Stangely I do not remember any arrows seen. Maybe there was a difference in the variants of the paper done right? One of them had active transport, other had facilitated diffusion because the question specifically said 'the concentration of the calcium ions inside the cell is thousand times less than the concentration outside.' How do these ions move into the cells?
The ions can only move into the cells by facilitated diffusion in that case.
I think there was a variation in the question in both the variants.
That energy level had to do with denitrifying bacteria and decomposing bacteria present in the soil which would increase the energy flow by decomposing amino acids found in tissues (decomposing) and by decomposing the nitrogen compounds to nitrogen (denitrifying bacteria). Mostly denitrifying bacteria as they obtain energy directly by breaking down nitrogen compounds while decomposing bacteria obtain energy by feeding on dead tissue.
For that TMP-1 structure, it had to do with DNA unwinds, mRNA replication, moves out, ribosome, translation, amino acid coded and finally packaged by the Golgi body and leaves via the cell membrane. A number of organelles could be involved from nucleolus to nucleus to ribosomes to Golgi body to cell membrane.
Hopefully the paper was not that bad.
A change in genetical code would result in mutation and would result in different cells hence repair, growth would not be able to take place. In other words, yes characteristics would be changed of the cell.