PBL Assignment - A Virtual Study of Mendel's Plant Height Alleles200 points total
Mendel's discovery of the principles of genetics is the most important unifying theory in biology. These principles describe the nature of genes and how they genetically interact to control gene expression. Since Mendel's time, a great amount of research has led to our understanding of the structure and expression of genes. Genes are made of DNA. The DNA is transcribed into RNA, which in turn is a substrate for the translation process that makes proteins. The proteins can act as enzymes in a biochemical pathway, agents that control gene expression or as structural components of the cell. These proteins are directly responsible for the phenotype of the organism. A change in the DNA sequence of the gene can directly affect the function of the protein. These changes may include a nucleotide substitution, or the addition or deletion of nucleotides from the sequence. All can have direct effects on the expression of the protein. An altered protein structure can lead to a new phenotype. In genetic terminology, an individual with a new phenotype is called a mutant.
Specifically, we will investigate the differences in gene structure of the pea gibberellin 3- hydroxylase gene. This gene is responsible for plant height in pea (and other species). A specific form of gibberellic acid (GA), a plant hormone, is necessary for stem elongation. If the correct form of the hormone, GA1, is not present, the stem doesn't elongate, and the plant is shorter in stature. A functional version of gibberellin 3- hydroxylase is necessary to convert GA20 to GA1. The mutated form of the protein cannot make the conversion. If you remember, plant height was one of the seven traits Mendel studied. The gene responsible for this trait is called Le. You will use bioinformatic tools to learn the nature of the Le mutants.
Computer scientists have written programs that allow geneticists to study gene sequences. The most important programs align two sequences and permit a detailed study of their sequence differences. We will use a program, MultAlin, which is available over the Internet. To use the program, you simply paste the sequences you wish to compare into the "Sequence box", set a few parameters, and have the program align the sequences.
1. Carefully go through the alignment and look for differences. Do you see any? What differences do you see?
2. The sequences you analyzed represent the mRNAs for each of the two alleles. (The information for the one intron is not included.) The sequences begin with the three base pair ATG start codon that encodes the amino acid methionine. Using this information, can you figure out the amino acid change that would result from this mutation? The Genetic Code is included below for reference.
Many mutants in nature are result of simple changes. But by no means is that the only type of change that could occur. Since Mendel's time other Le mutants have been discovered. In each case, the plant is shorter than the tall wild type plant. Some mutants (le-2) were actually derived from Mendel's original dwarf mutant plant. le-2 is even shorter than le-1. So the question is: What are the structural differences in the various mutants.
3. What differences do you see?
4. What specific amino acid changes do you predict for certain mutants?
5. Do you observe a new mutant changes? If so, describe those.
6. Can you determine which mutants are related?
7. What information supports your conclusion?
8. What differences do you see between le-1 and le-2? Remember these two mutants are related?
9. What is different about this mutant compared to the others?
10. What other mutant appears to be closely related to le-2*?
The Genetic Code