BioSec 2012: Mohammad

Energy and Enzymes

I summarized this chapter earlier:

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Catalyst called enzymes speed up the rates of reaction without the need for an increase in temperature.

Phosphatases: A group of enzymes catalyze the removal of phosphates groups from a range of molecules.

Energy: The capacity to do work e.g build a protein from a group of amino acids or pump sucrose across a cell membrane.

First law of thermodynamics: Energy can be transformed from one place to another, but it cannot be created or destroyed.

Second law of thermodynamics: The total disorder (entropy) of a system and its surroundings always increases.

It takes energy to maintain low entropy or the “orderness” of things.

Cells are always breaking down and new ones are always being created by the synthesis of a huge array of proteins, carbohydrates and lipid molecules.

Free energy: The portion of a system’s energy that is available to do work.

Spontaneous reactions:

1- Reactions tend to be spontaneous if the products have less potential energy than the reactants.

2- Reactions tend to be spontaneous when the products are less ordered than the reactants.

3- Change in free energy indicated whether a reaction is spontaneous. The free energy change as the system goes from initial to final states is the sum of the changes in the energy content and entropy.

Point of chemical equilibrium: a state in which reaction does not stop but rather a state in which the rate of the forward reaction equals the rate of the backward reactions.

The change in free energy of life is always negative as organisms constantly take in energy-rich molecules and use them to do work. Organisms reach equilibrium only when they die.

Exergonic reaction: A reaction that releases free energy. Products contain less free energy than the reactants

Endergonic reaction: The products contain more free energy than the reactants.The reactants involved in the reaction need to gain free energy from the surroundings to form products of the reaction. Catabolic pathway: Energy is released by the breakdown of complex molecules to simpler compounds e.g. cellular respiration

Anabolic pathway: Energy is consumed to build complex molecules from more simple ones. e.g. photosynthesis.

Cells supplies energy to drive endergonic reactions using ATP (adenosine triphosphate)

ATP contains free enegry from high energy phosphate bonds.

Removal of one or two of the three phosphate groups is a spontaneous reaction that relieves the repulsion of the negatively charged phosphate groups and releases large amounts of free energy.

The breakdown of ATP is a hydrolysis reaction and results in the formation of ADP (adenosine diphosphate) and a molecule of inorganic phosphate.

Hydrolysis of ATP produces free energy (heat).

How do living cells link the hydrolysis of ATP to an endergonic reaction such that the energy is not wasted as heat?: Energy coupling: An enzyme brings ATP and the reactant molecule into close association.

Energy in carbohydrates, fats and proteins consumed in food is used in the energy requiring endergonic process that combines ADP and Pi.

The continued breakdown and resynthesis of ATP is called the ATP cycle.

A spontaneous reaction does not mean that it proceeds rapidly.

Activation Energy: initial energy required to start a reaction and tranform molecules into transition state where bonds are stable and are ready to be broken.

Enzymes act as a catalyst by lowering the activation energy required by molecules in reactants to start a reaction.

Enzymes speed-up the rate of spontaneous exergonic reactions.

Enzymes do not supply free energy to the reaction.

Three main mechanisms in which an Enzyme lowers activation Energy:

1- Bringing the reacting molecules together

2- Exposing the reactant molecule to altered charge environments that promote catalysis

3- Changing the shape of a substrate molecule

Temperature and pH levels have a significant effect on enzyme activity and thus the reaction rates. The optimum pH level for an enzyme depends on the pH level of its environment. If Temperature becomes too high the enzyme of denatured.

As the enzyme concentration increases the rate of catalysis increases.

Competitive Enzyme inhibition: enzyme inhibitors bind to the enzyme’s active site

Non-competitive inhibitors: enzyme inhibitors bind to a location on the enzyme other than the active site.

Enzyme inhibition is important to the cell since it controls the presence of multiple active enzymes at the same time. (allosteric regulation).

Feedback inhibition provides a mechanism to prevent the wasting of cell’s energy. If the concentration of the inhibitor increases the enzyme action is inhibited, if the concentration of the inhibitor decreases, the enzyme is activated.

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Are we really evolving software via trial and error as opposed to properly and specifically designing them?

Is it possible to properly design a piece of software to do exactly what we want it to do and nothing else considering that it will be part of a bigger system?

mo_brain.core.1

With all the complex biological systems how can computer scientists acquire all that knowledge? Do we need to acquire all that knowledge before making a decision whether this is useful in terms of computer system's security of not? How long or how much effort needs to be spent in such a process?

From the few chapters that we've read, a thought that goes through my mind: Can we completely understand how a biological system works in full? If we ever do, can we ever fully understand how it interacts with its environment (drugs, foriegn organisms,etc.), can we ever understand the full short or long term implications of changing a minor thing in a biological system?. Even though we consider a software system or a collection of systems as complex structures, relatively speaking and compared to a biological system them seem quite small, deterministic and controllable.

How much can computer scientists take from biology? Can we take sub systems from biology or do we need to go full out replicating existing biological systems?

There seems to be alot of diversity in biology, yet diverse organims can affect each other for example a human getting sick from a bird through a certain strain of bird flu but most of the times diversity provides protection. Can diversity of computer systems provide security?

Can't wait to see how the immune system works and how its evolution happens "online" or during the organisms life.

Biology tends to build things in a bottom up fashion, a fully connected graphs that get pruned with time. Humans tends to engineer systems differently.

"Attacking" a cell affects many other parts or systems within the organism.

A human attacking a computer system tends to make sure his attack does not affect other parts of the system that may trigger alarms or suspicions. That is possible because components of a computer system unlike a biological system could be completely isolated from each other.

Several communication paths are used to relay messages between cells. Membrane receptors resemble a software interface to the system where embedded receptors resemble exposed APIs.

The amazing complexity of the biological pathways amazes me for example:

Originator --> Specific receptor site-binding molecules --> Receptors --> phosphorylation of protein --> Enzyme kicked into action --> Second messengers activated --> FEEDBACK LOOP TO CONTROL PROCESS

Can we enhance a system's security by obscurity or added complexity?

If we were to design a computer system based on biology/evolution, a self replicating, code generating system; what would we gain? how would that system look like?

Can we create an artificial immune system that is as good as a biological one? Can we consider all computer systems in the world to be part of one parent biological organism with one big distributed artificial immune system (a distributed OS)?