I got a sign-in bonus $5000 from the company that hired me,and was given a 1099-misc with report $5000 in box 7. how should I report this on my 1040? Can I pay employee's portion of combination of Social Security and Medicare(7.65%) only, instead of paying both the employee's and employer's portion(7.65% x 2)?

1099-misc (nonemployee compensation) income:
You will report your income and business related expenses on schedule C or C-EZ (Form 1040). Then you put net income (or loss) on line 12 of Form 1040. This income is subject to SE tax at 15.3% (this is shown on line 57 of Form 1040).
Even though schedule C treats you as a self employed, which may not be correct for you, this is how you must report this income. Your U.S. Tax Return: Tax Filing by Self Employed Sole Proprietor or Independent Contractor