First three Groups with Highest Marks should have specific points

Question

my table

+------+-------+---------+-------+--------+
| Name | Group1| Section | Marks | Points |
+------+-------+---------+-------+--------+
| S1   | G1             


        

Answer 1

You can do an update join to achieve what you want;

UPDATE students
JOIN (
  SELECT marks, (@sp:=@sp-2) a
  FROM (
    SELECT distinct marks FROM students
    WHERE section='class1' AND group1 IS NOT NULL
    GROUP BY group1 ORDER BY marks DESC LIMIT 3
  ) b, (SELECT @sp:=7) c
) d
SET students.points = d.a 
WHERE students.marks = d.marks
  AND section='class1'
  AND group1 IS NOT NULL;

(posted this answer also to your second question where you seemed to ask for an update statement without noticing that it was a duplicate, moved it here)

An SQLfiddle to test with.