Genomics,proteomics and comparative genomics
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This document provides an introduction to genomics, proteomics, and comparative genomics. It discusses the central dogma of molecular biology involving DNA replication, transcription, and translation. It describes DNA and RNA structure and explains how genetic information flows from DNA to protein. The document also discusses genome sequencing, gene mapping, and how comparative analysis of genomes from different species can provide insights into evolutionary relationships and biological functions.
Genomics,proteomics and comparative genomics
- 1. Genomics, Proteomics and Comparative Genomics- Basic Concepts Dr. Nusaifa Beevi.P Associate Professor, PG Department of Botany, Iqbal College, Peringammala
- 2. INTRODUCTION • DNA- the most impt biomolecule which carry genetic informn. • Making Proteins is a key operation of all living organisms • DNA (nucleus) does not directly serve as a template for the ordering of aminoacids for their polymerization in to proteins (ribosomes in the cytoplasm). • So it requires the involvement of an intermediate molecule in transferring information from DNA in the nucleus, to the cytoplasm. • This intermediary molecule is the RNA. • These three classes of biomolecules play equally important role and constitute the central principle upon which all living activities depend. • This principle is called central dogma of molecular biology, which involved 3 processes viz; replicaion, transcription and translation (flow of genetic information).
- 3. CENTRAL DOGMA OF MOLECULAR BIOLOGY • DNA REPLICATION • Each time a cell divides, each of its double strands of DNA splits into two single strands. Each of these single strands acts as a template for a new strand of complementary DNA. As a result, each new cell has its own complete genome. This process is known as DNA replication. • DNA biosynthesis proceeds in the 5′- to 3′-direction. • TRANSCRIPTION • Transcription is the process by which DNA is copied (transcribed) to mRNA, which carries the information needed for protein synthesis. Transcription takes place in two broad steps. • TRANSLATION • The mRNA formed in transcription is transported out of the nucleus, into the cytoplasm, to the ribosome (the cell's protein synthesis factory). Here, it directs protein synthesis.
- 4. Polymerization of nucleotides occurs only in the 5’—3’ direction. So polymerization occurs ‘forwards’ in one strand and ;backwards (3’— 5’) in the other. The synthesis of 5’—3’ (forward) strand is continuous and it proceeds in non-stop manner (leading). The synthesis of 3’—5’ strand is semi-discontnous and proceed backward with several unconnected polynucleotides called okazaki fragments (lagging). They later joined together through phosphodiester bonds and DNA ligase.
- 5. • In the flow of information in cells, nucleotide sequences and amino acid sequences, serves as informational macromolecules. • The amino acid sequence of protein is analogous to the letters of the alphabet, determined by the nucleotide sequence of DNA. • 20 genetically encoded amino acids are naturally incorporated in to polypeptides and are called standard amino acids. • They assighned both 3-letter and 1-letter code
- 7. Properties of Genetic Material • From the Hershey and Chase experiment, the fact was established that DNA acts as a genetic material. But later, studies revealed that in some viruses (e.g., Tobacco Mosaic Viruses, bacteriophage, etc.) RNA is the genetic material. • Following are the criteria that a molecule must fulfil to act as a genetic material: • (i) It should be able to replicate. • (ii) It should be chemically and structurally stable. • (iii) It should provide the scope for slow changes • (iv) It should be able to express itself in the form of ‘Mendelian characters’. According to these criteria, both DNA and RNA have the ability to direct their duplications (because of the rule of base pairing and complementarity), whereas the other molecules in the living system, fail to duplicate, e.g., protein.
- 8. Chargaff's rules • Through careful experimentation, Erwin Chargaff discovered four rules that lead to the discovery of the double helix structure of DNA. These are called Chargaff's rule 1. The quantitative base composition of DNA varies with species, but it remains the same among the members of a species. 2. DNA contains equal amounts of purines and pyrimidines. I e. (A+G) = (C+T) or (A+G) / (C+T) = 1 3. The molar content of guanine units is equal to that of cytosine units, and the adenine units is equal to the thymine units. i.e A=T and G=C or A/T=G/C=1 4. The base ratio (A+T) / (G+C) is not equal to 1, but is different in different species and the same and constant among the members of a given species.
- 9. Chemical Bonding in DNA Glycosidic bonding:- Sugar links with purines or pyrimidines and forms deoxyribo nucleosides like deoxyadenosine, deoxyguanosine, Deoxycytidine and deoxythymidine, Ester bonds:- Deoxyribo nucleosides link with phosphoric acid through this bond and forms deoxyribo nucleotides like deoxy adenylic acid, deoxyguanylicacid, Deoxy cytidylicacid and deoxythymidylic acid. These nucleotodes undergo condensation polmerization through C-3 and C-5 phosphodiester bonds and form polynucleotide chains. Two such chains coil around each other and interlink through hydrogen bonding and form a DNA molecule.
- 10. Levels of DNA structure Primary structure:- Formation of nucleotides and their condensation polymerization to form single poly nucleotide chains Secondary structure:- DNA double helix or duplex Tertiary structure:- represented by the coiling and compaction of the DNA duplex to form nucleosomes, and then its supercoiling and further compaction to form a solenoid structure, characteristic of eukaryotic chromatin.
- 11. Molecular Organization of DNA First explained by the Nobel laureates James Watson and Francis Crick in 1953. So called as Watson and Crick double helical model. They were honoured with Nobel Prize for this discovery, in 1962 It is based on X-ray diffraction studies of Rosalind Franklin and Maurice Wilkins and also on Chargaffs rule of base pairing. A/c to them DNA molecule is in the form of a spiral ladder It is formed of two complementary, antiparallel polynucleotide chains, twisted around a common axis in the form of a right - handed double helix. The two chains are held together and the double helical structure is stabilized by inter chain hydrogen bonds between complementary bases and also by the ‘stacking interaction’ b/w adjacent base pairs.
- 12. Molecular Organization of DNA • The two chains are complementary and anti-parallel with opposite polarity. • The inter nucleotide phospho diester bonds run from C-3 to C-5 in one strand, and from C-5 to C-3 in the other. • In each polynucleotide chain, the constituent molecules are arranged in two series, one outer and one inner layer. • The outer layer consists of pentose sugar alternate with phosphate group and forms the back bone of the chain. • Nitrogenous bases are arranged along the inner side, perpendicular to the long axis of the chain. • They stack one above the other in the centre of the double helix • Externally, each base links with a sugar molecule through glycosidic bonds and internally, it non-covalently links with a corresponding base of the companion strand through hydrogen bonds and forms a base-pair.
- 13. GENOMICS • In the field of molecular biology and genetics genome is the genetic material of an organism. • Genome is defined as the full complement of genetic information, both coding and non coding. • It also include the mitochondrial DNA and chloroplast DNA. • The study of genome of an organism is called genomics. • It basically involve analysis of nucleotide sequence of genomes using computational methods (sequencing of genome). • The availability of genome sequences revolutionized many areas of biology
- 14. IMPORTANCE OF GENOMICS • Provides a map of the genetic make up of a cell. • Gives an idea of how the cell responds at the genetic level to different situations. • More than 3000 whole genomes have been sequenced till date and added to public databases. • This enables researchers to compare the genomes of different organisms, to see how the genes function in different circumstances, how they interact, how they control over one another or how differences in the genomes are reflected in the phenotype.
- 15. HISTORY OF GENOMICS • 1903- Chromosome theory of heredity (W,S.Sutton & T. Bovery). • 1932- First linkage map constructed.( T.H.Morgan) • 1970- First DNA sequencing (Frederic Sanger). • 1977- Bacteriophage phi X 174 (ΦX174) (first virus) – sequenced. • 1995- The first bacteria to have its entire genome sequenced • 2004- Human Genome Project published. • DNA bar coding • DNA libraries • DNA sequencing. • Computer algorithms • Genetic maps and physical maps. • PCR technique
- 16. BASIC PRINCIPLES OF GENOMICS • Eukaryotic genes with informative or coding sequences, interspaced with long stretches of non-informative or non-coding ‘silent ‘ or ‘spacer’ sequences. • The non-coding regions are called junk DNA. • The coding units are called exons. • Exons are actually interspaced by introns. • All exons may undergo transcription and translation and find their expression in the primary, intermediate and final products(pre-mRNA, mature mRNA and proteins). • Introns are only transcribed to the pre-mRNA
- 17. BASIC PRINCIPLES OF GENOMICS • Introns are sliced out during the post-transcriptional chemical processing of immature mRNA- “m RNA splicing” • Introns appear only in the primary mRNA transcript and never in mature mRNA and proteins. This primary mRNA transcript is also called heterogenous nuclear RNA (hn mRNA) or precursor mRNA (pre-mRNA) • So eukaryotic genes are expressed only after splicing. • Discovered in 1977 by Richard.J.Roberts and Philip Sharp. • All split genes begins with an exon, and also end with the same. • The presence of introns is neither essential nor deleterious to the organism.
- 18. BASIC PRINCIPLES OF GENOMICS-SPLIT GENES
- 19. ABOUT THE HUMAN GENOME • The human genome consists of 3.2 billion nucleotides, of which barely 1.4% is coding sequences. • The difference in the composition of genomes between two human individuals is only 0.1%.ie. A difference in merely 25 genes. • Our nearest relative is the chimpanzee, with 99% similarity. • About 8500 disease associated genes have been identified for about 7000 genetically inherited diseases. • In more than 1000 of these diseases, the location of the defective gene has been determined in particular chromosomes by linkage analysis. • The changes are due to deletions, insertions, inversions or translocations.
- 20. BROAD COVERAGE OF GENOMICS • Structural genomics: Understanding the content of genome and is concerned with genome mapping, genome sequencing and genome manipulations. • Functional genomics: Identification of genes and their respective functions • Comparative genomics: Analysis and comparison of genomes from different species. It includes animal genomics, plant genomics, microbial genomics etc..
- 21. STRUCTURAL GENOMICS • Concerned with understanding the content of genome. • First step is genome mapping (to prepare genetic and physical maps of its chromosomes). • A genetic map is analogous to a highway map that shows the locations of major towns and cities, here it provides a rough approximation of the locations of the genes, in relation to the locatoin of other known genes. • A physical map is analogous to a neighbourhood map that shows the location of every house along a street, and are based on the direct analysis of DNA, and they place genes in relations to distance measured in number of base pairs, kilobases or megabases. • Physical map has higher resolution and accuracy.
- 22. Genetic Maps Vs Physical Maps • Genetic Maps : Order and location of markers assigned to chromosome on the basis of linkage analysis. Distance measured in Morgans (M) • Physical Maps : Actual structure of genetic material. At highest level DNA sequence. Distance measured in bp (Mbp/Kbp)
- 23. TECHNIQUES FOR CREATING PHYSICAL MAPS • Restriction Mapping : determine the position of restriction sites on DNA • Sequence Tagged Sites (STS) Mapping : locates the positions of short unique sequences of DNA • Flourescent in situ hybridization (FISH) : markers can be visually mapped to locations on chromosomes. • DNA sequencing: technique of determining the sequence of individual nucleotides in a DNA molecule or gene.
- 24. Functional Genomics • Probing genome sequences for meaning. It include: Identifying genes Recognizing their organization Understanding their function Goal of functional genomics include identifying all the mRNA molecules transcribed (transcriptome) from a genome and all the proteins encoded by the genome(proteome). It means to understand the relationship b/w genome and phenotype. It make use of the wet-lab analysis and bioinformatics for the study of gene expression
- 25. Gene Functions - Homology Searches • It is the first employed computational method for understanding gene function. • It depends on comparing DNA and Protein sequences from same and different organisms. • Databases containing genes and proteins in a wide array of organisms are available for homology searches. • Evolutionary related genes are called homologous • Homologous genes found in different species that are evolved from the same gene in a common ancestor are called orthologos. • Homologous genes in the same organism arising by gene duplication of a single gene in the evolutionary past are called paralogos.
- 26. Other Sequence Comparison/Protein domain • Domains are protein regions that have specific shape/function. • Each protein domain has an arrangement of amino acids common to that domain. • Molecular functions of many such domains has already been determined and stored as databases. • The sequence from a newly identified gene can be scanned against a database of known domains. • The function of already identified domain can provide information about a possible function of the new gene.
- 27. PROTEOMICS • A branch of Functional genomics • Study of identification and determination of amount, localization and interaction of all proteins,of a cell/tissue /organism. • Definition- Large scale study of protein properties such as expression levels, post translational modifications, and interactions with other molecules to obtain global view of cellular processes at the protein level • It has three categories
- 28. Categories of proteomics • Structural proteomics:- Includes a large scale determination of 3D structure of protein complexes • Functional proteomics:- Study of the analysis of functions of proteome with the help of functional inactivation of protein to elucidate the role of target protein • Expression proteomics:- Study of protein expression of entire protein through protein profiling with the help of 2D gel electrophoresis and mass spectroscopy.
- 29. COMPARATIVE GENOMICS • Genomic features (genomic structural land marks like DNA sequence, genes, gene order, regulatory sequences) of different organisms are compared. • Helps to study the biological similarities and differences as well as evolutionary relationships between organisms. • With the explosion in the number of genome project , which is due to the advancement in DNA sequencing technologies, it is possible to deal with many genomes in a single study.
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