UB Senior Science (2012) by Jeremy Buie

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UB Senior Science (2012)

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Brainard

Buie

Krista

Wilkin

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CK-12 Foundation is a non-proﬁt organization with a mission to reduce the cost of textbook materials for the K-12 market both in the U.S. and worldwide. Using an open-content, web-based collaborative model termed the FlexBook®, CK-12 intends to pioneer the generation and distribution of high-quality educational content that will serve both as core text as well as provide an adaptive environment for learning, powered through the FlexBook Platform®. Copyright © 2011 CK-12 Foundation, www.ck12.org The names “CK-12” and “CK12” and associated logos and the terms “FlexBook®,” and “FlexBook Platform®,” (collectively “CK-12 Marks”) are trademarks and service marks of CK-12 Foundation and are protected by federal, state, and international laws. Any form of reproduction of this book in any format or medium, in whole or in sections must include the referral attribution link http://www.ck12.org/saythanks (placed in a visible location) in addition to the following terms. Except as otherwise noted, all CK-12 Content (including CK-12 Curriculum Material) is made available to Users in accordance with the Creative Commons Attribution/Non-Commercial/Share Alike 3.0 Unported (CC-BY-NC-SA) License (http://creativecommons.org/licenses/by-nc-sa/3.0/), as amended and updated by Creative Commons from time to time (the “CC License”), which is incorporated herein by this reference. Complete terms can be found at http://www.ck12.org/terms. Printed: June 15, 2012

Authors Jean Brainard, Jeremy Buie, Thomas Krista, Douglas Wilkin

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Contents 1 Introduction to Digestion and Nutrition - Student Edition (Human Biology)

1.1

Human Biology: An Interdisciplinary Life Science Curriculum . . . . . . . . . . . . . . . . .

1.2

Introduction to Digestion and Nutrition . . . . . . . . . . . . . . . . . . . . . . . . . . . . .

2 Food and the Digestive System

2.1

Food and Nutrients . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .

2.2

Choosing Healthy Foods . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .

2.3

The Digestive System . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .

3 Biotechnology

3.1

Lesson 10.1: DNA Technology

. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .

3.2

Lesson 10.2: Biotechnology . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .

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Chapter 1 Introduction to Digestion and Nutrition - Student Edition (Human Biology) 1.1 Human Biology: An Interdisciplinary Life Science Curriculum An inquiry-based guide for the middle school student. Originally developed by the Program in Human Biology at Stanford University and EVERYDAY LEARNINGr Donated to CK-12 Foundation under the Creative Commons Attibution-NonCommercial-ShareAlike (CCBY-NC-SA) license. This license allows others to use, distribute, and create derivative works based on that content.

1.2 Introduction to Digestion and Nutrition Contents 1. 2. 3. 4. 5. 6. 7. 8.

Why Do We Eat? Food Is Fuel Mouth to Stomach in One Swallow A Journey through the Intestine Food for life Staying Healthy Food Nutrient Chart Glossary

Authors H. Craig Heller, Principal Investigator

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Mary L. Kiely, Project Director

Text Authors H. Craig Heller, James V. Lawry

Activity Authors James V. Lawry, Stan Ogren, Marjorie Gray, Geraldine Horsma

Project Editor Dennis McKee

Photo Credits • • • • • • • • • •

1 (top center): Bernd Wittich/Visuals Unlimited 2 (bottom center): Robert E. Daemmrich/Tony Stone Images 14 (top center): Phil Degginger/Tony Stone Images 24 (top center): AP/Wide World Photos 34 (top center): Cabisco/Visuals Unlimited 47 (top center): “The Field Museum” #A76851, Chicago, Illinois 48 (top center): W.A. Banaszewski/Visuals Unlimited 48 (middle left): Corbis-Bettmann 48 (bottom left): James Mayo/Chicago Tribune 56 (top center): Terry Donnelly/West Stock

Data Sources • Food Nutrient chart: Morrill, Judi, Sheri Bakun, and Suzanne Murphy. Are You Eating Right? San Jose: Department of Nutrition and Food Science, San Jose State University, 1992. Whitney, Eleanor Noss, and Sharon Rady Rolfes. Understanding Nutrition, 7th ed. St. Paul: West Information Publishing Group, 1996. • FAO information: Food and Agriculture Organization (FAO), Food Security and Nutrition. Prepared for the 1996 World Food Summit.

Originally Published by Everyday Learning Corporation Everyday Learning Development Staﬀ Editorial Steve Mico, Leslie Morrison, Susan Zeitner www.ck12.org

Production/Design Fran Brown, Annette Davis, Jess Schaal, Norma Underwood

ISBN 1-57039-683-3 Stanford University’s Middle Grades Life Science Curriculum Project was supported by grants from the National Science Foundation, Carnegie Corporation of New York, and The David and Lucile Packard Foundation. The content of the Human Biology curriculum is the sole responsibility of Stanford University’s Middle Grades Life Science Curriculum Project and does not necessarily reﬂect the views or opinions of the National Science Foundation, Carnegie Corporation of New York, or The David and Lucile Packard Foundation.

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Chapter 2 Food and the Digestive System 2.1 Food and Nutrients Lesson Objectives • • • •

Explain why the body needs food. Identify the roles of carbohydrates, proteins, and lipids. Give examples of vitamins and minerals, and state their functions. Explain why water is a nutrient.

Check Your Understanding • What are the four types of organic compounds? • What do all cells need in order to function? • What are muscles made of?

Introduction Did you ever hear the old saying “An apple a day keeps the doctor away”? Do apples really prevent you from getting sick? Probably not, but eating apples and other fresh fruits can help keep you healthy. The girl shown in Figure 2.1 is eating fresh vegetables as part of a healthy meal. Why do you need foods like these for good health? What role does food play in the body?

Why We Need Food Your body needs food for three reasons: • Food gives your body energy. You need energy for everything you do. • Food provides building materials for your body. Your body needs building materials so it can grow and repair itself. • Food contains substances that help control body processes. Your body processes must be kept in balance for good health. For example, your body needs the right balance of water and salts. www.ck12.org

Figure 2.1: This girl is eating a salad of tomatoes and leafy green vegetables. Fresh vegetables such as these are excellent food choices for good health. For all these reasons, you must have a steady supply of nutrients. Nutrients are chemicals in food that your body needs. There are six types of nutrients: carbohydrates, proteins, lipids, vitamins, minerals, and water. Carbohydrates, proteins, and lipids give your body energy. Proteins provide building materials. Proteins, vitamins, and minerals help control body processes.

Nutrients that Provide Energy Molecules of carbohydrates, proteins, and lipids contain energy. When your body digests food, it breaks down the molecules of these nutrients. This releases the energy so your body can use it. The energy in food is measured in units called Calories.

Carbohydrates Carbohydrates are nutrients that include sugars, starches, and ďŹ ber. How many grams of carbohydrates you need each day are shown in Figure 2.2. It also shows some foods that are good sources of carbohydrates. Sugars are small, simple carbohydrates that are found in foods such as fruits and milk. The sugar found in fruits is called fructose. The sugar found in milk is called lactose. These sugars are broken down by the body to form glucose, the simplest sugar of all. Glucose is used by cells for energy. Remember the discussion of cellular respiration in the Cell Functions chapter? Cellular respiration turns glucose into the usable form of chemical energy, ATP. One gram of sugar provides your body with four Calories of energy. Some people cannot digest lactose, the sugar in milk. This condition is called lactose intolerance. If people with this condition drink milk, they may have cramping, bloating, and gas. To avoid these symptoms, they should not drink milk, or else they should drink special, lactose-free milk. Starches are large, complex carbohydrates. They are found in foods such as vegetables and grains. Starches are broken down by the body into sugars that provide energy. Like sugar, one gram of starch provides your body with four Calories of energy.

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Figure 2.2: Up to the age of 13 years, you need about 130 grams of carbohydrates a day. Most of the carbohydrates should be complex. They are broken down by the body more slowly than simple carbohydrates. Therefore, they provide energy longer and more steadily. What other foods do you think are good sources of complex carbohydrates? Fiber is another type of large, complex carbohydrate. Unlike sugars and starches, fiber does not provide energy. However, it has other important roles in the body. There are two types of fiber found in food: soluble fiber and insoluble fiber. Each type has a different role. • Soluble fiber dissolves in water. It helps keep sugar and fat at normal levels in the blood. • Insoluble fiber does not dissolve in water. As it moves through the large intestine, it absorbs water. This helps keep food waste moist so it can pass easily out of the body. Eating foods high in fiber helps fill you up without providing too many Calories. Most fruits and vegetables are high in fiber. Some examples are shown in Figure 2.3.

Proteins Proteins are nutrients made up of smaller molecules called amino acids. As discussed in the Introduction to Living Things chapter, the amino acids are arranged like ”beads on a string.” These amino acid chains then fold up into a three-dimensional molecule. Proteins have several important roles in the body. For example, proteins: • • • •

Make up muscles. Help control body processes. Help the body ﬁght oﬀ bacteria and other “foreign invaders.” Carry substances in the blood.

If you eat more proteins than you need for these purposes, the extra proteins are used for energy. One gram of protein provides four Calories of energy. This is the same amount as one gram of sugar or starch. How many grams of proteins you need each day are shown in Figure 2.4. It also shows some foods that are good sources of proteins. There are many diﬀerent amino acids, the building blocks of proteins, but your body needs only 20 of them. Your body can make ten of these amino acids from simpler substances. The other ten amino acids must come from the proteins in foods. These ten are called essential amino acids. Only animal foods, such www.ck12.org

Figure 2.3: Between the ages of 9 and 13 years, girls need about 26 grams of fiber a day, and boys need about 31 grams of fiber a day. Do you know other foods that are high in fiber?

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Figure 2.4: Between the ages of 9 and 13 years, you need about 34 grams of proteins a day. What other foods do you think are good sources of proteins? as milk and meat, contain all ten essential amino acids in a single food. Plant foods are missing one or more essential amino acids. However, by eating a combination of plant foods, such as beans and rice, you can get all ten essential amino acids.

Lipids Lipids are nutrients such as fats that store energy. The heart and skeletal muscles rely mainly on lipids for energy. One gram of lipids provides nine Calories of energy. This is more than twice the amount provided by carbohydrates or proteins. Lipids have several other roles in the body. For example, lipids: • • • •

Protect nerves. Help control blood pressure. Help blood to clot. Make up the membranes that surround cells.

Fats are one type of lipid. Fat is the main form in which the body stores energy. Stored fat gives your body an energy reserve. It’s like having money in a savings account. It’s there in case you need it. Stored fat also cushions and protects internal organs. In addition, it insulates the body. It helps keep you warm in cold weather. Fats and other lipids are necessary for life. However, they can be harmful if you eat too much of them, or the wrong type of fats. Fats can build up in the blood and damage blood vessels. This increases the risk of heart disease. There are two types of lipids: saturated lipids and unsaturated lipids. • Saturated lipids are harmful even in very small amounts. They should be avoided as much as possible. Saturated fats are found mainly in animal foods, such as meats, whole milk, and eggs. Saturated fats increase cholesterol levels in the blood. Cholesterol is a fatty substance that is found naturally in the body. Too much cholesterol in the blood can lead to heart disease. It is best to limit the amount of saturated fats in your diet. • Unsaturated lipids are found mainly in plant foods, such as vegetable oil, olive oil, and nuts. Unsaturated lipids are also found in ﬁsh such as salmon. Unsaturated lipids are needed in small amounts for good health because your body cannot make them. Most lipids and fats in your diet should be unsaturated. www.ck12.org

Another type of lipid is called trans fat. Trans fat is manufactured and added to certain foods to keep them fresher for longer. Foods that contain trans fats include cakes, cookies, fried foods, and margarine. Eating foods that contain trans fats increases the risk of heart disease. You should do your best to eat fewer foods that contain it. Beginning in 2010, California will ban trans fats from restaurant products, and, beginning in 2011, from all retail baked goods.

Vitamins and Minerals Vitamins and minerals are also nutrients. They do not provide energy. However, they are needed for good health.

Vitamins Vitamins are substances that the body needs in small amounts to function properly. Humans need 13 diﬀerent vitamins. Some of them are listed in Table (2.1) . The table also shows how much of each vitamin you need each day. Vitamins have many roles in the body. For example, Vitamin A helps maintain good vision. Vitamin B9 helps form red blood cells. Vitamin K is needed for blood to clot when you have a cut or other wound. Table 2.1: Vitamins Needed For Good Health Vitamin

One Reason You Need It

Some Foods that Have It

How Much of It You Need Each Day (at ages 9–13 years)

Vitamin A

Needed for good vision

Vitamin B1

Needed nerves

600 �g (1 �g = 1 x 10-6 g) 0.9 mg (1 mg = 1 x 10-3 g)

Vitamin B3

Needed for healthy skin and nerves Needed to make red blood cells Needed for healthy nerves Needed for growth and repair of tissues Needed for healthy bones and teeth Needed for blood to clot

Carrots, spinach, milk, eggs Whole wheat, peas, meat, beans, fish, peanuts Beets, liver, pork, turkey, fish, peanuts Liver, peas, dried beans, green leafy vegetables Meat, liver, milk, shellfish, eggs Oranges, grapefruits, red peppers, broccoli Milk, salmon, tuna, eggs Spinach, Brussels sprouts, milk, eggs

Vitamin B9 Vitamin B12 Vitamin C Vitamin D Vitamin K

for

healthy

12 mg 300 �g 1.8 �g 45 mg 5 �g 60 �g

Some vitamins are produced in the body. For example, vitamin D is made in the skin when it is exposed to sunlight. Vitamins B12 and K are produced by bacteria that normally live inside the body. Most other vitamins must come from foods. Foods that are good sources of vitamins are listed in Table 1. They include whole grains, vegetables, fruits, and milk. Not getting enough vitamins can cause health problems. For example, too little vitamin C causes a disease called scurvy. People with scurvy have bleeding gums, nosebleeds, and other symptoms. Getting too much

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of some vitamins can also cause health problems. The vitamins to watch out for are vitamins A, D, E, and K. These vitamins are stored by the body, so they can build up to high levels. Very high levels of these vitamins can even cause death, although this is very rare.

Minerals Minerals are chemical elements that are needed for body processes. Minerals that you need in relatively large amounts are listed in Table (2.2). Minerals that you need in smaller amounts include iodine, iron, and zinc. Minerals have many important roles in the body. For example, calcium and phosphorus are needed for strong bones and teeth. Potassium and sodium are needed for muscles and nerves to work normally. Table 2.2: Minerals Needed For Good Health. Mineral

One Reason You Need It

Some Foods that Have It

How Much of It You Need Each Day (at ages 9â&#x20AC;&#x201C;13 years)

Calcium

Needed for strong bones and teeth Needed for proper balance of water and salts in body Needed for strong bones

Milk, soy milk, green leafy vegetables Table salt, most packaged foods

1,300 mg

Whole grains, green leafy vegetables, nuts Meat, poultry, whole grains\ Meats, grains, bananas, orange juice Table salt, most packaged foods

240 mg

Chloride

Magnesium Phosphorus Potassium Sodium

Needed for strong bones and teeth Needed for muscles and nerves to work normally Needed for muscles and nerves to work normally

2.3 g

1,250 mg 4.5 g 1.5 g

Your body cannot produce any of the minerals that it needs. Instead, you must get minerals from the foods you eat. Good sources of minerals are listed in Table (2.2). They include milk, green leafy vegetables, and whole grains. Not getting enough minerals can cause health problems. For example, too little calcium may cause osteoporosis. This is a disease in which bones become soft and break easily. Getting too much of some minerals can also cause health problems. Many people get too much sodium. Sodium is added to most packaged foods. People often add more sodium to their food by using table salt (sodium chloride). Too much sodium causes high blood pressure in some people.

Water Did you know that water is also a nutrient? By weight, your cells are about two-thirds water, so you cannot live without it. In fact, you can survive for only a few days without water. You lose water in each breath you exhale. You also lose water in sweat and urine. If you do not take in enough water to replace the water that you lose, you may develop dehydration. Symptoms of dehydration include dry mouth, headaches, and feeling dizzy. Dehydration can be very serious. Severe dehydration can even cause death. www.ck12.org

When you exercise, especially on a hot day, you lose more water in sweat than you usually do. You need to drink extra water before, during, and after exercise. The children in Figure 2.5 are drinking water while playing outside on a warm day. They need to drink water to avoid dehydration.

Figure 2.5: When you are active outside on a warm day, it’s important to drink plenty of water. You need to replace the water you lose in sweat. Getting too much water can also be dangerous. Excessive water may cause a condition called hyponatremia. In this condition, water collects in the brain and causes it to swell. Hyponatremia can cause death. It requires emergency medical care.

Lesson Summary • The body needs food for energy, building materials, and substances that help control body processes. • Carbohydrates, proteins, and lipids provide energy and have other important roles in the body. • Vitamins and minerals do not provide energy but are needed in small amounts for the body to function properly. • The body must have water to survive.

Review Questions 1. What are three reasons that your body needs food? 2. Which nutrients can be used for energy? 3. Name two types of ﬁber and state the role of each type of ﬁber in the body.

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4. What are some foods that are good sources of vitamin C? 5. What are two minerals that are needed for strong bones and teeth? 6. List some of the functions of proteins in the body. Based on your list, predict health problems people might have if they do not get enough proteins in foods. 7. Your body needs 20 diﬀerent amino acids. Why do you need to get only ten of these amino acids from food? Name foods you can eat to get these ten amino acids. 8. Compare and contrast saturated and unsaturated lipids. 9. Identify three vitamins that are produced in the body. How are they produced? 10. Why do you need to drink extra water when you exercise on a hot day? What might happen if you did not drink extra water?

Further Reading / Supplemental Links • Alexandra Powe Allred. Nutrition. Perfection Learning, 2005. • Ann Douglas and Julie Douglas. Body Talk: The Straight Facts on Fitness, Nutrition, and Feeling Great about Yourself! Maple Tree Press, 2006. • DK Publishing. Food. DK Children, 2005. • Donna Shryer. Body Fuel: A Guide to Good Nutrition. Marshall Cavendish Children’s Books, 2007. • Linda Bickerstaﬀ. Nutrition Sense. Rosen Central, 2008. • CK–12. High School Biology. Chapter 38, Lesson 1. • http://www.nlm.nih.gov/medlineplus/ency/article/002404.htm • http://www.textbookofbacteriology.net/normalflora.html • http://en.wikipedia.org/wiki/Vitamins • http://www.alexandrapoweallred.com/

Vocabulary calories Units used to measure the energy in food. carbohydrates Nutrients that include sugars, starches, and ﬁber; give your body energy; organic compound. essential amino acids Amino acids that must come from the proteins in foods; you cannot make these amino acids. insoluble ﬁber Large, complex carbohydrate; does not dissolve in water; moves through the large intestine and helps keep food waste moist so it can pass easily out of the body. lipids Nutrients such as fats that are rich in energy; organic compound. minerals Chemical elements that are needed for body processes. nutrients Chemicals in food that your body needs. proteins Nutrients made up of smaller molecules called amino acids; give your body energy; help control body processes; organic compound. www.ck12.org

saturated fats Found mainly in animal foods, such as meats, whole milk, and eggs; increase cholesterol levels in the blood. soluble ﬁber Large, complex carbohydrate; dissolves in water; helps keep sugar and fat at normal levels in the blood. starch Large, complex carbohydrate; found in foods such as vegetables and grains; broken down by the body into sugars that provide energy. trans fat Manufactured and added to certain foods to keep them fresher for longer. Foods that contain trans fats include cakes, cookies, fried foods, and margarine. unsaturated lipids Found mainly in plant foods, such as vegetable oil, olive oil, and nuts; also found in ﬁsh such as salmon. vitamins Substances that the body needs in small amounts to function properly.

Points to Consider • Think about how you can be sure you are getting enough nutrients? • Do you think knowing the nutrients in the foods you eat are important? • Do you have to keep track of all the nutrients you eat, or is there an easier way to choose foods that provide the nutrients you need?

2.2 Choosing Healthy Foods Lesson Objectives • State how to use MyPyramid to get the proper balance of nutrients. • Describe how to read food labels to choose foods wisely. • Explain how to balance food with exercise.

Check Your Understanding • What is a nutrient? • Why do you need extra energy when you exercise?

Introduction Foods such as whole grain breads, fresh fruits, and fish provide nutrients you need for good health. However, various foods provide different nutrients. You also need different amounts of each nutrient. How can you choose the right mix of foods to get the proper balance of nutrients? Two tools can help you choose foods wisely: MyPyramid and food labels.

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MyPyramid MyPyramid is a diagram that shows how much you should eat each day of foods from six diﬀerent food groups. It recommends the amount of nutrients you need based on your age, your sex, and your levels of activity. MyPyramid is shown in Figure 2.6. The six food groups in MyPyramid are: • • • • • •

Grains—such as bread, rice, pasta, and cereal. Vegetables—such as spinach, broccoli, carrots, and sweet potatoes. Fruits—such as oranges, apples, bananas, and strawberries. Oils—such as vegetable oil, canola oil, olive oil, and peanut oil. Milk—such as milk, yogurt, cottage cheese, and other cheeses. Meat and beans—such as chicken, ﬁsh, soybeans, and kidney beans.

Figure 2.6: MyPyramid can help you choose foods wisely for good health. Each colored band represents a diﬀerent food group. The key shows which food group each color represents. Which colored band of MyPyramid is widest? Which food group does it represent?

Using MyPyramid In MyPyramid, each food group is represented by a band of a diﬀerent color. For example, grains are represented by an orange band, and vegetables are represented by a green band. The wider the band, the more foods you should choose from that food group each day. The orange band in MyPyramid is the widest band. This means that you should choose more foods from the grain group than from any other single food group. The green, blue, and red bands are also relatively wide. Therefore, you should choose plenty of foods from the vegetable, milk, and fruit groups, as well. You should choose the fewest foods from the food group with the narrowest band. Which band is narrowest? Which food group does it represent?

Healthy Eating Guidelines Did you ever hear the saying, “variety is the spice of life”? Variety is also the basis of a healthy eating plan. When you choose foods based on MyPyramid, you should choose a variety of diﬀerent foods. Follow these www.ck12.org

guidelines to make the wisest food choices for good health. Keep in mind that nutritional guidelines may change throughout life. As food provides energy and nutrients for growth and development, nutritional requirements may vary with body weight, age, sex, activity, and body functioning. • Make at least half your daily grain choices whole grains. Examples of whole grains are whole wheat bread, whole wheat pasta, and brown rice. • Choose a variety of different vegetables each day. Be sure to include both dark green vegetables, such as spinach and broccoli, and orange vegetables, such as carrots and sweet potatoes. • Choose a variety of different fruits each day. Select mainly fresh fruits rather than canned fruits and whole fruits instead of fruit juices. • When choosing oils, go for unsaturated oils, such as olive oil, canola oil, or vegetable oil. • Choose low-fat or fat-free milk and other dairy products. For example, select fat-free yogurt and low-fat cheese. • For meats, choose fish, chicken, and lean cuts of beef. Also, be sure to include beans, nuts, and seeds.

What about Ice Cream, Cookies, and Potato Chips? Are you wondering where foods like ice cream, cookies, and potato chips ﬁt into MyPyramid? The white tip of MyPyramid represents foods such as these. These are foods that should be eaten only in very small amounts and not very often. Such foods contain very few nutrients, and are called nutrient-poor. Instead, they are high in fats, sugars, and sodium, but low in other nutrients. Fats, sugars, and sodium are nutrients that you should limit in a healthy eating plan. Ice cream, cookies, and potato chips are also high in Calories. Eating too much of them may lead to unhealthy weight gain.

MyPlate In June 2011, the United States Department of Agriculture replaced My Pyramid with MyPlate. MyPlate depicts the relative daily portions of various food groups. See http://www.choosemyplate.gov/ for further information. The following guidelines accompany MyPlate: 1. Balancing Calories • Enjoy your food, but eat less. • Avoid oversized portions. 2. Foods to Increase • Make half your plate fruits and vegetables. • Make at least half your grains whole grains. • Switch to fat-free or low-fat (1%) milk. 3. Foods to Reduce • Compare sodium in foods like soup, bread, and frozen meals � and choose the foods with lower numbers. • Drink water instead of sugary drinks.

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Figure 2.7: MyPlate is a visual guideline for balanced eating, replacing MyPyramid in 2011.

Food Labels In the United States, packaged foods are required by law to have nutrition facts labels. A nutrition facts label shows the nutrients in a food. Packaged foods are also required to list their ingredients. An ingredient is a speciﬁc item that a food contains.

Using Nutrition Facts Labels An example of a nutrition facts label is shown in Figure 2.8. The information listed at the right of the label tells you what to look for. At the top of the label, look for the serving size. The serving size tells you how much of the food you should eat to get the nutrients listed on the label. A cup of food from the label in Figure 2.8 is a serving. The Calories in one serving are listed next. In this food, there are 250 Calories per serving. Next on the nutrition facts label, look for the percent daily values (% DV) of nutrients. A food is low in a nutrient if the percent daily value of the nutrient is 5% or less. The healthiest foods are low in nutrients such as fats and sodium. A food is high in a nutrient if the percent daily value of the nutrient is 20% or more. The healthiest foods are high in nutrients such as ﬁber and proteins. Look at the percent daily values on the food label in Figure 2.8. Which nutrients have values of 5% or less? These are the nutrients that are low in this food. They include ﬁber, vitamin A, vitamin C, and iron. Which nutrients have values of 20% or more? These are the nutrients that are high in this food. They include sodium, potassium, and calcium.

Using Ingredients Lists The food label in Figure 2.9 includes the list of ingredients in a diﬀerent food. The ingredients on food labels are always listed in descending order. This means that the main ingredient is listed ﬁrst. The main www.ck12.org

Figure 2.8: Reading nutrition facts labels can help you choose healthy foods. Look at the nutrition facts label shown here. Do you think this food is a good choice for a healthy eating plan? Why or why not?

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ingredient is the ingredient that is present in the food in the greatest amount. As you go down the list, the ingredients are present in smaller and smaller amounts.

Figure 2.9: This food label includes the list of ingredients in the food. The main ingredient is enriched wheat ﬂour, followed by high-fructose corn syrup. Why should you avoid foods with ingredients such as these at the top of the ingredients list? Reading the ingredients lists on food labels can help you choose the healthiest foods. At the top of the list, look for ingredients such as whole grains, vegetables, milk, and fruits. These are the ingredients you need in the greatest amounts for balanced eating. Avoid foods that list fats, oils, sugar, or salt at the top of the list. For good health, you should avoid getting too much of these ingredients. Be aware that ingredients such as corn syrup are sugars. You should also use moderation when eating foods that contain ingredients such as white ﬂour or white rice. These ingredients have been processed, and processing removes nutrients. The word ”enriched” is a clue that an ingredient has been processed. Ingredients are enriched with added nutrients to replace those lost during processing. However, enriched ingredients are still likely to have fewer nutrients than unprocessed ingredients.

Balancing Food with Exercise Look at MyPyramid in Figure 2.6. Note the person walking up the side of the pyramid. This shows that exercise is important for balanced eating. Exercise helps you use any extra energy in the foods you eat. The more active you are, the more energy you use. You should try to get at least an hour of physical activity just about every day. Figure 2.10 shows some activities that can help you use extra energy. Any unused energy in food is stored in the body as fat. This is true whether the extra energy comes from carbohydrates, proteins, or lipids. What happens if you take in more energy than you use, day after day? You will store more and more fat and become overweight. Eventually, you may become obese. Obesity is having a very high percentage of body fat. Obese people are at least 20 percent heavier than their healthy weight range. The excess body fat of obesity is linked to many diseases. Obese people often have serious www.ck12.org

Figure 2.10: All of these activities are good ways to exercise and use extra energy. The Calories given for each activity are the number of Calories used in an hour by a person that weighs 100 pounds. Which of these activities uses the most Calories? Which of the activities do you enjoy?

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health problems, such as diabetes, high blood pressure, and high cholesterol. They are also more likely to develop arthritis and some types of cancer. People that remain obese throughout adulthood usually do not live as long as people that stay within a healthy weight range. The current generation of children and teens is the ﬁrst generation in our history that may have a shorter life than their parents. The reason is their high rate of obesity and the health problems associated with obesity. You can avoid gaining weight and becoming obese. The choice is yours. Choose healthy foods by using MyPyramid and reading food labels. Then get plenty of exercise to balance the energy in the foods you eat.

Lesson Summary • MyPyramid shows how much you should eat each day of foods from six diﬀerent food groups. • Reading food labels can help you choose the healthiest foods. • Regular exercise helps you use extra energy and avoid unhealthy weight gain.

Review Questions 1. 2. 3. 4. 5. 6. 7. 8. 9.

List the six food groups represented by MyPyramid. Which food group contains soybeans, kidney beans, and fish? What guideline should you follow in choosing foods from the grains food group? Which ingredient is always listed first on a food label? What happens if you take in more energy than you use, day after day? Explain how you can use MyPyramid to choose foods that provide the proper balance of nutrients. Why should you limit foods like ice cream and potato chips in a healthy eating plan? Explain how you can use food labels to choose foods that are high in fiber. Why should you try to avoid foods with processed ingredients? What are some examples of processed ingredients? 10. How does physical activity help prevent obesity?

Further Reading / Supplemental Links • Eric Schlosser and Charles Wilson. Chew on This: Everything You Don’t Want to Know about Fast Food. Houghton Miﬄin, 2006. • John Burstein. The Shape of Good Nutrition: The Food Pyramid. Crabtree Publishing Company, 2008. • Rose McCarthy. Food Labels: Using Nutrition Information to Create a Healthy Diet. Rosen Publishing Group, 2008. • Sandra Giddens. Making Smart Choices about Food, Nutrition, and Lifestyle. Rosen Central, 2008. CK–12. High School Biology. Chapter 38, Lesson 1. • • • • •

http://www.cfsan.fda.gov/~acrobat/nutfacts.pdf http://www.cfsan.fda.gov/~dms/foodlab.html http://www.health.gov/dietaryguidelines/dga2005/document/pdf/DGA2005.pdf http://www.mypyramid.gov http://www.newswise.com/articles/view/537296

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• http://www.nlm.nih.gov/medlineplus/ency/article/002459.htm • http://www.nlm.nih.gov/medlineplus/exerciseforchildren.html • http://www.prb.org/Articles/2005/WillRisingChildhoodObesityDecreaseUSLifeExpectancy. aspx • http://www.sciencemag.org/cgi/content/summary/307/5716/1716 • http://en.wikipedia.org/wiki

Vocabulary enriched Term used for an ingredient that has been processed; ingredients are enriched with added nutrients to replace those lost during processing; likely to have fewer nutrients than unprocessed ingredients. ingredient A speciﬁc item that a food contains. main ingredient The ingredient that is present in the food in the greatest amount. MyPlate Visual representation of the relative daily portions of various food groups; replaced MyPyramid in 2011. MyPyramid Diagram that shows how much you should eat each day of foods from six diﬀerent food groups. nutrition facts label The label on packaged food that shows the nutrients in the food. obesity Having a very high percentage of body fat; obese people are at least 20 percent heavier than their healthy weight range. serving size Tells you how much of the food you should eat to get the nutrients listed on the label.

Points to Consider • Discuss how foods may be broken down into nutrients that your body can use? For example, how do you think an apple becomes simple sugars that your body can use for energy? Or how might a piece of cheese become proteins that your body can use for building materials?

2.3 The Digestive System Lesson Objectives • • • • •

State the functions of the digestive system. Explain the role of enzymes in digestion. Describe the digestive organs and their functions. Explain the roles of helpful bacteria in the digestive system. List ways to help keep your digestive system healthy.

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Check Your Understanding • What is a chemical reaction? • What is an enzyme? • What are bacteria?

Introduction Nutrients in the foods you eat are needed by the cells of your body. How do the nutrients in foods get to your body cells? What organs and processes break down the foods and make the nutrients available to cells? The organs are those of the digestive system. The processes are digestion and absorption.

What Does the Digestive System Do? The digestive system is the body system that breaks down food and absorbs nutrients. It also gets rid of solid food waste. The main organs of the digestive system are shown in Figure 2.11.

Figure 2.11: This drawing shows the major organs of the digestive system. Trace the path of food through the organs of the digestive system as you read about them in this lesson. Digestion is the process of breaking down food into nutrients. There are two types of digestion: mechanical digestion and chemical digestion. In mechanical digestion, large chunks of food are broken down into small pieces. This is a physical process. In chemical digestion, large food molecules are broken down into small nutrient molecules. This is a chemical process. Absorption is the process in which substances are taken up by the blood. After food is broken down into small nutrient molecules, the molecules are absorbed by the blood. Then the nutrient molecules travel in the bloodstream to cells throughout the body. www.ck12.org

Some substances in food cannot be broken down into nutrients. They remain behind in the digestive system after the nutrients are absorbed. Any substances in food that cannot be digested and absorbed pass out of the body as solid waste. The process of passing solid food waste out of the body is called elimination.

The Role of Enzymes in Digestion Chemical digestion could not take place without the help of digestive enzymes. An enzyme is a protein that speeds up chemical reactions in the body. Digestive enzymes speed up chemical reactions that break down large food molecules into small nutrient molecules. Did you ever use a wrench, like the one in Figure 2.12, to tighten a bolt? You could tighten a bolt with your fingers, but it would be difficult and slow. If you use a wrench, you can tighten a bolt much more easily and quickly. Enzymes are like wrenches. They make it much easier and quicker for chemical reactions to take place. Like a wrench, enzymes can also be used over and over again. But you need the appropriate size and shape of the wrench to efficiently tighten the bolt, just like each enzyme is specific for the reaction it helps.

Figure 2.12: Turning a bolt with a wrench is easier and quicker than trying to turn a bolt with your ﬁngers. How is a wrench like an enzyme? Digestive enzymes are secreted by the organs of the digestive system. Examples of digestive enzymes are: • Amylase is produced by the mouth. It helps break down large starches molecules into smaller sugar molecules. • Pepsin is produced by the stomach. Pepsin is a protease; it helps break down proteins into amino acids. • Trypsin is produced in the pancreas. Trypsin is a protease; it cleaves peptide chains. • Pancreatic lipase is secreted by the pancreas. It is a lipase, used to break apart fats.

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â&#x20AC;˘ Deoxyribonuclease and ribonuclease are nucleases secreted by the pancreas. They are enzymes that break bonds in nucleic acid backbones.

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Bile salts are bile acids whose main function is to facilitate the processing of dietary fat. Bile acids are made in the liver. Upon eating a meal, the contents of the gallbladder are secreted into the intestine, where bile acids break down dietary fats. Bile acids serve other functions, including eliminating cholesterol from the body.

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Hormones and Digestion If you are a typical teenager, you like to eat. Chances are, if you could, you would be eating in class right now. For your body to break down, absorb and distribute the nutrients, and maintain homeostasis, requires both the digestive system and endocrine system to work together. Digestive hormones are made by cells lining the stomach and small intestine. These hormones cross into the blood where they can aﬀect other parts of the digestive system. Some of these hormones are listed below. • Gastrin-Stimulates gastric acid secretion. • Cholecystokinin-Stimulates secretion of pancreatic enzymes, and contraction and emptying of the gall bladder. • Secretin-Stimulates secretion of water and bicarbonate from the pancreas and bile ducts. • Ghrelin-A strong stimulant for appetite and feeding. • Gastric inhibitory polypeptide-Inhibits gastric secretion; also causes the release of insulin in response to elevated blood glucose concentration.

Digestive Organs and Their Roles The mouth and stomach are just two of the organs of the digestive system. Other digestive system organs are the esophagus, small intestine, and large intestine. From Figure 2.11, you can see that the digestive organs form a long tube. In adults, this tube is about 9 meters (30 feet) long! At one end of the tube is the mouth. At the other end is the anus. Food enters the mouth and then passes through the rest of the digestive system. Food waste leaves the body through the anus. The organs of the digestive system are lined with muscles. The muscles contract, or tighten, to push food through the system. This is shown in Figure 2.13. The muscles contract in waves. The waves pass through the digestive system like waves through a Slinky®. This movement of muscle contractions is called peristalsis. Without peristalsis, food would not be able to move through the digestive system. Peristalsis is an involuntary process, which means that it occurs without your conscious control.

Figure 2.13: This diagram shows how muscles push food through the digestive system. Muscle contractions travel through the system in waves, pushing the food ahead of them. This is called peristalsis. The liver, gall bladder, and pancreas are also organs of the digestive system. They are shown in Figure www.ck12.org

2.14. Food does not pass through these three organs. However, these organs are important for digestion. They secrete or store enzymes or other chemicals that are needed to help digest food chemically.

Figure 2.14: This drawing shows the liver, gall bladder, and pancreas. These organs are part of the digestive system. Food does not pass through them, but they secrete substances needed for chemical digestion.

Mouth, Esophagus, and Stomach The mouth is the first organ that food enters. However, digestion may start even before you put the first bite of food into your mouth. Just seeing or smelling food can cause the release of saliva and digestive enzymes in your mouth. Once you start eating, saliva wets the food, which makes it easier to break up and swallow. Digestive enzymes, including amylase, start breaking down starches into sugars. Your tongue helps mix the food with the saliva and enzymes. Your teeth also help digest food. Your front teeth are sharp. They cut and tear food when you bite into it. Your back teeth are broad and flat. They grind food into smaller pieces when you chew. Chewing is part of mechanical digestion. Your tongue pushes the food to the back of your mouth so you can swallow it. When you swallow, the lump of chewed food passes down your throat to your esophagus. The esophagus is a narrow tube that carries food from the throat to the stomach. Food moves through the esophagus because of peristalsis. At the lower end of the esophagus, a circular muscle controls the opening to the stomach. The muscle relaxes to let food pass into the stomach. Then the muscle contracts

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again to prevent food from passing back into the esophagus. Some people think that gravity moves food through the esophagus. If that were true, food would move through the esophagus only when you are sitting or standing upright. In fact, because of peristalsis, food can move through the esophagus no matter what position you are in—even upside down. Just don’t try to swallow food when you upside down! You could choke if you try to swallow when you are not upright. The stomach is a sac-like organ at the end of the esophagus. It has thick muscular walls. The muscles alternately contract and relax. This churns the food and helps break it into smaller pieces. The churning also mixes the food with the enzyme pepsin and other chemicals that are secreted by the stomach. The pepsin and other chemicals help digest proteins chemically. Water, salt, and simple sugars can be absorbed into the blood from the stomach. Most other substances are broken down further in the small intestine before they are absorbed. The stomach stores food until the small intestine is ready to receive it. A circular muscle controls the opening between the stomach and small intestine. When the small intestine is empty, the muscle relaxes. This lets food pass from the stomach into the small intestine.

Small Intestine The small intestine is narrow tube that starts at the stomach and ends at the large intestine (see Figure 2.11). In adults, the small intestine is about 7 meters (23 feet) long. It is made up of three parts: the duodenum, jejunum, and ileum. Each part has different functions. The duodenum is the first part of the small intestine. This is where most chemical digestion takes place. Many enzymes and other chemicals are secreted here. Some are secreted by the duodenum itself. Others are secreted by the pancreas or liver. The jejunum is the second part of the small intestine. This is where most nutrients are absorbed into the blood. The jejunum is lined with tiny “fingers” called villi. A magnified picture of villi is shown in Figure 2.15. Villi contain microscopic blood vessels. Nutrients are absorbed into the blood through these tiny vessels. There are millions of villi, so altogether there is a very large area for absorption to take place. In fact, villi make the inner surface area of the small intestine 1,000 times larger than it would be without them. The entire inner surface area of the small intestine is about as big as a basketball court! The ileum is the third part of the small intestine. Like the jejunum, the ileum is covered with villi. A few remaining nutrients are absorbed in the ileum. From the ileum, any remaining food waste passes into the large intestine. The small intestine is much longer than the large intestine. So why is it called “small”? If you compare the small and large intestines in Figure 2.11, you will see why. The small intestine is smaller in width that the large intestine.

Large Intestine The large intestine is a relatively wide tube that connects the small intestine with the anus. In adults, it is about 1.5 meters (5 feet) long. Waste enters the large intestine from the small intestine in a liquid state. As the waste moves through the large intestine, excess water is absorbed from it. After the excess water is absorbed, the remaining solid waste is called feces. Circular muscles control the anus. They relax to let the feces pass out of the body through the anus. After feces pass out of the body, they are called stool. The excretion of stool is referred to as a bowel movement. www.ck12.org

Figure 2.15: This is what the villi lining the small intestine look like when magniﬁed. Each one is actually only about 1 millimeter long. Villi are just barely visible with the unaided eye.

Liver The liver has a wide range of functions, a few of which are blood detoxification, maintaining glucose balance, protein synthesis, and production of biochemicals necessary for digestion. The liver is necessary for survival; there is currently no way to compensate for the absence of liver function. The liver is one of the most important organs in the body when it comes to detoxifying or getting rid of foreign substances or toxins, especially from the gut. The liver filters blood from the intestine. This filtering process can remove a wide range of microorganisms such as bacteria, fungi, viruses and parasites from the blood. Almost 2 quarts of blood pass through the liver every minute. The liver also has several roles in maintaining glucose levels, including gluconeogenesis (the synthesis of glucose from certain amino acids, lactate or glycerol), glycogenolysis (the breakdown of glycogen into glucose), and glycogenesis (the formation of glycogen from glucose).

Bacteria in the Digestive System The large intestine provides a home for trillions of bacteria. Most of these bacteria are helpful. They have several roles in the body. For example, intestinal bacteria: • • • •

Produce vitamins B12 and K. Control the growth of harmful bacteria. Break down poisons in the large intestine. Break down some substances in food that cannot be digested, such as ﬁber and some starches and sugars.

Keeping Your Digestive System Healthy Most of the time, you probably aren’t aware of your digestive system. It works well without causing any problems. However, most people have problems with their digestive system at least once in awhile. Did

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you ever eat something that didn’t “agree” with you? Maybe you had a stomachache or felt sick to your stomach. Maybe you had diarrhea. These could be symptoms of foodborne illness.

Foodborne Illness Harmful bacteria can enter your digestive system in food and make you sick. This is called foodborne illness. The bacteria, or the toxins they produce, may cause vomiting or cramping, in addition to the symptoms mentioned above. You can help prevent foodborne illness by following a few simple rules: • Keep hot foods hot and cold foods cold. This helps prevent any bacteria in the foods from multiplying. • Wash your hands before you prepare or eat food. This helps prevent bacteria on your hands from getting on the food. • Wash your hands after you touch raw foods such as meats, poultry, ﬁsh, or eggs. These foods often contain bacteria that your hands could transfer to your mouth. • Cook meats, poultry, ﬁsh, and eggs thoroughly before eating them. The heat of cooking kills any bacteria the foods may contain so they cannot make you sick.

Food Allergies Food allergies are like other allergies. They occur when the immune system reacts to harmless substances as though they were harmful. Almost 10 percent of children have food allergies. Some of the foods most likely to cause allergies are shown in Figure 2.16. Eating foods you are allergic to may cause vomiting, diarrhea, or skin rashes. Some people are very allergic to certain foods. Eating even tiny amounts of the foods causes them to have serious symptoms, such as difficulty breathing. If they eat the foods by accident, they may need emergency medical treatment. If you think you may have food allergies, a doctor can test you to find out for sure. The tests will identify which foods you are allergic to. Then you can avoid eating these foods. This is the best way to prevent the symptoms of food allergies. To avoid the foods you are allergic to, you may have to read food labels carefully. This is especially likely if you are allergic to common food ingredients, such as soybeans, wheat, or peanuts. A food intolerance, or food sensitivity, is different to a food allergy. A food intolerance happens when the digestive system is unable to break down a certain type of food. This can result in stomach cramping, diarrhea, tiredness, and weight loss. Food intolerances are often mistakenly called allergies. Lactose intolerance is a food intolerance. A person who is lactose intolerant does not make enough lactase, the enzyme that breaks down the milk sugar lactose. About 75 percent of the world’s population is lactose intolerant.

Constipation Constipation means that a person has three bowel movement or less each week. The stools may also be hard and dry. Sometimes the stools are diﬀicult or painful to pass. The person may feel “draggy” and full. Some people think they should have a bowel movement every day. This is not necessarily true. There is no “right” number of bowel movements. What is normal for one person may not be normal for another. It depends on the foods they eat, how much they exercise, and other factors. At one time or another, almost everyone has constipation. In most cases, it lasts for a short time and isn’t serious. However, constipation can be very uncomfortable. You can follow these tips to help prevent it: www.ck12.org

Figure 2.16: Some of the foods that commonly cause allergies are shown here. They include nuts, eggs, ďŹ sh, milk, and shellďŹ sh. Are you allergic to any of these foods?

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• • • •

Eat enough high-ﬁber foods, including vegetables, fruits, beans, and whole grains. Drink plenty of water and other liquids. Exercise regularly. Don’t ignore the urge to have a bowel movement.

Following these tips will help keep your digestive system working properly. It will help you feel good and stay healthy.

Lesson Summary • The digestive system breaks down food, absorbs nutrients, and gets rid of food wastes. • Digestive enzymes speed up the reactions of chemical digestion. • The main organs of the digestive system are the mouth, esophagus, stomach, small intestine, and large intestine. • Bacteria in the large intestine produce vitamins and have other roles in the body. • You can follow simple tips to help keep your digestive system healthy.

Review Questions 1. 2. 3. 4. 5. 6. 7. 8.

What are three functions of the digestive system? Describe the roles of the mouth in digestion. In which organs of the digestive system does absorption of nutrients take place? Identify two roles of helpful bacteria in the large intestine. List two rules that can help prevent foodborne illness. Explain the role of enzymes in digestion. Give examples to illustrate your answer. Describe peristalsis, and explain why it is necessary for digestion. How can the inner surface area of the small intestine be as big as a basketball court? How does this help the small intestine absorb nutrients? 9. Assume a person has an illness that prevents the large intestine from doing its normal job. Why might the person have diarrhea? 10. Explain why eating high-ﬁber foods can help prevent constipation.

Further Reading / Supplemental Links CK–12, High School Biology, Chapter 38, Lesson 2. • Carol Ballard. The Digestive System. Heinemann Library, 2003. • Robert J. Sullivan. Digestion and Nutrition. Chelsea House Publications, 2004. • Sherri Mabry Gordon. Peanut Butter, Milk, and Other Deadly Threats: What You Should Know about Food Allergies. Enslow Publishers, 2006. • Steve Parker. Break It Down: The Digestive System. Raintree, 2006. • http://digestive.niddk.nih.gov/ddiseases/pubs/bacteria • http://digestive.niddk.nih.gov/ddiseases/pubs/constipation_ez • http://hypertextbook.com/facts/2001/AnneMarieThomasino.shtml • http://kalishresearch.com/a_gluten.html • http://physiwiki.wetpaint.com/page/Chapter+4:+Enzymes+and+Energy?t=anon • http://www.biologyinmotion.com/minilec/wrench.html www.ck12.org

• http://www.fsis.usda.gov/Factsheets/Cleanliness_Helps_Prevent_Foodborne_Illness/index. asp • http://www.mayoclinic.com/health/food-allergies/AA00057 • http://www.textbookofbacteriology.net/normalflora.html • http://en.wikipedia.org/wiki/Stomach

Vocabulary absorption Process in which substances are taken up by the blood; after food is broken down into small nutrient molecules, the molecules are absorbed by the blood. chemical digestion Digestion in which large food molecules are broken down into small nutrient molecules. constipation Having three or less bowel movements each week. digestion Process of breaking down food into nutrients. digestive system Body system that breaks down food, absorbs nutrients, and gets rid of solid food waste. duodenum The ﬁrst part of the small intestine; where most chemical digestion takes place. elimination The process in which solid food waste passes out of the body. enzyme A substance, usually a protein, that speeds up chemical reactions in the body. esophagus The narrow tube that carries food from the throat to the stomach. food allergies A condition in which the immune system reacts to harmless substances in food as though they were harmful. foodborne illness An illness caused by harmful bacteria that enter the digestive system in food. food intolerance Occurs when the digestive system is unable to break down a certain type of food. ileum The third part of the small intestine; covered with villi; the few remaining nutrients are absorbed in the ileum. jejunum The second part of the small intestine; where most nutrients are absorbed into the blood; lined with tiny “ﬁngers” called villi. large intestine The relatively wide tube between the small intestine and anus where excess water is absorbed from food waste. mechanical digestion Digestion in which large chunks of food are broken down into small pieces. peristalsis Involuntary muscle contractions which push food through the digestive system.

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small intestine The narrow tube between the stomach and large intestine where most chemical digestion and absorption of nutrients take place. stomach The sac-like organ at the end of the esophagus where proteins are digested. villi Contain microscopic blood vessels; nutrients are absorbed into the blood through these tiny vessels; located on the jejunum and the ileum.

Points to Consider â&#x20AC;˘ After nutrients are absorbed into the blood, think about how the blood could carry them to all the cells of the body. How does the blood travel? What keeps the blood moving?

Image Sources (1) CK-12 Foundation. http://www.kikkomanusa.com/_images/uploaded_images/420C6A.jpg http://commons.wikimedia.org/wiki/Image:DarkRedKidney.jpg http://www.iom.edu/Object.File/Master/21/372/0.pdf http://www.youngwomenshealth.org/protein.html. (a)GNU-FDL (b)GNU Free Documentation (c)Public Domain. (2) CK-12 Foundation. http://www.mypyramid.gov/. Public Domain. (3) http://kalishresearch.com/a_gluten.html. GNU-FDL. (4) http://www.water.ca.gov/swp/images/geography/Kids.jpg. Public Domain. (5) http://www.choosemyplate.gov/. Public Domian. (6) CK-12 Foundation. http://en.wikipedia.org/wiki/Image:BauchOrgane_wn.png. GNU-FDL. (7) Jean Brainard. . CC-BY-SA. (8) http://commons.wikimedia.org/wiki/File:Eggs_in_carton.jpg http://commons.wikimedia.org/wiki/Image:Rainbow_Trout.jpg http://commons.wikimedia.org/wiki/Image:Milk_glass.jpg http://commons.wikimedia.org/wiki/Image:Garnelen_im_Verkauf_fcm.jpg http://commons.wikimedia.org/wiki/Image:Shellfish.jpg. (a)Public Domain (b)CC-BY-SA (c)Public Domain (d)CC-BY-SA (e)Public Domain (f)CC-BY-SA. (9) http://www.hud.gov/local/ny/news/2005-06-27.cfm http://commons.wikimedia.org/wiki/Image:Walking.jpg http://whatscookingamerica.net/Information/CalorieBurnChart.htm http://www.cdc.gov/nchs/data/nhanes/growthcharts/set1clinical/cj41l022.pdf http://www.cdc.gov/nchs/data/nhanes/growthcharts/set2/chart%2003.pdf http://www.self.com/health/activity/calculators/soccer basketball. (a)GNU Free Documentation (b)Public Domain (c)CC-BY_SA 2.0 (d)Public Domain. (10) CK-12 Foundation. http://commons.wikimedia.org/wiki/Image:Mixed_bread_loaves.jpg http://commons.wikimedia.org/wiki/Image:Acornsquash.jpg http://whatscookingamerica.net/NutritionalChart.htm http://www.annecollins.com/dietary-carbs/carbs-in-veggies.htm http://www.carbohydrate-counter.org/. (a)Public Domain (b)CC-BY-SA 2.0 (c)Public Domain. www.ck12.org

(11) http://www.ehponline.org/docs/2006/114-2/saladgirl.jpg. Public Domain. (12) http://en.wikibooks.or/w/index.php?title=File: Anatomy_and_physiology_of_animals_Peristalis.jpg&#38;filetimestamp=20071126004402. CC-BY. (13) CK-12 Foundation. http://commons.wikimedia.org/wiki/Image:Green_peas.jpg http://commons.wikimedia.org/wiki/Image:PearPhoto.jpg http://commons.wikimedia.org/wiki/File:Avocado.jpeg http://www.bellaonline.com/articles/art49482.asp http://www.iom.edu/Object.File/Master/21/372/0.pdf http://www.mayoclinic.com/health/high-fiber-foods/NU00582. (a)Public Domain (b)GNU-FDL (c)GNU-FDL (d)Public Domain. (14) http://commons.wikimedia.org/wiki/Image:Digestivetract.gif. Public Domain. (15) HHS. http://www.health.gov/dietaryguidelines/dga2005/healthieryou/images/img_tips_ food_label.gif. Public Domain. (16) http://images1.comstock.com/Imagewarehouse/RF/SITECS/NLWMCompingVersions/0003000/ 3500-3999/KS3516.jpg. GNU Free Documentation.

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Chapter 3 Biotechnology 3.1 Lesson 10.1: DNA Technology Lesson Objectives • • • • • •

What is meant by DNA technology? What is the Human Genome Project? Describe the goals of the Human Genome Project. Describe gene cloning and the processes involved. What is PCR? Describe the processes involved in PCR.

Introduction Is it really possible to clone people? Another question is, should we clone people? Are scientific fantasies, such as depicted on TV shows such as Star Trek or in the movie GATTACA, actually a possibility? Who can really say? How, really, will science affect our future? The answers partially lie in the field of biotechnology. Biotechnology is technology based on biological applications. These applications are increasingly used in medicine, agriculture and food science. Biotechnology combines many features of biology, including genetics, molecular biology, biochemistry, embryology, and cell biology. Many aspects of biotechnology center around DNA and its applications, otherwise known as DNA technology. We could devote a whole textbook to current applications of biotechnology; in this chapter, however, we will focus on the applications towards medicine and the extension into the forensic sciences. First, though, we need to understand DNA technology.

DNA Technology What is DNA technology? Is it using and manipulating DNA to help people? Is it using DNA to make better medicines and individualized treatments? Is it analyzing DNA to determine predispositions to genetic diseases? The answers to these questions, and many more, is yes. And the answers to many of these issues begin with the Human Genome Project. www.ck12.org

The Human Genome Project If we are all 99.9% genetically identical, what makes us different? How does that 0.1% make us tall or short, light or dark, develop cancer or not? To understand that 0.1%, we also need to understand the other 99.9%. Understanding the human genome is the goal of The Human Genome Project (HGP). This project, publicly funded by the United States Department of Energy (DOE) (Figure 3.2); and the National Human Genome Research Institute (NHGRI), part of the National Institutes of Health (NIH), may be one of the landmark scientific events of our lifetime. Our Molecular Selves video discusses the human genome, and is available at http://www.genome. gov/25520211 or http://www.youtube.com/watch?v=XuUpnAz5y1g&#38;feature=related. The goal of the HGP is to understand the genetic make-up of the human species by determining the DNA sequence of the human genome (Figure 3.3);and the genome of a few model organisms. However, it is not just determining the 3 billion bases; it is understanding what they mean. Today, all 3 billion base pairs have been sequenced, and the genes in that sequence are in the process of being identified and characterized. A preliminary estimate of the number of genes in the human genome is around 22,000 to 23,000. The sequence of the human DNA is stored in databases available to anyone on the Internet. The U.S. National Center for Biotechnology Information (NCBI), part of the NIH, as well as comparable organizations in Europe and Japan, maintain the genomic sequences in a database known as Genbank. Protein sequences are also maintained in this database. The sequences in these databases are the combined sequences of anonymous donors, and as such do not yet address the individual differences that make us unique. However, the known sequence does lay the foundation to identify the unique differences among all of us. Most of the currently identified variations among individuals will be single nucleotide polymorphisms, or SNPs. A SNP (pronounced ”snip”) is a DNA sequence variation occurring at a single nucleotide in the genome. For example, two sequenced DNA fragments from different individuals, GGATCTA to GGATTTA, contain a difference in a single nucleotide. If this base change occurs in a gene, the base change then results in two alleles: the C allele and the T allele. Remember an allele is an alternative form of a gene. Almost all common SNPs have only two alleles. The effect of these SNPs on protein structure and function, and any effect on the resulting phenotype, is an extensive field of study.

Gene Cloning You probably have heard of cloning. Whereas cloning of humans has many ethical issues associated with it, the cloning of genes has been ongoing for well over 30 years, with cloning of animals occurring more recently. Gene cloning, also known as molecular cloning, refers to the process of isolating a DNA sequence of interest for the purpose of making multiple copies of it. The identical copies are clones. In 1973, Stanley Cohen and Herbert Boyer developed techniques to make recombinant DNA, a form of artiﬁcial DNA. Recombinant DNA is engineered through the combination of two or more DNA strands, combining DNA sequences which would not normally occur together. In other words, selected DNA (or the DNA of ”interest”) is inserted into an existing organismal genome, such as a bacterial plasmid DNA or some other sort of vector. The recombinant DNA can then be inserted into another cell, such as a bacterial cell, for ampliﬁcation and possibly production of the resulting protein. This process is called transformation, the genetic alteration of a cell resulting from the uptake, incorporation, and expression of foreign genetic material. Recombinant DNA technology was made possible by the discovery of restriction endonucleases.

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Figure 3.1: Human Genome Project; An introduction to the ongoing Human Genome Project. The dynamic 3D animation will take you ”inside” for a close up look at the complexity of the cell. Completed in 2003, the Human Genome Project (HGP) was a 13-year project coordinated by the U.S. Department of Energy and the National Institutes of Health. During the early years of the HGP, the Wellcome Trust (U.K.) became a major partner; additional contributions came from Japan, France, Germany, China, and others. See our history page for more information. Project goals were to identify all the approximately 20,000-25,000 genes in human DNA, determine the sequences of the 3 billion chemical base pairs that make up human DNA, store this information in databases, improve tools for data analysis, transfer related technologies to the private sector, and address the ethical, legal, and social issues (ELSI) that may arise from the project. Though the HGP is finished, analyses of the data will continue for many years. Follow this ongoing research on our Progress page. An important feature of the HGP project was the federal government’s long-standing dedication to the transfer of technology to the private sector. By licensing technologies to private companies and awarding grants for innovative research, the project catalyzed the multibillion-dollar U.S. biotechnology industry and fostered the development of new medical applications. Knowledge about the effects of DNA variations among individuals can lead to revolutionary new ways to diagnose, treat, and someday prevent the thousands of disorders that affect us. Besides providing clues to understanding human biology, learning about nonhuman organisms’ DNA sequences can lead to an understanding of their natural capabilities that can be applied toward solving challenges in health care, agriculture, energy production, environmental remediation, and carbon sequestration. A genome is all the DNA in an organism, including its genes. Genes carry information for making all the proteins required by all organisms. These proteins determine, among other things, how the organism looks, how well its body metabolizes food or fights infection, and sometimes even how it behaves. DNA is made up of four similar chemicals (called bases and abbreviated A, T, C, and G) that are repeated millions or billions of times throughout a genome. The human genome, for example, has 3 billion pairs of bases. The particular order of As, Ts, Cs, and Gs is extremely important. The order underlies all of life’s diversity, even dictating whether an organism is human or another species such as yeast, rice, or fruit fly, all of which have their own genomes and are themselves the focus of genome projects. Because all organisms are related through similarities in DNA sequences, insights gained from nonhuman genomes often lead to new knowledge about human biology. Producer: NIH Contact Information: http://www.genome.gov/Pages/EducationKit/ Creative Commons license: Attribution-NonCommercial-NoDerivs (Watch Youtube Video) http://www.youtube.com/v/XuUpnAz5y1g?f=videos38;c=ytapi-CK12Fo undation-Flexrwikiimport-fg5akohk-038;d=AT8BNcsNZiISDLhsoSt-gq IO88HsQjpE1a8d1GxQnGDm38;app=youtube_gdata

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Figure 3.2: The Human Genome Project logo of the DOE.

Figure 3.3: A depiction of DNA sequence analysis. Note the 4 colors utilized, each representing a separate base.

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Restriction Enzyme Digestion and Ligation In the classical restriction enzyme digestion and ligation cloning protocols, cloning of any DNA fragment essentially involves four steps: 1. 2. 3. 4.

isolation of the DNA of interest (or target DNA) ligation transfection (or transformation) a screening/selection procedure.

For an overview of cloning, see http://www.hhmi.org/biointeractive/media/DNAi_genetic_eng-sm. mov.

Isolation of DNA Initially, the DNA fragment to be cloned needs to be isolated. This DNA of interest may be a gene, part of a gene, a promoter, or another segment of DNA, and is frequently isolated by the Polymerase Chain Reaction (PCR) or restriction enzyme digestion. A restriction enzyme (or restriction endonuclease) is an enzyme that cuts double-stranded DNA at a speciﬁc sequence (Table 3.1). The enzyme makes two incisions, one through each strand of the double helix, without damaging the nitrogenous bases. This produces either overlapping ends (also known as sticky ends) or blunt ends. Table 3.1: A.

G↓ AATTC

CTTAA↑ G

CCC↓ GGG GGG↑ CCC

A. EcoRI digestion produces overlapping ”sticky” ends: The enzyme cleaves between the G and A on both strands. B. SmaII restriction enzyme cleavage produces ”blunt” ends. The enzyme cleaves between the G and C on both strands. (Source: Created by: Doug Wilkin, License: CC-BY-SA) The 1978 Nobel Prize in Medicine was awarded to Daniel Nathans and Hamilton Smith for the discovery of restriction endonucleases. The ﬁrst practical use of their work was the manipulation of E. coli bacteria to produce human insulin for diabetics.

Ligation Once the DNA of interest is isolated, a ligation procedure is necessary to insert the ampliﬁed fragment into a vector to produce the recombinant DNA molecule. Restriction fragments (or a fragment and a plasmid/vector) can be spliced together, provided their ends are complementary. Blunt end ligation is also possible. The plasmid or vector (which is usually circular) is digested with restriction enzymes, opening up the vector to allow insertion of the target DNA. The two DNAs are then incubated with DNA ligase, an enzyme that can attach together strands of DNA with double strand breaks. This produces the recombinant DNA molecule. Figure 3.4 depicts a plasmid with two additional segments of DNA ligated into the plasmid, producing the recombinant DNA molecule. Figure 3.5 depicts DNA before and after ligation. www.ck12.org

Figure 3.4: This image shows a line drawing of a plasmid. The plasmid is drawn as two concentric circles that are very close together, with two large segments and one small segment depicted. The two large segments (1 and 2) indicate antibiotic resistances usually used in a screening procedure, and the small segment (3) indicates an origin of replication. The resulting DNA is a recombinant DNA molecule.

Figure 3.5: Sticky ends produced by restriction enzyme digestion can be joined with the enzyme DNA ligase.

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Transfection and Selection Following ligation, the recombinant DNA is placed into a host cell, usually bacterial, in a process called transfection or transformation. Finally, the transfected cells are cultured. Many of these cultures may not contain a plasmid with the target DNA as the transfection process is not usually 100% successful, so the appropriate cultures with the DNA of interest must be selected. Many plasmids/vectors include selectable markers - usually some sort of antibiotic resistance (Figure 3.4). When cultures are grown in the presence of an antibiotic, only bacteria transfected with the vector containing resistance to that antibiotic should grow. However, these selection procedures do not guarantee that the DNA of insert is present in the cells. Further analysis of the resulting colonies is required to conﬁrm that cloning was successful. This may be accomplished by means of a process known as PCR (see below) or restriction fragment analysis, both of which need to be followed by gel electrophoresis and/or DNA sequencing (DNA sequence analysis). DNA sequence analysis (the analysis of the order of the nitrogenous bases that make up the DNA), PCR, or restriction fragment analysis will all determine if the plasmid/vector contains the insert. Restriction fragment analysis is digestion of isolated plasmid/vector DNA with restriction enzymes. If the isolated DNA contains the target DNA, that fragment will be excised by the restriction enzyme digestion. Gel electrophoresis will separate DNA molecules based on size and charge. Examples are shown in Figure 3.6.

Gel Electrophoresis Gel electrophoresis is an analytical technique used to separate DNA fragments by size and charge. Notice in Figure 3.6 that the ”gels” are rectangular in shape. The gels are made of a gelatin-like material of either agarose or polyacrylamide. An electric field, with a positive charge applied at one end of the gel, and a negative charge at the other end, forces the fragments to migrate through the gel. DNA molecules migrate from negative to positive charges due to the net negative charge of the phosphate groups in the DNA backbone. Longer molecules migrate more slowly through the gel matrix. After the separation is completed, DNA fragments of different lengths can be visualized using a fluorescent dye specific for DNA, such as ethidium bromide. The resulting stained gel shows bands correspond to DNA molecules of different lengths, which also correspond to different molecular weights. Band size is usually determined by comparison to DNA ladders containing DNA fragments of known length. Gel electrophoresis can also be used to separate RNA molecules and proteins. Recombinant DNA technology (5d, 5e) is discussed in the following videos and animations: http:// www.youtube.com/watch?v=x2jUMG2E-ic (4:36), http://www.youtube.com/watch?v=Jy15BWVxTC0 (0:50), http://www.youtube.com/watch?v=sjwNtQYLKeU&#38;feature=related (7:20), http://www.youtube. com/watch?v=Fi63VjfhsfI (3:59).

The Polymerase Chain Reaction The Polymerase Chain Reaction (PCR) is used to amplify specific regions of a DNA strand millions of times. A region may be a number of loci, a single gene, a part of a gene, or a non-coding sequence. This technique produces a useful quantity of DNA for analysis, be it medical, forensic or some other form of analysis. Amplification of DNA from as little as a single cell is possible. Whole genome amplification is also possible. PCR utilizes a heat stable DNA polymerase, Taq polymerase, named after the thermophilic bacterium Thermus aquaticus, from which it was originally isolated. T. aquaticus is a bacterium that lives in hot springs and hydrothermal vents, and Taq polymerase is able to withstand the high temperatures required www.ck12.org

Figure 3.6: Agarose gel following agarose gel electrophoresis on UV light box: In the gel with UV illumination (left), the ethidium bromide stained DNA glows pink; Right, photo of a gel. Far left: DNA ladder of fragments of known length. Lane 1: A PCR product of just over 500 bases. Lane 2: Restriction digest showing the 500 base fragment cut from a 4.5 kb plasmid vector.

Figure 3.7: A 3D animation illustrating the process by which a protein is mass-produced using spliced DNA and bacterial replication. For more animation samples, please visit: www.demonstratives.com. (Watch Youtube Video) http://www.youtube.com/v/x2jUMG2E-ic?f=videos38;c=ytapi-CK12Fo undation-Flexrwikiimport-fg5akohk-038;d=AT8BNcsNZiISDLhsoSt-gq IO88HsQjpE1a8d1GxQnGDm38;app=youtube_gdata

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Figure 3.8: A easy to understand animation on Gene Cloning. Based on the popular diagram in the Campbell Reese Honors Biology Text Book The Song is Thunder by Boys like Girls. I do not Own the SONG OR THE TEXT BOOK Duhhhâ&#x20AC;&#x17E; (Watch Youtube Video) http://www.youtube.com/v/Jy15BWVxTC0?f=videos38;c=ytapi-CK12Fo undation-Flexrwikiimport-fg5akohk-038;d=AT8BNcsNZiISDLhsoSt-gq IO88HsQjpE1a8d1GxQnGDm38;app=youtube_gdata

Figure 3.9: Animation demonstrating the concept and key steps of molecular cloning (Watch Youtube Video) http://www.youtube.com/v/sjwNtQYLKeU?f=videos38;c=ytapi-CK12Fo undation-Flexrwikiimport-fg5akohk-038;d=AT8BNcsNZiISDLhsoSt-gq IO88HsQjpE1a8d1GxQnGDm38;app=youtube_gdata

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Figure 3.10: How Gel Electrophoresis works. Ilistrated using a video editor as well as animations made in Scientific Visualization(Cinema 4d R11). Message or comment me for tutorial ideas! (Watch Youtube Video) http://www.youtube.com/v/Fi63VjfhsfI?f=videos38;c=ytapi-CK12Fo undation-Flexrwikiimport-fg5akohk-038;d=AT8BNcsNZiISDLhsoSt-gq IO88HsQjpE1a8d1GxQnGDm38;app=youtube_gdata to denature DNA during PCR (discussed below). Taq polymerase’s optimum temperature for activity is between 75°C and 80°C. Recently other DNA polymerases have also been used for PCR. A basic PCR involves a series of repeating cycles involving three main steps (see Figure 3.11): 1. denaturation of the double stranded DNA 2. annealing of specific oligonucleotide primers 3. extension of the primers to amplify the region of DNA of interest These steps will be discussed in additional detail below. The oligonucleotide primers are single stranded pieces of DNA that correspond to the 5’ and 3’ ends of the DNA region to be amplified. These primers will anneal to the corresponding segment of denatured DNA. Taq Polymerase, in the presence of free deoxynucleotide triphosphates (dNTPs), will extend the primers to create double stranded DNA. After many cycles of denaturation, annealing and extension, the region between the two primers will be amplified. The PCR is commonly carried out in a thermal cycler, a machine that automatically allows heating and cooling of the reactions to control the temperature required at each reaction step (see below). The PCR usually consists of a series of about 30 to 35 cycles. Most commonly, PCR is carried out in three repeating steps, with some modifications for the first and last step. PCR is usually performed in small tubes or wells in a tray, each often beginning with the complete genome of the species being studied. As only a specific sequence from that genome is of interest, the sequence specific primers are targeted to that sequence. PCR is done with all the building blocks necessary to create DNA: template DNA, primers, dNTPs, and a polymerase. The three basic steps of PCR (Figure 3.11) are: • Denaturation step: This step is the first regular cycling event and consists of heating the reaction to 94 - 98°C for 30 to 60 seconds. It disrupts the hydrogen bonds between complementary bases of the DNA strands, yielding single strands of DNA. • Annealing step: The reaction temperature is lowered to 50-65°C for 30 to 60 seconds, allowing annealing of the primers to the single-stranded DNA template. Stable hydrogen bonds form between

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the DNA strand (the template) and the primers when the primer sequence very closely matches the complementary template sequence. Primers are usually 17 - 22 nucleotides long and are carefully designed to bind to only one site in the genome. The polymerase binds to the primer-template hybrid and begins DNA synthesis. • Extension step: A temperature of around 72°C is used for this step, which is close to the optimum temperature of Taq polymerase. At this step the Taq polymerase extends the primer by adding dNTPs, using one DNA strand as a template to create a the other (new) DNA strand. The extension time depends on the length of the DNA fragment to be ampliﬁed. As a standard, at its optimum temperature, the DNA polymerase will polymerize a thousand bases in one minute.

Figure 3.11: PCR: A repeating cycle of denaturation (1), annealing (2), and extension (3). Notice that initially there is a double strand of DNA, and after denaturation, the DNA is single stranded. In the annealing step (2), single stranded primers bind. These primers are extended by Taq Polymerase, represented by the green ball (3). Utilizing the PCR, DNA can be amplified millions of times to generate quantities of DNA that can be used for a number of purposes. These include the use of DNA for prenatal or genetic testing, such as testing for a specific mutation. PCR has revolutionized the fields of biotechnology, human genetics, and a number of other sciences. Many of the applications will be discussed in the following lesson. PCR was developed www.ck12.org

in 1983 by Kary Mullis. Due to the importance of this process and the significance it has had on scientific research, Dr. Mullis was awarded the Nobel Prize in Chemistry in 1993, just 10 years after his discovery. To say that PCR, molecular cloning and the Human Genome Project has revolutionized biology and medicine would be an understatement. These efforts have led to numerous accolades, including Nobel prizes, and more may follow. Some of the ways that these discoveries have shaped our lives are the focus of the next lesson.

Lesson Summary • Biotechnology is technology based on biological applications, combining many features of Biology including genetics, molecular biology, biochemistry, embryology, and cell biology. • The goal of the Human Genome Project is to understand the genetic make-up of the human species by determining the DNA sequence of the human genome and the genome of a few model organisms. • Gene cloning, also known as molecular cloning, refers to the process of isolating a DNA sequence of interest for the purpose of making multiple copies of it (cloning). • Classic gene cloning involves the following steps: 1. 2. 3. 4. 5.

Restriction enzyme digestion and ligation Isolation of DNA Ligation Transfection and Selection Gel electrophoresis

• The Polymerase Chain Reaction (PCR) is used to amplify millions of times speciﬁc regions of a DNA strand. This can be a number of loci, a single gene, a part of a gene, or a non-coding sequence. • PCR usually involves the following steps: 1. Denaturation step 2. Annealing step 3. Extension step

Review Questions 1. 2. 3. 4. 5. 6. 7. 8. 9.

Why are biotechnology and DNA technology considered the same? What are the goals of the Human Genome Project? Is the DNA sequence information generated by the HGP available to anyone, and if so, how? How are gene cloning and recombinant DNA related? Describe the process of gene cloning. How does gel electrophoresis analyze DNA? What is PCR? What allows PCR to be done at high temperatures? Describe the PCR process.

Further Reading / Supplemental Links • http://www.genome.gov/HGP • http://www.ornl.gov/sci/techresources/Human_Genome/home.shtml

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• • • • • •

http://biotech.about.com/od/cloning/tp/DNAcloning.htm http://croptechnology.unl.edu/viewLesson.cgi?LessonID=957884601 http://www.pcrstation.com/ http://nobelprize.org/educational_games/chemistry/pcr/index.html http://en.wikipedia.org http://www.vtaide.com/png/cloning.htm

Vocabulary biotechnology Technology based on biological applications. gel electrophoresis An analytical technique used to separate DNA fragments by size and charge. Genbank The U.S. National Center for Biotechnology Information, part of the National Institutes of Health, which maintains the genomic sequences in a database. gene cloning The process of isolating a DNA sequence of interest for the purpose of making multiple copies of it. The Human Genome Project A project to understand the genetic make-up of the human species by determining the DNA sequence of the human genome and the genome of a few model organisms. plasmid (or vector) A small circular piece of DNA that carries the recombinant DNA into a host organism for cloning. polymerase chain reaction (PCR) A repeating series of cycles used to amplify millions of times speciﬁc regions of a DNA strand. recombinant DNA Engineered through the combination of two or more DNA strands that combine DNA sequences which would not normally occur together. restriction enzyme (or restriction endonuclease) An enzyme that cuts double-stranded DNA. Taq polymerase Named after the thermophilic bacterium Thermus aquaticus from which it was originally isolated, is the heat-stable polymerase used in the PCR reaction.

Points to Consider • The Human Genome Project, gene cloning, and PCR are some of the most remarkable scientiﬁc achievements of the recent past. But how can these milestones make our lives better? • Medicine and food science are just two of the categories that beneﬁt from biotechnology. Speculate on how our lives are made better by these achievements.

3.2 Lesson 10.2: Biotechnology Lesson Objectives • Describe various applications of biotechnology as related to medicine, agriculture and forensic science. www.ck12.org

• • • • •

How is DNA technology related to genetic testing and prenatal diagnosis? Why is biotechnology so important in agriculture? Why is DNA analysis the most important tool of the forensic scientist? Describe forensic STR analysis. Discuss some of the ELSI associated with biotechnology.

Introduction Scientists have sequenced a consensus version of the human genome. Now what? Do we know what all the genes are or what they do? Not yet. Do we know what phenotypes are associated with mutations in the genes? For many genes, or even most genes, we do not. Do we even know exactly how many genes we have? Not exactly. And we are far away from knowing what makes us all unique. So how does this information help us? The Human Genome Project has been labeled a landmark scientiﬁc event. But what can we do with this information? There are many applications of genetic information, including applications in medicine and agriculture. The applications of genetics to forensic science have become one of the most important aspects of the criminal justice system. And of course, these applications raise many ethical questions. These applications and questions will be the focus of this lesson. Biotechnology: The Invisible Revolution (I&E 1m) can be seen at http://www.youtube.com/ watch?v=OcG9q9cPqm4.

Figure 3.12: Biotechnology: The Invisible Revolution (Watch Youtube Video) http://www.youtube.com/v/OcG9q9cPqm4?f=videos38;c=ytapi-CK12Fo undation-Flexrwikiimport-fg5akohk-038;d=AT8BNcsNZiISDLhsoSt-gq IO88HsQjpE1a8d1GxQnGDm38;app=youtube_gdata ”What does biotechnology have to do with me?” (5c, I&E 1m) is discussed in the following video: http://www.youtube.com/watch?v=rrT5BT_7HdI&#38;feature=related (10:01).

Applications of DNA Technology: Medicine As discussed in the ﬁrst lesson of this chapter, the Human Genome Project has opened up many applications to take advantage of what we know about our genome in order to help us. Many of these applications are

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Figure 3.13: Project for Biology 111. 3dB. Wed Pm. Biotechnology Project on Gene Therapy. Rebecca Proctor, Chiquetta Silver, and Shamonia Wright. (Watch Youtube Video) http://www.youtube.com/v/rrT5BT_7HdI?f=videos38;c=ytapi-CK12Fo undation-Flexrwikiimport-fg5akohk-038;d=AT8BNcsNZiISDLhsoSt-gq IO88HsQjpE1a8d1GxQnGDm38;app=youtube_gdata medically related. Others will be legally related. And yet still other uses of DNA technology include those in agriculture and the food sciences. Understanding and curing genetic diseases is the ultimate goal of human geneticists. As discussed in the Human Genetics chapter, gene therapy is the insertion of a new gene into an individual’s cells and tissues to treat a disease, replacing a mutant disease-causing allele with a normal, non-mutant allele. Of course, the findings of the Human Genome Project are significant in determining the disease-causing alleles. In the 1920s, there was no known way to produce insulin, which was needed by people to remove excess sugar from the bloodstream. People with diabetes either lack insulin, produce low levels of insulin, or are resistant to insulin, and thus they may need external insulin to control blood glucose levels. This problem was solved, at least temporarily, when it was found that insulin from a pig’s pancreas could be used in humans. This method was the primary solution for diabetes until recently. The problem with insulin production was raised again: there were not enough pigs to provide the quantities of insulin needed. Scientists needed to devise another way. This led to one of the biggest breakthroughs in recombinant DNA technology: the cloning of the human insulin gene. By methods discussed in the first lesson in this chapter, the specific gene sequence that codes for human insulin was introduced into the bacteria E. coli. The transformed gene altered the genetic makeup of the bacterial cells, such that in a 24 hour period, billions of E. coli containing the human insulin gene resulted, producing human insulin to be administered to patients. Though the production of human insulin by recombinant DNA procedures is an extremely significant event, many other aspects of DNA technology are beginning to become reality. In medicine, modern biotechnology provides significant applications in such areas as pharmacogenomics, genetic testing (and prenatal diagnosis), and gene therapy. These applications use our knowledge of biology to improve our health and our lives. Many of these medical applications are based on the findings of the Human Genome Project.

Pharmacogenomics Currently, millions of individuals with high cholesterol take a similar type of drug. You may know of people who take a medicine to help with their cholesterol levels. However, these drugs probably work slightly diﬀerently in many of those people. In some, it lowers their cholesterol signiﬁcantly; in others it www.ck12.org

may lower it only moderately; and in some, it may have no effect at all. Why the difference? Because of the genetic background of all people. Pharmacogenomics, a combination of pharmacology and genomics (the study of the genome) that refers to the study of the relationship between pharmaceuticals and genetics, may explain and simplify this problem. Pharmacogenomics is the study of how the genetic inheritance of an individual affects his or her body’s response to drugs. In other words, pharmacogenomics will lead to the design and production of drugs that are adapted to each person’s genetic makeup. Pharmacogenomics will result in the following benefits: 1. Development of tailor-made medicines. Using pharmacogenomics, pharmaceutical companies will be able to create drugs based on the proteins, enzymes and RNA molecules that are associated with specific genes and diseases. These tailor-made drugs promise not only to maximize the beneficial effects of the medicine, but also to decrease damage to nearby healthy cells. 2. More accurate methods of determining appropriate drug dosages. Knowing a patient’s genetics will enable doctors to determine how well his or her body can process and metabolize a medicine. This will allow doctors to prescribe the proper levels of the medicine, allowing the medicine to have optimal results. 3. Improvements in the drug discovery and approval process. Once the genes and proteins associated with a disease are known, the discovery of new medicines will be made easier using these genes and proteins as targets for the medicine. In addition to creating much more beneficial medicines, this could significantly shorten the drug discovery process. 4. Better vaccines. Safer vaccines can be designed and produced by organisms transformed with DNA sequences from an antigen. These vaccines will trigger the immune response without the risks of infection. They will be capable of being engineered to carry several strains of pathogen at once, combining several vaccines into one.

Genetic Testing and Prenatal Diagnosis Let’s propose a hypothetical situation: unfortunately, your family is predisposed to develop a genetic disease. You and your spouse want to have a baby, but you want to know the likelihood of the child developing the disease. This scenario could happen to anyone. As we learn more and more about disease causing genes, it will become easier to test for mutations in those genes. Currently, is there any way to determine if a baby will develop a disease due to a known mutation? Is it possible to screen for a mutation in a developing baby? Yes. Genetic testing involves the direct examination of DNA sequences. A scientist scans, by any number of methods, a patient’s DNA for mutated sequences. Genetic testing can be used to: • • • • • • • •

Diagnose a disease. Confirm a diagnosis. Provide information about the course of a disease. Confirm the existence of a disease. Predict the risk of future development of a disease in otherwise healthy individuals or their children. Identify carriers (unaffected individuals who are heterozygous for a recessive disease gene). Perform prenatal diagnostic screening. Perform newborn screening.

Consultations with human geneticists and genetic counselors are an important ﬁrst step in genetic testing.

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They will most likely prescribe some sort of prenatal screening (see the Human Genetics chapter). Prenatal screening (also known as prenatal diagnosis or testing) is the testing for diseases or conditions in a fetus or embryo before it is born. Methods may involve amniocentesis or chorionic villus sampling to remove fetal cells. DNA can be isolated from these cells and analyzed. If the mutation that results in the phenotype is known, that specific mutation can be tested, either through restriction fragment length polymorphism analysis or, more likely, through PCR and DNA sequence analysis. As it is the baby’s DNA that is being analyzed, the analysis will determine if the developing baby will have the mutation and develop the phenotype, or not have the mutation. Parents can then be informed of the probability of the baby developing the disease. In human genetics, preimplantation genetic diagnosis (PIGD) is genetic analysis performed on embryos prior to implantation. PIGD is considered an alternative to prenatal diagnosis. Its main advantage is that it avoids selective pregnancy termination, as the method makes it highly likely that the baby will be free of the disease in question. In PIGD, in vitro fertilization is used to obtain embryos for analysis. DNA is isolated from developing embryos prior to implantation, and specific genetic loci are screened for mutations, usually using PCR based analysis. Embryos that lack the specific mutation can then be implanted into the mother, thereby guaranteeing that the developing baby will not have the specific mutation analyzed for (and thus not have the disease associated with that mutation).

Applications of DNA Technology: Agriculture Biotechnology has many other useful applications besides those that are medically related. Many of these are in agriculture and food science. These include the development of transgenic crops - the placement of genes into plants to give the crop a beneﬁcial trait. Beneﬁts include:

• • • • • •

Improved yield from crops. Reduced vulnerability of crops to environmental stresses. Increased nutritional qualities of food crops. Improved taste, texture or appearance of food. Reduced dependence on fertilizers, pesticides and other agrochemicals. Production of vaccines.

Biotechnology in agriculture (5c, I&E 1m) is discussed at http://www.youtube.com/watch?v= IY3mfgbe-0c (6:40).

Improved Yield from Crops Using biotechnology techniques, one or two genes may be transferred into a crop to give a new trait to that crop. This is done in the hope of increasing its yield. However, these increases in yield have proved to be difficult to achieve. Current genetic engineering techniques work best for single gene effects - that is traits inherited in a simple Mendelian fashion. Many of the genetic characteristics associated with crop yield, such as enhanced growth, are controlled by a large number of genes, each of which just has a slight effect on the overall yield. There is, therefore, still much research, including genetic research, to be done in this area. www.ck12.org

Figure 3.14: Doc Sanders talks about modern Biotechnology in Agriculture and it’s impact on producing aﬀordable food world wide. (Watch Youtube Video) http://www.youtube.com/v/IY3mfgbe-0c?f=videos38;c=ytapi-CK12Fo undation-Flexrwikiimport-fg5akohk-038;d=AT8BNcsNZiISDLhsoSt-gq IO88HsQjpE1a8d1GxQnGDm38;app=youtube_gdata

Reduced Vulnerability to Environmental Stresses Crops are obviously dependent on environmental conditions. Drought can destroy crop yields, as can too much rain or floods. But what if crops could be developed to withstand these harsh conditions? Biotechnology will allow the development of crops containing genes that will enable them to withstand biotic and abiotic stresses. For example, drought and excessively salty soil are two significant factors affecting crop productivity. But there are crops that can withstand these harsh conditions. Why? Probably because of that plant’s genetics. So biotechnologists are studying plants that can cope with these extreme conditions, trying to identify and isolate the genes that control these beneficial traits. The genes could then be transferred into more desirable crops, with the hope of producing the same phenotypes in those crops. Thale cress (Figure 3.15), a species of Arabidopsis (Arabidopsis thaliana), is a tiny weed that is often used for plant research because it is very easy to grow and its genome has been extensively characterized. Scientists have identified a gene from this plant, At-DBF2, that confers resistance to some environmental stresses. When this gene is inserted into tomato and tobacco cells, the cells were able to withstand environmental stresses like salt, drought, cold and heat far better than ordinary cells. If these preliminary results prove successful in larger trials, then At-DBF2 genes could help in engineering crops that can better withstand harsh environments. Researchers have also created transgenic rice plants that are resistant to rice yellow mottle virus (RYMV). In Africa, this virus destroys much of the rice crops and makes the surviving plants more susceptible to fungal infections.

Increased Nutritional Qualities of Crops Maybe you’ve heard over and over that eating beans is good for you. True? Well, maybe. But what if it were possible to increase the nutritional qualities of food? One would think that would be beneﬁcial to society. So, can biotechnology be used to do just that? Scientists are working on modifying proteins in foods to increase their nutritional qualities. Also, proteins in legumes and cereals may be transformed to provide all the amino acids needed by human beings for a balanced diet.

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Figure 3.15: Thale cress.

Improved Taste, Texture or Appearance of Food Have you ever gone to the grocery store, bought some fruit and never gotten around to eating it? Maybe you haven’t, but I bet your parents have. Modern biotechnology can be used to slow down the process of spoilage so that fruit can ripen longer on the plant and then be transported to the consumer with a still reasonable shelf life. This is extremely important in parts of the world where time from harvest to the consumer may be longer than in other areas. In addition to improving the taste, texture and appearance of fruit, it will also extend the usable life of the fruit. As the world population grows and grows, this may become a fairly important issue. Extending the life of fruit can expand the market for farmers in developing countries due to the reduction in spoilage. This has successfully been demonstrated in the tomato. The ﬁrst genetically modiﬁed food product was a tomato which was transformed to delay its ripening. Researchers in Indonesia, Malaysia, Thailand, Philippines and Vietnam are currently working on delayed-ripening papayas.

Reduced Dependence on Fertilizers, Pesticides and Other Agrochemicals There is growing concern regarding the use of pesticides in agriculture. Therefore, many of the current commercial applications of modern biotechnology in agriculture are focused on reducing the dependence of farmers on these chemicals. For example, Bacillus thuringiensis (Bt) is a soil bacterium that produces a protein that can act as an insecticide, known as the Bt toxin. But it is a protein, not a foreign chemical. Could this protein be used in crops instead of pesticides? Traditionally, an insecticidal spray has been produced from these bacteria. As a spray, the Bt toxin is in an inactive state and requires digestion by an insect to become active and have any eﬀect. Crop plants have now been engineered to contain and express the genes for the Bt toxin, which they produce in its active form. When an insect ingests the transgenic crop, it stops feeding and soon thereafter dies as a result of the Bt toxin binding to its gut wall. Bt corn is now commercially available in a number of countries to control corn borer (a lepidopteran insect like moths and butterﬂies), which is otherwise controlled by insecticidal spraying. www.ck12.org

Figure 3.16: Kenyans examining genetically modiďŹ ed insect resistant transgenic Bt corn.

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In addition to insects, weeds have also been a menace to farmers - just ask anyone with a garden how much they hate weeds. They can quickly compete for water and nutrients needed by other plants. Sure, farmers can use herbicides to kill weeds, but do these chemicals also harm the crops? Can biotechnology help with this issue? Some crops have also been genetically engineered to acquire tolerance to the herbicides allowing the crops to grow, but killing the weeds. But the lack of cost eﬀective herbicides with a broad range of activity - that do not harm crops - is a problem in weed management. Multiple applications of numerous herbicides are routinely needed to control the wide range of weeds that are harmful to crops. And at times these herbicides are being used as a preventive measure – that is, spraying to prevent weeds from developing rather than spraying after weeds form. So these chemicals are being added to crops. This practice is followed by mechanical and/or hand weeding to control weeds that are not controlled by the chemicals. Crops that are tolerant of herbicides would obviously be a tremendous beneﬁt to farmers (Figure 3.16). The introduction of herbicide tolerant crops has the potential to reduce the number of chemicals needed during a growing season, thereby increasing crop yield due to improved weed management and decreased harm to the crops. In 2001, 626,000 square kilometers of transgenic crops were planted. Seventy-seven percent of the transgenic crops were developed for herbicide tolerance in soybean, corn, and cotton, 15% were Bt crops for insect resistance, and 8% were developed with genes for both insect resistance and herbicide tolerance in cotton and corn.

Production of Vaccines in Crop Plants Many little children hate shots. And many children in parts of the world do not even have access to vaccines. But what if these vaccines were available in an edible form? Modern biotechnology is increasingly being applied for novel uses other than food. Banana trees and tomato plants have been genetically engineered to produce vaccines in their fruit. If future clinical trials prove successful, the advantages of edible vaccines would be enormous, especially for developing countries. The transgenic plants could be grown locally and cheaply. Edible vaccines would not require the use of syringes, which, in addition to being unpleasant, can be a source of infections if contaminated.

Applications of DNA Technology: Animal Cloning DNA technology has proved very beneficial to humans. Transgenic animals are animals that have incorporated a gene from another species into their genome (Figure 3.17). They are used as experimental models to perform phenotypic tests with genes whose function is unknown, or to generate animals that are susceptible to certain compounds or stresses for testing purposes. Other applications include the production of human hormones, such as insulin. Many times these animals are rodents, such as mice, or fruit flies (Drosophila melanogaster). Fruit flies are extremely useful as genetic models to study the effects of genetic changes on development. But transgenic animals just have one novel gene. What about a whole new genome? It could be argued that human cloning is one of the techniques of modern biotechnology. It involves the removal of the nucleus from one cell and its placement in an unfertilized egg cell whose nucleus has either been deactivated or removed. Theoretically this would result in an individual genetically identical to the donor. Of course, there are many ethical issues associated with human cloning. But animal cloning is arguably a different story. In February 1997, Ian Wilmut and his colleagues at the Roslin Institute announced the successful cloning of a sheep named Dolly from the mammary glands of an adult female (Figure 3.18). Dolly was the first mammal to be cloned from an adult somatic cell. The cloning of Dolly made it apparent to many that the techniques used to produce her could someday be used to clone human beings. This resulted in www.ck12.org

Figure 3.17: GloFish: the first genetically modified animal to be sold as a pet. GloFish are transgenic zebrafish transfected with a natural fluorescence gene.

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tremendous controversy because of its ethical implications. After cloning was successfully demonstrated by Dolly’s creators, many other large mammals, including horses and bulls, were cloned. Cloning is now considered a promising tool for preserving endangered species.

Figure 3.18: Dolly the sheep and her ﬁrst-born lamb Bonnie. Dolly was the ﬁrst large mammal to be cloned. This picture shows that a cloned animal can perform many, if not all, of the same functions as a non-cloned animal. In animal cloning, the nucleus from a somatic cell is inserted into an egg cell in which the nucleus has been removed. The resulting cell is cultivated and after a few divisions, the egg cell is placed into a uterus where it is allowed to develop into a fetus that is genetically identical to the donor of the original nucleus (Figure 3.19). For an animation of cloning, see http://www.dnalc.org/resources/animations/ cloning101.html.

Applications of DNA Technology: Forensic DNA Analysis You know that DNA can be used to distinguish individuals from each other. You may have heard that DNA can also be used to match evidence and suspects and help solve crimes. This is demonstrated on shows like CSI: Crime Scene Investigation. But how is this done? How is a “genetic fingerprint,” a DNA pattern unique to each individual (except identical twins) created? Genetic fingerprinting, or DNA fingerprinting, distinguishes between individuals of the same species using only samples of their DNA. DNA fingerprinting has thus become one of the most powerful tools of the forensic scientist, enabling law enforcement personnel to match biological evidence from crime scenes to suspects. As any two humans have the majority of their DNA sequence in common, those sequences which demonstrate high variability www.ck12.org

Figure 3.19: Reproductive cloning: The nucleus is removed from a somatic cell and fused with a denucleated egg cell. The resulting cell may develop into a colony of cloned cells, which is placed into a surrogate mother. In therapeutic cloning, the resulting cells are grown in tissue culture; an animal is not produced, but genetically identical cells are produced.

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must be analyzed. This DNA analysis was first developed using DNA hybridization techniques, but now is almost exclusively PCR-based. DNA fingerprinting was developed by Sir Alec Jeffreys in 1985. Genetic fingerprinting exploits highly variable repeating sequences. Two categories of these sequences are microsatellites and minisatellites. Microsatellites, also known as short tandem repeats (STRs), consist of adjacent repeating units of 2 - 10 bases in length, for example (GATC)n , where GATC is a tetranucleotide (4 base) repeat and n refers to the number of repeats. It is the number of repeating units at a given locus that is variable. An STR profile can be created for any individual by analyzing a series of STRs (Figure 3.20). Two unrelated humans will be unlikely to have the same numbers of repeats at a given locus. In STR profiling, PCR is used to obtain enough DNA to then detect the number of repeats at 13 specific loci. PCR products are separated by gel or capillary electrophoresis. By examining enough STR loci and counting how many repeats of a specific STR sequence there are at a given locus, it is possible to create a unique genetic profile of an individual. STR analysis has become the prevalent analysis method for determining genetic profiles in forensic cases. It is possible to establish a match that is extremely unlikely to have arisen by coincidence, except in the case of identical twins, who will have identical genetic profiles. The polymorphisms (different in the number of repeats) displayed at each STR region will be shared by approximately 5 - 20% of individuals. When analyzing STRs at multiple loci, such as the 13 STRs analyzed in forensic DNA analysis, it is the unique combinations of these polymorphisms in an individual that makes this method unmatched as an identification tool. The more STR regions that are analyzed in an individual the more discriminating the test becomes. Capillary electrophoresis is similar to gel electrophoresis but uses a capillary tube filled with the gelatin material. Genetic fingerprinting is used in forensic science to match suspects to samples of blood, hair, saliva or semen, or other sources of DNA. It has also led to several exonerations of formerly convicted suspects. Genetic fingerprinting is also used for identifying human remains, testing for paternity, matching organ donors, studying populations of wild animals, and establishing the province or composition of foods. It has also been used to generate hypotheses on the pattern of the human migration. In the United States, DNA fingerprint profiles generated from the 13 STR loci are stored in CODIS, The Combined DNA Index System, maintained by the Federal Bureau of Investigation. As of 2007, CODIS maintained over 4.5 million profiles. Profiles maintained in CODIS are compiled from both suspects and evidence, and therefore are used to help solve criminal cases. Profiles of missing persons are also maintained in CODIS. The true power of STR analysis is in its statistical power of discrimination. Because the 13 loci are independently assorted, the laws of probabilities can be applied. This means that if someone has the genotype of ABC at three independent loci, then the probability of having that specific genotype is the probability of having type A times the probability of having type B times the probability of having type C. This has resulted in the ability to generate match probabilities of 1 in a quintillion (1 with 18 zeros after it) or more, that is, the chance of two samples matching by coincidence is greater than the number of people on the planet, or the number of people that have ever lived! The development of PCR has enabled STR analysis to become the method of choice for DNA identification. Prior to PCR, other methods were utilized. These include restriction fragment length polymorphism (RFLP) analysis and Southern blot analysis.

RFLP Analysis: Restriction Fragment Length Polymorphism Prior to the development of PCR, restriction enzyme digestion of DNA followed by Southern blot analysis was used for DNA ﬁngerprinting. This analysis is based on the polymorphic nature of restriction enzyme sites among diﬀerent individuals, hence restriction fragment length polymorphisms are formed after www.ck12.org

Figure 3.20: The CODIS loci analyzed by STR analysis. Notice they are spread over 14 chromosomes, and that two are on the X and Y chromosomes.

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digestion of DNA with these enzymes. A Southern blot, named after its inventor Edwin Southern, is a method used to check for the presence of a specific DNA sequence in a DNA sample. Once an individual’s DNA is digested with a specific restriction enzyme, the resulting fragments are analyzed by Southern blot analysis. These fragments will produce a specific pattern for that individual. Southern blotting is also used for other molecular biology procedures, including gene identification and isolation. Other blotting methods that employ similar principles have been developed. These include the western blot and northern blot. These procedures analyze proteins and RNA respectively. RFLP and Southern blot analysis involved several steps: 1. First, the DNA being analyzed is cut into different-sized pieces using restriction enzymes. 2. The resulting DNA fragments are separated by gel electrophoresis. 3. Next, an alkaline solution or heat is applied to the gel so that the DNA denatures and separates into single strands. 4. Nitrocellulose paper is pressed evenly against the gel and then baked so the DNA is permanently attached to it. The DNA is now ready to be analyzed using a radioactive single-stranded DNA probe in a hybridization reaction. 5. After hybridization, excess probe is washed from the membrane, and the pattern of hybridization is visualized on X-ray film by autoradiography (Figure 3.21).

Figure 3.21: Mutations can create or abolish restriction enzyme (RE) recognition sites, thus affecting quantities and length of DNA fragments resulting from RE digestion. Hybridization is when two genetic sequences bind together because of the hydrogen bonds that form between the base pairs. To make hybridization work, the radioactive probe has to be denatured so that it is single-stranded. The denatured probe and the Southern blot are incubated together, allowing the probe to bind to the corresponding fragment on the Southern blot. The probe will bond to the denatured DNA wherever it finds a fit. Hybridization of a probe made to a variable segment of DNA will produce a DNA fingerprint pattern specific for an individual. This procedure has a number of steps and is very labor intensive. PCR-based methods are much simpler. www.ck12.org

Ethical, Legal, and Social Issues Imagine someone analyzes part of your DNA. Who controls that information? What if your health insurance company found out you were predisposed to develop a devastating genetic disease. Might they decide to cancel your insurance? Privacy issues concerning genetic information is a growing issue in this day and age, especially among those who donate DNA for large-scale sequence-variation studies. Other concerns have been to anticipate how the resulting data may affect concepts of race and ethnicity; identify potential uses (or misuses) of genetic data in workplaces, schools, and courts; identify commercial uses; and foresee impacts of genetic advances on the concepts of humanity and personal responsibility. ELSI stands for Ethical, Legal and Social Issues. It’s a term associated with the Human Genome project. This project didn’t only have the goal to identify all the approximately 20,000 – 24,000 genes in the human genome, but also to address the ELSI that might arise from the project. The U.S. Department of Energy (DOE) and the National Human Genome Research Institute (NHGRI) of the National Institutes of Health (NIH) devoted 3% to 5% of their annual human genome research budget toward studying ethical, legal, and social issues surrounding the availability of your genetic information. This represents the world’s largest bioethics program and has become a model for ELSI programs around the world. Rapid advances in DNA-based research, human genetics, and their applications have resulted in new and complex ethical and legal issues for society. ELSI programs that identify and address these implications have been an integral part of the Human Genome Project since its inception. These programs have resulted in a body of work that promotes education and helps guide the conduct of genetic research and the development of related medical and public policies. ELSI programs address the following issues, among others: • Privacy and confidentiality issues concerning personal genetic information. • The fairness in the use of personal genetic information by insurers, employers, courts, schools, adoption agencies, and the military, among others. • The psychological impact and stigmatization due to an individual’s genetic differences. • Clinical issues. These include the education of doctors and other health service providers, patients, and the general public in the capabilities and uses of genetic information, and the scientific/medical limitations of genetic testing. Clinical issues also include the implementation of standards and qualitycontrol measures in genetic testing procedures. • Reproductive issues. These include adequate informed consent for complex and potentially controversial procedures, and the use of genetic information in making decisions concerning reproductive options. • Uncertainties associated with genetic testing. The current and future uncertainties associated with testing for susceptibilities to a genetic condition raise many ethical issues, as does the testing for predisposition to a complex condition (such as heart disease) linked to multiple genes and geneenvironment interactions. • Health and environmental issues concerning genetically modified foods and microbes. • Commercialization of genetic products including property rights, such as patents and copyrights, and issues concerning the accessibility to genetic data and materials. Biotechnology will have a tremendous impact on our future - of this there is no doubt. Is society entering some dangerous areas? Well, many of these issues have never been analyzed until now. With the discovery of countless amounts of genetic information and the development of its applications, many questions need to be addressed. • Who should have access to personal genetic information, and how will it be used?

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• Who owns and controls genetic information? • How does personal genetic information affect an individual and society’s perceptions of that individual? • How does genomic information affect members of minority communities? • How reliable and useful is fetal genetic testing? • How will genetic tests be evaluated and regulated for accuracy, reliability, and utility? • How do we prepare the public to make informed choices? • Should testing be performed when no treatment is available? • Should parents have the right to have their minor children tested for adult-onset diseases? • Are genetic tests reliable and interpretable by the medical community? • Where is the line between medical treatment and enhancement? • Are genetically modified foods and other products safe for humans and the environment? • How will these technologies affect developing nations’ dependence on the West? • Who owns genes and other pieces of DNA? • Will patenting DNA sequences limit their accessibility and development into useful products?

Are scientiﬁc fantasies, such as those depicted on TV shows such as Star Trek or in the movie GATTACA http://www.youtube.com/watch?v=ZppWok6SX88&#38;feature=related, a possibility? Who can really say? How, really, will biotechnology aﬀect our future? It seems as if the possibilities are endless.

Figure 3.22: http://zuguide.com/Gattaca.html A science-fiction film set in the near future, it’s about a world controlled by the Gattaca Corporation, where everyone is categorized according to their DNA. Ethan Hawke stars as Vincent, a man whose genes have been deemed inferior by the powers-that-be. He dreams of traveling to space, but is considered fit only for menial jobs. He manages to take some genetic material from an angry disabled man (Jude Law) who is genetically superior. Uma Thurman is the woman who falls in love with Vincent, without knowing who he really is. Directed by Andrew Niccol. With Alan Arkin. Categories: Drama, Romance, Sci-Fi, Thriller. Year: 1997. For more trailers with Ethan Hawke, please see http://zuguide.com/Ethan-Hawke.html. Also, for movie previews starring Jude Law, see http://zuguide.com/Jude-Law.html. Trailers with Uma Thurman, can be seen at http://zuguide.com/Uma-Thurman.html. (Watch Youtube Video) http://www.youtube.com/v/ZppWok6SX88?f=videos38;c=ytapi-CK12Fo undation-Flexrwikiimport-fg5akohk-038;d=AT8BNcsNZiISDLhsoSt-gq IO88HsQjpE1a8d1GxQnGDm38;app=youtube_gdata

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Lesson Summary • In medicine, modern biotechnology provides signiﬁcant applications in such areas as pharmacogenomics, genetic testing (prenatal diagnosis), and gene therapy. • Pharmacogenomics, the combination of pharmacology and genomics, is the study of the relationship between pharmaceuticals and genetics. • Pharmacogenomics will result in the following beneﬁts: 1. 2. 3. 4.

Development of tailor-made medicines. More accurate methods of determining appropriate drug dosages. Improvements in the drug discovery and approval process. Better vaccines.

• Genetic testing involves the direct examination of DNA sequences. • Genetic testing can be used to: diagnose a disease; confirm a diagnosis; provide prognostic information about the course of a disease; confirm the existence of a disease; predict the risk of future development of a disease in otherwise healthy individuals or their children; screen for carriers (unaffected individuals who are heterozygous for a disease gene); perform prenatal diagnostic screening; and perform newborn screening. • Biotechnology in agriculture includes the development of transgenic crops - the placement of genes into plants to give the crop a beneficial trait. Benefits include improved yield from crops, reduced vulnerability of crops to environmental stresses, increased nutritional qualities of food crops, improved taste, texture or appearance of food, reduced dependence on fertilizers, pesticides and other agrochemicals, and production of vaccines. • Transgenic animals are animals that have incorporated a gene from another species into their genome. They are used as experimental models to perform phenotypic tests with genes whose function is unknown, or to generate animals that are susceptible to certain compounds or stresses for testing purposes. Other applications include the production of human hormones, such as insulin. • Animal cloning is the generation of genetically identical animals using DNA from a donor animal, not a gamete. Dolly, a sheep, was the first mammal to be cloned from an adult somatic cell. • Genetic fingerprinting, or DNA fingerprinting, distinguishes between individuals of the same species using only samples of their DNA. DNA fingerprinting has thus become one of the most powerful tools of the forensic scientist, enabling law enforcement personnel to match biological evidence from crime scenes to suspects. • ELSI stands for Ethical, Legal and Social Issues. This is a term associated with the Human Genome project. Rapid advances in DNA-based research, human genetics, and their applications have resulted in new and complex ethical and legal issues for society. ELSI programs that identify and address these implications have been an integral part of the Human Genome Project since its inception. These programs have resulted in a body of work that promotes education and helps guide the conduct of genetic research and the development of related medical and public policies.

Review Questions 1. 2. 3. 4. 5. 6.

List applications of DNA technology. List how DNA technology is used in agriculture. How is DNA technology used in medicine? What are some of the beneﬁts of pharmacogenomics? Describe how pharmacogenomics will result in specialty medicines. What are potential uses of genetic testing?

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7. Describe how DNA technology can improve yield from crops. 8. Describe how DNA technology can be used to reduce vulnerability to environmental stresses. Why is this important? State an example. 9. What is the difference between a transgenic animal and a cloned animal? 10. Who was Dolly? Why was she important? 11. What is a DNA fingerprint and how is it used? 12. What is STR profiling? 13. Describe why ELSI programs are important. 14. List some ELSI issues.

Further Reading / Supplemental Links • http://www.genome.gov • http://www.dna.gov/basics/http://www.ornl.gov/sci/techresources/Human_Genome/medicine/ pharma.shtml • http://www.ornl.gov/sci/techresources/Human_Genome/medicine/pharma.shtml • http://www.ornl.gov/sci/techresources/Human_Genome/medicine/genetherapy.shtml • http://www.ama-assn.org/ama/pub/category/2306.html • http://www.americanheart.org/presenter.jhtml?identifier=4566 • http://www.ift.org/cms/ • http://www.pub.ac.za/projects/dnakits.html • http://www.fda.gov/cvm/CloningRA_FAQConsumers.htm • http://www.aavs.org/animalcloning_overview.html • http://www.FBI.gov • http://www.ornl.gov/sci/techresources/Human_Genome/elsi/forensics.shtml • http://www.dna.gov/basics/analysishistory/ • http://www.genome.gov/ELSI/ • http://www.lbl.gov/Education/ELSI/ • http://en.wikipedia.org/wiki/Main_Page

Vocabulary CODIS The Combined DNA Index System, is maintained by the Federal Bureau of Investigation and stores DNA profiles. ELSI Ethical, Legal and Social Issues. This term is associated with the Human Genome Project. genetic fingerprinting (DNA fingerprinting) Creates a unique DNA pattern that distinguishes between individuals of the same species using only samples of their DNA. genetic testing The direct examination of DNA sequences for mutated sequence. microsatellites (short tandem repeats) Adjacent repeating units of 2 - 10 bases in length, for example (GATC)n , where GATC is a tetranucleotide repeat and n refers to the number of repeats. pharmacogenomics The combination of pharmacology and genomics, is the study of the relationship between pharmaceuticals and genetics. It is the study of how the genetic inheritance of an individual affects his or her body’s response to drugs. www.ck12.org

preimplantation genetic diagnosis (PGD) Genetic analysis performed on embryos prior to implantation. prenatal diagnosis (prenatal screening) Testing for diseases or conditions in a fetus or embryo before it is born. Methods may involve amniocentesis or chorionic villus sampling to remove fetal cells. restriction fragment length polymorphism (RFLP) Analysis that analyzes the differences between restriction enzyme sites. southern blot Named after its inventor Edwin Southern, is a method used to check for the presence of a specific DNA sequence in a DNA sample. STR profiling Analyzes 13 STR loci to create a DNA profile utilized in forensic analysis. transgenic animals Animals that have incorporated a gene from another species into their genome. transgenic crops The result of placement of genes into plants to give the crop a beneficial trait.

Points to Consider We have spent the past few chapters discussing genetics, molecular biology, and their implications. These are implicitly related to evolution. • Can you hypothesize on the relationship between genetics and evolution? • Why is an understanding of the principals of DNA and inheritance essential to understand evolution?

Image Sources (1) http://commons.wikimedia.org/wiki/Image:Cloning_diagram_english.png. GNU-FDL. (2) http://en.wikipedia.org/wiki/Image:Codis_profile.jpg. Public Domain. (3) http://commons.wikimedia.org/wiki/Image:Ligation.svg. GNU-FDL. (4) The Human Genome Project logo of the DOE.. Public Domain. (5) The Roslin Institute. http://en.wikipedia.org/wiki/Image:Dolly_the_sheep2-thumb.jpg. (6) http://commons.wikimedia.org/wiki/File:Btcornafrica.jpg. CC-BY 2.5. (7) http://commons.wikimedia.org/wiki/Image:PCR.svg. GNU-FDL. (8) http://commons.wikimedia.org/wiki/Image:DNA_sequence.png. Public Domain. (9) http://en.wikipedia.org/wiki/File:GloFish.jpg. The photographer of this work allows anyone to use it for any purpose including unrestricted redistribution, commercial use, and modiﬁcation. (10) http://commons.wikimedia.org/wiki/Image:Example_plasmid.png. GNU-FDL. (11) Thale cress.. GNU-FDL. (12) http://www.ncbi.nlm.nih.gov/projects/genome/probe/doc/TechRFLP.shtml. Public Domain. (13) http://en.wikipedia.org/wiki/File:Agarosegelphoto.jpg. GNU-FDL.