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Unit 2: Chemistry of life

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This unit is part of the Biology library. Browse videos, articles, and exercises by topic.

Elements and atoms

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Module 2: The Chemistry of Life

The chemistry of life.

All life exists within the context of its environment. Each environment is characterized by its biological, physical, and chemical properties. Since organisms are adapted to a specific environment, radical changes in these conditions often result in injury to the individual or possibly extinction of the species. Recent reports of declining frog populations, for example, have been correlated with increased ultraviolet radiation from the sun (specifically UVB). Chemical reactions that take place inside of an organism are dependent upon both internal and external chemical and physical properties. We will explore some of these properties in today’s lab.

Part 1: pH Chemistry

Although water is generally regarded as a stable compound, individual water molecules are constantly gaining, losing, and swapping hydrogen atoms. This process is represented by the following chemical reaction:

H 2 O ↔ OH + H

Pure water with a pH of 7 has equal numbers of hydrogen and hydroxide ions at any given moment. Water is considered to be a neutral substance. The pH of any solution can be determined by calculating the total concentration of hydrogen ions in the solution.

What is a MOLE?

A mole is a term used to describe the quantity of something. If you have a mole of paperclips, that means you have paperclips. This is similar to the way we use the word “dozen.” We know that if you have a dozen paperclips, it means you have 12 of them.

1 dozen = 12

1 mole = 6.02×10 23

Scientists measure acidity using the pH scale. The pH scale ranges from 0 to 14, and the numbers represent the concentration of hydrogen ions –1  in the substance. For example, battery acid, with a pH of 1, has 1×10 moles of hydrogen ions per liter of solution. Ammonia, which is a very basic substance with a pH of 12, has 1×10 –12 moles of hydrogen ions per liter of solution. The more acidic the solution, the more hydrogen ions it contains.

Excessive changes in pH can cause metabolic and ecological problems. For example, the pH of your blood is carefully kept between 7.35 and 7.45. Any deviation above or below this range will result in alkalosis or acidosis, and both conditions can be deadly. Acid rain, on the other hand, can dissolve toxic metals from the soil particles into the soil solution and impair plant growth. As we will soon see, plant health is a factor that quickly affects most other life forms on the planet.

• pH paper (1–14)
• Plastic tray with wells

Following the instructions given by your teacher, measure the pH of each solution using pH paper.  Record the pH of these items below.

• Distilled water
• Lemon juice

Part 2: Buffers

Buffers are molecules that resist changes in pH. They can take up and release excess hydrogen ions in a solution and therefore prevent drastic changes in pH, regardless of whether acid or base is added to the solution. The net result is that the pH of the solution remains relatively stable (until the buffer is overwhelmed). Buffers are commonly found in dissolved minerals, soils, and in living organisms.

For example, buffers can play a protective role in lake ecosystems. In a lowland lake, acid rain causes very little fluctuation in pH because these lakes are typically high in organic molecules that act as buffers. A lake with little buffering capacity, such as a high alpine lake low in organic molecules, will experience a much greater change in overall pH as a result of acid precipitation.

• Tap water (H 2 O)
• 2 beakers (250 mL)
• 1g NaHCO 3 (baking soda)
• 0.001 M HCl (hydrochloric acid)
• Fill two beakers with 50 ml of tap water. Label one beaker “buffered” and label the other beaker “unbuffered.”
• Add 1 gram of baking soda to the “buffered” beaker. Swirl to dissolve.
• Using the pH strips, measure the pH of both beakers. Record all measurements in Table 1.
• Add 10 ml of 0.001 M HCl (hydrochloric acid) to each beaker and swirl.
• Measure the pH of the two beakers and record.
• Repeat steps 3–5 until you have added a total of 50 ml of 0.001 M HCl to each beaker.

Record the pH of your buffered and unbuffered solutions after each addition of 10 mL of hydrochloric acid to each beaker.

Data Analysis

Illustrate the buffering capacity of each solution by graphing your results below. Place the volume of  HCl on the x-axis and the pH value on the y-axis. Don’t forget to give your graph a title.

You can download this  graph paper template  to complete this portion.

Part 3: Buffers in the Blood

Bicarbonate ions act as a powerful buffer in your blood. They are created when carbon dioxide (CO 2 ), produced during cellular respiration, reacts with water:

CO 2  + H 2 O ↔ H 2 CO 3 ↔ HCO 3– + H+

Notice that hydrogen ions are also generated, which increases the acidity of blood and decreases the pH. In your body, the hydrogen ions are absorbed by hemoglobin molecules on your red blood cells. Meanwhile, the bicarbonate ions circulate in the blood plasma, preventing rapid pH changes. As your blood circulates past the metabolizing cells, more and more CO 2 enters your bloodstream and turns to bicarbonate ions. By the time the blood reaches the lungs, it is full of bicarbonate and hydrogen ions. The bicarbonate and hydrogen ions now combine and the reaction goes from right to left, releasing the CO 2 , which is now breathed out. In this exercise, you will bubble CO 2 into tap water and demonstrate the change in pH as carbonic acid is formed. You will use the pH indicator phenol red, which turns yellow in acidic conditions and magenta (red- purple) in basic conditions.

• Drinking straw
• Ehrlenmeyer flask (250 mL)
• Obtain a small flask and a straw, and fill the flask approximately ¼ full with tap water.
• Measure the pH of the water using the pH paper.
• Add 6–7 drops of phenol red to the flask.
• Do not swirl the flask (this may introduce CO 2 into the solution!), but agitate gently to mix the solution.
• Record the initial color of the water.
• Using a straw, blow air bubbles into the solution and observe any color changes.
• Record the final pH of the solution.

Lab Questions

• What happens when carbon dioxide combines with water?
• Why did the phenol red solution turn color after you blew air bubbles into it?
• If a person holds her breath, CO 2 builds up in the bloodstream. What effect does this have on blood pH?
• If a person hyperventilates, too much CO 2 is removed from the bloodstream. What effect does this have on blood pH?
• Why is “breathing into a bag” a good treatment for a hyperventilating patient?
• Why is pH homeostasis so critical in living organisms?

Part 4: Polar and Nonpolar Compounds

• 2 test tubes
• Obtain two test tubes and add 5 ml of water and 5 ml of oil into each tube. Allow the tubes to stand for one minute. Record the appearance of the tubes and label the ingredients in the tube.
• Add ≈6 drops of beet juice extract to tube #1 and ≈6 drops of chili oil to tube #2. Allow diffusion to take place for 1–2 minutes. Record the appearance of the tubes.
• Shake each tube gently and let stand for several minutes. Record the appearance of the tubes.
• Next add a few drops of detergent to each tube; shake gently and observe. Record the appearance the tube.

Download this page to record the appearance of the tubes at every step .

• What happens when lipids and water are combined? Why?
• How do beet juice extract and chili oil differ in their chemical properties? How do you know?
• Explain what happened when the tubes were shaken. What happened after the detergent was added? How can you explain these results?
• How is the phospholipid bilayer that makes up a cell membrane both hydrophilic and hydrophobic?
• What is a surfactant? How does it work?
• Biology Labs. Authored by : Wendy Riggs. Provided by : College of the Redwoods. Located at : http://www.redwoods.edu/ . License : CC BY: Attribution

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Chapter 2: Introduction to the Chemistry of Life

The elements carbon, hydrogen, nitrogen, oxygen, sulfur, and phosphorus are the key building blocks of the chemicals found in living things. They form the carbohydrates, nucleic acids, proteins, and lipids (all of which will be defined later in this chapter) that are the fundamental molecular components of all organisms. In this chapter, we will discuss these important building blocks and learn how the unique properties of the atoms of different elements affect their interactions with other atoms to form the molecules of life. These interactions determine what atoms combine and the ultimate shape of the molecules and macromolecules, that shape will determine their function.

Food provides an organism with nutrients—the matter it needs to survive. Many of these critical nutrients come in the form of biological macromolecules, or large molecules necessary for life. These macromolecules are built from different combinations of smaller organic molecules. What specific types of biological macromolecules do living things require? How are these molecules formed? What functions do they serve? In this chapter, we will explore these questions.

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Viewed from space, Earth offers no clues about the diversity of life forms that reside there. Scientists believe that the first forms of life on Earth were microorganisms that existed for billions of years in the ocean before plants and animals appeared. The mammals, birds, and flowers so familiar to us are all relatively recent, originating 130 to 250 million years ago. The earliest representatives of the genus Homo , to which we belong, have inhabited this planet for only the last 2.5 million years, and only in the last 300,000 years have humans started looking like we do today.

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Module 2: The Chemistry of Life

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Introduction:

All life exists within the context of its environment. Each environment is characterized by its biological, physical, and chemical properties. Since organisms are adapted to a specific environment, radical changes in these conditions often result in injury to the individual or possibly extinction of the species. Recent reports of declining frog populations, for example, have been correlated with increased ultraviolet radiation from the sun (specifically UVB). Chemical reactions that take place inside of an organism are dependent upon both internal and external chemical and physical properties. We will explore some of these properties in today’s lab.

Part 1: pH Chemistry

Although water is generally regarded as a stable compound, individual water molecules are constantly gaining, losing, and swapping hydrogen atoms. This process is represented by the following chemical reaction:

H 2 O ↔ OH + H

Pure water with a pH of 7 has equal numbers of hydrogen and hydroxide ions at any given moment. Water is considered to be a neutral substance. The pH of any solution can be determined by calculating the total concentration of hydrogen ions in the solution.

what is a mole?

A mole is a term used to describe the quantity of something. If you have a mole of paperclips, that means you have paperclips. This is similar to the way we use the word “dozen.” We know that if you have a dozen paperclips, it means you have 12 of them.

1 dozen = 12

1 mole = 6.02 × 10 23

Scientists measure acidity using the pH scale. The pH scale ranges from 0 to 14, and the numbers represent the concentration of hydrogen ions in the substance. For example, battery acid, with a pH of 1, has 1×10 moles of hydrogen ions per liter of solution. Ammonia, which is a very basic substance with a pH of 12, has 1×10 –12 moles of hydrogen ions per liter of solution. The more acidic the solution, the more hydrogen ions it contains.

Excessive changes in pH can cause metabolic and ecological problems. For example, the pH of your blood is carefully kept between 7.35 and 7.45. Any deviation above or below this range will result in alkalosis or acidosis, and both conditions can be deadly. Acid rain, on the other hand, can dissolve toxic metals from the soil particles into the soil solution and impair plant growth. As we will soon see, plant health is a factor that quickly affects most other life forms on the planet.

• pH paper (1–14)
• Plastic tray with wells

Following the instructions given by your teacher, measure the pH of each solution using pH paper. Record the pH of these items below.

• Distilled Water
• Lemon Juice

Buffers are molecules that resist changes in pH. They can take up and release excess hydrogen ions in a solution and therefore prevent drastic changes in pH, regardless of whether acid or base is added to the solution. The net result is that the pH of the solution remains relatively stable (until the buffer is overwhelmed). Buffers are commonly found in dissolved minerals, soils, and in living organisms.

For example, buffers can play a protective role in lake ecosystems. In a lowland lake, acid rain causes very little fluctuation in pH because these lakes are typically high in organic molecules that act as buffers. A lake with little buffering capacity, such as a high alpine lake low in organic molecules, will experience a much greater change in overall pH as a result of acid precipitation.

• pH Paper (1–14)
• Tap Water (H 2 O)
• 2 Beakers (250 mL)
• 1 g. of NaHCO 3 (baking soda)
• 0.001 M of HCl (hydrochloric acid)
• Fill two beakers with 50 ml of tap water. Label one beaker “buffered” and label the other beaker “unbuffered.”
• Add 1 gram of baking soda to the “buffered” beaker. Swirl to dissolve.
• Using the pH strips, measure the pH of both beakers. Record all measurements in Table 1.
• Add 10 ml of 0.001 M HCl (hydrochloric acid) to each beaker and swirl.
• Measure the pH of the two beakers and record.
• Repeat steps 3–5 until you have added a total of 50 ml of 0.001 M HCl to each beaker.

Record the pH of your buffered and unbuffered solutions after each addition of 10 mL of hydrochloric acid to each beaker.

Data Analysis:

Illustrate the buffering capacity of each solution by graphing your results below. Place the volume of HCl on the x-axis and the pH value on the y-axis. Don’t forget to give your graph a title.

You can download this graph paper template to complete this portion.

Bicarbonate ions act as a powerful buffer in your blood. They are created when carbon dioxide (CO 2 ), produced during cellular respiration, reacts with water:

CO 2 + H 2 O ↔ H 2 CO 3 ↔ HCO 3 – + H +

Notice that hydrogen ions are also generated, which increases the blood acidity and decreases the pH. In your body, the hydrogen ions are absorbed by hemoglobin molecules on your red blood cells. Meanwhile, the bicarbonate ions circulate in the blood plasma, preventing rapid pH changes. As your blood circulates past the metabolizing cells, more and more CO 2 enters your bloodstream and turns to bicarbonate ions. By the time the blood reaches the lungs, it is full of bicarbonate and hydrogen ions. The bicarbonate and hydrogen ions now combine and the reaction goes from right to left, releasing the CO 2 , which is now breathed out. In this exercise, you will bubble CO 2 into tap water and demonstrate the change in pH as carbonic acid is formed. You will use the pH indicator phenol red, which turns yellow in acidic conditions and magenta (red-purple) in basic conditions.

• Drinking Straw
• Erlenmeyer Flask (250 mL)
• Obtain a small flask and a straw, and fill the flask approximately ¼ full with tap water.
• Measure the pH of the water using the pH paper.
• Add 6–7 drops of phenol red to the flask.
• Do not swirl the flask (this may introduce CO 2 into the solution!), but agitate gently to mix the solution.
• Record the initial color of the water.
• Using a straw, blow air bubbles into the solution and observe any color changes.
• Record the final pH of the solution.

Lab Questions:

1. What happens when carbon dioxide combines with water?

2. Why did the phenol red solution turn color after you blew air bubbles into it?

3. If a person holds her breath, CO2 builds up in the bloodstream. What effect does this have on blood pH?

4. If a person hyperventilates, too much CO2 is removed from the bloodstream. What effect does this have on blood pH?

5. Why is “breathing into a bag” a good treatment for a hyperventilating patient?

6. Why is pH homeostasis so critical in living organisms?

• 2 Test Tubes
• Obtain two test tubes and add 5 ml of water and 5 ml of oil into each tube. Allow the tubes to stand for one minute. Record the appearance of the tubes and label the ingredients in the tube.
• Add ≈6 drops of beet juice extract to tube #1 and ≈6 drops of chili oil to tube #2. Allow diffusion to take place for 1–2 minutes. Record the appearance of the tubes.
• Shake each tube gently and let stand for several minutes. Record the appearance of the tubes.
• Next, add a few drops of detergent to each tube; shake gently and observe. Record the appearance of the tubes.

Download this page to record the appearance of the tubes at every step .

1. What happens when lipids and water are combined? Why?

2. How do beet juice extract and chili oil differ in their chemical properties? How do you know?

3. Explain what happened when the tubes were shaken. What happened after the detergent was added? How can you explain these results?

4. How is the phospholipid bilayer that makes up a cell membrane both hydrophilic and hydrophobic?

5. What is a surfactant? How does it work?