What is difference between High quality and low quality proteins
"Low quality" vs. "high quality" protein does not refer to anything about the linkages between amino acids in proteins. Instead, these terms are used in a nutritional context to refer to whether an individual protein source is sufficient as a sole source of protein in someones' diet.

Essential amino acids are the amino acids that humans cannot synthesize; other amino acids can be synthesized from these, but they do not need to be part of the diet. Not all sources of protein have sufficient quantities of all of the essential amino acids. Low-quality protein sources are also referred to as "incomplete" and high-quality sources as "complete."

Meat products are typically "high quality" because they contain all of the essential amino acids together. Therefore, if you subsisted on various foods but only got your protein from one animal source, you would be okay.

Some plant products do not have all the essential amino acids in large concentrations. However, if you combine protein sources from different "low quality" plant sources that together cover these deficiencies, there is no disadvantage compared to a single "high quality" source.

In the digestive process, all you take out of the proteins you eat is the individual amino acids (generally): that means that only the amino acid composition matters, not the strength or quality of the bonds between amino acids. If someone tries to tell you otherwise, they are probably just trying to sell you something.

Here is a paper that talks about some of these issues, and addresses some of the myths about balancing proteins. The quick summary is that problems develop if you get your sole protein from a source that is low in a particular essential amino acids over a long time period, but there is no need to ensure every meal contain all the amino acids.

It is possible for people on unusual protein diets, either because they are avoiding animal products or using incomplete protein supplements, to develop a particular amino acid deficiency. Otherwise, as long as all amino acids are supplied, there is no difference on health or muscles to consuming "low quality" vs "high quality" proteins.



References:

Young, V. R., &amp; Pellett, P. L. (1994). Plant proteins in relation to human protein and amino acid nutrition. The American journal of clinical nutrition, 59(5), 1203S-1212S.