Question

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

Short answer

Answer: The exposed 3'-OH group plays a vital role in DNA replication by serving as the site for the formation of phosphodiester bonds with incoming nucleotides, which allows for the elongation of the growing daughter strand. The 3'-OH group ensures the accurate synthesis of complementary DNA strands according to the base pairing rules and provides energy for the formation of new bonds by interacting with the 5'-phosphate group of the incoming nucleotide.

Step-by-step solution

Understand DNA replication

DNA replication is the process by which a DNA molecule is copied to produce two identical DNA molecules. During this process, the DNA double helix is unwound and the two existing strands serve as templates for the synthesis of new complementary strands, called daughter strands.

The role of the 3'-OH group in DNA replication

Key to DNA replication is the addition of free nucleotide triphosphates (dNTPs) to the growing daughter strand according to the base pairing rule. This process occurs at the 3'-end of the daughter strand, which has a free 3'-OH (hydroxyl) group available for bonding with an incoming dNTP. The exposed 3'-OH group is essential for the formation of the phosphodiester bond between the incoming dNTP and the growing DNA strand.

The mechanism of addition to the 3'-end

A phosphodiester bond is formed between the exposed 3'-OH group on the last nucleotide of the growing daughter strand and the 5'-phosphate group of the incoming dNTP. This reaction is catalyzed by the enzyme DNA polymerase. The released energy from the hydrolysis of the two terminal phosphate groups of the incoming dNTP provides the energy necessary for the formation of the phosphodiester bond.

Elongation and termination

DNA polymerases continue adding nucleotides to the growing daughter strand, with exposed 3'-OH groups serving as the anchoring sites for incoming dNTPs, until the entire template strand is copied. Once the replication process is complete, the new DNA molecules consist of a continuous, complementary daughter strand created from the 5' to 3' direction, synthesized from the exposed 3'-OH groups of the preceding nucleotides. In conclusion, the exposed 3'-OH group on the growing daughter strand plays a vital role in the elongation process during DNA replication. It serves as the site for the formation of phosphodiester bonds with incoming nucleotides and ensures the accurate synthesis of complementary DNA strands according to the base pairing rules.

Key concepts

3'-OH Group Role

The exposed 3'-OH (hydroxyl) group at the end of the growing DNA strand is the linchpin in the process of DNA replication. Why is it so critical? This group participates in the elongation process by providing a point of attachment for incoming nucleotides. But it's not just about being a docking station. The 3'-OH group is chemically reactive, which is precisely what's needed to form the crucial bond with the new nucleotide.

During replication, each nucleotide that's added to a daughter strand arrives in the form of a deoxynucleoside triphosphate (dNTP). These dNTPs have a section called the phosphate group that needs to connect to something – that 'something' is the 3'-OH group. When the two meet, a reaction occurs that releases two phosphate molecules, providing the energy needed for the connection and leaving behind a single phosphate. This creates the necessary link—called a phosphodiester bond.

Without the 3'-OH group's active role, DNA replication would be a non-starter because there would be no chemically feasible way to extend the DNA chain.

Phosphodiester Bond Formation

When a new nucleotide is incorporated into the DNA strand, it's the phosphodiester bond that secures its place in the genetic code. This bond is the backbone of DNA structure, connecting the phosphate group of one nucleotide to the 3'-OH group of the previous nucleotide in the chain.

Let's get into a tad more detail: Imagine each nucleotide as a car in a train. The phosphodiester bond is like the coupling between the cars, enabling the train to be pulled along the tracks without the cars becoming separated. This bond is essential for maintaining the integrity and stability of the DNA molecule, ensuring that the genetic information is preserved and passed on accurately during cell division.

The formation of a phosphodiester bond during DNA replication is a two-step process. First, the 3'-OH group attacks the alpha-phosphate of the incoming dNTP. Then, a molecule of pyrophosphate is released. This action forms the new bond and, at the same time, helps drive the reaction forward because the release of pyrophosphate is energetically favorable.

DNA Polymerase Function

DNA polymerase is like the director of an orchestra in the symphony of DNA replication. This enzyme's job is to oversee the addition of new nucleotides in accordance with the existing template strand.

But DNA polymerase isn't just copying; it's editing too. The enzyme has a proofreading function that corrects errors during DNA replication, ensuring that each new strand is as close to a perfect copy as possible. It scans the newly added nucleotides and if an incorrect nucleotide is detected, it's excised, and the correct one is inserted—all with astonishing speed and accuracy.

Without DNA polymerase, cells could not divide, and organisms could not grow or repair tissues. This enzyme is absolutely critical for life as we know it.

Nucleotide Addition Mechanism

The actual incorporation of a nucleotide into the growing DNA strand is a well-choreographed process that rests on the shoulders of the 3'-OH group, phosphodiester bond formation, and the enzyme DNA polymerase. How does this dance unfold?

First, DNA polymerase selects a nucleotide whose base complements the corresponding base on the template strand (adenine pairs with thymine, cytosine with guanine). It guides the nucleotide into position such that its 5'-phosphate group aligns with the 3'-OH group at the end of the growing strand.

When they're perfectly paired, the 3'-OH group attacks the phosphate, releasing energy as a byproduct and fusing the nucleotide securely to the strand. This dance step is repeated, one nucleotide at a time, zipping along the DNA and assembling a brand-new sister strand. In this intricate mechanism, the interplay of chemical groups, energy transactions, and the guiding hand of DNA polymerase result in the creation of life's essential molecule—DNA.