Lab 3 Organic Molecules of Biological Importance

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1 Name Biology 3 ID Number Lab 3 Organic Molecules of Biological Importance Section 1 - Organic Molecules Section 2 - Functional Groups Section 3 - From Building Blocks to Macromolecules Section 4 - Carbohydrates Section 5 - Lipids Section 6 - Nucleic Acids Section 7 - Proteins Section 8 - The Roles of Biologically Important Organic Molecules Section 9 - Enzymes and Denaturation Section 10 -The Effect of Temperature on Enzyme Activity Objectives Upon completion of this laboratory exercise, you should be able to: 1. Recognize the difference between organic and inorganic compounds from both chemical and structural formulas. 2. Recognize the various functional groups and the macromolecules in which they are found. 3. Recognize the four categories of biologically important molecules (carbohydrates, lipids, proteins, and nucleic acids) from their chemical and structural formulas as well as their building blocks. 4. Differentiate between anabolic and catabolic reactions, dehydration (condensation) and hydrolysis, as well as endergonic and exergonic reactions. Be able to relate these processes to complexity, water, and energy. 5. Define saccharide, monosaccharide, disaccharide, polysaccharide, starch, and glycogen. 6. Describe the difference between saturated fatty acids and unsaturated fatty acids. 7. Recognize an emulsion and the hydrophobic and hydrophilic portions of phospholipids. 8. Define a peptide bond. 9. Recognize diagrams and descriptions of the four levels of protein complexity. 10. Recognize the major roles of carbohydrates, lipids, proteins, and nucleic acids in living organisms. 11. Define denaturation as it relates to enzyme activity and protein complexity. 12. Recognize the effect of temperature on the structure of a protein and how it affects the rate of enzyme activity. 13. In a given experiment, list the experimental variable and the controlled variables. 14. Analyze the results of an experiment. 3.1

2 Section 1 Organic Molecules Define organic molecule: How do organic molecules differ from inorganic molecules? For each of the molecules in the table below, determine if they are organic or inorganic. Substance Chemical Formula Organic or Inorganic? Water H 2 O Glucose C 6 H 12 O 6 Ammonia NH 3 Oxygen Gas O 2 Methane CH 4 Glycine NH 2 CH 2 COOH List the four categories of biologically important organic compounds Section 2 Functional Groups Define a functional group: 3.2

3 For each of functional groups listed in the table below, list the category of biologically important molecules in which you would find them. Functional Group Chemical Formula Structural Formula Categories where you would find these functional groups Hydroxyl -OH O H Acid (Carboxyl) -COOH Amino -NH 2 C O N H H O H O Phosphate -PO 4 2- O P O O Section 3 From Building Blocks to Macromolecules Define dehydration: The organic molecules we will study are all produced by bonding together smaller building blocks. In the diagram above circle the atoms you need to remove to bond the subunits together. In the diagram above circle the bonds that were formed. In this example, how many water molecules were formed? Define an anabolic reaction: 3.3

4 What molecule would you need to add to break the subunits apart? Describe the difference between dehydration (condensation) and hydrolysis. Define a catabolic reaction: Define an endergonic reaction: Define an exergonic reaction: Match the following relationships by circling the correct answer. Complexity Energy Dehydration (Condensation) Anabolic or Catabolic Endergonic or Exergonic Hydrolysis Anabolic or Catabolic Endergoinc or Exergonic Section 4 Carbohydrates In this section you will be using your molecular model kits to build two molecules which will be used later in the section. If you leave lab in the middle of this section, you will need to build the molecules again! Briefly describe a carbohydrate. List four examples of molecules that are included in the carbohydrates. 1) 3) 2) 4) 3.4

5 Examine the examples of the carbohydrates in the following table. Name Chemical formula Name Chemical formula Erythrose C 4 H 8 O 4 Glucose C 6 H 12 O 6 Ribose C 5 H 10 O 5 Fructose C 6 H 12 O 6 Summarize the numerical relationship among the three elements; this same numerical relationship is found in all monosaccharides. C H O Monosaccharide: the building block of the carbohydrates. Using the molecular model kit build a molecule of glucose. This will be easier if you: 1) remember to only use short bonds when attaching an atom of hydrogen, and 2) build the ring structure first. Step one, build the ring: Use all long bonds here! Step two, add the side groups: Use long bonds for oxygen and short bonds for hydrogen! GLUCOSE Save your glucose model, you will need it later! 3.5

6 Define the following: Saccharide Monosaccharide Disaccharide Polysaccharide Using the remaining pieces in your molecular model kit, construct a molecule of fructose. Step one - build the ring: Use all long bonds here! Step two - add the side groups: Use long bonds for oxygen and short bonds for hydrogen! FRUCTOSE How do glucose and fructose compare: Do they have the same elements? Do they have the same number of atoms of each element? How are the molecules different? 3.6

7 Using dehydration (condensation) reactions to build macromolecules. By combining your glucose and fructose models you will build sucrose. Study the following molecules of glucose and fructose. When you combine them using dehydration, what three atoms would you need to remove? What molecule would be produced when the three atoms are combined? Will the reaction combining glucose and fructose into sucrose be anabolic or catabolic? On the diagram, circle the three atoms you will remove. Now combine your models of glucose and fructose, to produce sucrose. Using your model of sucrose, fill-in the three missing atoms (boxes) and draw in the two missing bonds. + Take your model to the instructor to have it checked. 3.7

8 Section 5 Lipids Define a lipid: List four examples of molecules that are included in the lipid category. 1) 3) 2) 4) The building block of lipids. Identify each of the following structural formulas for the building blocks of a triglyceride or phospholipid as shown in the program. Triglycerides Define a saturated fat: Define an unsaturated fat: What makes a triglyceride either a fat or oil? 3.8

9 Complete the drawing of the structural formula for a generic triglyceride as shown in the program. H H H H C C C H O O O Phospholipids How does a phospholipid differ from a triglyceride? On the diagram of a phospholipid at the right label the: hydrophilic end hydrophobic end Describe the role of an emulsifying agent. Draw the arrangement of an emulsifying agent surrounding a lipid droplet. Describe how this arrangement allows lipids to move through solutions such as your blood. 3.9

10 Section 6 Nucleic Acids List two examples of nucleic acids. 1) 2) The nucleotide is the building block of nucleic acids. It is composed of three subunits, a sugar (either deoxyribose or ribose), a phosphate group, and a nitrogenous base. In the diagram of the nucleotide, label the: Phosphate group, Sugar, and the Nitrogenous Base Section 7 Proteins Define a protein: Amino Acid: the building block of proteins. Draw the general structural formula for an amino acid. Label the amino end and the acid (carboxyl) end of the molecule. What does the R represent? 3.10

11 Building a dipeptide. Define a peptide bond: Is this a covalent or hydrogen bond? Is it a strong or weak bond? Using your molecular model kit, build the two following amino acids. glycine alanine When you combine them into a dipeptide using dehydration, what three atoms would you need to remove? On the diagram of the two amino acids above, circle the three atoms you will remove. What molecule would be produced when the three atoms are combined? Will the reaction combining alanine and gylcine into the dipeptide be anabolic or catabolic? Will it be dehydration (condensation) or hydrolysis? 3.11

12 If you were to eat a dipeptide such as the one you built, your digestive system would have to break it down. What molecule would your body have to add to the dipeptide in order to break it down? Will the reaction be anabolic or catabolic? Will it be dehydration (condensation) or hydrolysis? Find the display of Levels of Protein Complexity and complete the table below. Level of Complexity Brief Written Description Type of Bond Diagrammatic Representation Primary Secondary Tertiary Quaternary 3.12

13 Section 8 Roles of Biologically Important Organic Molecules Molecule Examples Role Glucose Carbohydrates Starch Glycogen Cellulose Triglycerides Lipids Phospholipids Cholesterol Nucleic Acids Proteins DNA RNA Fibrous Enzymes Section 9 Enzymes and Denaturation Let s look at a chemical reaction and the role of an enzyme a little more closely. In the following diagram label the reactants, the enzyme, the enzyme active site, and the product as shown in the program. 3.13

14 As you have seen, proteins are very complex molecules. They have very specific shapes and perform very specific tasks in living organisms. Their shape relies on the bonds between the amino acids. From building your dipeptide, you know that you formed a covalent bond. These strong bonds between the amino acids establish the primary structure of a protein. The secondary, tertiary, and quaternary structures are held in place by hydrogen bonds between portions of the molecule; in many cases the hydrogen bonds form through interactions of atoms within the R groups. Are hydrogen bonds strong or weak? Certain conditions such as extreme ph or high temperature can break hydrogen bonds. Which levels of protein complexity will be affected by denaturation?,, and If an enzyme, which is a protein, loses its specific shape, it will no longer function and the protein is said to be denatured. Last week, did you find evidence that certain ph solutions could denature the protein tyrosinase? Section 10 The Effect of Temperature on Enzyme Activity Last week you performed an experiment to determine the effect of ph on enzyme activity. Here is the reaction: 2C 6 H 6 O 2 + O 2 TYROSINASE 2C 6 H 4 O 2 + 2H 2 O PYROCATECHOL OXYGEN QUINONE WATER Take a minute to review what you discovered last week. List the reactants for this reaction: and. List the products for this reaction: and. 3.14

15 List the enzyme for this reaction:. Which product was yellow in color?. This color change told you if there was a reaction and if so, how active the enzyme was. Was the enzyme active at all ph levels? Now that you have reviewed, you will perform an experiment to determine if changing the temperature will affect the activity of the enzyme tyrosinase. 1. Obtain three clean test tubes and a wooden test tube holder. 2. Using the wax pencils provided, label the tubes A, B, and C. Also place your initials or some identifying mark on each tube so you will be able to identify your tubes. 3. Fill each tube ¼ full of D.I. water. Note: This is a smaller volume than last week. 4. To each tube add 10 drops of tyrosinase (enzyme). 5. Place tube A in the cold water bath. 6. Place tube C in the hot block. 7. Keep tube B in the wooden holder (take it with you to your desk). 8. Leave the tubes in each respective temperature for a full 10 minutes. This will allow the water/tyrosinase mixture to equilibrate to each temperature. 9. After the 10 minutes, leave the tubes in the cold water bath and the hot block; add 10 drops of pyrocatechol to each tube. 10. Allow the tubes to remain at each temperature for an additional 2 minutes. 11. Remove the tubes and immediately compare them to the standards on display. Remember you will need to look directly down the tube (hold them over a white background) to determine the color of the solution. 12. Record your results in the following data table. 13. Also record the temperature for each tube. The cold water bath and hot block temperatures are given to you on the front of the bath and block. You will need to read the room temperature on the digital thermometer on the demonstration table. 14. Save your tubes to be checked by the instructor with your completed table and graph. 3.15

16 Test Tube A B C Experimental Temperature in o C Enzyme Activity (0 = not yellow, + = slightly yellow, ++ = moderately yellow, +++ = strongly yellow) 15. Using this data, graph your results. (Hint: remember how you made your graph last week.) Enzyme Activity Temperature o C 16. Bring your tubes to the instructor to have your tubes and graph checked. 17. When you have had the instructor sign off your experiment, wash your test tubes, wipe off your wax pencil marks and return them and your wooden block to their proper locations. 18. Complete the following questions regarding this experiment. Analysis of your experiment and data: What variable were you testing in this experiment? (Hint: What was different for each tube?) What variables are you holding constant in the experiment? At which experimental temperature was there no enzyme activity? How do you know there was no activity? Why is there no activity? (Hint: What happens to hydrogen bonds at high temperatures?) Why is there less activity in the coldest temperature? (Hint: Increasing temperature increases the amount of energy available.) 3.16

17 Self Test 1. Arrange the following in order from smallest, least complex, to largest, most complex. 1. amino acid 2. nitrogen atom 3. protein molecule 4. electron 5. hydrogen atom a b c d e Which of the following molecules is organic? a. H 2 O b. NH 3 c. CH 4 d. CH 3 OH e. both c and d are organic 3. When you break sucrose into glucose and fructose this would be a(n): a. anabolic reaction b. catabolic reaction c. dehydration reaction d. hydrolysis reaction e. both b and d are correct 4. Lipids can be carried in solution by: a. enzymes b. phospholipids c. monosaccharides d. steroids e. activation energy 5. When you chemically combine (bond) two amino acids together you produce a: a. dipeptide b. peptide bond c. molecule of water d. all of these 6. Which of the following relationships is mismatched? a. Nucleotides nucleic acids b. Steroids triglycerides c. Amino acids proteins d. Monosaccharides ---- polysaccharides 3.17

18 7. Label the molecules or groups with their correct names. Molecule/group name a. b. c. d. e. f. C O O H C 5 H 10 O 5 g. 3.18