Question

Question 1. (33 points) a. (11 points) Briefly describe in words, and with a clear figure, how COVID-19 proteins would be digested into peptides after infecting a host cell? b. (11 points) Briefly describe in words, and with a clear figure, the ultimate fate of COVID-19-derived peptides following infection of a host cell? What specific host cell protein(s) bind COVID-19-derived peptides after they are digested and shuffled through the infected cell? Where would these protein(s) take digested COVID-19 peptides? c. (11 points) Briefly describe in words, and with a clear figure, what type of T cell (CD4+ or CD8+) would you predict to bind a digested COVID-19 peptide? In which part of the body would this binding occur? Which protein(s) on the T-cell and infected cell would participate in this intercellular interaction, and what are their functions?

Answer 1

Viruses are acellular organisms, most possess only one type of nucleic acid, either DNA or RNA and they reproduce only within living cells. All virions are constructed around a nucleocapsid core which is composed of nucleic acid (either DNA or RNA) held within a protein coat called capsid. Capsids are large macromolecular structures that self-assemble from many copies of one or a few types of proteins (protomers). The various morphological types of viruses primarily result from the combination of a particular type of capsid symmetry with the presence or absence of an envelope, which is a lipid layer external to the nucleocapsid. Viral Reproduction Viruses require host cell for reproduction, the first step in the life cycle of a virus is attachment to the host cell. This is followed by entry of either the nucleocapsid or the viral nucleic acid into the host. If the nucleocapsid enters, uncoating of the genome usually occurs before further steps can occur. Once free in the cytoplasm, genes encoded by the viral genome are expressed. This allows the virus to take control of the host's cell biosynthetic machinery so that new virions can be made. New virions are constructed by self-assembly of coat proteins with the nucleic acids, and finally the mature virions are released from the host.

ICTV Taxon (Baltimore System Group)	Genome Size (kbp or kb)	Nucleic acid	Capsid symmetry	Presence of envelope
Coronaviridae (IV)	27-31	RNA single stranded	Helical	Yes

Entry into the Host Cell

· Viruses penetrate the plasma membrane and enter a host cell shortly after adsorption. Adsorption to the host cell is mediated by an interaction between receptors on the surface of the host cells and molecules on the surface of the virion. Vertebrate viruses show tropism, they only infect certain organisms, and sometimes, certain tissues within the host.

· Fusion may involve envelope glycoproteins that bind to plasma membrane proteins. After attachement to the host cell, membrane lipids rearrange, the adjacent halves of the contacting membranes merge, and a proteinaceous fusion pore forms. The nucleocapsid then enters the host cell cytoplasm, where a viral polymerase, associated with the nucleocapsid, begins transcribing the virus RNA while it is still within the capsid.

· RNA viruses have one thing common: they must encode an RNA-dependant RNA polymerase; which is used to synthesize mRNA or to replicate the RNA genome. Viruses with positive strand RNA genome (like Coronavirus) most likely use their + strand RNA genome as a giant mRNA, and host ribosomes synthesize an enormous peptide that is often cleaved by both host and virus-encoded enzymes to form the mature proteins.

· RNA-dependant RNA polymerase catalyzes the synthesis of a (-) strand RNA from the (+) strand genome forming a ds-RNA called the replicative form. The replicative form is used as the template for synthesis of (+) strand RNA molecules.

· Sometimes, a polyprotein is synthesized from viral mRNA, which is later cleaved to give rise to all the peptides or proteins required by the virus to complete its life cycle. RNA-dependant RNA polymerase is able to initiate mRNA synthesis at internal sites along the template RNA. RNA splicing is also used to generate different transcripts and therefore different proteins.

Viral Proteins are presented as antigens:

1. Antigen presenting cells can internalize antigens by phagocytosis, endocytosis or by both. Once an antigen is internalized, it is degraded into peptides within compartments of the endocytic processing pathway. Internalized antigen moves from early to late endosomes and finally to lysosomes, encountering hydrolytic enzymes and a lower pH in each compartment.

2. Within the compartments of the endocytic pathway, antigen is degraded into oligopepetides of about 13-18 residues, which bind to class II MHC molecules (therefore should be presented to CD4+ T cells).

EXOGENDUS PATHWAY CLASS 0 MHC 7 CLASS I MHC bind invariant chain Blocking binding of antigen RER CLASS I MHC 1 @ Mhe is routed through Golgi to endocytic pathusay compartment ③ Invariant chain degraded 9 ③ CLIP fragment Exogenous Ag is taken up, degraded, routed to endocytic pathway compartments 6 HLA-DM mediates exchange of CLIP fragment for Ag peptide - PRESENTED TO CD4+ T CELLS