Last update: doc. MUDr. Alena Stoklasová, CSc. (29.08.2023)
The main topics of the course include:
1) Principles of general, inorganic, physical and organic chemistry important for understanding biochemical processes. They include interactions between molecules, selected biogenic elements and their compounds, isomerism, biochemically significant organic compounds and their transformations typical of the organism, nomenclature, thermodynamics and kinetics of chemical reactions focused on biological systems, catalysis, enzymes, coenzymes and vitamins, solutions and their properties, acid-base processes, oxidation-reduction processes and biological oxidations, amino acids, peptides and proteins.
2) Basic aspects of metabolism focus on the overall overview of metabolism, electron transport chain and formation of high energy compounds, formation of reactive oxygen and nitrogen species, citric acid cycle, metabolism of carbohydrates and nucleic acids; protein synthesis.
3) Basic laboratory techniques in biochemistry focus on potentiometry, spectrophotometry and chromatography and their use for characteristics of buffers, determination of catalytic concentration of enzymes, influencing the results of laboratory examinations (analytical errors), or protein separation.
Learning outcomes:
1.The student will consolidate his/her knowledge of the course of chemical reactions in application to living systems and their influence by external conditions.
2.The student acquires a basic idea of the relationships between metabolic processes, which he/she will use in their more detailed study, including regulations at various levels in related subjects.
3.The student will get acquainted with the basic laboratory techniques used in the biochemical laboratory and will be able to process the results and their evaluation.
4.The student will be able to use the acquired knowledge in solving model case reports.
Entry requirements
Last update: doc. MUDr. Alena Stoklasová, CSc. (29.08.2023)
Completion of courses: Anatomy II; Histology and Embryology II
Aim of the course
Last update: doc. MUDr. Alena Stoklasová, CSc. (29.08.2023)
The aim of the course is to provide knowledge of chemistry that is necessary for understanding chemical principles applied in biochemistry and other related subjects and to acquaint students with the importance and function of nucleic acids, proteins and enzymes, metabolsim of carbohydrates, with the bioenergetics of living systems and the links of anabolic and catabolic pathways. As part of the laboratory classes, the student gains orientation in a biochemical laboratory, learns basic laboratory techniques, learns to process the results of measurements into protocols and evaluate them. The teaching of the subject consists of lectures (providing a theoretical basis), laboratory classes (to acquire skills in individual laboratory procedures) and seminars (where knowledge is applied and practiced).
Requirements to the exam
Last update: doc. MUDr. Alena Stoklasová, CSc. (29.08.2023)
Credit:
1) Attendance at classes
Maximum of three absences in classes of Biochemistry I in the semester is allowed.For the first two absences in the semester, you must inform the authorized person Assoc. Prof. A. Stoklasová, M.D., Ph.D. in advance, but it is not necessary to provide any documentation. Starting on the 3rd absence and onwards, only cases documented by valid medical certificates or official documents will be considered. The documents must be sent to authorized person. The guarantor of the subject will consider it individually and decides whether the excuse is legitimate and acceptable. The guarantor’s decision is not appealable
2) Active participation in classes, documented by
- completed and submitted homework assignments for laboratory classes and seminars (in MOODLE). In the case of an absence from the class, all homework assignments must be submitted no later than by the end of the semester.
- protocols of attended laboratory classes signed by a teacher. In the case of an absence from the laboratory class, special assignment (defined in MOODLE) must be completed no later than by the end of the semester.
3) Satisfactory results of examination
Average from all graded tests, oral examinations, and graded assignments must be at least 3.00 or better. In the case of absence, substitute tests must be completed no later than by the end of the semester and the date must be settled with Assoc. Prof. A. Stoklasová via e-mail.
4) Credit test
The result must be graded at least 3.00 or better (66 %).
Manual and topics of written tests and oral examinations are available in MOODLE.
Failure to meet the contidtions (1-4) will result in “Non credited” grade. Student has the right to two retakes for fulfilment of criterion (3) and (4) for the course credit. The retake will have a form of examination covering all topics of Biochemistry I.
In the event of a forced transition to online teaching, lectures and seminars will take place as planned in an online mode. Worksheets will be available in MOODLE, their submission will be limited in time and processing will be controlled. The materials will also include test questions. Testing will be in an online mode in various forms including essay. For laboratory classes, short videos will be prepared introducing students to the relevant technique and will be supplemented by the processing of given data and their evaluation.
If the lessons will take place without restrictions and some of the students will be in quarantine or ill for a long time, they are obliged to immediately notify Assoc. Prof. A. Stoklasová (via e-mail). Individual replacement of lessons will be agreed during their absence.
Consultations can be arranged individually and must be agreed in advance with the teacher by email.
Inspection of the tests: It is possible for one week from the date of writing, upon agreement with Assoc. Prof. A. Stoklasová (contact via e-mail).
Note: The pre-term for the biochemistry exam in the summer semester is also conditioned by the results in the winter semester. It is allowed to those who had an average at least 2.00 or better in the winter semester and the result of the credit test was also at least 2.00 or better.
Syllabus
Last update: doc. MUDr. Alena Stoklasová, CSc. (29.08.2023)
Lectures
Introduction to Study (Stoklasová 1)
Effect of ionizing Radiation on Living Systems. Radioisotopes in Medicine. (Hroch 2)
Chemical Thermodynamics - the Laws of Thermodynamics, Enthalpy, Entropy, Free Energy. Spontaneity of Chemical Change. Chemical Equilibrium. Equilibrium Constant. Le Chatelier´s Principle. (Hroch 1)
Chemical Kinetics. Reaction Rates and Factors that Influence them. Activation Energy and the Activated Complex. Catalysts and Mechanism of their Effect. (Hroch 1)
Anabolism and Catabolism. High Energy Compounds. (Řezáčová 1)
Solutions and their Properties. Solubility, Concentration of Solutions. Solutions of Electrolytes, Ionization Constant. Activity (effective concentration). Colloidal and Osmotic Properties of Solutions. Components of the Blood. (Havelek 3)
Acids and Bases. The Dissociation of Water. The pH Scale. Salts, Hydrolysis of Salts, Solubility Product. Buffers, Characterization, pH, Capacity. Buffers of the Blood. (Havelek 2)
Important Organic Compounds in Biochemistry. Hydrocarbons and their Derivatives. Alkanes, Alkenes, Alkynes, Cycloalkanes, Aromatic Hydrocarbones; Alkyl- and Aryl Halides, Amino-, Nitro-derivatives of Hydrocarbons; Thiols, Sulphides, Disulphides, Sulphonic Acids; Alcohols, Phenols; Aldehydes, Ketones; Carboxylic Acids and their Derivatives. Urea and its Derivatives. Typical Reactions. (Muthná 4)
Heterocyclic Compounds with one or more Heteroatoms. An Introduction to the Chemistry of Alkaloids. Vitamins as Cofactors of Enzymes. (Stoklasová 2)
Amino Acids and their Properties. Important Peptides. Proteins - Amino Acid Composition, Conformation of Proteins - Types of Bonds and Interactions. Physical and Chemical Properties. (Mrkvicová 1)
Enzymes - Characterization, Mechanism of their Action. Kinetics of Enzymic Reactions, Michaelis Constant. Environmental Effects Influencing Enzyme Activity. Inhibition of Enzyme Activity. Nomeclature and Classification of Enzymes. Enzymes in Medicine. (Mrkvicová 2)
Introduction to Metabolism. Citric Acid Cycle and its Regulation. The Pyruvate Dehydrogenase Complex. (Řezáčová 1)
Oxidation and Reduction in Living Systems. Biological Oxidation. Reactive Oxygen and Nitrogen Species. (Řezáčová 2)
The Electron Transport Chain and its Components. The Mechanism of Oxidative Phosphorylation. (Řezáčová 2)
Carbohydrates - Classification, Structure, Formation of Hemiacetal and Glycosidic Linkage, Properties, Basic Reactions. Digestion and Absorption in the Gastrointestinal Tract. Glycolysis, Gluconeogenesis, Pentose Phosphate Pathway, Metabolism of Glycogen, Fructose, Galactose and Uronic acids and their Regulation. (Řezáčová 4)
Synthesis and Degradation of Purine and Pyrimidine Nucleotides. (Beránek 2)
Biosynthesis of Nucleic Acids - Replication and Transcription. Proteosynthesis. (Beránek 2)
Laboratory classes & seminars
Prof. Martin Beránek, Dr., Ph.D.
Prof. Martina Řezáčová, M.D., Ph.D.
Prof. Jiri Stulik, M.D., Ph.D.
Assoc. Prof. Radim Havelek, Dr, Ph.D.
Assoc. Prof. Miloš Hroch, Ing., Ph.D.
Assoc. Prof. Alena Stoklasová, M.D., Ph.D.
Renata Köhlerová, MS, Ph.D.
Alena Mrkvicová, MS, Ph.D..
Darina Muthná, Dr., Ph.D.
Eva Peterová, MS, Ph.D.
Darja Koutová, MS, Ph.D.
Martin Uher, Dr., Ph.D.
Seminars
Chemical Reactions.Thermodynamics and Kinetics of Chemical Reactions. Basic Calculations in Chemistry.
Solutions, pH, Bufers. Electrolytes, Electrolytic Dissociation. The Bronstedt-Lowry Concept. The pH of Acids and Bases. Buffers. Basic Calculations. Collodidal Solutions. Osmotic Pressure. Test.
Organic Compounds Important in Biochemistry I. Hydrocarbons, Alcohols, Phenols, Quinones, Nitrogen- and Halogen-derivatives, Sulphur-containing Compounds, Aldehydes, Ketones, their Reactions. Test.
Organic Compounds Important in Biochemistry II. Organic Acids, their Reactions. Urea and its Derivatives. Importance in Biochemistry. Test.
Heterocycles. Alkaloids. Vitamins as a Component of Enzymes. Importance in Biochemistry. Test.
Synthetic Materials Important in Medicine. Isoprenoids, Vitamins Soluble in Fat. Importance in Medicine.
Amino Acids, Peptides, Proteins, their Properties.
Introduction to Metabolism. The Citric Acid Cycle. Substrate Phosphorylation. Test.
Enzymes. Kinetics of Enzyme reactions. The Michaelis Constant. Factors Affecting the Rate of Enzyme Catalyzed Reactions. Isoenzymes and their Importance in Clinical Practise.
Biological Oxidation. Bioenergetics. The Electron Transport Chain and Oxidative Phosphorylation. Reactive Oxygen and Nitrogen Species. Enzymes Involved in their Metabolism. Test.
Carbohydrates I: Structure, Properties. Digestion and Transport of Carbohydrates. Metabolism of Glucose - Glycolysis, Gluconeogenesis.
Carbohydrates II:Pentose Phosphate Pathway, Metabolism of Glycogen, Fructose, Galactose and Uronic Acids.
Meeting with an Expert: Study of Genes and Nucleic Acids. Proteomics. Importance in Medicine.
Credit test.
Laboratory classes
Laboratory Practice and Safety Rules. Introduction to Spectrophotometry.
Potenciometry. Weak Acid - Titration Curve.
Spectrophotometry. Determination of ferrous Ions Concentration.
The pH Measurement. Determination of Capacity of Acetate Buffer. Buffer Capacity of Proteins.
Factors Influencing Laboratory Results. Accuracy of Measurement.
Properties of Enzymes - the Influence of pH, Temperature, Concentration and Substrate Specificity.
Kinetics of Enzymatic Reactions.
General Properties of Amino Acids and Proteins. Determination of Isoelectric Point of Proteins.
Gel Permeation Chromatography. "Desalting" of Proteins.
Notes:
Attendance at laboratory classes and seminars is COMPULSORY and a register is kept. Substitution of written tests must be consulted with Asssoc. Prof. Stoklasová in case of your unavoidable absence (e. g. illness). Before starting laboratory class, do not forget laboratory coat and change your shoes (with rubber sole - no shoe covers). Calculator is necessary. Laboratory manual is available in MOODLE.
Literature
Last update: doc. MUDr. Alena Stoklasová, CSc. (29.08.2023)
Compulsory literature
1. R. Y. Ouellette Introduction to General, Organic and Biological Chemistry. 3rd ed., Mac Millan Publ.Company, New York, 1992. ISBN 0-02-390245-0 (or the latest edition available)
2. R. K. Murray et al. Harper's Biochemistry. 24th ed., Appleton and Lange, Stamford, USA, 1996.ISBN 0-8385-3612-3. (or the latest edition available)
3. J.W. Baynes et M. H. Dominiczak Medical Biochemistry. 4th ed., Elsevier 2014. ISBN 978-1-4557-4580-7
Materials prepared by the teachers – MOODLE (presentations, lectures, materials for home preparation, worksheets)
Recommend literature
1. Z. Durackova et al. Medical Chemistry. Asklepios, Bratislava, 1993. ISBN 80-7167-003-0
2. P. C. Champe and R.A.Harvey Biochemistry. Lippincott Co, 1987. ISBN 0-397-50801-8 (or the latest edition available)
3. Z. Orszaghova, I. Zitnanova et al. Medical Chemistry, Univerzita Komenskeho v Bratislave, 2008, ISBN 978-80-223-2426-7
