Bio chem Consider the folding funnel theory for proteins. As a first approximati
ID: 1009318 • Letter: B
Question
Bio chem
Consider the folding funnel theory for proteins. As a first approximation, the folding funnel does a reasonable job accounting for certain thermodynamic, kinetic, and mechanistic aspects of the folding process when one only considers the protein as the thermodynamic system. However once you start redefining the system to include water and/or asking more sophisticated questions, the original folding funnel idea becomes inadequate. One must then start making more specific assumptions about the funnel model, or modify the model all together.
1) What is the significance of the steepness of the funnel given that gravity has no meaning? Be as specific as possible and provide all necessary rationale for your answer?
2) When a real marble rolls down a real funnel (plastic or glass), friction between the marble and the funnel affects the speed and trajectory of the marble down the funnel. For the funnel theory, assume that the funnel does have mass. What is the funnel made of? What is the origin, significance and potential impact of any frictional forces that occur as the protein moves down the funnel? Be as specific as possible and provide all necessary rationale for your answer.
3) Chemical mechanisms involved with simple process, such as SN1 and similar multi-step organic chemistry mechanisms, require that steps in these mechanisms are ordered, sequential and obligatory. In other words, each step must occur in a particular order, one at a time (not simultaneously), and all steps must occur in order to go from reactant to product.
This is not likely true for more complex chemical processes, such as protein folding.
For example, the folding funnel model indicates that there are multiple, parallel folding pathways for a particular protein to fold. We represent this idea in the funnel model as a marble taking different trajectories down the funnel each time the protein folds.
If the marble does not contact exactly the same points on the surface area of the funnel in each trajectory down the funnel, then theoretically, it is not sampling the same folding intermediates. This is not consistent with the obligatory nature of chemical intermediates in chemical mechanisms,
How can the funnel model be modified to ensure that the same obligatory intermediates are sampled by the protein and still be consistent with multiple, parallel folding pathways? Be as specific as possible and provide all necessary rationale for your answer
Explanation / Answer
Consider the folding funnel theory for proteins. As a first approximation, the folding funnel does a reasonable job accounting for certain thermodynamic, kinetic, and mechanistic aspects of the folding process when one only considers the protein as the thermodynamic system. However once you start redefining the system to include water and/or asking more sophisticated questions, the original folding funnel idea becomes inadequate. One must then start making more specific assumptions about the funnel model, or modify the model all together.
a)
1.A kilogram of iron weighs more than a kilogram of feathers.
2.Weight and mass are the same thing; weight is not considered as a gravitational force.
3.There must be air for gravity to take effect; therefore, there is no gravity on the moon, nor is there gravity out in
space.
4.Earth’s magnetism and spin are connected with gravity.
5.Things fall naturally without the need for a force.
6.Heavier things fall faster than light things.
7.Gravity only acts on an object when it begins to fall and when falling.Gravity ceases to act when the object
lands on the ground and becomes stationary.
8.All objects can be moved with equal ease in the absence of gravity.
b)When a real marble rolls down a real funnel (plastic or glass), friction between the marble and the funnel affects the speed and trajectory of the marble down the funnel. For the funnel theory, assume that the funnel does have mass. What is the funnel made of? What is the origin, significance and potential impact of any frictional forces that occur as the protein moves down the funnel?
Friction removes some of the energy of the rolling marble causing it to drop down into the well.
When the marble drops down into the well some of its gravitational potential energy is converted into kinetic energy.
1.The potential energy of the marble is converted to kinetic energy so that as the marble drops down it has a higher velocity.
2.Not only does the marble go around in a smaller circle as it drops down into the gravity well, it travels around at a higher velocity.
3.The result is that the marble completes orbits much more rapidly near the center of the well.
c)Chemical mechanisms involved with simple process, such as SN1 and similar multi-step organic chemistry mechanisms, require that steps in these mechanisms are ordered, sequential and obligatory. In other words, each step must occur in a particular order, one at a time (not simultaneously), and all steps must occur in order to go from reactant to product. This is not likely true for more complex chemical processes, such as protein folding.
In any chemical change, some bonds are broken and new ones are made. Quite often, these changes are too complicated to happen in one simple stage. Instead, the reaction may involve a series of small changes one after the other.
A reaction mechanism describes the one or more steps involved in the reaction in a way which makes it clear exactly how the various bonds are broken and made.
Related Questions
Navigate
Integrity-first tutoring: explanations and feedback only — we do not complete graded work. Learn more.