Why does the DNA codon ACG code for threonine in the RNA codon table?

[nomadreid]

TL;DR

mRNA codon eventual matches to amino acids are straightforward. But in a DNA double helix, it seems that, for example, referring to a ACG DNA codon is referring not to the end result (amino acid) of the ACG in the strand on which the ACG is found but to the end result of the complementary TGC on the other strand. If not.... then I'm confused. More detail in main text.

I refer to the tables on https://en.wikipedia.org/wiki/DNA_and_RNA_codon_tables

In both the DNA and the RNA codon tables, ACG codes for threonine. But the transcription of the ACG from the DNA to the mRNA ends up with UGC (which would code for Cysteine). So should I assume that when the DNA table talks about the ACG coding for threonine, it is talking about the TGC on the complementary DNA strand which would transcribe to ACG on the mRNA (which would code for threonine as promised)?

If not, then what step am I missing? Thanks.

 

[pinball1970]

Summary: mRNA codon eventual matches to amino acids are straightforward. But in a DNA double helix, it seems that, for example, referring to a ACG DNA codon is referring not to the end result (amino acid) of the ACG in the strand on which the ACG is found but to the end result of the complementary TGC on the other strand. If not... then I'm confused. More detail in main text.

I refer to the tables on https://en.wikipedia.org/wiki/DNA_and_RNA_codon_tables

In both the DNA and the RNA codon tables, ACG codes for threonine. But the transcription of the ACG from the DNA to the mRNA ends up with UGC (which would code for Cysteine). So should I assume that when the DNA table talks about the ACG coding for threonine, it is talking about the TGC on the complementary DNA strand which would transcribe to ACG on the mRNA (which would code for threonine as promised)?

If not, then what step am I missing? Thanks

Not read about protein synthesis for a bit!

Yes just looks like a complimentary. ACG complimentary is UGC in mRNA.
Have a read through these.

https://en.m.wikipedia.org/wiki/Complementarity_(molecular_biology)

https://en.m.wikipedia.org/wiki/Protein_biosynthesis

 

[nomadreid]

Thanks, pinball1970. Also relevant to my question, which I found since I posted, are
https://en.wikipedia.org/wiki/Coding_strand
and, a bit less directly,
https://en.wikipedia.org/wiki/Sense_strand

 

[pinball1970]

Thanks, pinball1970. Also relevant to my question, which I found since I posted, are
https://en.wikipedia.org/wiki/Coding_strand
and, a bit less directly,
https://en.wikipedia.org/wiki/Sense_strand

I read it and I immediately clenched, reminded my of biochemistry from Uni or even A levels!
Not my forte.
Don't forget you have Jim Bill Atty Rive Teeth and loads of others know this stuff like I know the Beatles. If you need specifics.

 

[BillTre]

Although I have a good understanding of what is going on in the translation process (making proteins based in the sequences encoded in DNA), I am not too good at remembering the names for all the different little bits of sequence. These are the things of tests to me. If I were going to be tested on them, I would have to re-memorize them. Looking the names up is the logical path (for me) once the understanding of the process is acquired.

There are a lot of complementary relationships were a codon binds to an anticodon or a complementary strand (or DNA) or where the sense strand or the antisense strand templates the production of a complementary strand during replication.
Understanding these somewhat complex relationships would be my goal if I were learning this initially.
There are more then one path of information flow here:

• DNA --> new DNA strand (template directed replication)
• DNA --> mRNA (template directed transcription)
• DNA --> tRNA (also template directed transcription I think)
• DNA --> rRNA's (also template directed transcription I think)
• tRNA --> tRNA loaded with the correct amino acids (recognition by specific aminoacyl tRNA transferases of both the amino acids and RNA sequence)
• tRNA binds to mRNA in ribosome by a codon anti-codon interaction
• animo acid sequence is produced from the order of amino acids delivered to the ribosome by the combination of the loaded tRNAs and mRNA
• the sense strand of a piece of DNA encoding a protein is defined by whether it is the strand from which an RNA is transcribed for protein production. If there are two genes in the same place being transcribed in different directions (on different strands of the DNA), the same strand could be sense or antisense depending on which gene you are talking about.
• There are also the base differences between RNA (AUCG) and DNA (ATCG) to contend with. U and T act equivalently in base pairing.

 

[nomadreid]

Thanks, BillTre. I have a lot to go through; I thought that the DNA to tRNA was only via mRNA, and that rRNA acted as an enzyme for the mRNA--tRNA transcription. I must read more; the point about sense/antisense is the one that I was referring to originally, and your answer seems to say that both strands can be used, which is a very enlightening fact. Thanks!

 

[Bruzote]

Although I have a good understanding of what is going on in the translation process (making proteins based in the sequences encoded in DNA), I am not too good at remembering the names for all the different little bits of sequence.

A good understanding? I can't speak for you, but if that refers to the general limit of your expertise, you might be in the same boat as folks like me without realizing it. I thought I had a good understanding based on my high school and college education. For what was known during those years, I did have a good "basic" understanding.

One quick journey down the rabbit hole of Wikipedia link chasing revealed the gadzillion complexities of the "basic" process of gene transcription that were not known about in the past. Initiation of transcription, introns, extrons, suppression, etc. are pretty important to know about if you want to understand how the genome becomes realized. Leaving them out in a basic model yields a model that misses a lot of key factors affecting when and how transcription is accomplished.

Heck, even realizing how much unused stuff is just floating around, disappearing and reappearing, is surprising to me. Despite reading countless articles and watching videos, I can't seem to reach an end of what seems to be essential parts and processes that make transcription work. I see now that genomics, proteomics and related fields are incredibly rich not only due to the organisms under study or gene/protein under study, but also rich in what processes and "auxiliary" molecules one might focus on as well as the pressure of keeping with the evolving knowledge.

My hats are off to those in this field. From my perspective, it looks like the golden days of being a genetics expert have been over for many decades and I just didn't know. (I suppose most fields of knowledge become like that for aging folks.) AFAIK, there is no way someone can follow or at least catch up quickly on all the key events transpiring in the field of genomics. The top scientists surely have gross areas of ignorance at this point.

Kind of like how there was a time a microbiologist might be an expert in pretty much all developed areas of yeast knowledge. Now they are experts in various areas and sub-specialties, with too much to know for anybody to be expert in all of them. Amazing.

Again, I have no idea of you knew about this, but your question - as read by neophytes - might imply that transcription is quite straightforward, when it is not. It is very complex and awe-inspiring.

 

[BillTre]

The original post was about base pairs and coding for amino acids in a protein sequence.
You are going way beyond that. Should be a new thread.

You seem to be going through an intellectual period of being overwhelmed with a highly complex subject.
Too many details to handle all at once.

Take a smaller scale approach to the subjects and learn them in detail one by one. They will then build in each other and it will become easier (due to many shared concepts).
You will never know all the details. No one does, but you can choose which details to become familiar with. Be strategic. A molecules-up approach is one way, but there are others.

From my perspective, it looks like the golden days of being a genetics expert have been over for many decades and I just didn't know.

My interpretation is that there has been an ongoing golden age in biology in general (much but not all in genetics), since the structure DNA was described (1953, when I was born). It has gone through some periods with a particular focus (like basic molecular biology in the 1960 and 1970s).
Its still going on and more stuff is being worked out and new avenues of important data acquisition are still being developed (for example the ability to look at expression of all the genes in a cell, or more rapid acquiition of detailed protein structures).
This is not something that seems to be slowing down to me. Its building on recent successes and moving right along.
To me it is a very exciting time in biology.

 

[J Boogie]

It might clear up some confusion to learn the polymerase, as it is moving along the DNA, is moving from the 5' ("five prime") to the 3' ("three prime") direction, that is, only one strand is translated by the polymerase as it moves along. This is called the "sense" strand, the complimentary strand is "anti-sense".

As it goes down the helix the protein complex unzips the helix, exposing the sense strand to the polymerase. As it goes past, the nucleotides reform the hydrogen bonds that keep the DNA in the double-strand configuration, safe from further meddling.

 

[nomadreid]

the polymerase, as it is moving along the DNA, is moving from the 5' ("five prime") to the 3' ("three prime") direction, that is, only one strand is translated

Thanks, J Boogie.
If I understand correctly, this chooses the strand which has
(5') the end which has the fifth carbon in the sugar ring of the deoxyribose at its terminus to
(3') the end with the hydroxyl group of the third carbon in the sugar ring at its terminus

This brings up two questions for which I would be grateful for clarification:
(a) Does this mean the other strand never gets read? (seems like a waste...)
(b) (my original question) Is the designation of the gene from the anti-sense strand (as in the example given in the original post)?

 

[Bruzote]

The original post was about base pairs and coding for amino acids in a protein sequence.
You are going way beyond that. Should be a new thread.

You seem to be going through an intellectual period of being overwhelmed with a highly complex subject.
Too many details to handle all at once.

Take a smaller scale approach to the subjects and learn them in detail one by one. They will then build in each other and it will become easier (due to many shared concepts).
You will never know all the details. No one does, but you can choose which details to become familiar with. Be strategic. A molecules-up approach is one way, but there are others.My interpretation is that there has been an ongoing golden age in biology in general (much but not all in genetics), since the structure DNA was described (1953, when I was born). It has gone through some periods with a particular focus (like basic molecular biology in the 1960 and 1970s).
Its still going on and more stuff is being worked out and new avenues of important data acquisition are still being developed (for example the ability to look at expression of all the genes in a cell, or more rapid acquiition of detailed protein structures).
This is not something that seems to be slowing down to me. Its building on recent successes and moving right along.
To me it is a very exciting time in biology.

Thanks for your genuinely kind reproach. Regrettably, I forgot about forum etiquette after being on regular social media where topical boundaries are rarely a concern. Your advice about learning is so obviously wise, but no less challenging to follow in the face of so many exciting opportunities to discover and master knowledge.

 

[Godot_]

Thanks, J Boogie.
If I understand correctly, this chooses the strand which has
(5') the end which has the fifth carbon in the sugar ring of the deoxyribose at its terminus to
(3') the end with the hydroxyl group of the third carbon in the sugar ring at its terminus

This brings up two questions for which I would be grateful for clarification:
(a) Does this mean the other strand never gets read? (seems like a waste...)
(b) (my original question) Is the designation of the gene from the anti-sense strand (as in the example given in the original post)?

the other strand is simply duplicated the other way round. And there are quite a few examples where working genes are encoded there, in the same space, also different genes in different ORFs (open reading frames). Supposedly this is the big evolutionary benefit conveyed by third-base redundancy.

A college undergrad level genetics- or molecular / cell biology textbook would go into sufficient depth.

Please, when you're talking about nucleotide triplets, do include whether it's the codogenic or anticodogenic strand (or sense/antisense). Also, with polymerase, DNA-polymerase and RNA-polymerase are different beasts - though both only work 5'-to-3'. Plus, there also are DNA-directed- and RNA-directed- -RNA and -DNA polymerases.

To add to the answer to your initial question:
The codon tables refer to the tRNA sequence. Hence the mRNA is antisense, whereas the tRNA again is sense direction. Convenient, as it facilitates geneticists' "reading" or translating gene sequences into protein AA sequences...

 

[nomadreid]

The codon tables refer to the tRNA sequence. Hence the mRNA is antisense, whereas the tRNA again is sense direction. Convenient, as it facilitates geneticists' "reading" or translating gene sequences into protein AA sequences...

Thanks, Godot. An answer worth waiting for...