I think your question reflects a problems with the way we “tell stories” to help students understand and remember concepts. A cell does not “know” what to do any more than a cloud “knows” what it’s doing. However, people understand and remember stories that have actors, so telling this kind of story can be helpful. (Pretending that non-human things have human characteristics is called “anthropomorphism”). For example, I might tell my students that a plant growing in a hot dry climate “wants to keep its stomata closed as much as it can so that it doesn’t dry out.” I don’t really think the plant “wants” anything; it’s just a shortcut for saying that plants that keep their stomata closed as much as possible in hot dry climates tend to leave comparatively more offspring than plants that do not.

Atoms do not “know” how to line up, their interactions occur as a result of forces like attractions between opposite charges. Many different molecules form on their own, but very few are self-replicating. DNA is. I don’t really have the time or space to get into the entire history of life, but DNA acts as a pattern for its “mirror image,” which can then act as a pattern for the original. No outside intelligence is needed, it is just due to forces within and between molecules. Cells do what they do because DNA can be used to make proteins that make the cell and control its actions. This is similar to the way a cloud forms, moves, and rains without any outside programming or will of its own.

This is a fantastic question because it means you are really trying to understand big questions. There are many areas of science and philosophy that you might want to explore.

Good question. It's still a mystery just how life got started.

Life, from what we can tell, is a chemical reaction. The "programming" of life is just what those chemicals do in the right amounts and in the right temperature, etc. This would imply that if you got all of the right chemicals together int he right amounts by sheer chance, you would get life. However, the first life that could have formed by such random interactions had to have been much simpler than even the simplest forms of life on the planet today, and even so no scientist has been able to make it happen in the laboratory. We don't know how it happened.

This is an excellent question, and it's a question that we know a fair bit about, but there are a lot of specific details that people are still working to figure out right now. In general though, the instructions that tell a cell what to do are encoded in the cell's DNA. The process by which it carries out these instructions follows from the laws of nature, biology, chemistry and physics. Essentially, all the functions of a cell are carried out by proteins, which are generally large molecules with a particular shape. These protein molecules are long chains that are folded in such a way as to develop a very particular shape that can help it do its job. These proteins do everything from helping you move your muscles to helping regulate the healthy functioning of a cell. The instructions for making the proteins are written into the DNA. In reality, the information in the DNA needs to be rewritten into RNA (a similar code, but using a slightly different language, so to speak). The code in the RNA is then "read" by ribosomes (other molecular machines made in a similar but slightly different way). These ribosomes read the code and start making the protein one piece at a time. The protein then begins folding in on itself to develop the shape it needs to fulfill it's job. There are a lot of details I'm glossing over here, but in general, that's how it works. This process is called the central dogma of biology and you can read more about it here.

As I've said, there are a lot of details still being worked out, but in general, molecules come together and interact through the usual physical and chemical laws that we know to produce all of the effects we see in biology today.

How all of this got started is another question, but the idea is that there are some molecules, that when put together, naturally start replicating themselves. For a more in depth treatment of this, you can watch this video: click here to watch video which has lots of information on this subject and more.

That's a fantastic question. A lot of times we use words like "programmed" or "designed" to describe how things like cells, and bodies operate. But this is a little misleading because, really, nobody sat down and planned out how it the cell was going to work, but rather the cell evolved. This means essentially that a very very long process of trial and error and some good luck occurred over millions of years to develop the cell as it is today. All the cells that operated poorly or inefficiently died out over this incredibly long time period while the best model to date is the one that we get to study today. This is a process called natural selection, and is the theory that the vast majority of scientists use to explain how organisms came to be the way we see them now.

The cells of the first organisms on the planet probably looked a tremendously different and a lot less complicated than today's cells. But the organisms that those cells created were also much less complicated and underwent many changes and mutations. The mutations that were unfavorable died out and the ones that were favorable survived. This process repeated itself over and over until present day, and it will continue into the future for as long as life on Earth continues.