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AP Biology, Chapter 5, 9th ed. The Structure and Function of Large Biological molecules The Molecules of Life 1. List the four major classes of biological macromolecules in all known life forms. Carbohydrates Lipids Proteins Nucleic acids 1.D.2.b. Molecular and genetic evidence from extant and extinct organisms indicates that all organisms on Earth share a common ancestral origin of life. 1.D.2.b.1. Scientific evidence includes molecular building blocks that are common to all life forms. 1.D.2.b.2. Scientific evidence includes a common genetic code. 5.1 Macromolecules and polymers, built from monomers Intro The Synthesis and Breakdown of Polymers 2. Describe the construction and deconstruction of biological polymers. Polymers ("many part") are made from monomers ("one part") Put together by condensation by removing water = dehydration Taken apart by adding water = hydrolysis The Diversity of Polymers 3. Explain how organic polymers contribute to biological diversity. Organisms use 40-50 common monomers There are many combinations of those in long linear sequences 5.2 Carbohydrates serve as fuel and building material Intro Sugars 4. Describe the distinguishing characteristics of carbohydrates and explain how they are classified. Chemical characteristics Polyhydroxylated (1C:2H:1O) aldehydes, ketones, alcohols and acids Very polar while carrying appreciable energy Provide carbon skeletons for biosynthesis Classification Number of carbon atoms per monomer (triose, tetrose, pentose, hexose) Number of monomers (mono-, di-, polysaccharide) Position of carbonyl (aldose vs. ketose) 5. Distinguish significant monosaccharides and disaccharides. Mono-: a single sugar unit Glucose A hexose Import for energy, raw material for biosynthesis Found in ring form Ribose and deoxyribose are the pentoses of nucleic acids Di-: two monosaccharides with a glycosidic linkage Maltose = two glucoses Lactose = glucose + galactose; milk sugar Sucrose = glucose +fructose; transported in plants 6. Identify a glycosidic linkage and describe how it is formed. Glycosidic linkages form between hydroxyl groups Water is removed, one O atom link sugars Polysaccharides Intro Storage Polysaccharides 7. Describe the structure and functions of polysaccharides. Storage Starch Helical 1-4 linked glucose polymers, may be branched Energy storage in plants Hydrolysed using amylase Glycogen Highly branched glucose polymers Energy storage in liver and muscle Structural Polysaccharides Structural Cellulose: very long, unbranched, 1-4 linked, beta glucose in plants; “insoluble” fiber Chitin: many linked acetylglucosamine in arthropod and fungus cell walls Chondroitin: polymers of acetylgalactosamine and glucuronic acid in cartilage 8. Distinguish the glycosidic linkages found in starch and cellulose and explain why the difference is biologically important. Starch: glucose in alpha rings; 1-4 linkages digestible by us Cellulose: glucose in beta rings; 1-4 linkages not digestible by us 4.A.1: The subcomponents of biological molecules and their sequence determine the properties of that molecule. 4.A.1.a. Structure and function of polymers are derived from the way their monomers are assembled. 4. Carbohydrates are composed of sugar monomers whose structures and bonding with each other by dehydration synthesis determine the properties and functions of the molecules. Illustrative examples include: cellulose versus starch. 4.A.1.b. Directionality influences structure and function of the polymer. 3. The nature of the bonding between carbohydrate subunits determines their relative orientation in the carbohydrate, which then determines the secondary structure of the carbohydrate. 5.3 Lipids are a diverse group of hydrophobic molecules Intro 9. Describe what distinguishes lipids from other major classes of macromolecules. "Does not include polymers"; but fatty acids are made from 2C units Generally hydrophobic; except for steroid hormones Mostly hydrocarbon Generally small Fats 10. Describe the building-block molecules, unique properties, and biological importance of fats, phospholipids, and steroids. Fats = glycerol + 3 fatty acids with ester linkages = triacylglycerol Saturated (with H): no double bonds, straight, solid Unsaturated: double bonds, kinked, liquid Ester linkages are largely hidden; whole molecule is nonpolar Functions Stores > twices as much energy as carbodrates Insoluble in water so conserves water Insulates and cushions Phospholipids Triglyceride with one fatty acid replaced by PO4 PO4 is charged and hydrophilic, fatty acids are hydrophobic Forms membranes and micelles with PO4 sticking out Steroids Composed of four fused HC rings; hydrophilic functional groups may be added Cholesterol stabilizes membrane structure Steroid hormones have >1 hydrophilic functional group 4.A.1: The subcomponents of biological molecules and their sequence determine the properties of that molecule. 4.A.1.a. Structure and function of polymers are derived from the way their monomers are assembled. 3. In general, lipids are nonpolar; however, phospholipids exhibit structural properties, with polar regions that interact with other polar molecules such as water, and with nonpolar regions where differences in saturation determine the structure and function of lipids. 5.4 Proteins include a diversity of structures, resulting in a wide range of 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. Composed of 20 amino acids; the most structurally diverse Functions Structural support (collagen) Transport of other substances (hemoglobin) Signaling (insulin) Movement (myosin and actin) Defense (antibodies) Catalysts (enzymes) Polypeptides Intro 12. Differentiate polypeptide and protein. Polypeptide = a chain of amino acids Protein = folded, trimmed, combined, modified (finished), functional Amino Acid Monomers 13. 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. Components: amino, carboxyl, H, R (variable) group Side chain classes: nonpolar, polar, acidic, basic Amino Acid Polymers 14. Identify a peptide bond and explain how it is formed. Peptide bond links amino and carboxyl groups on adjacent amino acids In a structure: N-C w/double bonded O Amide bond is formed by dehydration Protein Structure and Function Intro 15. Explain what determines protein conformation and why it is important. Amino acid sequence mainly determines conformation Matching shapes determine interactions between molecules Substrate-enzyme Hormone-receptor protein Antibiotic-target protein Four Levels of Protein Structure 16. Define primary structure and describe how it may be deduced in the laboratory. Primary structure = amino acid sequence Determination (Sanger, 1958) Cut with sequence-specific proteases, characterize fragments Identify the amino- and carboxy-terminal amino acids 4.A.1.b. Directionality influences structure and function of the polymer. 2. Proteins have an amino (NH2) end and a carboxyl (COOH) end, and consist of a linear sequence of amino acids connected by the formation of peptide bonds by dehydration synthesis between the amino and carboxyl groups of adjacent monomers. 17. Describe the two types of secondary protein structure. Explain the role of hydrogen bonds in maintaining the structure. α helix: coil stabilized by H-bonds between every fourth amino acid β pleated sheet Parallel straight stretches of amino acids, carbonyls staggered Carbonyls H-bond with aligned strand 18. Define tertiary structure and list the stabilizing interactions. Sequence folds between secondary structures Interactions between R-groups Hydrophobic side chains fold in for water soluble proteins Hydrogen bonds Van der Waals interactions stabilize at close range Disulfide bridges form between non-adjacent cysteines Ionic bonds between basic and acidic side chains 19. Using collagen and hemoglobin as examples, describe quaternary protein structure. Quaternary = more than one amino acid chain bound together Collagen: three helical amino acid chains wound into a triple helix Hemoglobin: 2 alpha + 2 beta chains + 4 hemes 4.A.1: The subcomponents of biological molecules and their sequence determine the properties of that molecule. 4.A.1.a. Structure and function of polymers are derived from the way their monomers are assembled. 2. In proteins, the specific order of amino acids in a polypeptide (primary structure) interacts with the environment to determine the overall shape of the protein, which also involves secondary tertiary and quaternary structure and, thus, its function. The R group of an amino acid can be categorized by chemical properties (hydrophobic, hydrophilic and ionic), and the interactions of these R groups determine structure and function of that region of the protein. Sickle-Cell Disease: A Change in Primary Structure 20. Exemplify the significance of even slight changes in primary structure. Sickle-cell: one amino acid changed Changed protein shape, altered cell shape symptoms What Determines Protein Structure? 21. Define denaturation and explain how proteins may be denatured. Denaturation of protein = loss of shape and therefore function By heat, change in pH, organic solvents, polar solutes like urea Protein Folding in the Cell 22. Define the protein folding problem. So far, not able to predict protein structure from primary sequence Stages, intermediate structures involved 23. Describe the role of chaperonins in protein folding. = cylindrical chambers that accept unfolded polypeptides Provide folding environment without interfering influences 5.5 Nucleic acids store, transmit, and help express hereditary information Intro 24. Define gene in the traditional sense. Segment of DNA that defines the primary structure of a polypeptide 25. Describe the characteristics that distinguish nucleic acids from the other major groups of macromolecules. Polymers of 4 nucleotides Order = coded information Complementary strands allow replication The Roles of Nucleic Acids 26. Summarize the functions of nucleic acids. DNA is a stable, stored form of information giving traits RNAs are working copies of the information in DNA Semi-conservative replication allows transmission to offspring The Components of Nucleic Acids 27. List the major components of a nucleotide, and describe how these monomers are linked to form a nucleic acid. Nucleotide = nitrogen base+pentose+phosphate Phosphates link the 3' and 5' carbons on adjacent pentoses 28. Distinguish pyrimidine and purine nitrogen bases. Pyrimidine bases One ring Thymine, cytosine, uracil Purine bases Two rings Adenine, guanine Nucleotide Polymers The Structures of DNA and RNA Molecules 29. Differentiate the three-dimensional structures of DNA and RNA. DNA Double helix Strands anti-parallel: 3’ 5’, 5’ 3’ Complementary base pairs in center: A-T, G-C RNA Mainly single stranded May fold back on itself and base pair 4.A.1.b. Directionality influences structure and function of the polymer. 1. Nucleic acids have ends, defined by the 3' and 5' carbons of the sugar in the nucleotide, that determine the direction in which complementary nucleotides are added during DNA synthesis and the direction in which transcription occurs (from 5' to 3'). 3.A.1.b. DNA and RNA molecules have structural similarities and differences that define function. 1. Both have three components — sugar, phosphate and a nitrogenous base — which form nucleotide units that are connected by covalent bonds to form a linear molecule with 3' and 5' ends, with the nitrogenous bases perpendicular to the sugar-phosphate backbone. 2. The basic structural differences include: i. DNA contains deoxyribose (RNA contains ribose). ii. RNA contains uracil in lieu of thymine in DNA. iii. DNA is usually double stranded, RNA is usually single stranded. iv. The two DNA strands in double-stranded DNA are antiparallel in directionality. 3. Both DNA and RNA exhibit specific nucleotide base pairing that is conserved through evolution: adenine pairs with thymine or uracil (A-T or A-U) and cytosine pairs with guanine (C-G). i. Purines (G and A) have a double ring structure. ii. Pyrimidines (C, T and U) have a single ring structure. DNA and Proteins as Tape Measures of Evolution 30. Explain how the structure of DNA and proteins can be used to document the hereditary background of an organism. Assume descent with modification and a constant rate of mutation Phyogenetic trees showing relatedness can be constructed Number of changes is proportional to time since divergence 4.A.1: The subcomponents of biological molecules and their sequence determine the properties of that molecule. 4.A.1.a. Structure and function of polymers are derived from the way their monomers are assembled. 1. In nucleic acids, biological information is encoded in sequences of nucleotide monomers. Each nucleotide has structural components: a five-carbon sugar (deoxyribose or ribose), a phosphate and a nitrogen base (adenine, thymine, guanine, cytosine or uracil). DNA and RNA differ in function and differ slightly in structure, and these structural differences account for the differing functions. The Theme of Emergent Properties in the Chemistry of Life