Biochemistry

obligatory courses

The course is intended for the students of the major “Use of Physics in Biology and Medicine” (Molecular Biophysics, Molecular Modelling And Bioinformatics). The students should be acknowledged with the problems included in the program of the following courses: General Chemistry, Organic Chemistry, Bioorganic Chemistry.

Classroom

The course will acknowledge the students with the basic problems of a modern biochemistry, the knowledge of which shall allow understanding of tasks and challenges of medicine and pharmacology of the 21st century. Basic components and processes of cell metabolism, with consideration of enzymatic transformations, gene expression and energetic processes will be discussed.

Proteins – primary, secondary, tertiary and quaternary structure. Molecular evolution of the proteins, ordination of the proteins.

Enzymes. Terminology and units, specificity, ordination and nomenclature of the enzymes. Enzymatic kinetics – the Michaelis Theory. Types of inhibition and activation of enzymes. Allostery. Regulation of enzyme activity. Mechanism of enzyme functioning – structure of an active site, catalytic mechanisms. Enzymatic complexes. Co-enzymes.

Metabolism of the proteins. Proteolytic enzymes. Transamination, decarboxylation, oxidative deamination. Urea cycle.

Nucleic acids. Primary structure. Biosynthesis from precursors. DNA – secondary and tertiary structure. RNA: t-RNA, m-RNA, r-RNA. Enzymes that cleave nucleic acids. Genetic functions: DNA replication, RNA transcription. Mechanism of genetic information transmission. Genetic code. Translation – protein biosynthesis.

Carbohydrates – structure and metabolism. Mono-, di- and polysaccharides of animal and plant origin. Glycosides. Hydrolysis and phosphorolysis of polysaccharides. Glycolysis and fermentation. Substrate phosphorylation. Urea cycle. Pentose phosphate pathway. Gluconeogenesis. Photosynthesis. Calvin cycle.

Lipids – structure and metabolism. Proper fats, phospholipids, glycolipids, steroids, waxes, isoprenoids, vitamins. Metabolism: digestion of lipids, β-oxidation of fatty acids, biosynthesis of fatty acids, glycerides and phospholipids.

Biological oxidation – basics of bioenergetics. Electron transport chain. Electron carriers and their oxidoreductive potentials. Mechanism of oxidative phosphorylation according to Mitchell. Comparison of energetic balance of oxidative and substrate phosphorylation. Mitochondrion structure.

Photosynthesis – light process. Structure of the chloroplast. Dyes of the antennae complex. Photochemical pumping of the chlorophyll. Photosystem 1 and 2. Electron transport in the processes of cyclic and acyclic phosphorylation.

Structure of cell organelles – localisation of biochemical processes. Cell membrane – structure, chemical composition. Mechanisms and energetics of active and passive membrane transport. Membrane canals and pores, carriers, co-transport, ionophores. ATP-ase sodium/potassium pump in the membrane. Calcium pump. Cell nucleus – structure of the prokaryotic and eukaryotic chromosome, plasmids, transposones. Mitochondrial biochemistry, biochemical functions of the endoplasmic reticulum of the ribosomes.

Metabolic interdependencies. Stages of cell catabolism. Inflows and outflows from the Krebs cycle to the pool of proteins, carbohydrates and lipids.

After finishing this course the student:

knows the outline of a living cell structure and its basic organelles (cell nucleus, mitochondrion, chloroplasts, extracellular walls and membranes, intracellular membranes). He knows the chemical and physicochemical characteristics of the basic structural compounds of the cell: proteins, carbohydrates, nucleic acids, lipids. He understands the metabolic role of enzymes, hormones, deoxy-and rybonucleic acids, co-enzymes, sugars and mineral components of the cell. He knows the functions and the role of the main pathways, metabolic cycles and cellular processes (replication, transcription, translation, glycolysis, fermentation, Krebs cycle, pentose phosphate cycle, gluconeogenesis, beta-oxidation of fatty acids, biosynthesis of fats, urea cycle). He understands the physical (thermodynamical and electron) basis of the processes of energy transformation in living cells, in the electron transport chain and during photosynthesis.

Passing of two written tests during a semester is required. Obtaining positive grades may be a reason for an exam dispensation. Exam in a written form, in doubtful cases also in oral form.