Problem 79 - 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 \(3^{\prime}-\) ATC-5'.)

Step-by-Step Solution

Answer

The base sequence of the complementary strand for the given DNA single strand \(5^{\prime} -\)GCATTGGC-\(3^{\prime}\) is \(3^{\prime} -\)CGGTTACG-\(5^{\prime}\).

Step 1: 1. Understand the base pairing rules

In a DNA molecule, the bases found in the nucleotides always pair in a specific way: - Adenine (A) pairs with Thymine (T) - Guanine (G) pairs with Cytosine (C) This is known as the Watson-Crick base pairing rule.

Step 2: 2. Examine the given DNA strand and orientation

The given DNA strand has the sequence: \(5^{\prime} -\)GCATTGGC-\(3^{\prime}\) Notice that the given DNA strand is oriented in the 5' to 3' direction, as indicated by the \(5^{\prime}\) and \(3^{\prime}\) symbols.

Step 3: 3. Determine the complementary base sequence

Using the Watson-Crick base pairing rules, we can find the complementary base sequence of the given strand: - 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 So, the complementary base sequence is: CGTAACCG

Step 4: 4. Write the complementary strand in antiparallel fashion

Now that we have the complementary base sequence, we need to write it in the antiparallel fashion. The given strand has the direction \(5^{\prime}-3^{\prime}\), so the complementary strand must have a direction of \(3^{\prime}-5^{\prime}\). This means we need to reverse the complementary base sequence. So, the complementary strand in antiparallel fashion is: \(3^{\prime} -\)CGGTTACG-\(5^{\prime}\)

Step 5: 5. Conclusion

The base sequence of the complementary strand for the given DNA single strand \((5^{\prime} -\)GCATTGGC-\(3^{\prime})\) is \((3^{\prime} -\)CGGTTACG-\(5^{\prime})\).

Key Concepts

Watson-Crick Base Pairing Rule

One of the fundamental principles governing the structure of DNA is the Watson-Crick base pairing rule. This rule describes how nucleotide bases form hydrogen bonds in DNA, ensuring the genetic code is accurately copied and transmitted. According to this rule, adenine (A) always pairs with thymine (T), and guanine (G) pairs with cytosine (C). The pairing is very specific: A will not pair with G or C, and likewise, T will not pair with C or G. This specificity is due to the shapes and chemical properties of the bases, which allow for precise hydrogen bonding patterns.

When DNA replicates, these rules ensure that each new strand is a perfect complement to the original, preserving the genetic information. For students trying to determine the complementary strand of a given DNA sequence, remembering the acronym 'AT/GC' can be a helpful mnemonic device. This concept is at the heart of understanding genetic encoding and decoding in all living organisms.

DNA Strand Orientation

Nucleic acids, like DNA, are directional molecules. This directionality is a cornerstone of their function. DNA is made up of nucleotides that have a 5' end (five prime end) and a 3' end (three prime end). These refer to the carbon numbers in the DNA's sugar backbone; the 5' carbon has a phosphate group attached, while the 3' end has a hydroxyl group. This structure means that a single strand of DNA has a direction, indicated by 5' to 3'. All DNA polymerases, the enzymes responsible for copying DNA, add new nucleotides only to the 3' end, making this orientation critical for the process of replication and transcription.

Understanding this orientation is also essential when piecing together complementary DNA strands. Students often make the mistake of not paying attention to this aspect, which can lead to errors in predicting the sequence of the complementary strand. Always start from the 3' end of the original strand to determine the sequence of the new strand in the direction from the 5' to the 3' end.

Antiparallel DNA Strands

DNA's double-helix structure consists of two strands that run in opposite directions; this is referred to as antiparallel. As the DNA strands are paired, one runs in the 5' to 3' direction, and the other runs in the 3' to 5' direction. This antiparallel arrangement is key for many cellular processes, including DNA replication and transcription. It allows the enzymes that duplicate DNA to read the templates and build complements simultaneously during replication.

This antiparallel nature can be a source of confusion for students as they often assume the strands run parallel in the same direction. Remembering that the strands are oriented in opposite directions is crucial when determining the complementary sequence of a DNA strand. The given sequence must be read and rewritten in reverse order to maintain the antiparallel structure. For instance, if one strand in a DNA molecule runs 5' to 3', the complementary strand must be aligned from 3' to 5'. Keeping this in mind can aid students in correctly visualizing and writing DNA sequences.