Molecular Biology Basics Relevant to Computational Analysis
1. Central Dogma of Molecular Biology: This is the process by which the information in genes (DNA) is converted into a cellular function. It encompasses three main processes:
- DNA Replication: The process where DNA makes an exact copy of itself.
- Transcription: The synthesis of RNA from a DNA template.
- Translation: The synthesis of proteins based on the information in mRNA.
In simple terms: DNA -> RNA -> Protein.
2. Genes and Genomes:
- Gene: A segment of DNA that contains the instructions to make a protein. Genes are transcribed into RNA and then translated into protein.
- Genome: The complete set of genetic material in an organism, encompassing all its genes and other elements.
3. Genetic Code: The genetic code is a set of rules that translates nucleotide sequences in mRNA to amino acid sequences in proteins. There are 64 possible codons (triplets of nucleotides) and 20 amino acids, making some amino acids encoded by more than one codon.
4. Mutations: Changes in the DNA sequence are called mutations. These can be beneficial, neutral, or harmful. Mutations can lead to variations in protein sequences and functions.
Introduction to Biological Data Types
1. DNA: Deoxyribonucleic acid (DNA) is a double-stranded molecule that stores the genetic information of an organism. Its structure consists of two complementary strands twisted around each other in a double helix. Each strand is made up of four nucleotides: Adenine (A), Thymine (T), Cytosine (C), and Guanine (G). In bioinformatics, DNA sequences are represented as strings of these letters.
2. RNA: Ribonucleic acid (RNA) is typically a single-stranded molecule involved in protein synthesis (as mRNA), as a key structural and functional component of ribosomes (as rRNA), in transport of amino acids to the ribosome (as tRNA), and in various other cellular processes. Unlike DNA, RNA contains Uracil (U) instead of Thymine (T).
Types of RNA:
- mRNA (Messenger RNA): Carries the genetic code from the DNA to the ribosomes, where proteins are synthesized.
- tRNA (Transfer RNA): Transports specific amino acids to the ribosome during protein synthesis.
- rRNA (Ribosomal RNA): A major component of ribosomes.
- miRNA (Micro RNA) and siRNA (Small Interfering RNA): Involved in gene regulation.
3. Protein Sequences: Proteins are chains of amino acids and play crucial roles in almost every cellular process. The sequence of amino acids in a protein determines its structure and function. In bioinformatics, protein sequences are represented as strings of amino acid abbreviations (e.g., ‘M’ for Methionine, ‘A’ for Alanine, etc.).
Protein structure:
- Primary: Linear sequence of amino acids.
- Secondary: Local folding patterns, like alpha-helices and beta-sheets.
- Tertiary: Three-dimensional shape of the protein.
- Quaternary: Arrangement of multiple protein subunits.
Each data type (DNA, RNA, and protein sequences) serves as a foundation for various computational analyses, from sequence alignment and phylogenetics to structure prediction and functional annotation. Proper understanding of these data types and the underlying molecular biology is crucial for meaningful computational analyses in bioinformatics and computational biology.