1. Chs. 4 & 5 - Carbon and Organic Molecules Why are carbon compounds key to the variety of life?

2.  Although cells are 70-95% water, the rest consists mostly of carbon-based compounds.  Carbohydrates, lipids, proteins and nucleic acids are all composed of carbon atoms bonded to each other and to atoms of other elements. These other elements commonly include hydrogen (H), oxygen (O), nitrogen (N), sulfur (S), and phosphorus (P). A. Introduction

3.  The study of carbon compounds, organic chemistry, focuses on any compound with carbon and hydrogen (organic compounds). Organic compounds can range from the simple (methane - CH 4 ) to complex molecules, like proteins, that may weigh over 100,000 daltons. B. Organic chemistry is the study of carbon compounds Rhodopsin, a protein that acts as a light receptor in the eye http://blog.soton.ac.uk/magres/?page_id=70/ https://en.wikipedia.org/wiki/Methane

4. LINK to Theory of Knowledge:Vitalism – see p. 17 in your IB Biology study guide  Vitalism = theory that “living organisms were composed of organic chemicals that could only produced in living organisms because a ‘vital force’ was needed.”( Allott, p.17 )  “[P]eople thought that 'organic' chemicals…could not be made artificially, but had to be extracted from living animals.”( http://humantouchofchemistry.com/urea-and-the-beginnings-of-organic-chemistry.htm )  How could this theory be tested?

5. Urea’s discovery & synthesis  Hilaire Rouelle discovered urea from urine in 1773. Urea is a simple organic compound.  Friedrich Wohler accidentally created urea in 1828.  THUS, this was the first organic compound that was created artificially and this DISPROVED vitalism http://andromeda.rutgers.edu/~huskey/images/urea.jpg

6.  With a total of 6 electrons, a carbon atom has 2 in the first shell and 4 in the second shell. How many bonds will carbon tend to form? C. Carbon atoms are the most versatile building blocks of molecules Carbon usually completes its valence shell by sharing electrons with other atoms in four covalent bonds.

7. For each molecule below, count the number of bonds surrounding each carbon atom.

8. Hydrocarbons are organic molecules that consist of only carbon and hydrogen atoms.

9.  Fats are biological molecules that have long hydrocarbon tails attached to a non-hydrocarbon component. Hydrocarbon tails

10. 1)molecular formula C 4 H 10 2) SIMILARITY: Same molecular formula DIFFERENCE: butane has a straight skeleton and isobutane has a branched skeleton. Isomers are compounds that have the same molecular formula but different structures and therefore different chemical properties. Study the two molecules to the right. 1)State the molecular formula for butane and iso-butane. 2)State how they are similar and how they are different. Command term: STATE = Give a specific name, value or brief answer without explanation or calculation.

11. 1. What are the six major elements that make up living matter? 2. What kinds of bonds join these elements in living matter? 3. How many covalent bonds does carbon form? The chemical elements of life: a review carbon, oxygen, hydrogen, and nitrogen, with smaller amounts of sulfur and phosphorus. covalent bonds 4

12.  Macromolecules = large molecules (possibly made of 1000’s of atoms) formed when cells join together smaller organic molecules.  Four major classes of macromolecules: Carbohydrates Lipids Proteins Nucleic acids. D. Ch. 5 – Macromolecules Introduction Molecules to scale

13.  Three of the four classes of macromolecules form chainlike molecules called polymers. Polymers consist of many similar or identical building blocks linked by covalent bonds.  The repeated units are small molecules called monomers. Most macromolecules are polymers

14. The reaction that joins monomers to form polymers involves hydroxyl groups  Hydroxyl groups are made of an oxygen (O) bonded to a hydrogen (H) and to the carbon skeleton.  Looks like –OH  The bond between the O and H is a polar covalent bond

15.  Significance of the polar covalent bond in hydroxyl groups Because of these polar covalent bonds, hydroxyl groups improve the solubility of organic molecules. Organic compounds with hydroxyl groups are alcohols and their names typically end in -ol. (e.g., GLYCEROL, ETHANOL)

16.  Condensation (dehydration synthesis) reactions join smaller molecules to form larger molecules with the removal of water. Remember that body builders take ANABOLIC steroids to BUILD their muscles! See macromole app Glycosidic Linkage o One monomer provides a hydroxyl group and the other provides a hydrogen and together these form water. o This process requires energy and is aided by enzymes. o ANABOLIC reactions are those that synthesize complex molecules from simpler molecules.

17.  Hydrolysis reactions break apart larger molecules into smaller ones with the addition of water. In hydrolysis as the covalent bond is broken a hydrogen atom and hydroxyl group(-OH) from a split water molecule attaches where the covalent bond used to be. Hydrolysis reactions dominate the digestive process, guided by specific enzymes. CATABOLISM = the breakdown of complex molecules into simpler molecules.

18. Hydrolysis Song (to the tune of “My Boyfriend’s Back”)  The H’s are back and so are the O’s  Hey-Nah, Hey Nah, HYDROLYSIS  The starch turns to glucose and proteins to aminos  Hey-Nah, Hey Nah, HYDROLYSIS  Hey, it’s DIGESTION in the body  Hey, it’s how we SPLIT the macromole(cules)  The H’s are back and so are the O’s  Hey-Nah, Hey Nah, HYDROLYSIS

19. Review 1.What reaction does the diagram to the right represent? 2. Which molecule represents a monomer? 3.Which molecules represent polymers? 4.What is the source of the H and OH on molecules C and D? 5.What is the opposite reaction to this one? Molecule A Molecule B Molecule CMolecule D hydrolysis Molecule D Molecules A & C H2O/water Condensation reaction/dehydration synthesis reaction

20.  Carbohydrates are organic molecules made from the elements C, H and O.  All carbohydrates have a 2:1 ratio between hydrogen and oxygen.  The simplest carbohydrates are monosaccharides or simple sugars (1 ring).  Disaccharides, double sugars (2 ring), consist of two monosaccharides joined by dehydration synthesis.  Polysaccharides are polymers (many rings) of monosaccharides joined together. E. Carbohydrates HYDRATE refers to WATER = H 2 O (2H:1O)

21.  Monosaccharides, particularly glucose, are a major fuel for cellular work.  While often drawn as a linear skeleton, in aqueous solutions, monosaccharides form rings. Sugars, the smallest carbohydrates serve as a source of energy

22.  Monosaccharides generally have molecular formulas that are some multiple of CH 2 O. For example, glucose has the formula C 6 H 12 O 6. Most names for sugars end in -ose.  Monosaccharides include glucose, galactose and fructose. Sugars, the smallest carbohydrates, serve as a source of energy

23.  Monosaccharides can be classified by the number of carbons in the backbone. Glucose and other six (6) carbon sugars are hexoses. Five (5) carbon backbones are pentoses Three (3) carbon sugars are trioses.

24. What word can we use to describe glucose, galactose and fructose? ISOMERS

25. Draw the molecular structure of a glucose molecule. http://www.dbriers.com/tutorials/2012/11/draw-the-structure-of-glucose-molecule/ NOTE: Each vertex has a carbon atom

26. If carbohydrates have multiple –OH groups, will they tend to be hydrophilic or hydrophobic? Why?  Hydrophilic, because of the polar covalent bonds between the O and H of the –OH groups. Will simple sugars tend to dissolve in water? Why or why not?  Yes, they will dissolve because of their polar nature.

27.  Two monosaccharides can join with a glycosidic linkage to form a disaccharide via dehydration synthesis. Maltose, malt sugar, is formed by joining two glucose molecules. Sucrose, table sugar, is formed by joining glucose and fructose and is the major transport form of sugars in plants. Lactose, milk sugar, is formed by joining glucose and galactose. Several people lack the enzyme to digest this sugar and are “lactose intolerant”. View disaccharides in Macromole

28. Dehydration Synthesis: Glucose +Glucose  Maltose +Water

29. Use what you know to figure out the molecular formula for maltose.  If the molecular formula for glucose is C 6 H 12 O 6 and 2 glucose molecules are needed to synthesize one maltose molecule through dehydration synthesis, what is the molecular formula for maltose? C 6 H 12 O 6 + C 6 H 12 O 6 + H 2 O C 12 H 22 O 11

30.  Dehydration synthesis of sucrose

31. If glucose and fructose are isomers, then what is the molecular formula for sucrose?  Same as maltose: C 12 H 22 O 11

32. Dehydration synthesis/condensation of lactose http://www.indiana.edu/~ensiweb/lessons/tp.1.gif

33. Review Match the disaccharide with the monosaccharides that form each. 1. Maltose 2. Sucrose 3. Lactose A.Glucose + galactose B.Glucose + glucose C.Glucose + fructose B C A

34. Review Match the disaccharide with the descriptions. 1. Transports energy in the phloem of plants 2. Provides energy to baby mammals 3. Has the molecular formula C 12 H 22 O 11 A.Maltose B.Sucrose C.Lactose B C A, B, C

35.  Polysaccharides are polymers of hundreds to thousands of monosaccharides joined by glycosidic linkages.  Functions of polysaccharides: energy storage macromolecule that is hydrolyzed as needed. building materials for the cell or whole organism. Polysaccharides, the polymers of sugars, have storage and structural roles View Starch and Cellulose in Macromole

36.  Plants store starch within plastids, including chloroplasts.  Plants can store surplus glucose in starch and withdraw it when needed for energy or carbon.  Animals that feed on plants, especially parts rich in starch, can also access this starch to support their own metabolism. Plant Polysaccharides include starch and cellulose…

37.  Starch is a storage polysaccharide composed entirely of glucose monomers. One unbranched form of starch, amylose, forms a helix and has only 1,4 linkages. Branched forms, like amylopectin, have both 1,4 and 1,6 linkages. Glucose can load and unload more rapidly since there are more points for glucose to join or detach.

38.  One key difference among polysaccharides develops from 2 possible ring structures of glucose. These two ring forms differ in whether the hydroxyl group attached to the number 1 carbon is fixed above (beta glucose) or below (alpha glucose) the ring plane.

39.  Starch is a polysaccharide of alpha glucose monomers.

40.  Structural polysaccharides form strong building materials.  Cellulose is a major component of the tough wall of plant cells. Cellulose is also a polymer of glucose monomers, but using beta glucose monomers.

42.  The enzymes that digest starch cannot hydrolyze the beta linkages in cellulose. Cellulose in our food passes through the digestive tract and is eliminated in feces as “insoluble fiber”.  Some microbes can digest cellulose to its glucose monomers through the use of cellulase enzymes.  Many eukaryotic herbivores, like cows and termites, have symbiotic relationships with cellulolytic microbes, allowing them access to this rich source of energy.

43.  Animals also store glucose in a polysaccharide called glycogen.  Glycogen is highly branched.  Humans and other vertebrates store glycogen in the liver and muscles, but only have about a one day supply. Insert Fig. 5.6b - glycogen Look at the structure above. Identify whether glycogen is made of alpha or beta glucose monomers. Explain how you know.

44.  Another important structural polysaccharide is chitin, used in the exoskeletons of arthropods (including insects, spiders, and crustaceans). Chitin is similar to cellulose, except that it contains a nitrogen-containing appendage on each glucose.  Chitin also forms the structural support for the cell walls of many fungi. https:// en.wikip edia.org /wiki/N- Acetylgl ucosami ne

45. Try to make a word map for carbohydrates. Target word category example Organic macromolecules carbohydrates monosaccharidesdisaccharidespolysaccharides Is like... Properties are... Is like... Properties are... Contains C, H, & O with 2 H: 1 O ratio Often seen with ring structure Is like... Properties are... Hydrophilic, can join together through dehydration synthesis examples include Are like …

46. Match the term(s) with its (their) description or definition. 1. Used in insect exoskeletons & fungus cell walls 2. Coiled structure 3. Used in plant cell walls 4. Energy storage molecule in plants 5. Energy storage molecule in animals 6. Contains alpha 1-4 glycosidic linkages A.Chitin B.Cellulose C.Glycogen D.Starch/ Amylose A C D, C D B

47.  Lipids are highly diverse in form and function. Examples: fats, waxes, oils, steroids Functions: energy storage, structure, insulation, hormones  The unifying feature of lipids is that they can have little or no affinity for water. (hydrophobic) This is because their structures are dominated by nonpolar covalent bonds.  Lipids have C, H, and O but a H : O ratio greater than 2:1. C. Lipids

48.  Fats are large molecules assembled from smaller molecules by dehydration reactions.  A fat is constructed from two kinds of smaller molecules, glycerol and fatty acids.  One glycerol + 3 fatty acids combine to form a fat molecule + 3 water molecules.  Fats can store large amounts of energy and insulate and cushion organs. Fats are one example of a lipid.

49. Glycerol (an alcohol) consists of a three carbon skeleton with a hydroxyl group (-OH) attached to each…ho-ho-ho… http://appadvice.com/a ppnn/2010/07/dear- santa-ipad

50.  A carboxyl group (-COOH) consists of a carbon atom with a double bond with an oxygen atom and a single bond to a hydroxyl group. Compounds with carboxyl groups are organic acids. A carboxyl group acts as an acid because the molecule can release H + in solution. Fatty acids and amino acids have carboxyl groups.

51. A fatty acid consists of a carboxyl group (-COOH) attached to a long carbon skeleton, often 16 to 18 carbons long. NOTE: Where do the -H and –OH come from for forming water during dehydration synthesis?

52.  The many nonpolar C-H bonds in the long hydrocarbon skeleton make fats hydrophobic.  In a fat, three fatty acids are joined to glycerol by ester linkages, creating a triacylglycerol or triglycergeride.

53.  The three fatty acids in a fat can be the same or different.  Fatty acids may vary in length (number of carbons) and in the number and locations of double bonds. If there are no carbon-carbon double bonds, then the molecule is a saturated fatty acid - a hydrogen at every possible position. Straight chain

54. If there are one or more carbon-carbon double bonds, then the molecule is an unsaturated fatty acid - formed by the removal of hydrogen atoms from the carbon skeleton. Unsaturated fatty acids have a kink (bend) wherever there is a double bond. Monounsaturated fatty acids – have one double bond between the carbons Polyunsaturated fatty acids - have more than one double bond between the carbons

55. Draw a saturated fatty acid 1. Draw a carboxyl (- COOH) group – start with C, then double bond O, then add -OH 2. Draw a carbon chain. 3. Add hydrogen atoms around the carbon chain. C = O _ OH C C C H H H H H H H

56.  Saturated fats... contain saturated fatty acids are solid at room temperature make up most animal fats in a diet may contribute to cardiovascular disease (atherosclerosis) through plaque deposits.  Unsaturated fats... Contain unsaturated fatty acids are liquid are room temperature (known as oils)  The kinks provided by the double bonds prevent the molecules from packing tightly together. Are found in plant and fish fats

57. What is a hydrogenated oil?  Food scientists can break the double bond between the carbons in an unsaturated fatty acid and add hydrogen.  This converts a substance that was liquid at room temperature to a solid at room temperature. http://www.indiana.edu/~oso/Fat/FatImg/Hydrogenation.jpg OIL SHORTENING

58. What is a TRANS fatty acid?  An unsaturated fatty acid can be chemically modified to make it structurally straight and more likely to stick to the walls of the arteries. http://www.indiana.edu/~oso/Fat/trans.html

59. Match the term with its description or definition. 1. Contains more than one carbon- carbon double bonds 2. Contains carboxyl group 3. All carbon atoms in the chain connected by single bonds. 4. Bent molecule that releases H + ions in solution 5. Straight acidic molecule 6. Contains one carbon-carbon double bond. A.Saturated fatty acid B.Polyunsaturated fatty acid C.Monounsaturated fatty acid D.Trans unsaturated fatty acid E. Cis unsaturated fatty acid A, D all A B C B, C, E

60.  Major function = energy storage A gram of fat stores more than twice as much energy as a gram of a polysaccharide. Plants use starch for energy storage when mobility is not a concern but use oils when dispersal and packing is important, as in seeds. Humans and other mammals store fats as long-term energy reserves in adipose cells.  Cushioning for vital organs  Insulation This subcutaneous layer is especially thick in whales, seals, and most other marine mammals. FUNCTIONS of FATS

61. 1. Contrast the use of fats and carbo- hydrates for energy storage in humans.  Fats/lipids contain over twice as much energy per gram than do carbohydrates.  Fats are a more efficient molecule for long term energy storage than carbohydrates.  Carbohydrates are easier to build and take apart. 2. Explain why starch is a polymer and a triglyceride is not.  Starch is made of a chain of glucose molecules, whereas a triglyceride has a carbon backbone of glycerol with three fatty acids attached. It is NOT a chain of glycerols or a chain of fatty acids.

62.  Components of a phospholipid glycerol two fatty acids phosphate group at the third position.  A phosphate group (-OPO 3 2- ) consists of phosphorus bound to four oxygen atoms (three with single bonds and one with a double bond).  The phosphate group carries a negative charge. Phospholipids are major components of cell membranes

63. Amphipathic nature of phospholipids Having a charge on one side of the phospholipid (hydrophilic) and no charge on the other side (hydrophobic) makes this molecule have different personalities on either end. (i.e., Amphipathic) This “double” personality is key to how the structure of a membrane is adaptive to its function of transport for the cell.

64. The interaction of phospholipids with water is complex. The fatty acid tails are hydrophobic (water fearing), but the phosphate group and its attachments form a hydrophilic (water loving) head. Negative charge no charge (nonpolar) Look at this diagram. Which fatty acid is saturated and which is unsaturated? How do you know?

65.  At the surface of a cell, phospholipids are arranged as a bilayer. Again, the hydrophilic heads are on the outside in contact with the aqueous solution and the hydrophobic tails form the core. The phospholipid bilayer forms a barrier between the cell and the external environment.  They are the major component of membranes. Hydrophilic heads Hydrophobic tails Hydrophilic heads

66. Phospholipid Song (to the tune of “Oh My Darling”) Oh, my lipid Phos-pho-lipid Oh, my lipid ‘Round the cell You are made of Fat-ty a-cids And a phos-phate head as well. Add the backbone Made of glyc’rol Add the backbone To join three All together = Phospholipids Make the cells of you and me Oh, my lipid Phos-pho-lipid Oh, my lipid ‘Round the cell Hy-dro-pho-bic Fat-ty a-cids Fear the water they re-pel Oh, my lipid Phos-pho-lipid Oh, my lipid ‘Round the cell Hy-dro-phil-ic Are the phos-phates Touching water, there they dwell

67.  Steroids are lipids with a carbon skeleton consisting of four fused carbon rings. Different steroids are created by varying functional groups attached to the rings. Steroids include cholesterol and certain hormones

68.  Cholesterol, an important steroid, is a component in animal cell membranes.  Cholesterol is also the precursor from which all other steroids are synthesized. Many of these other steroids are hormones, including the vertebrate sex hormones.  While cholesterol is clearly an essential molecule, high levels of cholesterol in the blood may contribute to cardiovascular disease.

69. Try to make a word map for lipids. Target word category example Organic macromolecules lipids FATSPHOSPHOLIPIDSSTEROIDS Is like... Properties are... Is like... Properties are... Contains C, H, & O with H:O ratio much greater than 2:1 hydrophobic Is like... Properties are... Many nonpolar C-H bonds

70. Lipids review 1. True or False: All lipids are fats. 2. What are the three components that are attached to a glycerol molecule in a phospholipid? 3. Sketch a diagram of a phospholipid. Where are these found in a cell? 4. Describe the structure of a steroid. 5. Why is cholesterol such an important steroid? Phosphate, 2 fatty acids 4 fused carbon rings Part of cell membranes, precursor to steroid hormones, too much in blood can cause heart disease Cell membrane

71. What do these have in common? RUBISCO IMMUNOGLOBULINS COLLAGEN in skin SPIDER SILK https://en.wikipedia.org/wi ki/Collagen

72. These functions include  Growth and maintenance building materials  Regulatory roles enzymes, hormones, antibodies  Energy production calories  NOTE: Almost all enzymes in a cell are proteins. These regulate metabolism by selectively accelerating chemical reactions. Proteins Proteins are instrumental in about everything that an organism does.

73. http://pinoykcin.blogspot.com/2011/01/proteins-and-amino-acids.html

74. Diversity of Proteins  Humans have tens of thousands of different proteins, each with its own structure and function.  Each human has his own set of proteins, his proteome.  Each cell has its own proteome, which can change with its environmental conditions. See IB Study Guide p.24

75.  Proteins are the most structurally complex molecules known. Each type of protein has a complex three- dimensional shape or conformation.  All protein polymers are constructed from the same set of 20 monomers, called amino acids.  Polymers of amino acids are called polypeptides.  A protein consists of one or more polypeptides folded and coiled into a specific conformation.

76. Amino Acid/Protein Song: How to draw an amino acid To the tune of “Take a Walk on the Wild Side”

77. Central carbon met a COOH on the way... C C O OH Said he’d be protein for a day....

78. C C O OH Three strong bonds made so far.... Took an H and took an “R”.... H R

79. C C O OH H R They said, “Hey, carbon, take an NH 2 on the side.... N H H They said, “Hey, carbon, take an NH 2 on the side.”

80. And the molecules said, “COOH -- COOH, COOH,...” C C O OH H R N H H

81.  Amino acids consist of four components attached to a central carbon.  These components include a hydrogen atom, a carboxyl group, an amino group, and a variable R group (or side chain). Differences in R groups produce the 20 different amino acids. A polypeptide is a polymer of amino acids connected in a specific sequence C R H C OHOH O N H H Basic amino acid

82.  An amino group (-NH 2 ) consists of a nitrogen atom attached to two hydrogen atoms and the carbon skeleton. Organic compounds with amino groups are amines. The amino group acts as a base because ammonia can pick up a hydrogen ion (H + ) from the solution. Amino acids, the building blocks of proteins, have amino and carboxyl groups.

83.  The twenty (20) different R groups may be as simple as a hydrogen atom (as in the amino acid glutamine) to a carbon skeleton with various functional groups attached.  The physical and chemical characteristics of the R group determine the unique characteristics of a particular amino acid.  These R groups can be hydrophobic, hydrophilic or charged (ionic) Variety of Amino Acids

84.  One group of amino acids has hydrophobic R groups.

85.  A sulfhydryl group (-SH) consists of a sulfur atom bonded to a hydrogen atom and to the backbone. This group resembles a hydroxyl group in shape. Sulfhydryl groups help stabilize the structure of proteins.

86. Another group of amino acids has polar R groups, making them hydrophilic.

87.  The last group of amino acids includes those with functional groups that are charged (ionized) at cellular pH. Some R groups are bases, others are acids.

88.  Amino acids are joined together when a dehydration reaction removes a hydroxyl group from the carboxyl end of one amino acid and a hydrogen from the amino group of another. The resulting covalent bond is called a peptide bond. See Macromole The Peptide Bond

89. Draw two amino acids and then show the condensation/dehydration synthesis reaction to form a dipeptide and water. C R H C OHOH O N H H amino acid C R H C OHOH O N H H + C R H C OHOH O N H C R H C O N H H dipeptide Peptide bond + O-HO-H H water

90.  The repeated sequence (N-C- C) is the polypeptide backbone.  Attached to the backbone are the various R groups.  Polypeptides range in size from a few monomers to thousands. Repeating the process over and over creates a long polypeptide chain. At one end is an amino acid with a free amino group and at the other is an amino acid with a free carboxyl group. DO NOW: Circle the peptide bonds on the polypeptide.

91. Review about amino acids  How are all amino acids the same?  How are amino acids different?  How can living organisms build such a large variety of polypeptides? Central carbon, carboxyl group, amino group, H atom. R group – can be hydrophilic, hydrophobic, electrically charged Change the type and sequence of the amino acids in each chain.

92.  A functional proteins consists of one or more polypeptides that have been precisely twisted, folded, and coiled into a unique shape.  It is the order of amino acids that determines what the three-dimensional conformation will be. We need 3D glasses to appreciate proteins!

93.  A protein’s specific conformation determines its function.  In almost every case, the function depends on its ability to recognize and bind to some other molecule. For example, antibodies bind to particular foreign substances that fit their binding sites. Enzymes recognize and bind to specific substrates, facilitating a chemical reaction. Neurotransmitters pass signals from one cell to another by binding to receptor sites on proteins in the membrane of the receiving cell.

94.  The primary structure of a protein is its unique sequence of amino acids (which amino acid is 1 st,2 nd,etc). Lysozyme, an enzyme that attacks bacteria, consists of a polypeptide chain of 129 amino acids. The precise primary structure of a protein is determined by inherited genetic information in DNA. Macromole Primary Structure

95.  Even a slight change in primary structure can affect a protein’s conformation and ability to function.  In individuals with sickle cell disease, abnormal hemoglobins, oxygen- carrying proteins, develop because of a single amino acid substitution. These abnormal hemoglobins crystallize, deforming the red blood cells and leading to clogs in tiny blood vessels.

97.  The secondary structure of a protein results from hydrogen bonds at regular intervals along the polypeptide backbone. Typical shapes that develop from secondary structure are coils (an alpha helix) or folds (beta pleated sheets).

98.  The structural properties of silk are due to beta pleated sheets. The presence of so many hydrogen bonds makes each silk fiber stronger than steel. Beta pleated sheets look like a folded fan. See Macromole app Beta Sheets and more Beta Sheets

99.  Tertiary structure is determined by a variety of interactions among R groups and between R groups and the polypeptide backbone. These interactions include hydrogen bonds among polar and/or charged areas, ionic bonds between charged R groups, and hydrophobic interactions and van der Waals interactions among hydrophobic R groups.

100.  While these three interactions are relatively weak, disulfide bridges, strong covalent bonds that form between the sulfhydryl groups (SH) of cysteine monomers, stabilize the structure.

101.  Quarternary structure results from the union of two or more polypeptide subunits. o Collagen is a fibrous protein of three polypeptides that are supercoiled like a rope. o This provides the structural strength for their role in connective tissue. See Macromole App Structural: Collagen

102.  Quarternary structure results from the union of two or more polypeptide subunits. Hemoglobin is a globular protein with two copies of two kinds of polypeptides. Hemoglobin also contains a nonprotein heme group containing iron. A CONJUGATED PROTEIN like hemoglobin consists of a protein with a nonprotein substance.

104. Protein Structure Review 1. Results from H bonds at regular intervals along the polypeptide backbone 2. The sequence of amino acids 3. the union of two or more polypeptide subunits 4. Determined by H bonds, ionic bonds & hydrophobic interactions 5. Alpha helix & pleated sheet A.Primary structure B.Secondary structure C.Tertiary structure D.Quaternary structure B A D C&D B

105.  A protein’s conformation can change in response to the physical and chemical conditions.  Alterations in pH, salt concentration, temperature, or other factors can unravel or denature a protein. These forces disrupt the hydrogen bonds, ionic bonds, and disulfide bridges that maintain the protein’s shape.  Some proteins can return to their functional shape after denaturation, but others cannot, especially in the crowded environment of the cell.

107. What levels of structure of a protein can be disrupted while still allowing renaturation to occur?  Maybe quaternary or some tertiary structure

108. What is metabolism?  METABOLISM = the web of all enzyme-catalyzed reactions in a cell or organism

109.  A catalyst is a chemical agent that speeds up the rate of a reaction  It is NOT consumed by the reaction.  An enzyme is a catalytic protein. Therefore it is made of amino acids coiled together with 4  3  2  1 structure. I. Enzymes are proteins that speed up metabolic reactions by lowering energy barriers Click here for HOW ENZYMES WORK animation

110.  Activation energy is the amount of energy necessary to push the reactants over an energy barrier. The difference between the free energy of the products and the free energy of the reactants is the delta G (∆G).

111.  Enzyme speed up reactions by lowering E A.  Enzymes do not change delta G since they act to simply hasten reactions that would occur eventually.

112.  A substrate is a reactant which binds to an enzyme.  When a substrate or substrates binds to an enzyme, the enzyme catalyzes the conversion of the substrate to the product.  Enzyme + Substrate  Enzyme-Substrate Complex  Product +enzyme Sucrase is an enzyme that binds to sucrose and breaks the disaccharide into fructose and glucose. (enzymes end in “ase”) Enzymes are substrate specific animation

113.  The active site of an enzyme is typically a pocket or groove on the surface of the protein into which the substrate fits.

114. Enzymes have complex shapes that determine their function.

115.  The specificity of an enzyme is due to the fit between the active site and that of the substrate.  Substrates fit into enzymes like keys fit into locks…The LOCK and KEY HYPOTHESIS  As the substrate binds, the enzyme changes shape leading to a tighter INDUCED FIT, bringing chemical groups in position to catalyze the reaction. Enzymes have complex shapes that determine their function.

116.  In most cases substrates are held in the active site by weak interactions, such as hydrogen bonds and van der Waal forces. R groups of a few amino acids in the active site catalyze the conversion of substrate to product. The active site is an enzyme’s catalytic center

118.  A single enzyme molecule can catalyze thousands or more reactions a second.  Enzymes are unaffected by the reaction and are reusable.  Most metabolic enzymes can catalyze a reaction in both the forward and reverse direction. The actual direction depends on the relative concentrations of products and reactants. Enzymes catalyze reactions in the direction of equilibrium.

119. You Are My Enzyme (to the tune of “You are my sunshine”  You are my enzyme  My protein enzyme.  You make my cell reactions go!  You are specific,  Reused, unchang-ed  And make substrates change like so.  You are my enzyme  My protein enzyme.  You dwarf the substrates in my cells.  pH and temp’ture  And concentration  Are the factors keeping you well. Catalyst – speeds up reactions Work on reactants called substrates Bigger than substrates pH, temperature and concentration of enzyme and substrate determine the reaction rate of an enzyme

120.  The rate that a specific number of enzymes converts substrates to products depends in part on substrate concentrations.  At low substrate concentrations, an increase in substrate speeds binding to available active sites.  However, there is a limit to how fast a reaction can occur. At some substrate concentrations, the active sites on all enzymes are engaged, called enzyme saturation. The only way to increase productivity at this point is to add more enzyme molecules. * Assume constant enzyme concentration

121. Match the letters to the statements.  http://sahiljhamb.files.wordpress.com/2013/05/substare.jpg http://sahiljhamb.files.wordpress.com/2013/05/substare.jpg http://www.dynamicscience.com.au/tester/ solutions1/biology/enzrates.html 1.All enzymes present are working at maximum rate. 2. Amount of product produced over time with enzyme 3. Reaction rate zero. 3. Amount of product produced over time without enzyme. 4. Inc. substrate conc. leads to increased rxn rate. 5. Substrate concentration is very low. A B C red line D E blue line B C E A D D

122.  Temperature has a major impact on reaction rate. As temperature increases, collisions between substrates and active sites occur more frequently as molecules move faster. However, at some point thermal agitation begins to disrupt the weak bonds that stabilize the protein’s active conformation and the protein denatures. Each enzyme has an optimal temperature.

123. Increased temperature leads to higher kinetic energy and more successful collisions Increased temperature beyond optimum leads to breakage of weak forces holding 3D shape of protein (denaturation). Substrate no longer binds effectively to active site. What are the optimum temperatures of human enzymes and heat-tolerant bacteria?

124.  Because pH also influences shape and therefore reaction rate, each enzyme has an optimal pH too.  This falls between pH 6 - 8 for most enzymes.

125. However, digestive enzymes in the stomach are designed to work best at pH 2 while those in the intestine are optimal at pH 8, both matching their working environments.

126. Salt concentrations  Just as enzymes are affected by charged hydrogen and hydroxide ions, they will be affected by charged salt particles.  There will be an optimal salt concentration for each enzyme.

127. Eggs are proteins that are affected by environmental changes!

129. They can bind permanently or reversibly to the enzyme. Some inorganic cofactors include zinc, iron, and copper.  Examples of organic coenzymes, include vitamins or molecules derived from vitamins. Many enzymes require nonprotein helpers, cofactors, for catalytic activity. (They help the substrate fit into the enzyme) http://www.chem guide.co.uk/organi cprops/aminoacids /enzymes.html

131. Metabolic pathways consist of chains and cycles of enzyme- catalyzed reactions. https://www.studyblue.com/notes/note/n/microbial- metabolism-/deck/10602 http://newenglandconsortium.org/for- professionals/acute-illness-protocols/urea- cycle-disorders/neonate-infant-child-with- hyperammonemia/

132.  Binding by inhibitor molecules prevent enzymes from catalyzing reactions.  If the inhibitor binds to the same site as the substrate, then it blocks substrate binding via competitive inhibition.  Carbon monoxide is a competitive inhibitor blocking oxygen’s active site in hemoglobin. J. Control over enzyme action

133. http://mednhealth.com/carbon-monoxide-poisoning.html

134.  If the inhibitor binds somewhere other than the active site, it blocks substrate binding via noncompetitive inhibition.  Binding by the inhibitor causes the enzyme to change shape, rendering the active site less effective or completely unable to bind the substrate and catalyze the reaction. Enzymes that can change their shape are called ALLOSTERIC.

135. http://www.tokresource.org/tok_classes/biobiobi o/biomenu/enzymes/

136. Inhibition helps explain negative feedback cycles! The end product becomes the inhibitor that ultimately stops the reaction. This is a way to maintain homeostasis…

137. Use of Immobilized enzymes in Industry  Enzymes can be attached to a solid substrate, such as a bead or a filter.  The production of lactose- free milk uses immobilized enzymes.  Lactose in the milk is digested to glucose and galactose sugars that do not cause gas and bloating of lactose in those who are lactose intolerant. http://ib.bioninja.com. au/_Media/lactose- free_milk_med.jpeg

138. What is the advantage of immobilized enzymes in industry?  Can keep reusing the same enzymes for many substrates.  This saves money. http://www.abpischools.org.uk/page/modules/ enzymes/enzymes8.cfm?coSiteNavigation_allTo pic=1

139. Review: Enzyme Activity

140. Give five factors that affect the activity of enzymes  Temperature  pH  Salt concentration  Enzyme concentration  Substrate concentration  Presence of inhibitors

141. What are the two products when hydrogen peroxide is in the presence of peroxidase (catalase)?  Water  Free oxygen

142. Why does the paper disc float as a result of this reaction?  Bubbles of the free oxygen that is released as a product of H 2 O 2 decomposition stick to the paper disc and make it rise.

143. What happens when enzyme shape is altered?  the active site could become denatured and the substrate would no longer fit so the reaction rate would decrease.  If the enzyme started in another configuration (not optimal), the active site could be renatured and the reaction rate would increase. http://www.dls.ym.edu.tw/ol_biology2/ultr anet/Denaturing.gif

144. In a reaction with catalase and hydrogen peroxide, which graph represents the results if a competitive inhibitor is introduced? Time Amount of product Action with no inhibitor

145. In order to maintain the initial rate of an enzymatically controlled reaction, which of the following should be done?  A) add more enzyme  B) increase the temperature  C) add more substrate  D) change the pH  E) more than one of the above

146. In order to increase the initial rate of an enzymatically controlled reaction, which of the following should be done?  A) add more enzyme  B) increase the temperature  C) add more substrate  D) lower the pH to 1  E) more than one of the above Explain how those factors increase the reaction rate.

147. In a reaction with catalase and hydrogen peroxide, which one acts as the substrate?  Hydrogen peroxide  Catalase  Water  Oxygen

148. If a lab group accidentally poured more than 50 mL of buffer into the graduated cylinder, what would you expect to happen?  Reaction rate would increase because of the presence of more substrate molecules.  Reaction rate would increase because of a higher concentration of enzyme on the disk.  Reaction rate would decrease because of a lower concentration of substrate.  Reaction rate would decrease because the enzyme would be denatured.

149. Which arrow represents the activation energy without enzyme? a b c a b c

150. Which arrow represents the change in free energy (∆G)? a b c a b c

151. Which arrow represents the activation energy with enzyme? a b c a b c

152. What is the optimal temperature range for this enzyme? A. 0-10 B. 35-45 C. 10-20 D. 25-35

153. Why is the rate of reaction zero when the temperature reaches 48 degrees? A. There is no more substrate to catalyze. B. The enzyme is completely denatured. C. The pH level becomes toxic to the reaction. D. The weak hydrogen and ionic bonds holding the enzyme’s conformation are broken. E. more than one of the above 0

154. Which line represents the action of toothpickase under colder temperatures than the control group? A B C Explain why…

155. Which line represents the action of toothpickase under warmer temperatures than the control group? A B C Explain why…

156. Which line represents the action of toothpickase in the presence of a competitive inhibitor? A B C Explain why…

157. Which line represents the action of toothpickase when the amount of enzyme is doubled? A B C Explain why…

158. Which line represents the action of toothpickase in when 100 toothpicks rather than 50 were on the paper plate? a b c Explain why…

159.  There are two types of nucleic acids: ribonucleic acid (RNA) and deoxyribonucleic acid (DNA)  Adenosine triphosphate (ATP) is a building block for RNA.  DNA provides direction for its own replication.  DNA also directs RNA synthesis and, through RNA, controls protein synthesis.  ATP is the key molecule of energy used by the cell. Nucleic acids store and transmit hereditary information

160.  Each nucleotide consists of three parts: a nitrogen base, a pentose sugar, and a phosphate group. Nucleic acids, like DNA and RNA, have negatively charged phosphate groups which allow them to be drawn towards a positive charge in an electric field. One function of phosphate groups is to transfer energy between organic molecules, as with ATP, a nucleotide. A nucleic acid strand is a polymer of nucleotides http://study.com/academy/lesson/nucleic-acids-function-structure-quiz.html

161. Remember: Thy-Cy-Py

162.  The nitrogen bases, rings of carbon and nitrogen, come in two types: purines and pyrimidines. Pyrimidines have a single six- membered ring. The three different pyrimidines, cytosine (C), thymine (T), and uracil (U) differ in atoms attached to the ring. Purines have a double ring: a six- membered ring joined to a five- membered ring. The two purines are adenine (A) and guanine (G).

163.  The five carbon sugar joined to the nitrogen base is ribose in nucleotides of RNA and deoxyribose in DNA. The only difference between the sugars is the lack of an oxygen atom on carbon two in deoxyribose. The combination of a pentose sugar and nitrogenous base is a nucleoside.  The addition of a phosphate group creates the building block known as a nucleotide.

164. Draw the pentose sugar ribose  Start with a pentagon with an O at the top vertex.

165.  Nucleic acids are synthesized using dehydration synthesis.  The process occurs by connecting the sugars of one nucleotide to the phosphate of the next with a phosphodiester link.  This creates a repeating backbone of sugar-phosphate units with the nitrogen bases as rungs.

166. Circle 2 more nucleotides.

167.  An RNA molecule is single polynucleotide chain which is a single helix.  DNA molecules have two polynucleotide strands that spiral around an imaginary axis to form a double helix. The double helix was first proposed as the structure of DNA in 1953 by James Watson and Francis Crick. Inheritance is based on replication of the DNA double helix http://static.planetminecraft. com/files/resource_media/sc reenshot/1336/dna_6339076 _lrg.jpg

168. List at least 3 similarities between DNA and RNA  Both are made up of chains of nucleotides, each of which is made up of a phosphate group, a pentose sugar, and a nitrogenous base.  Both contain the N-Bases adenine, guanine, and cytosine.  Both contain a sugar-phosphate backbone.  Both are negatively charged because of the phosphate groups.

169. Contrast DNA and RNA in at least 3 ways Characteristic DNARNA # of strands21 N-basesThymineUracil Pentose (5- carbon) sugar DeoxyriboseRibose FunctionCodes for RNACodes for polypeptide Location in eukaryotic cell Nucleus, mitochondria, chloroplasts Nucleus and cytoplasm