Carbon and the Molecular Diversity of Life Chapter 4

Organic chemistry is the study of carbon compounds Organic chemistry -- Branch of chemistry that specializes in the study of carbon compounds; includes most compounds important to life. Organic chemistry -- Branch of chemistry that specializes in the study of carbon compounds; includes most compounds important to life. Great variety of structures and functions of organic molecules are due to carbon’s ability of carbon to bond with itself and many other elements. Great variety of structures and functions of organic molecules are due to carbon’s ability of carbon to bond with itself and many other elements. Pioneers of organic chemistry began to synthesize organic compounds from inorganic molecules. Pioneers of organic chemistry began to synthesize organic compounds from inorganic molecules. Friedrich Wohler (1828) synthesized urea. Friedrich Wohler (1828) synthesized urea. Stanley Miller (1953) demonstrated the possibility that organic compounds could have been produced under the chemical conditions of primordial Earth. Stanley Miller (1953) demonstrated the possibility that organic compounds could have been produced under the chemical conditions of primordial Earth.

Miller-Urey Apparatus

Carbon atoms are versatile building blocks The kinds and number of bonds carbon will form are determined by its tetravalent electron configuration. (4 valence e-) The kinds and number of bonds carbon will form are determined by its tetravalent electron configuration. (4 valence e-) Completes its outer energy shell by sharing valence electrons in four covalent bonds. (Not likely to form ionic bonds.) Completes its outer energy shell by sharing valence electrons in four covalent bonds. (Not likely to form ionic bonds.) Carbon atom is a central point from which the molecule branches off into four directions; results in large, complex molecules. Carbon atom is a central point from which the molecule branches off into four directions; results in large, complex molecules. An organic molecule's 3-dimensional shape will affect its function. An organic molecule's 3-dimensional shape will affect its function. When carbon forms four single covalent bonds, the four e- orbitals angle from the carbon atom to form a tetrahedron. When carbon forms four single covalent bonds, the four e- orbitals angle from the carbon atom to form a tetrahedron.

Methane/Ethane/Ethene

Variation in carbon skeletons. Carbon chains may vary in: Carbon chains may vary in: Length.Length. Shape (straight chain, branched, ring).Shape (straight chain, branched, ring). Number and location of double bonds.Number and location of double bonds. Other elements covalently bonded to available sites.Other elements covalently bonded to available sites. This variation in carbon skeletons contributes to the complexity and diversity of organic molecules. This variation in carbon skeletons contributes to the complexity and diversity of organic molecules. Hydrocarbons -- Molecules containing only carbon and hydrogen. Hydrocarbons -- Molecules containing only carbon and hydrogen. Major components of fossil fuels produced from the organic remains of organisms living millions of years ago, though they are not prevalent in living organisms. Major components of fossil fuels produced from the organic remains of organisms living millions of years ago, though they are not prevalent in living organisms. Hydrocarbon chains are hydrophobic because the C-C and C-H bonds are nonpolar. Hydrocarbon chains are hydrophobic because the C-C and C-H bonds are nonpolar.

Isomers Isomers -- Compounds with the same molecular formula but with different structures and different properties. Isomers -- Compounds with the same molecular formula but with different structures and different properties. 1. Structural isomers -- Isomers that differ in the covalent arrangement of their atoms. 1. Structural isomers -- Isomers that differ in the covalent arrangement of their atoms. Number of possible isomers increases as the carbon skeleton size increases. Number of possible isomers increases as the carbon skeleton size increases. May also differ in the location of double bonds. May also differ in the location of double bonds.

Isomers (cont) Geometric isomers -- Same covalent relationships, but differ in spatial arrangements. Geometric isomers -- Same covalent relationships, but differ in spatial arrangements. Result from the fact that atoms cannot rotate freely around double bonds. Result from the fact that atoms cannot rotate freely around double bonds. Subtle differences between isomers affects their biological activity. Subtle differences between isomers affects their biological activity.

Isomers (cont) Enantiomers -- Isomers that are mirror images of each other. Enantiomers -- Isomers that are mirror images of each other. When four different atoms or groups of atoms are bonded to the same carbon (asymmetric carbon). When four different atoms or groups of atoms are bonded to the same carbon (asymmetric carbon). Two different spatial arrangements of the four groups are mirror images. Two different spatial arrangements of the four groups are mirror images. Usually one form is biologically active and its mirror image is not. Usually one form is biologically active and its mirror image is not. L-isomer (levo/left) L-isomer (levo/left) D-isomer (dextro/right) D-isomer (dextro/right)

Thalidomide: Very different enantiomers

Functional groups also contribute to the molecular diversity of life Functional groups -- Small groups of atoms bonded to the carbon skeleton of organic molecules. T Functional groups -- Small groups of atoms bonded to the carbon skeleton of organic molecules. T Functional groups: Functional groups: Have specific chemical and physical properties.Have specific chemical and physical properties. Are commonly the chemically reactive regions of the molecule.Are commonly the chemically reactive regions of the molecule. Behave consistently from one organic molecule to another.Behave consistently from one organic molecule to another. Depending upon their number and arrangement, determine chemical properties of organic molecules in which they occur. Depending upon their number and arrangement, determine chemical properties of organic molecules in which they occur.

Hydroxyl Group (R--OH) Functional group that consists of a hydrogen atom bonded to an oxygen atom, which in turn is bonded to carbon. Functional group that consists of a hydrogen atom bonded to an oxygen atom, which in turn is bonded to carbon. Is a polar group (O-H bond is polar covalent). Is a polar group (O-H bond is polar covalent). Makes the molecule to which it is attached water soluble. Makes the molecule to which it is attached water soluble. Hydrogen bonds form between polar water molecules and hydroxyl group. Hydrogen bonds form between polar water molecules and hydroxyl group. Organic compounds with hydroxyl groups are called alcohols. Organic compounds with hydroxyl groups are called alcohols.

Carbonyl Group (R--C=O) Functional group that consists of a carbon atom double-bonded to oxygen (- CO). Functional group that consists of a carbon atom double-bonded to oxygen (- CO). Is a polar group (O can hydrogen bond) Is a polar group (O can hydrogen bond) Molecules with this functional group are water soluble. Molecules with this functional group are water soluble. Is a functional group found in sugars. Is a functional group found in sugars. If carbonyl is at the end off the carbon skeleton, the compound is an aldehyde. If carbonyl is at the end off the carbon skeleton, the compound is an aldehyde. If the carbonyl is NOT at the end of the carbon skeleton, the compound is a ketone. If the carbonyl is NOT at the end of the carbon skeleton, the compound is a ketone.

Carboxyl Group (R—COOH) Carboxyl Group (R—COOH) Functional group that consists of a carbon atom which is both double-bonded to an oxygen and single- bonded to the oxygen of a hydroxyl group. Functional group that consists of a carbon atom which is both double-bonded to an oxygen and single- bonded to the oxygen of a hydroxyl group. Is a polar group and water soluble. Is a polar group and water soluble. Since it donates protons, this group has acidic properties. Since it donates protons, this group has acidic properties. Compounds with this functional group are called carboxylic acids. Compounds with this functional group are called carboxylic acids.

Amino Group (R--NH 2 ) Functional group that consists of a nitrogen atom bonded to two hydrogens and to the carbon skeleton. Functional group that consists of a nitrogen atom bonded to two hydrogens and to the carbon skeleton. Is a polar group and soluble in water. Is a polar group and soluble in water. Acts as a weak base; the nitrogen can accept a proton. Acts as a weak base; the nitrogen can accept a proton. Organic compounds with this function group are called amines. Organic compounds with this function group are called amines.

Sulfhydryl Group (R--SH) Functional group which consists of an atom of (- sulfur bonded to an atom of hydrogen SH). Functional group which consists of an atom of (- sulfur bonded to an atom of hydrogen SH). Help stabilize the structure of proteins. Help stabilize the structure of proteins. Organic compounds with this functional group are called thiols. Organic compounds with this functional group are called thiols.

Phosphate Group (R--PO 4 ) Functional group in which the phosphate is attached to carbon skeleton by O. Functional group in which the phosphate is attached to carbon skeleton by O. Loss of two protons leaves the phosphate group with a negative charge; has acid properties. Loss of two protons leaves the phosphate group with a negative charge; has acid properties. Polar group and soluble in water. Polar group and soluble in water. Organic phosphates are important in cellular energy storage and transfer (ATP). Organic phosphates are important in cellular energy storage and transfer (ATP).

Nomenclature 1 C: methane 1 C: methane 2 C: ethane (C-C) 2 C: ethane (C-C) 3 C: propane (C-C-C) 3 C: propane (C-C-C) Ethene (C=C) Ethene (C=C) Ethyne (C=C) Ethyne (C=C) Propanol (C-C-C-OH) Propanol (C-C-C-OH) Propanal/Acetone (C-C-C=O) Propanal/Acetone (C-C-C=O)