First, what Mac OS are you using?
Secondly, what is the exact model of your MacBook Pro? Also, how much memory do you have?
Third, are you making backups to an external device?
Fourth, how much free space is left on your internal drive?
Now, for using Disk Utility to repair your internal drive, as long as you are using OS 10.7 or above, there is a hidden Recovery partition on your internal drive from where you would run Disk Utility to do the repair. This link describes how to boot to that partition, and what can be done from there:
https://support.apple.com/en-us/HT201314
One other thing: get rid of CleanMyMac! That software can cause more harm than good. As it is, you are doing some useful maintenance on your drive. You should also clean off anything you do not need. You should also consider using the excellent third party, free software called Onyx. That venerable product has been around for a long time, and it is rock solid. The version you need to obtain depends on which OS you are using. This link shows what versions are available (and you can download the applicable version directly form there):
http://www.titanium.free.fr/onyx.html
Additionally, if you have a "standard" hard drive (ie, not an SSD), it helps to optimize the drive, both at the Volume and Partition levels. I'm not sure if Disk Utility can do that efficiently. I have the excellent third party disk maintenance/repair software called TechTool Pro, and two of its useful features is Volume Optimization and File Optimization. I haver SSDs in each of my Macs, so Volume Optimization does not apply.
Finally, check your StartUp Items folders. There could be some software that starts up when you boot your machine which you do not need to run.