Chemical Principles: Carbon.

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1 Chemical Principles: Carbon

2 Chapter 4: Carbon: The Backbone of Life
Although cells are mostly% water, the rest consists 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 What is so special about carbon?

3 The electron configuration of carbon gives it the ability to:
make more covalent bonds than other elements make single, double or triple bonds bond with many other elements impart shape to molecules

4 Carbon can form up to four covalent bonds
Molecular Formula Structural Formula Ball-and-Stick Model Space-Filling Model Name (a) Methane (b) Ethane Figure 4.3 The shapes of three simple organic molecules (c) Ethene (ethylene) Sharing one pair of electrons = single covalent bond Sharing two pairs = double covalent bond

5 Carbon can form covalent bonds with other elements
Carbon dioxide: CO2 Carbon shares four pairs of electrons with oxygen (highest oxidation state) Urea Carbon shares two pairs of electrons with oxygen and two with nitrogen

6 (commonly called isobutane)
Carbon’s bonding properties can impart shape to molecules like these hydrocarbons Ethane Propane 1-Butene 2-Butene (a) Length (c) Double bonds Figure 4.5 Variation in carbon skeletons Butane 2-Methylpropane (commonly called isobutane) Cyclohexane Benzene (b) Branching (d) Rings

7 Isomers provide many different shapes Pentane 2-methyl butane
(a) Structural isomers cis isomer: The two Xs are on the same side. trans isomer: The two Xs are on opposite sides. (b) Geometric isomers Figure 4.7 Three types of isomers L isomer D isomer (c) Enantiomers

8 Effective Enantiomer Ineffective Enantiomer Drug Condition Pain;
inflammation Ibuprofen S-Ibuprofen R-Ibuprofen Figure 4.8 The pharmacological importance of enantiomers Albuterol Asthma R-Albuterol S-Albuterol

9 A small number of chemical groups are key to the functioning of biological molecules
Distinctive properties of organic molecules depend not only on the carbon skeleton but also on the molecular components attached to it A number of characteristic groups are often attached to skeletons of organic molecules Functional groups are the components of organic molecules that are most commonly involved in chemical reactions The number and arrangement of functional groups give each molecule its unique properties

10 Example-Different functional groups
make a difference at the biological level Testosterone Estradiol Figure 4.9 A comparison of chemical groups of female (estradiol) and male (testosterone) sex hormones

11 The seven functional groups that are most important in the chemistry of life:
Hydroxyl group: -OH Carbonyl group: -C=O Carboxyl group: -COOH Amino group: -NH2 Sulfhydryl group: -SH Phosphate group: -PO4 Methyl group: -CH3

12 Figure 4.10 Some biologically important chemical groups
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).

13 Figure 4.10 Some biologically important chemical groups
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.

14 Hydroxyl Carbonyl Carboxylic Amino Sulfhydryl Phosphate Methyl

15 Why is carbon special for life?
Carbon was thought to have supernatural properties that placed it at the center of living systems Reflected in the name of the branch of chemistry that deals with carbon: organic chemistry Vitalism was the idea that carbon compounds could only be produced by living organisms,

16 Vitalism dropped out of the picture when chemists first synthesized organic compounds in their labs
Mechanism is the view that all natural phenomena are governed by the same physical and chemical laws The mechanistic view allows scientists to take a reductionist approach to the study of living systems (and to this course)

17 What makes carbon “special”?
makes more bonds than other elements makes single, double or triple bonds bonds with many other elements imparts shape to molecules These properties are the result of electron configuration-not magic!