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What are the senses of 'spike protein' in the context of sars-cov-2? Please give me an idea of how many 'spike proteins' in each sense there would be per spike, and per virus, to help me get an idea of what exactly is being referred to in each sense of the phrase.

Here are some actual examples:

https://childrenshealthdefense.org/defender/moderna-pfizer-vaccines-blood-clots-inflammation-brain-heart/ The injected spike protein was also found in the lung, spleen, kidney and liver of the mice. [The protein here is clearly more than one molecule.]

https://www.news-medical.net/health/What-are-Spike-Proteins.aspx The viral envelope of coronaviruses is typically made up of three proteins that include the membrane protein (M), the envelope protein (E), and the spike protein (S). [The protein here is clearly more than one molecule.]

https://www.sciencenewsforstudents.org/article/explainer-what-is-a-spike-protein Members of the coronavirus family have sharp bumps that protrude from the surface of their outer envelopes. Those bumps are known as spike proteins.[Sounds like individual molecules are being referred to this time. By the way, "sharp" is flat wrong, no pun intended, since the bumps are not pointed and hence "spike" is a bit of a misnomer. "Stud" or "knob" would seem to make much more sense and indeed they are often referred to as "studs".]

https://globalbiodefense.com/2020/12/22/what-is-the-spike-protein-and-why-are-mutations-on-it-important/ The spike protein is composed of a linear chain of 1,273 amino acids, neatly folded into a structure, which is studded with up to 23 sugar molecules. Spike proteins like to stick together and three separate spike molecules bind to each other to form a functional "trimeric" unit.['up to'? Wouldn't it be a different molecule if it had a different number of 'studs'? The spike molecule is one and the spike molecule is three? Doesn't the spike molecule have a unique name? How about I coin one: 'the thousand two hundred seventy-three plus sugars molecule'? But it does sound like individual molecules are being referred to.]

https://en.wikipedia.org/wiki/Peplomer "Peplomer (sic)[Gr. peplos = robe, (woman’s) dress + Gr. meros = part] (also called a spike) is one of the knoblike structures (spikes), generally composed of glycoproteins (spike protein (sic)), projecting from the lipid bilayer of the surface envelope of an enveloped virus." but on the side of the same part of the page is the image of a single peplomer (correct me if I'm wrong) https://upload.wikimedia.org/wikipedia/commons/thumb/0/02/Novel_Coronavirus_SARS-CoV-2_Spike_Protein_%2849583626473%29.jpg/330px-Novel_Coronavirus_SARS-CoV-2_Spike_Protein_%2849583626473%29.jpg which is captioned: "3D print of the peplomers (sic) of SARS-CoV-2". [glycoproteins are spike protein?; a single peplomer is peplomers? Also, I see six colors in that peplomer. How does that fit with it being a 'trimer']

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    Your question needs prior research. Specifically, you need a basic understanding of what proteins are. You seem to be mixing them up with molecules – Carey Gregory Apr 17 at 15:47
  • 1. I have done a lot of amateur research about this and I have read a lot about proteins and about the sars-cov-2 virus and related matters. In my opinion the fault lies with the scientists who are attempting to communicate with the intelligent lay person, and are not being clear about in which sense the word 'protein' is being used. 2. You are the one who is mixed up. Proteins are molecules. Please look up the word. – Matthew Christopher Bartsh Apr 17 at 22:28
  • "Proteins are large, complex molecules that play many critical roles in the body." -medlineplus.gov/genetics/understanding/howgeneswork/protein – Matthew Christopher Bartsh Apr 17 at 22:31
  • medicinenet.com/proteins/definition.htm Proteins: Large molecules composed of one or more chains of amino acids in a specific order determined by the base sequence of nucleotides in the DNA coding for the protein. – Matthew Christopher Bartsh Apr 17 at 22:33
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    There are way too many questions here. Narrow it down to one. – Bryan Krause Apr 18 at 3:46
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From Wikipedia:

The spikes are the most distinguishing feature of coronaviruses and are responsible for the corona- or halo-like surface. On average a coronavirus particle has 74 surface spikes.[54] Each spike is about 20 nm long and is composed of a trimer of the S protein. The S protein is in turn composed of an S1 and S2 subunit.

So, a spike protein in its native conformation is a single protein consisting of a trimer of a 2-subunit dimer. "Quaternary structure" is a critical organizing feature of proteins, and it's typical to refer to a cluster of polypeptide chains as a single unit, and occasionally to refer to the individual components as separate proteins as well if they tend to function both together and separately. Anyone working in biology is familiar with this. Additionally, in case it isn't clear, a "protein" is not necessarily a covalently linked chain of atoms like a polypeptide chain is, but may instead be held together in part by hydrogen bonds or other intermolecular forces.

"Protein" is often used as an uncountable noun, for example when talking about protein in diet when someone says a meal has "10 g protein" you do not infer they mean a single polypeptide weighing 10 grams. Like "fish" and "fishes", plural "proteins" often refers to "multiple varieties of protein" rather than "multiple molecules". In other cases, when it makes sense to count individual molecules, protein can also be used as a countable noun.

The injected spike protein was also found in the lung, spleen, kidney and liver of the mice

This refers to multiple protein molecules (obviously), all of the same uncountable category ("spike protein").

The viral envelope of coronaviruses is typically made up of three proteins that include the membrane protein (M), the envelope protein (E), and the spike protein (S).

This refers to three types of protein that "make up" the viral envelope; that is, the viral envelope is made up of constituent parts of these types. The number is not specified, but you can safely assume it's used in the uncountable noun sense.

Members of the coronavirus family have sharp bumps that protrude from the surface of their outer envelopes. Those bumps are known as spike proteins

Each bump is, like written above, an individual trimer. The author here is using protein as a countable noun which nonetheless makes sense here because they are not talking about spike protein contained in some soup, but rather the individual "spikes" visible under a microscope that each consist of a single fully assembled spike protein.

The spike protein is composed of a linear chain of 1,273 amino acids, neatly folded into a structure, which is studded with up to 23 sugar molecules. Spike proteins like to stick together and three separate spike molecules bind to each other to form a functional "trimeric" unit

Spike proteins are glycoproteins, so they aren't just an amino acid chain, they are modified with sugars. I infer from this sentence that there is some probability that the number of attached sugar molecules varies. It's still the same protein just like a boat is a boat no matter how many crew members you put on it. One can still assume that the function of the boat depends somewhat on the crew members yet it isn't a different boat if the crew is absent. This paragraph is clearly not written for an expert audience; someone is trying to describe the biology in terms for an interested but non-technical audience. That said, there's nothing wrong with them referring to both the individual polypeptide subunits as "spike protein" as well as the assembled trimer as "spike protein".

If you wanted to be specific about the S1 and S2 subunits or the individual component molecules you would use specific language to do that, but it gets incredibly clunky in descriptive language to refer to biological molecules by long, complicated, definitive names, as well as clunky and confusing to create new names for each to keep them separate. You're probably familiar with other proteins referred to this way, for example you may be familiar with hemoglobin, the protein that assists in carrying oxygen in blood. Hemoglobin is a heterotetramer made out of two alpha and two beta subunits. HBA1 is a protein. HBA2 is a protein. HBB is a protein. Two HBA1 proteins with two HBB proteins together makes one hemoglobin protein.

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  • Anyone writing for the public (and maybe sometimes also for professionals) should take pains to be clear, even if it involves using a few extra words. For example, if you mean "a mixture of five types of protein", you shouldn't just write "five proteins". Likewise, if you are referring to five protein molecules, you shouldn't just write, "five proteins". A bit of clunkiness is a small price to pay for clarity. Seemingly you think my question was not a useful one. People can skim over long names and yet benefit a lot from them, because they can see what is what. – Matthew Christopher Bartsh Apr 30 at 18:43
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    @MatthewChristopherBartsh I read all your examples and their usage is correct and clear to the intended audience in every one of them. I find your grammatical critique rather pedantic and pointless. You should write to the editors of the journals that published the articles and recommend that they do better editing. – Carey Gregory May 1 at 0:54
  • @CareyGregory The writing is unclear. The topic is of great importance. The intended audience was laymen at least in part in every case. There's nothing pedantic about pointing that out. I find your objections rather saddening. – Matthew Christopher Bartsh May 1 at 1:16
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    @Matthew The thing is, the public doesn't need those details. They have no relevance to someone who can't gather exactly what is needed, whereas an expert (or just someone with general biology experience, like me - I'm a neuroscientist and hardly work with molecular biology at all) does understand it. If you were to spell everything out then the articles would get extremely long - it wouldn't be just the one case you identified here, it would be all the other language too. Language that is overly verbose is not good at conveying anything because it loses focus on what matters. – Bryan Krause May 1 at 3:04
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    @Matthew I think you've come to StackExchange mostly to argue your ideas about language, to suggest the whole world change to conform to your ideas. That's not the purpose of the site and it's going to just lead to your disappointment. – Bryan Krause May 1 at 14:06

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