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

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 H2O

Glucose C6H12O6

Ammonia NH3

Oxygen Gas O2

Methane CH4

Glycine NH2CH2COOH

ŻŹReturn to the program. List the four categories of biologically important organic compounds.

1. 3.

2. 4.

Section 2 – Functional Groups

Define a functional group:

3.2

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

Acid (Carboxyl) -COOH

Amino -NH2

Phosphate -PO42-

O H

ŻŹReturn to the program. 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: ŻŹReturn to the program.

N H H

O P O

O

O

Section 3 – From Building Blocks to Macromolecules

C O

O H

3.3

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

ŻŹReturn to the program.

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)

ŻŹReturn to the program.

3.4

Examine the examples of the carbohydrates in the following table. Name Chemical formula Name Chemical formula

Erythrose C4H8O4 Glucose C6H12O6

Ribose C5H10O5 Fructose C6H12O6 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! ŻŹReturn to the program.

3.5

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? ŻŹReturn to the program. 3.6

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. ŻŹReturn to the program.

3.7

Section 5 – Lipids

Define a lipid: List four examples of molecules that are included in the lipid category.

1) 3)

2) 4)

ŻŹReturn to the program. 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. __________________________ __________________________ __________________________ __________________________ ŻŹReturn to the program. Triglycerides Define a saturated fat: Define an unsaturated fat: What makes a triglyceride either a fat or oil?

3.8

Complete the drawing of the structural formula for a generic triglyceride as shown in the program.

H H C ŻŹReturn to the program. Phospholipids How does a phospholipid differ from a triglyceride? On the diagram of a phospholipid at the right label the:

x hydrophilic end x 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. ŻŹReturn to the program.

H

CH

C

O

O

H O

3.9

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 ŻŹReturn to the program.

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? ŻŹReturn to the program.

3.10

Building a dipeptide. Define a peptide bond: Is this a covalent or hydrogen bond? ______________ Is it a strong or weak bond? ______________ ŻŹReturn to the program. Using your molecular model kit, build the two following amino acids.

glycine alanine ŻŹReturn to the program. 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

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? _______________ ŻŹReturn to the program. 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

ŻŹReturn to the program.

3.12

Section 8 – Roles of Biologically Important Organic Molecules

Molecule Examples Role

Carbohydrates

Glucose

Starch

Glycogen

Cellulose

Lipids

Triglycerides

Phospholipids

Cholesterol

Nucleic Acids DNA

RNA

Proteins Fibrous

Enzymes

ŻŹReturn to the program. 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. ŻŹReturn to the program.

3.13

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? _____ ŻŹReturn to the program.

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:

TYROSINASE 2C6H6O2 + O2 2C6H4O2 + 2H2O

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

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? ______ ŻŹReturn to the program. 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

Test Tube Experimental Temperature in oC

Enzyme Activity (0 = not yellow, + = slightly yellow,

++ = moderately yellow, +++ = strongly yellow)

A

B

C

15. Using this data, graph your results. (Hint: remember how you made your graph last

week.)

10 20 30 40 50 60 70 80 90 Temperature oC

+++

Enzy

me

Act

ivity

++

+

0

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

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. 5 4 2 1 3 b. 4 5 2 3 1 c. 5 4 1 2 3 d. 3 1 2 5 4 e. 4 5 2 1 3

2. Which of the following molecules is organic?

a. H2O b. NH3 c. CH4 d. CH3OH 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

7. Label the molecules or groups with their correct names.

3.18

Molecule/group name a.

b.

c.

d.

e.

f.

C5H10O5

g.

C O

O H