AP Biology, Chapter 5
The Structure and Function of Macromolecules

Summary
Introduction
	1. List the four major classes of biological macromolecules.
		a. Carbohydrates
		b. Lipids
		c. Proteins
		d. Nucleic acids
POLYMER PRINCIPLES
	Intro
	Most macromolecules are polymers
		2. Describe the construction and deconstruction of biological polymers.
			a. Polymers ("many part") are made from monomers ("one part")
			b. Put together by condensation by removing water = dehydration
			c. Taken apart by adding  water = hydrolysis
	An immense variety of polymers can be built from a small set of monomers
		3. Explain how organic polymers contribute to biological diversity.
			a. Organisms use 40-50 common monomers
			b. There are many combinations of those in long linear sequences
CARBOHYDRATES – FUEL AND BUILDING MATERIAL
	Intro
	Sugars, the smallest carbohydrates, serve as fuel and carbon sources
		4. Describe the distinguishing characteristics of carbohydrates and explain how they are 
		classified.
			a. Chemical characteristics
				i. Polyhydroxylated (1C:2H:1O) aldehydes, ketones, or alcohol
				ii. Very polar while carrying appreciable energy
			b. Classification
				i. Number of carbon atoms per monomer (triose, tetrose, pentose, 
				hexose)
				ii. Number of monomers (mono-, di-, polysaccharide)
				iii. Position of carbonyl (aldose vs. ketose)
		5. Distinguish significant monosaccharides and disaccharides.
			a. Mono-: a single sugar unit
				i. Glucose is most import for energy, raw material for biosynthesis
				ii. Found in ring form
				iii. Ribose and deoxyribose are the pentoses of nucleic acids
			b. Di-: two monosaccharides with a glycosidic linkage
				i. Maltose = two glucoses
				ii. Lactose = glucose + galactose; milk sugar
				iii. Sucrose = glucose +fructose; transported in plants
		6. Identify a glycosidic linkage and describe how it is formed.
			a. Glycosidic linkages form between hydroxyl groups
			b. Water is removed, one O atom link sugars
	Polysaccharides, the polymers of sugars, have storage and structural roles
		7. Describe the structure and functions of polysaccharides.
			a. Storage
				i. Starch
					. Helical 1-4 linked glucose polymers, may be branched
					. Energy storage in plants
				ii. Glycogen
					. Highly branched glucose polymers
					. Energy storage in liver and muscle
			b. Structural
				i. Cellulose: very long, unbranched, 1-4 linked, beta glucose in plants
				ii. Chitin: many linked acetylglucosamine in arthropod and fungus cell 
				walls
				iii. Chondroitin: acetylgalactosamine and glucuronic acid in cartilage
		8. Distinguish the glycosidic linkages found in starch and cellulose and explain why the 
		difference is biologically important.
			a. Starch: glucose in alpha ring form; 1-4 linkages digestible by us
			b. Cellulose: glucose in beta ring form; 1-4 linkages not digestible by us

LIPIDS – DIVERSE HYDROPHOBIC MOLECULES
	Intro
		9. Describe what distinguishes lipids from other major classes of macromolecules.
			a. "Does not include polymers"; but fatty acids are made from 2C units
			b. Generally hydrophobic; except for steroid hormones
			c. Mostly hydrocarbon
			d. Generally small
	Fats store large amounts of energy
		10. Describe the building-block molecules, unique properties, and biological importance 
		of fats, phospholipids, and steroids.
			a. Fats = glycerol + 3 fatty acids with ester linkages = triglycerides
				i. Saturated (with H): no double bonds, straight, solid
				ii. Unsaturated: double bonds, kinked, liquid
			b. Ester linkages are largely hidden; whole molecule is nonpolar
			c. Functions
				i. Stores > twices as much energy as carbodrates
				ii. Insoluble in water so conserves water
				ii. Insulates and cushions
	Phospholipids are major components of cell membranes
			a. Triglyceride with one fatty acid replaced by PO4
			b. PO4 is charged and hydrophilic, fatty acids are hydrophobic
			c. Forms membranes and micelles with PO4 sticking out
	Steroids include cholesterol and certain hormones
			a. Composed of four fused HC rings; hydrophilic functional groups may be added
			b. Cholesterol stabilizes membrane structure
			c. Steroid hormones have >1 hydrophilic functional group

PROTEINS – MANY STRUCTURES, MANY FUNCTIONS
	Intro
		11. Describe the characteristics that distinguish proteins from the other major classes of 
		macromolecules and explain the biologically important functions of this group.
			a. Composed of 20 amino acids; the most structurally diverse
			b. Functions
				i. Structural support (collagen)
				ii. Transport of other substances (hemoglobin)
				iii. Signaling (insulin)
				iv. Movement (myosin and actin)
				v. Defense (antibodies)
				vi. Control metabolism (enzymes)
	A polypeptide is a polymer of amino acids connected in a specific sequence
		12. List the four major components of an amino acid. Explain how amino acids may be 
		grouped according to the physical and chemical properties of the side chains.
			a. Components: amino, carboxyl, H, R (variable) group
			b. Side chain classes: nonpolar, polar, acidic, basic
		13. Identify a peptide bond and explain how it is formed.
			a. Peptide bond links amino and carboxyl groups on adjacent amino acids
			b. Amide bond is formed by dehydration
	A protein’s function depends on its specific conformation
		14. Explain what determines protein conformation and why it is important.
			a. Amino acid sequence mainly determines conformation
			b. Conformation or shape determines the proteins interactions with other 
			molecules
			c. Protein conformation may be affected by modification
				i. Clipping part out or off
				ii. Adding sugars or ions
			d. Also affected by temperature, pH
		15. Define primary structure and describe how it may be deduced in the laboratory.
			a. Primary structure = amino acid sequence
			b. Determination
				i. Cut with sequence-specific proteases, characterize fragments
				i. Chemically identify the amino- and carboxy-terminal amino acids
		16. Describe the two types of secondary protein structure. Explain the role of hydrogen 
		bonds in maintaining the structure.
			a. Alpha helix: coil stabilized by H-bonds between every fourth amino acid
			b. Pleated sheet
				i. Parallel straight stretches of amino acids with carbonyls aligned
				ii. Carbonyls H-bond with aligned starnd
		17. Explain how weak interactions and disulfide bridges contribute to tertiary protein 
		structure.
			a. Alpha helix and pleated sheets are short segments with in protein
			b. Sequence folds between them and stabilizes
				i. Hydrophobic side chains fold in for soluble proteins
				ii. Van der Waals interactions stabilize at close range
				iii. Disulfide bridges form between non-adjacent cysteines
				iv. Ionic bonds also form between basic and acidic side chains
		18. Using collagen and hemoglobin as examples, describe quaternary protein structure.
			a. Quaternary = more than one amino acid chain bound together
			c. Collagen: three helical amino acid chains wound into a triple helix
			d. Hemoglobin: 2 alpha + 2 beta chains + heme
		19. Define denaturation and explain how proteins may be denatured.
			a. Denaturation of protein = loss of shape and therefore function
			b. By heat, change in pH, organic solvents, polar solutes like urea

NUCLEIC ACIDS – INFORMATIONAL POLYMERS
	Intro
		20. Describe the characteristics that distinguish nucleic acids from the other major 
		groups of macromolecules.
			a. Polymers of 4 nucleotides 
			b. Order = coded information
			c. Complementary strands allow replication
	Nucleic acids store and transmit hereditary information
		21. Summarize the functions of nucleic acids.
			a. DNA is a stable, stored form of information giving traits
			b. RNAs are working copies of the information in DNA
			c. Semi-conservative replication allows transmission to offspring 
	A nucleic acid strand is a polymer of nucleotides
		22. List the major components of a nucleotide, and describe how these monomers are 
		linked to form a nucleic acid.
			a. Nucleotide = nitrogen base+pentose+phosphate
			b. Phosphates link the 3' and 5' carbons on adjacent pentoses
		23. Distinguish pyrimidine and purine.
			a. Pyrimidine bases
				i. One ring
				ii. Thymine, cytosine, uracil
			b. Purine bases
				i. Two rings
				ii. Adenine, guanine
	Inheritance is based on replication of the DNA double helix
		24. Briefly describe the three-dimensional structure of DNA.
			a. Double helix, 1953, Watson and Crick
			b. Bases in defined pairs in the center: AT, GC
	We can use DNA and proteins as tape measures of evolution
		25. Explain how the structure of DNA and proteins can be used to document the 
		hereditary background of an organism.
			a. Assume descent with modification and a constant rate of mutation
			b. Phyogenetic trees showing relatedness can be constructed
			c. Number of changes is proportional to time since divergence