Nonsensical Point Mutations

Discussion in 'Biology & Genetics' started by Jake Arave, Nov 25, 2014.

  1. Jake Arave Ethologist Registered Senior Member

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    165
    What are some implications of Nonsensical Mutations?

    NOW INSERT

    Assuming that the stop codon (in this case) is moved to an incorrect location to create the full functional protein, what are the implications? I would appreciate if someone could point me in the right direction to find out more about specific Point Mutations, and the phenotypic representation of said mutations.
    I understand that this question isn't really in any sort of specific direction, and I hope that someone is able to give me a reputable source of information on NPM's.
     
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  3. Jake Arave Ethologist Registered Senior Member

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    165
    Found the information I needed.
     
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  5. wellwisher Banned Banned

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    Proteins within cells will fold into exact 3-D folds. These folds are not subject to chance due to thermal movement, but are exact and reproducible. This exact folding is due to the interaction of water and the protein and the need to minimize potential between the two in the context of water hydrogen bonding to itself and the protein; water and oil effect. If we change the protein, even a little, we also change the fold into another exact 3-D shape. The new shape will impact how the protein will orientate itself in 3-D and how its internal energy is distributed, thereby changing the way it interacts, flexes and conforms.

    In general, if the new amino acid(s) are more reduced, this will tighten up the protein section and/or tuck this section away from the surface. While more oxidized amino acids will loosen up the local fold and/or shift this section more to the surface. These changes in 3-D can add puckers and dents, which can alter the way the internal energy is distributed and the way it is released during conformational changes. It can also impact the surface active site.

    Protein activity and folds, are not isolated affects, but are also dependent on the water, with few protein working properly with any other solvent besides water. There is a special connection between water and protein, that is the key to the equation.

    Water self bonds, via hydrogen bonding, and can also pack in semi-stable 3-D clusters. The size of this cluster is about the same as basic protein sub-unit. This evolved for a reason. With a slight change of hydrogen bonding energy, these water clusters can shift between high and low density conformations. The high density water shape lowers its local volume in the local water and is needed to create liquid space so proteins can expand. Water is like a being in a crowded rock concert, very hard to move. To move to get refreshments, gaps need to open up.

    The low density water is fluffier and takes up more volume. This reduces the local liquid space and pushes proteins tighter. These two water conformations not only have different volumes and change local pressure, but they also define different free energy contents within the cluster. The free energy is connected to enthalpy and entropy and also help with protein energy dynamics beyond pressure.

    The surface of the protein helps to define the potential within the adjacent water. The adjacent water is also impacted by the potential of the bulk water, allowing all the proteins and the cell to integrate. Changes in protein can lock the water out of coordination, thereby creating a ripple effect.

    For example, in a protein train, where many reactions needs to occur sequentially, expansion of the water near one protein coordinates with the collapse of the water in the next, so the shapes changes can coordinate in the dense water; beating hearts 180 degree out of phase. If we change one protein in the train, its local water can the entire train, if the water clusters tend to remain open or closed, too long for the train. It may still work but be rate limiting.
     
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  7. The. Ring. Banned Banned

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    It is not a math problem that can be understood fully by viewing it in this fashion. The interaction with the environment, and the way this gives the organism an advantage in reproducing, is what is important, and this can not be seen in your equations, even though it is clearly there. When we can see this, then we will understand the equation, we can not do this as of yet.
     

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