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 cellCrick-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

• 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 DifferenceProkaryotes• 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 determination90% - X ray crystallography9% - NMR Spectroscopyhttp://fold.it/portal/

Biotechnology• 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 hoursCycle 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 • 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)

PPIs are involved in many biological processes:• 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/ )

Why protein-protein interactions (PPI)?

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/Biology-based+data

• Learning goals