Chemotaxis

Basic flagellar structure/behavior:  Some bacteria move using organelles known as a flagellum.  These are rotary motors powered by ion gradients (batteries).    The motor drives a helical propeller.  The basic motor can rotate in either a clockwise or a counterclockwise wise direction.

Because their three dimensional structure, when the flagellum rotates in one direction (clockwise - check), the bacteria moves forward; when rotating in the opposite direction, the bacteria tumbles.

Typically, the motor turns so the bacteria swims forward.   When the flagellar motor switches, the bacteria tumbles, and then when it switch back, it swims off in a new direction. 

The ability to control chemotaxis depends upon controlling the probability of this switching. 

expand discuss about probability?

Gradients:  Bacteria only display chemotaxis when they are placed in a gradient of a particular chemical.  The idea of a gradient involves differences in concentration. 

A gradient will form between any two point in a solution if the concentrations of a particular dissolved molecule are different at the two point – the larger the difference in concentrations the larger the gradient.  The direction of the gradient is from the higher to the lower concentration. 

In the absence of other factors, gradients are inherently unstable – they require a constant input of energy to maintain.  A stable gradient, that is one that persists of over time, is an example of a steady state system.  

The random movement of molecules in solution will lead to a net flux of molecules away from the area high concentration into the area of low concentration.    This movement, known as diffusion, is driven by the random (non-directional) movements of molecules.  

The movement of molecule is due to the kinetic energy, which is described by the equation

E_kinetic = Sum 1/2 m_iv^_i2

where the total kinetic energy of the system is the sum of the kinetic energies of each particle i, with mass m_i and velocity v_i.  The total energy of the system (E_system) is a function of its temperature and its mass, so that

E_system = ƒ(T,m) = E_kinetic + E_potential

[there must a term for entropy here]

where ƒ means function, T for temperature and m for mass of the system.  The term E_potential refers to energy stored in the organization of the system, and one form of stored energy is concentration gradients. 

Only if molecules are removed from the area of low concentration or added to the area of high concentration (or both together) can a gradient be maintained.  Adding or removing molecules from specific regions involves the input of energy. 

Neither the existence nor the movement of molecules can be experienced directly.  We can either use complex machinery to demonstrate that they exist , or we can infer their existence through scientific thinking.   

There are ways to directly visualize this movement; the most direct is known as Brownian motion, a fact recognized by Albert Einstein and subject of one his three classic scientific papers published in 1905.   [tutorial about random walking here?]

Sensing gradients:  Bacteria are no more than a few microns long, and even large gradients differ in concentration just too small to recognize. 

But, if a bacteria is swimming, it can determine whether the concentration is increasing or decreasing over time.  

When the concentration (of an increasing) is increasing, tumbling is suppressed - the motor runs mostly forward; when the concentration decreases, it reverses

• There is a process by which bacteria swarm together.  Given what you know about chemotaxis, and the fact that bacteria can secrete chemical that are attractive to their relatives, devise and describe a a plausible scenario for how this works. 
• READ the very, very short paper by Park et al (2003) Motion to form a quorum and describe how they deduced the nature of chemoattractant involved.