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Chapter 2

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MICB 201
Wade Bingle

MICB 201 Chapter 2: Learning Objectives/Outcomes (2012W T1) Define the terms: coccus, bacillus, spirillum, vibrio, hypha, mycelium and plasma in the context of prokaryotic cell shape. Coccus – berry/sphere Bacillus – rod Spirillum – spiral/helix/coil Vibrio – comma shaped (rod with bend) Hypha – web/thread Mycelium – many hypha, means fungus Plasma – fluid – indicates a very variable/irregular shape Compare Bacteria and Archaea with respect to cell shape, multicellularity and cellular differentiation. You basically can‟t tell a bacterium from an archeael organism without genome analysis. Basically, you can‟t tell them by cell shape most of the time. Only bacteria can differentiate, Archaea cannot. They can both be multicellular if they want. Appreciate the diversity exhibited by prokaryotes in terms of cell size in relation to other organisms. They have an enormous diversity with respect to size. Such as the bacteria T.namibiensus and E.fishelsoni which are bigger than eurkaryotic cells and are big enough to see without a microscope. On the other hand, they can be smaller than some viruses. Explain the importance of cell SA: V relationships in nutrient acquisition and waste disposal. SA:V is important. Surface area is related to how fast nutrients are acquired and how fast waste is disposed of. Volume is related to how much nutrients are required and how much waste is produced. As the size of a cell increases, the SA:V decreases because volume increases more quickly than surface area. Everything the cell needs or has to get rid of MUST go through the cytoplasmic membrane the amount relates to the membranes surface area While the amount of food and other materials from the outside and the amount of waste a cell disposes of relates to its volume Describe two ways some prokaryotes can modify their effective SA:V ratio. (1): Forming a large metabolically inactive membrane-bound vacuole (2): Synthesizing an invaginated (folded) cytoplasmic membrane (providing a much greater surface area) Describe how some prokaryotes modify their effective surface area to volume ratio using membrane invagination and vacuole formation. Some cells are very large. That means their SA:V is small relative to other smaller cells. Therefore they must seek to increase it. They can do this by using vacuole formation, which decreases the effective volume of the cell because the vacuole may be metabolically inactive. Invagination increases surface area that the cell can use. Stalks may also be used. Describe the composition and organization of the prokaryotic cytoplasmic membrane. The bacterial and archaeal cytoplasmic membrane is a bilayered structure about 10 nm thick composed of phospholipids just like eukaryotes. Each half is called a leaflet. Embedded in the lipid bilayer are proteins that are integral and may span both leaflets or just one. 50:50 lipid to protein by weight but 30:1 phospholipids molecules to a protein. The phospholipid has a head that may be an amino acid or sugar bonded to glycerol-phosphate. The glycerol is actually connected to phosphate and also to two hydrocarbon tails (fatty acids). All Archaea use an ether group –C – O – C- to connect the glycerol to the fatty acid tails. Most bacteria use an ester linkage (-COO-) to do this, but some may use the ether. The hydrocarbon tails of bacterial membrane phospholipids are unbranched most of the time. In Archaea there are methyl branches off the main hydrocarbon chain. Appreciate that the molecular structures of bacterial and archaeal phospholipid exhibit differences. As said earlier, all Archaea use an ether linkage which is –O – C – O- to link glycerol phosphate to the fatty acid hydrocarbon tails while most Bacteria/Euk use an ester linkage instead. Archaea also have branching (methyl groups) and Bacteria/Euk usually do not have branches. Also, the stereochemistry of the glycerol phosphate group. Bacteria and euk phospholipids use the D stereoisomer of the glycerol while Archaea use the L stereoisomer. Describe the mechanisms of passive and active transport of nutrients in prokaryotes and the different ways energy can be supplied to the later process (eg. ABC transporters, H+ gradients) Permeases are the proteins that are used in cytoplasmic membrane. Diffusion occurs which is passive transport. This is for small molecules that tend to be nonpolar, uncharged. Oxygen, carbon dioxide and water pass through the membrane directly. This is because phospholipids are not chemically bonded to each other e.g. covalently. Large or charged chemicals must also pass through into or out of the cell. Permeases are the proteins used for this purpose. Each permease transports a different chemical. That is, permeases are specific. Permeases may be for facilitated diffusion/passive transport or for active transport. For facilitated diffusion, the molecule binds to the permease and it changes conformation. Then it goes through. Molecules can just as easily leave the cell as entering using the permease. However, backward transport is generally prevented by consuming the molecule that needs to be transported upon entry. Prokaryotes usually live in hypertonic solutions. Chemicals/nutrients must be accumulated inside the cell. In order to work against the concentration gradient, the cell uses active transport methods. Active transport is the utilization of energy to move a chemical from an area of low to high concentration. As with facilitated diffusion, a chemical-specific transmembrane permease must be used. One method of active transport in prokaryotes is via ATP consumption. This involves ABC transporters which are ATP-Binding Cassette Transporters. These are found in all 3 domains. They are important. Consists of a transporter protein that is transmembrane and forms a pore through the CM. On the cytoplasmic end there is a nucleotide-binding site where ATP can bind to be used. On the other side, it depends. In Gram negative cells there is a OM so you can have periplasmic proteins floating around. For Gram positive cells the proteins are attached to the membrane, anchored to the membrane. These binding proteins bind to the chemical and pass them on to the transmembrane transporter protein in the CM. Conformational changes in the transporter protein promoted by energy from ATP consumption move the chemical into the cell. Another method is cotransport. This is also active transport and uses a concentration gradient rather than consuming ATP. Protons can be transported from the periplasm across the CM to the cytoplasm. There are no periplasmic binding proteins in this process. Aquaporins are proteins that move water across bilayers faster than simple diffusion allows. They are common in many eukaryotes including plants and mammals. They are not that common in microbes. Describe the nature of the prokaryotic cytoplasm and why the shape of phospholipids is important in delineating this compartment. The cytoplasm has loads of ribosome and contains the nucleoid. There are usually no membrane bound compartments. The shape of phospholipids determine the shape of the cytoplasm. The cytoplasm is both a concentrated solution of protein and a dense suspension of ribosomes, mRNA, tRNA and other random molecules. 10s of thousands ribosomes per cell. Proteins account for 50% of the cell dry weight. Phospholipids have two HC tails making them like a cylinder. In water, these phospholipids pack into vesicles containing an internal aqueous compartment. If phospholipids had one tail then bad. Obviously. Allows for internal aqueous compartment. Explain what the terms Gram-positive and Gram-negative mean. They refer to how bacterial cells show up when fixed to a slide and stained with two dyes. It is related to the cell wall structure but not much can be implied. It is basically a method of categorizing bacterial cells based on how they show up under the dyes. Gram positive cells stain purple while Gram negative cells stain red. Without resort to detailed molecular structures, describe the composition, structure and function of peptidoglycan in Gram-negative and Gram-positive bacteria. Peptidoglycan is a polysaccharide that exists in the cell wall of both Gram positive and Gram negative cells. It is not found in any domain other than Bacteria. PG is a huge mesh like molecule composed of two parts – the glycan chain and the tetrapeptides that connect the glycan chains. The glycan chain is made up of two subunits that are joined by an O-glycosidic bond. They are called NAM and NAG which stand for N-acetylmuramic acid and N-acetylglucosamine. The O-linkages are strong covalent bonds. The tetrapeptide is a sequence of 4 AA that are joined by strong covalent bonds in peptide linkages. The N-acetylmuramic acids of the glycan chains are crosslinked to each other through amino acid 3 and amino acid 4 of their tetrapeptides. Amino acid 4 is always alanine and Amino acid 3 is important because it must possess a free NH3+ group – the crosslink is formed from the –COO- group of Ala (AA4) and the –NH3+ group of AA3. In Gram negative bacteria, the tetrapeptides are directly cross linked to each other. In Gram positive bacteria, there may be up to 5 additional amino acids in a peptide interbridge. Gram positive PG has a higher degree of cross linking than Gram negative PG. As much as 80% of the NAMs in G+ bacteria can be crosslinked while less than 50% of the NAMs are cross linked in G- bacteria and can be as low as 20%. 20% to 50% cross linkage in the NAMs for Gram negative bacteria, up to 80% for Gram positive bacteria and Gram positive bacteria have an interbridge b/t NAMs that is up to 5 AA long. The AA of the tetrapeptide alternate L and D configurations. Perhaps to prevent degradation. Without resort to detailed molecular structures explain the differences between the composition and structure of Gram-negative and Gram-positive cell walls. Basically, the Gram-negative bacteria has an outer membrane (which contains porins and possibly permeases), then underneath some space, then the peptidoglycan layer which is like 3-5 layers thick and then some more space btw this is in the periplasm and then the cytoplasmic membrane. In Gram positive bacteria, there is no OM but there is peptidoglycan layer which is very thick. CM as usual. About 30% of cultured bacteria are Gram positive. Gram positive cell wall layers can have as many as 20 layers of PG producing a structure hundreds of nm thick. Gram positive cell walls contain polymers of phosphorylated sugar alcohols based on ribitol and glycerol and these are called teichoic acids. They are further classified into just teichoic acids or lipoteichoic acids. If the teichoic acid polymer is anchored to a sugar in the headgroup in a cell membrane phospho or glycolipid, it is called a lipoteichoic acid. If it is linked to the peptidoglycan NAM, then it is simply called teichoic acid. Both poke through the PG mesh and into the environment, not sure what they are for though. Unlike previously believed, Gram positive cells do have a periplasm between the PG and the cell membrane. The Gram negative cell wall is the most common bacterial cell wall type, accounting for about 50% of cultured bacteria. Gram positive cell walls only have about 1 to 2 layers of peptidoglycan. External to the PG is the outer membrane which is a bilayer structure that is made out of lipopolysaccharide, phospholipid and protein. The outer membrane contains phospholipids but only on the inner leaflet. In the outer leaflet there are other lipid molecules called LPS – lipopolysaccharide. There are three regions that the LPS is divided into. Lipid A, R-core and O-polysaccharide. Lipid A is made of several hydrocarbon tails and is the thing that is inserted into the membrane. The R core is a negatively charged that is made of many sugars. The O-polysaccharide is what extends outwards from the cell and attached to the R-group. Obviously made of sugars, but uncharged unlike the R-core which is made out of charged sugars (negative). Specific sugars can differ and sometimes the O-polysaccharide is not there. The outer membrane contains proteins – lipoproteins and porins. Lipoproteins are proteins with hydrocarbon tails (the lipid part). They HC tail is embedded in the outer membrane and the protein part is covalently bonded to the peptidoglycan. Thus the lipoprotein anchors the outer membrane to the peptidoglycan. The outer membrane lipid bilayer is even less fluid and less permeable than the CM. This is due to stronger lateral interactions b/t the lipopolysacchardide molecules than between phospholipids. There are also Calcium 2+ and Magnesium 2+ ions present in the outer leaflet of the outer membrane which help stabilize the negative charge of the LPS R-core. Therefore there are ionic bonds which stabilize the membrane and make it less fluid. It links the adjacent LPS molecules. Second, LPS has more than 2 HC per tail (sometimes 6) resulting in increased hydrophobic effect and increased lateral interactions (IDID) because of the increased SA. State the prevalence and distribution of the Gram-positive and Gram-negative cell wall types in the bacterial domain. 30% of cultured organisms are G+, 50% G-. Without resort to detailed molecular structures, describe the composition, structure and function of the Gram-negative outer membrane. The Gram negative outer membrane is made out of phospholipids and LPS which stands for lipopolysaccharide molecules which are made out of many hydrocarbon tails (more than 2), R-core (negative charge) and O-polysaccharide. Same width as CM which is about 10 nm. Less fluid because of the lateral interactions (more hydrocarbon) and also more ionic because MG2+ and Ca2+. There are porins and lipoproteins in the Gram negative outer membrane. The lipoproteins have two hydrocarbon tails which are embedded in the inner leaflet of the outer membrane and the protein is covalently bonded to PG which means the function is to attach the OM to the PG. Other than lipoproteins, there are porins that are transmembrane proteins. Because the OM is such an effective barrier against permeation, need some porins for transport. Porins are for small nutrient molecules (charged and uncharged) and this is passive/facilitated transport – facilitated diffusion. Porins form water-filled channels or pores in the OM. Some porins are general and allow passage of all chemicals that are small enough. Others are c
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