Chapter 4 – Carbon and Molecular Diversity of Life Living organisms consist mostly of carbon-based compounds Carbon is unparalleled in its ability to form large, complex, and diverse molecules Proteins, DNA, carbohydrates, and other molecules that distinguish living matter are all composed of carbon compounds Copyright © 2002 Pearson Education, Inc., publishing as Benjamin Cummings

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 volcanoes, could have been a stage in the origin of life © 2011 Pearson Education, Inc.

Cooled “rain” containing organic molecules Cold water Figure 4.2 EXPERIMENT “Atmosphere” CH4 Water vapor Electrode NH3 H2 Condenser Cooled “rain” containing organic molecules Cold water Figure 4.2 Inquiry: Can organic molecules form under conditions believed to simulate those on the early Earth? H2O “sea” Sample for chemical analysis

Organic chemistry is the study of carbon compounds The study of carbon compounds, organic chemistry, focuses on any compound with carbon (organic compounds). Organic compounds are not only come from biological processes, they can be synthesized by non-living reactions. Organic compounds can range from simple molecules, such as CO2 or CH4, to complex molecules, like proteins, that may weigh over 100,000 daltons. Copyright © 2002 Pearson Education, Inc., publishing as Benjamin Cummings

Carbon atoms are the most versatile building blocks of molecules What is the electron configuration of carbon? Carbon has little tendency to form ionic bonds by loosing or gaining 4 electrons. Instead, carbon usually completes its valence shell by sharing electrons with other atoms in four covalent bonds. (tetravalence) Copyright © 2002 Pearson Education, Inc., publishing as Benjamin Cummings

Fig. 4.2 Copyright © 2002 Pearson Education, Inc., publishing as Benjamin Cummings

Variation in carbon skeletons contributes to the diversity of organic molecules Carbon chains form the skeletons of most organic molecules. The skeletons may vary in length and may be straight, branched, or arranged in closed rings. The carbon skeletons may also include double bonds. Copyright © 2002 Pearson Education, Inc., publishing as Benjamin Cummings

Fig. 4.4 Copyright © 2002 Pearson Education, Inc., publishing as Benjamin Cummings

Isomers Isomers are compounds with the same molecular formula but different structures and properties Structural isomers have different covalent arrangements of their atoms Cis-trans isomers have the same covalent bonds but differ in spatial arrangements Enantiomers are isomers that are mirror images of each other © 2011 Pearson Education, Inc.

(a) Structural isomers Figure 4.7 (a) Structural isomers (b) Cis-trans isomers cis isomer: The two Xs are on the same side. trans isomer: The two Xs are on opposite sides. (c) Enantiomers Figure 4.7 Three types of isomers, compounds with the same molecular formula but different structures. CO2H CO2H H NH2 NH2 H CH3 CH3 L isomer D isomer

Hydrocarbons are organic molecules that consist of only carbon and hydrogen atoms. Hydrocarbons are the major component of petroleum. Petroleum is a fossil fuel because it consists of the partially decomposed remains of organisms that lived millions of years ago. Fats are biological molecules that have long hydrocarbon tails attached to a non-hydrocarbon component. Fig. 4.5 Copyright © 2002 Pearson Education, Inc., publishing as Benjamin Cummings

Functional groups contribute to the molecular diversity of life The components of organic molecules that are most commonly involved in chemical reactions are known as functional groups Functional groups are attachments that replace one or more hydrogen atoms to the carbon skeleton of the hydrocarbon. Copyright © 2002 Pearson Education, Inc., publishing as Benjamin Cummings

The basic structure of testosterone (male hormone) and estradiol (female hormone) is identical. Both are steroids with four fused carbon rings, but they differ in the functional groups attached to the rings. These then interact with different targets in the body. Fig. 4.8 Copyright © 2002 Pearson Education, Inc., publishing as Benjamin Cummings

Functional groups contribute to the molecular diversity of life Functional groups that are most important to the chemistry of life: hydroxyl carbonyl carboxyl amino sulfhydryl phosphate methyl

In a hydroxyl group (-OH), a hydrogen atom forms a polar covalent bond with an oxygen atom, which forms a polar covalent bond to the carbon skeleton. Because of these polar covalent bonds hydroxyl groups improve the solubility of organic molecules. Organic compounds with hydroxyl groups are alcohols and their names typically end in -ol. Copyright © 2002 Pearson Education, Inc., publishing as Benjamin Cummings

A carbonyl group (>CO) consists of an oxygen atom joined to the carbon skeleton by a double bond. If the carbonyl group is on the end of the skeleton, the compound is an aldehyde. If not, then the compound is a ketone. Isomers with aldehydes versus ketones have different properties. Copyright © 2002 Pearson Education, Inc., publishing as Benjamin Cummings

A carboxyl group (-COOH) consists of a carbon atom with a double bond to an oxygen atom and a single bond to a hydroxyl group. Compounds with carboxyl groups are carboxylic acids. A carboxyl group acts as an acid because the combined electronegativities of the two adjacent oxygen atoms increase the dissociation of hydrogen as an ion (H+). Copyright © 2002 Pearson Education, Inc., publishing as Benjamin Cummings

An amino group (-NH2) consists of a nitrogen atom attached to two hydrogen atoms and the carbon skeleton. Organic compounds with amino groups are amines. The amino group acts as a base because ammonia can pick up a hydrogen ion (H+) from the solution. Amino acids, the building blocks of proteins, have amino and carboxyl groups. Copyright © 2002 Pearson Education, Inc., publishing as Benjamin Cummings

This group resembles a hydroxyl group in shape. A sulfhydryl group (-SH) consists of a sulfur atom bonded to a hydrogen atom and to the backbone. This group resembles a hydroxyl group in shape. Organic molecules with sulfhydryl groups are thiols. Sulfhydryl groups help stabilize the structure of proteins. Copyright © 2002 Pearson Education, Inc., publishing as Benjamin Cummings

A phosphate group (-OPO32-) consists of phosphorus bound to four oxygen atoms A phosphate group connects to the carbon backbone via one of its oxygen atoms. Phosphate groups are anions with two negative charges as two protons have dissociated from the oxygen atoms. One function of phosphate groups is to transfer energy between organic molecules. Copyright © 2002 Pearson Education, Inc., publishing as Benjamin Cummings

• Addition of a methyl group Figure 4.9g Methyl STRUCTURE Methylated compounds NAME OF COMPOUND EXAMPLE • Addition of a methyl group to DNA, or to molecules bound to DNA, affects the expression of genes. FUNCTIONAL PROPERTIES Figure 4.9 Exploring: Some Biologically Important Chemical Groups • Arrangement of methyl groups in male and female sex hormones affects their shape and function. 5-Methyl cytidine

The chemical elements of life: a review Living matter consists mainly of carbon, oxygen, hydrogen, and nitrogen, with smaller amounts of sulfur and phosphorus. These elements are linked by strong covalent bonds. Carbon with its four covalent bonds is the basic building block in molecular architecture. The great diversity of organic molecules with their special properties emerge from the unique arrangement of the carbon skeleton and the functional groups attached to the skeleton. Copyright © 2002 Pearson Education, Inc., publishing as Benjamin Cummings