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 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 cgi 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

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 hours Cycle of PCR steps DNA denaturation at 95 degrees C. Primer annealing at 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) Microarray (single or dual channel) SAGE SAGE EST/cDNA library 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. ( ) MIPS-Munich Information center for Protein Sequences. ( ) 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 It’s a curated pathway database. We can analyse,browse and download pathways Kyoto Encyclopedia of Genes and Genomes holds the current knowledge on molecular interaction networks, including metabolic pathways, regulatory pathways,and molecular complexes MetaCyc MetaCyc is a database of nonredundant, experimentally elucidated metabolic pathways

Readings based+data based+data Learning goals