DNA and RNA: The Nucleic acids Deoxyribonucleic acid, or DNA, is a complex molecule found in all living organisms. It is the chemical that genes are made of. An understanding of the organization of this molecule has answered many questions. Scientists now know how chromosomes can duplicate during cell division and transfer their genetic information to new chromosomes. Scientists also understand how chromosomes can direct the formation of specific proteins outside the nucleus while still in the nucleus. In this investigation you will: 1) Construct a portion of a DNA molecule 2) Show the replication of DNA 3) Construct a portion of an RNA molecule 4) Compare and contrast DNA and RNA in terms of there structure and function Materials: A bag filled DNA and RNA nucleotides. Procedure Part A. Structure of a DNA molecule The molecules that make up DNA are Deoxyribose, phosphoric acid and the four nitrogen bases (adenine, thymine, cytosine, and guanine). Each molecule of deoxyribose has one nitrogen base and one phosphoric acid chemically attached to it. The three molecules together form a monomer called a nucleotide. Remove from your bag four different nucleotides for DNA. 1) What is the only difference between the four nucleotides? _____________________________________________________ _____________________________________________________ A DNA molecule is “ladder-like” in shape. Deoxyribose and phosphoric acid alternate to form the sides (uprights) of the ladder and the nitrogen bases combine with each other to form the steps of the ladder. Using the four nucleotides that you have already have, select two more and connect all six nucleotides together to form a row in the following order from top to bottom: Cytosine nucleotide Thymine nucleotide Guanine nucleotide Adenine nucleotide Guanine nucleotide Cytosine nucleotide Let this represent the left half of the “ladder-like” DNA molecule with one upright side and six half steps. 2) Name the two molecules that alternate to form the uprights side of the ladder. ____________________________________________________ 3) Name the specific part of the nucleotide that the nitrogen bases attach to. ____________________________________________________ 4) Name the molecules or parts of the nucleotide that form the half steps of the “ladder-like” DNA molecule. ____________________________________________________ ____________________________________________________ Complete the “ladder-like” DNA molecule by adding the complementary nucleotides to the right side. You will have to turn the new nucleotides so you can see the lettering but it is upside down, in order for them to match up. Your completed model should look like a ladder with complementary nitrogen bases pairs as steps. What are the names of the four nitrogen bases in DNA? 5) Is the order of nitrogen bases the same from top to bottom on the right side of the model as it is on the left side of the model? (look at the steps) ______________________________________________________ 6) There are only two combinations of nitrogen bases that can make up the steps of the ladder. What are these two combinations? ______________________________________________________ ______________________________________________________ 7) Look carefully at the picture of the DNA molecule on Page 294 in your textbook. Look at the hydrogen bonds (doted lines) between adenine and thymine and between cytosine and guanine. Count the doted lines and explain why adenine can only bond with thymine and cytosine can only bond with guanine. _____________________________________________________ _____________________________________________________ _____________________________________________________ 8) In real life a Chromosome can be many thousands of nucleotide pairs long. If there were 9,478 adenine nucleotides in a strand of DNA, how many thymine nucleotides would you expect to find? ___________ Count up the number of guanine nucleotides in your model. Then count up the cytosine nucleotides in your model and make sure it backs up your answer for question number 8. 9) What are the three parts of a DNA nucleotide? (Use the specific names except for the nitrogen bases) ______________________________________________________ 10) The following is a list of the nitrogen bases on the left side of a DNA molecule. List the complementary bases that would make up the right side of the same DNA molecule. Thymine _____________________________ Adenine _____________________________ Guanine _____________________________ Guanine _____________________________ Cytosine _____________________________ Thymine _____________________________ Cytosine _____________________________ Adenine _____________________________ Part B. DNA replication Your DNA model represents a very short piece of a chromosome but its replication is same as the replication of the chromosomes in the nucleus of a cell. Separate the two halves of your DNA strand in to left and right where the nitrogen bases come together. A chromosome untwists and unzips like this with the help of an enzyme called DNA HELICASE. Using the left half of your model as a pattern, connect new complementary nucleotides to form a new right half to complete a DNA strand. Build a second DNA model by using the right half of the original model as a template (pattern), add new complementary nucleotides to form a new left half. 11) Do the two new ladder-like molecules contain the same number of steps? _______________ 12) Is the order of nitrogen base pairs the same for each DNA model from top to bottom? __________________________ 13) Are the two DNA molecules exact copies of each other? ____________________________________________________ 14) What is it about the nitrogen bases that ensures that when DNA replication occurs, the two new DNA strands are identical to the original? __________________________________________________ __________________________________________________ __________________________________________________ __________________________________________________ Part C. Structure of RNA and RNA transcription Besides ensuring the exact replication of chromosomes, complementary base pairing and the order of the nitrogen base pairs also serves a code that contains the instructions for directing the cells activities, and for what characteristics an organism will have. How does a cell “read” and “translate” the message held in the order of the nitrogen base pairs of DNA? That is where ribonucleic acid (RNA) comes in. RNA is also made up of nucleotides. (What are the three parts of a nucleotide?) The differences between DNA and RNA are that Ribose is the sugar group in RNA rather than Deoxyribose, and RNA has Uracil as a nitrogen base instead of Thymine, and RNA is made up a single strand of nucleotides instead of a double strand. It looks like half of the “ladder-like” structure. 15) Determine the molecular formulas for Ribose and Deoxyribose. (How many carbons, hydrogens, and oxygens are in each) Refer to the diagrams of the structural formulas for ribose and deoxyribose on the next page of this lab and count the C’s, H’s, and O’s. Add the proper subscripts to the letters below. (H2O) Ribose: C H O Deoxyribose: C H O 16) How are these two sugars different from each other? 17) Examine the shape of a uracil nucleotide. With which nitrogen base can uracil match up to form a complete step of the ladder? _______________________________________ The process of making RNA is called Transcription. Choose one of the two DNA strands in front of you and take it apart. With the DNA strand that is left you are going to construct an RNA molecule. Separate the DNA strand into left and right where the nitrogen base pairs come together. During transcription, an enzyme called RNA POLYMERASE untwists and unzips the DNA to separate the two halves like you just did. Using the right side of your DNA strand as a template (pattern) match up RNA nucleotides with their complements on the DNA strand. 18) Is the order of nitrogen bases in the RNA strand the same as the order of nitrogen bases in the unused left side of the original DNA strand? (with the exception of uracil replacing thymine) ________________ 19) Do the RNA half-rung nitrogen bases pair up exactly as they Would if this was DNA replication? (with the exception of uracil replacing thymine) __________________________ Move the RNA strand to the side and move the two halves of the DNA strand back together. (during transcription, the DNA strands are separated only temporarily) After the single stranded RNA is completed it leaves the nucleus and travels to the ribosomes to deliver the message from the DNA. 20) What are the three parts of an RNA nucleotide? (be specific) ______________________________________ 21) What is it about the nitrogen bases that ensures when RNA Transcription happens, the new RNA strand will carry the correct DNA message to the ribosomes? _____________________________________________________ _____________________________________________________ _____________________________________________________ _____________________________________________________ Analysis 1) Complete the following table by using an X to indicate which nucleic acid each characteristic applies to. DNA RNA Ribose Deoxyribose Phosphoric acid Adenine Thymine Uracil Guanine Cytosine Double strand of nucleotides Single strand of nucleotides Leaves the nucleus Stays in the nucleus Replication Transcription 2) Explain how the pairing of nitrogen bases ensures that the DNA code is accurately passed from one cell to the next through DNA replication. 3) We know that messenger RNA (mRNA) passes the message from the DNA to the rest of the cell. How do you know that by reading the mRNA the ribosome will know what the original DNA strand looked like?