Science Quiz

[Perfection]

Well, the charge is one thing, but the answer is incomplete

*hint* Think of lewis structures and ionic lattice structures.

 

[slothman]

It's +1 like Sodium. And the oxyidation state would imply that the 4 H's have no electrons while the Nitrogen has 8 valence, noble gas. Things like ZnCl2, the Zn+2 isn't noble gas.
EDIT: It also doesn't have any more electrons that will be taken away. H3O+ still has 1.

 

[Perfection]

Well, that's true but not what I was looking for,

I was looking for the fact that ammonium is nonpolar and the radius of each sorrounding hydrogen atom is small compared to the nitrogen, producing an almost spherical +1 nonpolar ion that exhibits very similar properties in crystal lattices as Na K Cs, whatever because they are also nonpolar spherical +1 ions.

We'll let you have the next one

 

[betazed]

I am going to resurrect this thread (why does it keep dying? )


In our genome three bases form a codon. In keeping with the evolution thread going on, can we design this in a better way? Is it advantageous to use 4 bases to form a codon? Or 5? Or 6?...

If so, why?


I understand this question is slightly subjective. So I will give it to the first reasonable guess.

 

[Perfection]

Well, since we have 21 different codon types (20 amino acids, and the stop), the minimum amount of bases to code it is 3.

I suppose having additional codons could help in some cases, translation errors would be reduced, however apperently the effiiciency in 3 outwieghs the stability of 4.

 

[betazed]

I suppose having additional codons could help in some cases, translation errors would be reduced,

You are almost there. Can you expand on that? What translational error will it reduce?

 

[Perfection]

Are you refering to wobble?

 

[betazed]

Are you refering to wobble?

No I am not. I do not know what wobble is? What is it?

 

[The Last Conformist]

Um, having four bases per codon ought increase translation errors, since the risk for a single one presumably is constant.

You could however arrange it so that most errors will result in an invalid codon; error detection. Two extra bases should allow some error correction, even.

 

[Zwelgje]

4 bases to encode an amino-acid will cause redundancy: there are many more posibilities to form a codon than there are a.a. so more codons will encode the same a.a. Hence a mutation in the last of the four bases will be a silent mutation as it will not cause an a.a. change. Hence 25% of point mutations will be silent. This on top of the numerous mutations that are silent now already with 3-base codons. In many cases the third base of a codon doesn't matter.
Anyway, apperently 3 bases works better than 4, 5 or 6. Otherwise we would have had any of those in stead of 3.

 

[Perfection]

No I am not. I do not know what wobble is? What is it?

Wobble refers to the fact that tRNA anticodons often are not made up of the traditional A U G C, there are other bases such as Inosine, which bonds to U C or A. The anticodon CCI can bind to GGU GGC GGA, that's why all those code for the same amino acid (in this case glycine), the benefit is now instead of having to have 61 tRNA molecules we can have less (about 45) thus further maximizing metabolic efficiency.

 

[betazed]

You could however arrange it so that most errors will result in an invalid codon; error detection. Two extra bases should allow some error correction, even.

TLC and ZWelgje is right.

Let's say ACG is a valid codon and CGA is also a valid codon. Then the string ACGACGACG contains the first codon three times or the second codon twice starting from the second base. Now the translation mechanism is known to do slippage errors technically called frame shifting. So there is a possibility that it will slip the first A and read CGA CGA G..

However, with 4 bases we can get only 21 unique codons IIRC (I will leave it you to write down the exact codon sequences) that are resistant to slippage errors. If you slip the the resultant 4-base codon will be a error code. In fact this way of doing codons is so economical and precise and resistant to faults that it was thought that this must be so.

@Zwelgje: I am not sure anyone has shown that having 4 bases is necessarily worse than using three. Can you think of any disadvantage? Sheer length does not mean anything since more than 90% of our DNA is just junk and increasing it a little more can do only so much harm whereas reducing slippage errors gives it great robustness.


Either perfection or TLC or Zwelgje can take the next one.

 

[Perfection]

@Betazed there are a number of flaws to your arguement, 4 codons is far worse than 3.

1. Your system is inneficent. You're saying that since junk DNA is inefficient than ineffiencies elsewhere are okay. This statement is flawed as "junk" DNA serves an evolutionary purpose as well as structural purposes, pormoter regions and other things. Additionally, DNA is small potatos to RNA, you've only got a few DNA molecules, while RNA is being churned out in large amounts, a hunk of mRNA is only good for a little while before it degrades and has to be replaced.
2. The accountability of slippage errors is not really a big thing. Sure you don't waste energy to produce the protien (unless the error is far down the protien where it will still cause a problem), but with thee codons the slippage error still often causes a stop sequence to come early giving another defective protien. In fact, with the exception of an insertion at the third nucleotide there is no case where a slippage error that would produce a bad protien in mRNA as it is and not in your idea (as mRNA requires a spefic start codon), it may be shorter but it would still be there (In fact slippage errors would be more likely given the longer sequence).
3. If you have a point mutation you're more than likely screwed. Let's say you have DNA with a point mutation, with you metheod it is more than likely the cell can't produce any protien off of it, and you're screwed. But in mRNA now, it's likely you'll get a very similar protien, and you're doing a lot better. So basicly any cell that has a point mutation in DNA in your system, it's screwed, so only the cells with little to no point mutations survive and evolution is shackled. However with a point mutation as the way it is, it's likely you'll produce a similar protien, and so you're doing okay, and it's possible that it might improve the protien.

 

[betazed]

@Betazed there are a number of flaws to your arguement, 4 codons is far worse than 3.

I am not sure you are correct, but you maybe. As I stated in my question there is a subjective aspect to this question as there are no clear-cut answers.

 

[Perfection]

I am not sure you are correct, but you maybe. As I stated in my question there is a subjective aspect to this question as there are no clear-cut answers.

Did you read the rest of my post?

 

[betazed]

Did you read the rest of my post?

Trust me. I always read the whole post.

 

[Perfection]

Trust me. I always read the whole post.

So then how can it be subjective? Your method only prevents the further elongation of an already produced defective protien that is often already prevented with the current system for a rare error which it will increase the occurance of at the price of a substantial increase of required materials and energy, the inability to deal with more common point mutations (which it increases the rate of), and seriously shackling evolution.

Unless you despise living things I'm baffled by how that can make thingss better!

 

[Perfection]

Why isn't the recently discovered planetoid Sedna a member of the Kuiper belt and what is it a member of?

 

[betazed]

So then how can it be subjective? Your method only prevents the further elongation of an already produced defective protien

But proteins are made only after the initial transcription phase has gone thru and in the new coding scheme the error can be caught in the transcription phase itself. So a frame shift does not cause a wrong protein to be created.

the inability to deal with more common point mutations (which it increases the rate of),

Why should it increase the rate of point mutations. Most point mutations will lead to an invalid code. Hence while the number of point mutations mught ne increased most of them will be caught. So the effective number of poit mutations that will lead to an erroneous protein will decrease.

and seriously shackling evolution.

Evolution does not depend on point mutations alone. Although it can be argued what the rate of evolution will be in such a scheme. Hence this is probably a valid point.

Also, you correctly pointed out that the cost is not just to DNA but also to RNA. Is that cost worth it? I am not sure. Hence that too could be a reason against this scheme.

Thinking about all this I said you are probably correct. I am logging off for the night. If you have any other arguments post it. I will attempt to answer them tomorrow.

 

[Perfection]

But proteins are made only after the initial transcription phase has gone thru and in the new coding scheme the error can be caught in the transcription phase itself. So a frame shift does not cause a wrong protein to be created.

Well, now we're altering the nuts and bolts of the RNA transcription process, adding a new step from transcription to translation.

Why should it increase the rate of point mutations.

More DNA=More chance for errors

Most point mutations will lead to an invalid code. Hence while the number of point mutations mught ne increased most of them will be caught. So the effective number of poit mutations that will lead to an erroneous protein will decrease.

Precisely, let's say that's a critical gene. In your scheme the cell dies, in the current scheme the cell produces a very similar protien that will often work instead. A good example is hemoglobin, now there is one point mutation that cause the sickle cell trait, however there are several that have no effect and produce a very similar protien, the key is in this case the elimination of a point mutated protien is a detriment not a benifactor.

Evolution does not depend on point mutations alone. Although it can be argued what the rate of evolution will be in such a scheme. Hence this is probably a valid point.

Well, while point mutations are certainly not the only mutations important in evolution, but they are very important, as they only bring about a small controlled change, making it much more likelt to come up with something good, this is evidenced by the structural similarity of many protiens, often changed by only a few base pairs.

Thinking about all this I said you are probably correct. I am logging off for the night. If you have any other arguments post it. I will attempt to answer them tomorrow.

Good night, then.