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Lecturer(s)
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Šebela Marek, prof. Mgr. Dr.
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Course content
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1. Amino acids and their chemical properties. Ionisation of functional groups, dissociation constant and isoelectric point. Proteinogenic amino acids. Essential amino acids. Peptide bond, Ramachandran plot. Significant natural and synthetic peptides (eg, insulin, ACTH). 2. Proteins, proteome and proteomics. Fibrilar and globular proteins, membrane proteins. Amino acid sequence. Four levels of protein structure, prediction and determination of protein structures. Sructural domains. Interactions in protein molecule. Basic methods for the biochemical study of proteins. 3. Enzymes. The importance of enzymes as biocatalysts. The principle of catalysis, the lock and key theory, the theory of induced fit, catalytic tunnel. Coenzymes and cofactors. Vitamins and trace elements. Enzyme substrates and inhibitors. Enzyme activity. Enzyme catalog. 4. Chemical reactions in living systems. The concept of the Gibbs energy, enthalpy and entropy. Endergonic and exergonic reaction. ´Macroergic compounds. Coupled reactions. Receptors and proteins binding ligands. 5. Carbohydrates, lipids, nucleic acids. Chemical structure and terminology. Glycogen, starch, glycoproteins. Phospholipids and glycolipids. Biological membranes. The sequences of nucleic acids, the genetic code. DNA double helix. The structure of RNA. Enzymatic degradation of carbohydrates, lipids and nucleic acids. 6. The concept of primary and secondary metabolism. Metabolomics. Inborn errors of metabolism. Degradation metabolism (catabolism) and gaining energy. Biosynthetic (anabolic) reactions. The importance of glycolysis, gluconeogenesis and the pentose phosphate pathway. 7. Pyruvate dehydrogenase reaction and the formation of acetyl CoA. The importance of the citric acid cycle. Anaplerotic and cataplerotic pathways.The Pasteur effect. 8. The concept of redox potential. Respiratory chain, cellular respiration. Chemiosmotic theory of ATP formation. Proton gradient and protonmotive force. Uncouplers of oxidative phosphorylation. 9. The principle of protein degradation. Proteolytic enzymes and their importance for proteomics. Pepsin, trypsin and chymotrypsin. Understanding the elimination of carbon skeletons of amino acids plus related metabolic disorders (phenylketonuria, cystinuria, etc.). Adrenalin and the concept of hormonal regulation. Glutamine and glutamate dehydrogenase. Urea cycle. 10. Degradation and biosynthesis of fatty acids. Ketonic bodies and their significance. Steroids, corticoids. Degradation of nucleic acids, uric acid, major inherited disorders of purine metabolism. 11. Cell cycle. Necrosis and apoptosis. DNA replication. Transcription and transcriptome. Ribosomal machinery. Protein synthesis in prokaryotes and eukaryotes - differences. Transfer RNA, initiation and elongation factors. Post-translational modification. Cellular protein transport. 12. Photosynthesis. Plant pigments and the photosynthetic apparatus. C3, C4 and CAM plants. Ribulose bisphosphate carboxylase. Calvin-Benson cycle.
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Learning activities and teaching methods
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Lecture
- Attendace
- 26 hours per semester
- Preparation for the Exam
- 55 hours per semester
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Learning outcomes
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The course is designed for students of Bioinformatics. In an adequate and concise form, students will learn about basic components of living matter with a special attention paid to biomacromolecules (proteins, nucleic acids, polysaccharides) and their structure. The basic principles of metabolic pathways will be explained.
Students become competent in biochemistry and will get acquainted with biomolecules and basic principles of metabolism and its regulation.
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Prerequisites
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successful passing of the subjects from the first two semesters of the study plan Bioinformatics (bachelor level), namely the subjects LRR/OBBC and KFC/SAM.
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Assessment methods and criteria
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Written exam
Successful passing of written examination - obtaining of at least 60% of credit points.
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Recommended literature
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Berg, M. J.; Tymoczko, L. J.; Stryer, L. (2012). Biochemistry. New York.
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Kodíček, M.; Valentová, O.; Hynek, R. (2018). Biochemie: chemický pohled na biologický svět. Praha.
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Koolman, J., Roehm, K. H. (2005). Color Atlas of Biochemistry. Stuttgart.
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Moore, J.T.; Langley, R. (2008). Biochemistry for Dummies. Hoboken, NJ.
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Smith, A.D., managing editor. (2000). Oxford Dictionary of Biochemistry and Molecular Biology. Oxford.
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Sofrová, D. a kol. (2009). Biochemie: Základní kurz. Praha.
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Vodrážka, Z. (2007). Biochemie. Praha.
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