In terms of your question, it is very difficult to assess EXACTLY what your tax penalty will be given the limited amount of information. However, generally speaking, your penalty will be assessed based on the following factors:
1. The amount you underpaid
2. The timing of when your payment was due for each period and remained unpaid
3. An interest charge (which ranges approximately 4 to 5 percent as published by the IRS on a quarterly basis).
In basic terms, this means that you will be charged an interest penalty for failure to make proper payment on time. Please note that "catching up" in the fourth quarter for the total underpayment would not eliminate penalties for being late in the first, second and/or third quarters.
Estimated payment penalties are assessed on each of the four quarters of the year. So if you make additional payment in the fourth quarter to compensate for the shortfall in the prior three quarters, you will still be assessed a penalty since proper payment was past due for the first three quarters.
If you are interested on why your estimated payments are below the required amount, it is important to review IRS Publication 505. The publication states you may owe a penalty if the total of your estimated tax payments did not equal at least the smaller of: 1.) 90 percent of your 2009 tax or 2.) 110 percent of your 2008 tax if your adjusted gross income (AGI) is greater than $150,000 and 100 percent of your 2008 tax if your AGI is less than $150,000.
It seems as though you may have been paying 100 percent of your 2008 tax when you probably should have been paying 110 percent. That may be the reason for the underpayment but it is difficult to assess based on the limited amount of information. Also, note that there are special rules for farmers and fisherman if you fall under this category.
If you are interested in calculating the actual penalty yourself you would need to complete IRS Form 2210. IRS Form 2220 is used for calculating the penalty for corporations.