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BIOL 1F90 Study Guide-Chapter 3

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Douglas Bruce

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BIOL 1F90 Study Guide: Chapter 3 Carbon- What makes it the chemical basis of all life?  Ability to form four covalent bonds with other atoms, including other carbon atoms. This is because carbon has 4 valence electrons in its outer shell and needs four additional electrons for its outer shell to be full o This allows a vast number of organic compounds to be formed from only a few chemical elements  Commonly form covalent bonds with other carbons and with hydrogen, oxygen, nitrogen and sulphur  Carbon bonds can also occur in configurations that are linear, ring like, or highly branched o These molecular shapes can produce molecules with a variety of functions  Hydrocarbons: molecules with predominately hydrogen-carbon bonds o Hydrophobic and not very soluble in water  When carbon forms polar covalent bonds with oxygen or nitrogen, the molecule is much more soluble in water because of the electrical attraction of polar water molecules  The ability of carbon to form both polar and nonpolar bonds contributes to its ability to serve as the backbone for an astonishing variety of molecules  Carbon atoms are stable at the different temperatures associated with life. o This property arises in part because the carbon atom is very small compared with most other atoms, and therefore the distance between carb atoms forming a carbon-carbon is quite short.  Shorter bonds tend to be stronger and more stable than longer bonds between two large atoms Functional Groups  Groups of atoms with special chemical features that contribute to the molecules’ properties  Each type of functional group exhibits the same properties in all molecules in which it occurs Table 3.1: Biologically Important functional groups that may be present in organic molecules Functional Group Formula/Properties* Examples of where found Amino Amino Acids (Proteins) Carbonyl Steroids, eicosanoids, waxes, proteins Ketone Glucose, glyceraldehyde Aldehyde Glucose, glyceraldehyde Carboxyl Amino acids, fatty acids Hydroxyl Steroids, alcohol, carbohydrates, some amino acids Methyl May bet attached to DNA, proteins, carbohydrates Phosphate Nucleic acids, ATP, attached to amino acids Sulphate May be attached to carbohydrates, proteins, lipids Sulphhydryl Proteins that contain the amino acids cysteine Isomers  Two structures with an identical molecular formula but different structures and characteristics  Structural isomers: contain the same atoms but in different bonding relationships, hence different properties  Stereoisomers: Identical bonding relationships, but the spatial positioning of the atoms differs in the two isomers  Two types of stereoisomers o 1. Geometric Isomers:  cis double bond: The two hydrogen atoms linked to the two carbons of a C=C double bond may be on the same side of the carbons  trans double bond: The hydrogens are on opposite sides o 2. Enantiomers: exist as a pair of molecules that are mirror image  Four different atoms can bind to a single carbon atom in two possible ways, designated as a left handed and a right handed structure  A pair of enantiomers share identical chemical properties but because of the different orientation of atoms in space, their ability to noncovanlently bind to other molecules are different Classes of Organic Molecules and macromolecules  Four major categories of macromolecules 1. Lipids 2. Carbohydrates 3. Nucleic Acids (DNA and RNA) 4. Proteins  Carbohydrates, Nucleic Acids and Proteins come from Polymers  Polymers: large molecules formed by the linkage of many smaller molecules (building blocks) called monomers  Monomers: smaller molecules/ building blocks  The structure and function of each type of macromolecule depends on o The nature of its monomers o The number of monomers linked together o The 3 Dimensional way in which the monomers are linked  Condensation reaction: two or more molecules combine into a large one, with the loss of a small molecule o Condense them to make a bond  Dehydration Reaction: A condensation reaction, but with the loss of a water molecule  Hydrolysis Reaction: A polymer is broken down into monomers o A water molecule of water is added back each time a monomer is released  Dehydration and Hydrolysis reactions within cells are both catalyzed by enzymes Carbohydrates Include Simple Sugars and Polymers Composed of Sugar- monomers  Carbohydrates: are composed of carbon, hydrogen, and oxygen atoms in the proportions represented by the general formula Cn(H2O)n o ‘n’ is a whole number o The prevalence of the OH groups with their polar covalent bonds make carbohydrates soluble in water o Other functional groups such as amino and carboxyl groups are also found in certain carbohydrates Sugars  Small carbohydrates that may taste sweet  Monosaccharide: Simplest sugar consisting of a single monomer unit o Can join together to form larger carbohydrates  Disaccharides: Carbohydrates composed of two monosaccharaides  Glycosidic bond: bond form between two sugar molecules Monosaccharaides  Simplest sugars  Most common types are those with five carbons called pentoses, or six carbons called hexoses.  Important pentoses o Ribose ( C H5O10 a5d deoxyribose (C H O5) 10 4  Important Hexose o Glucose (C H6O 12 6)  Different ways to depict structures; ring or linear Glucose Isomers  Structural Isomers: different arrangement of the same elements o Glucose and Galactose  Stereoisomers o Alpha Glucose: The first carbon’s hydroxyl group lies on the opposite side of the ring as the sixth carbon o Beta Glucose: It lies on the same side  Enantiomers: Mirror images o D and L- Glucose Disaccharides  Carbohydrates composed of two monosaccharaides  Joined by dehydration or condensation reaction o The linking of most monosaccharaides involves the removal of a hydroxyl group from one monosaccharide and a hydrogen atom from the other, and the bonding of the 2 sugars together through an oxygen atom o Glycosidic bond  Broken apart by hydrolysis  Ex. Sucrose, maltose, lactose Polysaccharides  Many monosaccharaides can be successively linked to form long polymers  Starch: Common name of the storage polysaccharide found in plants o Consists of two polysaccharides: Amylose and Amylopectin o Amylose cab pack itself more tightly than amylopectin because it can form a helical structure of linear chains o Amylopectin readily forms branched structures o Most plants typically have about 30% amylose and 70% amylopectin  Glycogen: Found in animal cells  Glycogen and Starch are examples of polysaccharides that are composed of thousands of alpha-D glucose molecules connected by alpha glycosidic linkages to form long branched chains  Both can readily have individual glucose molecules removed by hydrolysis, providing an efficient source of glucose  Other polysaccharides provide a structural role, rather than storing energy, and this is reflected in their different structure. o Ie. Cellulose, chitin,  Cellulose: A polymer of beta glucose held by beta glycosidic linkages Lipids are mostly Hydrophobic and are heterogeneous in structure and function  Lipids: Molecules composed predominantly of hydrogen and carbon atoms held together by non covalent bonds o Do not interact with water, therefore insoluble in water o Account for about 40% of the organic matter in the average human body o 2 times more energy than carbohydrates o Their hydrophobicity is their unifying characteristic Fats  A mixture of triglycerides, also known as triacylglycerols  A fatty acid chain is a chain of carbon and hydrogen atoms with a carboxyl group at the end, joined by a dehydration or condensation reaction + o Because the carboxyl group (COOH) releases a H in water to become COO , these molecules are called fatty acids  Broken apart by hydrolysis  Saturated Fatty Acids: When all the carbons in a fatty acid are linked by single covalent bonds o Solid at room temperature  Unsaturated fatty acids: A fatty acid containing one or more carbon- carbon double bonds o A fatty acid with one carbon-carbon double bond is a monounsaturated fatty acid o Two or more double bonds constitute a polyunsaturated fatty acid (liquid at room temperature)  Essential Fatty acids: Certain fatty acids that are necessary for good health o Must be obtained through the diet  Trans Fat: Monosaturated fat isomers or polyunsaturated fats that have the hydrogens in the trans- position, on opposite sides of the double bond  Fats are important for energy storage o 1 gram of fat stores more energy than 1 gram of glycogen or starch  Fats can also be structural in providing cushioning and insulation Phospholipids  Another class of lipids, similar in structure to triglycerides but with one important difference. The third hydroxyl group of glycerol is linked to a phosphate group instead of to a fatty acid  In most phospholipids, a small polar or charged nitrogen-containing molecule is attached to this phosphate o These groups constitute a polar hydrophilic (water loving) region at one end of the phospholipid  At the opposite end is the non polar, hydrophobic (water fearing) fatty acid chains  They are amphipathic  In water, the amphipathic nature of phospholipids allow them to organize into bilayers: o Polar ends facing out, interacting with water o Non Polar ends facing one other in the interior  The bilayer arrangement of phospholipids is critical for determining the structure of plasma membranes Steroids  Four fused rings of carbon atoms form the skeleton of all steroids  A few polar hydroxyl groups may be attached to this ring, but they are not numerous enough to make a steroid highly water soluble.  Sterols: Steroids with a hydroxyl group  Tiny differences in chemical structure can lead to profoundly different biological properties  Hormones estrogen vs testosterone Waxes  Contains hundreds of different compounds  All waxes contain one or more hydrocarbons and long structures that resemble fatty acid attached by its carboxyl group to another long hydrocarbon chain  Very non polar and thus repel water, providing a barrier to water loss o For this reason many pants and animals produce waxes that are typically secreted onto their surface Proteins are Polymers composed of Amino Acids  Proteins are polymers composed of hydrogen, oxygen, nitrogen, and small amounts of other elements, notably sulphur  Amino Acids: Mon
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