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BIO302 : Molecular Biology

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Course Info

Course Category

 Molecular Biology

Course Level

 Undergraduate

Credit Hours

 4

Pre-requisites

 N/A

Instructor

 Dr. Hamid Mukhtar
Post-Doc
(Harvard Medical School, Harvard University, USA). 2010-11 “Genome Engineering in Human Induced Pluripotent Stem Cells”

Course Contents

Introduction to Molecular Biology History of Molecular Biology Achievements of Molecular Biology Nucleic Acids Chemical composition of DNA Nucleoside & Nucleotide Types of Deoxyribonucleotides How do Deoxyribonucleotides Join? Structure of DNA Work of Franklin & Wilkins (1950s) Structure of DNA - 2 Chemical composition of RNA Types of Ribonucleotides Types of RNAs Structures of RNAs Nature of Genetic Material Griffith’s Experiments Transformation Experiments Avery, MacLeod, and McCarty’s experiment Hershey & Chase experiment Chemical composition of proteins Primary structure of proteins Secondary structure of proteins Alpha Helix Beta Pleated Sheets Tertiary Structure of Proteins Quaternary Structure of Proteins Genetic Materials in Viruses Organization of Genetic Material in Bacteria -1 Organization of Genetic Material in Bacteria - 2 Organization of Genetic Material in Eukaryotes Histone Proteins The Nucleosome The 30-nm Fiber - 1 The 30-nm Fiber - 2 Replication of DNA Experiment of Meselson & Stahl Chemistry of DNA Synthesis - 1 Chemistry of DNA Synthesis - 2 Mechanism of DNA Polymerase DNA Polymerases Resemble a Hand - 1 DNA Polymerases Resemble a Hand - 2 THE REPLICATION FORK THE RNA PRIMER THE DNA HELICASE TOPOISOMERASES INITIATION OF REPLICATION THE REPLICON MODEL FINISHING REPLICATION TYPE II TOPOISOMERASES TELOMERASE DNA mutations Nature of Mutations Replication errors Radiation Demage Cyclobutane pyrimidine dimer (6-4) Photoproducts x rays and gamma rays damage DNA instability in water water-mediated deamination water-mediated deamination (Conti..) Oxidative damage to DNA Oxidative damage to DNA (Conti..) Alkylation damage to DNA Alkylation damage to DNA (Conti..) DNA damage by PAHs DNA damage by aflatoxins Chemical cross-linking agents DNA damage by Psoralen DNA damage by Cisplatin Base analogs and interclating agents Direct reversal of DNA damage Photoreactivation CPD Photolyase Mechanism of CPD photolyase (6-4) Photolyase Damage Reversal by Dealkylation Dealkylation Enzymes Base Excision Repair Base Excision Repair Pathway Short Patch Repair Long Patch Repair Nucleotide Excision Repair Nucleotide Excision Repair of UV-induced Damage UvrA, UvrB, and UvrC Proteins The NER Pathway Mismatch Repair Mismatch Repair System in E. coli MutS, MutL, & MutH Proteins Mismatch Repair in Eukaryotes Human Mismatch repair system The Central Dogma The Adapter Hypothesis of Crick Discovery of the Transfer RNA Discovery of the messenger RNA Synthesis of RNA upon DNA Templates Establishing the Genetic code Transcription RNA polymerases Transcription Process Elongation during transcription Transcription cycle in Bacteria transition to the open step transition to the open step 2 Initial transcription Inchworming the Elongating Polymerases Termination of the Transcription Termination of the Transcription II Rho independent termination Transcription in Eukaryotes Formation of Pre-initiation Complex Promoter Escape General Transcription Factors General Transcription Factors (Conti...) The Mediator Complex RNA Elongation and Proofreading RNA Elongation and Proofreading (Conti...) Transcription Termination Polymerases I and III Polymerases I and III (Conti...) RNA Splicing How splicing site is determined Removal on Introns The Spliceosome The Splicing Pathway Self-Splicing Introns Group I Introns Finding the Splice Sites Correctly Alternative Spliceosome Alternative Splicing Alternative Splicing 2 Mutually Exclusive Splicing Regulation by Activators and Repressors Regulation by Activators and Repressors 2 Mechanism of RNA Editing Mechanism of RNA Editing 2 RNA Editing by Nucleotide Deamination RNA Editing by Nucleotide Deamination 2 Translation Messenger RNA Prokaryotic mRNAs Eukaryotic mRNAs Transfer RNA Secondary structure of tRNA Attachment of aminoacids to tRNAs The ribosomes Structure of Peptide Bonds Binding sites on the ribosomes on tRNA Initiation of translation the initiation factors Translation elongation The Ribosome is a ribozyme The translocation in the large subunits Termination of the Translation Termination of the Translation part 2 Nascent Polypeptide processing and folding Nascent Polypeptide processing and folding part 2 Signal Sequence Regulation by RNAs in Bacteria Regulation by RNAs in Bacteria part 2 RiboSwitches CRISPRs Regulation by RNAs in Eukaryoutes Promoters Enhancers and Silencers Monocistronic or Polycistronic mRNA mRNA has a very short life span Controlling the rate of mRNA synthesis Lactose operon Lac structural genes are regulated Regulation of Lac mRNA The operon Model Allolactose; the inducer of lactose operon The lac repressor The lac repressor2 Catabolite Repression Catabolite Repression 2 The cAMP?CRP complex Galactose Operon Galactose Operon 2 Tryptophan Operon Tryptophan Operon 2 Gene Expression Is Controlled by Regulatory Proteins Some Activators and Repressors Work by Allostery Cooperative Binding and Allostery Activators Recruit the Transcriptional Machinery Activators Recruit Nucleosome Modifiers Activators Recruit Additional Factors Single integration & combinatorial control Single integration & combinatorial control 2 Transcriptional Repressors Signal Transduction Pathways Plasmids as Vectors Plasmid Selection Systems pUC Plasmid Cloning Vectors Virus-based Cloning Vectors λ lambda Phage Vectors M13 Phage Vectors Cosmids & Phagemids Large Insert Capacity Cloning Vectors & YAC vectors Vectors Used in Eukaryotic Cells Practical-1- Lab safety protocols Practical-2- Introduction to laboratory equipment Practical-3- Preparing Tris Buffer Practical-4- working solution Practical-5- Isolation of nucleic acids Practical-6- Quantification of nucleic acids Practical-7- Restriction digestion of DNA Practical-8- Preparation of restriction maps Practical - 9- Gel electrophoresis Practical-10 - Polymerase chain reaction (PCR) Practical-11- Detection of mutations Practical - 12 - Restriction fragment length polymorphism. Practical - 13 - Preparation of chemically competent cells Practical - 14 - Transformation of bacteria with plasmid DNA Practical - 15 - Comparing plasmids of different molecular weights Practical - 16 - Molecular weights marker
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