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Chapter 5

Chapter 5. The Structure and Function of Macromolecules. Overview: The Molecules of Life Another level in the hierarchy of biological organization is reached when small organic molecules are joined together. Macromolecules are large molecules composed of smaller molecule.

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Chapter 5

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  1. Chapter 5 The Structure and Function of Macromolecules

  2. Overview: The Molecules of Life • Another level in the hierarchy of biological organization is reached when small organic molecules are joined together. • Macromolecules are large molecules composed of smaller molecule. • Are complex in their structures. Lecturer/ Iyad A. Elqouqa

  3. Key Concepts • Concept 5.1 Most macromolecules are polymers, built from monomers. • Concept 5.2 Carbohydrates serve as fuel and building material. • Concept 5.3 Lipids are a diverse group of hydrophobic molecules. • Concept 5.4 Proteins have many structures, resulting in a wide range of functions. • Concept 5.5 Nucleic acids store and transmit hereditary information. Lecturer/ Iyad A. Elqouqa

  4. Concept 5.1: Most macromolecules are polymers, built from monomers • Three of the classes of life’s organic molecules are polymers • Carbohydrates • Proteins • Nucleic acids Lecturer/ Iyad A. Elqouqa

  5. A polymer • Is a long molecule consisting of many similar building blocks called monomers Lecturer/ Iyad A. Elqouqa

  6. 1 HO H 3 2 H HO Unlinked monomer Short polymer Dehydration removes a watermolecule, forming a new bond H2O 1 2 3 4 HO H Longer polymer (a) Dehydration reaction in the synthesis of a polymer Figure 5.2A The Synthesis and Breakdown of Polymers • Monomers form larger molecules by condensation reactions called dehydration reactions Lecturer/ Iyad A. Elqouqa

  7. 1 3 HO 4 2 H Hydrolysis adds a watermolecule, breaking a bond H2O 1 2 H HO 3 H HO (b) Hydrolysis of a polymer Figure 5.2B • Polymers can disassemble by • Hydrolysis Lecturer/ Iyad A. Elqouqa

  8. The Diversity of Polymers • Each class of polymer • Is formed from a specific set of monomers 1 3 2 H HO Although organisms share the same limited number of monomer types, each organism is unique based on the arrangement of monomers into polymers. Lecturer/ Iyad A. Elqouqa

  9. Concept 5.2: Carbohydrates serve as fuel and building material • Carbohydrates • Include both sugars and their polymers Sugars: • Monosaccharides • Are the simplest sugars • Can be used for fuel • Can be converted into other organic molecules • Can be combined into polymers Lecturer/ Iyad A. Elqouqa

  10. Triose sugars(C3H6O3) Pentose sugars(C5H10O5) Hexose sugars(C6H12O6) H H H H O O O O C C C C H C OH H C OH H C OH H C OH H C OH H C OH HO C H HO C H Aldoses H H C OH H C OH HO C H H C OH H C OH H C OH Glyceraldehyde H C OH H C OH H Ribose H H Glucose Galactose H H H H C OH H C OH H C OH C O C O C O HO C H H C OH H C OH Ketoses H C OH H C OH H Dihydroxyacetone H C OH H C OH H C OH H Ribulose H Figure 5.3 Fructose • Examples of monosaccharides Lecturer/ Iyad A. Elqouqa

  11. O H 1 C 6CH2OH 6CH2OH 2 CH2OH H C OH 5C H 5C O O 6 3 H O H H H H H 5 HO C H HOH H HOH 4 4C 1 C 1C 4C 4 1 OH H H H C OH O HO OH 3 2 OH OH 5 OH 2 C C 3 C 2C 3 OH H C H OH 6 H H OH OH H C OH H (a) Linear and ring forms. Chemical equilibrium between the linear and ring structures greatly favors the formation of rings. To form the glucose ring, carbon 1 bonds to the oxygen attached to carbon 5. Figure 5.4 • Monosaccharides • May be linear • Can form rings Lecturer/ Iyad A. Elqouqa

  12. Disaccharides • Consist of two monosaccharides • Are joined by a glycosidic linkage Lecturer/ Iyad A. Elqouqa

  13. (a) Dehydration reaction in the synthesis of maltose. The bonding of two glucose units forms maltose. The glycosidic link joins the number 1 carbon of one glucose to the number 4 carbon of the second glucose. Joining the glucose monomers in a different way would result in a different disaccharide. CH2OH CH2OH CH2OH CH2OH O O O O H H H H H H H H 1–4glycosidiclinkage HOH HOH HOH HOH 4 1 H H H H OH OH O H OH HO HO OH O H H H H OH OH OH OH H2O Glucose Maltose Glucose CH2OH CH2OH CH2OH CH2OH O O O O 1–2glycosidiclinkage H H H H H H HOH HOH 2 1 H H HO H HO H Dehydration reaction in the synthesis of sucrose. Sucrose is a disaccharide formed from glucose and fructose.Notice that fructose,though a hexose like glucose, forms a five-sided ring. (b) OH H O O HO CH2OH HO CH2OH H OH H H OH H OH OH H2O Glucose Sucrose Fructose Figure 5.5 • Examples of disaccharides Lecturer/ Iyad A. Elqouqa

  14. Polysaccharides • Polysaccharides • Are polymers of sugars • Serve many roles in organisms Storage Polysaccharides • Starch • Is a polymer consisting entirely of glucose monomers Lecturer/ Iyad A. Elqouqa

  15. Chloroplast Starch 1 m Amylose Amylopectin (a) Starch: a plant polysaccharide Figure 5.6 Storage Polysaccharides • Starch • Is a polymer consisting entirely of glucose monomers • Is the major storage form of glucose in plants Lecturer/ Iyad A. Elqouqa

  16. Giycogen granules Mitochondria 0.5 m Glycogen Figure 5.6 (b) Glycogen: an animal polysaccharide • Glycogen • Consists of glucose monomers • Is the major storage form of glucose in animals Lecturer/ Iyad A. Elqouqa

  17. H O CH2OH C CH2OH OH H C H O O OH H H H H HO C H 4 4 1 OH H OH H HO OH H HO H C OH H OH OH H C OH H  glucose C  glucose H OH (a)  and  glucose ring structures CH2OH CH2OH CH2OH CH2OH O O O O 1 4 4 4 1 1 1 OH OH OH OH O O O O HO OH OH OH OH (b) Starch: 1– 4 linkage of  glucose monomers CH2OH CH2OH OH OH O O O O OH OH OH OH 4 O 1 HO OH O O CH2OH CH2OH OH OH (c) Cellulose: 1– 4 linkage of  glucose monomers Figure 5.7 A–C Structural Polysaccharides • Cellulose • Is a polymer of glucose • Has different glycosidic linkages than starch Lecturer/ Iyad A. Elqouqa

  18. About 80 cellulose molecules associate to form a microfibril, the main architectural unit of the plant cell wall. Cellulose microfibrils in a plant cell wall Microfibril Cell walls  0.5 m Plant cells OH OH CH2OH CH2OH O O O O OH OH OH OH O O O O O OH CH2OH OH CH2OH Cellulose molecules CH2OH OH CH2OH OH O O O O OH OH OH OH Parallel cellulose molecules are held together by hydrogen bonds between hydroxyl groups attached to carbon atoms 3 and 6. O O O O O OH CH2OH OH CH2OH CH2OH CH2OH OH OH O O O O OH OH OH OH O O O A cellulose molecule is an unbranched  glucose polymer. O O OH CH2OH OH CH2OH Figure 5.8 • Glucose monomer • Is a major component of the tough walls that enclose plant cells Lecturer/ Iyad A. Elqouqa

  19. Figure 5.9 • Cellulose is difficult to digest • Cows have microbes in their stomachs to facilitate this process Lecturer/ Iyad A. Elqouqa

  20. CH2OH O OH H H OH H H H NH O C CH3 OH (b) Chitin forms the exoskeleton of arthropods. This cicada is molting, shedding its old exoskeleton and emerging in adult form. (c) Chitin is used to make a strong and flexible surgical thread that decomposes after the wound or incision heals. (a) The structure of the chitin monomer. Figure 5.10 A–C • Chitin, another important structural polysaccharide • Is found in the exoskeleton of arthropods • Can be used as surgical thread Lecturer/ Iyad A. Elqouqa

  21. Concept 5.3: Lipids are a diverse group of hydrophobic molecules • Lipids • Are the one class of large biological molecules that do not consist of polymers • Share the common trait of being hydrophobic Lecturer/ Iyad A. Elqouqa

  22. C C C C C C C H C H O H` C C C C C C C C C HO H H H H H H H H H H H H H H H H C OH Fatty acid (palmitic acid) H C OH H Glycerol (a) Dehydration reaction in the synthesis of a fat Ester linkage O H H H H H H H H H H H H H H H H H H O C C C C C C C C C C C C C C C C C H H H H H H H H H H H H H H H O H H H H H H H H H H H H H H H O C H C C C C C C C H C C C C C C C C C H H H H H H H H H H H H H H H O H H H H H H H H H H H H H H H H H C O C C C C C C C C C C C C C C C C H H H H H H H H H H H H H H H H Fats • Fats • Are constructed from two types of smaller molecules, a single glycerol and usually three fatty acids H H H H H H H H O H H H H H H H H Figure 5.11 (b) Fat molecule (triacylglycerol) Lecturer/ Iyad A. Elqouqa

  23. Stearic acid Figure 5.12 (a) Saturated fat and fatty acid • Fatty acids • Vary in the length and number and locations of double bonds they contain. • Saturated fatty acids • Have the maximum number of hydrogen atoms possible • Have no double bonds Lecturer/ Iyad A. Elqouqa

  24. Oleic acid cis double bond causes bending Figure 5.12 (b) Unsaturated fat and fatty acid • Unsaturated fatty acids • Have one or more double bonds Lecturer/ Iyad A. Elqouqa

  25. Phospholipids • Phospholipids • Have only two fatty acids • Have a phosphate group instead of a third fatty acid Lecturer/ Iyad A. Elqouqa

  26. + CH2 Choline N(CH3)3 CH2 O Phosphate Hydrophilic head – P O O O CH2 CH CH2 Glycerol O O C O C O Fatty acids Hydrophilic head Hydrophobic tails Hydrophobic tails (c) Phospholipid symbol (b) Space-filling model Figure 5.13 (a) Structural formula • Phospholipid structure • Consists of a hydrophilic “head” and hydrophobic “tails” Lecturer/ Iyad A. Elqouqa

  27. WATER Hydrophilic head WATER Hydrophobic tail Figure 5.14 • The structure of phospholipids • Results in a bilayer arrangement found in cell membranes Lecturer/ Iyad A. Elqouqa

  28. H3C CH3 CH3 CH3 CH3 HO Figure 5.15 Steroids • Steroids • Are lipids characterized by a carbon skeleton consisting of four fused rings. One steroid, cholesterol • Is found in cell membranes • Is a precursor for some hormones Lecturer/ Iyad A. Elqouqa

  29. Concept 5.4: Proteins have many structures, resulting in a wide range of functions • Proteins Have many roles inside the cell Lecturer/ Iyad A. Elqouqa

  30. Table 5.1 • An overview of protein functions Lecturer/ Iyad A. Elqouqa

  31. Substrate binds to enzyme. 1 Active site is available for a molecule of substrate, the reactant on which the enzyme acts. 2 2 Substrate (sucrose) Glucose Enzyme (sucrase) OH H2O Fructose H O 4 Products are released. 3 Substrate is converted to products. Figure 5.16 • Enzymes • Are a type of protein that acts as a catalyst, speeding up chemical reactions Lecturer/ Iyad A. Elqouqa

  32. Polypeptides • Polypeptides • Are polymers of amino acids • A protein • Consists of one or more polypeptides Lecturer/ Iyad A. Elqouqa

  33. Amino Acid Monomers • Amino acids • Are organic molecules possessing both carboxyl and amino groups • Differ in their properties due to differing side chains, called R groups Lecturer/ Iyad A. Elqouqa

  34. CH3 CH3 CH3 CH CH2 CH3 CH3 H CH3 H3C CH3 CH2 CH O O O O O H3N+ C H3N+ C H3N+ H3N+ C C C C C C H3N+ C C O– O– O– O– O– H H H H H Valine (Val) Leucine (Leu) Isoleucine (Ile) Glycine (Gly) Alanine (Ala) Nonpolar CH3 CH2 S H2C CH2 O NH CH2 C C H2N CH2 CH2 O– CH2 O O O H H3N+ H3N+ C C C C H3N+ C C O– O– O– H H H Phenylalanine (Phe) Proline (Pro) Methionine (Met) Tryptophan (Trp) Figure 5.17 • 20 different amino acids make up proteins Lecturer/ Iyad A. Elqouqa

  35. OH NH2 O C NH2 O C OH SH CH2 CH3 OH Polar CH2 CH CH2 CH2 CH2 CH2 O O O O O O H3N+ C H3N+ C H3N+ C C H3N+ C C H3N+ C C C C C H3N+ C O– O– O– O– O– O– H H H H H H Glutamine (Gln) Tyrosine (Tyr) Asparagine (Asn) Cysteine (Cys) Serine (Ser) Threonine (Thr) Basic Acidic NH3+ NH2 NH+ O– O –O O CH2 C NH2+ C C NH Electrically charged CH2 CH2 CH2 CH2 CH2 O O CH2 CH2 C CH2 C H3N+ C H3N+ C O O– O– CH2 C H3N+ CH2 C H O H O– C C H3N+ CH2 H O O– C C H3N+ H O– H Lysine (Lys) Histidine (His) Arginine (Arg) Glutamic acid (Glu) Aspartic acid (Asp) Lecturer/ Iyad A. Elqouqa

  36. Peptidebond OH SH CH2 CH2 CH2 H H H C C H C C N C OH H C OH N N DESMOSOMES H O H O H O (a) H2O OH DESMOSOMES DESMOSOMES Side chains SH OH Peptidebond CH2 CH2 CH2 H H H N OH C C C C C H C N N Backbone H H O O H O Amino end(N-terminus) Carboxyl end(C-terminus) Figure 5.18 (b) Amino Acid Polymers • Amino acids • Are linked by peptide bonds OH Lecturer/ Iyad A. Elqouqa

  37. Determining the Amino Acid Sequence of a Polypeptide • The amino acid sequences of polypeptides • Were first determined using chemical means • Can now be determined by automated machines • Protein Conformation and Function • A protein’s specific conformation determines how it functions Lecturer/ Iyad A. Elqouqa

  38. Groove (a) A ribbon model Groove Figure 5.19 (b) A space-filling model • Two models of protein conformation Lecturer/ Iyad A. Elqouqa

  39. +H3NAmino end Pro Thr Gly Gly Amino acid subunits Thr Gly Glu Seu Lys Cys Pro Leu Met Val Lys Val Leu Asp Ala Arg Val Gly Ser Pro Ala Glu Lle Asp Thr Lys Ser Tyr Trp Lys Ala Leu Gly lle Ser Pro Phe His Glu His Ala Glu Val Thr Phe Val Ala Asn lle Thr Asp Ala Tyr Arg Ser Ala Arg Pro Gly Leu Leu Ser Pro Tyr Ser Tyr Ser Thr Thr Ala o Val c Val Glu Lys o Thr – Pro Asn Carboxyl end Figure 5.20 Four Levels of Protein Structure • Primary structure • Is the unique sequence of amino acids in a polypeptide Lecturer/ Iyad A. Elqouqa

  40. H H H H H H O O O O O O O H H H H H H R R R R R R R C C C C C C C C C C C C C N N N N N N N N N N N N N C C C C C C C C C C C C C C R R R R R R H H H H H H H O O O O O O O H H H H H H H  pleated sheet H O H H Amino acidsubunits C C N N N C C C R H O H H H H H H N N N N N N  helix C C O C H H H C C C R R R R R H H C C C C C C O O O O H C R O C C O H C O N N H C C H R H R Figure 5.20 • Secondary structure • Is the folding or coiling of the polypeptide into a repeating configuration • Includes the  helix and the  pleated sheet Lecturer/ Iyad A. Elqouqa

  41. Hydrophobic interactions and van der Waalsinteractions CH CH2 CH2 H3C CH3 OH Polypeptidebackbone H3C CH3 Hyrdogenbond CH O HO C CH2 CH2 S S CH2 Disulfide bridge O -O C CH2 CH2 NH3+ Ionic bond • Tertiary structure • Is the overall three-dimensional shape of a polypeptide • Results from interactions between amino acids and R groups Lecturer/ Iyad A. Elqouqa

  42. Polypeptidechain Collagen  Chains Iron Heme  Chains Hemoglobin • Quaternary structure • Is the overall protein structure that results from the aggregation of two or more polypeptide subunits Lecturer/ Iyad A. Elqouqa

  43. +H3N Amino end Amino acid subunits helix • The four levels of protein structure Lecturer/ Iyad A. Elqouqa

  44. Sickle-Cell Disease: A Simple Change in Primary Structure • Sickle-cell disease • Results from a single amino acid substitution in the protein hemoglobin Lecturer/ Iyad A. Elqouqa

  45. Normal hemoglobin Sickle-cell hemoglobin Primary structure Primary structure . . . . . . Exposed hydrophobic region Val His Leu Thr Pro Glul Glu Val His Leu Pro Glu Thr Val 5 6 7 3 4 5 6 7 1 2 1 2 3 4 Secondaryand tertiarystructures Secondaryand tertiarystructures  subunit  subunit     Quaternary structure Hemoglobin A Quaternary structure Hemoglobin S     Molecules interact with one another tocrystallize into a fiber, capacity to carry oxygen is greatly reduced. Function Molecules donot associatewith oneanother, eachcarries oxygen. Function 10 m 10 m Normal cells arefull of individualhemoglobinmolecules, eachcarrying oxygen Red bloodcell shape Red bloodcell shape Figure 5.21 • Hemoglobin structure and sickle-cell disease Fibers of abnormalhemoglobin deform cell into sickle shape. Lecturer/ Iyad A. Elqouqa

  46. What Determines Protein Conformation? • Protein conformation • Depends on the physical and chemical conditions of the protein’s environment Lecturer/ Iyad A. Elqouqa

  47. Denaturation Normal protein Denatured protein Renaturation Figure 5.22 • Denaturation • Is when a protein unravels and loses its native conformation Lecturer/ Iyad A. Elqouqa

  48. The Protein-Folding Problem • Most proteins • Probably go through several intermediate states on their way to a stable conformation Lecturer/ Iyad A. Elqouqa

  49. Correctlyfoldedprotein Polypeptide Cap Hollowcylinder The cap attaches, causing the cylinder to change shape insuch a way that it creates a hydrophilic environment for the folding of the polypeptide. The cap comesoff, and the properlyfolded protein is released. Chaperonin(fully assembled) Steps of ChaperoninAction: An unfolded poly- peptide enters the cylinder from one end. 2 1 3 Figure 5.23 • Chaperonins • Are protein molecules that assist in the proper folding of other proteins Lecturer/ Iyad A. Elqouqa

  50. X-raydiffraction pattern Photographic film Diffracted X-rays X-ray beam X-raysource Crystal Nucleic acid Protein (b) 3D computer model (a) X-ray diffraction pattern • X-ray crystallography • Is used to determine a protein’s three-dimensional structure Figure 5.24 Lecturer/ Iyad A. Elqouqa

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