The document provides an overview of genomics and proteomics. It defines genomics as the study of an organism's complete set of genes and discusses structural, functional and comparative genomics. It also defines proteomics as the study of the complete set of proteins and discusses structural, functional and expression proteomics. The key techniques discussed for both include sequencing, 2D gel electrophoresis, mass spectrometry and database searching.

1. WELCOME
TO
GENOMICS &
PROTEOMICS
Parul Kaushik

2. Presented by
PARUL KAUSHIK

3. Contents :-
 Genomics
 Structural genomics
 Functional genomics
 Sequencing of genomes
 Clone-by-clone Sequencing
 Shot gun sequencing
 Genome sequence
compilation
 Comparative genomics
 Application of genomics
 Limitations of genomics
 Proteomics
 Structural proteomics
 Functional proteomics
 Expression proteomics
 Proteomics analysis
 2-D protein gel
 Electrophoresis
 Mass spectrometry
 Database searching
Application of
 proteomics
Reference
Parul Kaushik

4. GENOMICS :-
The study of complete set of genes for an
organism
Term Given : By Thomas H.
Roderick (1987)
Classified into :
●Structural genomics
●Functional genomics
Parul Kaushik

5. Structural Genomics :-
Determine complete sequence of genomes
●Gene mapping
●Gene sequencing
●Genome analysis
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6. Functional genomics :-
Studies the functioning of genes
and metabolic pathways , analysis of
information derived from structural
genomics to a variety of functions
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7. Sequencing of genomes :-
● Sequence the entire genome by cutting it
into small pieces
● Fragment cloning & generation of genomic
library
● Assembled the pieces into a sequence for
the genome
● Sequencing of genomes by two approaches -
●Clone -by-clone sequencing
●Shot gun sequencing
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8. Clone -By -Clone sequencing :-
● Clones are arranged in contigs
● Create cosmid & plasmid clones
and arranged in contigs
● Each clone of contig is sequenced
until the entire genome is sequenced
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9. Shot gun sequencing :-
● For DNA sequences longer than 1000 bp
● Haemophilus influenzae the first organism to
have its genome completely sequenced,
By Craig Venter in 1995
● Randomly selected clones are sequenced
● DNA fragments may be overlapping or
non-overlapping
● Sequencing the each fragment and generate
the complete sequence of the genome by
assembling the all sequences
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10. Genome sequence compilation :-
● To ensure that the nucleotide
sequence of a genome is complete
and error-free , the genome is
sequenced more than once .
● Pseudomonas aeruginosa - sequenced
7 times
● Human genome - sequenced 12 times
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11. Comparative genomics :-
The study of
differences & similarities in genome
structure and organisations of different
organisms .
Objectives :-
●To understand the process of evolution
●To convert the DNA sequence data into
proteins of known functions
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12. Comparative
Genomics
Horizontal
gene
transfer
Genome
similarty
Gene
order
comparison
Phylogenetic
footprinting
Origin of
new
genes
Minimum
genome
size
Comparative
genomics
of
mitochondria
Conclusion
from
comparative
genomics
SNPs
Exon
Shuffling
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13. Exon shuffling :- New combination of exons
are produced by recombination within the
intervening sequences
Horizontal gene transfer :-
Genitic exchange between different
evolutionary lineages
Genome Similarity :-
The genomes of organisms differing remarkably
in appearance may be quite similar
●Human & mice share about 97.5 % of their DNA
Sequence
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14. SNPs :-
(Single Nucleotide Polymorphism)
●SNPs are single Base position in genomic DNA
at which different nucleotide occur in different
individual of a population
●Used to map genes involved in human
diseases
●Pharmacogenomics : The field of study that is
concerned with effect of genetic variation on
disease susceptibility and drug response
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15. SNPs:-
AGCT TGCGT
TCGAACGCA
AGCTA GCGT
TCGAT CGCA
AGCT CGCGT
TCGAG CGCA
AGCTG CGCA
TCGA CCGCA.
－
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16. Gene order comparison :-
●Comparing the gene order of two organisms
●If the gene order of two organisms is comparable ,
they termed as Syntenic
●Synteny benefit - Information on gene location
from a highly mapped organism can be used to locate
the corresponding gene in a poorly mapped relative
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17. Phylogenetic Footprinting :-
●A comparative analysis of genome
sequences of related species to detect
orthologous DNA sequences
●Allow the discovery of genes and regulatory
elements
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18. Origin of New genes :-
●Many of the new genes are most likely
prokaryotic genes that have been modified
●The alpha - helical eukaryotic domains
evolved from the condensed coiled structure
present in prokaryotes
●New genes could have arisen from
transposable elements
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19. Minimum genome size :-
Minimum 250- 350 genes are necessary for
the organisms to exist as independent , self -
replicating organisms.
Smallest genome size :
●For unicellular eukaryote - 2.9×10*6 bp
for the parasite Encephalitozoan cuniculi
●For vertebrate - 4×10*8 bp for Japanese
puffer fish ( Fugu rubripes)
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20. Comparative genomics of
Mitochondria :-
●Animal & fungal mtDNA is smaller than
plant mtDNA
●The animal & plant mtDNA are mtDNA are
derived genomes
●Mitochondria considered to have originated
from Rickettsia prowazekii, the causal agent of
epidemic typhus
●Genes from mtDNA have been transferred into
nucleus , ( has stopped in animals )
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21. Conclusion from comparative
genomics :-
In Prokaryotes :
● Genome size vary from 0.58×10*6 bp Mycoplasma
germitalium to 30×10*6 bp Bacillus megaterium
●Gene density is relatively constant at one gene per kilo
Base pair
●Some bacteria like Vibrio cholerae have two or more
circular chromosome
●E.coli genome has ~ 600 operon
●Frequency of paralogues increase with genome size
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22. In Eukaryote :-
● Gene density declines with genome size
●Fruit fly act as model organism for study of even complex human
diseases
●Genomes have large amount of repetitive DNA
● Transposable elements density :-
Human Genome - 44.4%
Arabidopsis thaliana - 10.5%
Drosophila melanogaster- 3.1%
Caenorhabditis elegant - 6.5%
●Difference in intron and exon structure
●Some bacterial species have more genes than lower eukaryotes
●Genomes of Archaea have similarities with eukaryotic genome
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23. Application of genomics :-
●In Genomic medicine
●In Synthetic biology &
Bioengineering
●In Conservation genomics
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24. Limitations of genomics :-
●Expensive technique
●High technical skill
●Laborious work
●Limited genes available
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25. PROTEOMICS :-
Study of the complete set of
Proteins
Types of proteomics :-
●Structural proteomics
●Functional proteomics
●Expression proteomics
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26. Structural proteomics :-
●Mapping out the 3-D structure
●Concern with nature of protein complex
●Build a body of structural information
●Explain how the expression of certain
proteins contributes in cell's unique
characteristics
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27. Functional proteomics :-
It refers to the use of proteomics
techniques to analyse the
characteristics of molecular protein
network involved in a living cell
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28. Expression proteomics :-
●It refers to the quantitative study of
protein expression between samples
differing by some variable
●Useful in identifying disease -specific
proteins
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29. Proteome analysis :-
●2-D protein gel electrophoresis
●Mass spectrometry
●Database searching
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30. 2-D protein gel electrophoresis:-
To study the abundance and post- translational modifications of several
hundred proteins
Use for the separation of both soluble and membrane proteins
fraction as well as Glycoprotein
 Protein extract
 Polyacrylamide gel
 Apply electric charge
 Separate proteins according to their
molecular weight
 Rotate 90 °
 Protein separation according to their
molecular mass
 Spots cut from gel
 Digest with enzyme
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31. Mass spectrometry :-
• Protein separated by 2 -D
• Stained spots subjected to in -gel digestion with trypsin
• Resulting peptides separated by
High performance liquid chromatography
• Eluting peptides subjected to tendon MS
• Ionization of peptides by Electrospray ionization
• First MS
• Peptides identified on the basis of their mass to charge ratio
• Selected peptide is fragmented by collision with an inert gas
• Second MS
• Separate resulting peptide fragment
• Protein identification
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32. Database searching :-
●Identification of proteins by mass requires access to protein sequence database
●The most commonly used database are -
SWISS-2D PAGE : For protein
identification
NCBI/ BLAST : Sequence database
SWISS-PROT : Sequence database
SWISS-MODEL : For 3- D structure
PROSITE : For domain structure
GenBank and EMBL : DNA Data banks
●A database provide information on abundance and post-translational modification ,
also on the intracellular localisation
of a subset of proteins
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33. Application of Proteomics :-
●Post- translation modifications
●Protein-protein interactions
●Protein- expression profiling
● Molecular medicine
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