Malnutrition, DNA replication, development, and schizophrenia homework problem
This material is replicated on a number of sites
as part of the
SERC Pedagogic Service Project
Initial Publication Date: November 4, 2009
Summary
At the beginning of a unit on DNA, DNA replication, and mitosis, students are given a short science news article summarizing a recent research paper linking folic acid deficiency and schizophrenia. This assignment links the science news article to figures and key techniques from a related journal article. In order to answer the questions, students must apply and transfer the knowledge they gained about DNA and DNA replication in the unit, and they must extend these ideas to think about the role of cell division in development.
Collapse
Learning Goals
The malnutrition and schizophrenia homework problem is given approximately one week before an exam. There are two key goals for the homework problems. First, students read about current research, learn research techniques, and interpret data connected to the material they have just been learning about. Second, the assignment helps students make explicit connections between the major concepts covered in the unit and that will be on the exam. Students generate a diagram in which they link all of the concepts covered in the unit and connect these concepts to the research article.
Concepts and content
- nucleotides and DNA base pairing
- RNA contains uracil
- DNA replication
- mutation
- DNA repair mechanisms
- gel electrophoresis
- mitotic cell division
- interpreting data from published scientific papers
- understanding research techniques
- application of concepts in a new context
- synthesis of concepts
- concept mapping
Context for Use
This assignment is used in an undergraduate introductory biology course, but could also be used in upper level courses, such as genetics. The graded homework problem allows student discussion of the questions and ideas, but requires individually generated answers and concept diagrams. Students are, therefore, accountable individually (as described in the accompanying module, students solve most of the problems collaboratively and are not graded for their work).
We give students the homework assignment about one week before the exam to ensure they have time to reread the short news article and begin working on the questions. Students have covered the concepts listed above in interactive lectures, and have worked several problems relating to DNA, DNA replication, and mitosis in-class in small groups prior to receiving this assignment. The final question asks students to synthesize all of the concepts from the unit and to connect the ideas to the research paper. We want them to spend sufficient time on this assignment as it is a useful tool to help them study for the exam, identify "holes" in their notes or understanding, and see that the various pieces connect before they are sitting in the classroom taking the exam. The online key is made available for student use before the exam.
Description and Teaching Materials
Student homework assignment Malnutrition, DNA replication, Development, and Schizophrenia
To complete this problem, you should reread the article on famine and schizophrenia and use your class notes. You may discuss ideas with others in the course, but the answers should be your own.
Below are two figures taken from a journal article about folic acid and DNA damage (Duthiea, S. J. and A. Hawdona. 1998. DNA instability (strand breakage, uracil misincorporation, and defective repair) is increased by folic acid depletion in human lymphocytes in vitro. The FASEB Journal 12: 1491-1497.) The authors investigated the relationship between folic acid, uracil misincorporation during DNA replication, and DNA stability.
Figure 1. The effect of folic acid concentration on DNA strand breakage and misincorporated uracil in human immune cell DNA. Immune cells were grown for 8 days in either folate-deficient medium or in medium supplemented with increasing concentrations of folic acid. Cells were incubated either with uracil DNA glycosylase in buffer (white bars) or buffer alone (black bars) Results are shown as the Mean ± Standard Error of the Mean (n=10). The black bars show us the background amount of DNA strand breakage that was occurring in the immune cells before the DNA was isolated. Adding the uracil DNA glycosylase enhanced the breakage.
Before you can interpret Figure 1, you need to know how the authors measured DNA damage in cells. The researchers cleverly made use of a naturally occurring event in cells to track DNA damage. Here is the method they reported in the paper:
Stimulation of DNA replication
In the paper, the authors exposed the cells to conditions that normally stimulate cell division, i.e. DNA replication. For 8 days some of these cells grew in media without folic acid and other cells were exposed to various concentrations of folic acid. When the cells replicate their DNA, new nucleotides are incorporated into the growing DNA chain. Normally, deoxyadenosine base pairs with thymidine and deoxycytidine base pairs with deoxyguanosine. If thymine is absent, uracil will be misincorporated into the DNA molecule (remember that folic acid is required for thymine synthesis). When uracil is incorporated into the chromosome, normal cells try to repair the mistake. As a first step in the repair process, the DNA backbone is cut to remove the uracil.
Identification of uracil in newly synthesized DNA
After growing the cells as outlined above, DNA was isolated from the cells (all proteins and lipids were removed). Remember that anywhere there was a misincorporated uracil there will be a break in the DNA. By purifying just the DNA, the authors removed all of the enzymes that would normally "fix" breaks in the DNA. That means that wherever a uracil was incorporated into the DNA molecule, there will now be a break in the DNA*.
Electrophoresis of the DNA in agarose (a jelly-like substance) on a microscope slide forms a comet shaped design. The head of the comet is the site where DNA was loaded and the tail of the comet contains DNA that has migrated the furthest. Remember that smaller chunks of DNA migrate the furthest from the well where DNA was loaded. In a comet assay, the small fragments of broken DNA migrate in the tail. DNA can actually be visualized by staining with a fluorescent molecule called DAPI, which binds and stains DNA. Do you predict that DNA containing high levels of uracil will be found in the tail or the head of the comet? (A bright tail means lots of small pieces of DNA and therefore a lot of uracil incorporation. DNA that has not been broken will stay in the head of the comet.)
1. Now that you understand the method, look back to Figure 1 and focus on the black bars. (See * below for details on the white bars if you are curious). Concisely explain your conclusions about folic acid and DNA damage based only on the information found in Figure 1. (5 points)
Figure 2. The effect of folic acid concentration on human immune cells. Immune cells were grown for up to 8 days in either folate-deficient medium (white circles) or in medium supplemented with 1 ng/ml (black circles), 10 ng/ml (black triangles) or 100 ng/ml (white diamonds) folic acid. Cell number is expressed per milliliter. Results are mean ± standard error of the mean (n=10).
2. Use only the information available to you from Figure 2. What can you conclude about the effect of folic acid concentration from Figure 2? (5 points)
3. Concisely explain how Figures 1 and 2 relate to each other. (5 points)
4. How do these two figures and your answer to number 3 support or contradict the article you read in class entitled "Association between famine and schizophrenia..."? In your response connect ALL of the following concepts we have covered in the course: nucleotides, folic acid, DNA, protein, DNA replication, mutation, and mitosis. Your answer should include both a written explanation and a visual representation that diagrams these connections; as a starting point for your visual representation, look at the "visual outline" shown below. A thoughtful response to this question should help you in studying for the exam. (10 points)
*You may be interested in why they added the uracil DNA glycosylase enzyme in Figure 1. Here is the rest of the story. You are NOT responsible for this information on the exam. After nuclear DNA was isolated, the enzyme uracil DNA glycosylase was added to the DNA. All DNA containing organisms contain a specific repair pathway, which removes uracil from DNA.
Uracil-DNA glycosylase carries out the first step in this repair pathway. The enzyme is exquisitely specific for the removal of uracil, but no other base, from DNA. The DNA is nicked when the uracil is removed. In an intact cell, repair of the DNA requires filling in the hole with the correct nucleotide and an enzyme to reseal the nick in the phosphodiester backbone of the DNA molecule. In the case of our isolated nuclear DNA there are no enzymes around to "fix" the DNA. That means that wherever a uracil was incorporated into the DNA molecule, the uracil-DNA glycosylase causes a break in the DNA that is not repaired. The added uracil DNA glycosylase enhances the normal cellular mechanisms. Notice in Figure 1 that in the presence of the enzyme (white bars) there is more DNA damage detected.
Below are two figures taken from a journal article about folic acid and DNA damage (Duthiea, S. J. and A. Hawdona. 1998. DNA instability (strand breakage, uracil misincorporation, and defective repair) is increased by folic acid depletion in human lymphocytes in vitro. The FASEB Journal 12: 1491-1497.) The authors investigated the relationship between folic acid, uracil misincorporation during DNA replication, and DNA stability.
Figure 1. The effect of folic acid concentration on DNA strand breakage and misincorporated uracil in human immune cell DNA. Immune cells were grown for 8 days in either folate-deficient medium or in medium supplemented with increasing concentrations of folic acid. Cells were incubated either with uracil DNA glycosylase in buffer (white bars) or buffer alone (black bars) Results are shown as the Mean ± Standard Error of the Mean (n=10). The black bars show us the background amount of DNA strand breakage that was occurring in the immune cells before the DNA was isolated. Adding the uracil DNA glycosylase enhanced the breakage.
Before you can interpret Figure 1, you need to know how the authors measured DNA damage in cells. The researchers cleverly made use of a naturally occurring event in cells to track DNA damage. Here is the method they reported in the paper:
Stimulation of DNA replication
In the paper, the authors exposed the cells to conditions that normally stimulate cell division, i.e. DNA replication. For 8 days some of these cells grew in media without folic acid and other cells were exposed to various concentrations of folic acid. When the cells replicate their DNA, new nucleotides are incorporated into the growing DNA chain. Normally, deoxyadenosine base pairs with thymidine and deoxycytidine base pairs with deoxyguanosine. If thymine is absent, uracil will be misincorporated into the DNA molecule (remember that folic acid is required for thymine synthesis). When uracil is incorporated into the chromosome, normal cells try to repair the mistake. As a first step in the repair process, the DNA backbone is cut to remove the uracil.
Identification of uracil in newly synthesized DNA
After growing the cells as outlined above, DNA was isolated from the cells (all proteins and lipids were removed). Remember that anywhere there was a misincorporated uracil there will be a break in the DNA. By purifying just the DNA, the authors removed all of the enzymes that would normally "fix" breaks in the DNA. That means that wherever a uracil was incorporated into the DNA molecule, there will now be a break in the DNA*.
Electrophoresis of the DNA in agarose (a jelly-like substance) on a microscope slide forms a comet shaped design. The head of the comet is the site where DNA was loaded and the tail of the comet contains DNA that has migrated the furthest. Remember that smaller chunks of DNA migrate the furthest from the well where DNA was loaded. In a comet assay, the small fragments of broken DNA migrate in the tail. DNA can actually be visualized by staining with a fluorescent molecule called DAPI, which binds and stains DNA. Do you predict that DNA containing high levels of uracil will be found in the tail or the head of the comet? (A bright tail means lots of small pieces of DNA and therefore a lot of uracil incorporation. DNA that has not been broken will stay in the head of the comet.)
.jpg){kind=link}
1. Now that you understand the method, look back to Figure 1 and focus on the black bars. (See * below for details on the white bars if you are curious). Concisely explain your conclusions about folic acid and DNA damage based only on the information found in Figure 1. (5 points)
Figure 2. The effect of folic acid concentration on human immune cells. Immune cells were grown for up to 8 days in either folate-deficient medium (white circles) or in medium supplemented with 1 ng/ml (black circles), 10 ng/ml (black triangles) or 100 ng/ml (white diamonds) folic acid. Cell number is expressed per milliliter. Results are mean ± standard error of the mean (n=10).
2. Use only the information available to you from Figure 2. What can you conclude about the effect of folic acid concentration from Figure 2? (5 points)
3. Concisely explain how Figures 1 and 2 relate to each other. (5 points)
4. How do these two figures and your answer to number 3 support or contradict the article you read in class entitled "Association between famine and schizophrenia..."? In your response connect ALL of the following concepts we have covered in the course: nucleotides, folic acid, DNA, protein, DNA replication, mutation, and mitosis. Your answer should include both a written explanation and a visual representation that diagrams these connections; as a starting point for your visual representation, look at the "visual outline" shown below. A thoughtful response to this question should help you in studying for the exam. (10 points)
*You may be interested in why they added the uracil DNA glycosylase enzyme in Figure 1. Here is the rest of the story. You are NOT responsible for this information on the exam. After nuclear DNA was isolated, the enzyme uracil DNA glycosylase was added to the DNA. All DNA containing organisms contain a specific repair pathway, which removes uracil from DNA.
Uracil-DNA glycosylase carries out the first step in this repair pathway. The enzyme is exquisitely specific for the removal of uracil, but no other base, from DNA. The DNA is nicked when the uracil is removed. In an intact cell, repair of the DNA requires filling in the hole with the correct nucleotide and an enzyme to reseal the nick in the phosphodiester backbone of the DNA molecule. In the case of our isolated nuclear DNA there are no enzymes around to "fix" the DNA. That means that wherever a uracil was incorporated into the DNA molecule, the uracil-DNA glycosylase causes a break in the DNA that is not repaired. The added uracil DNA glycosylase enhances the normal cellular mechanisms. Notice in Figure 1 that in the presence of the enzyme (white bars) there is more DNA damage detected.
Teaching Notes and Tips
Rationale
We began to use this type of homework problem a few years ago to give some structure to each unit. We introduce a topic with a current, interesting research story that can be used as a touchstone throughout the unit. Despite our best intentions, introductory students often see each topic as disconnected from the previous or subsequent topic. We felt that asking them to explicitly connect ideas while studying for the exam would be beneficial. We have found that it is challenging for students to construct their own framework of how the ideas in the unit fit together. However, by working through the process, they gain understanding of the concepts and they more easily recognize "gaps" in their understanding prior to the exam.After the assignment has been collected, we post a few excellent student concept maps to show the rest of the class the variety of approaches. Students often begin with many more paragraphs and words than we'd like to see. Many students are uncomfortable with the idea of using pictures or flow charts to connect the concepts. We tell students they are drawing these diagrams because it will help them see the connections between the various concepts and mechanisms we have covered, and that it is a useful skill to develop because scientists often work with models and draw pictures or diagrams. Some students need an additional one-on-one explanation of how this process will help their learning. We use this research-based, synthesis approach before each exam throughout the term, and we observe that as the students become more familiar with diagramming they begin to use fewer words and are more comfortable with the process.
Problem Design
We chose a research article that was accessible to introductory biology students and that related to the topic of DNA, DNA replication, and mitosis. We wrote a brief summary of the key methods in terms the students could understand, selected two key figures from the paper, and rewrote the figure legends for the students. We wanted students to practice writing concise answers and to be sure they were answering the questions based only on the data presented. The final question forces the student to construct connections between the various concepts we covered, and to practice using diagrams to answer scientific questions rather than essay-type answers.Timeline
We first hand out the short science news article for students to read in class at the beginning of the unit. We let students know that some of the terms and ideas will be new to them, but that we will be covering these topics in the upcoming unit. We then use interactive lectures and in-class, faculty-coached problems to help the students learn the related concepts. When appropriate, we refer back to the original science news article so they are reminded of the article and that what we are learning relates to a real world problem. We give students the homework assignment about one week before the exam to ensure they have time to reread the short news article and begin working on the questions. The final question asks students to synthesize all of the concepts from the unit and to connect the ideas to the research paper. We want them to spend sufficient time on this assignment as it is a useful tool to help them study for the exam, to identify "holes" in their notes or understanding, and to see that the various pieces connect before they are sitting in the classroom taking the exam. Faculty are available to help students work through the questions and to guide them when generating their concept maps.Once students have handed in the assignment we post an online key. We use this type of problem prior to each exam throughout the term. Before students begin work on the next assignment, we post sample keys that students generated to help them see there are multiple approaches and to spark their creativity.
Answer Key Malnutrition, DNA replication, Development, and Schizophrenia
1. Now that you understand the method, look back at Figure 1 and focus on the black bars. (See * below for details on the white bars if you are curious). Concisely explain your conclusions about folic acid and DNA damage based only on the information found in Figure 1. (5 points)
The amount of DNA damage in the cells decreases as the concentration of folic acid increases.
(Note: The authors used immune cells because they are easily obtained from people by drawing blood. It is much harder to study cells from other tissues, most people don't want to donate a chunk of their liver or skin!)
2. Use only the information available to you from Figure 2. What can you conclude about the effect of folic acid concentration from Figure 2? (5 points)
Cell growth requires folic acid; cell number increases when the concentration of folic acid increases. The greater the concentration of folic acid (up to 100 ng/ml), the greater the amount of cell division.
3. Concisely explain how Figures 1 and 2 relate to each other. (5 points)
Figure 2 shows how cell number is dependent on the concentration of folic acid, and Figure 1 shows the amount of DNA damage in cells grown in various folic acid concentrations. How do these two figures relate to each other? If DNA is damaged the cell won't divide, therefore, the cell number doesn't increase.
4. How do these two figures and your answer to number 3 support or contradict the article you read in class entitled Association between famine and schizophrenia...? In your response connect ALL of the following concepts we have covered in the course: nucleotides, folic acid, DNA, protein, DNA replication, mutation, and mitosis. Your answer should include both a written explanation and a visual representation that diagrams these connections; as a starting point for your visual representation, look at the "visual outline" shown below. A thoughtful response to this question should help you in studying for the exam. (10 points)
These figures support the article. The lack of dietary folic acid leads to DNA damage (Figure 1). DNA damage may result in mutations or chromosome breaks. If the DNA damage is severe (such as a chromosome break) and/or unable to be repaired, the cell doesn't divide and in some cases may die; cell number does not increase (Figure 2). We know that the developing embryo requires cell divisionin general, and brain cells need to divide during embryonic growth. Important note: these figures DON'T tell us which genes are mutated due to the DNA damage or where the damage occurred. We would have to do additional studies using different techniques to answer those questions. It is also likely that the mutations that result from lack of folic acid would not lead to just schizophrenia, but also to other diseases or developmental problems.We know, for example, that if a birth mother is malnourished, there are links to heart development problems in her offspring.The short article you read in class was written by researchers who study schizophrenia, so they focused on schizophrenia.
The amount of DNA damage in the cells decreases as the concentration of folic acid increases.
(Note: The authors used immune cells because they are easily obtained from people by drawing blood. It is much harder to study cells from other tissues, most people don't want to donate a chunk of their liver or skin!)
2. Use only the information available to you from Figure 2. What can you conclude about the effect of folic acid concentration from Figure 2? (5 points)
Cell growth requires folic acid; cell number increases when the concentration of folic acid increases. The greater the concentration of folic acid (up to 100 ng/ml), the greater the amount of cell division.
3. Concisely explain how Figures 1 and 2 relate to each other. (5 points)
Figure 2 shows how cell number is dependent on the concentration of folic acid, and Figure 1 shows the amount of DNA damage in cells grown in various folic acid concentrations. How do these two figures relate to each other? If DNA is damaged the cell won't divide, therefore, the cell number doesn't increase.
4. How do these two figures and your answer to number 3 support or contradict the article you read in class entitled Association between famine and schizophrenia...? In your response connect ALL of the following concepts we have covered in the course: nucleotides, folic acid, DNA, protein, DNA replication, mutation, and mitosis. Your answer should include both a written explanation and a visual representation that diagrams these connections; as a starting point for your visual representation, look at the "visual outline" shown below. A thoughtful response to this question should help you in studying for the exam. (10 points)
These figures support the article. The lack of dietary folic acid leads to DNA damage (Figure 1). DNA damage may result in mutations or chromosome breaks. If the DNA damage is severe (such as a chromosome break) and/or unable to be repaired, the cell doesn't divide and in some cases may die; cell number does not increase (Figure 2). We know that the developing embryo requires cell divisionin general, and brain cells need to divide during embryonic growth. Important note: these figures DON'T tell us which genes are mutated due to the DNA damage or where the damage occurred. We would have to do additional studies using different techniques to answer those questions. It is also likely that the mutations that result from lack of folic acid would not lead to just schizophrenia, but also to other diseases or developmental problems.We know, for example, that if a birth mother is malnourished, there are links to heart development problems in her offspring.The short article you read in class was written by researchers who study schizophrenia, so they focused on schizophrenia.
Share your modifications and improvements to this activity through the Community Contribution Tool »
Assessment
The malnutrition and schizophrenia problem is graded (see key above). Students receive written feedback and are encouraged to check the online key for additional details and examples of concept maps. Faculty can also assess how well students are connecting ideas by interacting informally with students as they work on the problem and raise questions. Because students have spent so much time and energy on this assignment, we include a closely related question on the exam.
References and Resources
Duthiea, S. J. and A. Hawdona. 1998. DNA instability (strand breakage, uracil misincorporation, and defective repair) is increased by folic acid depletion in human lymphocytes in vitro The FASEB Journal 12: 1491-1497.