1- A Quick Review of the Properties of Water

 

1. Compounds that have the capacity to form hydrogen bonds with water are said to be hydrophilic (water loving). Those without this capacity are hydrophobic (water fearing).

Is the molecule on the right hydrophilic or hydrophobic?  Explain your answer  

2. In addition to being polar, water molecules can dissociate into hydronium ions (H3O+, often described simply as H+) and hydroxide ions (OH-). The concentration of each of these ions in pure water is 10-7. Another way to say this is that the concentration of hydronium ions, or H+ ions, is one out of every 10 million molecules. Similarly, the concentration of OH- ions is one in 10 million molecules.

 

a. The H+ ion concentration of a solution can be represented as its pH value. The pH of a solution is defined as the negative logio of the hydrogen ion concentration. What is the pH of pure water?

 

b. Refer to the diagram of the molecule of acetic acid in question 1. The COOH group can ionize to release a H+ ion into solution. If you add acetic acid to water and raise the concentration of H+ ions to 10-4' what is the pH of this solution?

 

3. Life as we know it could not exist without water. All the chemical reactions of life occur in aqueous solution. Water molecules are polar and are capable of forming hydrogen bonds with other polar or charged molecules. As a result, water has the following properties:

Explain how these properties of water are related to the phenomena described in parts a-h below. More than one property may be used to explain a given phenomenon.

a. During the winter, air temperatures in the northern United States can remain below
0°C for months; however, the fish and other animals living in the lakes survive.

 

b. Many substances-for example, salt (NaCI) and sucrose-dissolve quickly in water.

 

c. When you pour water into a 25-ml graduated cylinder, a meniscus forms at the top of the water column.

 

d. Sweating and the evaporation of sweat from the body surface help reduce a human's body temperature.

 

e. A bottle contains a liquid mixture of equal parts water and mineral oil. You shake the bottle vigorously and then set it on the table. Although the law of entropy favors maximum randomness, this mixture separates into layers of oil over water.

 

f. Water drops that fall on a surface tend to form rounded drops or beads.

 

g. Water drops that fall on your car tend to bead or round up more after you polish (or wax) the car than before you polished it.

 

h. If you touch the edge of a paper towel to a drop of colored water, the water will move up into (or be absorbed by) the towel.

 

 

 

Activity 4/5.1 How can you identify organic macromolecules?

 

Refer to the figure (Some Simple Chemistry) on the next page when doing this activity.

 

Part A. Answer the questions. Then use your answers to develop simple rules for identifying carbohydrates, lipids, proteins, and nucleic acids.

 

1. What is the approximate C:H:O ratio in each of the following types of macromolecules?

2. Which of the compounds listed in question 1 can often be composed of C, H, and 0 alone?

3. Which of the compounds can be identified by looking at the C:H:O ratios alone?

4. What other elements are commonly associated with each of these four types of macromolecules?

 

Carbohydrates

Lipids

Proteins

Nucleic acids

Always contain P

 

 

 

 

Generally contain

no P

 

 

 

 

Always contain N

 

 

 

 

Generally contain

no N

 

 

 

 

Frequently contain

S

 

 

 

 

Generally contain

no S

 

 

 

 

 

 

5. Functional groups can modify the properties of organic molecules. In the table below, indicate whether each functional group is polar or nonpolar and hydrophobic or hydrophilic. Which of these functional groups are found in proteins and lipids?

Functional

group

Polar or

nonpolar

Hydrophobic

or hydrophilic

Found in all

proteins

Found in many

proteins

Found in many

lipids

-OH

 

 

 

 

 

-CH2

 

 

 

 

 

-COOH

 

 

 

 

 

-NH2

 

 

 

 

 

-SH

 

 

 

 

 

-P04

 

 

 

 

 

6. You want to use a radioactive tracer that will label only the protein in an RNA virus. Assume the virus is composed of only a protein coat and an RNA core. Which of the following would you use? Be sure to explain your answer.

 

a. Radioactive P            b. Radioactive N           c. Radioactive S            d. Radioactive C

7. Closely related macromolecules often have many characteristics in common. For example, they share many of the same chemical elements and functional groups. Therefore, to separate or distinguish closely related macromolecules, you need to determine how they differ and then target or label that difference.

 

a. What makes RNA different from DNA?

b. If you wanted to use a radioactive or fluorescent tag to label only the RNA in a cell and not the DNA, what compound(s) could you label that is/are specific for RNA?

c. If you wanted to label only the DNA, what compound(s) could you label?


 

8. Based on your answers to questions 1-7, what simple rule(s) can you use to identify the following macromolecules?

Carbohydrates

Lipids

Proteins

DNA versus RNA

Part B. Carbohydrate, lipid, protein, or nucleic acid? Name that structure!

 

Based on the rules you developed in Part A, identify the compounds below (and on the following page) as carbohydrates, lipids, amino acids, polypeptides, or nucleic acids. In addition, indicate whether each is likely to be polar or nonpolar, hydrophilic or hydrophobic.

 

Activity 4/5.2 What predictions can you make about the behavior of organic macromolecules if you know their structure?

 

1. Twenty amino acids are commonly utilized in the synthesis of proteins. These amino acids differ in the chemical properties of their side chains (also called R groups). What properties does each of the following R groups have? (Note: A side chain may display more than one of these properties.)

R Group

Basic, acidic, or

neutral

Polar or nonpolar

Hydrophilic or

hydrophobic

a.

 

 

 

C H2

 

 

 

NCH

CH3 CH3

 

 

 

b.

 

 

 

IH2

_O--CEO

 

 

 

c.

 

 

 

IH2

IH2

IH2

IH2

NH3'

 

 

 

d.

IH2

OH

 

 

 

 

 

 

2. Polypeptides and proteins are made up of linear sequences of amino acids. In its functional form, each protein has a specific three-dimensional structure or shape. Interactions among the individual amino acids and their side chains play a major role in determining this shape.

 

a. How are amino acids linked together to form polypeptides or proteins? What is this type of bond called?

b. Define the four structures of a protein.

c. What kinds of bonds hold each of these

structures together?

Primary:

 

Secondary:

 

Tertiary:

 

Quaternary:

 

3. Lipids as a group are defined as being hydrophobic, or insoluble in water. As a result, this group includes a fairly wide range of compounds-for example, fats, oils, waxes, an steroids like cholesterol.

 

  1. How are fatty acids and glycerol linked together to form fats (triglycerides)? b. What functions do fats serve in living organisms? c. How do phospholipids differ from triglycerides? d. What characteristics do phospholipids have that triglycerides do not have?

 

4. Use your understanding of the chemical characteristics of the four major types of macromolecules in living organisms to predict the outcome of the following

experiments. Be sure to explain your reasoning.

 

Experiment a: You stir 10 g of glucose and 10 ml of phospholipids in a 500-ml beaker that contains 200 ml of distilled water. Draw a diagram to show where and how the glucose and phospholipids would be distributed after you let the mixture settle for about 30 minutes.

Experiment b: You do Experiment a again, but this time you stir 10 g of glucose and 10 ml of phospholipids in a different 500-ml beaker that contains 200 ml of distilled water and 100 ml of oil. Draw a diagram to show where and how the glucose, phospholipids, and oil would be distributed after you let the solution settle for about 30 minutes.

Experiment c: To completely fill a sealed 500-ml glass container that contains 490 ml of distilled water, you inject 10 ml of phospholipids into it. (A small gasket allows the air to leave as you inject the phospholipids.) You shake this mixture vigorously and then let it settle for an hour or more. Draw a diagram to show how the phospholipids would be distributed in the container.

 

Experiment d: A globular protein that is ordinarily found in aqueous solution has these amino acids in its primary structure: glutamic acid, lysine, leucine, and tryptophan. Predict where you would find each amino acid: in the interior portion of the protein (away from water) or on the outside of the protein (facing water). (Refer to Figure 5.17, page 79.)

Experiment e: Drawn below is part of the tertiary structure of a protein showing the positions of two amino acids (aspartic acid and lysine). Replacing lysine with another amino acid in the protein may change the shape and function of the protein. Replacing lysine with which type(s) of amino acid(s) would lead to the least amount of change in the tertiary structure of this protein? (Refer to Figure 5.17, page 79.)

 

-NH3} -