21

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 ...


12

When a complex mixture of particles undergoes ultracentrifugation, they separate based on their shape and mass due to the force applied by the centrifuge and the counteracting frictional force of the solvent. You can read more about this procedure here. S stands for Svedberg, which is a measurement of the sedimentation rate of a particle. This is given by ...


11

The other two answers give nice detail, so I want to give a bit more mathematical answer here. First, the S you are talking about is Svedberg units (of sedimentation coefficient, named after Swedish chemist Theodor Svedberg), used to characterize the behavior of a particle in sedimentation process, especially centrifugation. One svedberg corresponds to ...


8

Summary Messenger RNAs that are recruited to the ribosome for protein synthesis in vivo, need to satisfy particular structural requirements and must interact with the protein initiation factors that deliver them to the ribosome. Generic single-stranded DNA (ssDNA) does not have these structural characteristics and so cannot be translated on ribosomes under ...


7

The wording of the question suggests that it may be useful to clarify the meaning of the numbers in the designations 70S, 50S, 30S etc. These are sedimentation coefficients in Svedberg units as determined in the analytical ultracentrifuge, and are an indication of size. All ribosomes have two subunits. The reference eubacterial ribosomes from E.coli are ...


6

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 ...


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.


6

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 ...


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

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

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 ...


5

When cells run out of amino acids, more and more of their tRNAs remain uncharged. This elevated ratio of uncharged/charged tRNAs trigger complex signalling pathways that control amino acid biosynthesis, general reduction of translation, halting ribosome biosynthesis, autophagy (includes ribophagy - digestion of ribosomes) to recycle cells' components, etc. ...


5

When does protein folding begin? With reference to time you have asked, it can be after the translation has occurred (called Translational protein folding) or while translation is still occuring (called Co-Translational protein folding). Here is the link to an article for basic understanding of co-translational protein folding. There is a lot of debate on ...


4

There are two general points that should be appreciated in relation to this question: Your statement that mitochondria “have prokaryotic ribosomes” is a misleading simplification. Although mitochondria and plastids are thought to be derived from eubacteria — and their ribosomes have some similarities in antibiotic sensitivity — the structures of their ...


4

Peptides that are destined to be either secreted or included in the cell membrane have a signal sequence that binds a protein called Signal Recognition Particle (SRP). The SRP will in turn bind to translocons--basically peptide tunnels in the RER membrane. You need to have this interaction between the translocon and the SRP in order to have stable ribosome ...


4

This is an intelligent question that highlights the ‘sleight of hand’ simplifications employed in many text books to make experimental science appear cleaner and more logical than is in fact the case. From what we now know about the requirement for an AUG initiation codon in protein biosynthesis these experiments should not have worked. The reason they did ...


4

According to this Wikipedia article: "The Shine-Dalgarno (SD) sequence is a ribosomal binding site in bacterial and archaeal messenger RNA, generally located around 8 bases upstream of the start codon AUG.1 The RNA sequence helps recruit the ribosome to the messenger RNA (mRNA) to initiate protein synthesis by aligning the ribosome with the ...


4

Ribosomes are the only means we know by which cells produce proteins. Consequently, all proteins are made by a ribosome, including the proteins that then become part of a new ribosome. It's never a question of "more proteins than required" because there are different types of proteins and to make a ribosome, you need those specific types of proteins known as ...


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

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 3'...


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 ...


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

Regarding protein synthesis rate, here's an attempt at an estimate from bioenergetics: ATP turnover in the human body is consider to be about 100 mol / day. Protein synthesis is estimated to require about 1/4 of ATP consumption in a mammalian cell, and one amino acid elongation requires about 5 ATP, so about 5 mol amino acids are elongated per day, which ...


3

Because Svedberg is not a measure of weight, but it is a measure of a relative sedimentation after centrifugation. "It is defined as the ratio of a particle's sedimentation velocity to the acceleration that is applied to it (causing the sedimentation)." The high number of S are correlated to the shape of the particles as well. https://en.wikipedia.org/...


3

My question is whether translation can be done, either naturally or artificially, through a ribosome reading (single-stranded) DNA directly. Ribosomes participate into the translation of mRNA into proteins. See the wikipedia article for more information If not, I would like to know what allows ssRNA to be translated and ssDNA not. The "if not" makes no ...


3

Prelude: Thinking about protein synthesis I remember the time when there were only two sites on the ribosome, and when it became clear there were more, I resented the need to make my lecture notes and my contribution to a venerable text book more complicated. So I am neither a devotee nor an expert on the exit site, but if asked to guess who was right (even ...


3

Nonambiguity refers to the fact that codon X will always code for the same amino acid. Degeneracy refers to the fact that an amino acid can be coded for by many codons. I rephrase the question to get to the gist of things: Why do certain mutations cause no difference for protein synthesis, while others make a big difference? Certain mutations can ...


2

Unequivocally, YES. Before DNA sequencing was used to deduce the sequence of cloned or reverse-transcribed RNA molecules, slower and more cumbersome direct sequencing of RNA was performed using the method of Sanger et al. (Sanger, F., Brownlee, G. G. and Barrel B. G. (1965) J. Mol. Biol. 13, pp. 373–398). This used ribonucleases in a manner somewhat ...


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