On page 190 of the evidence section, David Shenk cites Godfrey-Smith in order to state, "All the genes can code for, if they code for anything, is the primary structure (amino acid sequence) of a protein" (Shenk 190). What does this exactly mean? How can the genes only code for the amino acid sequences? What about the rest, such as secondary, tertiary, and quartenary structure of proteins? Would they be affected strictly by the environment? If genes only control the primary structure of proteins, how can genes have any control over other protein functions? Can the environment affect primary structure as well as the three other protein structures by changing the transcription factors that causes the gene expression? How would the environmental factors have an impact towards structural characteristics of secondary through quartenary structures, for example, beta-pleated sheets and disulfide bonds? Try to think of this prompt by relating to the biological theme, structure and function. Refer to chapters 5 and 18 for protein structure and transcription factors and gene expression in the Campbell. How would the environment affect the protein structure and its functions?
Genes hold the sequence necessary to make proteins that carry out the various functions of the cell. The sequence on a gene makes a blueprint for the necessary amino acids in a specific pattern. The primary structure of the protein is the arrangement of the amino acids. The secondary, tertiary and quaternary structure of proteins all come from chemical interactions between the amino acids. For example the secondary structure of ß-sheets is due to the hydrogen bonding of the amino acids which make that shape. Amino acids all have different properties including being hydrophobic, charged or uncharged, polar or non-polar. The final 3-D structure of the protein is called the tertiary structure. When two chains interact to create a protein that shows quaternary structure of the protein. In our current unit of the immune system the B cell receptor is made out of four polypeptide chains demonstrating the quaternary structure of a protein.The environment would not change the structure of the protein unless it can break the bonds between the amino acids which would cause the protein to breakdown. A way the environment could change the structure is by preventing the transcription of the gene in the first place. This could be done in a way that the necessary activators of a gene disappear and the necessary protein is not produced. Changing the secondary or any higher structure is the denaturing of the protein. If the primary structure is changed when one amino acid is switched to another the structure of the protein will not be able to perform the same function as the normal protein. The environment can change a protein which would be denaturation but this will not be a lasting effect. A permanent change will need to happen in the genes that code for the protein.
ReplyDeleteAyana Dambaeva (adambaeva@gmail.com)
http://www.johnkyrk.com/aminoacid.html
http://www.vivo.colostate.edu/hbooks/genetics/biotech/basics/prostruct.html
When David Shenk quotes Patrick Bateson on the function of genes, his main point is that genes are “several steps removed from the process of trait formation” (25-26). Shenk also told us multiple times that “I’m not a scientist, I’m a journalist” (David Shenk Skype sessions with AP Bio students). Therefore, I don’t think he was putting into full consideration the rest of the protein-developing process with the secondary, tertiary structures. Those are all important steps in full protein synthesis, but regardless, they’re still not necessarily “single-handedly responsible for normal function” (Shenk 25). Shenk is using the same argument for talent as well.
ReplyDeleteThis being said, you still cannot disregard the process of protein synthesis –probably one of the most important functions of living cells. As Ayana described so well, the secondary, tertiary and quaternary structure of proteins all come from chemical interactions that occur between the various amino acids that were organized in the primary structure, and environmental factors do in fact affect these proteins structures. Variables such as heat can change the patterns of the hydrogen bonds that lead up to the secondary structure. However, I don’t think the environment can’t directly change the transcription factors. RNA transcription is more of a mechanism, with “three stages […] initiation, elongation, and termination” (Campbell 332), and translation is based off of the transcription. The only things that can affect these processes are mutations, and we still don’t know the exact cause of all mutations. But we do know that they are “chemical changes in a single base pair of a gene” (Campbell 344) that can alter the rest of the genetic sequence. So clearly this demonstrates a relationship between structure and function that may or may not be directly affected by the environment; thus, I agree with Ayana that the environment can’t change structure of the protein unless it can break the bonds between the amino acids, causing the protein to denature.
http://www.vivo.colostate.edu/hbooks/genetics/biotech/basics/prostruct.html
Agnes Kwon (akwon0215@gmail.com)