Question

A short RNA molecule was isolated that demonstrated a hyperchromic shift (see Chapter 10 ), indicating secondary structure. Its sequence was determined to be 5'-AGGCGCCGACUCUACU-3' (a) Propose a two-dimensional model for this molecule. (b) What DNA sequence would give rise to this RNA molecule through transcription? (c) If the molecule were a tRNA fragment containing a CGA anticodon, what would the corresponding codon be? (d) If the molecule were an internal part of a message, what amino acid sequence would result from it following translation? (Refer to the code chart in Figure 13.7 .)

Short answer

Answer: The amino acid sequence resulting from translating the RNA molecule is Arg-Arg-Arg-Leu-Tyr.

Step-by-step solution

Identify the sequence of RNA molecule

The given RNA sequence is AGGCGCCGACUCUACU.

Form complementary base pairs

Base pairs for this RNA molecule can be formed as follows: - A pairs with U - G pairs with C In this case, we have a complementary base pairing as follows: AGGCGC ||||| UCCGCG CGAC ||| CGUC UACU ||| AUGA The proposed two-dimensional model looks like this: ``` AGGCGC 5'-UCCGCG-3' CGAC 3'-CGUC-5' UACU 5'-AUGA-3' ``` b) DNA Sequence corresponding to the RNA Molecule

Write the RNA sequence

The given RNA sequence is AGGCGCCGACUCUACU.

Replace RNA bases with their corresponding DNA bases

For the DNA molecule, the following substitutions can be made according to the base pair rules: - Replace A with T - Replace U with A - Replace G with C - Replace C with G So, the corresponding DNA sequence is: TCCGCGGCTGAGATGA c) Corresponding Codon for the CGA Anticodon

Write down the anticodon

The given anticodon is CGA.

Find the corresponding codon

The corresponding codon for CGA can be determined using base pair rules: - C pairs with G - G pairs with C - A pairs with U Thus, the corresponding codon is GCU. d) Amino Acid Sequence from the RNA Molecule

Write down the RNA sequence

The given RNA sequence is AGGCGCCGACUCUACU.

Divide the RNA sequence into codons

Divide the RNA sequence into groups of three nucleotides each (codons): AGG CGC CGA CUC UAC U.

Translate the codons into amino acids

Using a genetic code chart or a table, translate the codons into their corresponding amino acids: - AGG: Arginine (Arg) - CGC: Arginine (Arg) - CGA: Arginine (Arg) - CUC: Leucine (Leu) - UAC: Tyrosine (Tyr) - U: Incomplete codon (no amino acid) The amino acid sequence resulting from translating the RNA molecule is: Arg-Arg-Arg-Leu-Tyr.

Key concepts

RNA Secondary Structure

The beauty of RNA lies not only in its genetic role but also in the intriguing shapes it adopts, often referred to as the RNA secondary structure. Imagine a string of pearls that twists and folds upon itself - that's RNA for you.

Secondary structures arise when sequences within the same RNA molecule pair up due to base-pairing rules. In our exercise, the RNA sequence '5'-AGGCGCCGACUCUACU-3'' can form such pairings, involving A pairing with U and G pairing with C. These interactions can lead to structures like stems, loops, bulges, and hairpins.

This intrinsic property is crucial for functions such as catalysis in ribozymes or recognition sites in tRNA. And it's not just about form; these structures can dictate how RNA molecules interact with other biomolecules. The hyperchromic shift observed in the exercise indicates that we're dealing with structured RNA, possibly tRNA given its short length and iconic cloverleaf pattern.

Anticodon-Codon Pairing

Let's play matchmaker with the letters of life in anticodon-codon pairing. This is where tRNAs, the interpreters of the genetic code, come into play with their anticodons. An anticodon is a trio of nucleotides that pairs up with a complementary messenger RNA (mRNA) codon.

In our case, the CGA anticodon would snugly pair with the GCU codon, following the 'opposites attract' principle of base pairing. Think of it as the molecule's way of ensuring precision in translating the genetic information into proteins. Each tRNA carries a specific amino acid, and this pairing brings the right amino acid to the mRNA, akin to selecting the correct letter in a complex alphabet soup to spell words, which in our language are proteins.

Amino Acid Sequence

Have you ever wondered how life translates a bunch of letters into action? The RNA's string of nucleotides does just that, giving rise to an amino acid sequence, the building block of proteins. This linear sequence emerges through translation, where ribosomes read RNA codons three letters at a time.

Every three nucleotides, or codon, corresponds to a specific amino acid (or a stop signal), determined by the genetic code. For our exercise, this code spells out a series of amino acids like Arginine (Arg) and Tyrosine (Tyr), each brought to the party by a tRNA with a matching anticodon. The sequence Arg-Arg-Arg-Leu-Tyr emerges, ready to fold into a functional protein with its distinctive properties and roles. Just like beads on a necklace, the order and type of amino acids determine the final shape and function of the protein.

Genetic Code Chart

The genetic code chart is like a decoder ring for understanding life's instructions. It's a tabular representation of how sequences of nucleotides correspond to amino acids - the essential components of proteins. For students tackling genetic puzzles, this chart is invaluable, allowing them to translate the RNA sequence into the actual string of amino acids that make up a protein.

Given a sequence like 'AGGCGCCGACUCUACU', referring to the genetic code chart will help determine that 'AGG' reads as Arginine, 'CGC' also as Arginine, and so on, just as we decoded in our exercise. Armed with this chart, even the most cryptic strings of RNA can be deciphered into meaningful biological functions. It's like turning a secret message into a fully understood directive that informs the construction of proteins, essentially directing the very processes of life.