Chemistry of Carbon

1. Chemistry of Carbon Building Blocks of Life

2. Why study Carbon? • All of life is built on carbon • Cells • ~72% H2O • ~25% carbon compounds • Carbohydrates • Lipids • Proteins • Nucleic Acids • ~3% salts • Na, Cl, K…

3. Chemistry of Life • Organic chemistry is the study of carboncompounds • C atoms are versatile building blocks • bonding properties • 4 stable covalent bonds H C H H H

4. Complex molecules assembled like TinkerToys

5. Fig. 4-7b cis isomer: The two Xs are on the same side. trans isomer: The two Xs are on opposite sides. (b) Geometric isomers

6. Hydrocarbons • Combinations of C & H • Methane • not soluble in H2O • stable • very little attraction between molecules • a gas at room temperature methane(simplest HC)

7. Hydrocarbons can grow

8. Isomers • Molecules with same molecular formula but different structures (shapes) • different chemical properties • different biological functions 6 carbons 6 carbons 6 carbons

9. Form affects function • Structural differences create important functional significance • amino acid alanine • L-alanine used in proteins • but not D-alanine • medicines • L-version active • but not D-version • sometimes withtragic results… stereoisomers

10. Form affects function • Thalidomide • prescribed to pregnant women in 50s & 60s • reduced morning sickness, but… • stereoisomer caused severe birth defects

11. Diversity of molecules • Substitute other atoms or groups around the carbon • ethane vs. ethanol • H replaced by an hydroxyl group (–OH) • nonpolar vs. polar • gas vs. liquid • biological effects! ethanol (C2H5OH) ethane (C2H6)

12. Functional groups • Parts of organic molecules that are involved in chemical reactions • give organic molecules distinctive properties hydroxylamino carbonylsulfhydryl carboxylphosphate • Affect reactivity • increase solubility in water

13. Viva la difference! • Basic structure of male & female hormones is identical • identical carbon skeleton • attachment of different functional groups • interact with different targets in the body • different effects

14. Hydroxyl • –OH • organic compounds with OH = alcohols • names typically end in -ol • ethanol

15. Carbonyl • C=O • O double bonded to C • if C=O at end molecule = aldehyde • if C=O in middle of molecule = ketone

16. Carboxyl • –COOH • C double bonded to O & single bonded to OH group • compounds with COOH = acids • fatty acids • amino acids

17. Amino • -NH2 • N attached to 2 H • compounds with NH2 = amines • amino acids • NH2 acts as base • ammonia picks up H+ from solution

18. Sulfhydryl • –SH • S bonded to H • compounds with SH = thiols • SH groups stabilize the structure of proteins

19. Phosphate • –PO4 • P bound to 4 O • connects to C through an O • lots of O = lots of negative charge • highly reactive • transfers energy between organic molecules • ATP, GTP, etc.

20. CHEMICAL GROUP Hydroxyl Carboxyl Carbonyl STRUCTURE (may be written HO—) 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). 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–.) Fig. 4-10a Alcohols (their specific names usually end in -ol) NAME OF COMPOUND Carboxylic acids, or organic acids Ketones if the carbonyl group is within a carbon skeleton Aldehydes if the carbonyl group is at the end of the carbon skeleton EXAMPLE Acetone, the simplest ketone Ethanol, the alcohol present in alcoholic beverages Acetic acid, which gives vinegar its sour taste 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). Acetate ion Acetic acid Found in cells in the ionized form with a charge of 1– and called a carboxylate ion (here, specifically, the acetate ion).

21. CHEMICAL GROUP Methyl Amino Sulfhydryl Phosphate (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 Fig. 4-10b NAME OF COMPOUND Amines Thiols Organic phosphates Methylated compounds EXAMPLE Glycine Glycerol phosphate Cysteine Because it also has a carboxyl group, glycine is both an amine and a carboxylic acid; compounds with both groups are called amino acids. 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. 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. Has the potential to react with water, releasing energy. 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. (ionized) (nonionized) Ionized, with a charge of 1+, under cellular conditions.

22. Carboxyl NAME OF COMPOUND STRUCTURE Carboxylic acids, or organic acids Fig. 4-10c 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 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).

23. Amino STRUCTURE NAME OF COMPOUND Amines Fig. 4-10d EXAMPLE FUNCTIONAL PROPERTIES Acts as a base; can pick up an H+ from the surrounding solution (water, in living organisms). Glycine 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.

24. Sulfhydryl STRUCTURE NAME OF COMPOUND Thiols (may be written HS—) Fig. 4-10e 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 Cysteine is an important sulfur-containing amino acid.

25. Phosphate STRUCTURE NAME OF COMPOUND Organic phosphates Fig. 4-10f 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 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.

26. Methyl NAME OF COMPOUND STRUCTURE Methylated compounds Fig. 4-10g 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. 5-Methyl cytidine 5-Methyl cytidine is a component of DNA that has been modified by addition of the methyl group.

27. Macromolecules Building Blocksof Life

28. Macromolecules • Smaller organic molecules join together to form larger molecules • 4 major classes of macromolecules: • Proteins • Carbohydrates • Lipids • Nucleic Acids

29. H2O HO H HO H HO H Polymers • Long molecules built by linking repeating building blocks in a chain • Monomers • building blocks • repeated small units • Dehydration synthesis

30. H2O HO H HO H enzyme HO H How to build a polymer • Chemical reaction that • joins monomers by “taking” H2O out • one monomer donates OH– • other monomer donates H+ • together these form H2O Dehydration synthesis or Condensation reaction

31. H2O HO H enzyme H HO H HO How to break down a polymer • Chemical Reaction that breaks polymers • use H2O to breakdown polymers • reverse of dehydration synthesis • cleave off one monomer at a time • H2O is split into H+ and OH– • H+ & OH– attach to ends Hydrolysis

32. Any Questions??