What's the difference between CTT and TTA?

[Str1pe]

Hopefully this is a pretty simple question, but I'm more a rock guy...

CTT and TTA can both be used to make leucine. So to make leucine there is no difference to an organism's DNA whether it has CTT or TTA in the right place. But might the difference between CTT and TTA have other effects not related to the production of leucine?

 

[bobze]

Hopefully this is a pretty simple question, but I'm more a rock guy...

CTT and TTA can both be used to make leucine. So to make leucine there is no difference to an organism's DNA whether it has CTT or TTA in the right place. But might the difference between CTT and TTA have other effects not related to the production of leucine?

No, no difference. I suppose, it could make a difference if a regulatory element bound there as the "shape" of small segment would be different. But most DNA binding proteins don't bind in coding regions of genes. Rather to specific effector regions outside the coding region.

Minor clarification note, you've listed the non-coding strand of DNA.

The coding strand would be GAA or AAT. The mRNA would be CUU or UUA.

Probably going way beyond the scope of your question, but interesting nonetheless, is that since CUU/CUC/CUA all code for Leu, then they probably use the same tRNA.

tRNA can use a 5th base, inosine. Which when in the 5' (five-prime) position of the anticodon can recognize a U, C or A. So rather than having 3 different tRNAs you can have GAI, which would pair with all three. G and U can also form "wobble" base pairs with C or U and A or G, respectively, also reducing the number of tRNAs needed to recognize a codon.

 

[Ygggdrasil]

Most of the time, mutations that change the nucleic acid sequence but do not change the amino acid identity (called synonymous mutations) do not have any effect on an organism. There are, however, special cases where synonymous mutations do have an effect.

First, as bobze noted, synonymous mutations can change regulatory elements such as splice sites, which can change a protein's structure and function. There is also new research suggesting that synonymous mutations can affect protein folding, however. One mechanism may be through altering mRNA structure. If the mRNA folds back on itself to form a hairpin structure, the hairpin could impede the ribosome from translating the mRNA, causing the ribosome to pause. This pausing during protein synthesis might be useful to give the protein time to fold correctly before other segments of the protein are translated that might interfere with folding had a pause not occurred. Synonymous mutations which alter mRNA structure may be able to alter the efficiency of protein folding in this way.

Another way the cell can pause protein synthesis is by encountering a codon that corresponds to a rare tRNA. By mutating a codon for a rare tRNA to a more abundant tRNA or vice versa, synonymous mutations can alter translational pausing and may be able to affect protein folding.

 

[Str1pe]

Hmmm ... OK. Sounds like I have my work cut out for me. Thanks, fellas. :)