If you are having your income from 1099, it's your responsibilty to pay self employment taxes (Social security and Medicare) and you may have to pay income tax as well. While you can request the issuer of 1099 to withhold income taxes for you, mostly the issuers of 1099 don't withhold income taxes. To avoid owing taxes on your 1099 income at the time of tax filing, and also as per the IRS requirements, you should pay your taxes during the year also called as paying quarterly estimated taxes. This will also avoid you ending up paying interest/penalty later on.
To determine the amount of estimated taxes you should pay every quarter, you can calcuate your annual taxes using this TurboTax Tool. Once you know your estimated annual tax liability you calculated using the tool (Income tax and Self employment tax) you can divide the estimated tax liability by 4 and pay tax to the IRS. You can adjust the amount of your tax liability in the subsequent quarters based on increase or decrease in your income during the year. You can pay the quarterly taxes to the IRS on the due dates provided in this IRS link. You may send estimated tax payments with Form 1040-ES by mail, pay online, by phone or from your mobile device using the IRS2Go app. Visit Payments to view all payment options. When you file your Income Tax return, you may have a refund or you may have some tax laibility, this will be calculated based on your actual income and the taxes you already paid during the year. If you have a tax liability, it may not be that big at the end of the year because of quartely payments you made to the IRS during the year.
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