Question

Kornberg showed that nucleotides are added to the 3 '-end of each growing DNA strand. In what way does an exposed \(3^{\prime}\) - OH group participate in strand elongation?

Short answer

Short Answer: During DNA replication, the exposed 3'-OH group in a growing DNA strand participates in strand elongation by forming a phosphodiester bond with the phosphate group of the incoming nucleotide. This reaction is catalyzed by DNA polymerase, which reads the template strand and adds complementary nucleotides to the new strand. As new nucleotides are added to the 3'-end of the growing strand, the DNA strand extends in the 5'-3' direction.

Step-by-step solution

Understand the basic structure of DNA

DNA is a double-stranded, helical molecule composed of nucleotides, which are the building blocks of DNA. Each nucleotide consists of a sugar (deoxyribose), a phosphate group, and a nitrogenous base.

Understand the directionality of DNA strands

Each DNA strand has a 5' end and a 3' end. This notation represents the carbon atoms in the deoxyribose sugar molecule. The phosphate groups are attached to the 5' carbon atom, and the OH groups are attached to the 3' carbon atom. The two strands in the DNA double helix are antiparallel, meaning their 5'-3' orientation is opposite to each other.

Explain the role of DNA polymerase

During DNA replication, an enzyme called DNA polymerase is responsible for adding new nucleotides to the growing DNA strand. The polymerase reads the nucleotide sequence on the template strand and adds complementary nucleotides to the new strand.

Describing the role of the 3'-OH group in strand elongation

During DNA replication, the exposed 3'-OH group of a growing DNA strand participates in strand elongation by forming a phosphodiester bond with the phosphate group of the incoming nucleotide. DNA polymerase catalyzes this reaction, where the phosphate group of the new nucleotide is released, and the 3'-OH group on the growing strand attacks the alpha-phosphate of the incoming nucleotide, creating a new phosphodiester bond and extending the strand by one nucleotide. This process of adding new nucleotides to the 3'-end of the growing DNA strand continues until the entire template strand is replicated, ensuring that the new strand forms in the 5'-3' direction, which is complementary to the template strand.

Key concepts

The 3'-OH Group

In the structure of DNA, the 3'-OH group plays a vital role in the process of DNA replication. Located at the end of the growing DNA strand, it is attached to the 3' carbon of the deoxyribose sugar. This strand end is crucial because it is specifically where new nucleotides are added during replication.

The presence of the 3'-OH group enables the strand to elongate by forming a bond with an incoming nucleotide. This happens through a chemical reaction where the 3'-OH group attacks the phosphate group of the new nucleotide. This reaction not only helps to link the nucleotides together but also sets the direction in which the DNA strand elongates.

• The 3'-OH group ensures elongation towards the 3'-end of the strand.
• It plays a key role in establishing the structural directionality of DNA.

Understanding the importance of the 3'-OH group is fundamental to grasp how DNA copies itself during cell division.

DNA Polymerase

DNA polymerase is the pivotal enzyme in the process of DNA replication. It is often described as the 'builder' of the DNA strand. Its primary role is to read the original DNA strand, called the "template strand," and add matching nucleotides to build a new complementary strand.

During this process, DNA polymerase has a specific direction in which it works. It can only add new nucleotides to the 3'-end of a growing DNA strand. Because of this, the enzyme moves along the template strand in a 3'-to-5' direction while synthesizing the new strand from 5' to 3'.

• Reads the nucleotide sequence of the template strand.
• Adds complementary nucleotides to the new strand.
• Requires a primer to start synthesizing a new strand.

DNA polymerase is essential for accurate DNA replication, ensuring that the genetic information is copied correctly and passed on to the next generation of cells.

The Phosphodiester Bond

A key feature in the structure and function of DNA is the formation of phosphodiester bonds. These bonds are connections between the sugar of one nucleotide and the phosphate group of the next nucleotide. They form the "backbone" that links nucleotides together into a long, stable strand.

When DNA polymerase adds a nucleotide to a growing DNA chain, a phosphodiester bond is formed between the existing 3'-OH group of the last nucleotide and the phosphate group of the new nucleotide.

• Creates stability and continuity in the DNA strand.
• Ensures the integrity and proper sequence of DNA.

Without phosphodiester bonds, the DNA strand could not maintain its essential double helix structure. This bond formation is an energy-dependent process, often using the energy released from the cleaving of phosphate groups.

Antiparallel Strands

Understanding the concept of antiparallel strands is crucial to grasping DNA's structural configuration. DNA is composed of two strands that twist around each other to form a double helix. These strands run in opposite directions, a feature that is described as being "antiparallel."

In an antiparallel arrangement, one strand is oriented in a 5' to 3' direction while the opposite strand runs 3' to 5'. This orientation is vital for the interactions between the strands, such as hydrogen bonding between complementary base pairs, and for the proper functioning of enzymes like DNA polymerase during replication.

• Facilitates the correct alignment and interaction between the two strands.
• Essential for the semiconservative replication of DNA.

The antiparallel nature is foundational to DNA's ability to carry and transmit genetic information during cell division, ensuring each new cell receives an accurate copy of genetic material.