Assume that the sequence of bases shown below is present on one nucleotide chain of a DNA duplex and that the chain has opened up at a replication fork. Synthesis of an RNA primer occurs on this template starting at the base that is underlined.
In the intact RNA primer, which nucleotide has a free 3'-OH terminus?
3'.......GGCTACCTGGATTCA....5'

Verified step by step guidance

1. Step 1: Understand the problem. The DNA sequence provided is the template strand, and the RNA primer is synthesized complementary to this strand. The RNA primer starts at the underlined base, and we need to determine which nucleotide in the RNA primer has a free 3'-OH terminus.
2. Step 2: Identify the direction of synthesis. RNA primers are synthesized in the 5' to 3' direction, meaning the first nucleotide added will have a free 5'-phosphate group, and the last nucleotide added will have a free 3'-OH group.
3. Step 3: Determine the complementary RNA sequence. RNA bases pair with DNA bases as follows: Adenine (A) pairs with Uracil (U), Thymine (T) pairs with Adenine (A), Cytosine (C) pairs with Guanine (G), and Guanine (G) pairs with Cytosine (C). Use this pairing rule to transcribe the RNA primer starting at the underlined base.
4. Step 4: Locate the last nucleotide in the RNA primer. Once the RNA primer sequence is determined, identify the last nucleotide added during synthesis, as this will have the free 3'-OH terminus.
5. Step 5: Confirm the orientation of the RNA primer. Ensure that the RNA primer is written in the 5' to 3' direction, and verify that the nucleotide at the 3' end has the free hydroxyl (-OH) group.

Key Concepts

DNA Replication

DNA replication is the biological process by which a cell duplicates its DNA before cell division. It involves unwinding the double helix and synthesizing new strands complementary to the original template strands. This process is crucial for genetic continuity and is facilitated by enzymes such as DNA polymerase.

RNA Primer

An RNA primer is a short strand of RNA that provides a starting point for DNA synthesis during replication. It is synthesized by the enzyme primase and is essential because DNA polymerases cannot initiate synthesis without a free 3'-OH group. The RNA primer is later removed and replaced with DNA.

3'-OH Terminus

The 3'-OH terminus refers to the end of a nucleic acid strand that has a free hydroxyl group (-OH) attached to the third carbon of the sugar molecule. This free 3'-OH group is critical for the addition of new nucleotides during DNA or RNA synthesis, allowing the formation of phosphodiester bonds and elongation of the nucleic acid chain.