Chapter 4 Carbon Chemistry Carbon The Backbone of Life Living organisms consist mostly of carbon based compounds Carbon is unparalleled in its ability to form large complex and varied molecules Proteins DNA carbohydrates and other molecules that distinguish living matter are all composed of carbon compounds Organic chemistry is the study of carbon compounds Cells are 70 95 water the rest consists mostly of carbon based compounds Proteins DNA carbohydrates lipids and other biological molecules are all composed of carbon atoms bonded to other carbon atoms and to atoms of other elements o Other common elements Hydrogen H Oxygen O Nitrogen N Sulfur S Phosphorus P Organic Molecules and the Origin of Life on Earth Stanley Miller s classic experiment demonstrated the abiotic synthesis of organic compounds Experiments support the idea that abiotic synthesis of organic compounds perhaps near volcanos could have been a stage in the origin of life Carbon atoms can form diverse molecules by bonding to four other atoms Carbon has 6 electrons 6 e o 2 e in the first shell full o 4 e in the second shell 8 e needed to fill the second shell Carbon has little tendency to form ionic bonds by losing or gaining 4 electrons earlier concept electronegativity Carbon s tetravalence makes large complex molecules possible earlier concept valence CO 2 is the source for all organic molecules in organisms through the process of photosynthesis o CO 2 may be considered organic or inorganic A molecule s biological function is related to its shape 3 D shape of molecule is important for function Molecule s shape determined by arrangement of electron orbitals that are shared by the atoms involved in the bond For atoms with electrons in both s and p orbitals the formation of covalent bonds leads to hybridization of the orbitals to four new orbitals in the tetrahedron shape Example methane CH4 o All four hybrid orbitals are shared o Hydrogen nuclei at the corners of the tetrahedron In larger molecules the tetrahedral shape of carbon bonded to four other atoms is often a repeating motif Molecular diversity arising form carbon skeleton carbon backbone variation Functional groups contribute to the molecular diversity of life Functional groups chemical groups that replace one or more H atoms of the carbon skeleton of hydrocarbon Behave consistently from one organic molecule to another Number and arrangement of functional groups help give molecules unique properties Seven functional groups SIX are hydrophilic increase solubility in water 1 Hydroxyl group OH H atom forms a polar covalent bond with O atom which forms a polar covalent bond to the carbon skeleton Polar covalent bonds improve solubility of organic molecules 2 Carbonyl group C O Oxygen atom joined to the carbon skeleton by a double bond Ketone carbonyl group is not on the end Aldelhyde carbonyl group is on the end Isomers with aldehydes versus ketones have different properties 3 Carboxyl group COOH Carbon atom with a double bond to an oxygen atom and a single bond to a hydroxyl group Carboxylic acids compounds with carboxyl groups A carboxyl group acts as an acid because of combined electronegativities of two adjacent O atoms 4 Amino group NH 2 N atom attached to two H atoms and the carbon skeleton Amines organic compounds with amino groups Amino group acts as a base because like ammonia it can pick up a hydrogen ion H from the solution Amino acids have amino and carboxyl groups building blocks of proteins 5 Sulfhydryl group SH Sulfur atom S bonded to a H atom and to the backbone Resembles a hydroxyl group in shape Thiols organic molecules with sulfhydryl groups Sulfhydryl groups help stabilize the structure of proteins 6 Phosphate group OPO3 2 Phosphorus P bound to four O atoms three with single bonds and one with a double strand Connects to carbon backbone via one of its O atoms Anion with two negative charges two protons have dissociated from the O atoms One function is to transfer energy between organic molecules ATP An Important Source of Energy for Cellular Processes An important organic phosphate is adenosine triphosphate ATP ATP consists of an organic molecule called adenosine attached to a string of three phosphate groups ATP stores the potential to react with water hydrolysis a reaction that releases energy to be used by the cell Carbon atom C bonded to 3 H atoms and to the backbone 7 Methyl group CH3 Methylated compounds organic molecules with methyl groups NON POLAR NOT HYDROPHILIC
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