13 votes

Why do 60S & 40S ribosomal subunits make an 80S ribosome (not 100S)?

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 ...
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11 votes

Why do 60S & 40S ribosomal subunits make an 80S ribosome (not 100S)?

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 ...
11 votes

Can I use multiple bicistronic RBS sequences in a synthetic biological circuit?

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 ...
10 votes
Accepted

Peptides neither produced by the ribosome or the non-ribosomal peptide synthase complexes

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 ...
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8 votes
Accepted

Can ribosomes read ssDNA?

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 ...
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8 votes
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How can a good SD / Kozak sequence enhance translation efficiency?

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 ...
7 votes
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Structure of mitochondrial ribosomes

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 ...
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6 votes
Accepted

When does protein folding begin?

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 (...
6 votes
Accepted

Does the ribosome have protein kinase activity?

No — there is no ribosomal protein with protein kinase activity. It is difficult to provide conclusive evidence for a negative statement, but the two objective points I can make in support of my view ...
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5 votes

What signals a ribosome to stop production when the cell is out of available amino acids?

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 ...
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4 votes

What is the Shine–Dalgarno sequence?

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 ...
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4 votes

Translation of Poly-U in the Nirenberg and Matthaei experiment

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. ...
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4 votes
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Why does azithromycin not affect human mitochondria?

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 ...
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4 votes
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Why do ribosomes associate with rough endoplasmic reticulum but not other membranes?

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 ...
4 votes
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Ribosomes producing proteins, but need proteins to be produced?

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 ...
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3 votes

Can ribosomes read ssDNA?

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 ...
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3 votes
Accepted

How the size of ribosomes are calculated?

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 ...
3 votes
Accepted

How many proteins do all human ribosomes together produce per hour?

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 ...
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3 votes
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Is there an Exit site (E-site) on the eukaryotic ribosome?

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 ...
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3 votes
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The genetic code and the effect of point mutations on proteins

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 ...
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3 votes

How is Open Reading Frame (ORF) chosen?

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 ...
3 votes
Accepted

Does my reasoning about the first emergence of proteins make any sense?

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 ...
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3 votes

Can I use multiple bicistronic RBS sequences in a synthetic biological circuit?

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 ...
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2 votes

Ribosomal DNA references sequences

I may be jumping the gun here, but assuming that you haven't searched NCBI or ensembl, I'd do that first. Essentially all genomic information is maintained by a collaboration between US NIH, EU EBI ...
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2 votes
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Ribosomal DNA references sequences

For birds you can start by searching 18s in http://birdgenenames.org/cgnc/ But generally NCBI Nucleotide database, should provide you with all information and accession numbers. See this broad search:...
2 votes

How does a cell create/gain its initial ribosomes for protein synthesis?

Each daughter cell, following mitosis, will contain some ribosomes and DNA transcription machinery already, so it can already synthesise more ribosomes. In the case of the fertilised ovum, when the ...
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2 votes
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How does a cell create/gain its initial ribosomes for protein synthesis?

From the comment section: Cells divide and when they do the two daughter cells will not only have copies of the DNA but also of the organelles, the cellular machineries and the cell membrane which ...
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2 votes
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Sequence of ribosomal RNA

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 ...
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2 votes
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Identification of proteins in this animation of a ribosome translating mRNA

The protein involved in "pushing" the tRNA and mRNA is the elongation factor EF-G. The protein involved in "transporting" the tRNA is the elongation factor EF-Tu. Quoted from the Wikipedia articles: ...
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