Name: The Structure of DNA 06/08/11 Students will turn in: 1. Assignment 1: DNA Worksheet 2. Assignment 2: Poster Draw a poster of the ladder structure of DNA, labeled. 3. Assignment 3: The completed DNA model (Use the materials in the supplies basket obtained at the Course Orientation & tape small pieces of paper to label the model). Introduction Human chromosomes are structures composed of two long strands of deoxyribonucleic acid (DNA) combined with proteins. In 1953, two scientists, James D. Watson and Francis H. Crick, proposed a model for the structure of DNA. They described the molecule as a double helix (two spiraling strands), composed of nucleotides. Each nucleotide is composed of a phosphate unit (PO 4 ) joined to deoxyribose (the five-carbon sugar) along with a nitrogen-containing base. Each deoxyribose sugar has 5 carbon atoms, and each of the carbons has its own number (see figure below). One Nucleotide #5C #4C #1C #3C OH #2C 1
Name: Assignment 1: DNA Structure Worksheet Read, label, and answer all of the questions below. I. Nucleotides: DNA is composed of building blocks called nucleotides The carbon with the asterist in the figure of the 5-C sugar to the right. 2
Below: 1. Write N-base in the correct position at the end of the correct bond (line). 2. Write PO 4 in the correct position at the end of the correct bond (line). 3. Write OH in the correct position at the end of the correct bond (line). II. DNA is Composed of Two Polynucleotide Chains 3
1. Write Free 3 end and Free 5 end at the appropriate ends of the chain below. 2. Cross off all of the #3 C OH groups- only the OH groups. Don t cross off the C s or the phosphates. Draw a line from the #3 C s to the phosphate groups of the adjacent nucleotides. 3. Note: The OH group bonded to the #3 C in deoxyribose is not removed until the nucleotide bonds to another nucleotide below it. Therefore, do not cross off the Free 3 OH group (since it is not bonded to another nucleotide on that end). 4
III. Antiparallel Arrangement of the two Chains Label the DNA molecule as instructed on the next page. 5
1. Number the carbons in all of the deoxyribose sugars. 2. Draw bonds between the sugars and phosphates of adjacent nucleotides (cross off the OH groups between nucleotides bonded to each other- NOT at the Free 3 Ends). 3. Draw the weak bonds between the nitrogen bases (base pairs) as several dots between them. 4. Identify the Free 5 end and the Free 3 ends of both chains. This will indicate the antiparallel nature of the two chains with respect to one another. 6
ASSIGNMENT 2: Poster A computer generated illustration is not allowed. You must DRAW the ladder YOURSELF. Use a small poster to DRAW the structure of DNA in the form of a "ladder". Draw the "ladder" exactly as illustrated below. The extended ends of each long line represent the Free 5 End of that strand. The ends of the long lines where the line is not extended out is the Free 3 end of each strand. Remember, the strands are antiparallel (upside-down) with respect to each other. Clearly and completely draw and label the following in your ladder structure. Be sure all of these words are on your poster: 1. Strong bonds and Weak bonds 2. Deoxyribose 3. Phosphate group (PO 4 ) 4. Base pair 5. Adenine, Cytosine, Guanine, Thymine (Be specific in your drawing) 6. Circle and label one Nucleotide (Be very specific in what you are including in the nucleotide!). 7. Finally, indicate the Antiparallel nature of the chains by labeling all of the Free 3' and Free 5' ends (Ends 'sticking out' are the free 5' phosphates). Be sure you have the correct molecules at the 3' and 5' ends! Include a legend (key) if using abbreviations. 7
ASSIGNMENT 3: DNA Model Materials and instructions for this lab were adapted from Hubbard Scientific, Inc., DNA Model. Procedure: First, tally the materials. You must report any missing parts no later than the week before the assignment is due. The set of parts that you received at the orientation may contain extra parts. Don't feel that all parts must be used if there are extra. Please return any extra parts with the completed model. Do not write directly on the pieces. Use tape and small pieces of paper to label the model and don't forget your name! Materials: (Do not use glue or adhesive) 12 - Three prong "deoxyribose centers" (black) 12 - Two prong "phosphates" (red) 22 - Yellow connectors (Strong bonds between the sugar sand phosphates) 3 - Adenine straws (short red) 3 - Guanine straws (short gray) 3- Thymine straws (short blue) 3 - Cytosine straws (short green) 6 - Hydrogen bond-centers (white) 1 - Long gray stand 1 - Four prong center (gray or black) 3 - Medium green straws 8
Construct the Model 1. Construct the nucleotides by attaching each deoxyribose (black center) to a phosphate (red center) with a yellow connector. The prongs (of the phosphates and sugars) should be inserted into the center of the yellow connectors). Then attach one nitrogen base (red, green, blue, and gray straws) to each deoxyribose as shown below. Construct 12 nucleotides. Yellow Connector Nucleotide Black Red, Blue, Gray or Green Red 2. Assemble one strand of connected nucleotides, consisting of six nucleotides, by connecting the phosphate (red) of one nucleotide to the deoxyribose sugar (black) of the adjacent nucleotide using the remaining yellow connectors. Twist the connectors as needed. See the Figure below. From top to bottom, put the nitrogen bases on one strand in the following order: adenine, thymine, cytosine, guanine, adenine, cytosine. (ATCGAC) One connected strand of nucleotides. 3. Repeat the above procedure to build the second strand. Be sure to place the complementary nitrogen bases in the correct position. 9
4. Connect the base pairs using the white hydrogen bonds. See Figure below. 5. Allow the DNA model to remain upright by passing the long gray straw through the holes in the white hydrogen centers. Attach the three long green straws to the four prong center. Attach the remaining prong to the bottom of the long gray straw to serve as the stand. 6. Twist the DNA structure gently to form a double helix spiral. With paper and tape (don t write on the model) label the model with your name and BIOL 117HY. 7. ONE MORE THING! Be sure there is a free 3 (sugar only) and free 5 end (sugar attached to a phosphate) on both DNA strands ON THE MODEL using the model pieces. Then label all of the free 3 and free 5' ends on the model with tape and a piece of paper. 10