BIOCHEMISTRY II

Course ID: MWW-SE>BIOCHEM2
Course title: BIOCHEMISTRY II
Semester: 3 / Winter
ECTS: 5
Lectures/Classes: 30 / 30 hours
Field of study: Veterinary Medicine
Study cycle: 1st cycle
Type of course: compulsory
Prerequisites: General chemistry, organic chemistry
Contact person: prof. dr hab. Maciej Ugorski
Short description: The course provides students with the knowledge on chemical structure and biological properties of proteins, nucleic acids, carbohydrates and lipids, basic metabolic pathways in animal cells, their energetics and regulatory mechanisms as well as basic information pathways and recombinant DNA technology. The course provides some practical training in basic laboratory procedures. After completing the course student acquires the knowledge and terminology necessary to understand biochemistry, molecular biology, physiology, genetics,microbiology, etc.
Full description: 1. Amino acids, peptides and proteins (peptide bond and the primary structure of proteins, proteins’ secondary, tertiary and quaternary structure, examples of fibrillar proteins, the relationship between structure and function, myoglobin - oxygen storage mechanism, structure of hemoglobin, mechanism of oxygen transfer of by hemoglobin, allostery and cooperation mechanisms, Bohr effect). 2. Nucleic acids (structure and nomenclature of nucleotides, structure of DNA and RNA, the genetic code and its properties, DNA mutations – general knowledge, haemoglobinopathies). 3. Biological membranes (structure and properties of the membrane lipids, structure and properties of the membrane proteins, glycoproteins, mosaic model of biological membranes, cell signaling; membrane signal transduction mechanism, membrane transport and its types, transporters, channels and membrane pumps). 4. Enzymes (the definitions of the free energy and the activation energy, difference between the chemical catalysis and biocatalysis, general structure, classification and nomenclature of enzymes, small molecule cofactors of an enzyme activity, enzyme kinetics, regulatory mechanism of the enzyme action, the main types of enzyme inhibition). 5. Bioenergetics (basic concepts and definitions, the “high energy” compounds, and other energy stores in the animal organism - chemical properties, distribution, functions and significance, the mitochondrial respiratory chain – its structural basis and its function, oxidative phosphorylation, Krebs cycle - the course, adjustable, meaning). 6. The carbohydrate metabolism (structure, classification and properties of carbohydrates, glycolysis - meaning, mileage, regulation, the pyruvate metabolism, gluconeogenesis - meaning, mileage, regulation, the metabolism of glycogen - glycogenolysis course and glycogen synthesis, regulation of glycogenolysis and glycogen synthesis, protein kinases, lactose synthesis in mammary gland, and its catabolic pathway in animals and bacteria, the pentose-phosphate pathway - meaning, mileage, regulation, cellulose fermentation processes in animals). 7. The lipid metabolism (catabolism of fatty acids/β-oxidation - meaning, mileage, regulation, ketone bodies - formation, importance, biosynthesis of fatty acids - meaning, mileage, regulation, fatty acid derivatives – eicosanoids, the synthesis and breakdown of triacylglycerols, the synthesis of complex lipids, phospholipases and biologically active derivatives of inositol, steroidogenesis - importance, mileage, regulation, transport of cholesterol and triglycerides, bile acids, steroid hormones, vitamin D – structure and biological role). 8. The nitrogen compound metabolism (amino acid deamination reactions, oxidative deamination, urea cycle, catabolism of the amino acid carbon skeletons, the synthesis of nonessential amino acids, metabolism of one-carbon groups, amino acids as substrates for the synthesis of other physiologically important metabolites or hormones, porphyrin and heme metabolism, synthesis of purine nucleotides - adenylate, guanylate, synthesis of pyrimidine nucleotides - cytydylate, thymidylate and urydylate, catabolism of purine and pyrimidine nucleotides). 9. DNA replication (replicative fork - structure and function, DNA polymerases and other proteins comprising the replisome in Prokaryotes, DNA polymerases in Eukaryotes, types of mutations and their causes, mutagenesis and carcinogenesis, repairing systems of the DNA). 10. RNA synthesis and post-translational processing (transcription in Prokaryotes, transcription in Eukaryotes, post-transcriptional RNA processing in Eukaryotes, alternative splicing and its significance, differences in transcription between Prokaryotes and Eukaryotes). 11. Protein biosynthesis (structure and function of ribosomes and tRNA, synthesis of aminoacyl-tRNA, initiation of translation, elongation and termination of translation). 12. Protein targeting and their catabolism (signal sequences present in various proteins, transport of membrane, secretory and lysosomal proteins, chaperones and their role). 13. Regulation of gene expression in Prokaryotes and Eukaryotes (operon model of regulation of the gene expression, the lac operon as an example of the induced and negatively controlled operon, positive control by the catabolic repression - ara operon, negative control - trp operon, transcription attenuation, multi-level structure of chromatin, the gene regulatory sequences, transcription factors, combinatorial model of gene regulation, regulation of gene expression by steroid hormone). 14. Gene rearrangements (homologous recombination, site specific recombination, rearrangements of genes for L and H chains of immunoglobulins, transposons). 15. Recombinant DNA technology (tools in recombinant DNA technology, cloning using plasmid vectors, cDNA and genomic DNA libraries, expression vectors, recombinant proteins, DNA analysis by Southern and Northern blotting and restriction fragment length polymorphism (RFLP), DNA sequencing, polymerase chain reaction (PCR) and its use in the diagnostics, transgenic animals, somatic cloning, gene therapy.
Bibliography: 1. Mathews C.K. van Holde K.E. Ahern K.G.2000. Biochemistry. Benjamin / Cummings. San Francisco 2. Devlin T.M. 2006. Textbook of Biochemistry with Clinical Correlations. Wiley-Liss,John Wiley & Sons Inc. 3. Berg J.M. Tymoczko J.L. Stryer L. 2007. Biochemistry. W.F.Freeman & Co. New York 4. Voet G. Voet J.G. Pratt C.W. 2006. Fundamentals of Biochemistry, Life at the Molecular Level. John Wiley & Sons Inc. 5. Murray R.K., Granner D.K., Rodwell V.W. 2006. Harper’s Illustrated Biochemistry. Lange Medical Books / McGraw –Hill. New York
Learning outcomes: Knowledge: - describes structure andbiological properties of proteins, nucleid acids, sugers and lipids - knows the basic metabolic pathways in human cells - has a basic knowledge of enzymology, molecular biology and genetic engineering - describes the basic methods of marking and identification of proteins, nucleic acids, carbohydrates and lipids Skills: - basic skills in the preparation of solutions and perform basic biochemical calculations - ability to perform qualitative and quantitative determination of basic low-molecular organic compounds and macromolecules constituting the cells and body fluids - basic skills in the separation and isolation of biologically important macromolecules Social competences: - ability to work by self and team work in an analytical laboratory - students acquire a basic understanding of cell metabolism at the molecular level. This knowledge is essential for further studies in physiology, pathology and clinical aspects of veterinary medicine
Assessment methods and assessment criteria: Biochemistry I: 50% laboratory I + 50% lectures grade Biochemistry II: 50% laboratory II + 50% lectures grade Final grade: 50% laboratory grade + 50% exam grade

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