Replacing the genetic material

[truthSeeker]

Hi everyone ...
I have a new question about genetic codes (I'm really interested in this subject)
as we now , each codon consists of three nucleobases and there are four nucleobases , so there are 64 possible codons and because there is only 20 amino acids involved in genetic code translation , some amino acids are represented by two or more codons .

suppose that i picked an organism and examined its genetic material and then i synthetically constructed that genetic material but with replacing each codon in the original genetic code with another codon that represents the same amino acid .
and then i replaced the original genetic material with my synthetically constructed genetic material , suppose that the organism survived aftre the replacement , would this replacement affect the organism in any manner ?
The attached picture clarify the problem .
thanks in advance ...

[truthSeeker]

there are some lingual mistakes in the picture , forgive me

[JackBean]

in fact, it would. Organisms do not use all codons (there are 6 for some amino acids!), but they have rather some preferred codons, which they overuse. You can find some examples on the internet for sure.
So, for this reason, they of course do not produce the tRNA for all codons and thus it may become limiting. And that can be also problem with heterologous expression

[kolean]

Does it read forwards and backwards?

[Darby]

I read somewhere that the codons affect the methylation of the amino acids (or maybe different codons are prone to methylation, I've forgotten which) and the speed with which they can be translated, so there are effects.

[JackBean]

Does it read forwards and backwards?

What do you mean?

[truthSeeker]

@JackBean
but i've read that the anticodons of some tRNAs can pair with more than one codon due to a phenomenon , i guess it's called "Wobble base pair"

@kolean
it reads form where the start codon is

@Darby
please , can you explain more ?

[JackBean]

yeah, that's true, that makes it possible to be read all the codons by use of only some tRNAs

my guess, what Darby meant is that by changing GC content and rate of methylation places you change the overall transcription rate

[truthSeeker]

Actually , i don't know much about "methylation" , so explain it for me please ... and let me ask this question
"is this change in methylation places and the change in the overall transcription rate can have fatal effects , in other words , can it cause a missfunction in the cell ?"
thanks in advance

[kolean]

In humans, methylation occurs on the cytosine nucleotide. It is methylated by DNA methylases (DNMT1 - which is usually the maintenance DNA methylase as it has been found to be attached to the polymerase complex and prefers the hemi-methylated DNA strand, in which it methylates the other strand's cytosine during duplication, and DNMT3a and 3b which are de novo DNA methylases that follow certain factors for the methylation of cytosines during development, in which DNMT3L is a regulatory DNA methylase and may help guide the DNMT3s). Methylated DNA can then be bound by MBD (methyl binding domains) proteins/factors, which can then utilize many complexes to bind up the chromatin into heterochromatin (polycomb repressor complex 1 and 2 - PRC1 and PRC2), which also utilize methylation of histones (which may be another factor for you to consider).

Read forwards and backwards meant that the DNA is double stranded and can be read forwards on one strand (sense strand), while forward on the other strand (antisense strand). Thus appearing to be 'read' backwards in relation to the other strand. So an ATG start codon on the antisense stand would be CAT in the sense strand, which would produce a different transcript (possibly an antisense one - then you get into RNAi stuff, which would possibly mess up your sense transcript - its degradation or just repression of expression). Though ATG doesn't guarantee that the polymerase will 'read' that DNA, there is alittle more that the polymerase needs to bind to the DNA.