General Biology: Cell Structure Notes - Samara University PDF

Samara University College of Natural and Computational Sciences Department of Biology General Biology for remedial program student Prepared by: Sadik Hussen (MSc) 2023 MAR,...

Samara University College of Natural and Computational Sciences Department of Biology General Biology for remedial program student Prepared by: Sadik Hussen (MSc) 2023 MAR, Samara, Ethiopia 1  UNIT 3. discovery of the cell & the cell theory Cells were first discovered by English scientist called Robert Hooke in 1665. The first cells seen by Robert hook were dead cells. The first living cells were observed by a dutch scientist called Anton Van Leeuwenhoek He called tiny organism which he observed ‘’Animalcules’’ meaning little animals In the 1830‘s two German scientists proposed that all living things are composed of cells (their names were Mathias Schleiden and Theodore Schwann). A German pathologist, Rudolph Virchow extended this idea by contending that cells arise only from other cells (cells arise from pre-existing cells by cell division).  Formulation of the cell theory Matthias Schleiden (1838) o Is a German Botanist (study of plant) o said that all plants are composed of cells. Theodor Schwann(1839) o Is a German Zoologist (study of animals) o discovered that all animals are made of cells Rudolf Virchow (1855) o is a German physician o “ said that cells only come from preexisting cells". The combined work of Schleiden, Schwann and Virchow make up the cell theory (doctrine) 3.1. The Cell Theory (Cell Doctrine)  The cell theory (the cell doctrine) is a principle that states : 1. All living things (unicellular or multicellular organisms) are composed of one or more cells. 2. The cell is the basic, structural and functional unit of life (living things) (the cell is the smallest living unit of structure and function of all organisms) 3.All cells arise(comes) from pre-existing cells through cell division((continuity of life from one generation to another has a cellular basis).  3.2. Types of Cells  There are two basic classes(types) of cells 1. Prokaryotic Cells: are cells lacking membrane bounded nucleus and lack of membranous organelles. E.g. bacteria and cyanobacteria (Blue Green Algae) Fig.3.1. General structure of prokaryotic cells 2. Eukaryotic Cells: are cells they have membrane bounded nucleus and membranous organelles. E.g. Protists, fungi, plants and animals.  A typical eukaryotic cell has 3 major parts: 1. The plasma membrane: the outer boundary of the cell. 2. The cytoplasm: the intracellular fluid packed with organelles ( small structures that perform specific cell functions). 3. The nucleus: an organelle that controls cellular activities. Typically the nucleus resides near the cells center.  3.2. Cellular Organelles  Organelle is a specialized subunit within a cell that has a specific function of the cell.  In Eukaryotes an organelle is a membrane bound structure found within a cell.  Prokaryotes are cells that do not have membrane bound organelles. 3.3. organelle structure and function 1. Nucleus: is largest part of cell that surrounded by a double-layered membrane.  the nucleus governs most cellular activities and serves as the cell‘s master (the brain or “control center” of the cell).  Contains the DNA which makes up the chromosomes.  Surrounded (covered) by double nuclear membrane (nuclear envelope) which contains nuclear pores for allowing certain materials to enter and leave from the nucleus to cytoplasm.  2. Cytoplasm Is the whole internal structure of the cell without the nucleus. It is filled with jelly substance and consists of thousands of structures called organelles. It is a center for the chemical reaction of the cell. The major organelles that are found in the cytoplasm are : mitochondria, endoplasmic reticulum, Golgi complex. Ribosome, etc 3. Endoplasmic reticulum (ER):  is the network of internal membranes extending through the cytoplasm.  it connects the nucleus with the cell membrane.  there are two forms of endoplasmic reticulum in a cell. These are:  Rough endoplasmic reticulum  have ribosome on its membrane surface  it is involved in protein transport which is synthesized by ribosome.  Smooth endoplasmic reticulum  have no ribosome on its surface  it is concerned with lipid synthesis, carbohydrate metabolism and detoxification. 4. Golgi complex (Apparatus):  A series of flattened sacs that modifies, packages, stores and transports materials out of the cell(called as “shippers of the cell” ).  Looks like a stack of plates that Stores, modifies and packages proteins  Processing the raw material into finished products(the raw proteins from the ER are modified)  Sorting and directing finished product to their final destination 5. Lysosomes:  are membrane-enclosed sacs containing powerful hydrolytic enzymes capable of digesting and removing unwanted cellular debris and foreign materials.  Lysosomes serve as the intracellular “digestive system” 6. Ribosome :  are found attached to rough endoplasmic reticulum and some are free in the cytoplasm.  they are composed of RNA and protein.  are involved in protein synthesis. 8. Mitochondria: are the “power houses‘‘ of a cell; they extract energy from nutrients in food and transform it into usable form to energize cell activity.  Responsible for site of cellular respiration  Known as "Powerhouse of the cell“ because they carried out cellular respiration (contains respiratory enzymes that make ATP) (releases energy)  Contain their own DNA called mitochondrial DNA (mDNA)  Are site of cellular respiration to release energy for the cell to use (ATP)  Bound by a double membrane called inner and outer membranes  9. Chloroplasts  they highly participate in the process of photosynthesis which is a process by which plants synthesize their own food.  They are located in outer surface of the cell to receive enough light.  Chloroplasts are green colored due to the chlorophyll pigments found in its internal parts.  Are the site of photosynthesis (the conversion of light energy to chemical energy by chlorophyll in chloroplasts).  10. Vacuoles (the water tower of the cell)  Are membrane bound cytoplasmic spaces containing materials  Vacuoles are help to maintain water balance.  One Large central vacuole usually present in plant cells  Many smaller vacuoles are present in animal cells  Storage container for water, food, enzymes, wastes, pigments, etc.  Two Types: – Food vacuole--store and digest ingested food – Contractile vacuole- pumps excess water from cells to maintain homeostasis  11. Plasma/cell membrane  Is semi/ partially permeable membrane that controls the movement of substances in and out of the cell.  some of the substances that pass across the cell membrane are carbon dioxide, oxygen and water. It is made up of protein and lipid bi layer. Thus, it is called a lipoprotein layer.  The cell membrane is a living layer of a cell which is found on the external layer of animal cells, while in plant cells it is found next to the cell well.  Functions of Plasma membranes:  Regulated transport of substances- selectively transport of substances into or out of the cells.  Encloses the cell & defines cell boundaries-Enclosure and insulation of cells and organelles.  Maintains the essential differences between the cytosol (intracellular fluid) and the extra cellular environment.  Signal Transduction-production and transmission of signals.  Enzymatic catalysis of reactions.  Interactions with other cells- cell to cell communication  Anchoring of the cytoskeleton- adhesion/attachement of cells/organelles Structure of the cell membrane  Molecular composition of the cell membrane  All plasma membrane are made up of lipids and proteins plus small amount of carbohydrates. ► Lipids(membrane lipids)  Phospholipid bilayer  Cholesterol ► Proteins(membrane proteins)  Peripheral proteins  Integral proteins ► Carbohydrates(membrane carbohydrates)  Oligosaccharides on glycoprotein and Glycolipids 20 a) Membrane proteins- in the membrane it is present as enzyme protein, carrier protein and structural protein.  The enzyme proteins have catalytic activity  The carrier proteins help to transport materials in and out of the cell  The structural proteins play an important role to form the structure of membrane.  There are two classes of membrane proteins that compose cell membrane based on their position in/on the plasma membrane. 1. Peripheral proteins ( extrinsic proteins) 2. Integral proteins (intrinsic /transmembrane proteins) 1. Peripheral proteins ( Extrinsic Proteins)  Do not penetrate the lipid bilayer to any significant degree  they are anchor integral proteins to the cytoskeleton 2. Integral proteins (intrinsic /transmembrane proteins) ► Possess hydrophobic surfaces that can readily penetrate the lipid bilayer itself in the plasma membrane ► play an important role In moving substance across the membrane. b) Membrane Carbohydrate: Short-chain carbohydrate on the outer membrane surface serves as  participating in cell recognition and adhesion , either cell-cell signaling or cell pathogen interactions  they have a structural role as physical barrier. c) Membrane lipids are lipid bilayer of many cell membranes and is composed of 1. Phospholipids-are constructed from four components  Two fatty acid chains (non-polar tail group- hydrophobic)  A phosphate group (polar head group-hydrophilic)  An alcohol (glycerol or sphingosine) attached to the phosphate (polar head group-hydrophilic)  Nitrogen containing bases (polar head group-hydrophilic) (choline, serine, ethanolamine, inositol, etc) 2.Cholesterol  reduce the fluidity of the memberane. 3. Glycolipids  Serve as signaling molecules  Have thee main components (fatty acid, sugar and cerebroside)  Are type of compound lipids that contain glycan (carbohydrate)  found exclusively on the extracellular layer of the membrane  Constitute 2–10 % of the total lipid in plasma membranesand and they are most abundant in nervous tissue.  3. Cellular diversity  Cells are found in different organisms, and are very diverse in their size, shape and their internal structure and this also applies to cells found in the same organism.  This diversity is influenced by their roles and function within organism‘s body. 3.1. Cell Shape: Cells have different shapes due to appropriate function. 3.2. Cell size: The size of a cell is directly related to its level of activity and the rate that molecules move across its membranes.  In order to stay alive, a cell must have a constant supply of nutrients, oxygen, and other molecules. It must also be able to get rid of carbon dioxide and other waste products that are harmful to it. The larger a cell becomes, the more difficult it is to satisfy these requirements; consequently, most cells are very small.  A small cell has more surface area than a large cell for a given volume of cytoplasm.  Two basic Advantages of a cell to being small : 1. Small cells have large surface area to volume ratio than large cells (i.e., higher s/v) – support greater nutrient exchange (things can be moved in and out efficiently) per unit cell volume – tend to grow faster than larger cells 2. the cell's nucleus (the brain of the cell) can only control a certain amount of living, active cytoplasm.  3.4. Transport Across Cell Membranes  Not all particles can actually pass through a plasma membrane unaided.  Most biological molecules are unable to diffuse through the phospholipids bilayer, so the plasma membrane forms a barrier that blocks the free exchange of molecules between the cytoplasm and the external environment of the cell.  Specific transport proteins (carrier proteins and channel proteins) then mediate the selective passage of small molecules across the membrane, allowing the cell to control the composition of its cytoplasm 27 In general  Small non-polar molecules, such as O2 and N2 readily dissolve in lipid bilayers and therefore diffuse rapidly across them.  Small uncharged polar molecules, such as water and urea, also diffuse across a bilayer, able it much more slowly  By contrast, lipid bilayer is highly impermeable to charged molecules (ions) such as Na+ and K+ Cl-, HCO3-, small hydrophilic molecules like glucose, macromolecules like proteins and RNA can not freely diffuse through the plasma membrane 28  Types of Membrane Transport 1. Passive transport- the movement of substances from high concentration to lower concentration down concentration gradient without the expense of energy. Three types. Simple diffusion: through the phospholipid bilayer Facilitated diffusion: through channel proteins or aided by carrier proteins Osmosis: is the net movement of water from diluted solution to concentrated solution 2. Active transport- the movement of substances from lower concentration to high concentration against concentration gradient with the expense of energy. It Includes: Endocytosis Exocytosis 29  Diffusion  Diffusion is the random movement of molecules from region of high concentration to the region of low concentration.  Simple Diffusion: The simplest mechanism by which molecules can cross the plasma membrane is simple diffusion.  During simple diffusion, A molecule dissolves in the phospholipid bilayer and diffuses across it It does not need energy for the process. No membrane proteins are involved the direction of transport is determined simply by the relative concentrations of the molecule inside and outside of the cell. 30 ► The net flow of molecules is always downhill their concentration gradient—from a compartment with a high concentration to one with a lower concentration of the molecule ► Molecules that can pass through plasma membrane by simple diffusion are:  Gases (such as O2 and CO2)  Hydrophobic molecules (such as benzene)  Small polar but uncharged molecules (such as H2O and ethanol) are able to diffuse across the plasma membrane. ► Other biological molecules, however, are unable to dissolve in the hydrophobic interior of the phospholipid bilayer and can not diffuse freely through the plasma membrane. This includes:  Larger uncharged polar molecules such as glucose, proteins  Charged molecules of any size (including small ions such as H+, Na+, K+, and Cl-). 31  Facilitated Diffusion ► Facilitated diffusion like simple diffusion, involves  No external source of energy  The direction of the transport is down hill ► Facilitated diffusion differs from simple diffusion in that The transported molecules do not dissolve in the phospholipid bilayer. Instead, their passage is mediated by proteins that enable the transported molecules to cross the membrane without directly interacting with its hydrophobic interior.  It allows the movement of polar and charged molecules, such as carbohydrates, amino acids, nucleosides, and ions, to cross the plasma membrane. The direction of their transport is determined both by the concentration and voltage (electrical) differences- Electrochemical gradient 32  Types of proteins that mediate facilitated diffusion ► There are two types of proteins that mediate facilitated diffusion are 1. carrier proteins and 2. Channel proteins. Carrier proteins ( are also known as transporters) Carrier proteins transport a wide variety of ions and molecules across cell membranes. There are Three types of transporters have been identified 1. Uniporters 2. Symporters 3. Antiporters 33  Uniporters: transport a single type of molecule down its concentration gradient via facilitated diffusion Symporters are also known as Co- transporters  They transport two different solutes simultaneously in the same direction Antiporters: are also known as counter transporters  They transport two different solutes simultaneously but in opposite direction 34  Channel Proteins  They form a hydrophilic passageway across the membrane through which polar molecules or ions move  In contrast to carrier proteins, Channel proteins simply form open pores in the membrane, allowing small molecules of the appropriate size and charge to pass freely through the lipid bilayer. E.g. Porins: permit the free passage of ions and small polar molecules through the outer membranes of bacteria. Aquaporins: water channel proteins through which water molecules are able to cross the membrane much more rapidly than they can diffuse through the phospholipid bilayer. Ion Channels: are the best-characterized channel proteins which mediate the passage of ions across plasma membrane 35 Factors That affect the rate of Diffusion Distance : the shorter distance the faster diffusion Size of molecules: Smaller molecules, faster diffusion  Size of pores in membranes Temperature: Higher temperature, faster diffusion Steepness of Concentration gradient: Steeper gradient, faster diffusion 36  Osmosis ► Osmosis: is the diffusion of water through a selectively permeable membrane ► Water moves from high water area to low water area or from dilute(weak) solution to concentrated (strong) solution ► If two solutions have unequal solute concentration, the solution with higher solute concentration is known as Hypertonic (hyper= more than) and the one with low solute concentration is known as hypotonic (Hypo= less than). ► If the solute concentration of two solutions are equal the solutions are said to be Isotonic ( Iso= same) ►In cells, plasma membrane separates two aqueous solutions, one inside the cell(cytoplasm) and one outside (extracellular fluid). ►The direction of net diffusion of water is determined by solute concentration of either side 37  Tonicity: is a measure of the osmotic pressure (as defined by the water potential of the two solutions) of two solutions separated by a semi-permeable(selectively ) membrane Solution = Solute + Solvent (water)  there are three types of solution tonicity : these are ►Hypotonic solution- high amount of water + low amount of solute (dilute solution)- there is net water movement ►Hypertonic solution - high amount of solute + low amount of water (concentrated solution) – there is net solute ►Isotonic solution- the amount of water equals with the amount of solute (normal solution) - there is no net solute/water  Direction of Osmosis ► The net direction of osmosis depends on the relative concentration of solutes on the two sides (outside & inside) of the membrane. ► When the concentration of solute molecules outside the cell is lower than the concentration in the cytosol, the solution outside is hypotonic to the cytosol. In this situation, water diffuses into the cell until equilibrium is reached. ► When the concentration of solute molecules outside the cell is higher than the concentration in the cytosol, the solution outside is hypertonic to the cytosol. The water will diffuse out of the cell until equilibrium is established. ► When the concentration of solutes outside and inside the cell are equal, the outside solution is said to be isotonic to the cytosol. The water diffuses into and out of the cell at equal rates, so there is no net movement of water. 39 Lower concentration Higher concentration Same concentration of solute (sugar) of sugar of sugar H 20 H2O Selectively permeable mem- brane: sugar mole- H20 cules cannot pass through pores, but water molecules can Solutes Net flow of water Osmosis  Activity. 1 1. What will happen to plant cells and animal cells if placed in the following solutions? a) Hypotonic solution b) Hypertonic solution c) Isotonic solution 41  Effects of Osmosis on Water Balance of cells Animal cells: 1. If animal cells are placed in Hypotonic solution: ‾ Water moves into the cell and the Cells swell up and finally burst (lysis) ‾ The pressure will eventually burst the weak plasma membrane: this is called Haemolysis. 2. If animal cells are placed in Hypertonic solution: ‾ Water moves out (leaves ) of the cell and the Cells finally shrink a condition called crenation. 3. If animal cells are placed in Isotonic solution ‾ No net flow of water into or out of the cell. This maintains normal animal cell volume 42  Plant, Algal, Fungal and Bacterial Cells: 1. If Plant, algal, fungal and bacterial cells placed in Hypotonic solution  Unlike animal cells they are surrounded by a rigid cell wall  Because of the cell wall, the osmotic influx of water that occurs when such cells are placed in a hypotonic solution (even pure water) leads to an increase in intracellular pressure called osmotic pressure  The osmotic pressure also called turgor pressure, generated from the entry of water into the cytosol pushes the cytosol and the plasma membrane against the resistant cell wall. In this case the cell get turgid and turgidity maintains normal cell volume. 2. If Plant, algal, fungal and bacterial cells placed in Hypertonic solution  The water will diffuse out of the cell and the protoplasm of the cell shrink. The condition known as plasmolysis. 43 What will happen to plant and animal cells if placed in the following solutions? 44 Factors That Affect The Rate Of Osmosis Temperature: Higher temperature, more vigorous vibrations, higher diffusion of water Concentration gradient: Larger concentration gradient, faster osmosis. Surface area to volume ratio: Higher SA:V, faster osmosis Permeability of membrane (for water): More permeable, faster. Permeability of membrane (for solute): More permeable, reduce average rate of osmosis The distance the molecules have to move across. so the more distance between the two sides the slow the rate of osmosis. 45  Active Transport  Active Transport: is the pumping of molecules or ions through a plasma membrane against (uphill ) their concentration gradient (from low concentration to high concentration) with the expense of energy.  It requires:  Membrane protein called a transporter and  Energy input The source of energy can be from:  Hydrolysis of ATP  Light energy  Energy stored in ion gradients  Based on the source of energy for the transport active transport is divided into two  Primary active transport (Direct active transport)  Secondary active transport process (Indirect active transport) 46