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# 4.1: Chromosomes and DNA

Difficulty Level: At Grade Created by: CK-12

What is the composition of a chromosome?

Karyotyping was not introduced until the 1950s. However, as early as the 1920s, scientists agreed that chromosomes were made of two chemical substances-deoxyribonucleic acid (DNA) and protein. After these substances were identified, the next question was, “Which of these two substances carries the genetic information?” By 1952, results of several experiments led scientists to agree that DNA was the substance responsible for the inheritance of traits. In this section you will learn about DNA.

If DNA is responsible for the inheritance of traits, then what is a gene? We hear that word, and we read that word often. For example, “She is a good athlete, because it's in her genes.” “A test showed he carries a gene for cystic fibrosis.” “Fourteen percent of African Americans carry the gene for sickle-cell anemia.” “A gene for pest resistance was inserted into a new variety of potatoes.”

A gene is a segment or a region of DNA that codes for a specific trait. What a gene really codes for, however, is a specific protein molecule, and protein molecules are the basis for traits. The questions you now have to ask are, “How does the sequence of DNA code for a protein molecule, and how is the DNA code replicated from cell to cell and organism to organism, so they all have the ability to make specific proteins?” We'll answer the second question first. We'll answer it by learning more about DNA. It's very important to keep in mind that a chromosome is a long DNA molecule, and that the individual segments of that molecule are genes. Each gene is a DNA code that carries information for duplicating itself and for producing a protein molecule.

Figure 3.1 (a) Chromosomes are found in the nucleus of a cell. (b) Before cells divide, chromosomes duplicate themselves and become compact. The duplicated chromosomes remain together, thus appearing like an X. (c) Each chromosome consists of completed coils of DNA called chromatin. (d) DNA consists of two strands twisted into a helix.

Did You Know?

Rosalind Franklin was the first person to discover that DNA was in the form of a helix. She and another scientist named Maurice Wilkins used X-rays to investigate the structure of DNA. Watson and Crick later used the X-ray photographs to create their famous model of the DNA structure. Unfortunately, Rosalind Franklin did not share in the 1962 Nobel Prize with the other scientists because she died in 1958. The Nobel Prize is awarded only to living individuals.

In 1953, James D. Watson and Francis H. C. Crick, based on information about DNA from several different scientists, constructed a model of a DNA that explained what was known about DNA at the time. The construction of the model of the DNA molecule is considered to be one of the most important events in the history of biology. It allowed scientists to ask even more questions about how genes cause traits and variations. Despite the fact that the construction of this model is so important to genetics, it is interesting to note that Watson and Crick made their first successful model using pieces of cardboard. Later they made a more permanent tin model. Since that time, models of DNA have been made of almost every material imaginable, from glass to gum drops.

Why do we use models of structures, such as a model of DNA, in science?

## Activity 3-1: Precipitation and Spooling of DNA

Introduction

Deoxyribonucleic acid (DNA) is a long molecule that contains the genetic information for gene expression and for the continuity between generations. It is one of the important molecules required for life. What does DNA look like? What are some of its many unique properties? In this activity you have the opportunity to precipitate and spool DNA onto a rod. The DNA has been isolated from the nuclei of cells.

Materials

• 1 test tube containing 2ml\begin{align*}2\;\mathrm{ml}\end{align*} DNA in solution 4ml\begin{align*}4\;\mathrm{ml}\end{align*} (milliliter) of alcohol
• 1 50ml\begin{align*}50\;\mathrm{ml}\end{align*} beaker containing strong salt (NaCl)\begin{align*}(\mathrm{NaCl})\end{align*} solution and an eyedropper
• 1 wooden skewer
• Activity Report

Procedure

Step 1 Obtain a test tube containing the 2ml\begin{align*}2\;\mathrm{ml}\end{align*} (milliliter) sample of DNA. Examine the solution of DNA. Describe its appearance, color, and viscosity.

Step 2 Use tile eyedropper to add 4 or 5 drops of the salt solution to the test tube containing the DNA. Carefully hold the test tube in one hand and tap gently on the bottom of the tube to mix.

Step 3 Pour 4ml\begin{align*}4\;\mathrm{ml}\end{align*} of alcohol into the test tube by slowly trickling the entire contents of ethyl alcohol down the side of the test tube containing the DNA and the NaCl\begin{align*}\mathrm{NaCl}\end{align*}.

Step 4 Observe the interface between the two solutions. Do not mix the two layers.

Step 5 Place the wooden skewer all the way to the bottom of the test tube that contains the two-layered solution.

Step 6 Observe the interface as you rotate the skewer and wind (spool) the DNA that comes out of the solution onto the skewer. This is not a single DNA molecule, but thousands of molecules. If you have a partner, be sure to take turns spooling.

Step 7 Examine and touch the DNA on the skewer. Record the appearance, color, and texture of the DNA.

Step 8 When you are finished, ask your teacher what to do with your spooled DNA and supplies.

What is so special about DNA? What does it do and how does it work? DNA does two important things.

1. It stores and replicates genetic information.
2. It provides information for gene expression through protein synthesis.

Proteins are responsible for cell structure and are the products of gene expression.

DNA is frequently the subject of scientific study, and sometimes it is a point of controversy. Watch your local newspapers and select articles about chromosomes and DNA. Write a one-paragraph summary and one paragraph about your opinion and thoughts.

Figure 3.2 (a) Nucleotides consist of a sugar molecule, a phosphate molecule, and one of four nitrogen molecules. (b) The four nucleotides fit together like a lock and key, with guanine pairing with cytosine, and adenine pairing with thymine.

Did You Know?

In the early 1900s, police began using fingerprints to identify criminals. Today, police also use DNA testing-taking a genetic fingerprint-to identify criminals. Have you seen anything in your local newspaper about police and lawyers using DNA to convict criminals?

Remember that DNA is part of the chromosomes and is located in the nucleus of the cell. The structure of a DNA molecule is simple to learn. A DNA molecule is made up of four different, complex chemical molecules, called nucleotides. Each nucleotide is composed of a sugar molecule called deoxyribose, a phosphate molecule, and one of four nitrogen molecules (adenine, guanine, cyostine, and thymine). (See Figure 3.2.)

• A phosphate, a sugar, and an adenine molecule make up the adenine nucleotide.
• A phosphate, a sugar, and a thymine molecule make up a thymine nucleotide.
• A phosphate, a sugar, and a guanine molecule make up the guanine nucleotide.
• A phosphate, a sugar, and a cytosine molecule make up a cytosine nucleotide.

Nucleotides are joined together, one after the other, and form a helix chain. Two of these chains pair. When they pair, they then twist to form a double helix (Figure 3.3), which is a name that scientists use meaning two-chained coil or spring.

Figure 3.3 DNA looks like a twisting ladder, with the nucleotides as rungs, and the sugar and phosphate molecules making up the legs (uprights) of the ladder.

What Do You Think?

Science is partly a process of answering questions that produce more questions. What questions come to your mind from the discovery of DNA and its structure?

The structure of DNA is like a twisted ladder. The sugar and phosphates make up the uprights of the ladder. The rungs are made up of pairs of complimentary nitrogen bases. These pairs fit together like a lock and key fit together. They consist either of adenine joined to thymine or cytosine joined to guanine. Because the four nucleotides of DNA can be arranged in any sequence along the strand of DNA, an unlimited number of different DNA molecules are possible.

## Activity 3-2: Removing DNA from Thymus Cells

Introduction

What does DNA look like? Where is it found in the cell? How can DNA be removed from a cell so we can see it?

In this activity you answer these questions by treating cells so you can remove DNA. You use thymus cells from an animal whose thymus cells are similar to human thymus cells.

Materials

• Sample of fresh thymus cell in beaker
• Tap water in beaker
• Sand
• Liquid soap, clear
• Alcohol
• Cheesecloth square (several layers, 15×15cm\begin{align*}15 \times 15\;\mathrm{cm}\end{align*})
• Mortar and pestle
• Test tube
• Small funnel
• Test tube rack
• Wooden skewer
• Forceps
• Eyedropper
• Permanent marking pen
• Paper towels
• Black construction paper, 4×4cm\begin{align*}4 \times 4\;\mathrm{cm}\end{align*}
• Transparent tape
• Microscope, slides, and cover slips
• Safety goggles
• Activity Report

Procedure

Step 1 Obtain supplies for your team and arrange them at your lab station.

Step 2 Using forceps, place a sample of thymus tissue in the mortar (bowl). Add a pinch of sand and 1 to 2 dropperfuls of water. Use the pestle to grind the thymus well, adding a little more water as necessary to make a thick, soup like mixture. Answer question 1 on your Activity Report.

Step 3 Put a test tube into a test tube rack and place a small funnel in the test tube. Spread a cheesecloth square over the large opening at the top of the funnel.

Step 4 Carefully pour the thymus contents of your mortar in the cheesecloth square and allow the liquid to filter through the cheesecloth and funnel. Carefully draw together the edges of the cheesecloth and use tl1e forceps to help squeeze the remaining liquid from the thymus mixture. Now discard the cheesecloth and its contents into a special waste container as indicated by your teacher.

Step 5 Take a drop-of the thymus cell liquid from the test tube. Place it on a microscope slide, and put a cover slip carefully on top of the drop. Observe the slide under a microscope. Then, on your Activity Report, draw what you see. Add labels, if possible. Answer question 2.

Step 6 Add 3 to 4 drops of liquid soap to the liquid in your test tube. Carefully hold the test tube in one hand and gently tap on the bottom of the tube to mix. Answer question 3 on your Activity Report.

Step 7 Mark the level of the liquid in the test tube with a permanent marker.

Step 8 Tilt the test tube and slowly trickle an equal volume of alcohol down the inside of the test tube. Wait 30-60 seconds and carefully observe to see what happens at the interface (where the alcohol and thymus mixtures meet). Answer question 4 on your Activity Report.

Step 9 Place a wooden skewer in the test tube and twirl it. Carefully observe what happens as you twirl the skewer. Keep twirling the skewer until there is no further change. Answer question 5 on your Activity Report.

Step 10 Remove the skewer. Place the skewer on a paper towel and carefully blot it dry. Observe the DNA. What does it look like? How does it feel when you touch it? Record your observations on your Activity Report.

Step 11 Using clean, dry forceps, carefully remove the DNA from the skewer. Place the DNA on a small piece of black construction paper. Use clear tape to cover your specimen to keep it from drying out and to fasten the specimen onto the construction paper. Attach the paper to your Activity Report in the space provided. Complete question 6 on your Activity Report.

Step 12 Wash and dry all the glassware you used during the investigation. Store the materials appropriately.

Step 13 Design an alternative procedure you could use to explore different ways of removing thymus DNA. One example might be using different soaps. Another procedure might be using different types of alcohol. Record your ideas on the Activity Report. Share your experimental design with your class. Answer question 7 on the Activity Report.

Step 14 How would you modify your experimental design to use different sources for DNA? Which sources would you choose and why? Record your proposals on the Activity Report. Answer question 8.

Replication

One of DNA's most important functions is to make a copy of itself. In making copies of itself, DNA can pass from one generation of cells to the next. When a strand of DNA makes an exact copy of itself, the process is called replication. Replication or duplication of DNA occurs just before a cell divides. Replication is very important to the study of genetics and how traits and variations are passed along from generation to generation. How does the strand split during replication? The DNA molecule comes apart where the adenine and thymine meet and where the guanine and cytosine meet. The DNA molecule acts like it is unzipping as it begins to replicate. As the DNA is unzipping, spare pieces of nucleotides that are found in the nucleus are matched to the free ends of adenine, guanine, cytosine, and thymine. Thymine (T) bonds to adenine (A). Cytosine (C) bonds to guanine (G). Guanine (G) bonds to cytosine (C). Adenine (A) bonds to thymine (T). Two new molecules of DNA are formed that are identical to the original DNA molecule.

Did You Know?

All organisms have chromosomes that contain DNA. If all organisms contain DNA, what makes a tulip a tulip and not a dog? What makes a goldfish a goldfish and not a human? The DNA in various species differs in the number and arrangement of the four nucleotides-adenine, guanine, cytosine, and thymine. In fact, every organism has a unique sequence (order) of nucleotides making up the DNA.

Did You Know?

If you stretched out the DNA strand in a single cell, it would be about 6feet\begin{align*}6\;\mathrm{feet}\end{align*} long. Every cell in your body carries a complete set of DNA instructions. This is true even though most of the instructions don't affect the functions of that one cell. DNA is so compact that if you put all of the DNA molecules from all of your cells together, they would be about the size of an ice cube. However, uncoiled and stretched out end to end, the DNA strands would stretch to the sun and back many times!

Figure 3.4 (a) When DNA replicates, it unzips. It separates at the point where the nucleotides meet. (b) These two strands of DNA (c) then pick up extra nucleotides (d) until each strand has a complete set of paired nucleotides. The result is two identical strands of DNA.

## Activity 3-3: Building and Using a DNA Model

Introduction

How do nucleotides fit together to make a DNA molecule? What does this double helix molecule look like? In this activity you make a model of DNA. Then you make a copy of your model to learn more about the structure and function of DNA and how it replicates.

Materials

• Scissors
• 6 sets of different colored sheets
• Tape
• Resource
• Activity Report

Procedure

PART A-A DNA MODEL

Step 1 Working in pairs, cut out pieces from the template for each of the following.

C-cytosine, yellow

T-thymine, blue

G-guanine, green

P-phosphate, orange

D-deoxyribose (sugar), white

15 cytosine nucleotides containing the nitrogen base cytosine;

15 thymine nucleotides containing the nitrogen base thymine; and

15 guanine nucleotides containing the nitrogen base guanine.

Make an adenine nucleotide by taping together 1 adenine nitrogen base, 1 deoxyribose sugar, and 1 phosphate. Make 14 more adenine nucleotides.

Make 15 cytosine nucleotides. Each cytosine nucleotide is made of 1 cytosine, 1 deoxyribose sugar, and 1 phosphate.

Tape the 3 parts of each cytosine nucleotide together.

Make 15 thymine nucleotides. Each thymine nucleotide is made of 1 thymine, 1 deoxyribose sugar, and 1 phosphate. Tape the 3 parts of each thymine nucleotide together.

Make 15 guanine nucleotides. Each guanine nucleotide is made of 1 guanine, 1 deoxyribose sugar, and 1 phosphate. Tape the 3 parts of each guanine nucleotide together.

Step 2 Build a ladder consisting of 12 nucleotide pairs. Do not use more than 7 individual adenine, guanine, cytosine, or thymine nucleotides that you made. Tape the nucleotides together. Remember that adenine pairs with thymine and cytosine pairs with guanine. Save the remaining nucleotides for Part B of this activity.

Step 3 Hold both ends of the model and gently twist. You have made a “double helix.”

Step 4 Answer questions 1 through 5 on the Activity Report.

PART B-REPLICATION

Step 5 Gently untwist your DNA model from Part A and place it in front of you. Separate the 2 halves of your model by cutting between the nitrogen bases (A & T and C & G).

Step 6 Using the extra nucleotides you saved from Part A, add nucleotides to each of the DNA halves. Remember that adenine bonds (connects) with thymine, and cytosine bonds with guanine. Answer questions 6 and 7 on the Activity Report.

Many people have said that the discovery of DNA is the most important discovery of the 20th century. Do you agree? Why or why not? Find articles from newspapers or magazines about DNA. Use the articles to write your own article that might appear 10 years from now.

## Review Questions

1. What is a chromosome made of?
2. What is DNA made of?
3. What is a nucleotide?
4. What is a double helix? What is its structure?
5. Which nucleotide molecules pair together?
6. What happens to DNA during replication?

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