Billy T should transcribe and translate a gene, that will help him to visualise it
http://learn.genetics.utah.edu/content/begin/dna/transcribe/
Holy cow! That's awesome!
Billy T should transcribe and translate a gene, that will help him to visualise it
http://learn.genetics.utah.edu/content/begin/dna/transcribe/
OK I made my short string of RNA and earned by "good job" reward.Billy T should transcribe and translate a gene, that will help him to visualise it
http://learn.genetics.utah.edu/content/begin/dna/transcribe/
Ok, it seems like in my analogy to the whole parts stock room of the factory as the role of the tRNA was wrong. The tRNA is more like the individual storage boxes of the stock room. Thus, the tRNA must be much smaller than the mRNA and the stock room clerk is really stupid, not well orded. He just keeps throwing tRNA boxes at the ribosome factory until the amino acid in one of the tRNA boxes happens to be the one currently needed to build a little more of the polypetide or protein. (Is "polypetide" just a more chemically descriptive term for "protein"?)Just a quick answer:
tRNA is synthesized basically the same as other RNA (it gets modified on its way, but that is detail for now), but a difference is that it gets loaded with a specific amino acid on its way.
They are indeed floating around and to the ribosome (protein factory, if you want call it). And only if the tRNA arrives by chance with the right anticodon the amino acid will get hooked up. It is really that inefficient (if you want to call it that way). The tRNA are not ordered in a sequence specific way. Only if their anticodon triplet (one per tRNA species) corresponds to the codon just being read from the mRNA the it will get unloaded. Without mRNA there would be no template that would direct the the type of tRNA-AA being unloaded.
Maybe you want to take a quick peek on tRNA structures (e.g. in wikipedia or someplace else). They are very distinct and it is immediately clear that they are not used in a somewhat linear way as mRNA.
Double stranded DNA carries ALL the information needed by most organisms to be constructed (but a few simple organisms can function without it – sort of use RNA like coded information)
The two DNA stands are sugar molecules linked together by a phosphate bond and each sugar molecule has a binding site which can accept one of four other molecules.
Their names begin with letter A, G, C, & T (and I will not bother with the full names). The "not bound to the sugar" end of each of these four can also bind to another's “not sugar” end but only to one of the other three “letter molecules.” I.e. A-T bond and G-C can join their “not-bound-to-sugar” ends.
The length of these A-T and G-C molecules, here after just AT = TA & GC = CG, are approximately the same, so they can and do cross link the two DNA strands, like steps on a spiraling ladder. A short section of the “ladder steps”, flatten out to fit on 2D display, follows partially to illustrate why there is an equality sign in prior sentence.
53
AT
CG
GC
TA
GC
AT
CG
35[/]
Now while joined, the two strands are only storing the information.
The bonds at mid ladder steps must be broken to allow the encoded information to make RNA, which is single stranded and has U replacing the T as the molecule that binds the non-sugar-bound end of A. This splitting of the DNA starts at one end and as the RNA forms on the exposed bonds. Using lower case letters c, g, u & a for the RNA forming on the splitting above segment of DNA we have:
..…AT ….Ignore dots (They are here to prevent SF’s computer from reducing all adjacent spaces to one space).
.…C-G
...Gc.gC
..Ta…uA
.Gc….gC
Au……aT
Cg……cG
So the DNA section above has made TWO strips of RNA, but not yet shown as separated from the DNA single strands. I.e. when the top two also have helped make RNA we will have:
ugcacug & acgugac segments of RNA ,
but RNA also has a "backbone" of linked sugar molecules. Thus there is much missing in this description of the formation of RNA. Somehow from somewhere these sugar molecules must attach to the newly formed sequences that are given at start of this paragraph. Perhaps what joins to the exposed base of the DNA is not just one of the 4 letters (a,c, g or u) but the entire nucleotide illustrated in SAM's post 64? Probably, if it is really nucleotides that are attaching to the exposed bonding sites of the separated DNA, then as these nucleotides attach they also make the phosphate bonds between each other to make the "RNA's "backbone." Possibly as they form they also separate the fully assembled RNA from the DNA that helped it form; but this is my first question below.
(1a) How is the nascent RNA freed for the single strands of DNA?
(1b) As the RNA is freed from the DNA, there are many open bond sites. For example, in the left of the two RNAs made, the g at the bottom of my illustration could bind with the c of the third from top as cg is an allowed binding. Thus, one would expect the RNA to rapidly become 3D structures. Does 3D structure formation occur while separating* from the DNA, or later
(2) Once that RNA is freed, do the two strands of DNA rejoin together or do they break up to resupply unbound A, C, T & G back to the “soup.” I guess they rejoin as the T can only be reused if more DNA is to be made. (RNA needs u, not t.)
(3) Where do the 5 letter molecules A,C,G,T & U come from? I.e. how are they made? Are they really the four Nucleotides, Na,Nc,Ng & Nu that join up on the exposed binding sites of the splitting DNA, not just the "letter molecules"?
(4) As the RNA production process makes two closely related, but entirely different RNA sequences are both of use or is one broken up to “recycle” the “letter molecules”
(5) What starts the double strand DNA splitting (at only one of the two ends?)?
(6a) As both T and U can bind to the “non-sugar-bound” end of A, is it not a common RNA error to occasionally have tA instead of the correct uA?
(7) I assume that certain sequences of the RNA are “weak points” (or vulnerable to enzymes breaking or *) so that mRNA and tRNA (and probably more I do not know of) form.
--------------
*A speculation:
As noted in (1b) during the separation of the nascent RNA from the DNA, assuming it is also some "un-zipping” process, there should be 3D self-binding structures formed. (As speculated in question 1b.) Thus, as the RNA “unzips” from the DNA, one could imagine that a “chain of balls” forms. I.e. various size complex 3D structures with relatively short linear links of RNA letter molecules joining them are made. These “linear links" would often “snap” due to the independent Brownian motion of two adjacent 3D balls. Perhaps this is part reason why the long RNA copy of the information in the DNA breaks into useful smaller pieces like mRNA, tRNA, and others I do not yet know of. Perhaps some of the "junk DNA" is used to make the "weak linear links" in the first formed long RNA so it snaps apart the longer RNA into useful 3D "balls"?
The tRNA has the anticodon loop at one end, quite remote from where the amino acid would be held on the tRNA molecule. When the anticodon loop briefly binds to the “now being read” part of the mRNA, is its amino acid is released (inside the ribosome?) at the now forming protein? I.e. is the mRNA passing thur the ribosome roughtly the length of the tRNA away from the site where the protein is being assembled? (I guess “Yes.”) Thus, the ribosome must have a “slot” thur it that is orienting the tRNA with the protein being built near one end of the “slot” and the mRNA passing thru the other end of the slot. As the currently being read codon of the mRNA and the matching anticodon of the tRNA separate, does this create some force that moves the mRNA one codon step more thur the ribosome?
Also does the amino acid release by the tRNA require BOTH the mating with the mRNA codon AND the molecular “pulling” from the already partially built protein site it should occupy? I would guess answer to that is “Yes” because if only the mating of the anticodon and codon is required for release, then that mating should occur often in the soup; However, perhaps loss of the amino acid is not important as the tRNA can just get another form the soup. Comments?
However, it is my understanding that when the tRNA briefly adheres to the mRNA as the mRNA is being passed through the ribosome, that a sort of 'flag' of protein develops as the amino-acid is attached to the growing polypeptide chain.
The ribosome is composed of two sub-units, and I believe the 'slot' you reference, where the mRNA is read, is where those two sub-units are connected.
don't have a nice diagram to show you, but perhaps Roman does.
Also, the proteins need to take specific shapes [not just a long stream of amino-acids], and they fold upon themselves into highly specific and complex shapes, often via Sulfur bonding, and as to how that is guided I'm not certain. Protein functions can be activated/deactivated by shaping/unshaping of the protein depending upon the cellular chemistry at the moment. Again, Roman would likely know more about that than I.
I don't think so.... I am but a lowly undergrad with little talent for organic chemistry and only a handful of classes on genetics. ...
I am but a lowly undergrad
As far as I know, RNA cutting itself is rare. It may be common, and we just don't know it yet, but so far, most modification to mRNA and tRNA after synthesis is mediated by proteins.
Like a chain coming out of the end, you mean, for the amino acids bonded together?
There are two slots (three in prokaryotes? will have to look that up) in the large subunit of the ribosome-one that facilitates the anticodon pairing with the mRNA- where the mRNA is read, as you said. If it matches, the tRNA is passed along into the slot where the amino acid is removed, then passed on out (or into the third slot, then out, if the wiki is to be believed, for prokaryotes).
Thanks. Here is direct link to the 13 chapters (I think):... I was just ordering some reagents from Promega and came cross their ... Protocols & Applications Guide. It's not too bad at describing some of the basic techniques routinely employed in molecular biology research. ...