Chapter 4: Life is based on molecules with carbon (organic molecules)

1. Chapter 4: Life is based on molecules with carbon (organic molecules) • organic compounds • isomers • functional groups

2. Much of the chemistry of life is based on organic compounds • organic compounds have at least one carbon atom covalently bound to either: • another carbon atom • or to hydrogen • the chemistry of organic molecules is organized around the carbon atom

3. Discuss the chemistry of carbon. How does it typically bond? What does it typically bond to? What sort of shapes, angles, freedoms, etc. are associated with the bonds that it makes? • Draw a tetrahedron.

4. Organic Compounds • carbon atoms have six electrons – • 2 in level 1 • 4 in their valence (outer) shell (level 2) • carbon is not a strongly electron seeking element, and it does not readily give up its electrons; therefore: • carbon does not readily from ionic bonds • it almost always forms covalent bonds • carbon can form up to 4 covalent bonds (and typically does form all four)

5. Organic Compounds • wide diversity in organic compounds • over 5 million identified • variety partially because carbon tends to bond to carbon, hydrogen, oxygen, nitrogen, sulfur, and phosphorus • hydrocarbons – contain only hydrogen and carbon • single carbon-carbon bonds allow rotation around them and lend flexibility to molecules

6. Organic Compounds • building of organic macromolecules also leads to diversity • carbon works well as a molecular “backbone” for forming long chain molecules • stronger carbon-carbon bonds can be made with double and triple covalent bonds • carbon chains can branch

7. Organic Compounds • the shape of a molecule is important in determining its chemical and biological properties • When 4 separate bonds are formed by carbon… • formed at 109.5 degree angles • form a pyramid with a triangular base called a tetrahedron • When double bonds are formed… • angles are 120 or 180 degrees apart, and they all lie in the same plane

8. Organic Compounds • bond angles for carbon play a critical role in determining the shape of molecules • generally there is freedom to rotate around carbon to carbon single bonds but not double (or triple) bonds

9. Discuss the chemistry of carbon. How does it typically bond? What does it typically bond to? What sort of shapes, angles, freedoms, etc. are associated with the bonds that it makes? • Draw a tetrahedron.

10. Chapter 4: Life is based on molecules with carbon (organic molecules) • organic compounds • isomers • functional groups

11. Discuss isomers. What are they? What is the difference between structural isomers and stereoisomers? Between cis-trans isomers and enantiomers? • Draw an example of each of these: structural isomers cis-trans isomers enantiomers

12. What type of isomer situation is this? How do you know?

13. What type of isomer situation is this? How do you know?

14. What type of isomer situation is this? How do you know?

15. What type of isomer situation is this? How do you know?

16. What type of isomer situation is this? How do you know?

17. What type of isomer situation is this? How do you know?

18. Isomers • have the same molecular formula • have different structures • there are two kinds of isomers • structural isomers • stereoisomers

19. Isomers • structural isomers - substances with the same molecular formula that differ in the covalent arrangement of their atoms • example: ethanol and dimethyl ether (C2H6O)

20. Isomers • stereoisomers - substances with the same arrangement of covalent bonds, but the order in which the atoms are arranged in space is different • two types: enantiomers and diastereomers

21. Isomers • cis-trans isomers – diastereomers associated with compounds that have carbon-carbon double bonds • since there is no rotation around the double bond the other atoms attached to the carbons are stuck in place in relationship to each other • larger items together = cis; larger items opposite = trans • examples: trans-2-butene and cis-2-butene

22. Isomers • enantiomers – substances that are mirror images of each other and that cannot be superimposed on each other • sometimes called optical isomers (kind of a loose term, though)

23. Isomers • typically, only one form of an enatiomer pair is found in and/or used by organisms • the enantiomers are given designations such as [(+)- vs. (−)-] or [D- vs. L-] or [(R)- vs. (S)-] • biologically important enantiomers include • amino acids (found in proteins) – most are L-amino acids (e.g. L-leucine, L-alanine, etc) • sugars – most are D-sugars (e.g. D-glucose, D-fructose, etc.)

24. Discuss isomers. What are they? What is the difference between structural isomers and stereoisomers? Between cis-trans isomers and enantiomers? • Draw an example of each of these: structural isomers cis-trans isomers enantiomers

25. Chapter 4: Life is based on molecules with carbon (organic molecules) • organic compounds • isomers • functional groups

26. What is a functional group, and why is it useful to know them? Quiz each other on the names and chemistry of the functional groups in the notes.

27. Functional Groups • functional groups determine most of the reactive properties (functions) of organic molecules • functional groups are groups of atoms covalently bonded to a carbon backbone that give properties different from a C-H bond • the properties of the major classes of organic compounds (carbohydrates, lipids, proteins, and nucleic acids) are determined mostly by their functional groups • learn the seven functional groupson the following slides

28. Functional Groups

29. Functional Groups • hydroxyl group: polar; found in alcohols • carbonyl group: polar; found in aldehydes and ketones • carboxyl group: weakly acidic; found in organic acids (such as amino acids)

30. Functional Groups • amino group: weakly basic; found in such things as amino acids • sulfhydryl group: essentially nonpolar; found in some amino acids • phosphate group: weakly acidic; found in such things as phospholipids and nucleic acids • methyl group: nonpolar (thus hydrophobic); found in such things as lipids, other membrane components P