Problem 4 - Biochemistry: Concepts and Connections

Question

When polynucleotides are synthesized with repeating triplets of nucleotide residues, one, two, or three different polypeptide chains will be produced in cell-free synthesis. (a) Explain why these different results are possible. (b) Predict polypeptides produced when the following are used with an E. coli system: (GUA) \()_{11},(\mathrm{UUA})_{\mathrm{s}-}\)

Step-by-Step Solution

Answer

Different reading frames cause different polypeptide chains when using repeating triplet sequences.

Step 1: Understanding Codons

A codon consists of three nucleotides and codes for a specific amino acid. The genetic code is read in triplets starting from a fixed starting point.

Step 2: Translating (GUA) Sequence

For the sequence (GUA) repeated, the possible reading frames are GUA, UAG, and AGU. These correspond to different codons: GUA (Valine), UAG (Stop), and AGU (Serine). Depending on where translation starts, different sequences may be produced.

Step 3: Translating (UUA) Sequence

With (UUA) repeating, the reading frames are UUA, UAU, and AUU. These correspond to: UUA (Leucine), UAU (Tyrosine), AUU (Isoleucine). Each frame results in different polypeptide chains being synthesized.

Step 4: Explaining Multiple Polypeptides

Due to the repeating nature of the sequence and shifting reading frames, one sequence can produce different polypeptides. The start of translation may differ, causing variations in polypeptides synthesized.

Key Concepts

The Genetic Code

The genetic code is like the language of life. It's a set of rules by which information encoded in genetic material (DNA or mRNA) is translated into proteins by living cells. This code is made up of sequences of three nucleotides, also known as codons, with each codon corresponding to a specific amino acid or a stop signal during protein synthesis.

What makes the genetic code fascinating is its universality. Almost all organisms use the same genetic code, where, for example, the codon AUG is usually a start signal and also codes for Methionine.

This code has a couple of key features:

• **Redundancy**: Most amino acids are coded by more than one codon; for instance, leucine is coded by six codons.
• **Without overlap**: Codons are read one after another, without overlapping.

In synthetic or experimental scenarios, like the one we are discussing, understanding the genetic code is crucial. Be it naturally in cells, or in a laboratory setup, polynucleotide synthesis heavily relies on following the genetic code rules.

Codon Translation

Codon translation is the process of converting genetic information from mRNA sequences into proteins. Each mRNA sequence is like a blueprint that guides the synthesis of proteins by translating nucleotide sequences (codons) into amino acids, the building blocks of proteins.

The machinery responsible for this task is the ribosome, a cellular "factory" where translation occurs. *tRNA* (transfer RNA) plays a crucial role, as it brings the correct amino acid to the ribosome corresponding to the codon presented.

Here's a quick rundown of how translation works:

• **Initiation**: The ribosome assembles at the start codon (usually AUG).
• **Elongation**: tRNA matches its anticodon to the mRNA codon, and the ribosome forms a peptide bond between the growing polypeptide and the new amino acid.
• **Termination**: When a stop codon (UAA, UAG, UGA) is reached, the process concludes, and the newly synthesized protein is released.

This system ensures that the right proteins are synthesized as needed by the organism or, in the context of your exercise, within a controlled experiment.

Reading Frames

Reading frames are the different ways nucleotides in a strand of RNA or DNA can be grouped into codons for translation into proteins. With sequences of nucleotides, you can shift the grouping by one or two nucleotides to create different reading frames.

Because codons are read in groups of three nucleotides, a single strand can be read from three starting points. This results in three potential ways to group the nucleotides, each potentially coding for a different series of amino acids and thus, different proteins.

In the context of your exercise, when the sequence is (GUA), the reading frames would be:

• **GUA**: Valine
• **UAG**: Stop - usually halts translation
• **AGU**: Serine

Similarly, for the sequence (UUA), the reading frames are:

• **UUA**: Leucine
• **UAU**: Tyrosine
• **AUU**: Isoleucine

These variations in reading frames are why different polynucleotide sequences can produce multiple distinct polypeptides, depending on where translation begins.