During the course of a criminal case, the District Attorney usually offers some type of plea agreement. As with most negotiations, the initial offer is a starting point and it is up to the criminal defense attorney to reach a reasonable plea agreement with the DA.
If you reject the plea offer and decide to proceed with a Motion to Suppress or take the case to a jury trial, the plea agreement is withdrawn by the DA. If the Motion to Suppress is granted or if you are found Not Guilty, the plea discussions are moot.
The "penalty" aspect occurs when the Motion to Suppress is not granted or your are found guilty at trial. Once the DA begins additional work, plea agreements can be come less favorable - especially if the evidence against you is strong.
If you are facing criminal charges, your attorney should discuss the benefits and pitfalls of suppression motions and trials before rejecting any plea agreements.