## Posts Tagged ‘amino acids’

### Our Ribosome

November 23, 2008

When you think about nano-machines, which perform a complex mechanical operations at the molecular level, you might think of science-fiction and the promise of nanotechnology.  Well, one of the most incredible nanomachines is in our cells: the Ribosome!  The magnificent contraption created after hundreds of millions of years of evolution reads an mRNA strand as input, and outputs a protein made of amino acids.  (Yes, we read about these chilralitic wonders in a previous post.)

The ribosome is found in all living cells, both Eukaryotes (protozoa, algae, humans, etc . . .) and Prokaryotes (bacteria and archaea).  It is composed of 2 subunits, one large and one small.  For Prokaryotes the small subunit is labeled 30S, and the large subunit 50S.  For Eukaryotes, they are 40S and 60S respctively.  (The S is for Svedberg units, a measure of sedimentation.)  The are a composed of a complicated intertwining of proteins and rRNA and look like this:

The small subunit on the left contains an RNA molecule (cyan) and 20 proteins (dark blue); the large subunit on the right contains two RNA molecules (grey and slate) and more than 30 proteins (magenta). The image also shows a transfer RNA (orange) bound to the active site of the ribosome. (Harry Noller, UCSC)

Here’s how the process works in Prokaryotes:

1. After mRNA is transctibed from DNA, it reaches (I’m not sure how), the small Ribosome 30S subunit.  Attached to 30S are 2 initiation factors, IF1 and IF3, which keep 30S seperated from the larger 50S.  the mRNA contains a special start codon (usually AUG), which marks the beginning of the mRNA sequence to read for protien synthesis.  A codon is a set of 3 genetic bases, which corresponds to a specific amino acid, but more about that later.
2. IF2 binds to the intitiator tRNA which holds the start anticodon, and IF2 brings this initiator tRNA to the ribosome’s P-site.  If the initiator codon is AUG, the anticodon on the initiator tRNA will be UAC.  Those sequences will bind together.
3. Once IF2 engages, it deposits the initialtor tRNA at the P-site, then all IFs disengage.  This allows 50S to attach with 30S, surround the P-site.
4. The tRNA which contains the anticodon for the next codon triplet in the mRNA sequence is guided into the A-Site inside the ribosome.  Each tRNA contains an anticodon on one end and an amino acid on the other end.  It is these amino acids which will be bound through peptide bond formation to form our protein!
5. After the bond is formed, the tRNA in the P-site is ejected out of the ribosome, and the tRNA in the A-Site is ratcheted into its place.  Then the cycle repeats until the special stop codon on the mRNA is reached.
6. When the stop codon is reached, the subunits disengage, and IF1 and 2 re-engage 30S, starting the process all over gain.

There is a large amount of research into modeling this incredible process.  One example is this remarkable video produced by the Weizmann and Max-Planck Institutes:

UPDATE:  There is some debate as to the realism of this video.  Unfortunately I have not found much information on it, which leads me to believe that this video is only remotely representative of actual processes.   It is still quite instructive, so please just take it with a grain of salt.

### Life’s Handedness

November 11, 2008

Origin of life research is a facinating subject, but one of its most baffling findings is that all life that we know of on this planet has a certain chemical “handedness” or chirality.  Well there is some new research that shows why evolution might prefer a certain handedness: certain reactions are more effecient depending on the handedness of the chemicals.

UPDATE: An insightful comment brought up the fact that chirality is an important subject in physics as well.  It turns out this is a useful concept throughout the sciences (maybe because of its relationship to symmetry.)   Here’s some more detailed information I found online, as we go from concrete to abstract:

Biology – Amino Acids are the building blocks of proteins (a subject which I want to blog about another time) which are essential to life.  There are left-handed and right-handed versions of them, designated L and D respecitively.   In chemistry, there is in general no preference between the two, and most reactions will result in equal numbers of each (called racemic).  However, in nature generally only L-amino acids are found in proteins.  Why this “homochirality” occurs is under much debate, but the above (and simlar) research may point in some promising directions.

ChemistryChiral molecules are those for which the atomic pattern differs from its mirror image.  The differences can be described by the following:

1. Configuration (R/S) – The relative position of the atoms in a molecule as it relates to their atomic numbers.
2. Configuration (D/L) – The relative position of the atoms as it relates to the molecule glyceraldehyde.
3. Optical Activity (+/-) – How a solution of the molecule rotates polarized light.

PhysicsAccording to wikipedia: “The chirality of a particle is more abstract. It is determined by whether the particle transforms in a right or left-handed representation of the Poincaré group.”  Unfortunately I do not understand the slightest about this group (a 10-dimensional lie group which represents the isometries of Minkowski spacetime), so it will have to wait for its own blog posting after some research.  Anyway, what is so interesting about chirality in physics, and what our insightful commenter alluded to, is that the weak interaction (one of the 4 fundamental forces of nature) only acts on left-handed fermions!  Remember that fermions have half-integer spin and make-up all matter due to their adherence to the Paui Exclusion Principle,  Nature is sometimes not as symmetrical as we would like her to be.

Mathematics Again from wikipedia: “A figure is achiral if and only if its symmetry group contains at least one orientation-reversing isometry. (In Euclidean geometry any isometry can be written as $v\mapsto Av+b$ with an orthogonal matrix A and a vector b. The determinant of A is either 1 or -1 then. If it is -1 the isometry is orientation-reversing, otherwise it is orientation-preserving.)”