Cell Biology Notes - IB

Cell Biology Notes Water and Life The first cells that formed were essentially water trapped in a membrane Water can dissolve many chemicals, and allow for them to react Almost all biochemical reactions must take place in water Water has two major chemical prop...

Cell Biology Notes Water and Life The first cells that formed were essentially water trapped in a membrane Water can dissolve many chemicals, and allow for them to react Almost all biochemical reactions must take place in water Water has two major chemical properties that make it so important for life: ○ Its polar nature ○ Its shape Water’s Polar Nature Water is a polar molecule - it has a positive and negative pole Hydrogen and oxygen are bound together by covalent bonds ○ Intramolecular force This sharing is unequal, so the electrons are pulled closer to the oxygen ○ Oxygen has a partial negative charge (δ-) ○ Hydrogens have a partial positive charge (δ+) Water’s Polar Nature Because water molecules are bent, the hydrogens are on the same side, with oxygen on the other This gives water a positive pole (with hydrogens) and a negative pole (with oxygen) Hydrogen Bonds Water has partial charges, so the bonds between water molecules are weak, but still significant The attraction between two water molecules is known as a hydrogen bond ○ This is an intermolecular force Due to how numerous water particles are, they produce many hydrogen bonds which gives water unique properties Cohesion Water molecules are attracted to one another ○ They “stick” together due to hydrogen bonding ○ It takes energy to break these hydrogen bonds This is known as cohesion Living systems take advantage of this ○ Xylem in plants ○ Water-beetles Cohesion in Living Systems Xylem - as water molecules are pulled upwards, they pull up the water molecules behind them Surface Tension - organisms can stay on the surface of water by not breaking the cohesive forces between molecules Adhesion Many solids are polar, they attract other polar molecules This causes water to “stick” to solids easily ○ This is known as adhesion This can also cause movement - capillary action ○ The movement of water through a narrow tube ○ Hydrogen bonds form between water and solid ○ Water is pulled upwards - against gravity Solvent Properties of Water When a substance dissolves, the particles of that substance are separated and dispersed into a liquid ○ Liquid = solvent ○ Separated particles = solutes Water’s polar nature make it an excellent solvent ○ Water molecules make a “shell” around the solute particles Prevents them from clumping together  Any substance that dissolves in water (polar or charged) is considered hydrophilic - water-loving Substances that don’t dissolve in water (non-polar) are considered hydrophobic - water-fearing ○ They are not attracted to water Water is not a universal solvent, but it does dissolve many things useful for metabolism Metabolism Cytoplasm is mostly composed of water with various substances dissolved in it ○ Enzymes, solutes Enzymes allow for chemical reactions to take place ○ This is known as metabolism Without water, the components of the reaction could not reach the enzymes ○ Water is the medium for metabolism Transport Due to its fluid nature, water can transport dissolved substances in aqueous solutions ○ Plants: ions in xylem, sugar in phloem ○ Animals: nutrients, ions, gases in blood plasma Living in Water Organisms that live in water must contend with water’s physical properties Buoyancy - objects less dense than water float, and will sink if they are more dense ○ Living in water means you must control your density Ex. Air bladders, Gas vesicles Living In Water Viscosity - High viscosity (slower moving) liquids produce more friction and are more difficult to swim though ○ Ex. Saltwater is more viscous than Freshwater  Thermal Conductivity - The rate at which heat passes through a material ○ Water has a high thermal conductivity This means it absorbs heat from organisms living in it Osmosis Water Movement Water molecules are always moving As they move, hydrogen bonds are repeatedly broken and formed ○ Hydrogen bonds are not very strong Intermolecular attractions between water and solutes are stronger ○ This means water particles move slower as solutions If water is able to move from one area to another, it will always move in both directions But, there will be net movement towards the more concentrated solution ○ Due to the difference of speed of water molecules ○ This is known as osmosis Hypotonic - A solution with a low solute concentration (compared to the cell) Hypertonic - A solution with a high solute concentration (compared to the cell) Isotonic - A solution with an equal concentration Water will always move from a hypotonic solution to a hypertonic solution until they are isotonic to each other ○ No more net movement of water Tonicity Water Movement Cell membranes are very permeable to water, but not as readily permeable to most solutes There is often a difference in solute concentration on the inside compared to the outside of the cell Water movement can be controlled by the cell by either changing ○ The permeability of the membrane  ○ The concentration of solutes inside the cell Animal and Plant Cells If an animal cell is placed into a hypotonic solution, water rushes into the cell ○ This causes it to swell up and potentially burst - lysis If a plant cell is placed in a hypotonic solution, it will not burst - it becomes turgid ○ Why would this be? Why might this be good for the plant? Plant Cells If a plant cell is placed in a hypertonic solution - it will lose water and therefore pressure inside the cell The plant cells will become flaccid or limp There is not enough pressure pushing against the cell wall The cell membrane will eventually pull away from the cell wall ○ This is known as plasmolysis Medical Implications of Osmosis Hypertonic and Hypotonic solutions damage human cells (in particular RBCs) We want plasma to be isotonic to our red blood cells Medical solutions (IV drips) must be in isotonic solutions to be safe for use Developments in Microscopy Microscopes were first invented in the 17th century. They allowed for the discovery of cells.As microscopes have improved, our understanding of cells and tissues has improved dramatically. Compound light microscopes first allowed us to discover bacteria, chromosomes, mitosis, and meiosis. As microscopes advanced, we began to see the inner workings of cells At magnifications of more than 400X, it becomes harder to produce a focused image with just a light microscope  Electron Microscopes - which use beams of electrons were a vast improvement ○ These can magnify things up to 1,000,000X their original size ○ The images produced by these microscopes are also high resolution ○ Drawbacks: Cannot produce colour images, cells need to be dead in order to examine them Fluorescent Stains Most cell parts are white or colourless and need to be stained… but chemical stains may only bind to some chemicals in the sample but not others Fluorescent Stains use intense light sources (lasers, high power LED). ○ The light is absorbed by the sample and re-emitted by the sample, generating bright images Immunofluorescence Immunofluorescence is an advancement in fluorescent staining Antibodies are produced that bind to particular chemicals (antigens) in the sample A multi-coloured fluorescent image can then be produced showing where different chemicals are located Freeze-Fracture Electron Microscopy Produces images of surfaces within cells A cell is rapidly frozen, then broken with a steel blade - fracturing it The ice on the fractured surface is removed to enhance the texture - etching A replica is taken of the fracture and can then be examined with an electron microscope Best for showing texture of a cell part Cryogenic Electron Microscopy Typically used to research the structure of proteins A protein solution is flash frozen and analyzed with an electron microscope Because protein molecules can be randomly oriented, a computer algorithm analyzes the different patterns and generates a 3D image of the protein structure Organelles Cell Structure Cells are the fundamental unit of life All living organisms are made of cells ○ Some are multicellular, others are unicellular Cells come from other cells There are two major types of cells ○ Eukaryotic ○ Prokaryotic Structures Common to All Cells Prokaryotic and Eukaryotic cells have three common features: Plasma membrane - surround and protects the cell a. Controls what enters and exits b. Maintains concentration differences between the inside and outside Cytoplasm - aqueous solution inside the cell - site of many metabolic reactions DNA - Information for a cell to carry out its functions Prokaryotic Cells Prokaryotes are single-celled organisms with a simple cell structure that lacks membrane-bound organelles - no compartmentalisation Come in a variety of shapes: rods (bacilli), spheres (cocci), spirals (spirilla), commas (vibrio) or corkscrews (spirochetes) Prokaryotic cells do not have a nucleus DNA is found within a region of the cytoplasm known as the nucleoid ○ Has a light appearance when viewed with an electron microscope May also have additional DNA molecules (plasmids) that have been exchanged with other bacteria DNA in a prokaryotic cell is “naked” - it does not wrap around protein and is free in the cytoplasm Prokaryotes are classified into two different groups (domains) Bacteria - diverse group of organisms, many are pathogens Archaea - live in extreme environments Ribosomes in prokaryotic cell are small in size (70S) compared to eukaryotic cells Contain a cell wall, may have an additional outer covering as well Some have hair-like extensions, pili, which help with adhesion Some have a whip-like projection, a flagellum, for movement  Eukaryotic Cells Eukaryotes are organisms whose cells have a nucleus and are compartmentalized by membrane-bound organelles ○ This allows for greater specialization and efficiency within the cell Eukaryotic Cells Eukaryotes are organisms whose cells have a nucleus and are compartmentalized by membrane-bound organelles ○ This allows for greater specialization and efficiency within the cell ○ DNA is found in the double-membrane nucleus ○ DNA is wrapped around proteins (histones) ○ Ribosomes are larger (80S) ○ All eukaryotes have mitochondria, endoplasmic reticula, golgi body and vesicles Plant cells possess chloroplasts and have a large central sap vacuole Eukaryotic Cell Structures - Other Organelles Peroxisome - Digests toxic substances from metabolic reactions - similar to a lysosome Centrosome / Centrioles (animal cells) - Allow for chromosome movement during cellular division Eukaryotic Organisms Separated into four distinct kingdoms - based on structural and functional differences: ○ Animals - heterotrophic nutrition (ingestion) ○ Plants - autotrophic nutrition ○ Fungi - heterotrophic nutrition (absorption) ○ Protist - Any eukaryotic organism that is not an animal, plant or fungi - often unicellular Differences in Cell Structure Animal Plant Fungus Cell Wall None Cellulose Chitin Vacuoles Small Large and Central Large and Central Temporary Permanent Permanent Motility (movement) Motile Non-motile Non-motile Have Cilia and Flagella No Cilia or Flagella No Cilia or Flagella Organelles Centrioles Chloroplast No unique organelles Lysosome Processes of Life; Vital Processes that Living Things Must Undertake: 1. Homeostasis - Constant internal environment 2. Metabolism - Biochemical reactions in the cell 3. Nutrition - Obtaining chemicals required for energy, growth and repair 4. Excretion - Removal of waste 5. Growth - An increase in size or number of cells 6. Response to Stimuli - Sensing and reacting to environment 7. Reproduction - Production of offspring Atypical Cells in Eukaryotes Recall: all living organisms are made up of cells Typically have specific organelles: ex: a nucleus Some structures, however, do not follow the typical patterns Atypical Cells in Eukaryotes: Red Blood Cells Mature red blood cells are enucleated - They lack a nucleus Nucleus moves to edge of cytoplasm - The area of the cell containing the nucleus is pinched off - Phagocyte (white blood cell) destroys it Enucleation allows red blood cells to be smaller and more flexible - Without a nucleus, can’t repair itself; thus short lifespan (100-120 days) Atypical Cells in Eukaryotes: Phloem Sieve Tube Elements - In Phloem Sieve tubes, dividing walls between adjacent cells (cells that are side-by-side) have large pores for sap to pass through - During development, the nucleus, and most of the other cell contents break down. - The plasma membrane remains - Subunits in sieve tube called elements instead of cells because of the structure - Sieve tubes are alongside companion cells that have mitochondria and nucleus  - These cells help the sieve tube elements survive Atypical Cells in Eukaryotes: Skeletal Muscle - Cells are multinucleated (More than 1 nuclei) - Contains long cylindrical fibres that are formed from the fusion of individual cells - Fibres therefore have a continuous plasma membrane and multiple nuclei - Muscle fibre operates as a single functional unit, made of multiple cells fused together Should it be called a cell? Atypical Cells in Eukaryotes: Aseptate Fungal Hyphae - Hyphae (fungal roots) have walls (septa) that are between cells - If a hyphae lacks septa and cell membrane between cells, these are referred to as “nonseptate” hyphae - This results in a large multinucleate structure (AKA: coenocyte) Membrane Transport Cell Membranes Cell membranes enclose the cellular contents - separates them from the external environment ○ This allows the cell to maintain an internal environment that is separate from the external - homeostasis  Cell membranes have two properties that allow them to maintain homeostasis: ○ Semi-permeability ○ Selectivity Cell membranes have two major components: phospholipids and proteins Phospholipids Phospholipids have a polar head (glycerol and phosphate) and two nonpolar tails (fatty acids) The head is hydrophilic, the tails are hydrophobic This makes a phospholipid an amphipathic molecule Phospholipids spontaneously form bilayers in water ○ tails forming the center ○ heads on the outside The hydrophobic central layer restricts the  movement of most polar molecules Individual phospholipids are able to move - allowing the cell membrane to change shape (be fluid) Membrane Proteins The phospholipid bilayer is embedded with proteins - forming a mosaic These proteins can be: ○ Integral - permanently attached to the bilayer, typically transmembrane (cross the entire bilayer) ○ Peripheral - attach to the membrane surface Membrane Protein Functions Membrane proteins serve a variety of functions Junctions - Connect and join two cells together Enzymes - Carrying out metabolic functions on the membrane Transport - Facilitated diffusion and active transport Recognition - Identifying cells (antigens) Anchorage - Attachment points for cytoskeleton and extracellular matrix Transduction - Function as receptors for hormones Glycosylation Phospholipids and proteins can have carbohydrate chains added to them ○ This forms glycolipids and glycoproteins The carbohydrate extends to the extracellular side of the membrane and can function for adhesion and recognition Both also help the cell anchor to the extracellular matrix Simple Diffusion Diffusion - is the net movement of particles from high to low concentration - does not require energy Simple Diffusion occurs in cells for particles that can pass between the phospholipids Possible for small, nonpolar molecules (O2) Lipophilic (fat-loving)particles can also follow simple diffusion Charged particles (ions) cannot follow simple diffusion Osmosis Water can move in and out of cells freely, even though they are polar molecules ○ Small enough to cross through the phospholipid bilayer Many cells have aquaporins, water channel proteins ○ Greatly enhance the cell membrane’s permeability to water  Facilitated Diffusion For large, charged or polar molecules, diffusion is only possible through a channel protein ○ A transmembrane protein with a pore Particles still diffuse down their concentration gradient, using the channel protein as a passageway There are specific channel proteins for each solute Does not require ATP Active Transport Active transport requires particles to move from low to high concentrations ○ Creates an internal environment that is different than the external environment ○ Requires energy (ATP) This often requires pump proteins ○ Only move particles in one direction ○ Change shape to force particles up their concentration gradient Cell Compartmentalization Eukaryotic Cells Remember - Eukaryotic cells are more efficient than prokaryotic cells because they have discrete organelles Each organelle is specialized to carry out specific tasks Eukaryotic cells are compartmentalized Advantages of Compartmentalization Separation of the Nucleus and Cytoplasm ○ Keeping the DNA inside the nucleus keeps it safe! ○ Separation of Tasks Within the Cytoplasm ○ Enzymes and substrate can be more concentrated in a small area ○ Protection from harmful chemicals ○ pH can be maintained at different levels for different metabolic reactions ○ Organelles can be moved ○ Larger membrane surface area for processes that take place across a membrane Example: Garlic Cells Garlic cells contain a harmless substance - alliin in vacuoles An enzyme, alliinase, is stored in other parts of the cell When alliin and alliinase mix, alliin is converted to allicin ○ This has a strong smell and flavour and is toxic to some herbivores ○ This compound is not formed unless the cells are damaged causing the mixture Garlic cells contain a harmless substance - alliin in vacuoles An enzyme, alliinase, is stored in other parts of the cell When alliin and alliinase mix, alliin is converted to allicin ○ This has a strong smell and flavour and is toxic to some herbivores ○ This compound is not formed unless the cells are damaged causing the mixture Cell Specialization All living things are made up of cells But the individual cells in different tissues can be quite different from one another The function that a cell has helps determines its structure Cells vary in size, shape and organization SA:Volume Ratio Cell size is limited by the energy and material requirements needed to stay alive ○ Volume determines how much energy a cell consumes - larger cells consume more energy ○ Surface Area determines the rate of exchange with surroundings - larger surface area = increased exchange efficiency As a cell grows larger, its volume increases faster than its surface area Therefore, we get a decrease in the SA : Volume Ratio If the metabolic rate exceeds how quickly the cell can obtain material, the cell will die So it is best for cells to be small! Being Multicellular Multicellular organisms are formed by repeated cell division and the grouping of similar cell types Being multicellular allows organisms to exceed body limits caused by the SA:Vol ratio Rather than cells needing to grow larger, we just grow more of them Cell Specialization In multicellular organisms, cells become specialized to form different cell types Each cell does a small number of functions extremely efficiently ○ These different cells interact to achieve complex functions Differentiation Every cell in a multicellular organism is a clone of an original parent cell (except gametes) ○ The original parent cell is a fertilized egg (zygote) All cells that come from this will have identical DNA ○ Certain cells will express specific genes, others will express other genes Stem Cells Stem Cells are unspecialized cells with two key properties: ○ Self-Renewal - they can divide continuously ○ Potency - they have the ability to differentiate When a stem cell differentiates and becomes specialized, it cannot change again ○ Stem cells are limited in availability Types of Stem Cells There are three types of stem cells that are found at different stages of development: Totipotent - can form any cell type and divide into new organisms Pluripotent - can form any cell type Multipotent - can form a number of closely related cell types