Genomics and Protomics | Zoology Optional Notes for UPSC PDF Download

Genomics

Genomics is a relatively new discipline. Although the DNA was first isolated as early as 1869, it took more than one century for the first genomes to be sequenced. The term genomics was introduced recently by Thomas Roderick in 1986. Genomics describes the detailed study of the genome, its structural organization, and function using various modern methods including computational biology. It involves genome sequencing and computer-aided analysis to understand its structural organization and functions, genome mapping, and related studies. The term genome represents the complete genetic material, including both nuclear and cytoplasmic genes present in a cell. The Human Genome Project (HGP) has created the field of genomics, understanding genetic material on a large scale.

Concept of genomics

Thomas Roderich introduced the term genomics in 1986. It is a scientific method of mapping, sequencing, analyzing, and making use of genetic information for further use in multifarious areas. Genomics can be defined as the study of the molecular organization of genomes, their information contents, and the gene products they encode.

Types of genomics

In the last few years, some interesting findings have been recorded, and several new branches have emerged. Consequently, the area of genomics has quietly widened. However, genomics is broadly categorized into three types, namely, structural genomics, functional genomics, and comparative genomics.

• Structural Genomics: The process of finding out the sequences of genomes is called structural genomics. It deals with DNA sequencing, sequence assembly, sequence organization, and management. Structural genomics attempts to determine the structure of every protein encoded by the genome, rather than focusing on one particular protein.
• Functional Genomics: Functional genomics is the study and understanding of the function of genes. Based on structural genomics, the reconstruction of genome sequences is useful to find out the function that the genes perform. It gives an idea of the function of all gene sequences and their expression in an organism.
• Comparative Genomics: Comparative genomics involves comparing different genomes to predict the function of genes. It includes analyzing protein sets from completely sequenced genomes and using databases for comparative genomics.

Methods used for whole genome sequencing

Whole genome sequencing is a laboratory procedure that determines the order of bases in the genome of an organism. Some important methods used for whole genome sequencing are:

• Chemical Methods: Developed by Maxam and Gilbert in 1977, this method involves labeling a restriction fragment of DNA with 32p and chemically cleaving the DNA at specific residues in five different reactions. The fragments with the labeled terminus are seen.
• Whole Genome Shotgun Sequencing: Developed by J. Craig Venter and H. Smith, this method involves constructing a library of plasmid clones by isolating the chromosome from desired cells, fragmenting the DNA into small pieces, and attaching them to plasmid vectors. The DNA fragments are then sequenced using automated sequencers, and the resulting sequence data is analyzed and assembled to form the complete genome sequence.

Proteomics

Proteomics is the study of all the proteins produced by a cell. It involves the identification, analysis, and large-scale characterization of the proteome expressed by any cells, tissues, and organs under defined conditions. Proteomics helps understand the structure and function of different proteins, as well as protein-protein interactions in an organism.

Concept of proteomics

The total protein component in a cell or organism is referred to as the proteome. Proteomics deals with the study of proteomes, which is the total protein content of a cell or organism. It helps in understanding the alteration in protein expression during different stages of the life cycle or under stress conditions. Proteomics is important for drug development and understanding various biological processes.

Types of proteomics

The types of proteomics are as follows:

• Structural Proteomics: It involves mapping out the 3D structure and nature of protein complexes present in a particular cell organelle. The aim is to build a body of structural information that helps predict the structure and function of proteins.
• Functional Proteomics: It refers to the use of proteomics techniques to analyze the characteristics of molecular protein networks involved in a living cell. It helps understand the function of proteins and protein-protein interactions.
• Expression Proteomics: It involves the quantitative study of protein expression between samples differing by some variable. It is useful in identifying disease-specific proteins and understanding the development of diseases like cancer.

Methods used in proteome analysis

Some of the methods used in proteome analysis are:

• Sodium Dodecyl Sulphate Polyacrylamide Gel Electrophoresis (SDS-PAGE): It is a high-resolution method used universally for analyzing the mixture of proteins according to their respective size. The proteins are denatured and separated based on their size.
• Iso-electric Focusing (IEF): It separates proteins based on their isoelectric points, which is the pH at which the net charges on molecules are zero. Proteins migrate until they reach a region with a pH corresponding to their isoelectric points.
• Mass spectrometry: It is a technique used for identifying and characterizing proteins present in a sample. It measures the mass-to-charge ratio of ions and provides valuable information about protein structures and covalent modifications.

Bioinformatics

Bioinformatics is the field that combines biology, computer science, and information technology to manage and analyze biological data. It involves the application of computer technology to collect, store, analyze, and integrate biological and genetic information. Bioinformatics is used in various fields such as genomics, biotechnology, gene therapy, and agriculture.

Concept of bioinformatics

Bioinformatics is the application of information sciences to increase our understanding of biology, biochemistry, and biological data. It is the management and analysis of biological information stored in databases using computational tools and algorithms.

Database and its classification

A database is a repository of sequences that provide a centralized and homogeneous view of its contents. Databases are classified into sequence databases, which contain information about both proteins and nucleic acids, and structural databases, which contain information about protein sequences.

Data retrieval tools

There are several data retrieval tools used in bioinformatics, such as Entrez, OMIM, BLAST, and FASTA. These tools allow users to access and search nucleotide and protein sequence data, structural data, and information from the biomedical literature.