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I asked this in Chemistry and it was suggested to ask it here. I wondered how the genome, which afaik does not contain iron or calcium as "reference" copies, nonetheless produces an organism that uses certain elements. If it create proteins which bind preferentially to iron or calcium, how then are such elements routed to sites where they can be bound? Are there proteins in addition to those which bind to elements that are responsible for routing? I should mention that I am a software developer and imagine mechanisms analogous to computer code.

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  • $\begingroup$ Hi and welcome to Biology.SE! It's unclear to me whether you're wondering about iron uptake into blood from consumed food or iron uptake by cells from blood. Or are you asking how individual iron ions reach binding sites on iron-binding proteins? Chemically, proteins that bind ions are no different from proteins that bind other organic molecules, and the genome contains codes for proteins that specifically bind almost every class of chemicals out there. You can get some basics re:iron here: en.wikipedia.org/wiki/… $\endgroup$ – Armatus Sep 25 '18 at 7:55
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    $\begingroup$ We welcome new users to SE Biology, but unfortunately your question has problems which will be apparent when you take time to read the introductory tour and the help. First, you really have to show evidence of your own research before posting a question. if you had done this you would see the second problem, that your question is much too broad. Different elements are handled in different ways. You seem to think there is a general problem here in relation to the elemental composition of the genome, but I see none. Please explain further. $\endgroup$ – David Sep 25 '18 at 12:17
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    $\begingroup$ @com.prehensible please refrain from answering in the comments. Please turn this into an answer. I'll delete your comment shortly. Problem is that answers in disguise demotivates others from writing quality answers. $\endgroup$ – AliceD Sep 25 '18 at 17:29
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    $\begingroup$ As another software developer, I should point out that analogies between computer hardware or software and biological systems can be misleading sometimes. What do you mean by "reference copies" in the genome? $\endgroup$ – gilleain Sep 26 '18 at 7:54
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A wikipedia source gives you general informations and precise details about the locations and methods of absorption and distribution. Reading the page is well recommended, I will add the quote to save others time:

en.wikipedia.org/wiki/Human_iron_metabolism#Dietary_iron_uptake :

Like most mineral nutrients, the majority of the iron absorbed from digested food or supplements is absorbed in the duodenum by enterocytes of the duodenal lining. These cells have special molecules that allow them to move iron into the body. To be absorbed, dietary iron can be absorbed as part of a protein such as heme protein or iron must be in its ferrous Fe2+ form.

A ferric reductase enzyme on the enterocytes’ brush border, duodenal cytochrome B (Dcytb), reduces ferric Fe3+ to Fe2+.[9]

A protein called divalent metal transporter 1 (DMT1), which can transport several divalent metals across the plasma membrane, then transports iron across the enterocyte’s cell membrane into the cell.

These intestinal lining cells can then either store the iron as ferritin, which is accomplished by Fe3+ binding to apoferritin (in which case the iron will leave the body when the cell dies and is sloughed off into feces), or the cell can release it into the body via the only known iron exporter in mammals, ferroportin.

Hephaestin, a ferroxidase that can oxidize Fe2+ to Fe3+ and is found mainly in the small intestine, helps ferroportin transfer iron across the basolateral end of the intestine cells. In contrast, ferroportin is post-translationally repressed by hepcidin, a 25-amino acid peptide hormone.

The body regulates iron levels by regulating each of these steps. For instance, enterocytes synthesize more Dcytb, DMT1 and ferroportin in response to iron deficiency anemia.[10] Iron absorption from diet is enhanced in the presence of vitamin C and diminished by excess calcium, zinc, or manganese.

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  • $\begingroup$ The fundamental question is, how can an element be "recognized" without any sample to compare it to? How are proteins able to bind iron from among any number of things that might be encountered? $\endgroup$ – releseabe Sep 26 '18 at 12:07
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    $\begingroup$ Enzyms have specificity, a lock and key method, a preferential fit method. The DNA keeps information on millions of external constructs, it is only a code, so it can code anything, not only mineral specific enzymes, it can code about 146 heptillion different enzymes, which change randomly and are selected by evolution or equivalent purpose(for enzymes). If the enzymes are randomly generated to begin with, the coding/cell memory structure doesn't need to have a "reference" copy of the mineral. it's quite a complicated deep theory, you can embark on readings about enzyme specificity/history. $\endgroup$ – com.prehensible Sep 26 '18 at 13:39
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    $\begingroup$ By the way, nobody knows the precise science of enzyme binding and evolution, it's one of the most complex things in biology. you can learn lots of theories, dozens of well written research, about enzyme binding and evolution, for example here: plantphysiol.org/content/125/1/54 there's another website with all 10,000 or so enzymes known to science, and apparently 75k enzymes are expected in the human body, and a lot more proteins. So, in computing there is no parallel, and computers are good at simple biomimicry, but advanced copying of nature is generally too disorderly for pc's. $\endgroup$ – com.prehensible Sep 26 '18 at 13:50

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