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Project Summary

Difficulty	5  –  6
Time required	Very Short (a day or less)
Prerequisites	You should have studied Life Science
Material Availability	None required
Cost	Very Low (under $20)
Safety	No issues

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Objective

The goal of this project is to learn the basics about DNA sequences by examining some simple differences between groups of genes.

Introduction

DNA is double stranded (a double helix) and made up of base PAIRS. Adenine on one strand (represented with an "A") always pairs with thymine (represented with a "T") on the other strand. These are called A~T pairs regardless of which strand has the "A" and which the "T." Similarly, cytosine on one strand (represented with a "C") always pairs with guanine (represented with a "G") on the other strand, creating G~C pairs.

Scientists often represent DNA strands with a string of letters like this:

ATATTTGAAAGCTGTGTCTGTAAACTGATGGCTAACAAAACTAG

This string of letters represents only one strand, or one half of the DNA molecule. There is no need to write down the other strand because as we just described above, a "G" in one strand means there is automatically a "C" in the other strand, just as a "C" in one strand implies that the other contains a "G".

Now think of the human genome and all of the genes in it as a VERY large set of blueprints. Each blueprint is an instruction set for assembling one part or piece of a cell. Almost every cell in your body carries the same set of blueprints -- so what makes a cell in your brain different from a cell in your stomach? A neuron and a stomach lining cell are very different in their morphologies (how they look) and their functions (what job they do). The different shapes and functions are a result of the fact that those two cells use different portions of the complete blueprint set to construct themselves. The neuron uses the blueprints for parts involved in brain signaling, while the stomach cell does not. The stomach cell makes parts for secreting stomach enzymes to help in food digestion, while the brain cell does not. These kinds of blueprints (or genes) are often called "tissue specific" because they are used in some body parts and not in others. However, there are also some blueprints that are used in every cell in the body because the parts they represent are needed in every cell (like pieces used during cell division or making energy). These kinds of blueprints (or genes) are often called "housekeeping" because they represent a basic need of every cell and they "keep up" the basic functions of the cell.

How does the cell know which blueprints to use? Each gene (or blueprint) is has its own control panel that acts as a group of switches affecting when (during an organism's development), where (in the body) and how much a particular blueprint is used. Scientists are still working hard at being able to identify all of the pieces of a gene's control panel. One important part of the control panel that we know a lot about is the "promoter." The number and pattern of As, Ts, Gs and Cs in a promoter is important in determining whether the switch will act like a "housekeeping" switch or a "tissue specific" switch. As of today, scientists are just beginning to understand why this is true.

Terms, Concepts and Questions to Start Background Research

• DNA, gene
• Nucleotide bases (adenine, thymine, guanine, cytosine)

Bibliography

Background knowledge/info:

• Genetic Science Learning Center: http://gslc.genetics.utah.edu/units/basics/
• Understanding Genetics: http://www.thetech.org/genetics/ See the "Zooming into DNA" link.
• NHGRI Education: http://www.genome.gov/Education/ See the book "From Blueprint to You."
• The online encyclopedia Wikipedia has a slightly more advanced discussion of DNA. http://en.wikipedia.org/wiki/Deoxyribonucleic_acid

Experimental Procedure

In this experiment, you will compare housekeeping promoters to other genes by calculating the percentage of G~C content. This will make sense in a minute!

How to calculate the G~C pair content of a DNA sequence:

1. Count the total number of G's and C's. Try it for this sample:
   
   

        ATATTTGAAAGCTGTGTCTGTAAACTGATGGCTAACAAAACTAG

   You should get a total count of 15 (9 G's and 6 C's).
   
   
2. Now count the total number of letters (bases). You should get 44.
   
   
3. %G~C pair content = (Count of G's and C's / Total count of all bases)*100
   
   So, for our sample, the %G~C pair content = (15/44)*100 or 34%

Now, let's perform the experiment:

Step 1: Formulate your hypothesis. Which do you think might be true?

1. Housekeeping promoters will have lower G~C content than other genes,
2. Housekeeping promoters will have higher G~C content than other genes, or
3. Housekeeping promoters will have similar G~C content to other genes.

Step 2: Calculate the %G~C content for each sequence listed below on this page. We have provided partial DNA sequences for three housekeeping promoters, three tissue specific promoters, and for comparison, a number of additional genes of the sort that the promoters would regulate and control.

Time saver! Do the first couple sequences "by hand," but then you can use the %G~C Content Calculator. To use the calculator:

1. Copy and paste the DNA sequence you want to analyze into the box.
2. Press "Calculate" to count the bases and determine the %G~C content.
3. Record your results.
4. Press "Clear Form" to clear all the fields, preparing the calculator for its next count.

Step 3: Record your results in a table with the % G~C content in one column and the name of the sequence in the second column. Fill the table out as you do your calculations. It should look like this:

Step 4: Sort the rows of the table, so that the highest %G~C content is at the top, the next highest percentage appears second, the third highest percentage appears third, and so forth. When you are done, the very lowest %G~C content should be at the bottom.

If you need or want to do a graph for your science fair project (it's almost always a good idea to do so), you can also do a bar chart showing the %G~C content for each gene.

Step 5: Draw your conclusion. What can you say about housekeeping promoters? How does their %G~C content compare to tissue specific promoters? How does the %G~C content of the housekeeping promoters compare to other genes of the sort that the promoters would regulate and control (bone morphogenetic protein 7, leptin, opsin, and cystic fibrosis genes)?

DNA Sequences for Your Experiment

Here are the sequences to use for your experiment. Note that these are partial sequences for the molecules; the full sequence is generally much longer.

Housekeeping Promoters:

1. Heat Shock Protein 90 (HSP90): When proteins get over-heated, their folding and conformation gets messed up which often affects their function. Heat Shock Proteins repair the unfolded proteins back to their working state.

   GCGCGCTGGGCGGGCCCGTGGCTATATAAGGCAGGCGCGGGGGTGGCGCG

2. Glucose-6-phosphate Dehydrogenase (G6PD): This molecule is a member of a team that helps protect each cell from agents that damage important proteins.

   CAGGCGCCCGCCCCCGCCCCCGCCGATTAAATGGGCCGGCGGGGCTCAGC

3. Beta-actin (ACTB): Actin proteins help the cell make an internal "skeleton" that maintains the cell's proper shape.

   CGAGCGGCCGCGGCGGCGCCCTATAAAACCCAGCGGCGCGACGCGCCACC

Tissue Specific Promoters:

1. Bone Morphogenetic Protein 5 (BMP5): Bone morphogenetic proteins help induce the growth of new bone.

   TCCCAGCAGGGTTGTGCTTACACTACTCTTTAGATCTCTCTTGAAGAGGG

2. Hemoglobin Beta (HBB): Part of hemoglobin which carries iron molecules in blood cells.

   CAGGAGCCAGGGCTGGGCATAAAAGTCAGGGCAGAGCCATCTATTGCTTA

3. GABA Receptor A1 (GABRA1): An important receptor of chemical signals that travel only in the brain.

   TTTGCCCTGGGACGTATTACTACTGTCTTGGTAAAGAGAAATCTTTTGTT

Bone Morphogenetic Protein 7 Genes:

Here is a partial DNA sequence from humans, pig, rabbit, and sheep for the Bone Morphogenetic Protein 7 gene (BMP7). You will notice that the sequences are not exactly the same. Bone Morphogenetic Proteins represent signals found in the body that help induce bone growth.

1. Human BMP7

   AGAACCGCTCCAAGACGCCCAAGAACCAGGAAGCCCTGCGGATGGCCAACGTGGCAGAG
   AACAGCAGCAGCGACCAGAGGCAGGCCTGTAAGAAGCACGAGCTGTATGTCAGCTTCCG
   AGACCTGGGCTGGCAGGACTGGATCATCGCGCCTGAAGGCTACGCCGCCTACTACTGTG
   AGGGGGAGTGTGCCTTCCC

2. Pig BMP7

   AGAACCGCTCCAAGACGCCCAAGAACCAGGAAGCCCTGCGGGTGGCCAACGTCGCAGAG
   AACAGCAGCAGTGACCAGCGGCAGGCCTGTAAGAAGCATGAGCTCTACGTCAGCTTCCG
   GGACCTGGGCTGGCAAGACTGGATCATCGCGCCCGAAGGCTATGCCGCCTACTACTGCG
   AGGGGGAGTGCGCCTTCCC

3. Rabbit BMP7

   AGAACCGCTCCAAGGCACCCAAGAACCAAGAGGCGCTGCGAGTGGCCAACGTGGCAGAA
   AACAGCAGCAGTGACCAGCGGCAGGCGTGCAAGAAACACGAACTGTACGTCAGCTTCCG
   CGACCTGGGCTGGCAGGATTGGATCATTGCCCCGGAAGGCTACGCCGCCTACTACTGCG
   AGGGAGAGTGCGCCTTCCC

4. Sheep BMP7

   AGAATCGCTCCAAGGCGCCCAAGAACCAAGAAGCCCTGCGGGTGGCCAACGTCGCAGAA
   AACAGCAGCAGTGACCAGAGGCAGGCATGTAAGAAGCACGAGCTATACGTCAGCTTCCG
   GGACCTGGGCTGGCAGGATTGGATCATCGCACCCGAAGGCTATGCCGCCTACTACTGCG
   AGGGGGAGTGCGCCTTCCC

Leptin Genes:

Here is a partial DNA sequence from humans, cow, dog, and horse for Leptin (LEP), a signal found in the body that tells your brain how much fat you have stored away. Leptin may help regulate how hungry you feel. You will notice that the sequences are not exactly the same.

1. Human Leptin

   TGTGGCTTTGGCCCTATCTTTTCTATGTCCAAGCTGTGCCCATCCAAAAAGTCCAAGAT
   GACACCAAAACCCTCATCAAGACAATTGTCACCAGGATCAATGACATTTCACACACGCA
   GTCAGTCTCCTCCAAACAGAAAGTCACCGGTTTGGACTTCATTCCTGGGCTCCACCCCA
   TCCTGACCTTATCCAAGATGGACCAGACACTGGCAGTCTACCAACAGATCCTCACCAGT
   ATGCCTTCCAGAAACGTGATCCAAATATCCAACGACCTGGAGAACCTCCGGGATCTTCT
   TCACGTGCTGGCCTTCTCTAAGAGCTGCCACTTGCCCTGGGCCAGTGGCCTGGAGACCT
   TGGACAGCCTGGGGGGTGTCCTGGAAGCTTCAGGCTACTCCACAGAGGTGGTGGCCCTG
   AGCAGGCTGCAGG

2. Cow Leptin

   TGTGGCTTTGGCCCTATCTGTCTTACGTGGAGGCTGTGCCCATCCGCAAGGTCCAGGAT
   GACACCAAAACCCTCATTAAGACAATTGTCACCAGGATCAATGACATCTCACACACGCA
   GTCCGTCTCCTCCAAACAGAGGGTCACTGGTTTGGACTTCATCCCTGGGCTCCACCCTC
   TCCTGAGTTTGTCCAAGATGGACCAGACATTGGCGATCTACCAACAGATCCTCACCAGT
   CTGCCTTCCAGAAATGTGGTCCAAATATCCAATGACCTGGAGAACCTCCGGGACCTTCT
   CCACCTGCTGGCCGCCTCCAAGAGCTGCCCCTTGCCGCAGGTCAGGGCCCTGGAGAGCT
   TGGAGAGCTTGGGCGTTGTCCTGGAAGCTTCCCTCTACTCCACCGAGGTGGTGGCCCTG
   AGCCGGCTGCAGG

3. Dog Leptin

   TGTGGCTCTGGCCCTATCTGTCCTGTGTTGAAGCTGTGCCAATCCGAAAAGTCCAGGAC
   GACACCAAACCCCTCATCAAGACGATTGTCGCCAGGATCAATGACATTTCACACACTCA
   GTCTGTCTCCTCCCAACAGAGGGTCGCTGGTCTGGACTTCATTCCTGGGCTCCAACCAG
   TCCTGAGTTTGTCCAGGATGGGCCAGACGTTGGCCATATACCAACAGATCCTCAACAGT
   CTGCATTCCAGAAATGTGGTCCAAATATCTAATGACCTGGAGAACCTCCGGGACCTTCT
   CCACCTGCTGGCCTCCTCCAAGAGCTGCCCCTTGCCCCGGGCCAGGGGCCTGGAGACCT
   TTGAGAGCGTGGGCGGCGTCCTGGAAGCCTCACTCTACTCCACAGAAGTGGTGGCTCTG
   AACAGACTGCAGG

4. Horse Leptin

   TGTGGCTTTGGCCCTATCTGTTCTTCATTGAAGCTGTGCCCATCCGAAAAGTCCAGGAT
   GACACCAAAACCCTCATCAAGACGATTGTCACCAGGATCAATGACATTTCACACACGCA
   GTCAGTCTCCTCCAAACAGAGGGTCACTGGTTTGGACTTCATTCCTGGGCTTCACCCTG
   TCCTGAGTTTGTCCAAGATGGACCAGACATTGGCAATCTACCAACAGATCCTTACAAGT
   CTGCCTTCCAGAAATGTGATCCAGATATCTAATGACCTGGAGAACCTCCGGGACCTTCT
   CCACCTGCTGGCCTCCTCCAAGAGTTGCCCCTTGCCCCAGGCCAGGGGTCTGGAGACCT
   TGGCGAGCCTGGGCGGTGTCCTGGAAGCTTCACTCTACTCCACAGAGGTGGTAGCCCTG
   AGCAGGCTGCAGG

Other genes:

1. Here is a partial DNA sequence for the human Cystic Fibrosis gene (CFTR). In the body this gene's product is involved in making sure mucous doesn't build up in the lungs and that the pancreas secretes the right enzymes to help you digest your food. If this gene is damaged, a patient gets Cystic Fibrosis.

   ATATTTGAAAGCTGTGTCTGTAAACTGATGGCTAACAAAACTAGGATTTTGGTCACTTC
   TAAAATGGAACATTTAAAGAAAGCTGACAAAATATTAATTTTGAATGAAGGTAGCAGCT
   ATTTTTATGGGACATTTTCAGAACTCCAAAATCTACAGCCAGACTTTAGCTCAAAACTC
   ATGGGATGTGATTCTTTCGACCAATTTAGTGCAGAAAGAAGAAATTCAATCCTAACTGA
   GACCTTACACCGTTTCTCATTAGAAGGAGATGCTCCTGTCTCCTGGACAGAAACCAATC
   TTTTAAACAGACTGGAGAGTTTGGGGAAAAAAGGAAGAATTCTATTCTCAATCCAATCA
   ACTCTATACGAAAATTTTCCATTGTGCAAAAGACTCCCTTACAAATGAATGGCATCGAA
   GAGGATTCTGATGAGCCTTTAGAGAGAAGGCTGTCCTTAGTACCAGATTCTGAGCAGGG
   AGAGGCGATACTGCCTCGCATCAGCGTGATCAGCACTGGCCCCACGCTTCAGGCACGAA
   GGAGGCAGTCTGTCCTGAACCTGATGACACACTCAGTTAACCAAGGTCAGAACATTCAC
   CGAAAGACAACAGCATCCACACGAAAAGTGTCACTGGCCCCTCAGGCAAACTTGACTGA
   ACTGGATATATATTCAAGAAGGTTATCTCAAGAAACTGGCTTGGAAATAAGTGAAGAAA
   TTAACGAAGAAGACTTAAAGG

2. Here is a partial DNA sequence for human Opsin1 (OPS1MW) Opsins are involved in providing color vision in the eye. Changes in the function of an opsin protein can lead to color-blindness.

   CCCTTCGAAGGCCCGAATTACCACATCGCTCCCAGATGGGTGTACCACCTCACCAGTGT
   CTGGATGATCTTTGTGGTCATTGCATCCGTTTTCACAAATGGGCTTGTGCTGGCGGCCA
   CCATGAAGTTCAAGAAGCTGCGCCACCCGCTGAACTGGATCCTGGTGAACCTGGCGGTC
   GCTGACCTGGCAGAGACCGTCATCGCCAGCACTATCAGCGTTGTGAACCAGGTCTATGG
   CTACTTCGTGCTGGGCCACCCTATGTGTGTCCTGGAGGGCTACACCGTCTCCCTGTGTG
   GGATCACAGGTCTCTGGTCTCTGGCCATCATTTCCTGGGAGAGATGGATGGTGGTCTGC
   AAGCCCTTTGGCAATGTGAGATTTGATGCCAAGCTGGCCATCGTGGGCATTGCCTTCTC
   CTGGATCTGGGCTGCTGTGTGGACAGCCCCGCCCATCTTTGGTTGGAGCAGGTACTGGC
   CCCACGGCCTGAAGACTTCATGCGGCCCAGACGTGTTCAGCGGCAGCTCGTACCCCGGG
   GTGCAGTCTTACATGATTGTCCTCATGGTCACCTGCTGCATCACCCCACTCAGCATCAT
   CGTGCTCTGCTACCTCCAAGTGTGGCTGGCCATCCGAGCGGTGGCAAAGCAGCAGAAAG
   AGTCTGAATCCACCCAGAAGGCAGAGAAGGAAGTGACGCGCATGGTGGTGGTGATGGTC
   CTGGCATTCTGCTTCTGCTGGGGACCATACGCCTTCTTCGCATGCTTTGCTGCTGCCAA
   CCCTGGCTA

Variations

For the leptin and bone morphogenetic protein 7 genes you have data for different species. How would you describe the % G~C content for the same gene, but in different animals?

• For more science project ideas in this area of science, see Genetics & Genomics Project Ideas.

Credits

Author:	Shelley Force Aldred, Department of Genetics, Stanford University
Sponsor:	Molecular Sciences Institute (MSI), Berkeley, California
Management & Editing:	Ken Hess, The Kenneth Lafferty Hess Family Charitable Foundation

Last edit date: 2005-08-31 13:46:08

Career Focus

If you like this project, you might want to think about career opportunities in Genetics & Genomics.

Many decisions regarding a person's health depend on knowing the patient's genetic risk of having a disease. Genetic counselors help assess those risks, explain them to patients, and counsel individuals and families about their options. Learn more about this career: Genetic Counselor.