🧬Systems Biology Unit 2 – Molecular Biology: Genes to Metabolites

Key Concepts and Terminology

• Central dogma of molecular biology describes the flow of genetic information from DNA to RNA to proteins
• Genome refers to the complete set of genetic material in an organism and consists of DNA or RNA
• Genes are segments of DNA that encode instructions for making specific proteins or functional RNA molecules
• Transcription process by which genetic information in DNA is used to produce a complementary RNA strand
• Translation process by which the genetic code in mRNA is read by ribosomes to synthesize proteins
• Metabolites are small molecules involved in cellular metabolism (glucose, amino acids, lipids)
• Systems biology interdisciplinary field that studies complex biological systems as integrated wholes

DNA Structure and Function

• DNA (deoxyribonucleic acid) is a double-stranded helical molecule that carries genetic information
• Composed of four nucleotide bases: adenine (A), thymine (T), guanine (G), and cytosine (C)
  • A pairs with T and G pairs with C through hydrogen bonding
• Sugar-phosphate backbone provides structural stability and connects nucleotides
• Antiparallel structure means the two strands run in opposite directions (5' to 3' and 3' to 5')
• DNA replication is the process by which DNA is copied during cell division
  • Semiconservative replication each new DNA molecule contains one original strand and one newly synthesized strand
• DNA packaging involves wrapping around histone proteins to form nucleosomes and higher-order chromatin structures
• Mutations are changes in the DNA sequence that can alter gene function (point mutations, insertions, deletions)

Gene Expression and Regulation

• Gene expression is the process by which genetic information is used to synthesize functional gene products (proteins or RNA)
• Transcription initiation requires the binding of RNA polymerase and transcription factors to the promoter region
• Promoter region contains specific DNA sequences that regulate transcription initiation
• Enhancers are distant regulatory elements that can increase transcription rates
• Transcription factors are proteins that bind to specific DNA sequences and regulate gene expression
  • Activators increase transcription while repressors decrease transcription
• Alternative splicing allows a single gene to produce multiple mRNA variants and protein isoforms
• Epigenetic modifications (DNA methylation, histone modifications) can alter gene expression without changing the DNA sequence

Protein Synthesis and Modification

• Protein synthesis occurs through the process of translation on ribosomes
• Genetic code specifies the relationship between codons (triplets of nucleotides) and amino acids
  • 61 codons code for 20 amino acids while 3 codons serve as stop signals
• tRNA (transfer RNA) molecules carry specific amino acids and have anticodons complementary to mRNA codons
• Ribosomes are complex molecular machines that catalyze peptide bond formation between amino acids
• Post-translational modifications (phosphorylation, glycosylation) can alter protein function and stability
• Protein folding is the process by which a linear chain of amino acids adopts a specific three-dimensional structure
  • Chaperone proteins assist in proper folding and prevent aggregation
• Protein degradation occurs through the ubiquitin-proteasome system or lysosomal pathways

Metabolic Pathways and Networks

• Metabolism encompasses all chemical reactions involved in maintaining cellular function
• Metabolic pathways are series of enzymatic reactions that convert substrates into products
  • Examples include glycolysis, citric acid cycle, and fatty acid synthesis
• Enzymes are protein catalysts that lower activation energy and speed up reactions
• Cofactors are non-protein molecules (vitamins, minerals) required for enzyme function
• Metabolic regulation involves control of enzyme activity and pathway flux
  • Allosteric regulation occurs when a molecule binds to an enzyme at a site other than the active site
  • Feedback inhibition is a regulatory mechanism where the end product of a pathway inhibits an earlier enzyme
• Metabolic networks are complex interconnected systems of pathways and reactions
  • Flux balance analysis is a computational method used to study metabolic networks

Molecular Techniques and Tools

• Polymerase chain reaction (PCR) is a technique used to amplify specific DNA sequences
  • Requires primers, DNA polymerase, and thermal cycling
• DNA sequencing determines the precise order of nucleotides in a DNA molecule
  • Next-generation sequencing technologies enable high-throughput and cost-effective sequencing
• Gel electrophoresis separates DNA, RNA, or proteins based on size and charge
• Recombinant DNA technology involves manipulating and combining DNA from different sources
  • Restriction enzymes cut DNA at specific recognition sites
  • DNA ligase joins DNA fragments together
• CRISPR-Cas9 is a powerful genome editing tool that allows precise modification of DNA sequences
• Mass spectrometry is an analytical technique used to identify and quantify molecules based on their mass-to-charge ratio

Applications in Systems Biology

• Network analysis studies the complex interactions between genes, proteins, and metabolites
  • Gene regulatory networks describe the interactions between transcription factors and target genes
  • Protein-protein interaction networks map the physical contacts between proteins
• Metabolomics is the study of the complete set of metabolites in a biological system
  • Can identify biomarkers for disease diagnosis and monitoring
• Synthetic biology involves designing and constructing novel biological systems or organisms
  • Metabolic engineering modifies metabolic pathways to produce desired compounds
• Personalized medicine tailors treatments based on an individual's genetic profile
  • Pharmacogenomics studies how genetic variations influence drug response
• Systems biology approaches are used to study complex diseases (cancer, diabetes)
  • Integrates data from multiple omics technologies (genomics, transcriptomics, proteomics)

Challenges and Future Directions

• Data integration and analysis pose challenges due to the large volume and complexity of biological data
  • Requires advanced computational tools and bioinformatics pipelines
• Standardization and reproducibility are important for ensuring the reliability and comparability of results
• Incomplete knowledge of biological systems limits our ability to build accurate models
  • Iterative cycles of experimentation and modeling are needed to refine understanding
• Translating systems biology findings into clinical applications remains a challenge
  • Requires collaboration between researchers, clinicians, and industry partners
• Ethical considerations arise when manipulating biological systems or using personal genomic data
• Future directions include single-cell analysis, spatial omics, and integration of multi-scale data
  • Aim to provide a more comprehensive understanding of biological systems across different levels of organization