TS mam Bioinformatics Introduction

                                                
                                                What is Bioinformatics?
Application of computational tools on molecular data, including the means to acquire, analyze, or visualize such data.

• Bioinformatics is a relatively new interdisciplinary field that integrates computer science, mathematics, biology, and information technology to manage, analyze, and understand biological, biochemical and biophysical information.

• Bioinformatics is the development of computational methods for studying structure, function and evolution of genes, proteins and whole genomes.

                                                                                                                                                                                                               Molecular Bioinformatics

Molecular Bioinformatics involves the use of computational tools to discover new information in complex data sets (from the one-dimensional information of DNA through the two-dimensional information of RNA and the three-dimensional information of proteins, to the four-dimensional information of evolving living systems).

                           

                             
                                   
                                    Origin of bioinformatics and biological databases:
The first protein sequence reported was that of bovine insulin in 1956, consisting of 51 residue

(Amino Acids).
Nearly a decade later, the first nucleic acid sequence was reported, that of yeast tRNA alanine with 77 bases.
In 1965, Dayhoff gathered all the available sequence data to create the first bioinformatic database (Atlas of Protein Sequence and Structure).
The Protein DataBank followed in 1972 with a collection of ten X-ray crystallographic protein structures.The SWISSPROT protein sequence database began in 1987.




                              

                                                                       

Some Terminology

• Cell is a primary unit of life

• Cell consists of molecules, chemical reactions and a copy of the genome for that organism

• All life on this planet depends on three types of molecules: DNA, RNA and proteins

• DNA

– Holds information on how cell works

• RNA

– Acts to transfer short pieces of information to different parts of cell

– Provide templates to synthesize into protein

• Proteins

– Form enzymes that send signals to other cells and regulate gene activity

– Form body’s major components (e.g. hair, skin, etc.)


                                                            DNA - Deoxyribonucleic Acid

• Genetic material

• Consists of two long strands

• Each strand is made of:

– Phosphates

– Sugar

– Nucleotides

• A (adenine)

• G (guanine)

• C (cytosine)

• T (thymine)

.


                                               
                                                The Central Dogma of Molecular Biology
                                   

• Information has been transferred from DNA (information storage molecule) to RNA (information transfer molecule) to a specific protein (a functional, non-coding product)

                                       
                                                                       




                                                               
                                                               More Terminology

• Transcription of DNA – DNA transcribed into RNA – RNA exits as a single-strand unit and as a double- helix as well – RNA consist of A, C, G and U (uracil)

• Types of RNA – Messenger RNA – mRNA  – Transfer RNA – tRNA – Ribosomal RNA – rRNA

• Translation of Messenger RNA (mRNA):

– mRNA is translated into protein
 

• Proteins:

– linear polymers built from amino acids

 • The transfer of information from DNA to specific protein via RNA takes place according to the genetic code.

– The RNA sequence is divided into blocks of three letters

– This block is called CODON

– Each codon corresponds to the specific amino acid

• Four different nucleotides are used to build DNA and RNA molecules – A, G, C, T and A, G, C, U

• 20 different amino acids are used in protein synthesis

• Four nucleotides can be arranged in 64 different combinations of three.

• There are 64 = 4*4*4 different codons

• Some codons are redundant and some have special function to terminate the translation process

                                                    Why is bioinformatics important?

• Traditionally, research was carried out entirely at the experimental laboratory but the huge increase in the data in the genomic era has seen a need to incorporate computers into this research process.

• There are three central biological processes around which bioinformatics tools must be developed:

-DNA sequence determines protein sequence

-Protein sequence determines protein structure

-Protein structure determines protein function

                                                                  Major research areas

• Sequence analysis-A comparison of genes within a species or between different species can show similarities between protein functions.
 

• The comparison of sequences in order to find similar and dissimilar in compared sequences (sequence alignment)

• Identification of gene-structures, reading frames, distributions of introns and exons and regulatory elements

• Revealing the evolution and genetic diversity of organisms.

                                               
                                      Computational evolutionary biology-

• Evolutionary biology is the study of the origin and descent of species, as well as their change over time.  Informatics has assisted evolutionary biologists in several key ways;
it has enabled researchers to:

-trace the evolution of a large number of organisms by measuring changes in their DNA, rather than through physical taxonomy or physiological observations alone,

-build complex computational models of populations to predict the outcome of the system over time,

-and track and share information on an increasingly large number of species and organisms.

• Prediction of protein structure-

Protein structure prediction is another important application of bioinformatics.

• In the genomic branch of bioinformatics, homology is used to predict the function of a gene: if the sequence of gene A, whose function is known, is homologous to the sequence of gene B, whose function is unknown, one could infer that B may share A's function.

• MODELLER is one of the best software for Homology modelling. Protein Data Bank is the data base for 3D co- ordinates of a protein.

• Drug Designing- Drug design is the approach of finding drugs by design, based on their biological targets.

• Computer-assisted drug design uses computational chemistry to discover, enhance, or study drugs and related biologically active molecules.

• Phylogenetics- Predicting the genetic or evolutionary relation of set of organisms. Mitochondrial SNPs and Microsatellites (DNA repeats) are mostly used in Phylogenetics. MEGA, PAUP are PAUP* are some of the important software's. Maximum Parsimony and Maximum Likelyhood are mostly used methods.