All Study Guides Systems Biology Unit 2
🧬 Systems Biology Unit 2 – Molecular Biology: Genes to MetabolitesMolecular biology explores the intricate journey from genes to metabolites, unraveling the central dogma of DNA to RNA to proteins. This unit covers key processes like transcription, translation, and metabolic pathways, highlighting how genetic information flows and is expressed in living organisms.
Systems biology takes a holistic approach, examining how these molecular components interact within complex biological networks. By integrating various omics technologies and computational tools, researchers aim to understand and model the behavior of entire biological systems, from cells to organisms.
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
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
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