Transcript CELL - DSDHT

CELL
 Building blocks of life
 Chemical system able to maintain its structure and reproduce
 Cells  tissues  organs Organism
PROKARYOTES
 Primitive organisms
 Rigid cell walls
 DNA found in Nucleoid
EUKARYOTES
 Plasma membrane(animals) cell wall(plants)
 Large nucleus
 Chromosome
Overview of Prokaryotic and Eukaryotic cells
BLUE PRINT OF LIFE
• DNA – Deoxy ribose nucleic acid
• Instructions to make proteins for the cell
Crick-Watson model
 Double helical structure with complimentary binding
 A,G,C,T building blocks of DNA A=T , CΞG
 Anti parllel strands with 5’ and 3’ ends
CENTRAL DOGMA
GENE
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Part of DNA that can translate into a protein –Gene
Transcription : A,C,T,G -> A,C,U,G
RNA – mRNA , tRNA, rRNA
Every 3 bases in mRNA form a codon and codes for specific
amino acid
• Every 3 bases in tRNA has specific anticodon that binds to
specific codon.
• rRNA is a component of ribosome, helps in translation
Prokaryotic and Eukaryotic genes
The Difference
Prokaryotes
• Continuous stretch of genes
• Transcribed mRNA is directly translated by ribosomes
Eukaryotes
• Mix of introns and exons
• Post transcriptional changes
• Each gene has its own transcriptional control
GENE PREDICTION
• In Prokaryotes genes can be identified using ORFs
• In Eukaryotes genes can be identified by Hidden Markov
models (HMMs) for gene finding :
GeneMark,GeneMark.hmm, GLIMMER,GRAIL, GenScan /
GenomeScan, etc.
• http://genes.mit.edu/GENSCAN.html
• http://www.ncbi.nlm.nih.gov/genomes/MICROBES/glimmer_
3.cgi
Proteins
 Final output of Central dogma
 Long chains of amino acids – Primary structure
 α-helices, and β-sheets with h-bonds – Secondary structure
 α-helices, and β-sheets fold to globular structure with
hydrophobic interactions .- Tertiary Structure
 Disulphide bonds – Quaternary structure
Structure determination
90% - X ray crystallography
9% - NMR Spectroscopy
http://fold.it/portal/
Biotechnology
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It harnesses cellular and biomolecular processes to develop
technologies and products that help improve our lives and the
health of our planet.
• Using Biotechnology we can fetch information of various
activities at cellular level, such as genetic disorder, gene
regulation, protein -protein interactions, protein functions etc.
DNA HYBRIDISATION
Why Polymerase Chain Reaction
• PCR can make billions of copies of a target sequence of DNA
in a few hours
Cycle of PCR steps
• DNA denaturation at 95 degrees C.
• Primer annealing at 50-60 degrees C.
• DNA polymerization by a thermostable DNA polymerase at 72
degrees C.
Applications
• Forensic medicine.
• Preimplantation Genetic Diagnosis (PGD).
• Archeology.
• Paternity testing.
Why Gene expression analysis
 Changes to the cell’s internal or external environment can
lead to changes in gene expression.
 Most human diseases manifest through a mis-regulation of
gene expression
Techniques Used to Detect Gene Expression Level
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Microarray (single or dual channel)
SAGE
EST/cDNA library
Northern Blots
Subtractive hybridisation
Differential hybridisation
Representational difference analysis (RDA)
DNA/RNA Fingerprinting (RAP-PCR)
Differential Display (DD-PCR)
aCGH: array CGH (DNA level)
Why protein-protein interactions (PPI)?
 PPIs are involved in many biological processes:
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Signal transduction
Protein complexes or molecular machinery
Protein carrier
Protein modifications (phosphorylation)
 PPIs help to decipher the molecular mechanisms underlying the biological
functions, and enhance the approaches for drug discovery
High throughput experimental methods for discovering PPIs
 Yeast-two-hybrid
 Affinity purification followed by mass spectrometry (AP-MS)
PPIs Databases.
 DIP- Database of Interacting Protein.
(http://dip.doe-mbi.ucla.edu/ )
 MIPS-Munich Information center for Protein Sequences.
(http://mips.gsf.de/ )
PATHWAYS
 A metabolic pathway is a series of chemical reactions occurring within a
cell, catalyzed by enzymes, and resulting in either the formation of a
metabolic product to be used or stored by the cell, or the initiation of
another metabolic pathway.
 Networks of metabolite feedback pathways
 regulate gene and protein expression,
 also can mediate signaling between organisms.
Public resources for Pathways
 Reactome
http://www.reactome.org/
It’s a curated pathway database. We can analyse,browse and
download pathways
 Kyoto Encyclopedia of Genes and Genomes
http://www.genome.jp/kegg
holds the current knowledge on molecular interaction
networks, including metabolic pathways, regulatory
pathways,and molecular complexes
 MetaCyc
http://www.metacyc.org
MetaCyc is a database of nonredundant, experimentally
elucidated metabolic pathways
Readings
• http://dsdht.wikispaces.com/Biologybased+data
• Learning goals