1. Biochemistry

2. Carbon—Backbone of Biological Molecules Although cells are 70–95% water, the rest consists mostly of carbon-based compounds Carbon is unique in its ability to form large, complex, and diverse molecules Proteins, DNA, carbohydrates, and other molecules that distinguish living matter are all composed of carbon compounds

3. Organic chemistry-the study of carbon compounds Organic compounds range from simple molecules to colossal ones Most organic compounds contain hydrogen atoms in addition to carbon atoms With four valence electrons, carbon can form four covalent bonds with a variety of atoms Needs 4 electrons - single, double or triple bonds This tetravalence makes large, complex molecules possible - can form long chains or rings

4. Carbon Molecules In molecules with multiple carbons, each carbon bonded to four other atoms has a tetrahedral shape However, when two carbon atoms are joined by a double bond, the molecule has a flat shape Molecular Formula Structural Formula Ball-and-Stick Model Space-Filling Model Methane Ethane Ethene (ethylene)

5. Carbon Molecules The electron configuration of carbon gives it covalent compatibility with many different elements The valences of carbon and its most frequent partners (hydrogen, oxygen, and nitrogen) are the “building code” that governs the architecture of living molecules Hydrogen (valence = 1) Oxygen (valence = 2) Nitrogen (valence = 3) Carbon (valence = 4)

6. Carbon Skeleton Diversity Carbon is a versatile atom Carbon can use its bonds to form an endless diversity of carbon skeletons Carbon chains form the skeletons of most organic molecules Length Ethane Propane Butane 2-methylpropane (commonly called isobutane) Branching Double bonds Rings 1-Butene2-Butene CyclohexaneBenzene

7. Hydrocarbons Hydrocarbons are organic molecules consisting of only carbon and hydrogen Many organic molecules, such as fats, have hydrocarbon components Hydrocarbons can undergo reactions that release a large amount of energy

8. Functional Groups Distinctive properties of organic molecules depend not only on the carbon skeleton but also on the molecular components attached to it Certain groups of atoms called functional groups are often attached to skeletons of organic molecules Functional groups are the parts of molecules involved in chemical reactions The number and arrangement of functional groups give each molecule its unique properties

9. Functional Groups The six functional groups that are most important in the chemistry of life: –Hydroxyl group –Carbonyl group –Carboxyl group –Amino group –Sulfhydryl group –Phosphate group

10. Biochemistry: The Molecules of Life Within cells, small organic molecules are joined together to form larger molecules Macromolecules are large molecules composed of thousands of covalently connected atoms –Carbohydrates –Lipids –Proteins –Nucleic acids

11. Macromolecules - Polymers A polymer is a long molecule consisting of many similar building blocks called monomers Most macromolecules are polymers, built from monomers An immense variety of polymers can be built from a small set of monomers Three of the four classes of life’s organic molecules are polymers: –Carbohydrates –Proteins –Nucleic acids

12. Polymers Monomers form larger molecules by condensation reactions called dehydration reactions Polymers are disassembled to monomers by hydrolysis, a reaction that is essentially the reverse of the dehydration reaction Short polymer Unlinked monomer Dehydration removes a water molecule, forming a new bond Dehydration reaction in the synthesis of a polymer Longer polymer Hydrolysis adds a water molecule, breaking a bond Hydrolysis of a polymer

13. Carbohydrates Carbohydrates serve as fuel and building material They include sugars and the polymers of sugars The simplest carbohydrates are monosaccharides, or single (simple) sugars Carbohydrate macromolecules are polysaccharides, polymers composed of many sugar building blocks

14. Sugars Monosaccharides have molecular formulas that contain C, H, and O in an approximate ratio of 1:2:1 Monosaccharides are used for short term energy storage, and serve as structural components of larger organic molecules Glucose is the most common monosaccharide

15. Monosaccharides are classified by location of the carbonyl group and by number of carbons in the carbon skeleton 3 C = triose e.g. glyceraldehyde 4 C = tetrose 5 C = pentose e.g. ribose, deoxyribose 6 C = hexose e.g. glucose, fructose, galactose Monosaccharides in living organisms generally have 3C, 5C, or 6C: Monosaccharides

16. Triose sugars (C 3 H 6 O 3 ) Glyceraldehyde Aldoses Ketoses Pentose sugars (C 5 H 10 O 5 ) Ribose Hexose sugars (C 5 H 12 O 6 ) Glucose Galactose Dihydroxyacetone Ribulose Fructose

17. Monosaccharides Monosaccharides serve as a major fuel for cells and as raw material for building molecules The monosaccharides glucose and fructose are isomers –They have the same chemical formula –Their atoms are arranged differently Though often drawn as a linear skeleton, in aqueous solutions they form rings GlucoseFructose

18. Monosaccharides In aqueous solutions, monosaccharides form rings Linear and ring forms Abbreviated ring structure

19. Monosaccharides: Hexoses

20. H H H HH H OH O H O CH 2 OH Ribose Pentoses (5-carbon sugars) Deoxyribose HH 4 5 1 3 2 4 5 1 3 2 CH 2 OH Monosaccharides: Pentsoses

21. Disaccharides A disaccharide is formed when a dehydration reaction joins two monosaccharides Disaccharides are joined by the process of dehydration synthesis This covalent bond is called a glycosidic linkage Glucose Maltose Fructose Sucrose Glucose Dehydration reaction in the synthesis of maltose Dehydration reaction in the synthesis of sucrose 1–4 glycosidic linkage 1–2 glycosidic linkage

22. Disaccharides Lactose = Glucose + Galactose Maltose = Glucose + Glucose Sucrose = Glucose + Fructose The most common disaccharide is sucrose, common table sugar Sucrose is extracted from sugar cane and the roots of sugar beets

23. Polysaccharides Complex carbohydrates are called polysaccharides They are polymers of monosaccharides - long chains of simple sugar units Polysaccharides have storage and structural roles The structure and function of a polysaccharide are determined by its sugar monomers and the positions of glycosidic linkages (a) Starch (b) Glycogen (c) Cellulose

24. Storage Polysaccharides - Starch Starch, a storage polysaccharide of plants, consists entirely of glucose monomers Plants store surplus starch as granules within chloroplasts and other plastids ChloroplastStarch 1 µm Amylose Starch: a plant polysaccharide Amylopectin

25. Storage Polysaccharides - Glycogen Glycogen is a storage polysaccharide in animals Humans and other vertebrates store glycogen mainly in liver and muscle cells Mitochondria Glycogen granules 0.5 µm Glycogen Glycogen: an animal polysaccharide

26. Structural Polysaccharides Cellulose is a major component of the tough wall of plant cells Like starch, cellulose is a polymer of glucose, but the glycosidic linkages differ The difference is based on two ring forms for glucose: alpha (  ) and beta (  ) –Polymers with alpha glucose are helical –Polymers with beta glucose are straight a Glucose a and b glucose ring structures b Glucose Starch: 1–4 linkage of a glucose monomers. Cellulose: 1–4 linkage of b glucose monomers.

27. Cellulose Enzymes that digest starch by hydrolyzing alpha linkages can’t hydrolyze beta linkages in cellulose Cellulose in human food passes through the digestive tract as insoluble fiber Some microbes use enzymes to digest cellulose Many herbivores, from cows to termites, have symbiotic relationships with these microbes Cellulose molecules Cellulose microfibrils in a plant cell wall Cell walls Microfibril Plant cells 0.5 µm  Glucose monomer

28. Lipids Lipids are the one class of large biological molecules that do not form polymers Utilized for energy storage, membranes, insulation, protection Greasy or oily substances The unifying feature of lipids is having little or no affinity for water - insoluble in water Lipids are hydrophobic because  they consist mostly of hydrocarbons, which form nonpolar covalent bonds

29. Fats The most biologically important lipids are fats, phospholipids, and steroids Fats are constructed from two types of smaller molecules: glycerol and fatty acids Glycerol is a three-carbon alcohol with a hydroxyl group attached to each carbon A fatty acid consists of a carboxyl group attached to a long carbon skeleton Dehydration reaction in the synthesis of a fat Glycerol Fatty acid (palmitic acid)

30. Fatty Acids A fatty acid has a long hydrocarbon chain with a carboxyl group at one end. Fatty acids vary in length (number of carbons) and in the number and locations of double bonds Saturated fatty acids have the maximum number of hydrogen atoms possible and no double bonds Unsaturated fatty acids have one or more double bonds, –Monounsaturated (one double bond) –Polyunsaturated (more than one double bond) H can be added to unsaturated fatty acids using a process called hydrogenation The major function of fats is energy storage StearateOleate

31. Fats Fats separate from water because water molecules form hydrogen bonds with each other and exclude the fats In a fat, three fatty acids are joined to glycerol by an ester linkage, creating a triacylglycerol, or triglyceride

32. Glycerides Glycerol + 1 fatty acid = monoglycerideGlycerol + 1 fatty acid = monoglyceride Glycerol + 2 fatty acids = diglycerideGlycerol + 2 fatty acids = diglyceride Glycerol + 3 fatty acids = triglyceride (also called triacylglycerol or “fat”.)Glycerol + 3 fatty acids = triglyceride (also called triacylglycerol or “fat”.) Ester linkage Fat molecule (triacylglycerol)

33. Saturated Fats Fats made from saturated fatty acids are called saturated fats Most animal fats are saturated Saturated fats are solid at room temperature A diet rich in saturated fats may contribute to cardiovascular disease through plaque deposits Saturated fat and fatty acid. Stearic acid

34. Unsaturated Fats Fats made from unsaturated fatty acids are called unsaturated fats Plant fats and fish fats are usually unsaturated Plant fats and fish fats are liquid at room temperature and are called oils Unsaturated fat and fatty acid. Oleic acid cis double bond causes bending

35. Fat Sources Most animal fats contain saturated fatty acids and tend to be solid at room temperature Most plant fats contain unsaturated fatty acids. They tend to be liquid at room temperature, and are called oils.

36. Phospholipids In phospholipids, two of the –OH groups on glycerol are joined to fatty acids. The third –OH joins to a phosphate group which joins, in turn, to another polar group of atoms. The phosphate and polar groups are hydrophilic (polar head) while the hydrocarbon chains of the 2 fatty acids are hydrophobic (nonpolar tails). Structural formula Space-filling model Phospholipid symbol Hydrophilic head Hydrophobic tails Fatty acids Choline Phosphate Glycerol Hydrophobic tails Hydrophilic head

37. Phospholipids

38. Micelle Phospholipid bilayer Water Lipid head (hydrophilic) Lipid tail (hydrophobic) Phospholipids When phospholipids are added to water, they orient so that the nonpolar tails are shielded from contact with the polar H2O may form micelles Phosopholipids also may self-assemble into a bilayer, with the hydrophobic tails pointing toward the interior The structure of phospholipids results in a bilayer arrangement found in cell membranes

39. Steroids Steroids are lipids characterized by a carbon skeleton consisting of four fused rings Cholesterol, an important steroid, is a component in animal cell membranes Testosterone and estrogen function as sex hormones

40. Proteins Proteins have many structures, resulting in a wide range of functions They account for more than 50% of the dry mass of most cells Protein functions –Structural support / storage / movement - fibers –Catalysis - Enzymes –Defense against foreign substances– Immunoglobulins –Transport – globins, membrane transporters –Messengers for cellular communications - hormones

42. Proteins A protein is composed of one or more polypeptides that performs a function A polypeptide is a polymer of amino acids joined by peptide bonds to form a long chain Polypeptides range in length from a few monomers to more than a thousand Each polypeptide has a unique linear sequence of amino acids A protein consists of one or more polypeptides which are coiled and folded into a specific 3-D shape. The shape of a protein determines its function.

43. Amino Acids Amino acids are monomers of polypetides They composed of a carboxyl group, amino group, and an “R”Group Amino acids differ in their properties due to differing side chains, called R groups Cells use 20 amino acids to make thousands of proteins Amino group Carboxyl group  carbon

45. 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– Amino Acids

47. Amino Acids and Peptide Bonds Two amino acids can join by condensation to form a dipeptide plus H2O. The bond between 2 amino acids is called a peptide bond.

48. Protein Conformation and Function A functional protein consists of one or more polypeptides twisted, folded, and coiled into a unique shape The sequence of amino acids determines a protein’s three- dimensional conformation A protein’s conformation determines its function Ribbon models and space- filling models can depict a protein’s conformation A ribbon model Groove A space-filling model

49. 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 Amino acid subunits  pleated sheet  helix

50. Levels of Protein Structure

51. 51 Interactions that Contribute to a Protein’s Shape 51

52. 52

53. Enzymes as Catalysts To increase reaction rates: –Add Energy (Heat) - molecules move faster so they collide more frequently and with greater force. –Add a catalyst – a catalyst reduces the energy needed to reach the activation state, without being changed itself. Proteins that function as catalysts are called enzymes. Reactant Product CatalyzedUncatalyzed Product Reactant Activation energy Activation energy Energy supplied Energy released Copyright © The McGraw-Hill Companies, Inc. Permission required for reproduction or display. Activation Energy and Catalysis

54. Enzymes Are Biological Catalysts Enzymes are proteins that carry out most catalysis in living organisms. Unlike heat, enzymes are highly specific. Each enzyme typically speeds up only one or a few chemical reactions. Unique three-dimensional shape enables an enzyme to stabilize a temporary association between substrates. Because the enzyme itself is not changed or consumed in the reaction, only a small amount is needed, and can then be reused. Therefore, by controlling which enzymes are made, a cell can control which reactions take place in the cell.

55. Substrate Specificity of Enzymes Almost all enzymes are globular proteins with one or more active sites on their surface. The substrate is the reactant an enzyme acts on Reactants bind to the active site to form an enzyme-substrate complex. The 3-D shape of the active site and the substrates must match, like a lock and key Binding of the substrates causes the enzyme to adjust its shape slightly, leading to a better induced fit. When this happens, the substrates are brought close together and existing bonds are stressed. This reduces the amount of energy needed to reach the transition state. Substate Active site Enzyme Enzyme- substrate complex

56. 1 The substrate, sucrose, consists of glucose and fructose bonded together. Bond Enzyme Active site The substrate binds to the enzyme, forming an enzyme-substrate complex. 2 H2OH2O The binding of the substrate and enzyme places stress on the glucose-fructose bond, and the bond breaks. 3 Glucose Fructose Products are released, and the enzyme is free to bind other substrates. 4 The Catalytic Cycle Of An Enzyme

57. Conformational Change and Enzyme Activity In addition to primary structure, physical and chemical conditions can affect conformation Alternations in pH, salt concentration, temperature, or other environmental factors can cause a protein to unravel This loss of a protein’s native conformation is called denaturation A denatured protein is biologically inactive Denaturation Renaturation Denatured proteinNormal protein

58. Effects of Temperature and pH Each enzyme has an optimal temperature in which it can function Optimal temperature for enzyme of thermophilic Rate of reaction 0 20 40 80 100 Temperature (Cº) (a) Optimal temperature for two enzymes Optimal temperature for typical human enzyme (heat-tolerant) bacteria

59. Effects of Temperature and pH –Each enzyme has an optimal pH in which it can function Figure 8.18 Rate of reaction (b) Optimal pH for two enzymes Optimal pH for pepsin (stomach enzyme) Optimal pH for trypsin (intestinal enzyme) 1 02 34 5 6789

60. Nucleic Acids (DNA/RNA) 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

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

62. 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 5 end 3 end Nucleoside Nitrogenous base Phosphate group Nucleotide Pentose sugar

63. Nucleotide Monomers Nucleotide monomers are made up of nucleosides and phosphate groups Nucleoside = nitrogenous base + sugar There are two families of nitrogenous bases: –Pyrimidines have a single six- membered ring –Purines have a six-membered ring fused to a five-membered ring In DNA, the sugar is deoxyribose In RNA, the sugar is ribose Nitrogenous bases Pyrimidines Purines Pentose sugars Cytosine C Thymine (in DNA) T Uracil (in RNA) U Adenine A Guanine G Deoxyribose (in DNA) Nucleoside components Ribose (in RNA)

64. Nucleotide Polymers Nucleotide polymers are linked together, building 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

65. 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´ to 3´ directions from each other, an arrangement referred to as antiparallel One DNA molecule includes many genes The nitrogenous bases in DNA form hydrogen bonds in a complementary fashion: A always with T, and G always with C Sugar-phosphate backbone 3 end 5 end Base pair (joined by hydrogen bonding) Old strands Nucleotide about to be added to a new strand 5 end New strands 3 end 5 end 3 end 5 end

66. ATP Adenosine triphosphate (ATP), is the primary energy- transferring molecule in the cell ATP is the “energy currency” of the cell ATP consists of an organic molecule called adenosine attached to a string of three phosphate groups The energy stored in the bond that connects the third phosphate to the rest of the molecule supplies the energy needed for most cell activities

67. ATP ATP (adenosine triphosphate) –Is the cell’s energy shuttle –Provides energy for cellular functions O O O O CH 2 H OH H N HH O N C HC N C C N NH 2 Adenine Ribose Phosphate groups O O O O O O - --- CH

68. ATP Energy is released from ATP w hen the terminal phosphate bond is broken P Adenosine triphosphate (ATP) H2OH2O + Energy Inorganic phosphate Adenosine diphosphate (ADP) PP PPP i