23 - The Gene and Its Genetic Code

Understanding the significance of genetic information is crucial in molecular biology and genetics.

A gene is defined in various ways:
- Historically, it is viewed as a unit of heredity that dictates traits or characteristics passed from one generation to another.
- In molecular biology, a gene is a specific sequence of DNA that is transcribed into RNA and may be translated into proteins.

Not every gene produces a protein
- Some genes produce functional RNA molecules.
- functional RNA: RNA molecule that carries out a specific job in the cell (ex: tRNA, mRNA, and rRNA)
RNA’s function and its potential to be translated into proteins:
- RNA molecules are commonly involved in cellular functions
  - While others serve as templates for protein synthesis

A focus is placed on eukaryotic genes due to their complexity compared to prokaryotic genes.
- Eukaryotic genes may contain introns and exons
  - With the introns being removed during RNA processing
The DNA sequence of a gene determines the structure and function of the protein produced.
Exons: Coding segments of a gene that stay in the final mRNA
Introns: Non-coding segments of a gene that are removed during RNA processing, thus not included in the mature mRNA.
Coding Segments: Stretch of DNA or RNA that contains the actual instructions for building part of a protein
- These are vital portions of a gene that directly translate into amino acids
  - ultimately forming functional proteins essential for various cellular processes.

When discussing the genetic code:
- The change in the DNA sequence can alter the protein produced by that gene.
The genome browser example illustrates gene length and orientation, focusing on a specific gene called HEXA and its role in encoding a protein with hexokinase function.
Genes have defined nucleotide sequences with specific start and stop points
- which are important for transcription and translation processes.
Nucleotide Sequences: The order of the four DNA bases (A, T, C, G) along a DNA strand— makes up a gene (order of nucleotides in DNA)
DNA sequence: The precise order of nucleotides (A, T, C, G) that make up a DNA molecule— encoding genetic information (order of nucleotides in DNA or RNA)
nucleotide sequuence and dna sequence are basically the same thing, nucleotide particularly refers to the order in DNA or RNA, while dna sequence refers to the order of nucleotides in DNA

DNA is double-stranded
- with strands defined as forward (5' to 3' direction) and reverse (3' to 5' direction).
DNA polymerases and RNA polymerases read nucleic acids in the 5' to 3' direction.
The forward strand (5’ to 3’ direction) is typically the gene's coding strand (because it has the same nucleotide sequence as the mRNA that will be made)
- providing the sequence that will make up the mRNA
- which is complementary to the template strand used during transcription

3 nucleotides are needed to cover at least 20 amino acids
3 nucleotides make a codon
- can be translated into one amino acid
Enables the genetic code to specify the sequence of amino acids in proteins, which ultimately determines their structure and function.

Transcription: The process of synthesizing RNA from a DNA template using RNA polymerase.
The resulting mRNA from transcription is single-stranded and complementary to the DNA template strand
- converting the nucleotide sequence into a code for protein synthesis—RNA sequence is the genetic code that will later be read to make a protein
mRNA is synthesized in a direction consistent with the 5' to 3' orientation.
- RNA polymerase adds new nucleotides to the growing strand from 5’ to 3’— using DNA template strand as guide

Translation: The process which mRNA is decoded by ribosomes to produce a polypeptide (protein).
- Ribosomes read mRNA in sets of three nucleotides known as codons, each corresponding to a specific amino acid.
- Each codon makes one amino acid
There are 64 possible codons derived from combinations of four nucleotides (A, T, C, G in DNA; U replaces T in RNA) to encode 20 distinct amino acids
- allowing for redundancy in the genetic code—more than one codon can specify the same amino acid
Start Codon: The codon (AUG) that initiates translation, coding for methionine.
- All proteins start with methionine due to the universality of the start codon.
Stop Codons: Specific codons signaling the end of translation
- leading to the termination of protein synthesis

Types of Mutations:
- Silent mutations: Alter the nucleotide sequence without changing the corresponding amino acid (e.g. GGC to GGU still codes for glycine).
- Missense mutations: Result in a different amino acid being incorporated into the protein sequence, potentially altering protein function.
- Nonsense mutations: Introduce a premature stop codon, resulting in incomplete protein synthesis.
- Frameshift mutations: Caused by insertions or deletions that are not multiples of three, altering the reading frame and resulting in extensive changes to protein structure.
Contextual example: In muscular dystrophy, mutations in the dystrophin gene can be missense, frameshift, or nonsense, impacting the protein's functionality depending on their nature and position.

Key molecular biology techniques include:
- Polymerase Chain Reaction (PCR): Amplifies specific DNA sequences for analysis.
- Gel Electrophoresis: Used for separating DNA/RNA fragments based on size, allowing visualization of amplified products.
- Molecular Cloning: Involves transferring a gene from one organism into another, often utilizing recombinant DNA technology.
- Nucleotide Sequencing: Determines the exact sequence of nucleotides in a DNA molecule, revealing basis for functional characteristics of genes.

The complexity of eukaryotic genomes results in a large proportion of non-coding sequences (introns, regulatory elements) that play critical roles in gene expression regulation but do not directly code for proteins.
Understanding both coding and non-coding regions is essential for comprehending gene function at a higher level.

Knowledge of gene structure, function, transcription, translation, mutation impacts, and molecular biology techniques is fundamental to grasping the principles of molecular genetics and understanding how genetic information dictates biological functions in organisms.