With food, we consume proteins, but they do not get into our organisms. Instead, amino acids, of which they are made, do. Of these amino acids, we build our own proteins. And redundant amino acids (those that have not been used for making our proteins) are converted into glucose or are utilized in some other way. If we already have more than enough of glucose, the additional glucose made from amino acids (as well as all excess amounts of glucose) are converted into fats that are stored in our fat tissue.
Proteins are long chains of amino acids twisted in complex spatial structures. In a protein, both the sequence of amino acids in the chain and the spatial structure of the chain are important.
In living organisms, a part of proteins act as structural elements, like, for instance, collagen, which forms connecting tissues, tendons and ligaments, and is present in our bones and skin (in fact, collagen is not a single protein, but a whole group of proteins; there ae whole 28 types of collagen).
A considerable part of proteins are nanomachines. They perform certain functions. For instance, special proteins in our muscles facilitate contraction of our muscles, when the muscle cells receive certain signals. A special protein called hemoglobin transports oxygen to the cells of the organism and takes away carbon dioxide from them. Certain proteins in the membranes of the cells react to hormonal and other chemical signals (are receptors). A part of hormones are proteins (while others are steroids). Enzymes are proteins that facilitate or control certain biochemical reactions. All these nanomachines require energy for their operation, and they get it from the ATP molecules.
Since proteins are "machines", admission of such "machines" from another "factory" into our can be dangerous. And some of those "machines" (for instance, certain proteins of viruses and bacteria) are specially designed as "machines of war", weapons to attack our organism. This is why we do not absorb proteins from food, but disassemble them into "spare parts" and then absorb them (that is, amino acids). Appearance of any alien protein in our organism is perceived by our immune system as an alarm signal. Though, some simpler proteins are almost or completely the same in all organisms of a certain biological species or even several species. But even such proteins are disassembled before they are consumed, just in case, to avoid possible unexpected complications.
Amino acids are organic molecules composed of atoms of carbon, hydrogen, nitrogen and oxygen. In total, around 500 different amino acids are known. Besides, amino acids can be "right-handed" (R) or "left-handed" (S), like one of them is a reflection of the other in a mirror And the property of the same molecule are substantially different depending on whether it is R or S.
For making proteins of all living creatures on Earth, only 22 amino acids are used. Of them, 20 amino acids are encoded in the genetic code, and two more are added only to certain proteins in a different way (not through genetic encoding). One of these "uncoded" amino acids is present only in proteins of some bacteria, but not in our proteins.
Only one amino acid of those used by all forms of life on Earth is right-handed (R) – this is cysteine. All other amino acids of all forms of life on Earth are left-handed (S).
Short chains of amino acids (up to 10 in a chain) are called peptides. A peptide may have a special function of its own or as a part of a protein. Chains from 10 to 100 amino acids are usually called polypeptides, and those longer than 100 amino acids, proteins. Sometimes, any proteins are called polypeptides. Typical proteins include from several hundreds to several thousands of amino acids. The longest known protein contains around 27 thousand amino acids.
Eight out of 20 "encoded" amino acids, and one "unencoded", are "essential" (a better word would be irreplaceable) for us. We can obtain them only from food. Six amino acids are "conditionally nonessential", that is, we can synthesize them out of other amino acids, but not always. When there are certain metabolic disorders, they are not synthesized, and food becomes their only source. And six amino acids are "nonessential", that is, we can synthesize them out of other amino acids.
People on a vegetarian and, especially, vegan diet, need to ensure that all essential amino acids are present in their food in sufficient quantities. In certain plants, some of the essential amino acids may be absent or present in a very insufficient quantity. Therefore, such combinations of plants should be chosen that ensure all essential amino acids.
In proteins of the animal origin, all the amino acids we need are present in proportions that are close to those we need. Especially close these proportions are in red meat. Meat also contains most of the vitamins and minerals we need, but it does not contain omega-3 fatty acids (ALA, EPA, DHA) and does not contain fiber at all.
While working either as structural elements, or nanomachines, proteins eventually wear out and need replacement. This process of replacement continues all the time, for which cells synthesize proteins they need.
Structures of proteins are encoded in the genetic code (genome). The human genome contains between 20 and 22 thousand genes (different numbers in different people). Each gene is a separate code. But it encodes not just one protein, because not only the code as such is important, but also the way of its interpretation and implementation of this interpretation for the synthesis of proteins. This is why the total number of proteins encoded in our genetic code is estimated to be from 800 thousand to over 2 million.
For producing a protein, a cell makes a copy of the genetic code from a DNA molecule into a special RNA molecule, which is called mRNA. This molecule is then delivered to a "protein factory" – ribosome, which produces the required protein according to the provided "technical specification" in the form of the mRNA.
Obviously, for making a particular protein, all necessary spare parts (amino acids) must be available in sufficient quantities.
A source of amino acids can be not only food, but also disassembly of damaged proteins into spare parts, that is, into amino acids. These spare parts are then sorted, and most of them can be reused for new proteins. In hard times, when there is a shortage or no food for a long time, proteins of lower priority can be disassembled into amino acids for renewal of the most prioritized proteins.
In the organism, an excess of amino acids may occur, if we consume too much proteins. Or an excess of only certain amino acids may occur, if their fraction that we get from food exceeds the fraction required for making our own proteins. Excess amino acids are converted into glucose and are used as fuel, or are converted into substances that can be removed from the organism. Some of the substances produced in this process are poisonous. There is even such a condition – protein poisoning. It occurs in people who have to consume proteins almost exclusively because of the lack of other food, or consume too much proteins for some other reason.