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BIO1140 (690)

The Chemistry of Life

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Kathleen Gilmour

The Chemistry of Life Carbon Compounds -4 major macromolecule classes: 1) polypeptides (proteins) 2) nucleic acids 3) lipids 4) polysaccharides (carbohydrates) -biological molecules = organic molecules -made up of long carbon chains -mostly non-polar, covalent bonds; tend not to attract water and are good for water proofing -hold a lot of energy in their bonding arrangements -can create 4 covalent bonds with other atoms (carbon has a valence of 4); this is known as tetravalence which give molecules a 3-dimensional aspect -carbon molecules can be arranged in a variety of ways; there are typical patterns of arrangement known as function groups -monomers (small organic units) are polymerized into larger macromolecules (polymers) -organic molecules are different from inorganic molecules because all organic molecules are based on carbon -organic molecules are constructed from chains of carbon attached to each other and the varying shapes of biological molecules are a result of carbon's tetravalence -hydrocarbons consist of only hydrogen and carbon -form non-polar covalent bonds and can therefore bond with each other -non-polar covalent bonds means there is nothing for water to hold on to (not soluble in water) and therefore act as water proofing -electrons are fairly easily removed due to low electronegativity; this forms a source of potential energy -the easily removed electrons act as an energy source for living organisms -carbons act as the building blocks because of: -its ability to form 4 bonds which give it a more 3-dimensional aspect -its ability to form an infinitely long chain by binding to itself; new molecules can be made depending on the chain length -its ability to act as an intersection to cause branching along the chain; branch points allow for further diversification of form -its ability to contribute to double bonds (contribute to catalysis) and triple bonds (less biological significance)along the chain -its ability to participate in resonance forms (important for chemical reactions) -its ability to form rings with its carbon backbone (important in nitrogenous bases found in nucleic acids) -its ability to incorporate into functional groups, allowing it to modify its properties Functional Groups -collections of atoms of certain composition which bring give certain properties to a molecule -most functional groups act as hydrophilic structures -properties of a collection of atoms with the same functional group are consistent (have definite chemical properties) and give rise to new features if applied to another carbon skeleton -electronegative atoms such as oxygen and nitrogen are usually members of functional groups -they increase the solubility of a carbon skeleton in water -the polarity of most functional groups not only increase their solubility in water, but they also give rise to hydrogen bonding arrangements -carboxyl groups can give away hydrogens, making them acidic -amino groups tend to take hydrogens, making them basic Macromolecules -are a result of polymerization of smaller units called monomers -monosaccharides can be joined together by dehydration reactions -dehydration synthesis (condensation reaction) forms a covalent bond and brings the molecules together by moving H20 (H from 1 molecule and OH/hydroxyl from the other molecule) -H2O is removed and the sugars are linked by a glycosidic bond (covalent bond that joins a carbohydrate / sugar to another group) between 2 of their carbons -if a few sugars are joined (2-10 carbon chain), the polymer is called an oligosaccharide -if a large number of sugars are involved, the resulting polymers are macromolecules called polysaccharides -anabolic -two glucose molecules in the α configuration are joined by a bond between carbons 1 and 4, which is therefore called an α (1→4) glycosidic bond -hydrolysis is the opposite of dehydration synthesis; it breaks covalent bonds through the addition of water to separate off a monomer -catabolic Carbohydrates -include monomers/ simple sugars and polysaccharides -monosaccharide polymers = linked repeating units = polysaccharide -used for energy storage (i.e.: glycogen for animals and starch for plants) or for structural purposes (i.e.: cellulose and chitin) -cells typically use the D-glucose form (i.e.: carbohydrates use the D-conformation of the cell) -there is a reaction between the C-1 and C-5 to form a ring - β-D-glucose; the -OH projects above the main ring - α-D-glucose; the -OH projects below the main ring -condensation reaction of the C-1 and C-4 create a glycosidic bond / linkage - α-D-glucose glycosidic bonds = glycogen / starch H H |_O_| - β-D-glucose glycosidic bonds = more rigid = cellulose / chitin |\O \| -α - β naming reflects the asymmetrical carbon when it is in the ring form Simple Sugars -simple sugars like glucose are the major nutrient of the cell; their breakdown provides a source of cellular energy and the starting material for the synthesis of other cell constituents -monosaccharides - 1C : 2H : 1O ratio -have a carbonyl group (either a ketone or an aldehyde) which are fairly reactive -normally made up of a linear structure but the carbonyl will often react to form a ring structure through a covalent bond -by convention, the oxygen is placed at the top right for simple sugars -alpha conformation involves the hydroxyl group on the 1-C pointing downward; alpha bonds tend to create polysaccharides that can be broken down easily -these bonds allow enzymes to enter and break the bond during digestion since the long strand of polysaccharide are easily accessible by water surrounding them -e.g.: maltose (2 glucose), sucrose (glucose and fructose), lactose (galactose and glucose) -beta conformation involves the hydroxyl group on the 1-C being placed in an axial position pointing up and to the right -beta linked monosaccharides are harder to break because they pack tightly and hide the bonds from enzymatic digestion -cellulose (made up of mostly beta bonds) are used for structure in a cell because of their ability to resist most digestion -triose: monomers that contain 3 carbons (i.e.: glyceraldehyde0 -pentose: monomers that contain 5 carbons (i.e.: ribose) -hexose: monomers that contain 6 carbons (i.e.: mannose) -glucose and fructose are hexose sugars and have the same molecular formula but are structural isomers of each other (glucose = aldose sugar; fructose = ketose sugar) -swapping the H and the OH on the left and right of the sugar creates a new compound with very different properties Polysaccharides -long chains of monomers (simple sugars) -are storage forms of sugars and form structural components of the cell -polysaccharides and shorter polymers of sugars act as markers for a variety of cell recognition processes (i.e.: cell adhesion, protein transport to appropriate intracellular destinations) -the basic formula is (CH O2 n -sugars containing 5 or more carbons can cyclize to form ring structures, which are the predominant forms of these molecules within cells -cyclized sugars exist in either an α or β configuration of carbon 1 Polysaccharide Transport and Storage -long polysaccharides are difficult to transport because of their bulk; shorter saccharides are used for transport Storage -glycogen and starch are the storage forms of carbohydrates in animal and plant cells respectively -polymerization allows for storage of large amounts of glucose in a single molecule -starches (unbranched α 1-4 bonds) and glycogen (involved in animal muscles and the liver; branched α 1-4 bonds) involve the alpha conformation of polymerized glucose molecules - α conformations allow for solubility in water and can be broken down rapidly using enzymes -glycogen and amylopectin (1 form of starch) contain an occasional α (1-6) linkage (carbon 1 is joined to carbon 6) and lead to the formation of branches resulting from the joining of 2 separate α (1-4) linked chains - glycogen, starch, and cellulose are all composed entirely of glucose residues, which are joined by α (1→4) glycosidic bonds in glycogen and starch, but by β (1→4) bonds in cellulose -glycogen and one form of starch (amylopectin) also contain occasional α (1→6) bonds, which serve as branch points by joining two separate α (1→4) chains. -glucose is associated with blood sugar (monosaccharide) -sucrose is associated with sugar in plants (disaccharide) -structural polysaccharides involve the beta glycosidic linkages of glucose (i.e.: cellulose and chitin) - involve β 1-4 bonds which create linear structure that crystallize -cellulose is composed entirely of glucose molecules that are in the β conformation and is an unbranched polysaccharide and the linkages involve β (1- 4) bonds that allow cellulose to form long extended chains that pack side by side to form fibres, allowing for mechanical strength Cell Signalling -oligosaccharides and polysaccharides are important in a variety of cell signaling processes -oligosaccharides are frequently linked to proteins, where they serve as markers to target proteins for transport to the cell surface or incorporation into different subcellular organelles -oligosaccharides and polysaccharides also serve as markers on the surface of cells, playing important roles in cell recognition and the interactions between cells in tissues of multicellular organisms Lipids -all lipids are insoluble in water and soluble in non-polar solvents -most lipids play a role in signalling to a certain degree -not as large as other macromolecules -are no polymers (no repetition of subunits) -6 classes of lipids Phospholipid / Phosphoglycerides -composed of some fatty acids -phosphoglycerides are the main building block of membranes -major type of lipid in biological organisms -amphipathic (has hydrophilic and hydrophobic properties) -the head is charged and contains phosphate and other polar groups that allow it to interact with water -the tail contains long hydrocarbon tails that do no associate with water because it is rich in non-polar covalent bonds -when a number of phospholipids are put together in aqueous solution, they aggregate as a sphere to exclude as much water from the centre due to its amphipathic properties and this is called a micelle -phospholipids can also form a membrane (bilayered sheet) which forms the outer boundary of all cells -phospholipids are composed of 3 subunits: 1) polar head (hydrophilic) -phosphate group containing lots of oxygen (very electronegative) -may have an R group (i.e.: containing nitrogen) -R groups are always hydrophilic -common R groups include serine, ethanolamine, choline, and inositol -the phosphoglyceride is named based on the R group 2) glycerol -a 3-C molecule with 3 hydroxyl functional groups -a carboxyl group joins a hydroxyl group to the glycerol group 3) 2 fatty acids (hydrophobic) -long carbon chain -covalently linked to glycerol via an ester bond Fatty Acids -play a role as building blocks and energy storage -consist of a string of hydrocarbons with a carboxyl group at one end -the hydrocarbons are non-polar and the carboxyl group is polar / charged; because it has 2 regions of polarity, it is said to be amphipathic (part of it is polar and hydrophilic and the other part is non-polar and hydrophobic) -in cells, the length of the carbon chain is 14-22 -in membrane structure, it is usually 16-18 C -can be saturated or unsaturated -saturated fatty acids have a maximum number of H atoms bound to C -have a chemical formula of C H n 2n 2 -unsaturated fatty acids have double bonds and less than the maximum number of H atoms bound to C -if it has one double bond, it is said to be monounsaturated fatty acid (MUFA) -if it has multiple double bonds, it is said to be a polyunsaturated fatty acid (PUFA) -made up of a glycerol with 3 fatty acids (triglyceride / triglycerol) -the point where fatty acids join the glycerol is at each hydroxyl of the glycerol -not a component of membranes -serve as an energy storage form of lipid -saturated fatty acids create a relatively straight chain which allow them to be able to fit in a smaller area and pack more tightly, while being less flexible -animal fats tend to be saturated; cholesterol is used to make the membrane more fluid -unsaturated fats tend to have less than the maximum number of hydrogens because of double bonds -take up a larger space a
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