1. Copyright © 2006 Cynthia Garrard publishing under Canyon Design Chapter 5 - Macromolecules Overview: The Molecules of Life – Another level in the hierarchy of biological organization is reached when small organic molecules are joined together

2. Copyright © 2006 Cynthia Garrard publishing under Canyon Design Macromolecules – Are large molecules composed of smaller molecules – Are complex in their structures Figure 5.1

3. Copyright © 2006 Cynthia Garrard publishing under Canyon Design Polymers and Monomers Three of the classes of life’s organic molecules are polymers – Carbohydrates – Proteins – Nucleic acids

4. Copyright © 2006 Cynthia Garrard publishing under Canyon Design Polymers and Monomers A polymer – Is a long molecule consisting of many similar or identical building blocks called monomers A monomer – Is the subunit that serve as the building block of a polymer

5. Copyright © 2006 Cynthia Garrard publishing under Canyon Design Polymers and Monomers Dehydration reactions – condensation reaction that forms large molecules from monomers – Takes energy – Must have enzymes helping (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. Copyright © 2006 Cynthia Garrard publishing under Canyon Design Polymers and Monomers Polymers can disassemble by – Hydrolysis Releases energy (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. Copyright © 2006 Cynthia Garrard publishing under Canyon Design Polymers and Monomers There are only about 40 -50 monomers, yet there are 1000’s of different polymers – Possible through different linear sequences 1 2 3 HOH

8. Copyright © 2006 Cynthia Garrard publishing under Canyon Design Carbohydrates Monomer – monosaccharide or simple sugar – Example: Glucose, Fructose, Lactose – Major nutrient of cells – Joined together by glycosidic linkage Figure 5.3

9. Copyright © 2006 Cynthia Garrard publishing under Canyon Design Carbohydrates Monosaccharides – May be linear – Can form rings 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

10. Copyright © 2006 Cynthia Garrard publishing under Canyon Design Carbohydrates Polymer – is polysaccharide – Example: Starch, Glycogen, Cellulose

11. Copyright © 2006 Cynthia Garrard publishing under Canyon Design Carbohydrates Polysaccharide can be involved with storage Starch – Is a polymer consisting entirely of glucose monomers – Is found in plants Glycogen – Is found in animals Both are stored energy

12. Copyright © 2006 Cynthia Garrard publishing under Canyon Design Carbohydrates Polysaccharides involved in the structure of cells – Cellulose – in plants – Chitin – in insects Strength comes from the isomers of glucose and the 3D shape of the molecule

13. Copyright © 2006 Cynthia Garrard publishing under Canyon Design Carbohydrates Isomers of glucose - Differ in the location of the hydroxyl group bonded to the 1’ C Figure 5.7

14. Copyright © 2006 Cynthia Garrard publishing under Canyon Design Carbohydrates Different isomers can create different molecules Figure 5.7

15. Copyright © 2006 Cynthia Garrard publishing under Canyon Design Lipids – Are the one class of large biological molecules that do not consist of polymers – Share the common trait of being hydrophobic – Consist mostly of hydrocarbons – Have varied functions

16. Copyright © 2006 Cynthia Garrard publishing under Canyon Design Lipids Fats – Constructed from two types of smaller molecules: a single glycerol, and usually three fatty acids (b) Fat molecule (triacylglycerol) H H H H H H H H H H H H H H H H O Figure 5.11

17. Copyright © 2006 Cynthia Garrard publishing under Canyon Design Lipids Fats – Fatty acids are joined to the glycerol by ester linkages – Major function is energy storage

18. Copyright © 2006 Cynthia Garrard publishing under Canyon Design Fatty acids – Vary in the length and number and locations of double bonds they contain This results in different types of fatty acids – Saturated – Unsaturated

19. Copyright © 2006 Cynthia Garrard publishing under Canyon Design Lipids Saturated fatty acids – Have the maximum number of hydrogen atoms possible – Have no double bonds – Solid at room temp (a) Saturated fat and fatty acid Stearic acid Figure 5.12

20. Copyright © 2006 Cynthia Garrard publishing under Canyon Design Unsaturated fatty acids – Have one or more double bonds – Liquid at room temp (b) Unsaturated fat and fatty acid cis double bond causes bending Oleic acid Figure 5.12

21. Copyright © 2006 Cynthia Garrard publishing under Canyon Design Lipids Another type of lipid is the phospholipid Phospholipids – Have only two fatty acids – Have a phosphate group instead of a third fatty acid

22. Copyright © 2006 Cynthia Garrard publishing under Canyon Design Lipids Phospholipid structure – Consists of a hydrophilic “head” and hydrophobic “tails” 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

23. Copyright © 2006 Cynthia Garrard publishing under Canyon Design Lipids The structure of phospholipids – Results in a bilayer arrangement found in cell membranes Hydrophilic head WATER Hydrophobic tail Figure 5.14 We’ll spend more time with them in Chapter 7

24. Copyright © 2006 Cynthia Garrard publishing under Canyon Design Proteins Proteins have many structures, resulting in a wide range of functions – Proteins More than 50% of dry mass of cell Important in most everything organisms do Have many roles inside the cell – Examples: speed up rxns, storage, cellular communication, transport, movement, structural support, and defense

25. Copyright © 2006 Cynthia Garrard publishing under Canyon Design Protein Enzymes – Are a type of protein that acts as a catalyst, speeding up chemical reactions – Humans have 10,000 + different enzymes – Each enzyme does its specific job – Does not get used up or altered in the rxn

26. Copyright © 2006 Cynthia Garrard publishing under Canyon Design Protein Monomer – amino acid – Are organic molecules possessing both carboxyl and amino groups – 20 unique amino acids – Differ in their properties due to differing side chains, called R groups

27. Copyright © 2006 Cynthia Garrard publishing under Canyon Design Protein 20 different amino acids make up proteins 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–

28. Copyright © 2006 Cynthia Garrard publishing under Canyon Design

29. Protein Amino acids – Are linked by peptide bonds DESMOSOMES OH CH 2 C N H C H O HOH Peptide bond OH H H HH H H H H H H H H N N N N N SH Side chains SH OO OO O H2OH2O CH 2 C C C CCC C C C C Peptide bond Amino end (N-terminus) Backbone (a) Figure 5.18 (b) Carboxyl end (C-terminus)

30. Copyright © 2006 Cynthia Garrard publishing under Canyon Design Protein Polymer – polypeptide, which differs from a protein – Amino acids are joined by peptide bonds, amino group to carboxyl group – Each has a unique linear sequence Protein – Consists of one or more polypeptides

31. Copyright © 2006 Cynthia Garrard publishing under Canyon Design Protein To be functional, the protein’s polypeptide chain(s) must be precisely twisted, folded and coiled into the proper shape The linear sequence of the amino acids determine which polypeptide is formed and its proper 3D shape

32. Copyright © 2006 Cynthia Garrard publishing under Canyon Design Protein There are 4 levels of protein structure: Primary structure – Is the unique sequence of amino acids in a polypeptide 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

33. Copyright © 2006 Cynthia Garrard publishing under Canyon Design Protein Secondary structure – Is the folding or coiling of the polypeptide into a repeating configuration – Includes the  helix and the  pleated sheet Figure 5.20

34. Copyright © 2006 Cynthia Garrard publishing under Canyon Design Protein Tertiary structure – Is the overall three-dimensional shape of a polypeptide – Results from interactions between amino acids and R groups 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

35. Copyright © 2006 Cynthia Garrard publishing under Canyon Design Protein Quaternary structure – Is the overall protein structure that results from the aggregation of two or more polypeptide subunits Polypeptide chain Collagen  Chains  Chains Hemoglobin Iron Heme

36. Copyright © 2006 Cynthia Garrard publishing under Canyon Design Protein Protein conformation – Depends on the physical and chemical conditions of the protein’s environment Things like salt concentration, pH level and temperature can denature a protein

37. Copyright © 2006 Cynthia Garrard publishing under Canyon Design Protein Denaturing – when a protein unravels and loses its native conformation Denaturation Renaturation Denatured proteinNormal protein Figure 5.22

38. Copyright © 2006 Cynthia Garrard publishing under Canyon Design Protein Proteins have help folding properly in the form of chaperone proteins

39. Copyright © 2006 Cynthia Garrard publishing under Canyon Design Protein Chaperonins (chaperone proteins) – Are protein molecules that assist in the proper folding of other proteins 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

40. Copyright © 2006 Cynthia Garrard publishing under Canyon Design 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 nucleic acids

41. Copyright © 2006 Cynthia Garrard publishing under Canyon Design Nucleic Acids There are two types of nucleic acids – Deoxyribonucleic acid (DNA) – Stores information for the synthesis of specific proteins Directs RNA synthesis Directs protein synthesis through RNA – Ribonucleic acid (RNA) Multiple functions and types

42. Copyright © 2006 Cynthia Garrard publishing under Canyon Design Nucleic Acids Nucleic acids – Exist as polymers called polynucleotides (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

43. Copyright © 2006 Cynthia Garrard publishing under Canyon Design Nucleic acid Each polynucleotide – Consists of monomers called nucleotides 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 Nitrogenous base (1 of 4) Sugar (pentose or 5C) Phosphate group

44. Copyright © 2006 Cynthia Garrard publishing under Canyon Design Nucleic acid Nucleotides can be divided into two types – Pyrimidines – smaller, 1 6C ring Cytosine, thynine and uracil – Purines – larger, 1 6C ring and 1 5C ring Adenosine, guanine

45. Copyright © 2006 Cynthia Garrard publishing under Canyon Design Nucleic acid Before we move on, lets look closely at the sugar and count the carbons:

46. Copyright © 2006 Cynthia Garrard publishing under Canyon Design Nucleic acid Nucleotide polymers – Are made up of nucleotides linked by the–OH group on the 3´ carbon of one nucleotide and the phosphate on the 5´ carbon on the next – Monomers are joined by phosphodiester linkages between sugar / phosphate backbone, not bases

47. Copyright © 2006 Cynthia Garrard publishing under Canyon Design The DNA Double Helix Cellular DNA molecules – Have two polynucleotides that spiral around an imaginary axis – Form a double helix

48. Copyright © 2006 Cynthia Garrard publishing under Canyon Design The DNA double helix – Consists of two antiparallel nucleotide strands 3’ end Sugar-phosphate backbone Base pair (joined by hydrogen bonding) Old strands Nucleotide about to be added to a new strand A 3’ end 5’ end New strands 3’ end 5’ end Figure 5.27

49. Copyright © 2006 Cynthia Garrard publishing under Canyon Design The nitrogenous bases in DNA – Form hydrogen bonds in a complementary fashion (A with T only, and C with G only) The nitrogenous bases in RNA – Form hydrogen bonds in a complementary fashion (A with U only, and C with G only)