Chapter 5

1. Chapter 5 The Structure and Function of Macromolecules

2. Figure 5.1 Overview: The Molecules of Life Another level in the hierarchy of biological organization is reached when small organic molecules are joined together Macromolecules • Are large molecules composed of smaller molecules • Are complex in their structures

3. Organic Compounds • All compounds discovered can be classified into two broad categories: inorganic and organic • "Organic" = • The compounds of life consist of primarily 6 elements: "CHONPS"

4. Chemistry of CARBON is the chemistry of LIFE! • Carbon forms the “backbone” (framework) of all organic molecules • C has four e- in its outermost energy level, but needs 8 to fill it, so it readily forms covalent bonds!

5. Carbon, the basis for life • Carbon likes to bond, with other atoms and with itself • single bonds- • double bonds- • triple bonds-                

6. Concept 5.1: Most macromolecules are polymers, built from monomers Three of the classes of life’s organic molecules are polymers • Carbohydrates • Proteins • Nucleic acids • A polymer • Is a long molecule consisting of many similar building blocks called monomers

7. 1 HO H 3 2 H HO Unlinked monomer Short polymer Dehydration removes a watermolecule, forming a new bond H2O 1 2 3 4 HO H Longer polymer (a) Dehydration reaction in the synthesis of a polymer Figure 5.2A The Synthesis and Breakdown of Polymers • Monomers form larger molecules by condensation reactions called dehydration synthesis • These are sometimes called condensation rxns because a molecule of water is liberated when a bond is formed.

8. 1 3 HO 4 2 H Hydrolysis adds a watermolecule, breaking a bond H2O 1 2 H HO 3 H HO (b) Hydrolysis of a polymer Figure 5.2B Polymers • Polymers can disassemble by • Hydrolysis (water cleavage)

9. Concept 5.2: Carbohydrates serve as fuel and building material CARBOHYDRATES (= ENERGY) • - The most abundant organic compounds in nature • Include both sugars and their polymers (starches) • Most carbohydrates have the empirical formula (CH20)n. • Carbohydrates are composed of covalently bonded atoms of carbon, hydrogen, and oxygen.

10. O H 1 C 6CH2OH 6CH2OH 2 CH2OH H C OH 5C H 5C O O 6 3 H O H H H H H 5 HO C H HOH H HOH 4 4C 1 C 1C 4C 4 1 OH H H H C OH O HO OH 3 2 OH OH 5 OH 2 C C 3 C 2C 3 OH H C H OH 6 H H OH OH H C OH H (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. Figure 5.4 • Monosaccharides • May be linear • Can form rings (when aqueous)

11. There are Four Major Classes of Organic Compounds: Three main monosaccharides: • glucose- main source of energy for cells • fructose- sugar in fruits and honey (the sweetest monosaccharide) • galactose- sugar in milk and yogurt Monosaccharides - simple sugars; "building blocks of all carbs“ • C:H:O = approx. 1:2:1 • Example: C6H12O6 • May be linear • Can form rings (when aqueous)

12. A side note: Isomers These are compounds that have the same molecular formula but different three dimensional structures and hence different physical and/or chemical properties.

13. Another side note… Drawing organic molecules-  Sometimes even the carbons are not labeled, but are always assumed to be present at every 'bend or end' of the ring. Sometimes the drawings showing monosaccharides are simplified to show only the most important parts of the molecules. The same sequence of events diagrammed above could be shown as: Here the hydrogens that complete each molecule are simply 'understood' to be present, and are not included in the diagrams. There is also a specific way that the carbons in the molecule are numbered for reference, clockwise 

14. Disaccharides: “double sugars” • Disaccharides - two monosaccharides bonded together by condensation rxn’s to form glycosidic bonds • Examples: • glucose + fructose = sucrose (common table sugar) • glucose + galactose = lactose (major sugar in milk) This bond is called ana(alpha) 1,4 linkage. Why? Questions for review: 1) Why is this “joining” called a condensation (dehydration synthesis) reaction? 2) How could this bond be broken?

15. (a) 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. CH2OH CH2OH CH2OH CH2OH O O O O H H H H H H H H 1–4glycosidiclinkage HOH HOH HOH HOH 4 1 H H H H OH OH O H OH HO HO OH O H H H H OH OH OH OH H2O Glucose Maltose Glucose CH2OH CH2OH CH2OH CH2OH O O O O 1–2glycosidiclinkage H H H H H H HOH HOH 2 1 H H HO H HO H 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. (b) OH H O O HO CH2OH HO CH2OH H OH H H OH H OH OH H2O Glucose Sucrose Fructose Figure 5.5 Examples of disaccharides

16. Polysaccharides are polymers of sugars Examples: glycogen (animals), starch (plant), cellulose (plant fiber), chitin (insect) • Cell stores energy it doesn’t use by converting monosaccharides into disaccharides/polysaccharides A polysaccharide consists of three or more (usually hundreds of) monosaccharides, joined together by condensation reactions.

17. Chloroplast Starch 1 m Amylose Amylopectin (a) Starch: a plant polysaccharide Figure 5.6 Two different types of starches • Starch • Is a polymer consisting entirely of glucose monomers • Starch is the storage polysaccharide in plants and is an important reservoir for energy. • There are two common types of (plant) starch:

18. Starches 1) Amylose: the simplest starch, consisting of unbranched chains of hundreds of glucose molecules. Note: the [alpha] 1,4 glycosidic bond, (the glucose units are connected to the first and fourth carbons) 2) Amylopectin: large molecule consisting of short glucose chains with other glucose chains branching off of the main chain. • Note: the glucose units are linked by both [alpha] 1,4 AND [alpha] 1,6 bonds!

19. Giycogen granules Mitochondria 0.5 m Glycogen Figure 5.6 (b) Glycogen: an animal polysaccharide “animal” starch • Glycogen • Consists of linked, highly branched, glucose monomers • Is the major storage form of glucose in animals

20. Glycogen • Glycogen is the main energy storage polysaccharide in animals • Glycogen is composed of branching glucose chains, with more branches than amylopectin. • It is found in the liver and muscles and acts as the temporary storage form of glucose. The liver removes the excess glucose from the bloodstream, converts the glucose monomers to glycogen via condensation reactions, and stores it as glycogen. • When vertebrates need glucose for energy, glycogen is converted by hydrolysis back to glucose. • In glycogen, or animal starch, the glucose units are again joined by [alpha] 1,4 linkages to produce long chains, but side chains are linked to the main chain by [alpha] 1,6 linkages

21. Structural Polysaccharides • Cellulose is a structural polysaccharide and is the major building material made by plants. • It is the most abundant organic material on earth. • Cellulose is made up of long, straight glucose molecules. Cellulose is called a structural polysaccharide because it gives the plant cell its shape, is not soluble, and is very strong. • Cellulose is flexible when the plant cell is young. As the cell grows, the cellulose becomes thicker and more rigid.

22. Figure 5.9 Cellulose • Cellulose is indigestible to humans because the linkages are 1-4 beta linkages, and our enzymes can only break down 1-4 alpha linkages because the shapes are different. • Cellulose is the so-called "fiber" in our diets. • Some bacteria, protists, fungi, and lichens have enzymes that can break down cellulose. • For example, bacteria and protists found in the stomachs of termites and grazing animals break down the cellulose in the grass and wood to provide the animal with glucose

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

24. CH2OH O OH H H OH H H H NH O C CH3 OH (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. (a) The structure of the chitin monomer. Figure 5.10 A–C Other structural polysaccharides • Chitin, another important structural polysaccharide • Is found in the exoskeleton of arthropods • Chitin is very soft but is combined with CaCO3 (calcium carbonate or limestone) to become hard. Most animals cannot digest chitin • Can be used as surgical thread Pectin and carrageenan: These are extracted from algae.   Pectin and carrageenan are put into food items such as jellies, jams, yogurt, icecream , and milkshakes to give them a jelly-like or creamy consistency.

25. LIPIDS • Concept 5.3: Lipids are a diverse group of hydrophobic molecules • Are the one class of large biological molecules that do not consist of polymers • Lipids are a diverse group of molecules defined by their solubility rather than by their structures (Share the common trait of being hydrophobic) • Lipids dissolve in nonpolar solvents such as chloroform, ether, and benzene. • There are 5 classes of lipids: triglycerides, phospholipids, glycolipids, steroids, and waxes. • Fats, waxes, oils store energy very efficiently (concentrated energy) • Ratio of C:H:O is > than in carbs; LARGE # of C-H bonds

26. Triglycerides: Fats and Oils • Fat: solid at room temperature.Oil: liquid at room temperature. • Glycerol: Fatty acids usually have an even number of carbons, differ in the length of the carbon chain, and may contain single or double covalent bonds.

27. Triglycerides: Fats and oils • A triglyceride is composed of one glycerol molecule and three fatty acid molecules. • The synthesis of a triglyceride occurs when a glycerol molecule joins with three (of the seventy different) fatty acids. Fat molecule (triacylglycerol)

28. Stearic acid Figure 5.12 (a) Saturated fat and fatty acid Saturated fatty acids • Have the maximum number of hydrogen atoms possible • Have no double bonds Animal fats are usually saturated fats and solidify at room temperature.

29. Unsaturated fatty acids Figure 5.12 Oleic acid cis double bond causes bending (b) Unsaturated fat and fatty acid • Have one or more double bonds between carbons • This structure means that they have fewer hydrogens than the saturated fats; these are called unsaturated fats. • Unsaturated fats can be found in plants (olive oil, peanut oil, corn oil) more commonly than animals • Usually liquids at room temperature. • We can't make unsaturated fats, so we need to eat small amounts of unsaturated fats. • Polyunsaturated fats have more than one double bond.

30. Functions of Fats • Triglycerides (fats and oils) are a concentrated source of energy. • When the fat is combined with oxygen, the fats release a large amount of energy, more than twice as much per gram as carbohydrates. • Seeds store triglycerides, animals store energy as fat for lean seasons or migration or insulation, humans store fat under the skin and around internal organs. • Fat serves for insulation and flotation. • Storage fat serves as padding in your fingers and your bottom.

31. PHOSPHOLIPIDS: Important components of cell membranes • Have only two fatty acids • Have a phosphate group instead of a third fatty acid (attached to the glycerol) • Consists of a hydrophilic “head” and hydrophobic “tails”

32. Importance of phospholipids • The structure of phospholipids • Results in a bilayer arrangement found in cell membranes

33. Other Biologically Important Groups of Lipids Glycolipids: The third carbon in the glycerol molecule isn't bound to a phosphate group. Instead, it is bonded to a short carbohydrate chain (1-15 monosaccharides). The carbohydrate head is hydrophilic; thus glycolipids behave in the same way as phospholipids. They are also important components of the cell membrane.

34. Other Biologically Important Groups of Lipids Waxes: Waxes are similar in structure to triglycerides, but instead of glycerol there is a long chain alcohol. Because of their hydrophobic quality, waxes are found in many living things that need to conserve water. Insects have waxy cuticles, plants have wax on their leaves, fruit skins and petals have wax as an outer covering.

35. Steroids Steroids are not really that structurally similar to fatty acids or lipids. Since they are hydrophobic, however, they are called lipids. All steroids have four linked carbon rings. Steroids have a tail and many have an -OH group.

36. H3C CH3 CH3 CH3 CH3 HO Figure 5.15 Steroids • Cholesterol-  A major constituents of the cell membrane. When bombarded with ultraviolet light, it rearranged into vitamin D. When modified slightly, it makes sex hormones.

37. Steroids

38. Proteins • Concept 5.4: Proteins can be folded into many shapes, resulting in a wide range of functions • Proteins have many roles inside the cell • Proteins are large, complex organic molecules that are made of smaller monomer units, amino acids. • Proteins are naturally occurring biological molecules that are composed of amino acid monomers linked together through dehydration (condensation) reactions. • Amino Acids are the building blocks (monomers) of proteins. • There are 20 different amino acids.

39. Table 5.1 An overview of protein functions

40. Basic Structure of an Amino Acid Each amino acid has a carbon with four different groups attached. (1) Amine group, NH2 ,  (basic, can accept H+ and thus have a positive charge). (2) Carboxyl group, -COOH, acidic, can donate H+ and thus have a negative charge (-COO-) (3) Hydrogen (4) R group: (“variable” group) The R group is the portion of the amino acids that is different in each amino acid. In the amino acid glycine, the R group is replaced with an H atom.

41. CH3 CH3 CH3 CH CH2 CH3 CH3 H CH3 H3C CH3 CH2 CH O O O O O H3N+ C H3N+ C H3N+ H3N+ C C C C C C H3N+ C C O– O– O– O– O– H H H H H Valine (Val) Leucine (Leu) Isoleucine (Ile) Glycine (Gly) Alanine (Ala) Nonpolar CH3 CH2 S H2C CH2 O NH CH2 C C H2N CH2 CH2 O– CH2 O O O H H3N+ H3N+ C C C C H3N+ C C O– O– O– H H H Phenylalanine (Phe) Proline (Pro) Methionine (Met) Tryptophan (Trp) Figure 5.17 20 different amino acids make up proteins

42. R Groups   The R group of the amino acid determines the physical and chemical properties of the protein. R groups can be nonpolar, polar, acidic, or basic.

43. OH NH2 O C NH2 O C OH SH CH2 CH3 OH Polar CH2 CH CH2 CH2 CH2 CH2 O O O O O O H3N+ C H3N+ C H3N+ C C H3N+ C C H3N+ C C C C C H3N+ C O– O– O– O– O– O– H H H H H H Glutamine (Gln) Tyrosine (Tyr) Asparagine (Asn) Cysteine (Cys) Serine (Ser) Threonine (Thr) Basic Acidic NH3+ NH2 NH+ O– O –O O CH2 C NH2+ C C NH Electrically charged CH2 CH2 CH2 CH2 CH2 O O CH2 CH2 C CH2 C H3N+ C H3N+ C O O– O– CH2 C H3N+ CH2 C H O H O– C C H3N+ CH2 H O O– C C H3N+ H O– H Lysine (Lys) Histidine (His) Arginine (Arg) Glutamic acid (Glu) Aspartic acid (Asp)

44. R Groups They can also be the site of the addition of prosthetic groups, inorganic “add-ons” (vitamins, minerals) that are essential for the functioning of the protein. These prosthetic groups often determine the protein's function, as in hemoglobin. Minerals in our diets are often essential parts of prosthetic groups; for example, iron (Fe2+) in our diet is essential for the synthesis of the heme group the prosthetic group in hemoglobin.

45. Biological Sources and Utilization of Amino Acids How do the cells in the body obtain amino acids? Many foods contain proteins; the proteins are broken down into small pieces called peptides. Peptides are small (about 30 amino acids long) and are carried in the blood vessels. When a cell is actively making proteins, peptides are taken into the cell, broken down, and the constituent amino acids are reconfigured into a protein.

46. Peptidebond OH SH CH2 CH2 CH2 H H H C C H C C N C OH H C OH N N DESMOSOMES H O H O H O (a) H2O OH DESMOSOMES DESMOSOMES Side chains SH OH Peptidebond CH2 CH2 CH2 H H H N OH C C C C C H C N N Backbone H H O O H O Amino end(N-terminus) Carboxyl end(C-terminus) Figure 5.18 (b) Amino Acid Polymers • Amino acids • Are linked by peptide bonds OH

47. Determining the Amino Acid Sequence of a Polypeptide • Proteins have a three dimensional configuration which is determined by the amino acid sequence. • The amino acid sequences of polypeptides • Were first determined using chemical means • Can now be determined by automated machines http://en.wikipedia.org/wiki/Frederick_Sanger

48. Protein Conformation and Function • Proteins can be stringy or globular. The conformation of the protein is its three dimensional shape. • The function of the protein is determined by its conformation. A protein may have four different levels of structure that determine its conformation. • A protein’s specific conformation: • Determines how it functions. This is especially important in ENZYMES (which are all proteins) and HORMONES (many are proteins) that have to FIT specifically with a target cell receptor or with a substrate.

49. Substrate binds to enzyme. 1 Active site is available for a molecule of substrate, the reactant on which the enzyme acts. 2 2 Substrate (sucrose) Glucose Enzyme (sucrase) OH H2O Fructose H O 4 Products are released. 3 Substrate is converted to products. Figure 5.16 Enzymes • Are a type of protein that acts as a catalyst, speeding up chemical reactions

50. Groove (a) A ribbon model Groove (b) A space-filling model Figure 5.19 Two models of protein conformation