Biochemistry

1. Biochemistry The Structure and Function of Macromolecules

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. Space-Filling Model Molecular Formula Structural Formula Ball-and-Stick Model Methane Ethane Ethene (ethylene) 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

5. Hydrogen (valence = 1) Oxygen (valence = 2) Nitrogen (valence = 3) Carbon (valence = 4) 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

6. Propane Ethane Length 2-methylpropane (commonly called isobutane) Butane Branching 1-Butene 2-Butene Double bonds Cyclohexane Benzene Rings 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

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. Structural isomers differ in covalent partners, as shown in this example of two isomers of pentane. cis isomer: The two Xs are on the same side. trans isomer: The two Xs are on opposite sides. Geometric isomers differ in arrangement about a double bond. In these diagrams, X represents an atom or group of atoms attached to a double-bonded carbon. L isomer D isomer Enantiomers differ in spatial arrangement around an asymmetric carbon, resulting in molecules that are mirror images, like left and right hands. The two isomers are designated the L and D isomers from the Latin for left and right (levo and dextro). Enantiomers cannot be superimposed on each other. Isomers • Isomers are compounds with the same molecular formula but different structures and properties: • Structural isomers have different covalent arrangements of their atoms • Geometric isomers have the same covalent arrangements but differ in spatial arrangements • Enantiomers are isomers that are mirror images of each other

9. L-Dopa (effective against Parkinson’s disease) D-Dopa (biologically Inactive) Enantiomers • Enantiomers are important in the pharmaceutical industry • Two enantiomers of a drug may have different effects • Differing effects of enantiomers demonstrate that organisms are sensitive to even subtle variations in molecules

10. 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

11. 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

12. STRUCTURE (may be written HO—) Ethanol, the alcohol present in alcoholic beverages NAME OF COMPOUNDS FUNCTIONAL PROPERTIES Is polar as a result of the electronegative oxygen atom drawing electrons toward itself. Alcohols (their specific names usually end in -ol) Attracts water molecules, helping dissolve organic compounds such as sugars (see Figure 5.3).

13. Acetone, the simplest ketone EXAMPLE STRUCTURE Acetone, the simplest ketone Propanal, an aldehyde NAME OF COMPOUNDS Ketones if the carbonyl group is within a carbon skeleton FUNCTIONAL PROPERTIES Aldehydes if the carbonyl group is at the end of the carbon skeleton A ketone and an aldehyde may be structural isomers with different properties, as is the case for acetone and propanal.

14. EXAMPLE STRUCTURE Acetic acid, which gives vinegar its sour taste NAME OF COMPOUNDS FUNCTIONAL PROPERTIES Carboxylic acids, or organic acids Has acidic properties because it is a source of hydrogen ions. The covalent bond between oxygen and hydrogen is so polar that hydrogen ions (H+) tend to dissociate reversibly; for example, Acetic acid Acetate ion In cells, found in the ionic form, which is called a carboxylate group.

15. EXAMPLE STRUCTURE Glycine Because it also has a carboxyl group, glycine is both an amine and a carboxylic acid; compounds with both groups are called amino acids. FUNCTIONAL PROPERTIES NAME OF COMPOUNDS Acts as a base; can pick up a proton from the surrounding solution: Amine (nonionized) (ionized) Ionized, with a charge of 1+, under cellular conditions

16. EXAMPLE STRUCTURE (may be written HS—) Ethanethiol NAME OF COMPOUNDS FUNCTIONAL PROPERTIES Two sulfhydryl groups can interact to help stabilize protein structure (see Figure 5.20). Thiols

17. EXAMPLE STRUCTURE Glycerol phosphate NAME OF COMPOUNDS FUNCTIONAL PROPERTIES Makes the molecule of which it is a part an anion (negatively charged ion). Organic phosphates Can transfer energy between organic molecules.

18. 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

19. Biochemistry • Living organisms are composed of both inorganic and organic molecules • Inorganic molecules • Relatively small, simple molecules that usually lack C (a few have one C atom). • Examples: CO2, NH3, H2O, O2, H2 • Organic molecules • Larger, more complex, based on a backbone of C atoms (always contain C as a major part of their structure). • Examples: C6H12O6, C2H5COOH

20. 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

21. 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 Longer polymer Dehydration reaction in the synthesis of a polymer Hydrolysis adds a water molecule, breaking a bond Hydrolysis of a polymer

22. 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

23. 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

24. Monosaccharides • 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:

25. Triose sugars (C3H6O3) Pentosesugars (C5H10O5) Hexose sugars (C5H12O6) Aldoses Glyceraldehyde Ribose Galactose Glucose Ketoses Dihydroxyacetone Ribulose Fructose

26. Glucose Fructose 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

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

29. Triose (3-carbon sugar) Pentoses (5-carbon sugars) H O C CH2OH 5 CH2OH 5 1 O O OH OH C OH H 2 1 4 4 1 H H H H OH H C H H H H 3 3 2 2 3 H H OH OH OH Glyceraldehyde Ribose Deoxyribose 29

30. Dehydration reaction in the synthesis of maltose 1–4 glycosidic linkage Glucose Glucose Maltose Dehydration reaction in the synthesis of sucrose 1–2 glycosidic linkage Sucrose Fructose Glucose 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

31. 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

32. 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

33. Chloroplast Starch 1 µm Amylose Amylopectin Starch: a plant polysaccharide 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

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

35. a Glucose b Glucose a and b glucose ring structures Starch: 1–4 linkage of a glucose monomers. Cellulose: 1–4 linkage of b glucose monomers. 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

36. Cellulose microfibrils in a plant cell wall Cell walls Microfibril 0.5 µm Plant cells Cellulose molecules b Glucose monomer 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

37. Chitin • Chitin, another structural polysaccharide, is found in the exoskeleton of arthropods • Chitin also provides structural support for the cell walls of many fungi • Chitin can be used as surgical thread

38. 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

39. Fatty acid (palmitic acid) Glycerol Dehydration reaction in the synthesis of a fat 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

40. Stearate Oleate 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

41. Ester linkage Fat molecule (triacylglycerol) 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

43. Glycerides • Glycerol + 1 fatty acid = monoglyceride • Glycerol + 2 fatty acids = diglyceride • Glycerol + 3 fatty acids = triacylglycerol (also called a triglyceride or fat.)

44. Stearic acid Saturated fat and fatty acid. 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

45. Oleic acid cis double bond causes bending Unsaturated fat and fatty acid. 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

46. 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.

47. Choline Hydrophilic head Phosphate Glycerol Hydrophobic tails Fatty acids Hydrophilic head Hydrophobic tails Space-filling model Structural formula Phospholipid symbol 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).

49. Water Lipid head (hydrophilic) Lipid tail (hydrophobic) Micelle Water Water Phospholipid bilayer 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

50. WATER Hydrophilic head Hydrophobic tails WATER Phospholipids • The structure of phospholipids results in a bilayer arrangement found in cell membranes • Phospholipids are the major component of all cell membranes