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If you want to backup all databases, users, and authentication:

# mysqldump -u root -p --all-databases > d:\alldatabases.sql

This will prompt you for the root password, save all of the databases including the users and authentication information. Everything is saved.

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If you want to restore all databases then use

# mysql -u root -p < d:\alldatabases.sql

This will prompt for password and then restore all of the complete mysql databases and users with authentication.

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If you want to backup a specific database called companydb:

# mysqldump -u root -p companydb > d:\companydb.sql

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If you only want to restore a single database called companydb:

# mysql -u root -p companydb < d:\companydb.sql

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If you are upgrading to a more recent version, then it is good to run mysql_upgrade:

# mysql_upgrade -u root -p

This will both attempt to configure the tables properly and check for errors.