1. Chapter 4: Carbon

2. Carbon Overview: Carbon—The Backbone of Biological Molecules All living organisms are made up of chemicals based mostly on the element carbon Organic chemistry is the study of carbon compounds Overview: Carbon—The Backbone of Biological Molecules All living organisms are made up of chemicals based mostly on the element carbon Organic chemistry is the study of carbon compounds

3. The Formation of Bonds with Carbon  Carbon has FOUR unpaired valence electrons  This allows it to form FOUR covalent bonds with a variety of atoms  Carbon has FOUR unpaired valence electrons  This allows it to form FOUR covalent bonds with a variety of atoms

4. Versatility of Carbon The bonding versatility of carbon Allows it to form many diverse molecules, including carbon skeletons The bonding versatility of carbon Allows it to form many diverse molecules, including carbon skeletons (a) Methane (b) Ethane ( c) Ethene (ethylene) Molecular Formula Structural Formula Ball-and- Stick Model Space- Filling Model H H H H H H H H H H HH H H C C C CC CH 4 C2H6C2H6C2H6C2H6 C2H4C2H4C2H4C2H4 Name and Comments

5. Common Bonding Partners of Carbon The electron configuration of carbon Gives it covalent compatibility with many different elements The electron configuration of carbon Gives it covalent compatibility with many different elements HONCHydrogen (valence = 1) Oxygen (valence = 2 ) Nitrogen (valence = 3) Carbon (valence = 4)

6. Carbon chains Form the skeletons of most organic molecules Vary in length and shape 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 Length Branching Double bonds Rings Ethane Propane Butane 2-methylpropane (commonly called isobutane) 1-Butene 2-Butene Cyclohexane Benzene HHHHH

7. Hydrocarbons  Hydrocarbons  Are molecules consisting of only carbon (C) and hydrogen (H)  The bonds between the C and H atoms are non-polar covalent  This makes hydrocarbons hydrophobic  Hydrocarbons  Are molecules consisting of only carbon (C) and hydrogen (H)  The bonds between the C and H atoms are non-polar covalent  This makes hydrocarbons hydrophobic

8. Isomers  Isomers  Are molecules with the same molecular formula but different structures and properties Three types of isomers are: Structural Geometric Enantiomers  Isomers  Are molecules with the same molecular formula but different structures and properties Three types of isomers are: Structural Geometric Enantiomers

9. Structural isomers: Branching 2-methyl butane Pentane

10. Geometric isomers: Double Bonds cis isomer: The two Xs are on the same side. trans isomer: The two Xs are on opposite sides.

11. Enantiomers: Mirrored Images Asymmetric Carbon

12. The Functional Groups  Functional groups  Are the chemically reactive groups of atoms within an organic molecule  They behave consistently and characteristically, giving unique properties to the molecules possessing them.  Functional groups  Are the chemically reactive groups of atoms within an organic molecule  They behave consistently and characteristically, giving unique properties to the molecules possessing them.

13. STRUCTURE EXAMPLE NAME OF COMPOUND FUNCTIONAL PROPERTIES Methyl 5-Methyl cytidine is a component of DNA that has been modified by addition of the methyl group. 5-Methyl cytidine Methylated compounds 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.

14. Hydroxyl  Composition: Oxygen bonded to a Hydrogen atom as well as a Carbon  Structure: -C-OH  Methanol:  Can also be seen as HO-C-  Not to be confused with hydroxide ion (OH - )  Compounds containing hydroxyl groups are called alcohols  Makes molecules polar (hydrophilic)  Composition: Oxygen bonded to a Hydrogen atom as well as a Carbon  Structure: -C-OH  Methanol:  Can also be seen as HO-C-  Not to be confused with hydroxide ion (OH - )  Compounds containing hydroxyl groups are called alcohols  Makes molecules polar (hydrophilic)

15. Carbonyl  Composition: Oxygen double bonded to a Carbon  Structure: -C=O  Aldehyde: If at end of carbon skeleton  Ketone: If in middle of carbon skeleton  Composition: Oxygen double bonded to a Carbon  Structure: -C=O  Aldehyde: If at end of carbon skeleton  Ketone: If in middle of carbon skeleton

16. STRUCTURE EXAMPLE NAME OF COMPOUND FUNCTIONAL PROPERTIES Carboxyl Acetic acid, which gives vinegar its sour taste Carboxylic acids, or organic acids Has acidic properties because the covalent bond between oxygen and hydrogen is so polar; for example, Acetic acidAcetate ion

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

18. STRUCTURE EXAMPLE NAME OF COMPOUND FUNCTIONAL PROPERTIES Sulfhydryl (may be written HS—) Cysteine Cysteine is an important sulfur-containing amino acid. Thiols 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.

19. STRUCTURE EXAMPLE NAME OF COMPOUND FUNCTIONAL PROPERTIES Phosphate 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. Glycerol phosphate Organic phosphates 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). Has the potential to react with water, releasing energy.