1. Copyright © 2006 Cynthia Garrard publishing under Canyon Design Chapter 4 - Carbon All living organisms – Made of chemicals, based mostly on the element carbon Carbon is unparalleled in its ability to form large, complex and diverse molecules

2. Copyright © 2006 Cynthia Garrard publishing under Canyon Design Organic Chemistry Organic chemistry is the study of carbon compounds Organic compounds – Range from simple molecules to colossal ones

3. Copyright © 2006 Cynthia Garrard publishing under Canyon Design Molecular Diversity of Carbon Carbon chains – Form the skeletons of most organic molecules – Vary in length and shape H H H H H H H H H H H HHH H H H H H H H H H H H H H H H H HH H H HH HHH H HH HH H H H H H H H C C CCC CCCCCCC CCCCCCCC C C C C C C C C C C C C H H H H H H H (a) Length (b) Branching (c) Double bonds (d) Rings Ethane Propane Butane 2-methylpropane (commonly called isobutane) 1-Butene2-Butene Cyclohexane Benzene HH HHH Figure 4.5 A-D

4. Copyright © 2006 Cynthia Garrard publishing under Canyon Design Carbon’s Four Bonding Sites Remember electron configuration determines the kind and number of bonds an atom will form Carbon has __ valence electrons, it must form __ bonds Carbon is covalently compatible with many different elements

5. Copyright © 2006 Cynthia Garrard publishing under Canyon Design Carbon’s Four Bonding Sites The electron configuration of carbon – Gives it covalent compatibility with many different elements H O NC Hydrogen (valence = 1) Oxygen (valence = 2) Nitrogen (valence = 3) Carbon (valence = 4) Figure 4.4

6. Copyright © 2006 Cynthia Garrard publishing under Canyon Design Hydrocarbons – Are molecules consisting of only carbon and hydrogen – Are hydrophobic – Undergo reactions that release relatively large amounts of energy

7. Copyright © 2006 Cynthia Garrard publishing under Canyon Design Hydrocarbons – Are found in many of a cell’s organic molecules (a) A fat molecule (b) Mammalian adipose cells 100 µm Fat droplets (stained red) Figure 4.6 A, B

8. Copyright © 2006 Cynthia Garrard publishing under Canyon Design Isomers – Are molecules with the same molecular formula but different structures and properties Three types of isomers are – Structural – Geometric – Enantiomers (mirror)

9. Copyright © 2006 Cynthia Garrard publishing under Canyon Design Isomers Structural isomers – Differ in the covalent arrangement of atoms – Location of double bond(s) may also differ

10. Copyright © 2006 Cynthia Garrard publishing under Canyon Design Isomers Geometric isomers – Differ in spatial arrangements – Arrangements can be cis or tran

11. Copyright © 2006 Cynthia Garrard publishing under Canyon Design Isomers Enantiomers – Mirror images L-Dopa (effective against Parkinson’s disease) D-Dopa (biologicall y inactive) Figure 4.8

12. Copyright © 2006 Cynthia Garrard publishing under Canyon Design So, given a chemical formula, how do you know what a molecule should look like structurally?

13. Copyright © 2006 Cynthia Garrard publishing under Canyon Design Functional Groups Functional groups – Are the chemically reactive groups of atoms within an organic molecule – Behave consistently from one molecule to the next – The arrangement of the groups help give the molecule its properties

14. Copyright © 2006 Cynthia Garrard publishing under Canyon Design Functional Groups Six functional groups are important in the chemistry of life – Hydroxyl – Carbonyl – Carboxyl – Amino – Sulfhydryl – Phosphate

15. Copyright © 2006 Cynthia Garrard publishing under Canyon Design Functional Groups Some important functional groups of organic compounds FUNCTIONAL GROUP STRUCTURE (may be written HO ) HYDROXYL CARBONYL CARBOXYL OH 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 –.) When an oxygen atom is double- bonded to a carbon atom that is also bonded to a hydroxyl group, the entire assembly of atoms is called a carboxyl group (— COOH). C OO C OH Figure 4.10 The carbonyl group ( CO) consists of a carbon atom joined to an oxygen atom by a double bond. 

16. Copyright © 2006 Cynthia Garrard publishing under Canyon Design Functional Groups Some important functional groups of organic compounds Acetic acid, which gives vinegar its sour tatste NAME OF COMPOUNDS Alcohols (their specific names usually end in -ol) Ketones if the carbonyl group is within a carbon skeleton Aldehydes if the carbonyl group is at the end of the carbon skeleton Carboxylic acids, or organic acids EXAMPLE Propanal, an aldehyde Acetone, the simplest ketone Ethanol, the alcohol present in alcoholic beverages H H H HH CC OH H H H H H H H C C H C C C CCC O H O H H HH H O H Figure 4.10

17. Copyright © 2006 Cynthia Garrard publishing under Canyon Design Functional Groups Some important functional groups of organic compounds FUNCTIONAL PROPERTIES  Is polar as a result of the electronegative oxygen atom drawing electrons toward itself.  Attracts water molecules, helping dissolve organic compounds such as sugars (see Figure 5.3).  A ketone and an aldehyde may be structural isomers with different properties, as is the case for acetone and propanal.  Has acidic properties because it is a source of hydrogen ions. The covalent bond between oxygen and hydrogen is so polar that hydrogen ions (H + ) tend to dissociate reversibly; for example,  In cells, found in the ionic form, which is called a carboxylate group. H H C H H C O OH H H C O C OO + H + Figure 4.10

18. Copyright © 2006 Cynthia Garrard publishing under Canyon Design Functional Groups Some important functional groups of organic compounds The amino group (—NH 2 ) consists of a nitrogen atom bonded to two hydrogen atoms and to the carbon skeleton. AMINO SULFHYDRYL PHOSPHATE (may be written HS ) 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; abbreviated P. The phosphate group (—OPO 3 2– ) is an ionized form of a phosphoric acid group (— OPO 3 H 2 ; note the two hydrogens). N H H SH O P O OH Figure 4.10

19. Copyright © 2006 Cynthia Garrard publishing under Canyon Design Functional Groups Some important functional groups of organic compounds Because it also has a carboxyl group, glycine is both an amine and a carboxylic acid; compounds with both groups are called amino acids. Glycine Ethanethiol Glycerol phosphate O C HO C H H N H H H CC SH H H H H H OH CCCOPOO OO HHH O H Figure 4.10

20. Copyright © 2006 Cynthia Garrard publishing under Canyon Design Functional Groups Some important functional groups of organic compounds  Acts as a base; can pick up a proton from the surrounding solution:  Ionized, with a charge of 1+, under cellular conditions. (nonionized) (ionized) N H H H +N+NH H  Two sulfhydryl groups can interact to help stabilize protein structure (see Figure 5.20).  Makes the molecule of which it is a part an anion (negatively charged ion). Can transfer energy between organic molecules. Figure 4.10

21. Copyright © 2006 Cynthia Garrard publishing under Canyon Design The Chemical Elements of Life: A Review The versatility of carbon – Makes possible the great diversity of organic molecules