Questions tagged [ribosome]
Organelles responsible for protein synthesis in cells. They are distinguished into "free" and "membrane-bound" classes.
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In mRNA translation, why are there so many factors?
When the small ribosomal subunit binds to mRNA’s 5’-cap, it looks for the complex of three eLFs bound to the poly-A-binding protein (PABP), which circularises the mRNA. It is then this circular mRNA ...
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Can the UGA codon be used as a drop-in replacement when adapting genes for Paramecium?
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It is well established that Paramecium translate UAG and UAA mRNA codons to amino acid, although they are STOP codons ...
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What came first: the ribosome in which RNA is read, or the RNA to encode for the ribosome proteins? [duplicate]
It's a bit like the chicken-and-egg problem. Ribosomes need proteins because they are partially made of them. Where can they get their proteins? They read the base sequence in mRNA entering them, ...
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What prevents non-aminoacylated tRNA from binding to mRNA on the ribosome and disrupting protein synthesis?
Specific aminoacyl-tRNA synthetases catalyse a reaction in which a transfer RNA molecule with a given anticodon is covalently attached to its cognate amino acid (aminoacylated).
What factors favor the ...
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Does the ribosome have protein kinase activity?
The ribosome synthesizes proteins by translating the mRNA. The nascent peptide needs to go through the nascent polypeptide exit tunnel in the large ribosomal sub-unit before it reaches the cytosol ...
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How many times is a single strand of mRNA translated into a protein?
In other words, is the mRNA damaged or somehow "marked completed" in the translation process? Or does it pop out the other side of a ribosome ready to be translated again? If the latter, how ...
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Can I use multiple bicistronic RBS sequences in a synthetic biological circuit?
The bicistroninc RBS sequences (BCDs) developed by Mutalik et al. [1] aim to remove context sensitivity from translation and therefore ensure more predictable gene expression. However, I have been ...
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How can good Shine–Dalgarno or Kozak sequences enhance translation?
In prokaryotes the Shine-Dalgarno sequence, a polypurine consensus sequence near the initiation codon (usually AUG), is required for the mRNA to bind to the small ribosomal subunit, allowing ...
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Does my reasoning about the first emergence of proteins make any sense?
In order to make proteins, a cell uses ribosomes, which itself is a structure made out of proteins. The first ribosome couldn't have been created with the help of ribosomes though, as the ribosomes ...
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Why are some parts of an rRNA structure diagram not labelled?
I've been looking at this structure diagram of the 16S rRNA and have been wondering why some parts of the diagrams have labelled base pairs while other parts are just lines and dots. I'm new to this ...
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How is Open Reading Frame (ORF) chosen?
I understand that AUG is the "start codon", and, because of this, most proteins begin with methionine as their first amino acid.
However, this ORF problem on Rosalind.info states that "...
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Need either a [similar] ribosome to the following few | a heuristic for finding [similar] macromolecule given 20 others
Background :
Hi! I am running a small experiment dealing with structural heterogeneity of the ribosome, actually of ribosomes across all domains of life. It's entirely computational: I get cryoEM ...
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Peptides neither produced by the ribosome or the non-ribosomal peptide synthase complexes
I read in Wikipedia:
While there exist a wide range of peptides that are not synthesized by
ribosomes, the term nonribosomal peptide typically refers to a very
specific set of these as ...
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What is the charge of (bacterial) ribosome?
Ribosomes are negatively charged and thus electrostaticaly repelled from DNA. However, I could not find a good reference that would allow me to estimate the magnitude of negative charge on a ribosome. ...
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The genetic code and the effect of point mutations on proteins
I was asked a question, "Considering degenerate and non ambiguous nature of genetic code, Why is that certain mutations don't disturb the protein synthesis leading to synthesis of functional proteins ...
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How does a ribosome gather tRNAs at a fast enough rate for Translation?
There are many animations of the ribosome in action, and all I have seen show the correct tRNA neatly entering the ribosome and its amino acid being added to the growing protein chain. My question is ...
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How does a ribosome move along mRNA?
I've been reading around Wikipedia recently trying to learn more about various biomechanisms. I’m intrigued by ribosomes — with how small they are, they’re basically chemical machines from what I can ...
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Do ribosomes read mRNA?
So I understand that tRNA bonds to a codon (with an anticodon) in the translation process. I read in my biology textbook that the ribosomes "read" the mRNA strand.
Why do the ribosomes need to read ...
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Is there an Exit site (E-site) on the eukaryotic ribosome?
One of my professors mentioned something about the e-site (the exit site for the t-RNA) on a eukaryotic ribosome. There was a student in the class who objected, saying that there is no e-site on ...
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When does protein folding begin?
I had always assumed that protein folding is an independent activity that occurs after translation is complete. However, recently, I learned that intermolecular forces begin shaping the peptide bonds ...
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Can ribosomes read ssDNA?
My question is whether translation can be done, either naturally or artificially, through a ribosome reading (single-stranded) DNA directly. If not, I would like to know what allows ssRNA to be ...
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Eukaryotic equivalent of bacterial tmRNA
According to this Wikipedia article,
tmRNA is only found in bacteria, with its purpose being to “rescue stalled ribosomes”.
This brings me to the question of is there a eukaryotic equivalent of this ...
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Ribosomes producing proteins, but need proteins to be produced?
So according to my textbook:
RNA is used to create ribosomal RNA (known as rRNA) which is then combined with proteins to form the ribomsomes necessary for protein synthesis.
I'm a bit confused ...
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How rapidly do human mitochondrial ribosomes turn over?
How rapidly do human mitochondrial ribosomes turn over?
The inside of the mitochondrion is a highly oxidizing environment that can damage RNA and DNA. How long do mitochondrial ribosomes last before ...
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Why is translation so much faster in prokaryotes than eukaryotes?
Prokaryotes perform transcription and translation much faster than eukaryotes. If memory serves, a single 70S prokaryotic ribosome can incorporate around 20 amino acids per second, whereas the 80S ...
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How is mRNA directed out of the nucleus to its ultimate cytoplasmic location?
In the process of translation, I learnt that following formation the mRNA must exit the nucleus through a nuclear pore and attach to a ribosome.
My question is how does mRNA navigate itself out of ...
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Why do 60S & 40S ribosomal subunits make an 80S ribosome (not 100S)?
Why do 60S & 40S subunits make an 80S (not 100S) ribosome and, similarly, 50S & 30S make 70S? 60+40 is not equal to 80, nor is 50+30 equal to 70, so why are the subunits of the 80S and 70S ...
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Consensus sequence for selection of initiation codon in eukaryotes
In bacteria the AUG (or other) codon at which translation of mRNA is initiated is preceded at a precise distance by a sequence known as the Shine and Dalgarno sequence, to which the 30S subunit ...
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What is the Shine–Dalgarno sequence?
I am trying to understand the Shine–Dalgarno sequence. I currently know it is related to ribosomal binding sites, it is only found in prokaryote cells and it is in front of the initial codon. Also, ...
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Translation of Poly-U in the Nirenberg and Matthaei experiment
In the Nirenberg and Matthaei experiment the artificial mRNA, polyU, was translated into polyphenylalanine in a cell-free system, establishing that UUU was the codon for Phe. How did this work as the ...
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What causes the variable/conserved structure in the 16S rRNA gene?
See the image below for a visual representation of the 16S rRNA gene. It is composed of conserved and variable regions however I can't see to find a reasoning for why this is the case
Thanks
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How the size of ribosomes are calculated?
When I was studying microbiology, something didn't make sense to me. We all know ribosomes have two subunits; the large subunit and the small subunit. Such as for eukaryotic cells, the large subunit ...
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Why do ribosomes associate with rough endoplasmic reticulum but not other membranes?
As far as I am aware, all eukaryotic membranes consist of a lipid bilayer. Smooth endoplasmic reticulum (ER) and rough ER are distinguished by the presence of ribosome on the rough ER surface, but are ...
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How many proteins do all human ribosomes together produce per hour? [closed]
Very roughly how many proteins (chains) are synthesized in the human body per hour under normal conditions?
(And how many ribosomes does the human body have?)
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Why does azithromycin not affect human mitochondria?
Drugs like tetracyclines, macrolides and aminoglycosides bind to prokaryotic ribosomes. It is interesting that our body too having mitochondria, which have prokaryotic ribosomes, there is little(?) ...
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Structure of mitochondrial ribosomes
Is the ribosome found in mitochondrion and choloroplast formed of 30S and 50S subunits as in prokaryotes. I couldn't find any information on internet concerning it.
The general wikipedia page has no ...
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Identification of proteins in this animation of a ribosome translating mRNA
This gif is from this page
After each aminoacyl-tRNA enters the ribosome, one blue thing comes and pushes the whole tRNAs whats that? I couldn't find it anywhere.(maybe some elongation factor?)
Also ...
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Action of tetracycline on 30s ribosomal subunits
My question concerns the mode of action of 30s ribosomal antibiotc inhibitors — tetracyclines. According to some online resources, the antibiotics enter the A-site, which prevents other tRNA from ...
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What signals a ribosome to stop production when the cell is out of available amino acids?
In the production of a protein molecule, there have to be a ready supply of free-floating amino acids. When a given codon for adjoining, say, serine comes up, how are the serine molecules found out of ...
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Why does the inhibition of translation initiation cause the accumulation of 80S ribosomal monosomes?
As I have read in (1), inhibition of translation initiation will increase the number of 80S ribosomes while decreasing the fraction of polysomes due to the polysome-runoff. The net effect is to ...
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Are upstream activating factor (UAF) and upstream binding factor (UBF) the same thing?
During ribosome pre-40S and pre-60S synthesis, many sources state the importance of UAF or UBF in initiation complex of ribosome DNA transcription. None of the sources I've seen mentions the other ...
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Ribosomal DNA references sequences
I'm having a bit of trouble with searching for this piece of information. I'm doing a study related to phylogenetic susceptibility of hosts to pathogens (based on a recent Nature publication), ...
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Is there a cellular mechanism that detects Ribosomal damage?
What kinds of options, if any, do cells (Eukary and Prokary) have for detecting, and repairing damage in Ribosomes (of all types)? I am curious as to
what happens when a cell sustains damage of some ...
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How does a cell create/gain its initial ribosomes for protein synthesis?
I did some quick google searches for how a cellular organism generates or acquires its first ribosomes, but I found nothing. For instance, do the organisms initiating replication form extra Ribosomes ...
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Ribosomal RNA amount in a Drosophila cell
I am isolation RNA from Drosophila larvae brain with TRIzol method. What percentage of extracted RNA will be ribosomal RNA? I am only interested in mRNA, so I am trying to figure out whether I need to ...
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Termination of translation
What dissociates first - the last tRNA, mRNA and release factors or the subunits of ribosomes?
I tried searching this from Lehninger but couldn't get a clean answer.
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What exactly happens if during translation, an amino acid is not present?
Lets say that the cell wants to make a particular protein. Transcription of the appropriate gene is done and the mRNA is made. mRNA attaches to the ribosome and the translation is initiated in a "...
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How are the correct tRNAs transported to the ribosome?
I have been trying to understand how the tRNA transporting the correct amino acid required by the ribosome reaches the ribosome. The only way I can imagine this happening is that all types of tRNA+...
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How does GTP help in the step of codon recognition?
The anticodon of an incoming tRNA base pairs with the complementary mRNA codon in the A site.Hydrolysis of GTP increases the efficiency and accuracy of this step.
How does GTP do so ?
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What is the advantage of the way eukaryotes initiate translation?
The eukaryote and prokaryote mechanism for translation is slightly different. Is there any advantage of the eukaryote translation mechanism ?
Edit : I specifically want to know why eukaryotic ...
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