Molecular Biology

Molecular Biology is a branch of biology focusing on the molecular mechanisms that underlie the processes of biological phenomena. It encompasses the study of biomolecules such as DNA, RNA, and proteins, and examines their roles in replication, transcription, translation, and cellular regulation. By integrating techniques from genetics and biochemistry, molecular biology seeks to understand how molecular interactions govern the function and behavior of cells, ultimately contributing to our understanding of life, disease, and genetic inheritance.

1. Fundamental Concepts in Molecular Biology
   1. Central Dogma of Molecular Biology
      1. Overview of the Central Dogma
         1. Flow of genetic information from DNA to RNA to Protein
         2. Historical development and foundational experiments
      2. DNA Replication
         1. Initiation of replication
            1. Origin of replication in prokaryotes vs. eukaryotes
            2. Role of helicase and primase
         2. Elongation process
            1. Leading and lagging strands
            2. Role of DNA polymerases
            3. Okazaki fragments
         3. Termination of replication
            1. Telomere replication
            2. Role of telomerase
         4. Proofreading and error correction
            1. 3’ to 5’ exonuclease activity
            2. Mismatch repair
      3. Transcription
         1. Initiation
            1. Promoters and transcription factors
            2. RNA polymerase binding and assembly
         2. Elongation
            1. RNA chain elongation mechanism
            2. Role of elongation factors
         3. Termination
            1. Types of termination: rho-dependent and independent
            2. Post-termination processing
      4. Translation
         1. Initiation
            1. mRNA cap and tail recognition in eukaryotes
            2. Shine-Dalgarno sequence in prokaryotes
            3. Assembly of ribosomal subunits
         2. Elongation
            1. Role of tRNA and ribosomes
            2. Elongation factors and GTP hydrolysis
         3. Termination
            1. Stop codons and release factors
            2. Ribosome recycling
         4. Post-translational modifications
            1. Phosphorylation, glycosylation, and other modifications
   2. Genetic Code
      1. Codon structure
         1. Role of triplet codons
         2. Start and stop codons
      2. Redundancy and Wobble hypothesis
         1. Implications of degeneracy in the genetic code
         2. Flexibility in tRNA pairing
      3. Evolution of the genetic code
         1. Theories on origin and adaptation
         2. Universality and exceptions
   3. Structure and Function of Nucleic Acids
      1. DNA
         1. Double helix structure
            1. Watson-Crick model explanation
            2. Major and minor grooves
         2. DNA bases (adenine, thymine, cytosine, guanine)
            1. Complementary base pairing
            2. Hydrogen bonding
         3. DNA replication mechanisms
            1. Semi-conservative replication model
            2. Enzymes involved in the process
      2. RNA
         1. Structural differences from DNA
            1. Ribose sugar vs. deoxyribose
            2. Single-stranded nature
         2. mRNA, tRNA, rRNA
            1. Functional roles in gene expression
            2. Structural uniqueness
         3. RNA bases (adenine, uracil, cytosine, guanine)
            1. RNA folding and stability
         4. RNA processing and splicing
            1. Capping, polyadenylation, and splicing
            2. Role of spliceosomes and ribozymes
            3. Alternative splicing mechanisms
   4. Protein Structure and Function
      1. Amino acids and polypeptide chains
         1. Basic structure of amino acids
         2. Peptide bond formation
         3. Side chain properties and classifications
      2. Levels of protein structure
         1. Primary
            1. Sequence of amino acids
            2. Genetic determinants
         2. Secondary
            1. Alpha helices and beta sheets
            2. Hydrogen bonding patterns
         3. Tertiary
            1. Three-dimensional folding interactions
            2. Role of hydrophobic interactions, ionic bonds, and disulfide bridges
         4. Quaternary
            1. Multimeric protein complexes
            2. Functional implications
      3. Protein folding and function
         1. Chaperones and folding pathways
         2. Misfolding and diseases
            1. Prion diseases
            2. Alzheimer's and other conformational disorders
         3. Functional specificity and enzyme catalysis