🧬Molecular Biology Unit 1 – Introduction to Molecular Biology

Key Concepts and Terminology

• Molecular biology studies the structure, function, and interactions of biological macromolecules essential for life (nucleic acids, proteins, carbohydrates, and lipids)
• Nucleic acids (DNA and RNA) store and transmit genetic information
• Proteins perform a wide range of functions in living organisms (enzymes, structural components, signaling molecules, and more)
• Genome refers to an organism's complete set of genetic material
• Gene expression is the process by which genetic information is used to synthesize functional gene products (proteins or RNA)
• Mutations are changes in the DNA sequence that can lead to altered gene function or expression
• Recombinant DNA technology involves manipulating and combining DNA molecules from different sources to create novel genetic sequences
  • Enables the production of recombinant proteins (insulin) and genetically modified organisms (GMOs)

Structure of DNA and RNA

• DNA (deoxyribonucleic acid) is a double-stranded helical molecule composed of nucleotides
  • Each nucleotide consists of a sugar (deoxyribose), a phosphate group, and a nitrogenous base (adenine, thymine, guanine, or cytosine)
• DNA bases pair through hydrogen bonds (A with T and G with C) to form the double helix structure
• RNA (ribonucleic acid) is typically single-stranded and composed of nucleotides with a ribose sugar and the base uracil instead of thymine
  • RNA types include messenger RNA (mRNA), transfer RNA (tRNA), and ribosomal RNA (rRNA)
• DNA is more stable than RNA due to the absence of the 2' hydroxyl group on the sugar and the double-stranded structure
• DNA is primarily located in the nucleus, while RNA can be found in the nucleus and cytoplasm
• The antiparallel nature of DNA strands is crucial for replication and transcription processes

Central Dogma of Molecular Biology

• The central dogma describes the flow of genetic information in living organisms: DNA → RNA → Protein
• DNA serves as the template for its own replication and the synthesis of RNA through transcription
• RNA, specifically mRNA, acts as the intermediary to convey genetic information from DNA to ribosomes for protein synthesis (translation)
• The genetic code is the set of rules that defines how the sequence of nucleotides in mRNA is translated into the sequence of amino acids in a protein
• Reverse transcription, observed in retroviruses (HIV), allows the conversion of RNA back into DNA
• The central dogma emphasizes the unidirectional flow of genetic information, with rare exceptions (reverse transcription and RNA replication in some viruses)

Replication, Transcription, and Translation

• Replication is the process of copying DNA to produce two identical DNA molecules
  • Occurs during cell division to ensure each daughter cell receives a complete set of genetic material
• Replication is semiconservative, meaning each new DNA molecule contains one original strand and one newly synthesized strand
• DNA polymerase enzymes catalyze the addition of nucleotides to the growing DNA strand based on complementary base pairing with the template strand
• Transcription is the synthesis of RNA from a DNA template, catalyzed by RNA polymerase enzymes
  • Produces mRNA, tRNA, and rRNA
• Transcription factors and regulatory elements (promoters, enhancers) control the initiation and rate of transcription
• Translation is the process of synthesizing proteins using the genetic information in mRNA
  • Occurs at ribosomes in the cytoplasm
• tRNAs act as adaptor molecules, carrying specific amino acids to the ribosome and recognizing the corresponding codons in the mRNA sequence

Genetic Code and Protein Synthesis

• The genetic code is the set of rules that determines how the sequence of nucleotides in mRNA is translated into the sequence of amino acids in a protein
• Codons are three-nucleotide sequences in mRNA that specify a particular amino acid or a stop signal
• The genetic code is degenerate, meaning multiple codons can code for the same amino acid
  • Reduces the impact of point mutations and allows for codon bias in different organisms
• Start codons (AUG) initiate translation, while stop codons (UAA, UAG, UGA) terminate protein synthesis
• Ribosomes, composed of rRNA and proteins, catalyze the formation of peptide bonds between amino acids during translation
• Post-translational modifications (phosphorylation, glycosylation) can alter the structure, function, or localization of proteins

Gene Regulation and Expression

• Gene regulation controls the timing, location, and amount of gene expression in cells
• Prokaryotic gene regulation often involves operons, where multiple genes are under the control of a single promoter (lac operon)
  • Repressors and activators bind to specific DNA sequences to inhibit or promote transcription
• Eukaryotic gene regulation is more complex, with multiple levels of control (chromatin structure, transcription factors, RNA processing, and more)
• Epigenetic modifications (DNA methylation, histone modifications) can alter gene expression without changing the DNA sequence
  • Play crucial roles in development, cell differentiation, and disease
• Alternative splicing allows a single gene to produce multiple protein isoforms with different functions
• Gene expression can be quantified using techniques like RNA-seq, microarrays, and quantitative PCR (qPCR)

Molecular Biology Techniques

• Polymerase Chain Reaction (PCR) amplifies specific DNA sequences using primers, dNTPs, and a heat-stable DNA polymerase (Taq)
  • Enables the detection and quantification of DNA from small samples
• DNA sequencing determines the precise order of nucleotides in a DNA molecule
  • Next-generation sequencing (NGS) technologies allow for high-throughput, parallel sequencing of millions of DNA fragments
• Cloning involves inserting a DNA fragment into a vector (plasmid) and introducing it into a host cell (bacteria) for replication and expression
• CRISPR-Cas9 is a powerful genome editing tool that allows for precise modification of DNA sequences in living cells
  • Has applications in basic research, agriculture, and gene therapy
• Gel electrophoresis separates DNA, RNA, or proteins based on size and charge using an electric field applied to a gel matrix (agarose or polyacrylamide)
• Southern, Northern, and Western blotting techniques detect specific DNA, RNA, or protein molecules, respectively, using labeled probes

Real-World Applications and Future Directions

• Personalized medicine tailors treatments to an individual's genetic profile
  • Pharmacogenomics studies how genetic variations influence drug response and guides the development of targeted therapies
• Genetic testing can identify inherited disorders, predict disease risk, and guide family planning decisions
• Gene therapy aims to treat or cure genetic diseases by introducing functional copies of genes into cells
  • Recent successes in treating inherited retinal disorders (Luxturna) and spinal muscular atrophy (Zolgensma)
• Synthetic biology designs and constructs novel biological systems or organisms with desired functions
  • Applications in biofuel production, biosensors, and artificial organs
• Molecular diagnostics detects pathogens, monitors disease progression, and guides treatment decisions using molecular biology techniques (PCR, sequencing)
• CRISPR-based technologies have the potential to revolutionize agriculture (crop improvement), animal health, and environmental conservation
• Single-cell sequencing provides unprecedented insights into cellular heterogeneity and enables the study of rare cell types and developmental processes