Chapter 4: Carbon and the Molecular Diversity of Life

Overview: Carbon: The Backbone of Life Cells 70–95% water BUT the rest mostly carbon-based compounds “Carbon is unparalleled in its ability to form large, complex, and diverse molecules” Why? Important Carbon Compounds: Proteins DNA Carbohydrates, Molecules that distinguish living Carbon-rich  Copyright © 2008 Pearson Education, Inc., publishing as Pearson Benjamin Cummings

Concept 4.1: Organic chemistry is the study of carbon compounds Organic chemistry: study of compounds that contain carbon Simple molecules to colossal ones Organic compounds usually contain hydrogen too Vitalism: idea that organic compounds arise only in organisms disproved when chemists synthesized these compounds  Mechanism: the view that all natural phenomena are governed by physical and chemical laws  Copyright © 2008 Pearson Education, Inc., publishing as Pearson Benjamin Cummings

Concept 4.2: Carbon atoms can form diverse molecules by bonding to four other atoms Electron configuration = key to an atom’s characteristics Electron configuration determines: the kinds of bond number of bonds with other atoms (MANY) Tetravalence: Carbon has FOUR valence electrons  FOUR covalent bonds can be formed This makes large, complex molecules possible Tetrahedral shape: molecules with multiple carbons, when each carbon bonded to four other atoms HOWEVER, two carbon with double bond  flat shape “Building code that governs architecture of living molecule: Valences of carbon Its most frequent partners (hydrogen, oxygen, and nitrogen) O = C = O Copyright © 2008 Pearson Education, Inc., publishing as Pearson Benjamin Cummings

Fig. 4-3 Properties of molecules are influenced by characteristics of the covalent bonds: Orientation—length, angle, and direction of bonds between any two elements are always the same. Example: Methane always forms a tetrahedron. Molecular Formula Structural Formula Name Ball-and-Stick Model Space-Filling Model (a) Methane (b) Ethane Figure 4.3 The shapes of three simple organic molecules (c) Ethene (ethylene)

Hydrogen (valence = 1) Oxygen (valence = 2) Nitrogen (valence = 3) Fig. 4-4 Hydrogen (valence = 1) Oxygen (valence = 2) Nitrogen (valence = 3) Carbon (valence = 4) H O N C Figure 4.4 Valences of the major elements of organic molecules

Concept 2.2 Atoms Interact and Form Molecules Strength and stability—covalent bonds are very strong; it takes a lot of energy to break them. Multiple bonds Single—sharing 1 pair of electrons : C - H Double—sharing 2 pairs of electrons : C = C Triple—sharing 3 pairs of electrons : C N

Fig. 4-UN1 Urea

Concept 2.2 Atoms Interact and Form Molecules Two atoms of different elements do not always share electrons equally. The nucleus of one element may have greater electronegativity — the attractive force that an atomic nucleus exerts on electrons. Depends on the number of protons and the distance between the nucleus and electrons.

Table 2.3

Concept 2.2 Atoms Interact and Form Molecules If atoms have similar electronegativities, they share electrons equally (nonpolar covalent bond). If atoms have different electronegativities, electrons tend to be near the most attractive atom, forming a polar covalent bond.

Molecular Diversity Arising from Carbon Skeleton Variation Carbon chains form skeletons of most organic molecules length and shape Hydrocarbons: organic molecules consisting of only carbon and hydrogen Many organic molecules have hydrocarbon components Can undergo reactions that release a large amount of energy Copyright © 2008 Pearson Education, Inc., publishing as Pearson Benjamin Cummings

Fat droplets (stained red) Fig. 4-6 Fat droplets (stained red) Figure 4.6 The role of hydrocarbons in fats Hydrocarbon tails… insoluble in water... This is a pic of adipose tissue (fat tissue)- insulation; long-term energy storage! If a hydrocarbon has the greatest number of “openings” filled with hydrogen, then it is said to be SATURATED This means it is full and can hold no more If a hydrocarbon has a double bond, does it have the potential to hold more hydrogen than it has now? Yes…it is UNSATURATED 100 µm (a) Mammalian adipose cells (b) A fat molecule

Isomers Isomers: compounds with the same molecular formula but different structures and properties: Structural isomers: different covalent arrangements of their atoms Geometric isomers: the same covalent arrangements but differ in spatial arrangements Enantiomers: isomers that are mirror images of each other Same atoms arranged differently give diff properties Copyright © 2008 Pearson Education, Inc., publishing as Pearson Benjamin Cummings

Enantiomers are Important in the pharmaceutical industry Two enantiomers of a drug may have different effects  organisms are sensitive to even subtle variations in molecules Copyright © 2008 Pearson Education, Inc., publishing as Pearson Benjamin Cummings

Concept 4.3: A small number of chemical groups are key to the functioning of biological molecules Distinctive properties depend on the carbon skeleton molecular components attached to it Can be more than one Functional groups: the components of organic molecules that are most commonly involved in chemical reactions Number + arrangement of functional groups = unique properties Copyright © 2008 Pearson Education, Inc., publishing as Pearson Benjamin Cummings

Seven Most Important FUNctional groups in Chemistry of Life Hydroxyl group Carbonyl group Carboxyl group Amino group Sulfhydryl group Phosphate group Methyl group Copyright © 2008 Pearson Education, Inc., publishing as Pearson Benjamin Cummings

Figure 4.10 Some biologically important chemical groups Fig. 4-10a CHEMICAL GROUP Hydroxyl Carbonyl Carboxyl STRUCTURE (may be written HO—) In a hydroxyl group (—OH), a hydrogen atom is bonded to an oxygen atom, which in turn is bonded to the carbon skeleton of the organic molecule. (Do not confuse this functional group with the hydroxide ion, OH–.) The carbonyl group ( CO) consists of a carbon atom joined to an oxygen atom by a double bond. When an oxygen atom is double-bonded to a carbon atom that is also bonded to an —OH group, the entire assembly of atoms is called a carboxyl group (—COOH). NAME OF COMPOUND Alcohols (their specific names usually end in -ol) Ketones if the carbonyl group is within a carbon skeleton Carboxylic acids, or organic acids Aldehydes if the carbonyl group is at the end of the carbon skeleton EXAMPLE Ethanol, the alcohol present in alcoholic beverages Acetone, the simplest ketone Acetic acid, which gives vinegar its sour taste Figure 4.10 Some biologically important chemical groups Propanal, an aldehyde FUNCTIONAL PROPERTIES Is polar as a result of the electrons spending more time near the electronegative oxygen atom. A ketone and an aldehyde may be structural isomers with different properties, as is the case for acetone and propanal. Has acidic properties because the covalent bond between oxygen and hydrogen is so polar; for example, Can form hydrogen bonds with water molecules, helping dissolve organic compounds such as sugars. These two groups are also found in sugars, giving rise to two major groups of sugars: aldoses (containing an aldehyde) and ketoses (containing a ketone). Acetic acid Acetate ion Found in cells in the ionized form with a charge of 1– and called a carboxylate ion (here, specifically, the acetate ion).

Figure 4.10 Some biologically important chemical groups Fig. 4-10b CHEMICAL GROUP Amino Sulfhydryl Phosphate Methyl (may be written HS—) STRUCTURE The amino group (—NH2) consists of a nitrogen atom bonded to two hydrogen atoms and to the carbon skeleton. The sulfhydryl group consists of a sulfur atom bonded to an atom of hydrogen; resembles a hydroxyl group in shape. In a phosphate group, a phosphorus atom is bonded to four oxygen atoms; one oxygen is bonded to the carbon skeleton; two oxygens carry negative charges. The phosphate group (—OPO32–, abbreviated ) is an ionized form of a phosphoric acid group (—OPO3H2; note the two hydrogens). A methyl group consists of a carbon bonded to three hydrogen atoms. The methyl group may be attached to a carbon or to a different atom. P NAME OF COMPOUND Amines Thiols Organic phosphates Methylated compounds EXAMPLE Glycine Glycerol phosphate Because it also has a carboxyl group, glycine is both an amine and a carboxylic acid; compounds with both groups are called amino acids. Cysteine In addition to taking part in many important chemical reactions in cells, glycerol phosphate provides the backbone for phospholipids, the most prevalent molecules in cell membranes. 5-Methyl cytidine Cysteine is an important sulfur-containing amino acid. 5-Methyl cytidine is a component of DNA that has been modified by addition of the methyl group. Figure 4.10 Some biologically important chemical groups FUNCTIONAL PROPERTIES Acts as a base; can pick up an H+ from the surrounding solution (water, in living organisms). Two sulfhydryl groups can react, forming a covalent bond. This “cross-linking” helps stabilize protein structure. Contributes negative charge to the molecule of which it is a part (2– when at the end of a molecule; 1– when located internally in a chain of phosphates). Addition of a methyl group to DNA, or to molecules bound to DNA, affects expression of genes. Arrangement of methyl groups in male and female sex hormones affects their shape and function. Cross-linking of cysteines in hair proteins maintains the curliness or straightness of hair. Straight hair can be “permanently” curled by shaping it around curlers, then breaking and re-forming the cross-linking bonds. Has the potential to react with water, releasing energy. (nonionized) (ionized) Ionized, with a charge of 1+, under cellular conditions.

Carboxyl STRUCTURE NAME OF COMPOUND Carboxylic acids, or organic acids Fig. 4-10c Carboxyl STRUCTURE NAME OF COMPOUND Carboxylic acids, or organic acids EXAMPLE FUNCTIONAL PROPERTIES Has acidic properties because the covalent bond between oxygen and hydrogen is so polar; for example, Acetic acid, which gives vinegar its sour taste Figure 4.10 Some biologically important chemical groups—carbonyl group Acetic acid Acetate ion Found in cells in the ionized form with a charge of 1– and called a carboxylate ion (here, specifically, the acetate ion).

Amino STRUCTURE NAME OF COMPOUND Amines EXAMPLE FUNCTIONAL PROPERTIES Fig. 4-10d Amino STRUCTURE NAME OF COMPOUND Amines EXAMPLE FUNCTIONAL PROPERTIES Acts as a base; can pick up an H+ from the surrounding solution (water, in living organisms). Glycine Figure 4.10 Some biologically important chemical groups—amino group Because it also has a carboxyl group, glycine is both an amine and a carboxylic acid; compounds with both groups are called amino acids. (nonionized) (ionized) Ionized, with a charge of 1+, under cellular conditions.

Sulfhydryl STRUCTURE NAME OF COMPOUND Thiols (may be written HS—) Fig. 4-10e Sulfhydryl STRUCTURE NAME OF COMPOUND Thiols (may be written HS—) EXAMPLE FUNCTIONAL PROPERTIES Two sulfhydryl groups can react, forming a covalent bond. This “cross-linking” helps stabilize protein structure. Cross-linking of cysteines in hair proteins maintains the curliness or straightness of hair. Straight hair can be “permanently” curled by shaping it around curlers, then breaking and re-forming the cross-linking bonds. Cysteine Figure 4.10 Some biologically important chemical groups—sulfhydryl group Cysteine is an important sulfur-containing amino acid.

Phosphate STRUCTURE NAME OF COMPOUND Organic phosphates EXAMPLE Fig. 4-10f Phosphate STRUCTURE NAME OF COMPOUND Organic phosphates EXAMPLE FUNCTIONAL PROPERTIES Contributes negative charge to the molecule of which it is a part (2– when at the end of a molecule; 1– when located internally in a chain of phosphates). Glycerol phosphate Figure 4.10 Some biologically important chemical groups—phosphate group Has the potential to react with water, releasing energy. In addition to taking part in many important chemical reactions in cells, glycerol phosphate provides the backbone for phospholipids, the most prevalent molecules in cell membranes.

Methyl STRUCTURE NAME OF COMPOUND Methylated compounds EXAMPLE Fig. 4-10g Methyl STRUCTURE NAME OF COMPOUND Methylated compounds EXAMPLE FUNCTIONAL PROPERTIES Addition of a methyl group to DNA, or to molecules bound to DNA, affects expression of genes. Arrangement of methyl groups in male and female sex hormones affects their shape and function. Figure 4.10 Some biologically important chemical groups—methyl group 5-Methyl cytidine 5-Methyl cytidine is a component of DNA that has been modified by addition of the methyl group.

ATP: An Important Source of Energy for Cellular Processes Adenosine triphosphate (ATP): phosphate molecule that is the primary energy-transferring molecule in the cell adenosine attached to a string of three phosphate groups What did YOU use it for today? How did you get it? Copyright © 2008 Pearson Education, Inc., publishing as Pearson Benjamin Cummings

Reacts with H2O Energy ATP Inorganic phosphate ADP Adenosine Adenosine Fig. 4-UN4 Reacts with H2O P P P Adenosine P i P P Adenosine Energy ATP Inorganic phosphate ADP Hydrolysis--- water pops off the 3rd P- releasing energy for cellular metabolism. ATP is an unstable molecule which hydrolyzes to ADP and inorganic phosphate when it is in equilibrium with water. The high energy of this molecule comes from the two high-energy phosphate bonds.

You should now be able to: Explain how carbon’s electron configuration is key to its ability to form large, complex, diverse organic molecules Describe how carbon skeletons may vary and explain how this variation contributes to the diversity and complexity of organic molecules Distinguish among the three types of isomers: structural geometric enantiomer Name the major functional groups found in organic molecules; describe the basic structure of each functional group and outline the chemical properties of the organic molecules in which they occur Explain how ATP functions as the primary energy transfer molecule in living cells Copyright © 2008 Pearson Education, Inc., publishing as Pearson Benjamin Cummings