Introduction to Bioinformatics

• Bioinformatics combines biology, computer science, and mathematics to analyze biological data.
• It is the application of computational methods to address biological questions and solve biological problems.
• A simple view is Biological Data + Computer calculations.

Definition of Bioinformatics

• It is regular biology that is appropriately formatted to fit into a computer.
• Bioinformatics is the science of storing, retrieving, organizing, analyzing, and interpreting biological information, mainly from molecular biology experiments.
• It involves creating and using computational methods and tools to answer biological questions and solve biological problems, especially with large, complex datasets.

Bioinformatics as an Interdisciplinary Field

• Bioinformatics uses biology, chemistry, physics, computer science, computer programming, information, engineering, mathematics, and statistics to analyze and interpret biological data.
• Computational biology analyzes and interprets data using applied mathematics, informatics, statistics, and computer science to solve biological problems.

Why Bioinformatics is Important

• High-throughput technologies, like next-generation sequencing, generate biological data at an unprecedented rate.
• Bioinformatics helps researchers study molecular mechanisms by delving into DNA, RNA, Protein, and other interactions.
• Genomic sequencing has led to personalized medicine, agriculture, and evolutionary studies.
• Biological systems need bioinformatics to study intricate interactions between genes, proteins, and other molecules.
• Bioinformatics helps address global health issues, including infectious diseases, cancer, and drug resistance.

Bioinformatics Applications

• Biology applications include genomics, transcriptomics, proteomics, and evolution.
• Medicine applications include disease diagnosis, drug discovery and development, pharmacogenomics, and infectious disease epidemiology.

Key Areas

• Sequence Analysis: Identifying patterns, motifs, and functional elements in DNA, RNA, and protein sequences.
• Structural Bioinformatics: Predicting and analyzing the three-dimensional structures of proteins and nucleic acids using computational methods.
• Functional Genomics: Studying the functions and interactions of genes and proteins on a genome-wide scale.
• Comparative Genomics: Comparing genomes across different species to understand evolutionary relationships, genetic variation, genome evolution, gene function, and disease mechanisms

Course overview

• Bioinformatics course providing an introduction to the area of bioinformatics
• Topics include: biology overview, databases, the alignment problem, proteins and protein structure-function, and use of public databases.

Course contents

• Introduction to Bioinformatics: Includes applications in biology and medicine, the importance of mathematics, biological sequences (DNA, RNA, proteins), and biological databases/tools.
• Proteins I (Structure-function relationships): Covers protein structures, protein databases, database similarity search, and protein family analysis.
• Proteins II (Computational modeling): Includes structural analysis, three-dimensional comparative modeling, and protein interactions.
• Algorithms and simulations: Focuses on dynamic programming, clustering, classifications, string matching, and BLAST.

Why Mathematics

• Mathematics is a precise language which helps formulate ideas and assumptions unambiguously.
• It is a concise language where an equation can convey more than 1000 words.
• The same techniques relate across a range of scales.
• Mathematics is described as an old but trendy language with a rich toolbox, and the language best able to be understood by computers.

Importance of Mathematics

• Essential for statistical methods to analyze biological data like DNA sequences
• Bioinformatics algorithms rely on mathematical concepts to solve computational problems
• Mathematics is the language to model biological systems like gene regulatory networks, metabolic pathways, and protein-protein interactions.
• Its importance extends to data analysis, algorithm development, modeling biological systems, sequence analysis, and structural bioinformatics.

Course Evaluation

• End-term Examination: 50 points
• Mid-term Examination: 30 points
• Course Activities: 20 points
• Total: 100 points

Cells, DNA, and Genes

• Cells are structural building blocks that carry out specialized functions.
• Trillions of cells contain DNA packaged in chromosomes; they typically contain 46 chromosomes.
• Segments of DNA, known as genes, provide instructions which are used to make proteins that ensure specific functions.

Proteins and Amino Acids

• Proteins are made of amino acids and perform functions within living organisms.
• The function is determined by the amino acid sequence and three-dimensional structure influenced by interactions.
• Amino acids have carbon, hydrogen, oxygen, and nitrogen. Some have sulfur.
• The alpha carbon bonds to an amino group (-NH2), a carboxyl group (-COOH), a hydrogen atom (H), and a variable side chain (R group).
• There are 20 standard amino acids found in proteins.
• Amino acids are the building blocks that contribute to protein structure, function, and arrangement determine properties.
• All amino-acids have a pair of hooks NH2 and COOH groups to form peptidic bonds between the residues in the sequence.

Protein Sequences

• 20 blocks amino acid = 20 alphabet letter (ACDEFGHIKLMNPQRSTVWY)
• Polypeptide chain lengths range from 6 to almost 37,000 amino acid residues.
• There are 8M known protein sequences but only a few protein structures are known.

Protein Structures

• Primary Structure: A sequence of amino acids linked by peptide bonds.
• Secondary Structure: Regular bonds (hydrogen bonds) cause repeating structures of a polypeptide chain.
• Tertiary Structure: The three-dimensional shape of a peptide chain, determined by internal/external factors.
• Quaternary Structure: The structure formed by multiple peptide chains (subunits).

Three-Dimensional Protein Structure

• Biological properties depend on the 3D shape.
• Function is a direct consequence of its shape.
• Sequence determines structure determines Function