Problem 75 - Chemistry: The Central Science

Question

Imagine a single DNA strand containing a section with the following base sequence: \(5^{\prime}\) -GCATTGGC-3'. What is the base sequence of the complementary strand? (The two strands of DNA will come together in an antiparallel fashion: that is, \(5^{\prime}-\mathrm{TAG}-3^{\prime}\) will bind to \(3^{\prime}-\mathrm{ATC}-5^{\prime} .\) )

Step-by-Step Solution

Answer

The base sequence of the complementary strand is \(3^{\prime} -\text{ GCCGTAAC- }5^{\prime}\), considering the antiparallel arrangement of the DNA strands.

Step 1: Identify the complementary bases

Use the base pairing rules to determine the complementary bases for each base in the given sequence: - G pairs with C - C pairs with G - A pairs with T - T pairs with A - T pairs with A - G pairs with C - G pairs with C - C pairs with G

Step 2: Write down the complementary strand

Based on the complementary bases obtained in the previous step, write down the complementary strand in the parallel orientation (5' to 3'): \(5^{\prime} -\text{ CGTAACCG- }3^{\prime}\)

Step 3: Convert the complementary strand into antiparallel orientation

Since DNA strands bind in an antiparallel fashion, convert the complementary strand from parallel orientation (5' to 3') to antiparallel orientation (3' to 5'): \(3^{\prime} -\text{ GCCGTAAC- }5^{\prime}\)

Key Concepts

Complementary DNA strands

Understanding the concept of complementary DNA strands is crucial in grasping the basics of genetic encoding and replication. Each strand of DNA is made up of a sequence of nucleotides that contain a nitrogenous base. In DNA, these bases are adenine (A), thymine (T), guanine (G), and cytosine (C).

The two strands of DNA molecule are complementary to each other, meaning that the bases on one strand specifically pair with bases on the other strand: adenine with thymine and guanine with cytosine. In our exercise, given the sequence 5′ -GCATTGGC-3′, the complementary strand is determined by pairing G with C and vice versa, A with T and vice versa. Consequently, the sequence of the complementary strand would start with a G to pair with the C from the original strand, and so on. This precise pairing is the foundation of DNA replication and transcription.

When visualizing this pairing, think of each pair as a perfect puzzle match, with A-T and G-C as the corresponding pieces that create a stable DNA double helix structure.

Antiparallel DNA structure

The antiparallel DNA structure is a defining characteristic of the DNA double helix. What does 'antiparallel' mean? Essentially, it refers to the orientation of the two DNA strands. While they run parallel to each other in the sense that they are side by side, they also run in opposite directions.

In a DNA strand, orientation is indicated by the numbers 5′ and 3′ marking the highest to the lowest value consecutively, which refer to the carbon atoms in the sugar component of the DNA backbone. One strand runs 5′ to 3′ and the complementary strand runs 3′ to 5′. This means that the 5′ end of one strand is paired with the 3′ end of the other, creating a ladder-like structure where the rungs are comprised of the base pairs.

In our exercise, converting the complementary strand into the antiparallel orientation, as we move from 5′ -CGTAACCG- 3′ to 3′ -GCCGTAAC- 5′, ensures proper pairing with the original DNA strand. This orientation is critical for the enzymes that replicate and repair DNA, as they work in a direction-specific manner.

Nucleotide base pairing rules

The rules of nucleotide base pairing, often referred to as the Chargaff’s rules, are simple yet the key elements to the structure and function of DNA. They dictate how nucleotide bases naturally pair up with each other, which directly influences DNA replication and gene expression.

The base pairing rules are as follows:

• Adenine (A) always pairs with Thymine (T)
• Guanine (G) always pairs with Cytosine (C)

By following these rules, we can predict the sequence of the complementary DNA strand. For example, opposite a sequence of 5′ -GCATTGGC-3′, with G pairing with C and A with T, we'll derive 5′ -CGTAACCG-3′ as its complement.

Moreover, these rules are crucial for the exercise improvement advice provided. Ensuring that students understand the base pairing rules can help them to approach DNA-related exercises with confidence. As students apply these rules, they gain a better understanding of the molecular processes such as the making of mRNA during transcription, DNA replication during cell division, and ultimately, the entire central dogma of molecular biology.