1. Carbon and the Molecular Diversity of Life

2. Why study Carbon? All of life is built on carbon Cells ~72% H2O ~25% carbon compounds carbohydrates lipids proteins nucleic acids ~3% salts Na, Cl, K…

3. CHNOPS Carbon, Hydrogen, Nitrogen, Oxygen, Phosphorus, Sulfur

4. Properties of Carbon It can form up to 4 covalent bonds These can be single, double, or triple covalent bonds

5. Properties of Carbon  It likes to bond with itself, unlike most atoms  Thus it can form large molecules  These molecules can be chains, branches, or rings- shaped

6. Variations in Carbon Skeletons How can you create variations in carbon skeletons? Change the length of the carbon skeleton. The skeleton may be straight, branched, or arranged in closed rings Alter the number and location of double bonds. Change the elements or groups with which carbon bonds.

7. Diversity of Molecules Substitute other atoms or groups around the carbon ethane vs. ethanol H replaced by an hydroxyl group (–OH) nonpolar vs. polar gas vs. liquid biological effects! ethane (C 2 H6) ethanol (C2H5OH)

8. Hydrocarbons Combinations of C & H only non-polar not soluble in H2O Hydrophobic Can undergo reactions that release a relatively large amount of energy methane (simplest HC)

9. Form Affects Function Structural differences create important functional significance amino acid alanine L-alanine used in proteins but not D-alanine medicines L-version active but not D-version sometimes with tragic results… stereoisomers

10. Form Affects Function Thalidomide prescribed to pregnant women in 50s & 60s reduced morning sickness, but… stereoisomer caused severe birth defects

11. Chemical Groups There are SEVEN chemical groups most important in biology Hydroxyl Carbonyl Carboxyl Amino Sulfhydryl Phosphate Methyl 6 of the 7 chemical groups are considered functional groups Methyl group is NOT a functional group because it does not participate in chemical reactions, instead it acts as a recognizable tag on biological molecules

13. Functional Groups parts of organic molecules that are involved in chemical reactions give organic molecules distinctive properties hydroxyl amino carbonyl sulfhydryl carboxyl phosphate Affect reactivity makes hydrocarbons hydrophilic increase solubility in water

14. Viva la difference! Basic structure of male & female hormones is identical identical carbon skeleton attachment of different chemical / functional groups interact with different targets in the body different effects

15. Hydroxyl –OH organic compounds with OH = alcohols names typically end in -ol ethanol

17. Carbonyl C=O O double bonded to C if C=O at end molecule = aldehyde if C=O in middle of molecule = ketone

19. Carboxyl –COOH C double bonded to O & single bonded to OH group compounds with COOH = acids fatty acids amino acids

20. Carboxyl Group How did it get its name? COOH - This group consists of a carbon atom that is bonded to both a carbonyl and a hydroxyl group. Why is this group acidic? It donates H+ Compounds with this group are called carboxylic acids

22. Amino - NH2 N attached to 2 H compounds with NH2 = amines amino acids NH2 acts as base ammonia picks up H+ from solution

24. Sulfhydryl – SH S bonded to H compounds with SH = thiols SH groups help stabilize protein structure through disulfide bridges

25. Disulfide Bridge

27. Phosphate –PO4 P bound to 4 O connects to C through an O lots of O = lots of negative charge highly reactive transfers energy between organic molecules ATP, GTP, etc.

29. CARBON AND MOLECULAR DIVERSITY The structure and function of macromolecules: Carbohydrates, Lipids, Proteins and Nucleic Acids

30. Objectives Be familiar with how polymers are assembled and dismantled Understand that most organic macromolecules are polymers of smaller units Describe the properties of a carbohydrate Be able to distinguish between a monosaccharide, disaccharide and a polysaccharide. Be able to give examples of each kind of carbohydrate Know that the energy of a carbohydrate comes from its ability to donate electrons Describe the properties of a lipid Understand the 3 categories of lipids and the significance of each kind of lipid

31. POLYMER PRINCIPLES. Most macromolecules are polymers built from smaller units called monomers. Polymerization reactions are carried out through the elimination of water (condensation or dehydration synthesis) or the addition of water (hydrolysis). An immense variety of polymers can be built from a small set of monomers.

33. Depending on their size and configuration, carbohydrates serve as energy molecules or structural “building blocks” Carbohydrates are molecules built from monomer units with a chemical formulation of CH2O Three “size categories” of carbohydrates are recognized: Monosaccharide, Disaccharide, and Polysaccharide CARBOHYDRATES: FUEL AND BUILDING MATERIAL

34. Monosaccharides: Fuel and Building Material Monosaccharides, the smallest carbohydrates, serve as fuel and carbon sources

35. Examples of linear (chain) form structures for several monosaccharides What are these? Answer: Isomers of each other

36. Glycosidic Linkage Formation The junction between two monosaccharides is called a glycosidic linkage The structure of the disaccharide (types of monosaccharides used and glycosidic linkage position) is important in determining how the disaccharide functions

37. Polysaccharide Polysaccharides result from many monosaccharides being linked together Energy Storage Glycogen, Starch Structural Support Chitin, Cellulose Again, type of monosaccharide and glycosidic linkage structure are important

39. Importance of Carbohydrates Energy (electron donors) Building materials Used for cell-cell recognition (important to the immune system)

40. LIPIDS: DIVERSE HYDROPHOBIC MOLECULES Lipids store large amounts of energy 9 kcal/gram due to energy rich fatty acid chain Characteristics of fat Hydrophobic because of nonpolar FA chain Saturated versus unsaturated fats. Saturated FA chains form no more bonds, unsaturated FA chains can form more bonds

41. General Role of Lipids Functions of fat energy storage, cushioning, insulation Lipids store large amounts of energy 9 kcal/gram due to energy rich fatty acid chain Their fluid (pliable) nature makes then a good cushion as “Shockwaves” are dispersed Molecules can be close together making some fats good insulators

42. What are Lipids? Characteristics Tend to be Hydrophobic (water fearing) because of nonpolar components (lots of hydrocarbons (C-H)) Made from isoprene units combined to make chains Chains are made polar through the addition of a carboxyl group forming a Fatty acid Saturated versus unsaturated fats. Saturated FA chains form no more bonds, unsaturated FA chains can form more bonds

44. Kinds of Lipids Triglyceride (triacyclglycerol) Comprise many of the dietary oils and fats Functional differences arise from differences in hydrophobic chain type and position

45. Kinds of Lipids Phospholipid Comprises much of the Plasma Membrane (border around cell) Polar phosphate group coupled with nonpolar hydrocarbon chains make this molecule amphipathic

47. Steroids Isoprene chains form a 17 carbon ring system as core structure Steroid types vary depending on position and type of groups attached to ring system Comprise some hormones such as Testosterone, Estradiol, Cortisol, and Aldosterone Kinds of Lipids

48. Polypeptides Polypeptides are polymers built from the same set of 20 amino acids A protein consists of one or more polypeptides Copyright © 2008 Pearson Education, Inc., publishing as Pearson Benjamin Cummings

49. Amino Acid Monomers Amino acids are organic molecules with carboxyl and amino groups Amino acids differ in their properties due to differing side chains, called R groups Copyright © 2008 Pearson Education, Inc., publishing as Pearson Benjamin Cummings

50. Amino group Carboxyl group carbon

51. Nonpolar Glycine (Gly or G) Alanine (Ala or A) Valine (Val or V) Leucine (Leu or L) Isoleucine (Ile or I ) Methionine (Met or M) Phenylalanine (Phe or F) Trypotphan (Trp or W) Proline (Pro or P) Polar Serine (Ser or S) Threonine (Thr or T) Cysteine (Cys or C) Tyrosine (Tyr or Y) Asparagine (Asn or N) Glutamine (Gln or Q) Electrically charged AcidicBasic Aspartic acid (Asp or D) Glutamic acid (Glu or E) Lysine (Lys or K) Arginine (Arg or R) Histidine (His or H)

52. Nonpolar Glycine (Gly or G) Alanine (Ala or A) Valine (Val or V) Leucine (Leu or L) Isoleucine (Ile or I ) Methionine (Met or M) Phenylalanine (Phe or F) Tryptophan (Trp or W) Proline (Pro or P)

53. Polar Asparagine (Asn or N) Glutamine (Gln or Q) Serine (Ser or S) Threonine (Thr or T) Cysteine (Cys or C) Tyrosine (Tyr or Y)

54. Acidic Arginine (Arg or R) Histidine (His or H) Aspartic acid (Asp or D) Glutamic acid (Glu or E) Lysine (Lys or K) Basic Electrically charged

55. Amino Acid Polymers Amino acids are linked by peptide bonds A polypeptide is a polymer of amino acids Polypeptides range in length from a few to more than a thousand monomers Each polypeptide has a unique linear sequence of amino acids Copyright © 2008 Pearson Education, Inc., publishing as Pearson Benjamin Cummings

56. Peptide bond Amino end (N-terminus) Peptide bond Side chains Backbone Carboxyl end (C-terminus) (a) (b)

57. A ribbon model of lysozyme (a)(b) A space-filling model of lysozyme Groove A functional protein consists of one or more polypeptides twisted, folded, and coiled into a unique shape Protein Structure and Function

58. Four Levels of Protein Structure The primary structure of a protein is its unique sequence of amino acids Secondary structure, found in most proteins, consists of coils and folds in the polypeptide chain Tertiary structure is determined by interactions among various side chains (R groups) Quaternary structure results when a protein consists of multiple polypeptide chains Copyright © 2008 Pearson Education, Inc., publishing as Pearson Benjamin Cummings

59. Primary structure, the sequence of amino acids in a protein, is like the order of letters in a long word Primary structure is determined by inherited genetic information Copyright © 2008 Pearson Education, Inc., publishing as Pearson Benjamin Cummings 25 5 1

60. Secondary Structure Examples of amino acid subunits The coils and folds of secondary structure result from hydrogen bonds between repeating constituents of the polypeptide backbone Typical secondary structures are a coil called an  helix and a folded structure called a  pleated sheet

61. Abdominal glands of the spider secrete silk fibers made of a structural protein containing  pleated sheets. The radiating strands, made of dry silk fibers, maintain the shape of the web. The spiral strands (capture strands) are elastic, stretching in response to wind, rain, and the touch of insects.

62. Tertiary structure is determined by interactions between R groups, rather than interactions between backbone constituents These interactions between R groups include hydrogen bonds, ionic bonds, hydrophobic interactions, and van der Waals interactions Strong covalent bonds called disulfide bridges may reinforce the protein’s structure Copyright © 2008 Pearson Education, Inc., publishing as Pearson Benjamin Cummings

63. Quaternary structure results when two or more polypeptide chains form one macromolecule Collagen is a fibrous protein consisting of three polypeptides coiled like a rope Hemoglobin is a globular protein consisting of four polypeptides: two alpha and two beta chains Copyright © 2008 Pearson Education, Inc., publishing as Pearson Benjamin Cummings

64. Sickle-Cell Disease: A Change in Primary Structure A slight change in primary structure can affect a protein’s structure and ability to function Sickle-cell disease, an inherited blood disorder, results from a single amino acid substitution in the protein hemoglobin Copyright © 2008 Pearson Education, Inc., publishing as Pearson Benjamin Cummings

65. Primary structure Secondary and tertiary structures Quaternary structure Normal hemoglobin (top view) Primary structure Secondary and tertiary structures Quaternary structure Function  subunit Molecules do not associate with one another; each carries oxygen. Red blood cell shape Normal red blood cells are full of individual hemoglobin moledules, each carrying oxygen. 10 µm Normal hemoglobin     1234567 Val His Leu ThrPro Glu Red blood cell shape  subunit Exposed hydrophobic region Sickle-cell hemoglobin   Molecules interact with one another and crystallize into a fiber; capacity to carry oxygen is greatly reduced.   Fibers of abnormal hemoglobin deform red blood cell into sickle shape. 10 µm Sickle-cell hemoglobin GluPro Thr Leu His Val 1234567

66. What Determines Protein Structure? In addition to primary structure, physical and chemical conditions can affect structure Alterations in pH, salt concentration, temperature, or other environmental factors can cause a protein to unravel This loss of a protein’s native structure is called denaturation A denatured protein is biologically inactive Copyright © 2008 Pearson Education, Inc., publishing as Pearson Benjamin Cummings

67. Normal protein Denatured protein Denaturation Renaturation

68. Protein Folding in the Cell It is hard to predict a protein’s structure from its primary structure Most proteins probably go through several states on their way to a stable structure Chaperonins are protein molecules that assist the proper folding of other proteins Copyright © 2008 Pearson Education, Inc., publishing as Pearson Benjamin Cummings

69. Fig. 5-24 Hollow cylinder Cap Chaperonin (fully assembled) Polypeptide Steps of Chaperonin Action: An unfolded poly- peptide enters the cylinder from one end. 1 23 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

70. Nucleic acids store and transmit hereditary information The amino acid sequence of a polypeptide is programmed by a unit of inheritance called a gene Genes are made of DNA, a nucleic acid Copyright © 2008 Pearson Education, Inc., publishing as Pearson Benjamin Cummings

71. The Roles of Nucleic Acids There are two types of nucleic acids: Deoxyribonucleic acid (DNA) Ribonucleic acid (RNA) DNA provides directions for its own replication DNA directs synthesis of messenger RNA (mRNA) and, through mRNA, controls protein synthesis Protein synthesis occurs in ribosomes Copyright © 2008 Pearson Education, Inc., publishing as Pearson Benjamin Cummings

72. mRNA Synthesis of mRNA in the nucleus DNA NUCLEUS mRNA CYTOPLASM Movement of mRNA into cytoplasm via nuclear pore Ribosome Amino acids Polypeptide Synthesis of protein 1 2 3

73. The Structure of Nucleic Acids Nucleic acids are polymers called polynucleotides Each polynucleotide is made of monomers called nucleotides Each nucleotide consists of a nitrogenous base, a pentose sugar, and a phosphate group The portion of a nucleotide without the phosphate group is called a nucleoside Copyright © 2008 Pearson Education, Inc., publishing as Pearson Benjamin Cummings

74. Nucleotide Monomers Nucleoside = nitrogenous base + sugar There are two families of nitrogenous bases: Pyrimidines (cytosine, thymine, and uracil) have a single six- membered ring Purines (adenine and guanine) have a six-membered ring fused to a five-membered ring In DNA, the sugar is deoxyribose; in RNA, the sugar is ribose Nucleotide = nucleoside + phosphate group Copyright © 2008 Pearson Education, Inc., publishing as Pearson Benjamin Cummings

75. 5 end Nucleoside Nitrogenous base Phosphate group Sugar (pentose) (b) Nucleotide (a) Polynucleotide, or nucleic acid 3 end 3C3C 3C3C 5C5C 5C5C Nitrogenous bases Pyrimidines Cytosine (C) Thymine (T, in DNA)Uracil (U, in RNA) Purines Adenine (A)Guanine (G) Sugars Deoxyribose (in DNA) Ribose (in RNA) (c) Nucleoside components: sugars

76. 5' end 5'C 3'C 5'C 3'C 3' end (a) Polynucleotide, or nucleic acid (b) Nucleotide Nucleoside Nitrogenous base 3'C 5'C Phosphate group Sugar (pentose)

77. Nucleotide Polymers Nucleotide polymers are linked together to build a polynucleotide Adjacent nucleotides are joined by covalent bonds that form between the –OH group on the 3 carbon of one nucleotide and the phosphate on the 5 carbon on the next These links create a backbone of sugar-phosphate units with nitrogenous bases as appendages The sequence of bases along a DNA or mRNA polymer is unique for each gene Copyright © 2008 Pearson Education, Inc., publishing as Pearson Benjamin Cummings

78. The DNA Double Helix A DNA molecule has two polynucleotides spiraling around an imaginary axis, forming a double helix In the DNA double helix, the two backbones run in opposite 5 → 3 directions from each other, an arrangement referred to as antiparallel One DNA molecule includes many genes The nitrogenous bases in DNA pair up and form hydrogen bonds: adenine (A) always with thymine (T), and guanine (G) always with cytosine (C) Copyright © 2008 Pearson Education, Inc., publishing as Pearson Benjamin Cummings

79. Sugar-phosphate backbones 3' end 5' end Base pair (joined by hydrogen bonding) Old strands New strands Nucleotide about to be added to a new strand

80. DNA and Proteins as Tape Measures of Evolution The linear sequences of nucleotides in DNA molecules are passed from parents to offspring Two closely related species are more similar in DNA than are more distantly related species Molecular biology can be used to assess evolutionary kinship Copyright © 2008 Pearson Education, Inc., publishing as Pearson Benjamin Cummings