Background: popular science, addressed to all.
Biomachines are among the most efficient and small machines in the universe, that perform a host of vital functions imperative for the survival of a cell. Unzipping double stranded DNA at a fantastic speed of ~60 base pairs/sec, synthesizing proteins from the pool of amino acids in a cell by strictly following the instructions encoded in the RNA (with a very small chance of errors), bearing cargo to and from the cytoplasm of the cell to the outside (which are heavier than the weight of the motor itself) are just some the functions that biological motors perform. Basically, these are devices that perform active processes (ie, processes that require external input of energy), as opposed to purely thermal processes. The energy input for these motors is almost always through the hydrolysis of ATP (adinosine triphosphate), releasing ADP and a phosphate group.
A single strand of DNA in a cell is basically a series of bases (A, T, G, C), attached to a sugar-phosphate backbone. Among these four bases, A has the capability to bind to T and G to C. Thus, when two ssDNA (single stranded DNA) with complimentary bases come together, they pair up to form a double stranded DNA (dsDNA ). This double stranded molecule then twists into a helical structure to minimize free energy, yielding the much talked about helical structure of the DNA molecule. The entire DNA molecule, which could run into meters in length is compressed into the cell nucleus or diameter 4-5 microns!
This huge molecule contains the codes that tell the cell how to synthesize proteins from the pool of free amino acids, and proteins are what is necessary for the performance of almost every biological activity. So how does this huge, complex and highly charged molecule exactly contain the fundamental codes of life?
The entire code is in the order of bases on the DNA single strand. If there is a certain region of exposed ssDNA, then complementary base pairing takes place to produce a new molecule called RNA (ribonucleic acid). RNA differs from DNA in that the base T (thymine) is replaced by U (uracil). So how does a naked ssDNA strand ever get exposed? Whenever the cell has to read the code from a certain region the DNA, a motor called DNA helicase goes and sits on the DNA, binding to only one of it's strands. This helicase is powered by ATP hydrolysis, and is propelled forward at rates of ~60 base pairs per sec, prizing open the double strands. Following the helicase is another motor called the RNA polymerase, which catalysis the addition of complementary bases to form the RNA molecule.
Once the RNA molecule is in the cytoplasm of the cell, a highly complex motor called the ribosome sits on the RNA molecule and synthesizes proteins based on the sequential order of bases. A protein a basically a polypeptide (peptide bond is the CONH bond), resulting from peptide bond formation between many monomeric aminon acids. Generally there are 20 different types of amino acids that are used for the synthesis of proteins. These amono acids are attached to what is called an anticodon. An anticodon binds to the amino acid at one end, and has a set of 3 bases (A,T,G or U) at the other end. When the ribosome sits on the RNA, it reads three bases at a time. It then waits for the complementary anticodon to come and bind to it, thereby bringind with it the amino acid that is coded for by the set of three bases. Having catalysed the binding, the motor moves forward to read the next set of three bases and attach the corresponding anticodon. Now the amino acids attached to the codons have automatically been placed in an order dictated by the sequence of bases in the RNA (and hence the DNA). These form peptide linkages between them, giving rise to a protein. Of course the function of the protein largely depends on how the protein folds into it's three dimension structure, but that is another story.
This has been highly simplified, in that there are several more steps. At every stage, there is a possibility of error, and to rectify them, certain proofreading motors move along. Also, each motor exists in a variety of conformational stated, and ATP hydrolysis provides the energy to overcome the activation barrier between the states. Change in corformation is almost always responsible for propelling the motor forward.
Biological motors perform many other type of functions as well. Of importance are cargo bearing motors called Kinesin and Dinine. These motors carry cargo to and from the cytoplasm of the cell to the outside, moving on the microtubule filaments. Their dynamics is very rich in the sense that the track itself on which it modes is dynamic. It changes its length, and can even disintegrate any time. These cargo bearing motors can carry cargo that are heavier than the motor itself. Their movement on the microtubule is just like walking. They have two heads (or legs rather) that walk on the microtubule, alternately binding to it. The Kinesin carries cargo to the outide, while the Dinene carries it back into the cell. Also, while coming back, the kinesin becomes the cargo of the dinene, and vice versa.
Biological motors are of great physial interest as well, because they are among the most efficient engines in the universe. They have a rich dynamics resulting from a combination of mechanics and chemistry. Collective movement of motors on their respective tracks lead to interesting situations in traffic, and dynamic phase transitions are observed, both invitro and in vivo. Finally, it is only through millions of years of evolution that these motors achieved their present form.
Posted by: Aakash Basu.