Jim’s Discussion Notes

CARBON AND THE

MOLECULAR DIVERSITY

OF LIFE

A. The Importance of Carbon

· Although cells are 70-95% water, the rest consists mostly of carbon-based compounds.

· Proteins, DNA, carbohydrates, and other molecules that distinguish living matter from inorganic material are all composed of carbon atoms bonded to each other and to atoms of other elements.

· These other elements commonly include hydrogen (H), oxygen (O), nitrogen (N), sulfur (S), and phosphorus (P).

1. Organic chemistry is the study of carbon compounds

· The study of carbon compounds, organic chemistry, focuses on any compound with carbon (organic compounds).

· While the name, organic compounds, implies that these compounds can 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.

· The overall percentages of the major elements of life (C, H, O, N, S, and P) are quite uniform from one organism to another.

· However, because of carbon’s versatility, these few elements can be combined to build an inexhaustible variety of organic molecules.

· While the percentages of major elements do not differ within or among species, variations in organic molecules can distinguish even between individuals of a single species.

· The science of organic chemistry began in attempts to purify and improve the yield of products from other organisms.

· Later chemists learned to synthesize simple compounds in the laboratory, but they had no success with more complex compounds.

· The Swedish chemist Jons Jacob Berzelius was the first to make a distinction between organic compounds that seemed to arise only in living organisms and inorganic compounds from the nonliving world.

· This led early organic chemists to propose vitalism, the belief in a life outside the limits of physical and chemical laws.

· Support for vitalism began to wane as organic chemists learned to synthesize more complex organic compounds in the laboratory.

· In the early 1800s the German chemist Friedrich Wöhler and his students were able to synthesize urea from totally inorganic starting materials.

· In 1953, Stanley Miller at the University of Chicago was able to simulate chemical conditions on the primitive Earth to demonstrate the spontaneous synthesis of organic compounds.

· Organic chemists finally rejected vitalism and embraced mechanism.

· Under mechanism, all natural phenomena, including the processes of life, are governed by the same physical and chemical laws.

· Organic chemistry was redefined as the study of carbon compounds regardless of origin.

· Still, most organic compounds in an amazing diversity and complexity are produced by organisms.

· However, the same rules apply to inorganic and organic compounds alike.

2. Carbon atoms are the most versatile building blocks of molecules

· With a total of 6 electrons, a carbon atom has 2 in the first shell and 4 in the second shell.

· Carbon has little tendency to form ionic bonds by losing or gaining 4 electrons.

· Instead, carbon usually completes its valence shell by sharing electrons with other atoms in four covalent bonds.

· This tetravalence by carbon makes large, complex molecules possible.

· When carbon forms covalent bonds with four other atoms, they are arranged at the corners of an imaginary tetrahedron with bond angles near 109^o.

· While drawn flat, they are actually three-dimensional.

· When two carbon atoms are joined by a double bond, all bonds around the carbons are in the same plane.

· They have a flat, three-dimensional structure.

· The electron configuration of carbon gives it compatibility to form covalent bonds with many different elements.

· The valences of carbon and its partners can be viewed as the building code that governs the architecture of organic molecules.

· In carbon dioxide, one carbon atom forms two double bonds with two different oxygen atoms.

· The structural formula, O = C = O, shows that each atom has completed its valence shells.

· While CO₂ can be classified as either organic or inorganic, its importance to the living world is clear.

· CO₂ is the source for all organic molecules in organisms via the process of photosynthesis.

· Urea, CO(NH₂)₂, is another simple organic molecule in which each atom has enough covalent bonds to complete its valence shell.

3. 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.

· 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.

· Isomers are compounds that have the same molecular formula but different structures and therefore different chemical properties.

· For example, butane and isobutane have the same molecular formula C₄H₁₀, but butane has a straight skeleton and isobutane has a branched skeleton.

· The two butanes are structural isomers, molecules that have the same molecular formula but differ in the covalent arrangement of atoms.

· Geometric isomers are compounds with the same covalent partnerships that differ in their spatial arrangement around a carbon-carbon double bond.

· The double bond does not allow atoms to rotate freely around the bond axis.

· The biochemistry of vision involves a light-induced change in the structure of rhodopsin in the retina from one geometric isomer to another.

· Enantiomers are molecules that are mirror images of each other.

· Enantiomers are possible if there are four different atoms or groups of atoms bonded to a carbon.

· If this is true, it is possible to arrange the four groups in space in two different ways that are mirror images.

· They are like left-handed and right-handed versions.

· Usually one is biologically active, the other inactive.

· Even the subtle structural differences in two enantiomers have important functional significance because of emergent properties from the specific arrangements of atoms.

· One enantiomer of the drug thalidomide reduced morning sickness, its desired effect, but the other isomer caused severe birth defects.

· The L-Dopa isomer is an effective treatment of Parkinson’s disease, but the D-Dopa isomer is inactive.

B. Functional Groups

1. 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.

· Each functional group behaves consistently from one organic molecule to another.

· The number and arrangement of functional groups help give each molecule its unique properties.

· 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.

· There are six functional groups that are most important to the chemistry of life: hydroxyl, carbonyl, carboxyl, amino, sulfhydryl, and phosphate groups.

· All are hydrophilic and increase the solubility of organic compounds in water.

· 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.

· 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.

· 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⁺).

· 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.

· 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.

· A phosphate group (-OPO₃^2-) consists of phosphorus bound to four oxygen atoms (three with single bonds and one with a double bond).

· 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.

2. 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.