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Chapter 3

Chapter 3 bio 102

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BIOL 102
Wayne Snedden

Chapter 3: The Chemical Basis of Life II: Organic Molecules By the end of this unit you should be able to: o Explain the properties of carbon that make it the chemical basis of all life. o Appreciate the chemical characteristics of common functional groups of organic compounds. o Understand the differences between isomeric compounds. o Understand how small molecules can be assembled into larger molecules by dehydration reactions and how hydrolysis reactions can reverse this process. o List the four major classes of organic molecules and macromolecules found in living organisms. o Distinguish among different forms of carbohydrate molecules, including monosaccharides, disaccharides, and polysaccharides. o Relate the functions of plant and animal polysaccharides to their structure. o List the different classes of lipid molecules that are important in living organisms. o Understand the structure of triglycerides and how the structure and melting point are affected by the presence of saturated and unsaturated fatty acids. o Discuss why fats function more efficiently than carbohydrates as energy-storage molecules. o Relate phospholipids structure to its ability to form bilayers in aqueous environments. o Describe the chemical nature of steroids and give two examples of their biological function. o Give examples of the general types of functions that are carried out in cells by different types of proteins. o Explain how amino acids are joined to form a polypeptide, and distinguish between a polypeptide and protein. o Describe the levels of protein structure, and understand the bonding forces and factors that are important in determining polypeptide and protein shape. o Explain what domains are and their importance in proteins. o Describe the three components of nucleotides, and be able to number the carbons of the monomers sugar. o Understand what polarity means for a strand of DNA or RNA. o Distinguish between the structures of DNA and RNA. o Explain the term antiparallel and describe its importance for base pairing. o Describe how certain bases can pair with others to form a DNA double helix. 3.1 • vitalism - organic molecules were created by, and therefore imparted with a vital life force contained within a plant or an animal • this idea changed with experiments done by Friedrich Wohler • he attempted to synthesize ammonium cyanate (inorganic) but accidentally reacted to create a 3rd compound that when heated, presented similar crystals to organic urea • the fact that he synthesized urea not within a living outlet, it was a huge breakthrough • carbon - forms 4 covalent bonds because the valence only needs 4 e- to be complete • can form single or double bonds • carbon-carbon and carbon-hydrogen bonds are non-polar because close in electronegativity • hydrocarbons - hydrophobic, not soluble in water • carbon-carbon bond is a short and stable bond (small atom so therefore closer together) • functional groups ◦ • isomers - two structures with an identical molecular formula but different structures and characteristics • Structural isomers - contain the same atoms but in different bonding relationships • Stereoisomers - have identical bonding but spatial positioning of the atom differs from one to another ◦ geometric isomers - double bonds cause the other remaining bonds on the atom to be either cis (same side) or trans (opposite sides) ◦ enantiomers - a pair of molecules that are mirror images ▪ 4 different atoms can bind to one carbon atom in 2 possible ways ▪ properties are pretty much the same but the ability to noncovalently bind to other molecules like proteins can be different 3.2 • 4 macromolecules: lipids, carbohydrates, proteins and nucleic acid (RNA and DNA) • last 3 are found as polymers - large molecules formed by the linkage of many smaller molecules (monomers) • condensation reaction - two or more molecules combine into a larger one with the loss of a small molecule • dehydration reaction - when the lost molecule is water for a condensation rxn • hydrolysis reaction - cells break a polymer into a monomer and water is added back in every time a monomer is released • dehydration and hydrolysis are catalyzed by enzymes 3.3 • carbohydrates - CHO atoms Cn(H2O)n • most carbon atoms in a carbohydrate are linked to a hydrogen atom and a hydroxyl group (OH) • Sugars ◦ monosaccharides - single monomer unit (ex. glucose, ribose, hexose) ◦ ring structure ◦ there are many isomers of glucose (D-glucose, L-glucose) OR (a-glucose, b-glucose) --> just because the hydroxyl group lies on a different side ◦ disaccharides - composed of 2 monosaccharides with the help of glycosidic bonds (dehydration reaction) --> can have beta or alpha glycosidic linkage ◦ ex. sucrose --> composed of a-glucose and fructose linked by a a-glycosidic linkage between the 1st carbon of a-glucose and the fructose ◦ others, maltose, lactose + sucrose ◦ polysaccharides - long polymers of many monosaccharides ◦ starch is a common one ◦ the unbranched, linear fibres of adjacent cellulose molecules can be very closely packed and form hydrogen bonds between the multiple hydroxyl groups on the glucose molecules of one chain and the oxygen molecules on the neighbouring chain ◦ microfibrils in cellulose form stabilizing van der waal interactions, and most of the glucose molecules are not readily accessible for hydrolysis, making cellulose bad for energy storage but good for structural support ◦ chitin - sugar monomers within have nitrogen containing groups attached to them ◦ Glycosaminoglycans (GAGs) have amino acids and sulphate groups attached to them are also polysaccharides that are very important in animals --> part of connective tissue 3.4 • lipids - made of mostly hydrogen and carbon atoms held together by non-polar covalent bonds • hydrophobic and insoluble in water • triglycerides/triglycerols - glycerol bonded to 3 fatty acid chains • fatty acids are hydrocarbon chains with a carboxyl group on the end (COOH) • glycerol is linked to the carboxyl group of the fatty acids and in the process removes a water (dehydration reaction) --> creates ester bonds • saturated fatty acid - saturated in hydrogens, no double bonds • Unsaturated fatty acid - when there are c=c double bonds on the fatty acid chain (one double bond makes it monounsaturated, multiple makes it polyunsaturated) • fats you cannot synthesize in your body and can only get by your diet are called essential fatty acids • trans fats - in an unsaturated fatty acid when the hydrogens are situated in the trans position ◦ can be considered monounsaturated fat isomers or polyunsaturated fats that have hydrogen i
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