13

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 ...


11

That’s a great question and has lot of opportunities to explore. I am not sure anyone has followed up on this original BCD work systematically. We did try cloning these elements on a medium copy plasmids, in an operon design, driving multiple genes, and now I think about it, that was not a smart thing to do. Cloning was very challenging, probably due to ...


10

One peptide that comes to mind is the metabolically important reducing tripeptide glutathione — γ-L-Glutamyl-L-cysteinylglycine: This is synthesized from cysteine, glutamate and glycine by reactions catalysed by glutamate cysteine ligase and glutathione synthase: Synthesis of glutathione (GSH) — two subunits of glutamate cysteine ligase (GCL) are shown ...


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 ...


8

I would strongly recommend looking in more detail into available resources for SD and Kozak sequences, wikipedia basically answers these questions and has plenty of further reading if you desire to explore these questions. At the same time, remember that these are statistical processes involving thousands of molecules, rather than deterministic processes ...


7

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 ...


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

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 ...


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. ...


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

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

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

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 ...


4

As their name suggests, the majority of a ribosome's structure and function come from ribonucleic acid (RNA), not protein. While ribosomes are about 35%-40% protein on average, a majority of ribosomal proteins are not essential for the catalytic functions of the ribosome, and none are in direct contact with the catalytic reaction site where peptide bonds are ...


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

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

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

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

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 ...


3

Tl Dr: In the rosalind example they are showing the 3 reading frames that stem from the definition of a reading frame(non-overlapping triplets), not an example of open reading frames. Open reading frames are non-overlapping triplets between a start codon and a stop codon. Its important to step back and understand what is meant by reading frame first. It has ...


3

In the documentation for this recent cloning method from Richard Murray's group at Caltech (,https://doi.org/10.1021/acssynbio.8b00060) they include a parts library with various BCDs. I haven't tested this directly myself, but the warning they note for multiple BCDs is not that they are toxic, but that because they have long homologous regions that they are ...


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 ...


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 ...


Only top voted, non community-wiki answers of a minimum length are eligible