Question

Prompt: Coronavirus (Covid-19) is an enveloped virus. Enveloped viruses like Covid-19 are referred to as being “enveloped” because their virus particle is surrounded by a layer that resembles a cell membrane. The “Corona” part of coronavirus comes from the appearance of the virus particles under an electron microscope. Corona refers to “crown” or “wreath.” Proteins that stick out from the surface of the virus (called spike proteins) are responsible for the crown-like appearance.

Questions 1 and 2 I need help with:

1. To get sick by Covid-19, the virus needs to enter into our respiratory tract (nose or mouth). One way we can get infected by Covid-19 is by touching an infected surface and then touching our face.

Although alcohol-containing hand sanitizer does helps to protect us against Covid-19 and has certainly received a lot of press, washing our hands with soap and water is still the best and most effective approach to protect ourselves against the virus! Soap is an amphipathic molecule.

How does soap and water help to prevent infection by Covid-19? Use the details provided above and information you learned in the class to support your answer. Your answer should include a discussion about bonds and molecular interactions.

2. Spike proteins are transmembrane proteins that stick out from the surface of the virus particle. Covid-19 uses its spike proteins to attach to the cell when it is causing an infection.

What types of amino acids would you expect to find in the spike protein within the transmembrane portion of the protein? Conversely, what types of amino acids would you find in the spike protein at the top of the spike (ie. the region that is not in the envelope)? Explain your answer.

(By types of amino acids, I am not looking for specific names of amino acids. I want to know the characteristics of the amino acids that you would expect to find in these regions).

Answer 1

Corona Viruses are a family of viruses that have a characteristic spike protein crown resembling the crown, these are lipid enveloped viruses with single-strand RNA as genetic material. These virus particles possess these spike proteins (after which they are named Corona) that help them gain an entry in the host cells.
If you remember the soap is a detergent and thus has amphipathic nature. this means when you look at the chemical structure of the detergent or the soap molecules they have a hydrophobic tail and a hydrophilic head. By Hydrophobic I mean that it will repel water and thus would interact with the molecules of similar nature (the lipid layer of the coronavirus in our case) and the hydrophilic head group in the molecule will attract water or can easily interact with the water. So now say a person comes in contact with a surface that has coronavirus all over, there are chances that they will get those virus particles to stick to their hands. Once they get to use soap and water and thus wash their hands, they are bringing these amphipathic detergent molecules in contact with the virus, made up of lipid. That way the hydrophobic tail of the detergent will interact with the virus whereas the hydrophilic tail will interact with water and there would be the formation of micelles. That person will be continuously scrubbing their hands and that physical activity coupled with the formation of the micelles will lead to the destruction of the virus particles that were stuck on the hand surfaces. This way the soap and water can help prevent the infection by the SARS-CoV-2 virus.
Coming now to the second part of the question, you would have studied that the proteins are made up of amino acid monomers, polymerized by the amide linkages or the bonds. So there are 20 amino acids present in the body and have different chemical natures. Largely they could be grouped into polar and nonpolar amino acids. Polar amino acids are those which have the side chains that can easily interact with water or aqueous environment. Whereas the nonpolar amino acid is those that cannot do that and thus are hydrophobic in nature, this is largely due to the presence of the aromatic ring or uncharged chain in their molecular structure.
In order to answer the second question, you will also have to keep in mind the environment for the presence of the amino acids (thus the protein domain/protein they comprise). There are three locations for a protein to be present if it is associated with the lipid membrane (either surrounding a cell or a virus particle), Intracellular, extracellular in case of the cell, inside or outside the virus particle, and transmembrane, in case of both. Our focus would be on Coronavirus.

Now the transmembrane space is such that it has lipid molecules all over(for visualization imagine a sandwich model of the lipid bilayer), in that case, if a protein has to be present here in this space then it will have to have the stability and thus to help them maintain that the amino acids that make up that protein domain/component will have to be hydrophobic or nonpolar in nature, only that way this particular protein or protein domain can stay stable in the lipid, and thus transmembrane space. You can think of all the nonpolar amino acid's names which might make up the transmembrane domain of the protein (spike protein) (For example tryptophan, tyrosine, & phenylalanine). Thus the spike protein components that are embedded in the lipid membrane of the virus will have to be hydrophobic amino acids.

Coming to the exterior and interior side of the virus envelope, these two microenvironments will be aqueous in nature relative to the transmembrane. Thus the nature of the amino acids would be polar or hydrophilic in nature. This does not mean that all the amino acid that makes up the spike protein component, exterior or interior of the virus lipid membrane will be polar, but the majority of them. Over here you can think of some of the polar amino acids that can make up the exterior of the spike protein ( For an example glycine, alanine, serine & valine), Thus the spike protein components that are embedded/present outside the lipid membrane of the virus will have to be hydrophilic amino acids.