Student learning outcomes

At the completion of this exercise, the student will be able to:

1. Discuss the role of chemistry in the biological sciences.2. Define elements, atoms, atomic number, atomic mass, and isotopes.3. Define compounds and molecules.4. Differentiate among ionic, covalent, and hydrogen bonds.5. Distinguish between inorganic, organic, and biochemistry.6. Define solution, aqueous solution, solvent, and solute.7. Define and describe the properties of an acid and a base.8. Determine the pH of a substance.9. Define and describe the characteristics of carbohydrates. 10. Discuss the composition and functions of monosaccharaides, disaccharides and

polysaccharides. 11. Perform the Benedict’s Test for the presence of a reducing sugar.12. Perform the Iodine Test for the presence of starch.13. Define and describe the characteristics of lipids.14. Perform the Grease-Spot Test for the presence of a lipid.15. Perform the Sudan Test for the presence of lipid.16. Define and describe the characteristics of proteins.17. Perform the Biuret Test for the presence of a protein.18. Define and describe the characteristics of nucleic acids.

OVERVIEW

To develop a meaningful understanding of biology, a fundamental knowledge of chemistry is necessary (Fig. 5.2). Chemistry is the study of the composition, structure, properties, and interaction of matter. Matter is anything that occupies space and has mass. Matter, whether it is this page, a meteorite or a gallstone, is composed of elements. An element is a substance that cannot be broken down into other substances by ordinary chemical means. Although more than 112 elements have been described only 92 elements are naturally occurring; the others are human-made.”

Of the naturally occurring elements, approximately 25 are common to living systems. A typical human is composed of 65% oxygen (O), 18.5% carbon (C), 9.5% hydrogen (H), and 3.2% nitrogen (N). Other important elements in humans and other living systems include

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CHAPTER 5. CHEMISTRY: UNDERSTANDING THE COMPOSITION OF LIVING THINGS

phosphorus (P), sulfur (S), calcium (Ca), potassium (K), sodium (NA), chorine (Cl), magnesium (Mg), iron (Fe), and silicon (Si).

Elements are composed of atoms. An atom is the smallest part of an element that retains the properties of that element. Atoms are composed of a variety of subatomic particles, the best known of which are protons, neutrons, and electrons. Positively charged protons and uncharged neutrons can be found in the nucleus negatively charged electrons exist in orbitals surrounding the nucleus.

The atomic number of an element reflects the number of protons in the nucleus. For example, copper (Cu) has an atomic number of 29. The atomic mass of an element indicates the number of protons plus the number of neutrons in the nucleus. The atomic mass of copper is 63.546.The Atomic number mass reflects that the number of neutrons can vary in the nucleus. Atoms that have same number of protons and a varied number of neutrons are called isotopes. For example, the element tin (Sn) has 10 isotopes. Many isotopes are radioactive.

A molecule results from the chemical union of two or more atoms. Some molecules are simple, such as a molecule of oxygen (O2) and a molecule of water (H2O). Others are quite large, such as a molecule of chlorophyll (C55H72O5N4Mg). Compounds are molecules composed of different elements. Water and chlorophyll are compounds. Other examples of compounds are glucose (C6H12O6), hydrogen peroxide (H2O2), baking soda (NaHCO3) and ethyl alcohol (C2H5OH).

Atoms combine with other atoms by means of chemical bonds. Ionic compounds such as salt (NaCl) are held together by an attraction between positively and negatively charged ion. This loss or gain of electrons forms an ionic bond. When placed in water, ionic compounds dissociate (dissolve).

1) Covalent bonds - result from sharing of electrons. Covalent bonds are strong and are common in living systems.

2) Nonpolar covalent bonds - involve an equal sharing of electrons. Nonpolar covalent bonds between carbon and hydrogen from a stable framework for building larger molecules such as octane (C8H10).

3) Polar covalent bonds - involve an unequal sharing of electrons.

The most important polar molecule to life on Earth is water (H2O). Hydrogen bonds are weak bonds between the positively charged region of a hydrogen atom of a polar covalent molecule and the negatively charged region of oxygen or nitrogen of another polar covalent molecule. Hydrogen bonds give shape and three-dimensional structure to complex molecules such as proteins. Hydrogen bonds also provide water with several special properties.

In this chapter we divide the discussion of chemistry in inorganic chemistry and organic chemistry. Inorganic chemistry addresses chemical principles excluding the special properties of carbon. Organic chemistry addresses chemistry involving the special

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properties of carbon. Biochemistry, the study of the chemistry of life, will be discussed in late chapters.

EXERCISES IN INORGANIC CHEMISTRY

Understanding acids and bases

A solution is a liquid composed of a uniform mixture of two or more substances . In a solution, the dissolving medium is the solvent, and the dissolved substance(s) is the solute. One of the unique properties of water is that it is an excellent solvent. An aqueous solution uses water as the solvent. Some inorganic molecules are held together by ionic bonds. In an aqueous solution, these substances undergo dissociation and produce positive and negative ions. For example, sodium chloride (NaCl) dissociates into sodium ions (Na) and chloride ions (Cl). Substances that release ions in an aqueous solution are called electrolytes. Other biologically important electrolytes include potassium chloride (KCl), calcium chloride (CaCl2), and sodium bicarbonate (NaHCO3).

Although many people think that acids and bases are chemicals that are best left in the laboratory, many common substances are classified as acids or a base. These substances can be important and, in some instances, potentially dangerous to living systems.

Both inorganic and organic acids are common in nature. An acid is a substance that yields (donates) a hydrogen ion in solution. Acids share a number of structural characteristics and properties.

(1) Acids contribute one or more hydrogen atoms to a solution when they dissociates in water

(2) Acids have a sour taste. (Don’t taste unknown chemicals)(3) Acids may be corrosive or poisonous.(4) Acids react with certain metals to liberate hydrogen.(5) Acids neutralize bases.(6) Acids affect the color of certain indication.

Several common inorganic acids are:

Sulfuric acid (H2SO4)Nitric acid (HNO3)Phosphorous acid (H3PO4)Hydrochloric acid (HCl)

Some common organic acids are:Citric acid (lemon juice)Acetic acid (vinegar)Carbonic acid (carbonated water)Malic acid (apple juice)Formic acid (bee stings)Lactic acid (sour milk)

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Bases are commonly known as alkalines. These chemicals share several structural characteristics and properties.

(1) Bases decrease the hydrogen ion concentration of their aqueous solution or release hydroxide ions (OH-) in solution.

(2) Bases have a bitter taste.(3) Bases feel slippery.(4) Bases may be corrosive or poisonous.(5) Bases neutralize acids.(6) Bases affect the color of certain indicators.

Some common bases are sodium hydroxide (NaOH), calcium hydroxide (Ca(OH)2), and magnesium hydroxide (Mg(OH)2). Examples of industrial bases are potassium hydroxide, barium hydroxide, and strontium hydroxide.

Chemists use a variety of indicators to determine if a substance is an acid or a base.

(1) Acids turn blue litmus indicators, red, are colorless in phenolphthalein, and turn methyl orange indicator red.

(2) Bases turn red litmus indicators blue, turn phenolphthalein pink, and turn methyl` orange indicator yellow.

Using natural pH indicators

One of the most interesting properties of acids and bases is their ability to change the color of some plant materials. Purple cabbage and elderberry extracts respond in an amazing manner to an acidic or basic solution. In this activity, purple (red) cabbage is used to develop an acid or a base scale and determine the approximate pH value of various substances.

Chemistry: Understanding the composition of living things

(Biological molecules= Molecules of life)

A living cell is composed of a collection of molecules that are characterized as “organic”, because they contain carbon and hydrogen atoms. Scientists commonly recognize four classes of “biological molecules”: 1) Carbohydrates, 2) lipids, 3) proteins, and 4) nucleic acids. The presence of each of these molecules can be assessed by the application of a simple chemical test. During this laboratory exercise the student will learn how to test for the presence of three of these classes, leaving the nucleic acids for a later lab.

1. Carbohydrates – are composed of monosaccharaides (building blocks), which may be characterized by the number of carbon atoms they contain. They may also be characterized by the presence of a terminal aldehyde group, or an internal ketone group. The presence of ether of these two functional groups may be determined by testing a substance with Benedict’s reagent (solution), which reacts with these functional groups

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double-bonded oxygen atom to form a colored precipitate. See the explanation below:

A disaccharide may be formed by joining two monosaccharides. If all of the reactive aldehyde groups or ketone groups are involved in the formation of a bond between the two monosaccharides (as in sucrose), the disaccharide will react with Benedict’s reagent thus will generate a negative reaction (-). If at least one ketone or aldehyde group remain free to react (for example, maltose), it will generate a positive reaction (+) with Benedict’s reagent.

4) Sugars which possess a free aldehyde or ketone group are called reducing sugars, because they are oxidized (lose electrons (e-)) by the Cu2- in Benedict’s reagent. Likewise, these sugars are capable of reducing other molecules, such as Benedict’s reagent.

5) For example, glucose, maltose, and lactose will test (+) for a simple sugar test. Sucrose will test negative (-) with Benedict’s reagent.

Note: In solution, a number of monosaccharides, including fructose and ribose, exist in a ring form which modifies the original ketone and aldehyde groups, leaving them un-reactive to Benedict’s reagents. In other words, sugars generally need to be in the chain form (rather than the ring form) to react with Benedict’s reagent. When heated; sugars in the ring form can convert to chain form. Thus: If a reducing sugar is heated in the presence of Benedict’s reagent, the solution will change as follows.

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For example below is the molecule structure of glucose. Does glucose appear to be a reducing sugar? YES. Why? Because the presence of: terminal aldehyde group.

1. A positive (+) control - is the known standard of the experiment that will allow the researcher to verify the appearance of a positive reaction.

For example, glucose, maltose, and lactose will test (+) for simple sugar test.For example, potato will test (+) for starch with Iodine/Lugol’s Sol (I2KI)

2. A negative (-) control – is the known standard of the experiment that will allow the researcher to verify the appearance of a negative (-) reaction. In brief, water doesn’t possess any of the macromolecules studied (proteins, carbohydrates, and lipids).

For example sucrose will test negative (-) with Benedict’s reagents.For example water (ddH2 O) will test negative (-) for all macromolecules test.

STUDENT ACTIVITY BENEDICT’S SOLUTION

Materials

6) Hot plate7) 500 mL beaker8) Test tube rack and test tube

holder9) 10 test tube

10) Sharpie11) Metric ruler12) Dropper13) Benedict’s reagent

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14) Test solution: distilled water, clear diet soda, clear non-diet soda, pineapple juice, onion juice, potato juice, milk, glucose solution, sucrose solution, corn syrup, and tap water.

[Warning: Benedict’s reagent is corrosive. If it splashes onto your skin, wash the area immediately with soap and water.] Note: Label each transfer pipette with the name of the solutions that are distributed to you.

Procedure 5.5 Benedict’s Reagent test [Warning: Benedict reagent is the only solution you will heat up.]

1. Using a sharpie, label test tube 1-152. Pipette 2 mL of the correct stock solution into the test tubes, as described in Table 5.4.3. Add 2 mL of Benedict’s solution to each test tube agitate the mixture by shaking the test

tubes from side to side or with a vortex mixer, and record the color of the mixture in Table 5.4.

4. Heat the test tubes in boiling water for 3 minutes. Remove the test tube with a test tube holder, and record the color of each test tube in Table 5.4.

5. Discard all the solution according to the instructor’s directions. Wash each test tube and return them to your station.

Table 5.4 Benedict’s Reagent Test for Reducing SugarsTest Tube Solution

What color is itBefore heating?

What color is itafter heating? Conclusion

1 Distilled water

2 Glucose solution

3 Maltose solution

4 Lactose solution

5 Sucrose solution

6 Starch solution

7 Fructose solution

8 Lemon juice

9 Orange juice

10 Non-diet soda

11 Diet soda

12 Chicken broth

13 Meal Replacement

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Q. In the above test, rank the solution from non-reducing sugar to stronger reducing sugar.

1. __________________________ 8. _________________________

2. _________________________ 9. _________________________

3. _________________________ 10. _________________________

4. _________________________ 11. _________________________

5. _________________________ 12. _________________________

6. _________________________ 13. __________________________

7. _________________________ Q. Why was Benedict’s reagent used to test the urine of diabetics before more sophisticated methods were developed?

______________________________________________________________________________

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STUDENT ACTIVITY - IODINE TEST (I2Kl)

Iodine Test for StarchThe iodine test using iodine-potassium iodide (I2KI) has been developed to distinguish starch from other carbohydrates. Because starch is a coiled glucose polymer, the I2 KI solution interacts with the starch, producing a bluish black color. The I2KI does not react with non-coiled carbohydrates and remains a yellowish-brown color. Some carbohydrates, such as dextrin and glycogen, will produce an intermediate color reaction.

Materials

15) I2KI solution16) Test tube rack

17) 3-10 test tubes18) Sharpies

19) Metric ruler20) Dropper

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21) Test solution and material: distilled water, clear diet soda, clear non-diet soda, onion juice, potato juice, milk, glucose solution, sucrose solution, paper, and cotton

Procedure 5.6 Lugol’s reagent test [Warning: Do not heat up this solution!]

1. Using a sharpie, label test tube 1-112. For test tube 1-9, pipette 3 mL of the correct stock solution in each test tube, as described in

Table 5.5. For test tubes 10 and 11, place a small amount of paper and cotton. Record the color of each solution in Table 5.5.

3. Add 3 to 5 drops of Lugol’s [Iodine solution or reagent (I2KI)] solution to each test tube, agitate the mixture by shaking the test tubes from side to side or with a vortex mixer, and record the color of the mixture in Table 5.5.

4. Discard all the solution according to the instructor’s direction. Wash each test tube and return them to your station.

Table 5.5 Iodine test for starchTest Tube Solution

What color is itBefore heating?

What color is itafter heating? Conclusion

1 Distilled water

2 Starch solution

3 Diet soda

4 Non-diet soda

5 Onion Juice

6 Cream

7 Glucose solution

8 Potato juice

9 Chicken broth

10 Cotton

11 Paper

12 Meal Replacement

Q. Which substance contained starch?

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Q. Compare and contrast the reaction of potato juice and onion juice.

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Grease-spot test for lipids: You probably have noticed lipids are greasy, especially after eating a bag of potato chips. The grease-spot test is a simple test tube to identify the lipid nature of substance.

Materials

22) Brown paper bag or brown wrapping paper

23) Scissors

24) Rulers25) Dropper

26) Test substance: water, vegetable oil, egg white, soda, potato chip, honey, salad dressing, butter, rubbing alcohol, beef jerky

Procedure 5.7 Grease - Spot 1. Using a sharpie, label grocery bag piece 1-12.2. Place a drop of each test substance, as described in Table 5.6, on each labeled spot

grocery bag piece. Set aside to dry for 10 minutes.3. After 10 minutes, describe the appearance of each spot on the paper.4. Discard all the solution according to the instructor’s directions.

Table 5.6 Grease-spot test for a lipid

Paper Substance Result Conclusion

1 Distilled water

2 Vegetable oil

3 Egg albumin

4 Non-diet soda

5 Potato chips

6 Honey

7 Salad dressing

8 Butter

9 Alcohol

10 Chicken broth

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ACTIVITY - Grease Spot Test

11 Meal Replacement

Q. If you rub some nose grease (oil from bridge of the nose) on the paper, what will happen?

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STUDENT ACTIVITY - Sudan Test

Sudan test for a lipidA stain known as Sudan III combines with lipid molecules to produce a brilliant orange color. Sudan works by forming a hydrophobic interaction with nonpolar molecules. The more vivid the orange color, the greater the intensity of the interaction.

Materials

27)

28) Sudan III stain29) Filter paper30) Ruler

31) Pencil32) Forceps

33) Test substance: distilled water, whole milk, low-fat milk, skim milk, egg white, egg yolk, butter, margarine, corn syrup, and pineapple juice.

Procedure 5.8 Sudan Test1. Obtain several sheets of filter paper2. On the perimeter of the paper, draw several circles of 2 cm diameter spaced equally apart

(you may use a nickel to draw the circle). You may need more than one sheet of filter paper to make 12 circles.

3. Number each circle according to the substance in Table 5.7.4. Place 1 drop of each substance in the appropriate circle. Blot off any excess liquid and

allow the paper to dry completely.5. Obtain a bowl containing Sudan III stain.6. Dip the filter papers in the bowl and let them sit for 5 minutes.7. Remove the filter paper with forceps.8. Wash the filter paper in a pan of water for 1 minute.9. Examine the color in each circle and record the color in Table 5.7.10. Discard all the solution according to the instructor’s direction. Wash each test tube and

return them to your station.

Q. Which substance did react the greatest with Sudan III?

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______________________________________________________________________________

Q. Which substances did not react with Sudan III? ______________________________________________________________________________

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Table 5.7 Sudan III test for lipidPaper Substance Result Conclusion

1 Distilled water

2 Vegetable oil

3 Egg albumin

4 Non-diet soda

5 Potato chips

6 Honey

7 Salad dressing

8 Butter

9 Chicken broth

10 Meal Replacement

STUDENT ACTIVITY - Biuret's Reagent

Biuret test for proteinThe Biuret test is commonly used to detect the presence of a protein. The Biuret reagent is strong blue-green colored solution containing 1% copper sulfate (CuSO4), and sodium hydroxide (NaOH) or potassium hydroxide (KOH). The reagent changes color from blue-green to violet in the presence of proteins. The change in color results from the interaction between the copper ions and the peptide bonds of the protein. The more the peptide bonds, the darker is the resulting color.

Materials

34) Biuret reagent is extremely corrosive HANDLE WITH CARE!!!!35) 10 test tubes

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36) Sharpie 37) Dropper38) Test substance: distilled water, sucrose solution, whole milk, bread, ground peanuts,

chicken broth, vegetable oil, egg white, egg yolk, and albumin.

Procedure 5.9 Biuret’s Reagent[* Caution: Biuret reagent is extremely corrosive. Handle this chemical with great care. If you get some on your skin, wash the area with mild soap and water and notify your lab instructor. Carefully follow your instructor's directions regarding the use and disposal of Biuret reagent.]

[Warning: Do not heat up this solution!]

1. Using a sharpie, labeled test tube 1-6.2. Pipette 3 mL of the correct stock solution in each test tube, as described in Table 5.8.3. Add 2 mL of biuret’s reagent to each test tube and agitate the mixture by shaking the

test tubes from side to side or with a vortex mixer, and record the color of the mixture in Table 5.8.

4. Discard all the solution according to the instructor’s directions. Wash each test tube and return them to your station.

Q. Which substances were proteinaceous?

______________________________________________________________________________

______________________________________________________________________________

Table 5.8 Biuret’s Test for a proteinPaper Substance Color after Biuret Conclusion

1 Distilled water

2 Egg albumin

3 Sucrose solution

4 Chicken broth

5 Potato juice

6 Hamburger juice

7 Meal Replacement

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Procedure 5.10 test for unknown

Repeat each test with the unknown solutions and record your result in Table 5.9.

Table 5.9 Test for Unknown Solution

Unknown

Benedict’stest

Lugol’stest

Grease-spot test

Sudan IIItest

Biuret’stest

Name of theunknown

A

B

C

D

E

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Review Questions Chapter 5: Chemistry Understanding the Composition of Living Things

1. Compare and contrast an acid and a base, and provide examples of each.

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2. Distinguish between inorganic and organic molecule.

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3. Why was water or distilled water tested in each activity?

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___________________________________________ ____________________________________________Last Name, First Name [lab partner N0. 1] Last Name, First Name [lab partner N0. 2]

_______________________________ _______________________________Last Name, First Name [lab partner N0. 3] Last Name, First Name [lab partner N0. 4]

______________________ _______________ ___________________Section group # Date

4. Compare and contrast ionic and covalent bonds, and give an example of each?

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5. Describe what happens when a polar covalent and a nonpolar covalent substance are combined. Provide an example of a mixture with these components.

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6. Define monosaccharides. disaccharides, and polysaccharides, and provide two examples of each.

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7. What is a peptide bond?

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8. What are phospholipids, and where are they found?

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9. What is an essential amino acid?

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10. What is acid rain? Describe the impact of acid rain upon the environment.

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