Biochemical Engineering
Theory
- Introduction in Biochemical and Metabolic Engineering
- Basic concepts of metabolism
- Metabolic pathways in fermentations
- Enzyme kinetis synopsis
- Enzyme inhibition
- Allosteric enzymes - Concerted model
- Modeling of cellular reactions
- Control of metabolic pathways
- Analysis of metabolic flux
- Experimental methods for study and control of metabolism
- Metabolic control analysis
- Metabolic Engineering in action
- Material Balances
- Mass Transfer in Biochemical systems
- Factors Affecting Cellular Oxygen Demand
- Cell Growth Kinetics
- Basic principles of Reactor Engineering
Laboratory exercises
- Analysis of enzyme kinetic data using various computational and graphical methods to obtain kinetic parameters
- Regulatory action of inhibitors on enzyme activity - Identification and quantification of inhibitory effects
- Metabolic regulation of a yeast enzyme - Induction versus repression of α-glucosidase from Saccharomyces cerevisiae
- Simulation and control of metabolic pathways - Gepasi software
- Implementation of Gepasi software in metabolic control analysis
- Regulation of metabolic pathways for aminoacids overproduction - The case of lysine from Corynebacterium glutamicum
- Bioprocess simulation in bioreactors
Molecular Genetics
- Mutations and DNA Repair
Molecular mechanisms of spontaneous mutations. Induced mutations. Modification of DNA. DNA repair systems in prokaryotes, photoreactivation, mismatch repair, recombinational repair, SOS system. DNA repair systems in eukaryotes, non-homologous end-joining, the Ku heterodimer. Deficiencies in DNA repair systems and hereditary disorders.
- Genetic Recombination
Homologous recombination, site-specific recombination, bacteriophage integration, mechanism of integrase action. Chiasmata, crossing-over, Holliday junction, chromosomal pairing, synaptonemal complex. Gene conversion.
- Transposable Elements
Prokaryotic and eukaryotic transposable elements. Insertion sequences, transposase, transposition mechanisms, composite transposons. Controlling elements in Zea Mays and phenotypic diversity. The phenomenon of hybrid dysgenesis in Drosophila, P elements, copia transposons. The contribution of transposable elements in genomic instability. Transposable elements and regulation of gene expression. Importance of the mobile elements for the creation of genetic diversity
- Regulation of gene expression
Examples of general regulatory systems in prokaryotic organisms. Examples of positive and negative regulation of gene expression, lactose and arabinose operons. The phenomenon of attenuation in the tryptophan operon. Two-component sensory transduction systems. Transcriptional regulatory elements of eukaryotic genes. Structure and function of transcriptional activators, mechanisms of induction. Co-regulatory molecules, interactions with the basal transcription machinery, transcriptional repressors. Cooperative regulation in transcription. Insulators and mechanisms of action. Levels of DNA packaging and gene expression.
- Regulatory RNA Molecules
Bacterial regulatory RNA. Co-suppression of transgenes in plants. Principles and mechanisms of RNA interference. RNAi and epigenetic regulation. MicroRNA, structure, mechanism of processing, miRNA genes and their function.
- Epigenetic Modifications of the Genome:
Alternative chromatin states, chromatin remodeling, histone code, histone modification enzymes (acetylation, methylation). Epigenetic phenomena, position effect variegation, sex-linked genes and dosage compensation, inheritance of methylated DNA, genomic imprinting, epigenetic inheritance.
- Reorganization of DNA Sequences, Modifications of Phenotype and Gene Expression
Mating type switching in Saccharomyces cerevisiae, the MAT locus.
