AP Biology, Chapter 4
Carbon and the Molecular Diversity of Life

INTRODUCTION
THE IMPORTANCE OF CARBON
	Intro
	Organic chemistry is the study of organic compounds
		1. Distinguish organic and inorganic compounds and give examples of each.
			a. Organic contain carbon, inorganic do not
			b. Organic: methane, urea, octane; inorganic: ammonia, NaCl, H2S
		2. Describe the Miller experiment and its implications for chemical evolution.
			a. Miller simulated the chemistry of the early Earth
				i. Gases: H2O, H2, NH3, CH4
				ii. Liquid water
				iii. Sparks
				iv. Got complex organic goo
			b. Complex organic chemicals may appear from non-living sources
		3. Summarize the philosophies of vitalism and mechanism and explain how they 
		influenced the development of organic chemistry and mainstream biological thought.
			a. Vitalism: a life force exists separate from physics and chemistry
			b. Mechanism: physical and chemical laws explain life
			c. Artificial organic molecules functioned as natural; no life force
	Carbon atoms are the most versatile building blocks of molecules
		4. Explain how the tetravalence of the carbon atom contributes the structural complexity 
		of organic compounds.
			a. Carbon has 4 valence electrons, forms 4 covalent bonds
			b. Is not very electronegative, the bonds are relatively stable
			c. Can serve as branch points in complex molecules
		5. Review the valences of CHON.
			a. C, 4; H, 1; O, 2; N, 3
		6. Draw a structural formula for C3H8N2O.
	Variation in carbon skeleton contributes to the diversity of organic molecules
		7. Describe how carbon skeletons vary, and explain how this variation contributes to the 
		diversity and complexity of organic molecules.
			a. May be straight, branched, ringed
			b. Ex.: fatty acid, isopropanol, benzene
		8. Contrast alkanes, alkenes, and alkynes.
			a. Alkanes: no C-C double bonds
			b. Alkenes: at least one C-C double bond
			c. Alkynes: at least one C-C triple bond
		9. Draw a structural formula for a 15-carbon hydrocarbon.
		10. Why are hydrocarbons hydrophobic?
			a. Only have C and H
			b. C and have very similar electronegativities (C, 2.20; H, 2.55)
			c. C-H bonds are relatively non-polar, no hydrogen bonding
			d. When mixed with water, water molecules bind strongly to each other 
		11. Draw structural formulas for all isomers of pentene.
		12. Distinguish the three types of isomers: structural, geometric, and enantiomer.
			a. Structural: different arrangement of the same atoms
			b. Geometric: same atoms bound but a different arrangement across a double 
			bond
			c. Enantiomers
				i. Also called stereoisomers, chiral compounds and optical isomers
				ii. Mirror image arrangement of groups on the asymmetric carbon
				iii. Opposite forms called (+)- and (-)-, D- and L-, and left-and right-
					handed
				iv. Mixture of the two is a racemic mixture 
				v. Separated enantiomers rotate polarized light in opposite directions
		13. Why are enantiomers important in biology?
			a. One or the other is active
				i. L-amino acids are synthesized by cells and used in proteins
				ii. D-glucose can be used for energy, L- cannot
			b. Drugs may be mixtures
				i. Thalidomide: one active, the other teratogenic
				ii. Mixtures can be patented and the pure active enantiomer

FUNCTIONAL GROUPS
	Intro
	Functional groups also contribute to the molecular diversity of life
		13. Draw the structural formula for a 10-carbon molecule containing one of each of the 6 
		major functional groups.
		14. Differentiate the chemical properties of thiols, alcohols, organic phosphates, amines, 
		aldehydes, carboxylic acids, and ketones.
			a. Hydroxyl, -OH, alcohols
				i. Polar
				ii. Forms ester linkage with carboxyl
			b. Carbonyl, -C=O, aldehydes and ketones
				i. Polar
				ii. Aldehyde if on a terminal C, ketone if in the middle
			c. Carboxyl, -COOH, carboxylic acids
				i. Acidic
				ii. Forms amide bond with amino group
				iii. Forms ester with carbonyl
			d. Amino, -NH2, amines
				i. Base
				ii. Forms amide bonds with carboxyl
			e. Sulfhydryl, -SH, thiols
				i. Polar
				ii. Forms disulfide bridges to stabilize proteins
			f. Phosphate, -PO4, organic phosphates
				i. Acid
				ii. Stores energy when linked as ester
	The chemical elements of life: a review