What do proteins and amino acids manipulate?

Which things do proteins and amino acids change?

Amino acids are the building blocks of proteins, much like Lincoln Logs would be used to construct a model of Fort Ticonderoga.

Proteins are to all living things what resistors, transistors, and capacitors are to integrated circuits. In other words, proteins are the building blocks of life.

In a nutshell, they do not influence any component of you; instead, they make up who you are. One more example of “resistors, transistors, and capacitors” being used to achieve a particular effect is the formation of bones and other tissues during early gestation caused by specific genes’ actions.

Genes can be thought of as being analogous to the microprogramming found in a computer. Genes are responsible for encoding proteins, but the proteins themselves are not nearly as essential as the genes that provide their instructions.

It is probably as clear as mud. Perhaps someone else can explain it more transparently and concisely.

Why are amino acids known as amino acids?

At last, biology gives us a useful name! Like other building blocks that cells use, amino acids have parts that are the same and parts that are different.

In the case of amino acids, the common parts are used by the assembly machine (the ribosome) to put together each of the different parts. There are 20 amino acids, but they all have the same chassis.

Now, to your question! The basic building blocks of amino acids are:

An amino group (-NH2)
a carbon in the middle, called the “alpha carbon.” This carbon connects to the parts of the chassis as well as the amino acid’s “side chain” (also called the “R group” in the image below) or unique part.
a carboxylic acid group (-COOH)

So, an amino acid gets its name from the parts that all of its group members have in common. As shown in the image below from Wikipedia, these common elements are directly involved in “stitching together” a chain of amino acids, or making a protein: the carboxy group of one amino acid is joined to the amino group of the next… …and on and on and on…

Just so you know, these common parts are also used in alpha helices and beta sheets, which are two of the most common parts of the secondary structure of proteins.

Do all of the proteins we eat get broken down into amino acids and have no effect on us?

The short answer is no, but it’s not often that the proteins we eat have an effect on us. The vast majority of proteins do break down, and in almost all cases, they can no longer do their jobs. Even proteins that don’t break down almost never do anything similar to what they were made to do (think proteins involved in shell formation or plant fiber). Still, there are some exceptions.

Allergens. Powerful allergens can cause immune reactions before they are broken down. Of course, this often has bad or even deadly effects on the person using it.
Gut enzymes. What I mean is that some enzymes will continue to work in the gut for a short time after being eaten. Lactaid, which people who can’t digest lactose take to help them digest dairy, is the best example of this. These enzymes, on the other hand, usually only work for a short time and almost always only in the gut.
The disease that makes cows go crazy. This is the most scary example that comes to mind. Creutzfeldt-Jakob disease, which is like mad cow disease in people, is caused by a protein that can sometimes get into the bloodstream from the digestive tract. From there, the protein can sometimes cross the barrier between the blood and the brain. Depending on how similar the species is to humans, this can sometimes lead to a cascade of proteins that don’t fold right. This causes proteins to stick together in the brain, which causes the brain to turn into Swiss cheese. Not fun. It happens rarely, but often enough that people who lived in the UK in the 1990s can’t give blood in the US (or at least that used to be the rule). I don’t know if it still is).
Organisms that spread disease. This is a bit of a trick because the protein comes from a different living thing. Also, bacteria and other microbes make a lot of toxins that can hurt or kill humans if they eat them. Probably not what the person asking the question meant.

All of this being said, there are a number of products that make questionable claims about how the protein in them will help your health. The only functional proteins that could have a noticeable effect because of what they do naturally are the digestive enzymes that were talked about above. Even that is not very likely.