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Is that what they called junk? Why does a simple cell have the DNA code for everything else when it just needs a few codes to function? Wouldn't that be a wasteful?

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Why does a cell contain all DNA when it only needs a few genes ?

I interpret this question to mean "why does every cell contain the whole human genome even though it doesn't use it all, i.e. why does a liver cell contain the genes for eye color?"

If that is what you meant, then we can easily answer the first question in your actual text:

Is that what they called junk?

No, that is not what is called "junk DNA". "Junk DNA" can refer to many concepts, but generally it refers to parts of DNA that serve no function in the body: they are not transcribed into proteins, they don't serve to regulate other genes, and if you remove them or change their sequence this will have no effect on the overall organism. This means it refers to parts of DNA that are used nowhere in the body, not parts that are used in one place but not in others.

How much DNA is "junk", how useless it actually is, and why we have it are complex questions that don't all have known answers, but it is completely different from your headline question.

I don't have the time to look up a detailed answer to your first question so I will leave that to others, but here are some elements that might help:

1) I think cells use more genes than you realize. I don't know the proportion of genes that are used for the cell to live as a cell vs those that are used for the specific tasks this cell needs to do beyond maintaining itself and reproducing, but I'm pretty certain there is no cell in the body that "only needs a few genes". I would even guess all cells in the body use most of the genes they contain.

2) not all cells contain an unmodified copy of the whole genome. Some cells lose their nucleus, i.e. their DNA entirely (red blood cells); others multiply some genes that they use a lot.

3) having said all that, I would guess that liver cells indeed don't need the genes for eye color, yet they might have them. Consider that cells reproduce by copying themselves, and copying their whole genome. Is it more of a waste to keep the copy as it is, or to go around before or after the copying cutting out all the bits this specific cell won't use? Do I go around editing the code of my text editor and recompiling it to get rid of all the functionalities I don't use? I might save some space on my hard drive but it is very obviously not worth my time to do that either. If the extra DNA doesn't do enough harm, there is no reason it would be taken out; indeed the wasteful thing would be to do so.

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  1. Whether there is junk DNA

The common view of a gene is a sequence of DNA which, upon transcription, which I assume in your understanding is a process by which DNA is read by a RNA polymerase to produce mRNA, and upon translation, produces a functional protein to regulate cellular metabolism (sum of all chemical reactions in a cell). It is not until the discipline of epigenetics emerged that we discover that most of other non-protein-coding sequences have important regulatory functions on the protein-coding sequences. Without them, the cell simply has no clue as to when it should produce more of a protein and when it should produce less, or whether the protein should be produced at all. And of course, DNA also encodes information about rRNA, which is an integral component of ribosome, which you know, is imperative for protein synthesis. Thus, the ‘functions’ of the DNA cannot be limited to protein synthesis, and after extension of the concept of functions, the parts of DNA we can dispense with are incredibly small.

Then let it be argued that those small parts of DNA which really serve no functions are the junk DNA. In fact, even this view is untenable because the ‘functionless’ DNA may be situated between the important sequences that can subtly affect the chemical properties of the protein interactions during an important biochemical process. Specifically, consider NtrC, a bacterial transcription regulator that activates transcription by directly contacting the RNA polymerase. Note that the regulatory sequence (the part of DNA the protein binds to) is very distant from the promoter of the gene(the part of the gene that RNA polymerase binds to). To directly contact it, DNA looping must occur. It is a phenomenon in which an otherwise linear DNA macromolecule is looped out(imagine bending a wire so that two extreme end of the wire touches each other) to allow for the contacts between molecules. Since the protein has such biochemical properties that allow it to contact another protein at a distance, we do not know what will happen if the ‘junk DNA’ the DNA spacing the promoter and the regulatory sequence is deleted. It is well possible that the two proteins will not make contacts anymore. And DNA looping is also ubiquitously found in transcription regulation of eukaryotes.

  1. Why a cell needs to contain all the DNA when it only needs a few genes to function

Once the notion of junk DNA is found to be elusive. This question’s premises no longer hold. But let’s assume there are really genes that when deleted have no observable effects on the phenotypes of the cells or their health, why does not nature delete them during differentiation of stem cells? To explain it in evolutionary terms, there are two main mechanisms nature can design to keep the ‘functionless’ genes at bay during differentiation of stem cells. One is to silence them by wrapping them in a compacted nucleosomal structure, or to delete them once and for all. We do not know if nature has once experimented with deletion, if it has then this design must have endowed less fitness then the wrapping model. What reasons then can we speculate about the failure of the deletion model? To delete the useless sequences, there is a widespread effects on the length of the DNA, the resultant secondary structure (topology of the chromatin). And a protein must be designed to specifically recognise what genes to delete, together with the cooperation of nucleases. This is analogous to writing a computer code that contains information that specifies some of the codes to be deleted while not influencing the instructions of the code that follow, all while being consistent in the process. This is logically possible, and we can never say this design is entirely prohibited. But computationally this is not as elegant a solution than just genes in the DNA that code for a repressor protein for the ‘useless’ code when the right time has come, or by just using proteins to wrap around the sequences to render them unreadable.

  1. Whether ‘non-functional ‘ DNA constitutes a waste

Not at all.

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  • $\begingroup$ I expect you were downvoted because it's not the consensus that little to no DNA has no function. It isn't just about how non-coding DNA might have other functions; for example, looking at which parts of the genome show evidence of selection and which don't can serve as a proxy for them having a function or not, and by that metric most human DNA is indeed "junk". I also don't think it has been shown that most non-coding DNA has a regulatory function. Some yes, most no. Highest number I find is 40% here, and even that's a hypothetical. ncbi.nlm.nih.gov/pmc/articles/PMC3431477 $\endgroup$ – Oosaka Jul 18 '18 at 22:16

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