sarah99 let me see if I can help!
- Interferons have antiviral properties, so they're going to try and stop virus replication. In order for viruses to replicate, they're going to take over a host cell and its gene expression machinery, meaning interferons will pause gene expression to prevent viral proteins from being produced (aka preventing viral replication). I'm assuming it would just be preventing gene expression of viral genes, not the cell's genes. That said, the cell would probably have to be cleared from the body anyway because it's already virally infected. The interferons will just prevent the virus from spreading further.
- No. The proteome includes all the proteins expressed in an organism. This includes MHC I, but also other proteins in the organism too.
- Viruses and tumours/cancerous cells can downregulate the expression of MHC I markers, meaning they can be absent. Some may be present, presenting viral or tumour/cancer peptides (i.e. antigens). Some would function abnormally as well. NK cells will just look to see if normal MHC I markers are being expressed or stressed/abnormal markers, and if there's been any downregulation in the number of MHC I markers.