The pricing guide has this to say;
The number of I/O requests to storage made by your database instance depends on your queries, workload and data set. Cloud SQL will cache data in memory to serve your queries efficiently and to minimise the number of I/O requests.
In other words, neither of the two options, some queries may be served entirely from memory, generating no I/O, while some may generate many I/O requests. Optimising the database well with indexes will make your queries cheaper, generating table scans over large tables will cost more.
In short, same good practice rules apply as keeping a fast database as on a local machine, but not doing the optimisation won't just make your queries slower, but make them cost more.
Source: http://stackoverflow.com/questions/17633923/how-is-one-i-o-measured-in-google-app-engine
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