Gene Expression and the Genetic Code

Gene expression is the process that leads to the translation of genetic information from DNA into proteins.

The Central Dogma illustrates the flow of genetic information within a biological system.
DNA undergoes two key processes:
- Transcription: The process of copying a segment of DNA into RNA.
  - In prokaryotes: RNA is directly utilized as mRNA.
  - In eukaryotes: mRNA undergoes processing to become mature mRNA (i.e., capping, polyadenylation, splicing).
- Translation: The process of converting the RNA sequence into a polypeptide chain (protein).

The genetic code is a set of rules that determines how nucleotide sequences are translated into amino acids.

Codon: A triplet of nucleotides that correspond to a specific amino acid.
- Example of Nucleotide Sequence: AACGTAGTTTAGTAG
- Each codon represents one amino acid.

Each amino acid is represented by a specific codon.
The code indicates:
- How many letters make up a single "word" (which represents one amino acid).
- Distinguishing between words in the sequence (where genes start and end).
- Presence of punctuation in the genetic code.

Hypothesis on Codon Length:
- 1 nucleotide/codon: Only 4 possibilities (A, T, C, G).
- 2 nucleotides/codon: 16 possibilities (4 x 4).
- 3 nucleotides/codon: 64 possibilities (4 x 4 x 4).
It is deduced that codons must be at least triplet combinations to encode for amino acids effectively.

The genetic code consists of:
- 64 triplet codons that encode for 20 amino acids.
- The codon AUG functions as an initiation (start) codon.
- There are 3 codons that signify termination (stop codons).
- The code is described as degenerate; multiple codons can correspond to the same amino acid.

Investigated the relationship between a gene's nucleotide sequence and the corresponding amino acid sequence of the polypeptide it encodes.
- Organism used: Escherichia coli (E. coli)
- Specific gene studied: Gene for a subunit of tryptophan synthetase, designated as the trpA gene.
- Methodology: Mutations in the trpA gene were compared to expected amino acid substitutions.
- Impact: Illustrated a colinear relationship between DNA mutations and the order of amino acid sequence changes.

Results showed specific mutations in the trpA gene correlated with particular positions of altered amino acids in the produced polypeptide.
Examples of mutated amino acids included:
- Wild-type Amino acids: Lysine, Phenylalanine, Glutamic acid.
- Mutant Amino acids: Various mutations leading to altered functions including stops (represented as STOP).

A codon consists of three nucleotides.
The established starting point of each gene sets the reading frame for translation.
Important to note:
- Different point mutations may affect the same amino acid, but each nucleotide is part of only one codon.
- Codons for amino acids do not overlap, indicating that each point mutation typically results in the alteration of only one amino acid.

Frameshift mutations occur due to insertion or deletion of nucleotides, affecting the reading frame.
The phenotypic effects depend on whether the reading frame is restored after the mutation.
- Most amino acids have multiple codons (redundancy), providing some resilience against mutations.

A real-world example of deletion and insertion impacts on the sequence of a sentence may include:
- Original Sentence: "The cat ate the rat."
  - Deletion Example: "Thc ata tet her at…"
  - Insertion Example: "The cat tat eth era t…"
  - Both Deletion and Insertion: "Thc att ate the rat."