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Pregnancy Timeline by SemestersFetal liver is producing blood cellsHead may position into pelvisBrain convolutions beginFull TermWhite fat begins to be madeWhite fat begins to be madeHead may position into pelvisImmune system beginningImmune system beginningPeriod of rapid brain growthBrain convolutions beginLungs begin to produce surfactantSensory brain waves begin to activateSensory brain waves begin to activateInner Ear Bones HardenBone marrow starts making blood cellsBone marrow starts making blood cellsBrown fat surrounds lymphatic systemFetal sexual organs visibleFinger and toe prints appearFinger and toe prints appearHeartbeat can be detectedHeartbeat can be detectedBasic Brain Structure in PlaceThe Appearance of SomitesFirst Detectable Brain WavesA Four Chambered HeartBeginning Cerebral HemispheresFemale Reproductive SystemEnd of Embryonic PeriodEnd of Embryonic PeriodFirst Thin Layer of Skin AppearsThird TrimesterSecond TrimesterFirst TrimesterFertilizationDevelopmental Timeline
CLICK ON weeks 0 - 40 and follow along every 2 weeks of fetal development
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Home | Pregnancy Timeline | News Alerts |News Archive June 13, 2014

 

Molecules of transfer RNA (tRNA) bind to specific amino acids then carry them to cell factories called ribosomes. In the ribosome, amino acids are laced together to form proteins.




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Wobble identifies amino acids in gene coding

Proteins are produced in cells based on the "genetic code" (or rules) found within DNA and RNA. When the genetic code is accurately translated, proteins are produced. This is a very precise process, because mistakes can be disastrous.

Molecules called transfer RNA (tRNA) bind to specific amino acids and carry them to cell factories called ribosomes. In the ribosome, amino acids are put together, step by step, to form a protein.

This process is assisted by enzymes called synthetases. Mistakes can lead to misformed proteins so, thankfully, tRNA molecules are matched to their proper amino acids with great precision. But we still lack a fundamental understanding of the decision process that aligns amino acids so accurately.

In work recently published in Nature, scientists from RIKEN, along with colleagues from the University of Tokyo and other institutions, have identified a surprising mechanism allowing one enzyme — alanyl-tRNA synthetase — to assemble with its' amino acid — alanine — to properly configure a tRNA molecule.


Using Xray crystallography images of molecules, the group, led by Shigeyuki Yokoyama (in RIKEN's Structural Biology Laboratory) determined that an enzyme precisely identifies the proper tRNA thanks to the amount of "wobble" at its base pair. In this case, the "wobble" motion only allows alanine to be identified by the tRNA. Other amino acids, therefore, cannot come into contact with this enzyme's active region.


The group looked at a complex of alanyl-tRNA synthetase with the wild-type (or typical) tRNA, which has a wobble at its base pair made up of uracil and guanine. They then compared that complex with a variation where the guanine is replaced by adenine. This tRNA variant can bind to alanyl-tRNA synthetase, but was kept separated from the active region, in what Yokoyama calls a "non-reactive state."

The overall enzyme reaction was 100 times faster in the typical tRNA, and it turns out that the key is a change in the tRNA molecule caused by the difference in that single base pair. Thus, this small wobble is exploited by the enzyme to make recognition so accurate.


"This is a fascinating finding that may give us new insights into how living systems can so accurately translate their genetic code using processes that are — at their core — random.

"Our work is interesting in terms of the evolution of the genetic code. Especially as acceptor stem recognition is important to the concept of a 'second genetic code'.

"This paper may show a previously unknown mechanism of tRNA recognition inherited from a distant ancestor."


Shigeyuki Yokoyama, PhD, RIKEN Structural Biology Laboratory


Abstract
Ligation of tRNAs with their cognate amino acids, by aminoacyl-tRNA synthetases, establishes the genetic code. Throughout evolution, tRNAAla selection by alanyl-tRNA synthetase (AlaRS) has depended predominantly on a single wobble base pair in the acceptor stem, G3•U70, mainly on the kcat level. Here we report the crystal structures of an archaeal AlaRS in complex with tRNAAla with G3•U70 and its A3•U70 variant. AlaRS interacts with both the minor- and the major-groove sides of G3•U70, widening the major groove. The geometry difference between G3•U70 and A3•U70 is transmitted along the acceptor stem to the 3′-CCA region. Thus, the 3′-CCA region of tRNAAla with G3•U70 is oriented to the reactive route that reaches the active site, whereas that of the A3•U70 variant is folded back into the non-reactive route. This novel mechanism enables the single wobble pair to dominantly determine the specificity of tRNA selection, by an approximate 100-fold difference in kcat.


RIKEN is Japan's largest comprehensive research institution renowned for high-quality research in a diverse range of scientific disciplines. Founded in 1917 as a private research foundation in Tokyo, RIKEN has grown rapidly in size and scope, today encompassing a network of world-class research centers and institutes across Japan.

Insights into the geometry of genetic coding http://www.riken.jp/en/pr/press/2014/20140612_1/

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