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17

I found an oldish paper on this topic (from 1994). Here's a summary: Determination of the optimal aligned spacing between the Shine-Dalgarno sequence and the translation initiation codon of Escherichia coli mRNAs. by Chen, Bjerknes, Kumar, & Jay. Nucleic Acids Research. (1994) Experiment The authors constructed a series of synthetic RBS regions that ...


6

Here's an example in which the ribosome is fixed: During co-translational translocation, the ribosome is essentially anchored onto the ER membrane through the Sec61 complex. It certainly cannot move along the mRNA. The mRNA is fed through the ribosome and the nascent peptide traverses into the ER lumen.


5

Movement is relative. The real events happening in translation are the conformational changes of ribosome makes itself continuous reading the base sequentially. Please refer the biochemistry textbook or cell biology textbook. Indeed, if the ribosome is anchored, you may say the mRNA is moving.


5

The most important parts of the ribosome are not made by other ribosomes - 5 rRNA (ribosomal RNA) of the ribosome actually do most of the direct work of creating the protein and are made by RNA polymerase ( a protein, but not the ribosome). Then there are 92 ribosomal proteins, which as a rule bind to ribosomal RNA to support their structure and keep ...


5

The ribosome moves relative to the mRNA by, in effect, pulling itself along it. If both the ribosome and the mRNA are freely floating and not attached to anything else (as in jp89's answer), the relative amount of movement should depend on their relative masses. (Actually, it also depends on how much drag each of them experiences with respect to the ...


5

An interesting take on this question is addressed in Bokov and Steinberg's hypothesis. They have proposed the ribosome has evolved from a short length (~110bp) of RNA that did not have the translational activity that we associate with ribosomes today. Instead this short length of RNA carried out alternative functions on RNA in RNA based life. Then ...


4

As far as I can tell from the paper you linked to (Damiana et al) it is possible but inefficient: Naturally, we tried to translate ssDNA, but as previously described elsewhere, direct DNA translation was not really efficient in absence of antibiotics such as neomycin [5] and [6]. It seemed that the elongation phase was the limiting step in the ...


3

The protocol you are using will not only leave the sample with rRNA but also non coding RNA. Many RNA protocols will separate mRNA by affinity of a carrier to the polyA tail. This protocol references an older paper that estimates that only 5% of RNA is mRNA. I'd be surprised if this ratio changed by more than 2-3 fold in drosophila. I assume that %age ...


3

Shigeta's got a point: the ribosome is latched onto the mRNA so those two are intrinsically linked. You're really asking whether the ribosome comes off first or whether the tRNA does, but it's actually the new polypeptide, which makes sense: The stop codon is recognized by a protein, the polypeptide chain release factor (RF), which triggers the ...


3

Point to know : aminoacyl-tRNA binds to mRNA its not just t-RNA.. So if there is no Amino-acid there is no aminoacyl-tRNA of that aminoacid.. so if there is no aminoacyl-tRNA, the anticodon of tRNA doesn't form a bond with mRNA, so the protein production halts (until the Amino acid produced). If the protein is not formed within a certain long time, the ...


3

Basically, all 16S genes are highly conserved, i.e., they share much identical bases. This means one can bind the 16S gene piece (after DNA was cut) to a specific other piece of DNA, even if you don't know exactly the 16S gene bases. Everything else is discarded then. Now finally, using PCR the rest is amplified and sequenced. Sequencing 16S only is much ...


2

The mRNA moves during translation. It is essentially threaded through the ribosome. This has been known ever since polyribosomes were discovered; see paper here. Polyribosomes are a cluster of ribosomes that read a series of mRNA molecules. Often, the ribosomes in a polyribosome will be translating the same mRNA.


2

As far as I understand it (and I'll preface this by saying that initiation is not my strongest point), but prokaryotes utilize the beautiful AGGAGG Shine-Dalgarno sequence. Usually around 8bp upstream of the start codon, it is this sequence that the prokaryotic ribosome seeks out to initiate translation. It does this through a complementary region in the ...


2

It is not true that the anticodon of an uncharged tRNA can't bind to the mRNA. Bacteria have a mechanism called stringent response. This response is complicated, here is a shorter and simplified explanation. Further informations can be found at the wikipedia pages linked in the text. If during translation a certain amino acid is absent, an uncharged tRNA ...


1

just off the top of my head... since the ribosome is made of 2 large complexes which assemble and clamp onto the mRNA, I'd say it was the tRNA first, then the ribosome and mRNA would detach simultaneously.


1

The only way I can imagine this happening is that all types of tRNA+amino acid reach the ribosome, bombarding the ribosome, and the ribosome will 'accept' only the one that matches what it is waiting for. Yup, basically. This is an extremely cool figure showing the process. There are various elongation factors that aid the process, such as EF-Tu, which ...


1

GTP based structural changes (even motor actions) are very common in biological systems. For e.g. G-proteins, Rab-GTPase (vesicular transport), Ran-GTPase (Nuclear export/import). So all these GTP-bound proteins make use of an intrinsic or assisted GTPase activity to convert GTP to GDP. This conversion causes change in the structure of the associated ...


1

As far as I know it'spossible to reverse transcribe a rRNA gene, you may not get the best yields though. The secondary / tertiary structures will be a problem, however, there are reverse transcriptase's commercially available that can handle secondary structure: Thermo-X™ Reverse Transcriptase from Invitrogen or Sensiscript™ from Qiagen.



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