1. Chapter 5 The Structure and Function of Macromolecules 1

2. The Molecules of Life Overview: – Another level in the hierarchy of biological organization is reached when small organic molecules are joined together – Atom ---> molecule ---  compound – Big Idea 2: Biological systems utilize Free Energy and molecular Building Blocks to grow, reproduce, and maintain dynamic homeostasis. – Big Idea 3: Biological systems store, retrieve, transmit, and respond to information essential to life processes. 2

3. Macromolecules Most macromolecules are polymers, built from monomers Four classes of life’s organic molecules are polymers – Carbohydrates – Proteins – Nucleic acids – Lipids 3

4. A polymer – Is a long molecule consisting of many similar building blocks called monomers – Specific monomers make up each macromolecule – E.g. amino acids are the monomers for proteins 4

5. The Synthesis and Breakdown of Polymers Monomers form larger molecules by condensation reactions called dehydration synthesis 5 (a) Dehydration reaction in the synthesis of a polymer HOH 1 2 3 H 1 23 4 H H2OH2O Short polymer Unlinked monomer Longer polymer Dehydration removes a water molecule, forming a new bond Figure 5.2A

6. The Synthesis and Breakdown of Polymers Polymers can disassemble by – Hydrolysis (addition of water molecules) 6 (b) Hydrolysis of a polymer HO 1 2 3 H H 1 2 3 4 H2OH2O H Hydrolysis adds a water molecule, breaking a bond Figure 5.2B

7. Although organisms share the same limited number of monomer types, each organism is unique based on the arrangement of monomers into polymers An immense variety of polymers can be built from a small set of monomers 7

8. Sugars Monosaccharides – Are the simplest sugars – Can be used for fuel – Can be converted into other organic molecules – Can be combined into polymers 8 Carbohydrates Serve as fuel and building material Include both sugars and their polymers (starch, cellulose, etc.)

9. Examples of monosaccharides 9 Triose sugars (C 3 H 6 O 3 ) Pentose sugars (C 5 H 10 O 5 ) Hexose sugars (C 6 H 12 O 6 ) H C OH HO C H H C OH HO C H H C OH C O H C OH HO C H H C OH C O H H H HHH H H HHH H H H C CCC O O O O Aldoses Glyceraldehyde Ribose Glucose Galactose Dihydroxyacetone Ribulose Ketoses Fructose Figure 5.3

10. Monosaccharides – May be linear – Can form rings 10 H H C OH HO C H H C OH H C O C H 1 2 3 4 5 6 H OH 4C4C 6 CH 2 OH 5C5C H OH C H OH H 2 C 1C1C H O H OH 4C4C 5C5C 3 C H H OH OH H 2C2C 1 C OH H CH 2 OH H H OH HO H OH H 5 3 2 4 (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. OH 3 O H O O 6 1 Figure 5.4

11. 11 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. 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. (a) (b) H HO H H OH H OH O H CH 2 OH H HOHO H HOHHOH H OHOH O H OHOH H O H H OH H OH O H CH 2 OH H H2OH2O H2OH2O H H O H HO H OH O H CH 2 OH HO OH H CH 2 OH HOHHOH H H HO OH H CH 2 OH HOHHOH H O O H OH H CH 2 OH HOHHOH H O H OH CH 2 OH H HO O CH 2 OH H H OH O O 1 2 1 4 1– 4 glycosidic linkage 1–2 glycosidic linkage Glucose Fructose Maltose Sucrose OH H H Figure 5.5 Disaccharides – Consist of two monosaccharides – Are joined by a glycosidic linkage

12. Polysaccharides – Are polymers of sugars – Serve many roles in organisms 12

13. Storage Polysaccharides Starch – Is a polymer consisting entirely of glucose monomers – Is the major storage form of glucose in plants 13 Chloroplast Starch Amylose Amylopectin 1  m (a) Starch: a plant polysaccharide Figure 5.6

14. Glycogen – Consists of glucose monomers – Is the major storage form of glucose in animals 14 Mitochondria Giycogen granules 0.5  m (b) Glycogen: an animal polysaccharide Glycogen Figure 5.6

15. Structural Polysaccharides Cellulose – Is a polymer of glucose 15 – Has different glycosidic linkages than starch (c) Cellulose: 1– 4 linkage of  glucose monomers H O O CH 2 O H H OHOH H H OHOH OHOH H H HOHO 4 C C C C C C H H H HOHO OHOH H OHOH OHOH OHOH H O H H H OHOH OHOH H H HOHO 4 OHOH O OHOH OHOH HOHO 4 1 O O OHOH OHOH O O OHOH OHOH O OHOH OHOH O O O OHOH OHOH HOHO 4 O 1 OHOH O OHOH OHOH O O OHOH O OHOH O OHOH OHOH (a)  and  glucose ring structures (b) Starch: 1– 4 linkage of  glucose monomers 1  glucose  glucose CH 2 O H 1 4 4 1 1 Figure 5.7 A–C

16. – Is a major component of the tough walls that enclose plant cells 16 Plant cells 0.5  m Cell walls Cellulose microfibrils in a plant cell wall  Microfibril CH 2 OH OH OHOH O O O CH 2 OH O O OH O CH 2 OH OH O O CH 2 OH O O OHOH O O OHOH O O OH CH 2 OHOH O O CH 2 OH OH O CH 2 OH O O OHCH 2 OH OH  Glucose monomer O O O O O O Parallel cellulose molecules are held together by hydrogen bonds between hydroxyl groups attached to carbon atoms 3 and 6. About 80 cellulose molecules associate to form a microfibril, the main architectural unit of the plant cell wall. A cellulose molecule is an unbranched  glucose polymer. OH O O Cellulose molecules Figure 5.8

17. Cellulose is difficult to digest – Cows have microbes in their stomachs to facilitate this process 17 Figure 5.9

18. Chitin, another important structural polysaccharide – Is found in the exoskeleton of arthropods – Can be used as surgical thread 18 (a) The structure of the chitin monomer. O CH 2 O H OH H H H NH C CH 3 O H H (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. OH Figure 5.10 A–C

19. Lipids 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 19

20. Triglycerides (Fats) – Are constructed from two types of smaller molecules, a single glycerol and usually three fatty acids – Vary in the length and number and locations of double bonds they contain 20

21. (a) Saturated fat and fatty acid Stearic acid Figure 5.12 (b) Unsaturated fat and fatty acid cis double bond causes bending Oleic acid Figure 5.12 21 Saturated fatty acids – Have the maximum number of hydrogen atoms possible – Have no double bonds Unsaturated fatty acids – Have one or more double bonds

22. Phospholipids – Have only two fatty acids – Have a phosphate group instead of a third fatty acid 22

23. Phospholipid structure – Consists of a hydrophilic “head” and hydrophobic “tails” 23 CH 2 O P O O O CH CH 2 OO C O C O Phosphate Glycerol (a) Structural formula (b) Space-filling model Fatty acids (c) Phospholipid symbol Hydrophobic tails Hydrophilic head Hydrophobic tails – Hydrophilic head CH 2 Choline + Figure 5.13 N(CH 3 ) 3

24. The structure of phospholipids – Results in a bilayer arrangement found in cell membranes 24 Hydrophilic head WATER Hydrophobic tail Figure 5.14

25. Steroids – Are lipids characterized by a carbon skeleton consisting of four fused rings 25 E.g. Cholesterol – Is found in cell membranes – Is a precursor for some hormones HO CH 3 H3CH3C Figure 5.15

26. Proteins Proteins have many structures, resulting in a wide range of functions Proteins do most of the work in cells and act as enzymes Proteins are made of monomers called amino acids 26

27. An overview of protein functions 27 Table 5.1

28. Enzymes – Are a type of protein that acts as a catalyst, speeding up chemical reactions 28 Substrate (sucrose) Enzyme (sucrase) Glucose OH H O H2OH2O Fructose 3 Substrate is converted to products. 1 Active site is available for a molecule of substrate, the reactant on which the enzyme acts. Substrate binds to enzyme. 22 4 Products are released. Figure 5.16

29. Polypeptides – Are polymers (chains) of amino acids A protein – Consists of one or more polypeptides Amino acids – Are organic molecules possessing both carboxyl and amino groups – Differ in their properties due to differing side chains, called R groups 29

30. Twenty Amino Acids 20 different amino acids make up proteins 30 O O–O– H H3N+H3N+ C C O O–O– H CH 3 H3N+H3N+ C H C O O–O– C C O O–O– H H3N+H3N+ CH CH 3 CH 2 C H H3N+H3N+ CH 3 CH 2 CH C H H3N+H3N+ C CH 3 CH 2 C H3N+H3N+ H C O O–O– C H3N+H3N+ H C O O–O– NH H C O O–O– H3N+H3N+ C CH 2 H2CH2C H2NH2N C H C Nonpolar Glycine (Gly) Alanine (Ala) Valine (Val)Leucine (Leu)Isoleucine (Ile) Methionine (Met) Phenylalanine (Phe) C O O–O– Tryptophan (Trp) Proline (Pro) H3CH3C Figure 5.17 S O O–O–

31. 31

32. Amino Acid Polymers Amino acids – Are linked by peptide bonds 32

33. Protein Conformation and Function A protein’s specific conformation (shape) determines how it functions 33

34. Four Levels of Protein Structure Primary structure – Is the unique sequence of amino acids in a polypeptide 34 Figure 5.20 – Amino acid subunits + H 3 N Amino end o Carboxyl end o c Gly ProThr Gly Thr Gly Glu Seu Lys Cys Pro Leu Met Val Lys Val Leu Asp Ala Val Arg Gly Ser Pro Ala Gly lle Ser Pro Phe His Glu His Ala Glu Val Phe Thr Ala Asn Asp Ser Gly Pro Arg Tyr Thr lle Ala Leu Ser Pro Tyr Ser Tyr Ser Thr Ala Val Thr Asn Pro Lys Glu Thr Lys Ser Tyr Trp Lys Ala Leu Glu Lle Asp

35. Secondary structure – Is the folding or coiling of the polypeptide into a repeating configuration – Includes the  helix and the  pleated sheet 35 O C  helix  pleated sheet Amino acid subunits N C H C O C N H C O H R C N H C O H C R N H H R C O R C H N H C O H N C O R C H N H H C R C O C O C N H H R C C O N H H C R C O N H R C H C O N H H C R C O N H R C H C O N H H C R C O N H H C R N H O O C N C R C H O C H R N H O C R C H N H O C H C R N H C C N R H O C H C R N H O C R C H H C R N H C O C N H R C H C O N H C H H Figure 5.20

36. Tertiary structure – Is the overall three-dimensional shape of a polypeptide – Results from interactions between amino acids and R groups 36 CH 2 CH OHOH O C HO CH 2 NH 3 + C -O-O CH 2 O SS CH CH 3 H3CH3C H3CH3C Hydrophobic interactions and van der Waals interactions Polypeptide backbone Hyrdogen bond Ionic bond CH 2 Disulfide bridge

37. Quaternary structure – Is the overall protein structure that results from the aggregation of two or more polypeptide subunits 37 Polypeptide chain Collagen  Chains  Chains Hemoglobin Iron Heme

38. Review of Protein Structure 38 + H 3 N Amino end Amino acid subunits  helix

39. 39 Fibers of abnormal hemoglobin deform cell into sickle shape. Primary structure Secondary and tertiary structures Quaternary structure Function Red blood cell shape Hemoglobin A Molecules do not associate with one another, each carries oxygen. Normal cells are full of individual hemoglobin molecules, each carrying oxygen     10  m     Primary structure Secondary and tertiary structures Quaternary structure Function Red blood cell shape Hemoglobin S Molecules interact with one another to crystallize into a fiber, capacity to carry oxygen is greatly reduced.  subunit 12 3 4 567 34 567 21 Normal hemoglobin Sickle-cell hemoglobin... Figure 5.21 Exposed hydrophobic region ValThrHisLeuProGlulGluValHisLeu Thr Pro Val Glu Sickle-Cell Disease: A Simple Change in Primary Structure

40. What Determines Protein Conformation? Protein conformation Depends on the physical and chemical conditions of the protein’s environment Temperature, pH, etc. affect protein structure 40

41. Denaturation is when a protein unravels and loses its native conformation (shape) 41 Denaturation Renaturation Denatured proteinNormal protein Figure 5.22

42. The Protein-Folding Problem Most proteins – Probably go through several intermediate states on their way to a stable conformation – Denaturated proteins no longer work in their unfolded condition – Proteins may be denaturated by extreme changes in pH or temperature 42

43. Chaperonins – Are protein molecules that assist in the proper folding of other proteins 43 Hollow cylinder Cap Chaperonin (fully assembled) Steps of Chaperonin Action: An unfolded poly- peptide enters the cylinder from one end. The cap attaches, causing the cylinder to change shape in such a way that it creates a hydrophilic environment for the folding of the polypeptide. The cap comes off, and the properly folded protein is released. Correctly folded protein Polypeptide 2 1 3 Figure 5.23

44. X-ray crystallography – Is used to determine a protein’s three- dimensional structure 44 X-ray diffraction pattern Photographic film Diffracted X- rays X-ray source X-ray beam Crystal Nucleic acidProtein (a) X-ray diffraction pattern (b) 3D computer model Figure 5.24

45. Nucleic Acids Nucleic acids store and transmit hereditary information Genes – Are the units of inheritance – Program the amino acid sequence of polypeptides – Are made of nucleotide sequences on DNA 45

46. The Roles of Nucleic Acids There are two types of nucleic acids – Deoxyribonucleic acid (DNA) – Ribonucleic acid (RNA) 46

47. Deoxyribonucleic Acid DNA – Stores information for the synthesis of specific proteins – Found in the nucleus of cells – Directs RNA synthesis (transcription) – Directs protein synthesis through RNA (translation) 47 1 2 3 Synthesis of mRNA in the nucleus Movement of mRNA into cytoplasm via nuclear pore Synthesis of protein NUCLEUS CYTOPLASM DNA mRNA Ribosome Amino acids Polypeptide mRNA Figure 5.25

48. The Structure of Nucleic Acids – Consists of monomers called nucleotides – Sugar + phosphate + nitrogen base 48 (a) Polynucleotide, or nucleic acid 3’C 5’ end 5’C 3’C 5’C 3’ end OH Figure 5.26 O O O O Nitrogenous base Nucleoside O O OO OO P CH 2 5’C 3’C Phosphate group Pentose sugar (b) Nucleotide Figure 5.26 O

49. The Nitrogen bases: A, T, U, G, and C Purine Rings: Adenine, Guanine Pyrimidine Rings: Cytosine, Uracil, thymine 49

50. Nucleotide Polymers Nucleotide polymers are linked by phosphodiester bonds. – OH group on the 3´ carbon to phosphate of 5’ carbon on next molecule. 50

51. The DNA Double Helix Cellular DNA molecules – Have two anti-parallel strands that spiral around an imaginary axis forming a double helix – Are held together by hydrogen bonding between nitrogen bases on anti-paralle strands 51 complementary base pair rules: A with T only in DNA/ A with U only in RNA C with G only

52. DNA and Proteins as Tape Measures of Evolution Molecular comparisons – Help biologists sort out the evolutionary connections among species – We will come back to this in Investigation 3: Using BLAST to compare DNA sequences to determine evolutionary sequences 52

53. Big Ideas 2 and 3 Big Idea 2: Biological systems utilize Free Energy and molecular Building Blocks to grow, reproduce, and maintain dynamic homeostasis. Big Idea 3: Biological systems store, retrieve, transmit, and respond to information essential to life processes. 53