The Evidence-
In a footnote for page 25, David Shenk cites “Genes and Codes” by Godfrey-Smith to say that “All the genes can code for, if they code for anything, is the primary structure (amino acid sequence) of a protein” (190). If genes only code for amino acid sequences, does that mean that secondary through quartenary structure of proteins is affected only by the environment? How can genes have any control over protein function if genes only control the primary structure of proteins? How do environmental factors impact the formation of proteins, especially in secondary through quartenary structural aspects such as beta-pleated sheets, disulfide bonds, and so on? Can the environment affect primary structure as well by changing transcription factors that impact gene expression? Furthermore, relate to the biological theme of structure and function by analyzing how the environmental effects on a protein’s structure can affect the protein’s function as well. Also analyze how these protein functions impact the life of an organism. Refer to chapter 5 of Campbell for protein structure, and refer to chapter 18 for transcription factors and gene expression.
Aaron Zalewski (bitquest@yahoo.com)
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DeleteAlthough genes only code for amino acid sequences, the secondary through quaternary structures of proteins are directly affected by the primary structure. For instance, the tertiary structure "is the overall shape of the polypeptide resulting from interactions between the side chains (R groups) of the various amino acids" (Campbell 83). In other words, the primary structure (amino acid sequence) determines the tertiary structure (general shape), at least in part. While the effect of genes on secondary, tertiary, and quaternary structure of a protein is indirect, that effect most certainly exists via the genetic coding for amino acid chains. Sickle-cell anemia, for instance, is caused by a change in the quaternary structure of hemoglobin - however, it "is caused by the substitution of one amino acid (valine) for the normal one (glutamic acid) at a particular position in the primary structure of hemoglobin" (Campbell 84). The point mutation is not merely caused by the environment, either, seeing as, according to http://www.pnas.org/content/77/5/2853.abstract?sid=322875f8-1271-4d89-bcae-3bbb45a4c48d, sickle-cell anemia can be prenatally diagnosed, indicating that the disorder is caused by a flaw in the genetic code, not from environmental stimulus. This relates to the theme of structure and function because changes to the structure of the protein - that is, denaturation - affect the function of the protein.
DeleteEnvironmental factors affect the transcription of proteins by the epigenome, and "the epigenome can be altered by the environment" (p. 159), as Shenk says. The environment certainly can alter the primary structure of proteins; however, it is inaccurate to think of the environment's primary effect on proteins being the epigenomatic effect on proteins; it is more likely for environmental stresses to denature proteins through effects on the secondary and tertiary structures of the protein.
Also, the effect of the environment on protein structure at all levels most certainly affects the protein's function. When a protein's structure is changed, the protein can be denatured, making the protein cease to function in its original form. The denaturation of proteins affects the life of an organism; when the proteins in an organism cease to function, that organism cannot carry out those functions that the proteins required. When the proteins cease to function, then the organism dies. So yes, the proteins in an organism can easily affect the life of that organism; but the organism itself usually has self-regulating mechanisms to prevent the protein from being denatured except in extreme circumstances.
This relates to the theme of structure and function, the theme stating that a protein, organelle, or organ's structure determines the function of that protein, organelle, or organ. The relation lies in the fact that the substitution of one amino acid , or any other change in the structure of the protein being used, ultimately renders the protein non-functional.
Ari Bakke
Aribakke@gmail.com
It is inaccurate to say that secondary through quaternary structure of proteins are only affected by the environment because, just like Ari mentions, the primary structure of a protein (which is coded for by genes) has a huge affect on the secondary through quaternary structures of a protein. In the Campbell text on page 84 there is an example of how changing just one of the amino acids in the sequence of the hemoglobin protein can affect the quaternary structure of the protein. This ends up inhibiting hemoglobin from performing its function of carrying oxygen. Genes have complete control over what the eventual structure and function of protein will be, for building the correct sequence of amino acids will lead to the correct secondary through quaternary structures, which will lead to the correct protein function.
ReplyDeleteNow, having said that genes can control primary through quaternary structures of proteins, genes are not the only factor of the eventual structure and function of a protein, and the environment also has huge effects. One of the biggest ways that the environment can alter primary structure (which will change secondary-quaternary structure) is via mutagens that change the genes that code for proteins. Campbell talks about missense and nonsense mutations on pages 344-345, both of which can happen from environmental mutagens and change primary structure of proteins. Secondary structure can be altered when proteins are exposed to acidic or basic environments with high concentrations of H+ or OH- ions that will form hydrogen bonds with the ends of amino acids, causing the amino acids to be less likely to form hydrogen bonds with each other. Secondary and Tertiary structure can be altered through changes in environmental temperature. Changing the kinetic energy of the molecules in a protein will cause the molecules to be more or less likely to form hydrogen bonds with one another. The increased energy will also cause the molecules to spread out and denature the protein. Changing primary-tertiary structures with the environment can have an effect on quaternary structure.
At first glance, it seems like the environment’s effects on a protein are mostly negative, but along with denaturing and altering proteins, there are also specific conditions that cause a protein to work at optimal conditions. It would be a selective advantage for an organism to have proteins whose optimal conditions are the environment in which the organism lives in. Therefore the genes should make proteins that work for the organism’s environment. It is possible that the GxE interactions that Shenk talks about cause the genes to be altered so they manufacture proteins that work best in the environmental conditions that altered the genes in the first place.
Brad Tiller (brad.tiller@comcast.net)