Revised/commented

function executeOperationsOnNumbers(op)
{
    var num;
    // - Begin switch
    switch(op)
    {
        // - Begin first case
        case "checkPrime":
            var sum;
            // - Begin while loop
            while (true)
            {
                var data = window.prompt("Enter a positive number:");
                var number = parseInt(data, 10);
                sum = checkPrimeNumber(number);
                if (sum == true)
                {
                    break;
                }
            }
            // - End while loop
            //   Why is the below in braces {}?
            {
                var num = + number + " is a prime number"
                window.alert(num);
                output.innerHTML = num;
                console.log(num);
            }
            // - Each case should end with a break if the next
            //   case isn't supposed to execute as well
        // - End first case
    }
    // - End switch

        // - Begin second case - this needs to be inside the switch
        case "findPrime":
            var sum;
            // - Begin while loop
            while (true)
            {
                var data = window.prompt("Enter a positive number:");
                var number = parseInt(data, 10);
                sum = findPrimeNumbers(number);
                if(number > 0)
                {
                    break;
                }
            }
            // - End while loop
            //   Why is the below in braces {}?
            {
                var num = "There are " + sum.length
                + " prime numbers <= " + number + "\n"
                + "Prime Numbers <= " + number + ": " + sum

                window.alert(num);
                output.innerHTML = num;
                console.log(num);
            }
            // - Each case should end with a break if the next
            //   case isn't supposed to execute as well
        // - End second case

        // - Begin third case - this ALSO needs to be inside the switch
        case "calcSum":
            var sum;
            while (true)
            {
                var data = window.prompt("Enter a positive integer:");
                var number = parseInt(data, 10);
                sum = calculateSum(number);
                if (Number.isInteger(sum) && sum> 0)
                {
                    break;
                }
            }
            var num2 = "The sum of the integers from 1 to " + number + " is " + sum;
            window.alert(num2);
            output.innerHTML = num2;
            console.log(num2);
            // - Each case should end with a break if the next
            //   case isn't supposed to execute as well
        // - End third case

        default:
            console.log('default');
}