Bio Chapter 6 PDF

Chapter 6 The Fundamental Units of Life 1. The simplest unit of function in a larger system is a cell 2. The cell is also the simplest collection of matter that can live 3. All cells related to older cells To study cells, biologists use microscopes and the tools of biochemistry ------...

Chapter 6 The Fundamental Units of Life 1. The simplest unit of function in a larger system is a cell 2. The cell is also the simplest collection of matter that can live 3. All cells related to older cells To study cells, biologists use microscopes and the tools of biochemistry --------------------------------------------------------------------------------------------------------------------- Microscopy 1. Microscopes created in 1590 and refined throughout 1600 2. Renaissance scientists first used light microscopes, with light passing through the specimen, and the lenses would then refract the light into such a way where the image becomes magnified 3. Magnification is the ratio of an object's image to its real size; Resolution is the clarity of the image, and can be measured as the minimum distance 2 dots can be separated and still be distinguished as 2 dots 4. Details finer than 0.2 micrometers/ 200 nanometers cannot be distinguished with the light microscope, so most plant/animal/nucleus/bacteria/mitochondria can be seen 5. Contrast also plays a heavy role, as it accentuates differences in parts of the sample, and most improvement in microscopy have been due to innovations like staining or labeling 6. Cell walls first discovered by Robert Hooke in 1665, when he looked at dead cells from an oak tree through a microscope 7. Living cells had to be seen through Antoni van leeuwenhoek’s lens though, but many organelles can not be seen through light microscope 8. In the 1950’s, the electron microscope was created, in which a beam of electrons is blasted onto a specimen to see it. Resolution is inversely proportional to wavelength, and electron beams have short wavelengths, making them ideal for good resolution 9. Cell ultrastructure is the name given to the cell seen through an EM 10. The scanning electron microscope is used to see the surface of the cell. A sheet of gold usually is layered onto a cell, and the EB is sent towards it. The gold becomes excited, and this picture can be translated through the computer via an electronic signal. It is especially useful for depth of field, and seeing the 3d shape of the surface 11. The transmission electron microscope is used more for the internal than the surface. Through the usage of staining with heavy metals in the cell, the electrons become excited and once again provide and image, and instead of lenses, there are electromagnets that feed into a computer 12. Light microscopes allow living organisms to be seen, but EM don't, and the preparation of specimens can cause structures that don't exist to be interpreted as being there --------------------------------------------------------------------------------------------------------------------- Cell Fractionation 1. Cell fractionation splits the cell into different organelles and substructures to individually study them. Most often a centrifuge is used, where the spinning of cells through centrifugal force causes components to separate in layers called pellets. At low speeds, there are large pellets, and at high it is the opposite 2. Method is to blend cells up till homogeneous, called homogenization, and then you spin at different speeds and te, separating old and new, for different things. 1000g-nuclei and  cellular debris, 20000g- mitochondria and chloroplasts, 80000g for membranes, and 150000 for ribosomes 3. This fractionation allows researchers to collect bulk of cell parts and identify their tasks --------------------------------------------------------------------------------------------------------------------- Eukaryotic cells have internal membranes that compartmentalize their functions Comparing Prokaryotic and Eukaryotic cells 1. All cells have a cell membrane called the plasma membrane, which is selectively permeable. Enclosed in that plasma membrane is a jelly like substance called the cytosol/cytoplasm, where organelles are. All cells also have chromosomes/ribosomes 2. DNA is located in different parts of the cell however in eukaryotic/prokaryotic cells. For eukaryotic, the DNA is found in the nucleus, bounded by a double membrane. For prokaryotic, the DNA is located in a non membrane bound area called the nucleoid. 3. Eukaryotic cells are generally bigger than prokaryotic cells. This is due to cellular metabolism setting a limit on size. The smallest bacteria are known as mycoplasmas, with a size of 0.1 to 1 micrometers. Usually bacteria are between 1-5 micrometers, and eukaryotes are usually 10-100 micrometers. (Bacteria are prokaryotic, while eukaryotic aer animal/ plant) 4. The plasma membrane acts as a barrier that allows nutrients, oxygen, and wastes to leave the cell. For every portion of the plasma membrane only a certain amount of substance can cross or leave the cell, and at some point, the cell becomes so large that it is redundant to become larger. As a result, most large organisms don't have larger cells, instead they just have more cells, making them bigger as a whole. ------------------------------------------------------------------------------------------------------------------- A Panoramic View of the Eukaryotic Cell List of Organelles for Animals Flagellum- locomotion for some organelles, made of microtubule Centrosome-Region where microtubules are initiated, centrioles found here as well Cytoskeleton- reinforces cells shape, function, and has components made of proteins, Microfilaments Intermediate filaments Microtubules MicroVilli- projections that increase surface area (spikes) Peroxisome- produces hydrogen peroxide which then turns into water Mitochondria- cellular respiration and ATP made ER- Network of sacs and tubes, active in synthesis of proteins and membrane, has rough and smooth Nuclear envelope- Double membrane enveloping the nucleus, has holes that connect to ER Nucleolus- produces ribosomes, has one or more nucleoli Chromatin- material consisting of DNA and proteins, seen in chromosomes Plasma membrane- membrane enclosing the cell Ribosomes- make proteins, located like everywhere Golgi apparatus- organelle responsible for synthesis, modification, sorting, secretion, and sugar tagging of cell products/proteins Lysosome- place where macromolecules are hydrolyzed *Animals have lysosomes, centrosomes, and flagella ------------------------------------------------------------------------------------------------------------------- List of Organelles for Plants Nuclear envelope- Double membrane enveloping the nucleus, has holes that connect to ER Nucleolus- produces ribosomes, has one or more nucleoli Chromatin- material consisting of DNA and proteins, seen in chromosomes ER- Network of sacs and tubes, active in synthesis of proteins and membrane, has rough and smooth Ribosomes- make proteins, located like everywhere Central Vacuole- storage, breakdown of waste products, hydrolysis of macromolecules Cytoskeleton- reinforces cells shape, function, and has components made of proteins, Microfilaments Intermediate filaments Microtubules Chloroplast: photosynthetic organelle, converts energy from sun to chemical Plasmodesmata: channels through cell walls that connect cytoplasms of cells Cell wall- structural support, made of cellulose, polysaccharides, and proteins Plasma membrane- membrane enclosing the cell Peroxisome- produces hydrogen peroxide which then turns into water Mitochondria- cellular respiration and ATP made Golgi apparatus- organelle responsible for synthesis, modification, sorting, secretion, and sugar tagging of cell products/proteins *Plants contain chloroplasts, central vacuole, cell wall, plasmodesmata ---------------------------------------------------------------------------------------------- The eukaryotic cell’s genetic instructions are housed in the nucleus and carried out by the ribosomes The Nucleus: Information Central 1. The nucleus contains most of the genes in a eukaryotic cell, but some are in mitochondria/chloroplasts. Average nucleus is about 5 micrometers, the nuclear envelope containing the nucleus 2. The nuclear envelope is double membrane, each being a lipid bilayer, separated by a space of 20-40 nanometers, and it also contains pores about 100 nanometers. At the lip of each pore, the inner and outer membranes connect, with an intricate protein structure called the pore complex regulating what comes in and out ( mostly protein and RNA, with some large macromolecules). Except at the pores, the envelope is lined by nuclear lamina, a net of proteins that maintains shape of envelope, and there might be a nuclear matrix with the protein fibers going into the nuclear interior 3. Chromosomes are contained in the nucleus, but only sometimes. Most of the time, the chromatin that makes up these chromosomes is diffused, and when the cell is dividing, the chromatin strands coil into the bundles we know as chromosomes. Each eukaryotic species has a distinct number of chromosomes, and half that amount in its sex cells 4. The nucleolus is located in the nucleus, and it makes Ribosomal RNA (rRNA). It also makes small and large ribosomal units, through imported proteins and rRNA. There can be more than one nucleolus depending on species, and some research says that it might also help in cell division. 5. The nucleus directs protein synthesis through creating mRNA from DNA, and then that mRNA is transported through the nuclear pores into the cytoplasm, and reaches ribosomes that synthesize the protein --------------------------------------------------------------------------------------------------------------------- Ribosomes: Protein Factories 1. Ribosomes are made of rRNA and proteins, and create proteins. Free ribosomes are in the cytoplasm, and bound ribosomes are in the ER/Nuclear envelope’s outside of the nucleus. They can alternate in their locations, but depending on where the protein is synthesized, it has different applications. If synthesized in the cytoplasm, it will work inside the cell, and if synthesized on a bound portion, it will be used in the membrane, exported out of the cell, or used in different organelles. The endomembrane system regulates protein traffic and performs metabolic functions 1. The endomembrane system carries out synthesis of proteins and their transport to membranes/organelles/out of the cell, metabolism and movement of lipids, and detoxification of poisons. The parts of the system can be physically linked for transport, or be connected by vesicles (tiny sacs made of membrane, transporting whatever is inside) 2. The endomembrane consists of the nuclear envelope, the endoplasmic reticulum, the golgi apparatus, lysosomes, vacuoles, and plasma membrane. The Endoplasmic Reticulum: Biosynthetic Factory 1. ER is made of a network of membranous tubules and sacs called cisternae. The ER membrane is called the ER lumen, and separates cytosol and inner EAR. The ER is separated into smooth and rough ER Function of Smooth ER 1. The smooth ER synthesizes lipids, metabolizes carbs, and detoxifies drugs/poisons 2. Lipids, which include steroids, oils, and phospholipids, are made here, and cells like in the testes and ovaries that secrete hormones have an extensive amount of smooth ER. 3. Other enzymes in the smooth ER detoxify, like in the liver cells, and mostly consists of adding hydroxyl to the drug to break it up. Due to the smooth ER’s involvement in the detoxifying process, many sedatives, barbiturates, and alcohols/other drugs will cause the enzymes to become faster at the detoxification process, in turn inciting more usage of the drug to acquire the same effect. 4. This can also cause other drugs to be less accepted and detoxified, as the enzymes also take care of them. Ex. barbiturate abuse causing antibiotics and other drugs to be less accepted. Smooth ER also contains calcium ions that can be released for different reactions. Ex. muscle cells release to contract the muscle. Function of Rough ER 1. As a polypeptide chain grows from a bound ribosome, it is threaded into ER Lumen through nuclear pore, and it folds into its normal shape. Most of these proteins are glycoproteins, which have carbs covalently bonded to them. These proteins will leave through a transport vesicle, from the transitional ER, 2. Rough ER also produces its membrane, adding proteins and phospholipids. Polypeptides destined to be membrane bound are inserted into the ER by hydrophobic properties, and phospholipids are also made for the ER by things in the cytosol. The Golgi Apparatus 1. Transport vesicles end up at the golgi apparatus, where they are sorted, modified, or secreted. The Golgi also contains cisternae, (looking like pita bread?) and there can be hundreds of these. The inside of the cisternae are separated from the cytoplasm, and here  the vesicles from the ER connect to the cis side, and leave after maturing and being tagged into other locations from the trans side. 2. The carbohydrates of glycoproteins are often modified here, with sugar added and removed depending on the necessity, and some phospholipids are also modified here. The golgi also creates some macromolecules, like pectins and certain non cellulose polysaccharides. 3. The Golgi also tags products with phosphate groups or sugars, acting as zip codes for the areas that the products need to be shipped to. Lysosomes: Digestive Compartments 1. A lysosome is a sac of hydrolytic enzymes that animal cells use to digest macromolecules. They work best in acidic environments in the lysosomes, and so if they break, it is not that big of an issue. However, if a large number of lysosomes break, the cell can auto digest itself by accident. 2. Both the hydrolytic enzymes and the lysosomal membrane are made by the rough ER, and are probably produced through budding off the trans side of the golgi body. Lysosomes help in digestion of intracellular issues. Amoebas and other protists eat through a process known as phagocytosis, engulfing the smaller organism and taking it in. 3. Then, the food vacuole in which the smaller organism is contained comes in contact with a lysosome, where it will be digested into its macromolecules and other parts, used by the cell. Some human cells also do this, like the white blood cell macrophages, engulfing diseases and destroying the bacteria. 4. Sometimes, the damaged organelles in a cell can be digested, through a process similar to phagocytosis, called autophagy. Vacuoles: Diverse Maintenance Compartments 1. Vacuoles are membrane bound vesicles whose functions differ in different cells. Some like food vacuoles, have been mentioned already, others like contractile vacuoles, found in freshwater protists, pump out water from their systems if in excess.Plants and fungi have vacuoles that carry out hydrolysis. Large plants often have a large central vacuole, which holds reserves of important organic compounds. 2. It can also be used as a waste disposal site, a storage site for ions like potassium and chloride, color for petals and other stuff, or poison to get rid of predators. Vacuoles also absorb water, which is good for plant growth as cytoplasm is less needed, which takes more time to create. Mitochondria and chloroplasts change energy from one form to another 1. Mitochondria are sites of cellular respiration, creating ATP by extracting energy from sugar, fats and other fuels. Chloroplasts create chemical energy by absorbing solar energy and using it to form organic compounds like sugar and water 2. Mitochondria have 2 membranes separating them from the cytoplasm, and chloroplasts have 3-4 membranes. Their membrane proteins are made by free ribosomes, and by ribosomes inside themselves. A small amount of DNA is also in the mitochondria/chloroplasts, and this allows their proteins to be made in house. 3. The mitochondria/chloroplasts are semiautonomous, and reproduce/grow on their own. Mitochondria: Chemical energy Conversion 1. Basically all eukaryotic cells have mitochondria. Some have one large singular mitochondria, or they may have hundreds-thousands of separate organelles. They tend to  be 1-10 micrometers long. They move around, fuse, break and do a lot of the stuff cells usually do. 2. Mitochondria are enclosed by 2 phospholipid bilayer membranes, each having a unique collection of proteins. The outer is smooth, the inner with folds that increase surface area and are called cristae. The mitochondrial matrix is enclosed by the inner membrane, and here is where ATP is produced. The folds mentioned for surface area are necessary for increased productivity Chloroplasts: Capture of Light Energy 1. Chloroplasts come from a plant organelle family known as plastids. Chloroplasts contain chlorophyll (green pigment), enzymes and proteins that aid in photosynthetic production of sugar. They are usually 2 to 5 micrometers long 2. Chloroplasts have an inner and outer membrane that separates it from cytoplasm, and inside that there are membranes coiled up known as thylakoids. Thylakoids are layered up like poker chips into granum, and surrounding them is stroma, where DNA and ribosomes are held. 3. They also move around like the mitochondria, and move throughout the cytoskeleton, dividing and reproducing Peroxisomes: Oxidation 1. The peroxisome is a specialized metabolic compartment that is bounded by one membrane. Here, enzymes that transfer hydrogen from substrate join them with oxygen, to form Hydrogen Peroxide as a byproduct. Some functions include breaking down fatty acids through the use of oxygen, which make their way to the mitochondria and are used for energy. 2. Some peroxisomes in the liver detoxify alcohol, by removing hydrogen into the peroxide. The Peroxide is poisonous, but becomes water in the organelle as well. Specialized peroxisomes called glyoxysomes are seen in the fat storing area of plants, changing the stored fatty acids into usable sugars. 3. Peroxisomes are made of proteins from the cytosol, lipids made in the ER, and lipids made by itself too, and may split after becoming large. The cytoskeleton is a network of fibers that organizes structures and activities in the cell. 1. A cytoskeleton, which consists of fiber stretching throughout the cytoplasm, consists of microtubules, microfilaments and intermediate filaments Roles of the Cytoskeleton: Support, Motility, and Regulation 1. The cytoskeleton supports shape, which is important for animal cells that lack cell walls. It can be disassembled and reassembled in many different locations, to change the shape of the cell. 2. Cell movement sometimes relies on the cytoskeleton. It is called cell motility, and through the work of the cytoskeleton and motor proteins, this can occur. The motor protein will have a vesicle/ thing on top of it, that it then walks throughout the cytoskeleton to where it needs to be. Components of the cytoskeleton Microtubules 1. All eukaryotic cells have microtubules, hollow rods measuring about 25 nanometers in width and 200 nanometers to 25 micrometers in length. The walls that make the microtubule are hollow, and they are made of globular tubulin protein. Each of those proteins has 2 subunits, giving it the name dimer. One subunit is called an alpha, one is a  beta. The tubulin can be disassembled at a large rate, and reassembled at a different part of the cell with relative quickness. This is due to the 2 sides of the microtubule having a side that is much faster than the other at releasing all the tubulin. (known as the plus side) Centrosomes and centrioles 1. Microtubules emerge from a centrosome, which has a centrioles in it, and they basically just organize those microtubules, but aren't necessary Cilia and Flagella 1. Cilia/ Flagella are microtubules that extend from the cell, and allow for movement. Cilia can help move around liquid from the surface of a tissue, and so things like mucus can move around the ciliated lining of the trachea 2. Usually the motile cilia are 0.25 micrometers in width and 2-20 micrometers long. Flagella have the same diameter, but longer length at 10-200 micrometers. Cilia move back and forth, and have individual rowing power to change speed/ correct direction, like oars, while flagella have a more taillike appearance that pushes themselves 3. Cilium might also act as antennas, but this is more in non-motile cells, and usually there is only one per cell. This cilium indicates changes to the cell to allow the cell to adapt, and it is crucial in brain function and embryonic development 4. The similarity remains in both being made of microtubules surrounded by plasma membranes. 9 doublets of microtubules are arranged in ringlets, and 2 central ringlets run through it, and non-motile cilia have just the 9, none of the central 5. Both the flagella/cilia are anchored to the cell through a basal body, and in the flagella/ motile cilia, flexible cross linking proteins connect the space between the ringlets together in the outer portion. There are also large motor proteins reaching toward the next ringlet called dyneins, that walk around and cause movement between the microtubules Microfilaments (Actin Filaments) 1. Microfilaments are solid rods, 7 nanometers in diameter. They are called actin filaments as well, due the actin proteins in them. They are twisted double chains, and can be both linear as well as branching 2. They bear force that might be exerted on the cell, like cortical microfilaments in the plasma membrane. In doing so, the outer layer of the cytoplasm, called the cortex, has more gel consistency, and the inside a more fluid one. 3. They also make up microvilli (protrusions for surface area) and are also used in cell motility. The microfilaments are heavily noticeable in muscle cells, lined up against each other and contracting, alongside thicker filaments called myosin. Myosin acts like dyesins, contracting the muscles by walking against the actin filaments, shortening the cell. It can also be seen in the dividing of daughter cells 4. Can also be used by amoeba in pseudopodia, basically to crawl. They also help in cytoplasmic streaming, which just moves cytoplasm fast for stuff distribution Intermediate filaments 1. Their diameter is 8 to 12 nanometers, and they also focus on tension bearing. They are more permanent, and are left behind even after death. They essentially hold organelles in their respective places permanently, and hold the nucleus down. They also create the nuclear lamina surrounding the nuclear envelope Extracellular components and connections between cells help coordinate cellular activities Cell walls of Plants  1. Strong cell walls hold the plant up against gravity, are thicker than the membrane at 0.1 micrometers to several micrometers. Microfibrils made of cellulose are synthesized by an enzyme called cellulose synthase and added to the cell wall 2. Originally , the plant cell secretes a thin primary cell wall. The cellulose fibrils are oriented at right angles to the growth direction. Between those primary walls is a middle lamella, a thin layer rich in pectins. It essentially glues 2 cell walls together, and when teh plant matures both will harden, or a secondary cell wall can be formed between the plasma membrane and primary cell wall. Between these cell walls tunnel called plasmodesmata are found, interlinking the cells The extracellular matrix of animal cells 1. Even without a cell wall, there is still an extracellular matrix, mostly consisting of glycoproteins. The most abundant glycoprotein is collagen, which forms fibers outside the cell. That collagen is embedded in a network made of proteoglycans. The proteoglycan molecule is a small core protein with carbohydrate chains attached to it, making it 95% carb 2. Some cells are connected to other cells through different glycoproteins, like fibronectin. They bind to cell surface receptor proteins called integrins that are in the plasma membrane. All these glycoproteins communicate with other cells to change cell behavior and coordinate with others. Intercellular junctions Plasmodesmata in plant cells 1. Cell walls have plasmodesmata in their cell walls, connecting themselves to other plants' cytosol, with the plasma membrane running in between them. Water and small solutes can pass through the channel freely to other cells in need, as well as some RNA and proteins Tight junctions, desmosomes, and gap junctions in animal cells 1. Tight junctions consist of plasma membranes touching each other tightly, bound by proteins. They make us watertight basically 2. desmosomes/anchoring junctions fasten cells together like rivets holding sheets of plasma membrane together. Muscle tears may include their rupturing 3. Gap junctions/ communicating junctions provide cytoplasm channels like plasmodesmata, where things can be exchanged between cells For the love of god fuck this chapter