Introduction to Bioinformatics and Biocomputing

Bioinformatics (Biocomputing) Introduction

• Bioinformatics (Biocomputing) is the application of computational methods to study biological data.
• Bioinformatics is crucial due to the massive amount of biological data.
• Key computational techniques are used to model biological processes.
• These techniques are used to identify patterns, visualize data, and create simulations.
• Bioinformatics helps predict biological effects and behaviors.

Importance of Bioinformatics and Computational Biology

• Computational methods are used to analyze biological data due to the amount of data.
• This is vital for modeling biological processes.
• It also helps identify patterns and visualize operations.
• Computational biology makes it possible to create simulations and predict effects or behaviors.
• Using computational methods is more efficient, reducing time and resources needed for experimental processes.
• This process is helpful for identifying relationships between different factors.

General Introduction to Bioinformatics

• The field focuses on problems people are working on in biology.
• Key computational techniques required to solve biological problems by computation were discussed.
• The field helps answer how these methods and techniques contribute to biological research

What is Bioinformatics?

• Bioinformatics involves conceptualizing biology from a molecular (physical chemistry) perspective.
• Bioinformatics applies informatics techniques like math, computer science and statistics at a large scale.
• Bioinformatics is a practical field with multiple applications based on these techniques.

Scales of Life

• Biological levels range from atoms to the biosphere.
• This diagram illustrates different levels of life from the smallest (atomic) to the largest (organism).
• Included are molecules, cells, tissues and the biosphere.

Two Kinds of Cells

• Prokaryotes lack a nucleus and have circular genomes.
• Eukaryotes have a nucleus and have linear genomes.
• The genomes are organized into pairs.

DNA (Genotype) → Protein → Phenotype

• Differences between organisms come from differences in their DNA (genotypes).
• Genotypes determine the proteins produced, which influence the phenotype.

DNA: The Sequence of Life

• DNA contains unique genetic codes.
• DNA serves as instructions for protein production.
• DNA is made of deoxyribonucleic acid (DNA).
• DNA has four base pairs (A, C, G, T).

Molecular Biology Information - DNA

• Raw DNA sequences are analyzed.
• DNA sequences are parsed into genes.
• Genes consist of coding sequences (~1 KB per gene) with non-coding regions (introns).
• A human genome contains millions of bases.

Eukaryotic Genes: Exons and Introns

• Eukaryotic genes are composed of exons (coding) and introns (non-coding) regions.
• Introns are removed from the primary RNA transcript.
• Exons are joined together, allowing production of mature messenger RNA

RNA Transcription and Processing

• RNA is produced from DNA template through transcription.
• Pre-mRNA contains exons and introns.
• RNA splicing removes introns, joining exons to form mature mRNA.

Genes and Proteins

• A gene codes for a specific protein.
• The gene contains the sequence that determines the amino acid sequence of the corresponding protein.
• Proteins are composed of amino acids.

DNA to Protein

• Transcription produces mRNA from a DNA template.
• Translation uses mRNA to generate a protein.
• Amino acids combine to form proteins, essential for biological function.

DNA Transcription

• Transcription takes place in the cell nucleus.
• DNA is used as a template for converting into RNA.
• A strand of mRNA is produced, complementary to the DNA strand.

mRNA Translation

• mRNA is translated into amino acid chains to form proteins.
• mRNA sequence is read.
• A set of rules determine how mRNA translates to amino acid sequences.

Genes and Proteins

• One gene often encodes one protein.
• Protein production begins with a start codon and ends with a stop codon.
• Introns in eukaryotic genes are removed during splicing.

Codon to Amino Acid Table

• Codons are three-nucleotide sequences in mRNA that specify a particular amino acid.
• The genetic code provides the instructions for the translation.
• The table lists the correspondence between codons and amino acids.

Amino Acids

• Building blocks of proteins.
• 20 amino acids.
• Have distinct properties (electric charge, polarity) related to their side chains.

Protein Folding and Structure

• Protein amino acid sequence folds into a 3-D shape.
• Folding is a physical process.
• The 3-D shape influences function.
• Different structures imply different functions.

Protein Structure

• Protein structure diagrams are shown.
• Illustrations of protein structures.

Genetic Variant Effect Prediction

• Predicting the effect of genetic changes on protein function.
• Diagrams depicting genetic variations and possible effects are included.

Genetic Variations

• Causes of genetic variations, such as mistakes during DNA replication.
• Environmental impacts, transposable elements and horizontal DNA transfers cause genetic variations.
• There are types of variations like SNPs, Indels, Inversion and Duplication.

DNA: The Sequence of Life

• DNA sequences, chemical structures involved in biological processes.
• Genomes (complete set of an organism's DNA).
• The length of the DNA varies according to species.

DNA Sequence

• DNA's double-stranded structure and complementary base pairs (A-T, C-G).
• DNA strands have directions (5' to 3').

RNA

• RNA is a single-stranded molecule.
• RNA consists of four nucleotides (A, C, U, G).
• RNA is involved in protein production.

Proteins

• Proteins are chains of amino acids.
• Different proteins have different structures, hence have different functions.
• Proteins are essential for various biological functions.

Biological Sequences

• DNA, RNA, and proteins are biological sequences.
• DNA, RNA, and protein sequences have specific alphabets.

Obtaining Sequences

• Websites and resources for obtaining biological sequences.
• Databases for storing detailed information about genes, proteins, and other biological entities are mentioned.