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BIO302 : Molecular Biology

Course Overview

Course Synopsis

This course is designed for graduate students who will explore basic concepts about molecular biology topics starting from nucleic acids (DNA and RNA), genes, genome and then finally up to the gene expression level. This course will enable the students to get sufficient knowledge about the subject to carry out research in the same field.

Course Learning Outcomes

Understanding the central dogma of molecular biology

  • After the successful completion of this course, students will develop basic knowledge and skills in molecular biology and become aware of the complexity and harmony of the cell. As you proceed through the modules, you will become able to apply this knowledge, skill, and awareness to topics such as: structure and functions of DNA/RNA and proteins, DNA/RNA extraction, PCR, recombinant DNA technology, blotting techniques, concept of gene and chromosomes, transcription, translation and DNA replication.
  • This course is aimed to provide ample knowledge to the students which is sufficient to fulfill the requirements of their BS degree. Students will be able to develop classical understanding about molecular biology. An important objective is to provide a supportive environment for students to cultivate higher order thinking skills by synthesizing concepts and by analyzing and interpreting different questions.

Course Calendar

Introduction to Molecular Biology1
History of Molecular Biology2
Achievements of Molecular Biology3
Nucleic Acids4
Chemical composition of DNA5
Nucleoside & Nucleotide6
Types of Deoxyribonucleotides7
How do Deoxyribonucleotides Join?8
Structure of DNA9
Work of Franklin & Wilkins (1950s)10
Structure of DNA - 211
Chemical composition of RNA12
Types of Ribonucleotides13
Types of RNAs14
Structures of RNAs15
Nature of Genetic Material16
Griffith’s Experiments17
Transformation Experiments18
Avery, MacLeod, and McCarty’s experiment19
Hershey & Chase experiment20
Chemical composition of proteins21
Primary structure of proteins22
Secondary structure of proteins23
Alpha Helix24
Beta Pleated Sheets      Current Lesson25
Tertiary Structure of Proteins26
Quaternary Structure of Proteins27
Genetic Materials in Viruses28
Organization of Genetic Material in Bacteria -129
Organization of Genetic Material in Bacteria - 230
Organization of Genetic Material in Eukaryotes31
Histone Proteins32
The Nucleosome33
The 30-nm Fiber - 134
The 30-nm Fiber - 235
Replication of DNA36
Experiment of Meselson & Stahl37
Chemistry of DNA Synthesis - 138
Chemistry of DNA Synthesis - 239
Mechanism of DNA Polymerase40
DNA Polymerases Resemble a Hand - 141
DNA Polymerases Resemble a Hand - 242
DNA mutations52
Nature of Mutations53
Replication errors54
Radiation Demage55
Cyclobutane pyrimidine dimer56
(6-4) Photoproducts57
x rays and gamma rays damage58
DNA instability in water59
water-mediated deamination60
water-mediated deamination (Conti..)61
Oxidative damage to DNA62
Oxidative damage to DNA (Conti..)63
Alkylation damage to DNA64
Alkylation damage to DNA (Conti..)65
DNA damage by PAHs66
DNA damage by aflatoxins67
Chemical cross-linking agents68
DNA damage by Psoralen69
DNA damage by Cisplatin70
Base analogs and interclating agents71
Direct reversal of DNA damage72
CPD Photolyase74
Mechanism of CPD photolyase75
(6-4) Photolyase76
Damage Reversal by Dealkylation77
Dealkylation Enzymes78
Base Excision Repair79
Base Excision Repair Pathway80
Short Patch Repair81
Long Patch Repair82
Nucleotide Excision Repair83
Nucleotide Excision Repair of UV-induced Damage84
UvrA, UvrB, and UvrC Proteins85
The NER Pathway86
Mismatch Repair87
Mismatch Repair System in E. coli88
MutS, MutL, & MutH Proteins89
Mismatch Repair in Eukaryotes90
Human Mismatch repair system91
The Central Dogma92
The Adapter Hypothesis of Crick93
Discovery of the Transfer RNA94
Discovery of the messenger RNA95
Synthesis of RNA upon DNA Templates96
Establishing the Genetic code97
RNA polymerases99
Transcription Process100
Elongation during transcription101
Midterm Examination
Transcription cycle in Bacteria102
transition to the open step103
transition to the open step 2104
Initial transcription105
the Elongating Polymerases107
Termination of the Transcription108
Termination of the Transcription II109
Rho independent termination110
Transcription in Eukaryotes111
Formation of Pre-initiation Complex112
Promoter Escape113
General Transcription Factors114
General Transcription Factors (Conti...)115
The Mediator Complex116
RNA Elongation and Proofreading117
RNA Elongation and Proofreading (Conti...)118
Transcription Termination119
Polymerases I and III120
Polymerases I and III (Conti...)121
RNA Splicing122
How splicing site is determined123
Removal on Introns124
The Spliceosome125
The Splicing Pathway126
Self-Splicing Introns127
Group I Introns128
Finding the Splice Sites Correctly129
Alternative Spliceosome130
Alternative Splicing131
Alternative Splicing 2132
Mutually Exclusive Splicing133
Regulation by Activators and Repressors134
Regulation by Activators and Repressors 2135
Mechanism of RNA Editing136
Mechanism of RNA Editing 2137
RNA Editing by Nucleotide Deamination138
RNA Editing by Nucleotide Deamination 2139
Messenger RNA141
Prokaryotic mRNAs142
Eukaryotic mRNAs143
Transfer RNA144
Secondary structure of tRNA145
Attachment of aminoacids to tRNAs146
The ribosomes147
Structure of Peptide Bonds148
Binding sites on the ribosomes on tRNA149
Initiation of translation150
the initiation factors151
Translation elongation152
The Ribosome is a ribozyme153
The translocation in the large subunits154
Termination of the Translation155
Termination of the Translation part 2156
Nascent Polypeptide processing and folding157
Nascent Polypeptide processing and folding part 2158
Signal Sequence159
Regulation by RNAs in Bacteria160
Regulation by RNAs in Bacteria part 2161
Regulation by RNAs in Eukaryoutes164
Enhancers and Silencers166
Monocistronic or Polycistronic mRNA167
mRNA has a very short life span168
Controlling the rate of mRNA synthesis169
Lactose operon170
Lac structural genes are regulated171
Regulation of Lac mRNA172
The operon Model173
Allolactose; the inducer of lactose operon174
The lac repressor175
The lac repressor2176
Catabolite Repression177
Catabolite Repression 2178
The cAMP?CRP complex179
Galactose Operon180
Galactose Operon 2181
Tryptophan Operon182
Tryptophan Operon 2183
Gene Expression Is Controlled by Regulatory Proteins184
Some Activators and Repressors Work by Allostery185
Cooperative Binding and Allostery186
Activators Recruit the Transcriptional Machinery187
Activators Recruit Nucleosome Modifiers188
Activators Recruit Additional Factors189
Single integration & combinatorial control190
Single integration & combinatorial control 2191
Transcriptional Repressors192
Signal Transduction Pathways193
Plasmids as Vectors194
Plasmid Selection Systems195
pUC Plasmid Cloning Vectors196
Virus-based Cloning Vectors197
? lambda Phage Vectors198
M13 Phage Vectors199
Cosmids & Phagemids200
Large Insert Capacity Cloning Vectors & YAC vectors201
Vectors Used in Eukaryotic Cells202
Final term Examination
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