL ITS ORGANELLES 100 micrometers (μm). 5 micrometers (μm) CELL  All Cells Exhibit Basic Structural Similarities 1. Centrally located GENETIC MATERIAL ✓ Every cell contains DNA, the hereditary molecule. ✓ In PROKARYOTES, the simplest organisms, most of the genetic material lies in a single circular molecule of DNA (Plasmid). ✓ It typically resides near the center of the cell in an area called the nucleoid, not segregated from the rest of the cell’s interior by membranes.  All Cells Exhibit Basic Structural Similarities ✓ By contrast, the DNA of EUKARYOTES, which are more complex organisms, is encased within a double-membrane structure called the NUCLEUS.  All Cells Exhibit Basic Structural Similarities 2. The cytoplasm ✓ includes all the contents of a cell between the cell membrane and the nuclear envelope. It encompasses both the cytosol and the cellular organelles. ✓ Cytoplasm consists of cytosol, which is the liquid component, as well as organelles.  All Cells Exhibit Basic Structural Similarities 2. The cytoplasm ✓ In bacterial cells, the terms "cytoplasm" and "cytosol" are often used interchangeably, as bacterial cells lack membrane-bound organelles. Therefore, the entire content inside the bacterial cell membrane, including the fluid portion and all cellular structures, is commonly referred to as cytoplasm.  All Cells Exhibit Basic Structural Similarities 3. The plasma membrane (cell membrane) ✓ A plasma membrane encloses every cell, separating its contents from the surroundings. ✓ The plasma membrane is a phospholipid bilayer about 5 to 10 nm (5 to 10 billionths of a meter) thick, with proteins embedded in it. PROKARYOTE/PROKARYOTIC CELL  PROKARYOTE/PROKARYOTIC CELL The underlying difference between prokaryotes and eukaryotes is the existence of the NUCLEUS and membrane-bound organelles. Prokaryotic cell does not have NUCLEUS and lacks membrane-bound organelles. Organelles are specialized structures within a cell that perform specific functions, contributing to the overall structure, organization, and function of the cell. Membrane-bound organelles ✓ Organelles which are surrounded by a phospholipid bilayer or single layer (membrane). ✓ This allows organelles within the cells to control what enters and leaves it by using a selectively permeable membrane. Nonmembrane-bound organelle ✓ Simply means that the organelle doesn't have a membrane because they don't need to control their internal conditions. ✓ Prokaryotes include bacteria and archaea (single- celled organisms that include those that can survive in hostile environments) ✓ Bacterial cell walls are composed of peptidoglycan, and archaeal cell walls are made from a variety of polysaccharides and peptides. ✓ Archaeal membranes contain unusual lipids. ✓ Peptidoglycan, also known as murein, is a polymer consisting of sugars and amino acids that forms a mesh-like layer outside the plasma membrane of most bacteria, forming the cell wall.  GRAM POSITIVE GRAM NEGATIVE Inner most plasma membrane Inner most plasma membrane THICK peptidoglycan cell wall THIN peptidoglycan cell wall Outer Capsule Another plasma membrane More easily treatable with Outer Capsule antibiotics Harder to treat with antibiotics Stains purple/violet after Stains red/pink after Gram Stain Gram Stain  Prokaryotic Cells Lack Interior Organization ✓ Prokaryotes are the simplest organisms. ✓ They consist of cytoplasm surrounded by a plasma membrane, encased within a rigid cell wall. ✓ Importantly, they have no distinct interior compartments ✓ A prokaryotic cell is like a one-room cabin in which eating, sleeping, and watching TV all occur. ✓ Prokaryotes play a very important role in the ecology of living organisms. ✓ Some harvest light by photosynthesis; others break down dead organisms and recycle their components. ✓ Still others cause disease or have uses in many important industrial processes. ✓ The nucleoid (meaning nucleus-like) is an irregularly shaped region within the cell of a prokaryote that contains all or most of the genetic material, called genophore. ✓ A pilus is a thin, rigid fiber made of protein that protrudes from the cell surface. ✓ The primary function of pili are to attach a bacterial cell to specific surfaces or to other cells. ✓ Along the length of the pilus are adhesin proteins. ✓ These molecules aid in the attachment of the pilus and are specific to the target surface.  Many Prokaryotic Cells Move About by Means of Rotating Flagella ✓ Flagella (singular, flagellum) are long, threadlike structures protruding from the surface of a cell that are used in locomotion. Chlamydia Spirillum  BACTERIAL CELL Type of Cell Prokaryotic Cell Membrane Cytoplasm DNA (single circular ring called Plasmid) Genophore Ribosomes Cytoskeleton (simple cytoskeleton)  BACTERIAL CELL Cell Wall (made of PEPTIDOGLYCAN) Nuclear Membrane Nucleus (Nucleoid) ER (Endoplasmic Reticulum) Golgi Apparatus  BACTERIAL CELL Lysosomes Vesicles Vacuoles Present only is specific genera of filamentous bacteria Centrioles Mitochondria Chloroplasts Peroxisomes Size 0.2–10 micro meters EUKARYOTE/EUKARYOTIC CELL  EUKARYOTE/EUKARYOTIC CELL ✓ Existence of the NUCLEUS. ✓ Membrane-bound organelles are present ✓ There is a set of ENDOMEMBRANE SYSTEM  Endomembrane System The endomembrane system (endo- = “within”) is a group of membranes and organelles in eukaryotic cells that works together to modify, package, and transport lipids and proteins.  MEMBRANE-BOUND ORGANELLES Nucleus E N Rough ER D O M Smooth ER E M Golgi Apparatus/Body B R Vacuoles and Vesicles A N Lysosomes E Chloroplasts and other Plastids Mitochondria Peroxisomes NON-MEMBRANE-BOUND ORGANELLES Ribosome Cytoskeleton Centriole  PLASMA MEMBRANE / CELL MEMBRANE Separates cell from external environment; controls passage of organic molecules, ions, water, oxygen, and wastes into and out of the cell MEMBRANE-BOUND ORGANELLES NON-MEMBRANE-BOUND ORGANELLES E Nucleus* N Ribosome D Rough ER O Centriole M Smooth ER E Cytoskeleton M B Golgi Apparatus/Body R A Vacuoles and Vesicles N E Lysosomes Chloroplasts and other Plastids* Mitochondria* Peroxisomes  ANIMAL CELLS PLANT CELLS Type of Cells Eukaryotic Eukaryotic Cell Membrane Cytoplasm DNA in multiple chromosomes in multiple chromosomes (Linear) (Linear) Ribosomes Cytoskeleton  ANIMAL CELLS PLANT CELLS Cell Wall made of CELLULOSE Nuclear Membrane and Nucleus ER (Smooth and Rough) Golgi Apparatus Lysosomes  ANIMAL CELLS PLANT CELLS Vesicles Vacuoles Small Large Centrioles Mitochondria Chloroplasts Peroxisomes Glyoxisomes Size 10 to 30 micrometers 10 to 100 micrometers NUCLEUS NUCLEUS ✓ Is a membrane-bound organelle that stores, protects and expresses most of the genetic information (DNA) found in the cell. ✓ Since regulation of gene expression takes place in the nucleus, it is commonly called the control center of the cell. ✓ First described by the botanist Robert Brown in 1831. ✓ The largest and most easily seen organelle within a eukaryotic cell ✓ Acts as the cell’s information center ✓ Nuclei are roughly spherical in shape ✓ In animal cells they are typically located in the central region of the cell. ✓ Is the repository of the genetic information that enables the synthesis of nearly all proteins of a living eukaryotic cell. ✓ Most eukaryotic cells possess a single nucleus, although the cells of fungi and some other groups may have several to many nuclei. ✓ Mammalian erythrocytes (red blood cells) lose their nuclei when they mature. ✓ Many nuclei exhibit a dark-staining zone called a nucleolus (a region where intensive synthesis of ribosomal RNA is taking place.) Nuclear Envelope ✓ The surface of the nucleus is bounded by two phospholipid bilayer membranes, which together make up the nuclear envelope/membrane. ✓ The outer membrane of the nuclear envelope is continuous with the cytoplasm’s interior membrane system, called the endoplasmic reticulum ✓ Scattered over the surface of the nuclear envelope are what appear as shallow depressions but are, in fact, structures called nuclear pores. ✓ The pore allows ions and small molecules to diffuse freely between nucleoplasm and cytoplasm while controlling the passage of proteins and RNA–protein complexes. ✓ The inner surface of the nuclear envelope is covered with a network of fibers that make up the nuclear lamina. ✓ This is composed of intermediate filament fibers called nuclear lamins. ✓ Nuclear lamins give the nucleus its shape and is involved in the deconstruction and reconstruction of the nuclear envelope that accompanies cell division.  Definition of Terms 1. DNA (Deoxyribonucleic acid) ✓ a molecule composed of two chains (made of nucleotides) that coil around each other to form a double helix carrying the genetic instructions used in the growth, development, functioning and reproduction of all known living organisms and many viruses. 2. GENE ✓ is the basic physical and functional unit of heredity ✓ is a sequence of DNA or RNA that codes for a molecule that has a function. 3. HISTONES ✓ are proteins found in eukaryotic cell nuclei that package and order the DNA into structural units called nucleosomes. 4. NUCLEOSOME ✓ is a basic unit of DNA packaging in eukaryotes, consisting of a segment of DNA wound in sequence around eight histone protein cores. 5. CHROMATIN ✓ Is a complex of DNA, RNA, and protein found in eukaryotic cells. ✓ Its primary function is packaging very long DNA molecules into a more compact, denser shape, which prevents the strands from becoming tangled. ✓ Plays important roles in reinforcing the DNA during cell division, preventing DNA damage, and regulating gene expression and DNA replication. 6. CHROMOSOMES ✓ are thread-like structures in which DNA is tightly packaged within the nucleus. DNA packaging ✓In both prokaryotes and eukaryotes, DNA is the molecule that stores genetic information. ✓In eukaryotes, the DNA is divided into multiple linear chromosomes, which are organized with proteins into a complex structure called chromatin. ✓ Chromatin is usually in a more extended form that is organized in the nucleus ✓ When cells divide, the chromatin must be further compacted into a more highly condensed state that forms the X-shaped chromosomes visible in the light microscope. The NUCLEOLUS ✓A nucleolus consists of RNA and protein and is the site of ribosome production. ✓Before cells can synthesize proteins in large quantity, they must first construct a large number of ribosomes to carry out this synthesis. ENDOPLASMIC RETICULUM  ENDOPLASMIC RETICULUM ✓ endo = within plasma = cytoplasm reticulum = network ✓ The largest of the internal membranes is called the endoplasmic reticulum (ER). ✓ Single membrane-bound organelle ✓ Composed of a phospholipid bilayer embedded with proteins ✓ Is a membrane factory that specializes in the synthesis and transport of the protein and lipid components of most of the cell’s organelles. ✓ It consists of a network of tubular or saclike channels (cisternae) that extend throughout the cytoplasm and are continuous with the outer nuclear membrane. ✓ The folded membranes that form the cisternae of the endoplasmic reticulum can be: a. rough (granular) – Rough ER b. smooth (agranular) – Smooth ER Rough Endoplasmic Reticulum ✓ Characterized by the presence of numerous ribosomes located on the outer surface of the membranes. ✓ The proteins synthesized on the surface of the RER are destined to be exported from the cell, sent to lysosomes or vacuoles or embedded in the plasma membrane. ✓ These proteins enter the cisternal space as a first step in the pathway that will sort proteins to their eventual destinations. ✓ The RER also manufactures membranes by producing membrane proteins and phospholipid molecules. ✓ The membrane proteins are inserted into the ER’s own membrane, which can then expand and pinch off in the form of vesicles to be transferred to other locations. Smooth Endoplasmic Reticulum ✓ Regions of the ER with relatively few bound ribosomes or does not contain ribosomes or ribonucleoprotein particles. ✓ Appears more like a network of tubules than the flattened sacs of the RER ✓ The membranes of the SER contain many embedded enzymes. ✓ Enzymes anchored within the ER, for example, catalyze the synthesis of a variety of carbohydrates and lipids. ✓ Steroid hormones are synthesized in the SER as well. ✓ The majority of membrane lipids are assembled in the SER and then sent to the parts of the cell that need membrane components. ✓ Cells that carry out extensive lipid synthesis, such as those in the testes, intestine, and brain, have abundant SER. ✓Another role of the SER is the modification of foreign substances to make them less toxic. ✓In the liver, the enzymes of the SER carry out this detoxification. ✓Liver cells have extensive SER as well as enzymes that can process a variety of substances by chemically modifying them. GOLGI APPARATUS GOLGI APPARATUS/BODY/COMPLEX ✓ Flattened stacks of membranes, often interconnected with one another, form a complex called the Golgi apparatus/body/complex. ✓ These structures are named for Camillo Golgi, the 19th-century physician who first identified them. ✓ Primary function is to sort and package Proteins. ✓ They are especially abundant in glandular cells, which manufacture and secrete substances. ✓ The Golgi apparatus is the post office of the cell. *It functions in the collection, packaging, and distribution of molecules synthesized at one location and used at another within the cell or even outside of it. ✓ A Golgi apparatus has a front and a back, with distinctly different membrane compositions at these opposite ends. ✓ The front, or receiving end, is called the cis face and is usually located near ER while the trans face is concave in shape and face towards cytoplasm or away from ER. ✓ The trans face releases golgian vacuoles containing modified enzymes /proteins. VESICLES VESICLE ✓ is a large structure within a cell, or extracellular, consisting of liquid enclosed by a lipid bilayer. ✓ forms naturally during the processes of secretion (exocytosis), uptake (endocytosis) and transport of materials within the plasma membrane.  TYPES OF VESICLE ✓Transport vesicles ✓Secretory vesicles ✓Vacuoles* ✓Lysosomes* Transport Vesicles ✓ Can move molecules between locations inside the cell ✓ Example: Materials arrive at the cis face in transport vesicles that bud off the ER Secretory Vesicles ✓ Contain materials that are to be excreted from the cell. ✓ Within a larger organism, some cells are specialized to produce certain chemicals. ✓ These chemicals are stored in secretory vesicles and released when needed. VACUOLE VACUOLE ✓ A membrane-bound organelle which is present in all plant and fungal cells and some protist and animal ✓ Is essentially enclosed compartments which is filled with water containing inorganic and organic molecules including enzymes in solution. ✓ In animal cells, vacuoles perform mostly subordinate roles, assisting in larger processes of exocytosis and endocytosis. Plant Vacuoles ✓ Specialized membrane-bounded organelle ✓ Large central vacuole is seen in most plant cells ✓ Vacuole means “blank space,” referring to its appearance in the light microscope. ✓ The membrane surrounding this vacuole is called the TONOPLAST, because it contains channels for water that are used to help the cell maintain its tonicity, or osmotic balance. ✓ This allows the cell to expand and contract depending on conditions. ✓ Can serve as storage organelles for sugars, polysaccharides, organic acids and proteins ✓ Can be viewed as a micro-kidney inside each plant cell, filtering and sequestering potentially toxic ions from the cytosol. LYSOSOMES LYSOSOMES ✓ Membrane-bounded digestive vesicles, called lysosomes, are also components of the endomembrane system ✓ Arising from the Golgi apparatus, they contain high levels of degrading enzymes, which catalyze the rapid breakdown of proteins, nucleic acids, lipids, and carbohydrates. ✓ The enzymes of lysosomes are formed in the RER and are modified within the Golgi apparatus. ✓ Once modified, they leave the Golgi in secretory vesicles and fuse with endosomes to form lysosomes. ✓ An endosome is a membrane-bound compartment inside eukaryotic cells. It is a compartment of the endocytic membrane transport pathway originating from the trans Golgi membrane ✓ The lysosomal membrane acts as a protective shield between the powerful digestive enzymes within the lysosome and the cytoplasm, preventing their leakage into the cytoplasmic matrix. ✓ Throughout the lives of eukaryotic cells, lysosomal enzymes break down old organelles and recycle their component molecules. MICROBODIES *PEROXISOMES *GLYOXISOMES MICROBODIES ✓ Are small spherical membrane-bound organelles ✓ Two main types: Peroxisomes and Glyoxisomes Peroxisomes ✓ These are microbodies that carry out oxidation reactions and produce hydrogen peroxide as a by- product ✓ One of the major roles of peroxisomes is to break down fatty acids and produce energy in the form of ATP (Adenosine Triphosphate). ✓ The synthesis of lipids (ex: Cholesterol) can also occur in the peroxisomes. ✓ Another prominent role of peroxisomes involves the detoxification of toxins and drugs ✓ Unlike lysosomes, the protein found in peroxisomes are generated in free ribosomes found in the cytosol. Glyoxisomes ✓ Specialized peroxisome found in plant cells ✓ Responsible for oxidizing fatty acids into intermediates that are eventually converted into sugars that are used for energy ✓ In germinating plant cells, this is the major form of sugar production until chloroplasts mature to produce sugar via photosynthesis. MITOCHONDRIA MITOCHONDRIA (Mitochondrion) ✓ “Power Houses of the Cell” ✓ Site of Cellular Respiration and Energy Reproduction ✓ Typically tubular or sausage-shaped organelles that are found in all types of eukaryotic cells ✓ Bounded by two membranes: a smooth outer membrane and an inner folded membrane with numerous contiguous layers called cristae (singular, crista) that play a key role in ATP generation.  The cristae divide the mitochondrion into two compartments: a. matrix - lying inside the inner membrane b. outer compartment, or intermembrane space -lying between the two mitochondrial membranes ✓ On the surface of the inner membrane, and also embedded within it, are proteins that carry out oxidative metabolism. ✓ Oxidative metabolism is the oxygen-requiring process by which energy in macromolecules is used to produce ATP. ✓ Mitochondria have their own DNA. This circular DNA molecule contains several genes that produce proteins essential to the mitochondrion’s role in oxidative metabolism. ✓ Thus, the mitochondrion, in many respects, acts as a cell within a cell, maintaining its own genetic information specifying proteins for its unique functions. ✓ The mitochondria are not fully autonomous, however, because most of the genes that encode the enzymes used in oxidative metabolism are located in the cell nucleus.  PLASTIDS CHLOROPLASTS CHROMOPLASTS LEUCOPLASTS (AMYLOPLASTS) PLASTID (formed, molded) ✓ A membrane-bound organelle found in the cells of plants, algae, and some other eukaryotic organisms. ✓ Surrounded by a double membrane and contain their own DNA. ✓ The site of manufacture and storage of important chemical compounds used by the cells of autotrophic eukaryotes.  Types of Plastids 1. Chloroplasts 2. Chromoplasts 3. Leucoplasts CHLOROPLASTS ✓ Use light to generate ATP and sugars. ✓ Contain the photosynthetic pigment chlorophyll, which gives most plants their green color. ✓ Organelle where photosynthesis takes place. Thylakoid Thylakoid Membrane Thylakoid Space Granum ✓ Each chloroplast contains a system of flattened membranous sacs called THYLAKOIDS. ✓ Thylakoids contain the green pigment CHLOROPHYLL, the main molecule that absorbs light and captures light energy for the cell. ✓ Surrounding the thylakoid is a fluid matrix called the stroma. ✓ The enzymes used to synthesize glucose during photosynthesis are found in the stroma. ✓ Like mitochondria, chloroplasts contain DNA, but many of the genes that specify chloroplast components are also located in the nucleus. ✓ Some of the elements used in photosynthesis, including the specific protein components necessary to accomplish the reaction, are synthesized entirely within the chloroplast. CHROMOPLASTS ✓ Organelles responsible for pigment synthesis and storage in specific photosynthetic eukaryotes. ✓ Carrot root cells, for example, contain chromoplasts filled with the orange pigment carotene ✓ Chromoplasts in flower petal cells contain red, purple, yellow or white pigments. LEUCOPLASTS ✓ Lack pigment and a complex internal structure. ✓ In root cells and some other plant cells, leucoplasts may serve as starch-storage sites. ✓ A leucoplast that stores starch (amylose) is sometimes termed an amyloplast.  MITOCHONDRIA & CHLOROPLASTS COMPARISON ✓ Both have an outer membrane and an extensive inner membrane compartment. ✓ Both also have their own DNA but also have nuclear-encoded proteins. ✓ Mitochondria metabolize sugar to produce ATP. ✓ Chloroplasts harness light energy to produce ATP and synthesize sugars. ✓ Both mitochondria and chloroplasts arose by ENDOSYMBIOSIS, whereby a prokaryotic cell was engulfed by a eukaryotic precursor. RIBOSOMES RIBOSOMES ✓ Are the cell’s protein synthesis machinery ✓ Also known as large RNA–protein complexes outside the nucleus. ✓ Each ribosome is composed of two subunits and each subunit is composed of a combination of RNA, called ribosomal RNA (rRNA), and several dozen different proteins. ✓ The subunits join to form a functional ribosome only when they are actively synthesizing proteins. ✓ This complicated process requires the two other main forms of RNA: messenger RNA (mRNA), which carries coding information from DNA, and transfer RNA (tRNA), which carries amino acids. ✓ Ribosomes use the information in mRNA to direct the synthesis of a protein. ✓ Ribosomes can be thought of as “universal organelles,” because they are found in all cell types from all three domains of life.  2 Types of Ribosome 1. Free ribosomes ✓ synthesize proteins that are found in the cytoplasm, nuclear proteins, mitochondrial proteins, and proteins in other organelles not derived from the endomembrane system. 2. Membrane-associated ribosomes ✓ synthesize membrane proteins, proteins found in the endomembrane system (Rough Endoplasmic Reticulum), and proteins destined for export from the cell. CENTRIOLES Centrosomes ✓ Are microtubule-organizing centers ✓ The region surrounding the centrioles in almost all animal cells ✓ Also responsible for the reorganization of microtubules that occurs during cell division. ✓ The centrosomes of plants and fungi lack centrioles but still contain microtubule organizing centers. CENTRIOLES ✓ are barrel-shaped organelles found in the cells of animals and most protists. ✓ they occur in pairs, usually located at right angles to each other near the nuclear membranes. ✓ Surrounding the centrioles in the centrosome is the pericentriolar material, which contains ring-shaped structures composed of tubulin. ✓ Structures with this function are called microtubule organizing centers. CYTOSKELETON  An Internal Skeleton Supports the Shape of Cells ✓ The flexibility of different shapes of cells is made possible by a complex internal skeleton known as CYTOSKELETON. CYTOSKELETON ✓ Specialized internal structures in the cytosol that provide the “bones and muscles” of the cell. ✓ Maintains the cell’s shape and internal organization ✓ Permits movement of substances within the cell and movement of external projections (cilia or microvilli; flagella in sperm) outside the plasma membrane. The Cytoskeleton Is Composed of Three Types of Protein Fibers Spermatocyte Euglena Cilia, Flagella, and Microvilli CILIA and FLAGELLA ✓ Are small, hair-like projections from cells that are capable of wavelike movement. ✓ Cilia are numerous, short, hair-like projections from cells that, in humans, are used to move substances along the free cell surfaces in areas such as the respiratory and reproductive tracts ✓ Flagella are long, whip-like projections from cells. ✓ In humans, only sperm possess flagella, and each sperm has a single flagellum that enables movement. ✓ Both cilia and flagella contain microtubules that originate from centrioles positioned at the base of these flexible structures. MICROVILLI ✓ are extensions of the plasma membrane that are smaller and more numerous than cilia. ✓ They do not move like cilia or flagella, but they increase the surface area of the plasma membrane and, therefore, aid absorption of substances. ✓ Microvilli are abundant on the free surface of the cells lining the intestines.