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17

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 ...


9

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 ...


8

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 - ...


7

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 ...


6

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 ...


6

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 ...


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

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 ...


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), ...


5

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 ...


4

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 ...


4

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 ...


4

Hutchinson–Gilford progeria syndrome is almost always due to to a de novo mutation (i.e. not an inherited mutation) in the lamin A gene (LMNA). The mutation responsible is a C-to-T substitution at position 1824. Remarkably this doesn't change the encoded amino acid but rather creates a new splice donor site in the RNA transcript. When this splice site is ...


4

The process to which you refer is called tRNA charging and is catalyzed in the cytosol by a class of enzymes called aminoacyl tRNA synthetases.


4

Since the sequence starts with an initiation codon and ends with a stop codon I think it's safe to conclude that this is the coding strand. The coding strand has the same sequence as the transcribed RNA (except T>U). This is because it is the other strand of the DNA that is the template for the synthesis of an RNA. The RNA is indeed made 5'>3', but the ...


3

There are a few confusions here, I will try to get them resolved without adding more: First, a gene is always read in the 5' -> 3' direction, no matter on what strand of the double helix is is located. In the traditional way of writing down DNA the forward (or +) strand is written from left to right, the reverse (or -) strand from right to left. So even is ...


3

My understanding is that the antisense DNA strand (3'-5') makes the (sense) mRNA hence protein coding DNA strand where as the sense DNA strand (5'-3') is the non-proteins coding DNA strand. Hence the sense DNA produces antisense non-coding RNA, which ultimately acts as a translational regulator (http://en.wikipedia.org/wiki/Antisense_strand). The only reason ...


3

I think that there is no reason in principle why early evolution couldn't have landed on a translation mechanism going 3'>5'. There are, however, clear biochemical reasons why the transcript itself has to be made in a 5'>3' direction. So in this alternative world where the initiation signals would have been at the 3' end of the mRNA, the message would have ...


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

I commented that this was a duplicate, but reading the question more carefully you seem to be asking something slightly different. In the context of a 'start' these codons will be recognised by fMet-tRNA and a formyl-methionine will be inserted as the first amino acid. Subsequent occurrences of the same codon within the open reading frame will be translated ...


2

The mRNA moves during translation. It is essentially threaded through the ribosome. This has been known ever since polyribosomes were discovered; see paper here. Polyribosomes are a cluster of ribosomes that read a series of mRNA molecules. Often, the ribosomes in a polyribosome will be translating the same mRNA.


2

Sorry, but you started on the right track. What you're looking for is called the central dogma of protein synthesis. Genomic DNA is transcribed in the nucleus into messenger RNA (mRNA) by RNA polymerase. RNA polymerase is DNA-dependent; it needs a DNA template to make an RNA version of the message. The messenger RNA moves into the cytoplasm where it gets ...


2

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 ...


2

Some elements of response to your question. First, something about tRNA frequency. Even if there are six codons for a given amino acid, they are not equivalent because some will correspond to abundant tRNA, while others correspond to very minor tRNA. This has significant influence on the traduction speed, as the traduction will dramatically slow down on ...


2

The tRNA anticodons are both complementary and anti-parallel. That means for $5'-\text{AUG}-3'$, the tRNA anticodon would be $3'-\text{UAC}-5'$. The image has the mRNA oriented with the $5'$ end on the right end. It shows both, complementarity and anti-parallel configuration. The reference you cite might have cited the anticodons $3'\rightarrow 5'$ and ...


2

I can understand your confusion but it all makes sense. The basic idea is that what we call the "antisense" strand is actually the one being transcribed. However, since that is in effect a mirror image, it is much simpler to think in terms of the sense strand. To take a very simple example: 5' ATG 3' <-- sense strand 3' TAC 5' <-- antisense strand ...


1

just off the top of my head... since the ribosome is made of 2 large complexes which assemble and clamp onto the mRNA, I'd say it was the tRNA first, then the ribosome and mRNA would detach simultaneously.


1

The only way I can imagine this happening is that all types of tRNA+amino acid reach the ribosome, bombarding the ribosome, and the ribosome will 'accept' only the one that matches what it is waiting for. Yup, basically. This is an extremely cool figure showing the process. There are various elongation factors that aid the process, such as EF-Tu, which ...


1

EMBOSS has a tool for doing this: http://www.ebi.ac.uk/Tools/st/emboss_transeq/



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