Organic Molecules<br />
Six Functional Groups<br />
Six Functional Groups<br />
Early Origin-of-Life Experiments <br />Could the first steps of chemical evolution have occurred on ancient Earth?<br />To...
Figure 3-3<br />Nonpolar side chains<br />Glycine (G) Gly<br />Alanine (A) Ala<br />Valine (V) Val<br />Leucine (L) Leu<br...
The Nature of Side Chains <br />The 21 amino acids differ only in the variable side chain or R-group attached to the centr...
Primary Structure<br />A protein’s primary structure is its unique sequence of amino acids. <br />Because the amino acid R...
Figure 3-11<br />Normal amino acid sequence<br />Single change in amino acid sequence<br />4<br />5<br />6<br />7<br />4<b...
Secondary Structure<br />Secondarystructure results in part from hydrogen bonding between the carboxyl oxygen of one amino...
Hydrogen bonds form between peptide chains.<br />Hydrogen bonds<br />Secondary structures of proteins result.<br />-helix...
Tertiary Structure<br />The tertiarystructure of a polypeptide results from interactions between R-groups or between R-gro...
Tertiary Structures of Proteins<br />Interactions that determine the tertiary structure of proteins<br />Hydrogen bond bet...
Tertiary Structures of Proteins<br />Tertiary structures are diverse.<br />A tertiary structure composed mostly of -pleat...
Van der Waals Interactions<br />van der Waals interactions are electrical interactions between hydrophobic side chains. Al...
Quaternary Structure <br />Some proteins contain several distinct polypeptide subunits that interact to form a single stru...
Quaternary Structures of Proteins<br />Cro protein, a dimer<br />Hemoglobin, a tetramer<br />
Figure 3-14-Table 3-3<br />
Carbohydrates<br />
Simple Sugars<br />Monosaccharide<br />Single sugar<br />Ex. Glucose (blood sugar)<br /><ul><li>Disaccharide
     Two sugars
    Ex.  Sucrose, Lactose, Fructose</li></li></ul><li>Linear and Ring Forms<br />Linear form of glucose<br />Ring forms of...
Figure 5-4<br />Monosaccharides polymerize when hydroxyl groups react to form glycosidic linkages…<br />Maltose (a disacch...
Figure 5-4a<br />Monosaccharides polymerize when hydroxyl groups react to form glycosidic linkages…<br />-Glucose<br />Ma...
Figure 5-4b<br />…between various carbons and with various geometries.<br />Lactose (a disaccharide)<br />-Galactose<br /...
Polysaccharide<br />Complex Carbohydrate  ( Starch)<br />Ex.  Starch, Cellulose, Chitin<br />More than one ring structure<...
Cellulose, Chitin, Peptidoglycan<br />Cellulose in plant cell wall<br />Chitin in insect exoskeleton<br />Peptidoglycan in...
Figure 5-5a-Table 5-1<br />
Figure 5-5b-Table 5-1<br />
Figure 5-5c-Table 5-1<br />
Glycoproteins: Identification Badge for Cells<br />Glycoprotein<br />Outside<br />of cell<br />Inside<br />of cell<br />
Lipids<br />
Lipids –Fats, Oils, Waxes, Steroids (cholesterol)<br />Unsaturated<br />Comes from plants and is liquid at room temperatur...
Nucleic Acids<br />
Nucleic Acids<br />DNA<br />Deoxyribonucleic Acid<br />Phosphate, Deoxyribose sugar, Nitrogen Base<br />Double sided<br />...
Figure 4-1<br />Only in RNA<br />Only in DNA<br />Nucleotide<br />Nitrogen-containing bases<br />Nitrogenous base<br />Pho...
Figure 4-2<br />Condensation reaction<br />Phosphodiester linkage<br />
Figure 4-3<br />The sugar-phosphate<br />spine of RNA<br />The sequence of bases found in an RNA strandis written in the 5...
Figure 4-6b<br />Hydrogen bonds form between G-C pairs and A-T pairs.<br />Hydrogen bonds<br />5<br />3<br />Guanine<br ...
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Organic molecules

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Organic molecules

  1. 1. Organic Molecules<br />
  2. 2.
  3. 3. Six Functional Groups<br />
  4. 4. Six Functional Groups<br />
  5. 5. Early Origin-of-Life Experiments <br />Could the first steps of chemical evolution have occurred on ancient Earth?<br />To find out, Stanley Miller combined methane (CH4), ammonia (NH3), and hydrogen (H2) in a closed system with water, and applied heat and electricity as an energy source.<br />The products included hydrogen cyanide (HCN) and formaldehyde (H2CO), important precursors for more-complex organic molecules and amino acids.<br />In more recent experiments, amino acids and other organic molecules have been found to form easily under these conditions.<br />
  6. 6.
  7. 7. Figure 3-3<br />Nonpolar side chains<br />Glycine (G) Gly<br />Alanine (A) Ala<br />Valine (V) Val<br />Leucine (L) Leu<br />Isoleucine (I) Ile<br />No charged or electronegative atoms to form hydrogen bonds; not soluble in water<br />Methionine (M)<br />Met<br />Phenylalanine (F)<br />Phe<br />Tryptophan (W)<br />Trp<br />Proline (P)<br />Pro<br />Polar side chains<br />Partial charges can form hydrogen bonds; soluble in water<br />Serine (S)<br />Ser<br />Threonine (T)<br />Thr<br />Cysteine (C)<br />Cys<br />Tyrosine (Y)<br />Tyr<br />Asparagine (N) Asn<br />Glutamine (Q)<br />Gln<br />Acidic<br />Basic<br />Electrically charged<br />side chains<br />Charged side chains form hydrogen bonds; highly soluble in water<br />Aspartate (D)<br />Asp<br />Glutamate (E)<br />Glu<br />Lysine (K)<br />Lys<br />Arginine (R)<br />Arg<br />Histidine (H)<br />His<br />
  8. 8.
  9. 9.
  10. 10. The Nature of Side Chains <br />The 21 amino acids differ only in the variable side chain or R-group attached to the central carbon <br />R-groups differ in their size, shape, reactivity, and interactions with water. <br /> (1) Nonpolar R-groups: Do not form hydrogen bonds; coalesce in water<br /> (2) Polar R-groups: Form hydrogen bonds; readily dissolve in water <br />Amino acids with hydroxyl, amino, carboxyl, or sulfhydryl functional groups in their side chains are more chemically reactive than those with side chains composed of only carbon and hydrogen atoms.<br />
  11. 11. Primary Structure<br />A protein’s primary structure is its unique sequence of amino acids. <br />Because the amino acid R-groups affect a polypeptide’s properties and function, just a single amino acid change can radically alter protein function. <br />
  12. 12. Figure 3-11<br />Normal amino acid sequence<br />Single change in amino acid sequence<br />4<br />5<br />6<br />7<br />4<br />5<br />6<br />7<br />Normal red blood cells<br />Sickled red blood cells<br />
  13. 13. Secondary Structure<br />Secondarystructure results in part from hydrogen bonding between the carboxyl oxygen of one amino acid residue and the amino hydrogen of another. A polypeptide must bend to allow this hydrogen bonding—thus, -helices or -pleated sheets are formed.<br />Secondary structure depends on the primary structure—some amino acids are more likely to be involved in α-helices; while others, in β-pleated sheets. <br />Secondary Structure increases stability by way of the large number of hydrogen bonds.<br />
  14. 14. Hydrogen bonds form between peptide chains.<br />Hydrogen bonds<br />Secondary structures of proteins result.<br />-helix<br />-pleated sheet<br />Ribbon diagrams of secondary structure.<br />Arrowheads are at the carboxyl end of the arrows<br />-pleated sheet<br />-helix<br />
  15. 15. Tertiary Structure<br />The tertiarystructure of a polypeptide results from interactions between R-groups or between R-groups and the peptide backbone. These contacts cause the backbone to bend and fold, and contribute to the 3D shape of the polypeptide. <br />R-group interactions include hydrogen bonds, van der Waals interactions, covalent disulfide bonds, and ionic bonds. <br />Hydrogen bonds can form between hydrogen atoms and the carboxyl group in the peptide-bonded backbone, and between hydrogen atoms and atoms with partial negative charges in side chains. <br />
  16. 16. Tertiary Structures of Proteins<br />Interactions that determine the tertiary structure of proteins<br />Hydrogen bond between side chain and carboxyl oxygen<br />Ionic bond<br />Hydrophobic interactions (van der Waals interactions)<br />Hydrogen bond between two side chains<br />Disulfide bond<br />
  17. 17. Tertiary Structures of Proteins<br />Tertiary structures are diverse.<br />A tertiary structure composed mostly of -pleated sheets<br />A tertiary structure rich in disulfide bonds<br />A tertiary structure composed mostly of -helices<br />
  18. 18. Van der Waals Interactions<br />van der Waals interactions are electrical interactions between hydrophobic side chains. Although these interactions are weak, the large number of van der Waals interactions in a polypeptide significantly increases stability. <br />Covalent disulfide bonds form between sulfur-containing R-groups. <br />Ionic bonds form between groups that have full and opposing charges.<br />
  19. 19. Quaternary Structure <br />Some proteins contain several distinct polypeptide subunits that interact to form a single structure; the bonding of two or more subunits produces quaternarystructure. <br />The combined effects of primary, secondary, tertiary, and sometimes quaternary structure allow for amazing diversity in protein form and function. <br />
  20. 20. Quaternary Structures of Proteins<br />Cro protein, a dimer<br />Hemoglobin, a tetramer<br />
  21. 21. Figure 3-14-Table 3-3<br />
  22. 22. Carbohydrates<br />
  23. 23. Simple Sugars<br />Monosaccharide<br />Single sugar<br />Ex. Glucose (blood sugar)<br /><ul><li>Disaccharide
  24. 24. Two sugars
  25. 25. Ex. Sucrose, Lactose, Fructose</li></li></ul><li>Linear and Ring Forms<br />Linear form of glucose<br />Ring forms of glucose<br />Oxygen from the5-carbon bonds to the1-carbon, resulting in a ring structure<br />-Glucose<br />-Glucose<br />
  26. 26. Figure 5-4<br />Monosaccharides polymerize when hydroxyl groups react to form glycosidic linkages…<br />Maltose (a disaccharide)<br />-Glucose<br />-Glucose<br />The hydroxyl groups from the1-carbon and 4-carbon reactto produce an -1,4-glycosidiclinkage and water<br />…between various carbons and with various geometries.<br />Lactose (a disaccharide)<br />-Galactose<br />-Glucose<br />In this case, the hydroxyl groups fromthe 1-carbon and 4-carbon react toproduct a -1,4-glycosidic linkage<br />and water<br />
  27. 27. Figure 5-4a<br />Monosaccharides polymerize when hydroxyl groups react to form glycosidic linkages…<br />-Glucose<br />Maltose (a disaccharide)<br />-Glucose<br />The hydroxyl groups from the1-carbon and 4-carbon reactto produce an -1,4-glycosidiclinkage and water<br />
  28. 28. Figure 5-4b<br />…between various carbons and with various geometries.<br />Lactose (a disaccharide)<br />-Galactose<br />-Glucose<br />In this case, the hydroxyl groups fromthe 1-carbon and 4-carbon react toproduct a -1,4-glycosidic linkage<br />and water<br />
  29. 29. Polysaccharide<br />Complex Carbohydrate ( Starch)<br />Ex. Starch, Cellulose, Chitin<br />More than one ring structure<br />
  30. 30. Cellulose, Chitin, Peptidoglycan<br />Cellulose in plant cell wall<br />Chitin in insect exoskeleton<br />Peptidoglycan in bacterial cell wall<br />
  31. 31. Figure 5-5a-Table 5-1<br />
  32. 32. Figure 5-5b-Table 5-1<br />
  33. 33. Figure 5-5c-Table 5-1<br />
  34. 34. Glycoproteins: Identification Badge for Cells<br />Glycoprotein<br />Outside<br />of cell<br />Inside<br />of cell<br />
  35. 35. Lipids<br />
  36. 36. Lipids –Fats, Oils, Waxes, Steroids (cholesterol)<br />Unsaturated<br />Comes from plants and is liquid at room temperature<br />Ex. Corn oil, Olive oil, Sunflower oil<br />Better for you<br />Saturated<br />Comes from animals and is solid at room temperature<br />Ex. Bacon, animal fat<br />Bad for you <br />
  37. 37.
  38. 38.
  39. 39. Nucleic Acids<br />
  40. 40. Nucleic Acids<br />DNA<br />Deoxyribonucleic Acid<br />Phosphate, Deoxyribose sugar, Nitrogen Base<br />Double sided<br />Helical Structure<br />Found in nucleus<br />RNA<br />Ribonucleic Acid<br />Phosphate, Ribose sugar, Nitrogen Base<br />Single sided<br />Can be various places in the cell depending on type<br />
  41. 41. Figure 4-1<br />Only in RNA<br />Only in DNA<br />Nucleotide<br />Nitrogen-containing bases<br />Nitrogenous base<br />Phosphate group<br />Uracil (U)<br />Pyrimidines<br />Cytosine (C)<br />Thymine (T)<br />5-carbon sugar<br />Sugars<br />Guanine (G)<br />Adenine (A)<br />Ribose<br />Deoxyribose<br />Purines<br />
  42. 42. Figure 4-2<br />Condensation reaction<br />Phosphodiester linkage<br />
  43. 43. Figure 4-3<br />The sugar-phosphate<br />spine of RNA<br />The sequence of bases found in an RNA strandis written in the 5´  3´direction<br />Nitrogenousbases<br />3´ and 5´ carbonsjoined byphosphodiesterlinkage<br />Unlinked 3´ carbon:New nucleotidesare added here<br />
  44. 44. Figure 4-6b<br />Hydrogen bonds form between G-C pairs and A-T pairs.<br />Hydrogen bonds<br />5<br />3<br />Guanine<br />Cytosine<br />Sugar-phosphate backbone<br />Thymine<br />Adenine<br />DNA contains thymine,whereas RNA contains uracil<br />5<br />3<br />
  45. 45.
  46. 46. Majorgroove<br />Length of onecompleteturn of helix(10 rungs perturn) 3.4 nm<br />Minorgroove<br />Distancebetweenbases 0.34nm<br />Width of thehelix 2.0 nm<br />

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