Mendel had no way of knowing how his factors (genes) could produce plants that varied in phenotype. However, as our understanding of the molecular basis of genetics increases, so does our ability to explain Mendelian inheritance patterns.
Mendel discovered that the allele for smooth seeds is dominant over the wrinkled seed allele. How does one allele mask the expression of another? Often, the dominant allele codes for a protein that can effectively catalyze a reaction in a cell and produce a phenotype we recognize. The recessive allele, on the other hand, represents a mutant form that has an altered DNA sequence. The protein product that results from transcription and translation of that recessive (mutant) allele is defective. It cannot catalyze the reaction, and, therefore, does not produce a functional product. One copy of the normal allele is usually
enough to allow the cell to produce ample quantities of normal protein. Therefore, a heterozygous plant looks normal. A homozygous recessive plant, on the other hand, cannot make any normal protein from its two mutant alleles.
What is the difference between the smooth seed allele and the wrinkled seed one? The smooth pea phenotype (RR or Rr) produces an enzyme allowing the seeds to accumulate high levels of starch. Seeds with the rr genotype do not produce a functional form of that enzyme and so have high levels of sucrose rather than starch. The sucrose in the rr seeds causes them to absorb water during development. When they dry, they lose that water and shrivel. The RR and Rr seeds have lower levels of sucrose and do not absorb as much water during development; consequently, they do not shrivel when they dry. Recent molecular genetic studies have revealed that the r allele produces a defective enzyme because it has had an 800-nucleotide piece of DNA inserted into the gene. As you might expect, compared to the normal allele, transcription and translation of the allele carrying this insert produces a much different (and, in this case, nonfunctional) protein. How did the insert get there? The best guess is that a transposable element inserted into the pea chromosome at this location some time during the pea plant's evolutionary history.
Molecular genetics can also explain how other Mendelian traits are expressed. For example, as you recall, flower color in snapdragons is inherited as an incompletely dominant trait. In this case, one copy of the functional allele produces some red pigment, but two copies produce noticeably more pigment. Red-flowered plants therefore have two copies of an allele that is critical in the red pigment synthesis pathway and are RR. Pink-flowered plants have one copy of that allele, producing light red (pink) pigmentation, and are RR . (We use superscripts instead of upper and lowercase letters here because we are not looking at complete dominance). Finally, white plants have two copies of the defective allele (R R ) and cannot make the enzyme necessary for red pigment production.
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