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You are correct in thinking that since the translation of mRNA begins with AUG, which codes for methionine, then all proteins should contain a methionine at their N-terminus (aka start site). But, it is indeed not so. First of all, I want to mention about variations in start codon. As you say, AUG is not the only, but actually the most common, start codon, ...
answered Mar 4 '17 at 10:00
another 'Homo sapien'
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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 ...
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I think given that you're just getting started with genetics, you can say that the codons are interchangeable. This is generally true, though not technically correct. Here are a few reasons for why this is the case, though there's probably more:
Specific organisms use specific codons with different frequencies. This is usually related to the tRNA abundance ...
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A good question (if a little mixed up on transcription vs. translation!)
AUG is not always the start codon, but whatever the codon is it will always code for Methionine (or fMet, but still a variation on Met), even if the codon codes for a different amino acid otherwise. A separate transfer RNA (tRNAi, the initiator tRNA) is used for the arrangement of ...
10
This question is closely related, and the fascinating link posted by @JohnSmith is a good read.
In short, with a four-base system, and a codon size of 1, you get four possible amino acids. Silly system. A codon size of 2 gives 16. Not too shabby, but not a lot of room for growth, and not enough for those 20 amino acids. Codons of size 3 gives 64 - ...
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Actually, the start codon, no matter whether it is AUG or GUG/UGG, always encodes for Met. So the translation is initiated by tRNAfMet (prokaryotic translation). The 30s ribosome subunit binds to the Shine-Dalgarno sequence and then it scans the dowstream mRNA sequence for AUG and the tRNA loaded with Met, which has the CAU anticodon form the most stable ...
9
The NCBI translation table translates all alternative start sites as methionines. To my understanding, all translation is initiated by the fMet-tRNA. I don't know if there are any exceptions to this rule.
Regarding translation efficiency, I only found a 1985 paper in PNAS (Reddy et al, PNAS 82:5656-60), in which they compared the translation efficiency of ...
9
Translational coupling describes in how some cases an mRNA will code from more than one protein (i.e. will be polycistronic). Translational coupling is thought to be mostly used as a way to make a set of genes are translated at roughly the same amount in the cell.
Translational coupling is very common in prokaryotes and nearly half of e coli genes are ...
9
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
Take a look at this schematic of a mature mRNA.
[source]
The coding region (ie the part that is translated) is between the start and stop codons, but the 5' and 3' untranslated regions (UTRs) are also transcribed by RNA polymerase; these are part of the first and last exons, respectively. The transcription start site is labelled right in front of the 5' ...
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No, this will not happen. mRNAs are inspected in the nucleus before they are exported into the cytoplasm (at least in eukaryotes), where transcription and translation don't happen at the same place. This ensures that no mRNAs without stop codons or premature stop codons are exported. This phenomenon is called
"mRNA surveillance". mRNAs that do not pass this ...
7
Yes, tRNA can form dimers. For example it was shown that E. Coli tRNA GCC forms homodimers, i.e. two identical molecules interact with each other. In this case the dimerization occurs between the anti-codon loops (what was probably meant with UUU and AAA).
References:
Sequence and structure of naturally-occurring tRNA transcripts and site-directed variants ...
7
Aminoacyl-tRNA sythetases are highly specific to their corresponding amino acid. First, the activation site, where the amino acid binds, constitutes a complex network of intermolecular interactions. For example, threonine, catalyzed by threonyl-tRNA synthetase, is very similar to valine and serine. Valine has a methyl group instead of the hydroxy group of ...
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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 ...
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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.
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From the Methods section:
Human TfR in plasmid cDNA was a gift from Tim McGraw (Weill-Cornell
Medical College, New York, NY). Human TfR cDNA was subcloned in frame
with EGFP in the Clontech pEGFP-N1 vector at the XhoI and BamHI
restriction sites.
This TfR-GFP fusion protein does not have the endogenous TfR promoter. So it is not likely to be ...
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Genetic code and codons are always used with reference to RNA. When talking about DNA, the the sense strand of a gene is considered its sequence. The anti-sense strand though is the template for mRNA synthesis, does not represent the gene.
DNA-codon table has simply U replaced by T. Apart from a wikipedia article, I don't find the term being popularly (not ...
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There is a basic misconception in the question you have asked, which @biogirl has explained. There is only one start Codon in any mRNA and it defines the open reading frame.
All other AUGs in the open reading frame are simply codons that encode for the Amino Acid Methionine and have no function in the start of translation. There are factors other than AUG ...
6
Although the question shows considerable effort to achieve clarity, the way it is phrased as:
How many molecules of nucleoside triphosphate… [does] it take to release enough energy
still allows ambiguity, as I would not really regard the NTPs involved in protein synthesis “releasing energy”. So let us consider two reformulations of the question, as the ...
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Because the start codon is translated into methionine, it clearly can not be part of the 5'-untranslated region, as @Johnny writes in his answer.
The more contentious question would be for the stop codons and the 3'-untranslated region. Then it really is a question of semantics. One might argue that as no amino acid is inserted in response to these codons, ...
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 you pointed out, the repressor gene lacI is transcribed as a one mRNA, and three structural genes: lacZ, lacY and lacA are transcribed into a single polycistronic mRNA. The two mRNAs are translated independently of one another.
The polycisronic mRNA is not broken into pieces. Rather, it is translated by ribosomes (at least three, explanation below), ...
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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
The tRNA is not acting alone, it has the help of the Ribosome.
The Ribosome assembles at the beginning of the transcript and starts the translation at the first AUG codon. It then binds the first tRNA which fits to the mRNA. The tRNA is then moved from the A-position to the P-position and the next tRNA is binding (the move around and bind by chance. A nice ...
5
Wobble pairing is just a phenomenon and not a hard and fast rule. There are some justifications for why it should exist and that is why it is still called a hypothesis. And this statement is not true:"the base on the third position of the codon and that on the anticodon need not be complementary". The anticodon residue corresponding to the third residue of ...
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A good answer is already provided by @canadianer, but as with many things in biology it is important to keep in mind what organism and/or cell type we are talking about. Because the nuances of the answer to a question about a seemingly universal process sometimes actually depend on whether we want to know about bacteria, or fungi, or mammalian stem cells, ...
5
You mix up translation and transcription. Transcription creates mRNA from DNA template. Transcription also includes splicing, that is excision of introns so that mature mRNA contains only exons. In your example it goes like that:
DNA (chromosome): ---A----B--...--Dstop---E---
premature mRNA: A----B---...---Dstop--E---polyA
mature mRNA: AB..DstopE-polyA
...
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AUG functions as a start codon only when it is at the 1st position of the open reading frame. Whenever AUG is present in between, it codes for methionine amino acid. Go through the basics of translation from a good book.
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When ribosomes create peptides, Methionine is the starting amino acid. But, in many proteins, Methionine Aminopeptidases cut it off from N-terminus. This happens in cases when methionine is not required as starting amino acid (not required on N-terminus).
Source: https://en.m.wikipedia.org/wiki/Methionyl_aminopeptidase
I remembered the name of enzyme.
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I think the key to understanding this is to appreciate how different the initiation process is from the rest of translation.
The 30S ribosomal subunit recognises start codons via an interaction with the Shine-Dalgarno sequence that lies upstream in the mRNA. The remaining steps of initiation involve recruiting fMet-tRNA and, critically, placing it into the ...
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