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How important is DNA in the functioning of a cell?

Where do cells store the information to do all of the things they do? You probably know the answer to that question-in their DNA. But, do you know how information is organized in DNA? That is what you will learn about in this section. You also will learn how that information is copied accurately so that daughter cells get exactly the same information the parent cell has.

Figure 4.1 Nucleotides are joined together one after the other and form a helix chain. Two of these chains pair and then twist to form a double helix, which means “two-chained coil.”

DNA consists of repeating molecular units called nucleotides. Each nucleotide has three parts-a sugar, a phosphate, and a nucleotide base. There are four different nucleotide bases. The names of the four nucleotide bases are adenine (A), thymine (T), guanine (G), and cytosine (C). From now on, we will just use their initials: A, T, G, C. The DNA alphabet that codes for all of the information in DNA consists of only four letters corresponding to the four nucleotide bases. By stringing the nucleotides together in different sequences, the DNA stores information like strings of letters form words that store information.

The DNA molecule consists of two parallel strands of nucleotides. These two strands are twisted around each other to form a double helix. Think of a ladder made of flexible plastic. If you twisted that ladder, you would have a double helix. The rungs of the ladder consist of pairs of nucleotide bases, and the sides of the ladder consist of repeating sugar (deoxyribose) and phosphate groups. The pairs of nucleotide bases are not all of the possible combinations of A, T, G, C, however. Nucleotide base A can pair only with T, and G can pair only with C. This pairing is very important for the process by which the DNA molecule copies itself to produce identical copies.

Activity 4-1: 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 cells in a beaker
  • Sand
  • Liquid soap, clear in a beaker
  • Alcohol
  • Water, in a beaker
  • Cheesecloth square (several layers, 15 \times 15 \ cm)
  • Mortar and pestle
  • Test tube
  • Small funnel
  • Test tube rack
  • Wooden skewer
  • Forceps
  • 2 eyedroppers
  • Permanent marking pen
  • Paper towels
  • Black construction paper, 4 \times 4 \ cm
  • Transparent tape
  • Microscope, slides, and cover slips
  • Safety goggles
  • Activity Report

Procedure

Step 1 Obtain equipment for your team and arrange it at your lab station.

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

Step 3 Put a test tube into a test tube rack and place a small funnel into 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 into the cheesecloth square and allow the liquid to filter through the cheesecloth and funnel. Carefully draw together the edges of the cheesecloth and use the 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 and draw what you see on your Activity Report. Add labels, if possible. Answer question 2.

Step 6 Add three to four drops of liquid soap to the liquid in your test tube. Carefully hold the test tube in one hand and tap gently 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 to 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. What is wrapping around the skewer is DNA! 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 and place it on a small piece of black construction paper. Use clear tape to cover your specimen to keep it from drying out and to fasten it 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 to explore different ways of removing thymus DNA, such as using different soaps or 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.

How the Information in DNA Is Copied

A cell must copy its DNA before it can undergo cell division. This process is called replication. Replication is a complex job that must be done quickly. You might wonder just how quickly. Remember that a chromosome is one long DNA molecule. An average human chromosome may consist of 150 million nucleotide sequences. Remember the S phase of the cell cycle is the time over which replication takes place, and it lasts about six hours. So, how many sequences per second have to be replicated to copy an average human chromosome during the S phase?

What Do You Think?

What other processes use templates to produce a copy of something?

During replication, the DNA molecule starts to unwind at one end. An enzyme called a helicase helps it unwind. As the DNA molecule unwinds, the double strand splits right down the center, between the nucleotide base pairs forming two templates for DNA replication. The now unpaired nucleotide bases are free to combine with new partners. But, since a nucleotide base A can only combine with a T, and a C can only combine with a G, each strand combines with only the correct nucleotides to accurately recreate its complementary strand. Special enzymes carry out this neat and orderly replication process. These enzymes are called DNA polymerases.

Figure 4.2 Parental strands unwound. This picture shows a double helix. It is opened at the top to allow the DNA to be copied.

The DNA polymerases can only read the template DNA strand in one direction. Since the two strands of a DNA molecule run in opposite directions, the replication process is not the same on the two strands as the DNA unwinds. On one side, the DNA polymerase moves smoothly along the strand as the DNA unwinds and splits. This strand is called the continuous or leading strand. On the other side of the split, however, the DNA polymerase starts the process near the unwinding point and moves up the strand in the opposite direction. This strand is called the discontinuous or lagging strand. It has to have its gaps filled in by other enzymes before it is an exact copy of the original DNA molecule.

Now look at how this process occurs. In Figure 4.3, you can see the direction that the DNA polymerases work on the template DNA strands. Arrows show the direction of synthesis. Note on one side, replication proceeds “down” the strand; on the other strand, it proceeds up.

Figure 4.3 DNA synthesis in progress showing leading and lagging strands.

Figure 4.4 DNA is copied in this way. The exact nucleotide base sequence is copied in the direction shown by the arrows. The double helix is opened at the top of the diagram. Then each correct nucleotide base is added in exactly the right order. Perfect copies of the DNA sequence are made. Each chromosome is one long double helix DNA molecule. So this diagram shows how each chromosome is copied during cell division.

The DNA polymerase also checks its own work. It proofreads the new strand as it is made to make sure that all of the new nucleotide base pairs are correct. If a wrong nucleotide base is added to the growing strand, the DNA polymerase will cut it out and try again.

Activity 4-2: 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 will make a model of DNA and a copy of your model to learn more about the structure and function of DNA and how it replicates.

Materials

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

Procedure

Part A-A DNA Model

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

A-adenine, red

C-cytosine, yellow

T-thymine, blue

G-guanine, green

P-phosphate, orange

D-deoxyribose (sugar), white

Your task is to make a total of 60 nucleotides:

15 adenine nucleotides containing the nitrogen base adenine;

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 one adenine nitrogen base, one deoxyribose sugar, and one phosphate. Make 14 more adenine nucleotides.

Make 15 cytosine nucleotides. Each cytosine nucleotide is made of one cytosine, one deoxyribose sugar, and one phosphate. Tape the three parts of each cytosine nucleotide together.

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

Make 15 guanine nucleotides. Each guanine nucleotide is made of one guanine, one deoxyribose sugar, and one phosphate. Tape the three 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.

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 two 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.

Why DNA Is Important

Now you know how DNA codes for information and how that information is replicated so that each daughter cell gets exactly the same set of DNA instructions. Now let's discover the answers to these questions: How does the DNA code get used or expressed in a cell? What information is in this set of blueprints? How is the information put to work to make a cell do the things that it does?

Different regions of the DNA strand have different ways of influencing how a cell will do its work. Specific regions of the DNA called genes code for the production of specific proteins. These proteins are responsible for specific products and functions characteristic of the particular cell type. For example, muscle cells in your arm are different from nerve cells in your brain, yet both kinds of cells have the same DNA. The muscle cell and the nerve cell just use different portions of the DNA. They express different genes to make their specific protein products that carry out the specific functions of each cell type.

Proteins consist of chemicals called amino acids. The amino acids are bound together in long chains called polypeptides. You could think of amino acids as the alphabet that makes up the protein molecule. Proteins are produced when amino acids are added one by one at the ribosomes. The amino acid sequence of a protein gives that protein its character. The DNA code for a particular protein is stored in your genes.

Now you might realize that we have a problem based on cell structure. The DNA information is in the nucleus. But, the proteins are made at the ribosomes in the cytoplasm. Therefore, the blueprints are in the nucleus, but the protein factory is in the cytoplasm. So how do the ribosomes know how to make proteins? How does the genetic information flow from the nucleus to the cytoplasm of the cell?

The key to this problem is another type of nucleic acid called messenger ribonucleic acid (mRNA). Ribonucleic acids (RNA) are similar to deoxyribonucleic acid (DNA), but a little different in composition and shape. First, the sugar in RNA is different. It is ribose instead of deoxyribose. Second, RNA has a small difference in its nucleotide base alphabet. RNA uses the nucleotide base uracil (U) instead of thymine (T). U pairs with A in an RNA molecule. Whenever a gene is to be “expressed”-meaning that the protein for which it codes is to be made-its information is copied from the DNA gene as a messenger RNA (mRNA) molecule. The mRNA molecule then moves out of the nucleus into the cytoplasm and then to the ribosomes where it provides the information for making the protein molecule.

Transcription-Making Messenger RNA

The process of making a messenger RNA molecule from a segment of DNA is called transcription. Transcription is similar to replication. First, the DNA has to unwind, but unlike in replication, only the segment that corresponds to the gene to be transcribed unwinds. Then an enzyme, this time RNA polymerase, makes a complementary messenger RNA molecule from the DNA template.

Figure 4.5 Transcription of messenger RNA from the DNA template.

Let us look at the way transcription works. Suppose there is an original DNA sequence that looks like this:

DNA ATGCCGTGAA

It is transcribed to a complementary RNA sequence like this:

RNA UACGGCACUU

When a segment of DNA unwinds and the two strands separate, the RNA polymerase does not make complementary copies of both DNA strands. Only one strand of DNA contains the right information, or gene sequence, for making a specific protein. The mRNA produced by transcription contains the information for making this specific protein.

The Genetic Alphabet

The unique structure of a protein and the reason it can do a specific job is due to its specific sequence of amino acids. The information brought to the ribosome in the form of mRNA is the blueprint for the specific sequence of amino acids that makes a specific protein.

There is another challenge, however. Each strand of DNA or RNA contains combinations of the four-nucleotide bases, but there are twenty different amino acids that make up all of the proteins in your body. So, how do we use an alphabet of only four letters (A, T or U, C, and G), to write sentences using twenty possible words? Obviously, each word cannot be only one letter. Can each word be only two letters?

How many possible words can you make using four letters, two at a time? Try it and see, but the answer is less than twenty. This means that the minimum word length in the genetic vocabulary must consist of three letters. How many possible words will that allow? The correct answer is sixty-four, which is more than is needed to code for the twenty different amino acids.

Coding Use the following code and sequence to decode the secret message.

Code Key:

& \text{UUU = a} && \text{AUU = i} && \text{UCU = p} && \text{UGU = x}\\& \text{UUC = b} && \text{AUC = j} && \text{UCC = q} && \text{UGC = y}\\& \text{UUA = c} && \text{AUA = k} && \text{UCA = r} && \text{UGA = stop}\\& \text{UUG = d} && \text{AUG = start} && \text{UCG = s} && \text{UGG = z}\\\\& \text{CUU = e} && \text{GUU = l} && \text{UAU = t}\\& \text{CUC = f} && \text{GUC = m} && \text{UAC = u}\\& \text{CUA = g} && \text{GUA = n} && \text{UAA =v}\\& \text{CUG = h} && \text{GUG = o} && \text{UAG =w}

AUGCUGUACGUCUUCAUUGUGAUUUCGCUGUACGUCGUCAUUGUACUAUGA

Scientists did clever and important experiments in the 1950s to break the genetic code. Those experiments proved that the code is based on sets of three nucleotides. Thus, each word in the genetic vocabulary has three letters, or nucleotides. When a DNA sequence of three nucleotides is transcribed into an mRNA sequence of three nucleotides, that sequence codes for a specific amino acid.

Scientists also have discovered that some of the triplet nucleotide sequences are codes for start and stop signals that “tell” the mRNA when to start making a protein and when to stop making it. Each triplet of mRNA nucleotides is known as a codon. Some of the different codons instruct the RNA to make the same amino acid, just as some words in the English language have the same meaning even though they are spelled differently.

To learn how a triplet code works, consider the following sentences where each word is only three letters long.

  1. THE BAD CAT ATE THE OLD RAT AND THE RED BAT.
  2. SHE RAN AND SHE WON.
  3. SHE RAN AND GOT HER BAT AND SHE HIT HIS LEG.
  4. THE BOY GOT HIS BAT AND HAD FUN AND HIS MOM SAW HIM WIN THE BIG ONE FOR HER AND FOR HIM.

We can compare these examples of sentences with examples of different gene products (proteins) in several ways:

  • Each one of the sentences, like each gene, is made up of triplet codes. The genes have triplet codes of nucleotides, and the words in the sentences are each made up of three letters.
  • These sentences, like different genes, have different meanings. Each one tells a different story.
  • Some of the words appear in more than one of the sentences, just as some amino acids appear in more than one protein.
  • Some of the words appear more than once in the same sentence, just as some amino acids appear more than once in a protein.
  • Each of the sentences is a different length. Some sentences are short and so are some genes. Some sentences, such as sentence 4, are very long; some genes are very long.

Write a sentence in which each word is made up of three letters, but do not leave spaces between the words, and do not use a period at the end of the sentence. Use the Code Key in the Mini Activity: Coding. What rules do you have to use to read this sentence? Explain why RNA polymerase must have start and stop signals. What start and stop signals would make it possible for someone to read your message correctly?

Editing the Message

Has anyone in your class worked on a school newspaper or has anyone visited the offices where a city newspaper is produced? If so, have those students explain the job of the person who is called the editor. Writers almost always write too much, and all of the news that is written as copy will never fit into the newspaper unless it is edited. Parts have to be cut out, segments have to be rearranged, and the pieces that are to be printed have to be joined together in such a way that they make sense. A similar editing process takes place before mRNA leaves the nucleus.

There is usually more information in the DNA than is needed to make the proteins that the cell needs. So, before the mRNA leaves the nucleus, it is cut and spliced so that the message that reaches the ribosomes is different than the one that was transcribed directly from DNA.

Building a Protein Model Collect 50 pop beads or linker cubes. If possible, select pop beads having 20 different colors to represent the 20 different amino acids. Use any combination of colored pop beads to make a chain of 50 beads. Check with your classmates to see if anyone else has the same sequence of colored beads. What does this tell you about the number of possible proteins that can be made from 20 different amino acids?

Protein Synthesis

Now let's learn more about protein synthesis, which involves the translation of the mRNA message, and how the process takes place.

The edited mRNA is transported out to the cytoplasm where it travels to the ribosomes. Upon reaching the ribosome, the mRNA binds to it. The ribosome serves as the workbench on which the protein coded for by the mRNA is made or synthesized. But first, the “code” of the mRNA has to be translated.

What does translation mean when you are talking about languages? You might think of protein synthesis as going from one language to another. Since the “alphabet and words” of the mRNA code are different from the “words” of the protein, it is the job of the ribosome to decode the RNA message and translate it into protein.

Figure 4.6 Different codons and the amino acids coded by them.

There are hundreds of different languages spoken around the world. Why do you think there are so many languages? How would you investigate which languages are related to each other? Can you speak more than one language, or would you like to be able to? What are some advantages of being able to speak more than one language?

Figure 4.6 shows the different mRNA codons and the amino acid each codon translates into. For example, the triplet UUU codes for the amino acid phenylalanine (Phe). The triplet GAC codes for Aspartic acid (Asp). The triplet ACU codes for the amino acid Threonine (Thr). Notice different triplets can code for the same amino acid. There are also triplets that code for a STOP signal. This triplet stops the sequence of amino acids when the protein is complete. There is a triplet that means start. It tells the ribosome where to initiate the building of a protein.

More than one ribosome can read the mRNA at the same time, so many copies of that protein can be made at the same time by the different ribosomes that are attached to the mRNA. A ribosome starts to translate the mRNA at one end and moves along it translating as it goes. After completing the message, the ribosome is released from the mRNA molecule. This process is shown in the diagram in Figure 4.7

Figure 4.7 The ribosome reads the mRNA in one direction. More than one ribosome can translate the same message into protein at the same time. Each polypeptide chain grows as each amino acid is added, one by one, until the protein is complete.

Consider your answer to the Journal Writing on page 40 with respect to how you would investigate whether different languages are related. How could you investigate whether different animals are related based on their genetic codes and proteins? How could you tell which animals were more and which were less closely related?

Let's take a closer look at how amino acids are added to the growing polypeptide chain. The amino acids are added one by one to form the protein at the ribosomes. How do we know that ribosomes are the place where protein synthesis occurs? Scientists can take ribosomes out of a cell to see what they do. They can get ribosomes to make proteins outside of a cell, so they can study protein synthesis in vitro, which means “in glass” in a laboratory. To do this, scientists place ribosomes in a test tube with all of the other factors needed for protein synthesis. Then they add amino acids that are labeled or tagged with radioactivity. The scientists let the ribosomes work with these amino acids for certain lengths of time.

What are the results of this experiment? Where are amino acids added to the growing polypeptide chain? Are the new amino acids added

a. at the tip of the tail?

b. at the end nearest the ribosome?

c. somewhere in the middle of the polypeptide?

First, let's look at what the ribosome and growing protein look like before scientists add the labeled amino acids:

Figure 4.8 Diagram of ribosomes with different length chains of amino acids.

What does “poly” mean in the word polypeptide? What are some other words that use “poly” in this way?

Now, let's see how the growing polypeptide chains look after they are exposed to the labeled amino acids for two seconds. The labeled amino acids are indicated as colored circles, while the other amino acids are open circles.

Figure 4.9 Polypeptide chains at the ribosomes after exposure to labeled amino acids for two seconds. Only the most recently added amino acids are labeled.

Now, let's see how the growing polypeptide chains look after they were exposed to the labeled amino acids for one minute.

Figure 4.10 Polypeptide chains at the ribosomes after exposure to labeled amino acids for one minute. During one full minute, many amino acids are added.

You can see from Figure 4.10 that the polypeptide chain grows a lot during one minute. Many more amino acids have been added than in the two-second exposure in Figure 4.9. The longer the time of exposure of the ribosomes to the labeled amino acids, the more amino acids are incorporated into the growing polypeptide chain.

From this experiment you can see that the newly incorporated amino acids are added to the end of the chain that is next to the ribosome. So new amino acids are added to the polypeptide chain at the ribosome.

How do the amino acids necessary for creating the proteins get to the ribosomes? Another type of RNA, called transfer RNA (tRNA) brings the amino acids to the ribosomes.

In Figure 4.11 you can see that the transfer RNA has two main functional regions: the anticodon site and the amino acid binding site.

Figure 4.11 A tRNA molecule showing the amino acid and anticodon binding sites.

The amino acid binding site on the tRNA “picks up” a specific amino acid. The anticodon site on tRNA is complementary to a codon on the mRNA. Because of this complementarity between the tRNA and the mRNA, the tRNA molecules line up in a particular sequence along the mRNA. As a result, the amino acids are brought together in the sequence that is coded by the mRNA. Enzymes can then attach the amino acids to each other to form the polypeptide or protein specified by the mRNA.

  1. Write a code using the letters A, U, G, and C for the nucleotides in mRNA.
  2. Now design the triplets for the transfer RNAs that are complementary to this message.
  3. What would happen if, in the first triplet, the A was missing and the message began with a U?
  4. What else could you do that would change (mutate) the original message for making a functional protein into a meaningless message?

Review Questions

  1. Describe how DNA makes a copy of itself.
  2. Explain the role of DNA, mRNA, and amino acids in making a protein.
  3. What is the genetic code? How does it work?
  4. How are amino acids brought into the sequence that is specified by the mRNA code?

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