Question

Predicting Anticodons from Codons Most amino acids have more than one codon and attach to more than one tRNA, each with a different anticodon. Write all possible anticodons for the four codons of glycine: \(\left(5^{\prime}\right) \mathrm{GGU}, \mathrm{GGC}\), GGA, and GGG. a. From your answer, which of the positions in the anticodons are primary determinants of their codon specificity in the case of glycine? b. Which of these anticodon-codon pairings has/have a wobbly base pair? c. In which of the anticodon-codon pairings do all three positions exhibit strong Watson-Crick hydrogen bonding?

Short answer

a. First two positions are primary determinants. b. CCA with GGU has a wobbly base pair. c. GCC with GGC and CCC with GGG exhibit strong hydrogen bonding.

Step-by-step solution

Write given codons

The codons for glycine are given as follows: \( \text{GGU}, \text{GGC}, \text{GGA}, \text{GGG} \).

Identify anticodons

Anticodons are the complementary triplets recognized by tRNA. For the codons given, the anticodons will be: - \( \text{GGU} \rightarrow \text{CCA} \)- \( \text{GGC} \rightarrow \text{GCC} \)- \( \text{GGA} \rightarrow \text{UCC} \)- \( \text{GGG} \rightarrow \text{CCC} \)(Note: Anticodons are written in the direction of \(5' \) to \( 3' \)).

Primary determinant positions

In anticodons, the third position bases (wobble position) can exhibit flexibility in pairing. However, for glycine, the first two positions \(5' \) to \( 3' \) (\( C\) and \( G\) respectively) are the primary determinants, as they pair strongly with the codons.

Identify anticodon-codon pairs with wobbly base pairs

A wobbly base pair occurs when pairing is more flexible, often involving guanine (G) and uracil (U) pairs. For the anticodon \( \text{CCA} \) with codon \( \text{GGU} \), the third position \( A - U \) pair is a wobble base pair.

Identify strong hydrogen bonding pairs

Strong Watson-Crick hydrogen bonding occurs when all three bases follow traditional base pairing rules (A with U and G with C). For anticodon \( \text{GCC} \) with codon \( \text{GGC} \) and anticodon \( \text{CCC} \) with codon \( \text{GGG} \), all positions exhibit strong Watson-Crick base pairing.

Key concepts

Codon Specificity

Codon specificity is the unique feature of molecular genetics where each codon corresponds to a specific amino acid or gives a start or stop signal during protein synthesis. Codons are triplets of nucleotides in the mRNA sequence that determine the insertion of specific amino acids into a growing polypeptide chain. Each codon is "read" by tRNA molecules during translation to ensure proteins are built accurately.
For example, the codons for the amino acid glycine include GGU, GGC, GGA, and GGG. Despite having different nucleotide sequences, all these codons code for the same amino acid due to this specificity.

• GGU - Glycine
• GGC - Glycine
• GGA - Glycine
• GGG - Glycine

Understanding codon specificity is crucial because it highlights the robustness of genetic coding, allowing for diversity in genetic sequences without altering their protein products.

Anticodon-Codon Pairing

Anticodon-codon pairing is a critical concept in molecular biology referring to the interaction between the anticodon region of a tRNA molecule and the corresponding codon on an mRNA strand. This interaction ensures the correct amino acid is added to a growing polypeptide chain during protein synthesis.
Each tRNA molecule has an anticodon that is complementary to a specific mRNA codon. For instance, the anticodon for the mRNA codon GGU is CCA, but in the direction of 5' to 3', it reads ACC.

• Codon GGU pairs with anticodon CCA
• Codon GGC pairs with anticodon GCC
• Codon GGA pairs with anticodon UCC
• Codon GGG pairs with anticodon CCC

Correct matching is essential because errors in pairing can lead to the wrong amino acid being added, disrupting protein function and potentially leading to disease.

Wobble Base Pairing

Wobble base pairing is a feature of the genetic code that allows for some flexibility in the pairing between the third nucleotide of the codon and the first nucleotide of the anticodon, often referred to as the "wobble" position.
This flexibility allows one tRNA anticodon to recognize multiple codons that differ in their third nucleotide. For example, the anticodon CCA can pair with codons GGU and GGC. In this scenario, the guanine (G) can pair with uracil (U), which accounts for the wobble position between CCA and GGU.

• The wobble position is usually the third position in a codon.
• Wobble allows for redundancy in the genetic code.
• It helps explain why multiple codons can code for the same amino acid.

Wobble base pairing increases the efficiency of protein synthesis by minimizing the number of tRNA molecules needed, yet still maintaining accuracy in translation.

Watson-Crick Hydrogen Bonding

Watson-Crick hydrogen bonding describes the typical hydrogen bonding patterns found between base pairs in DNA and RNA. This involves adenine pairing with uracil (in RNA) and cytosine pairing with guanine, establishing strong and specific hydrogen bonds that are vital for accurate genetic translation and transcription.
For glycine codons and their anticodons, examples showing strong Watson-Crick hydrogen bonding occur when all three nucleotide positions follow these traditional base pairing rules.

• Anticodon GCC with codon GGC
• Anticodon CCC with codon GGG

This form of bonding is essential for maintaining the stability and integrity of the genetic code during translation, ensuring that proteins are synthesized correctly according to the genetic instructions.