Having a form as below, what should I do to my database or how should I structure my database so that for instance, a particular user will have all the three entries attached to him:
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<html>
<form action="processForm2.php" method="post">
        <p>First Entry</p>
        <div id="original">
        <select name="subject[]">
        <option>English</option>
        <option>Mathematics</option>
        <option>Physics</option>
        <option>Chemistry</option>
        <option>Biology</option>
        </select>
        <select name="grade[]">
        <option>A</option>
        <option>B</option>
        <option>C</option>
        </select>
        <select name="year[]">
        <option>2012</option>
        <option>2011</option>
        <option>2010</option>
        </select>
        </div>
        <p>Second Entry</p>
        <div id="original">
        <select name="subject[]">
        <option>English</option>
        <option>Mathematics</option>
        <option>Physics</option>
        <option>Chemistry</option>
        <option>Biology</option>
        </select>
        <select name="grade[]">
        <option>A</option>
        <option>B</option>
        <option>C</option>
        </select>
        <select name="year[]">
        <option>2012</option>
        <option>2011</option>
        <option>2010</option>
        </select>
        </div>
        <p>Third Entry</p>
        <div id="original">
        <select name="subject[]">
        <option>English</option>
        <option>Mathematics</option>
        <option>Physics</option>
        <option>Chemistry</option>
        <option>Biology</option>
        </select>
        <select name="grade[]">
        <option>A</option>
        <option>B</option>
        <option>C</option>
        </select>
        <select name="year[]">
        <option>2012</option>
        <option>2011</option>
        <option>2010</option>
        </select>
        </div>
    </form>
    </html>

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To submit my data to the database in mysql, I tried using a table "course" in a database with the respective numbers of Columns "email"(Primary key), "subject", "grade", "year". It complained of duplicate entries (Primary key). But when I changed the structure of the "course" table to "Id_no"(Primary key), "subject", "grade", "year", the data was submitted. But herein lies the big question? How do I associate the three entries to that one particular user using his email or his user ID???
PLEASE YOUR HELP WILL BE APPRECIATED!

Your case can be solved by using composite key (2 or more column together makes primary key of table)
You can make (email_id, subject, year) as primary key

If You already having single column primary key "id_no", so in that case make unique key of (email_id, subject, year)

So what you are saying is about me using a three primary key structure?
Well, what about me using something like this below:

Login_table: {"email_id", "Password"}.
Courses_table: {"Subject_id","grade", "year", "email_id"}.
Subject_id: {"Subject_id", "Subject"}.

yes, you are right

For courses table

Case 1 (if one person is going to learn subject only once in life time)
keep 2 cols (subject_id, email_id) as primary key

Case 2 (if one person is going to learn same subject again next year due failure)
keep 3 cols (subject_id, year, email_id) as primary key