Detailed requirements from medical chemistry and biochemistry
related to the individual questions from module B
(the details are not included in the list of questions used during examination)
1. Water as a solvent - polar properties, hydration sheath, hydrogen bonds, osmosis, osmotic
pressure, diffusion, dissociation equilibrium (dissociation constant), pH.
2. Chemical composition of cells - review: inorganic substances (water, ions, gases), and organic
compounds (macromolecular: structure and storage molecules, biocatalysts; energy substrates,
intermediates and products of metabolism) - properties, function. Conformation, configuration, and
isomerism of organic compounds. Types of chemical bonds.
Saccharides in details - structure, classification, chemical and physical properties, biological
importance, occurence in the nature; important sacharides: glucose, fructose, galactose, mannose,
ribose, 2-deoxyribose, glyceraldehyde, dihydroxyacetone, saccharose (sucrose), lactose, maltose,
starch, glycogen, cellulose; important terms: monosaccharides, disaccharides, oligosaccharides,
polysaccharides
(homopolysaccharides,
heteropolysaccharides),
glycosaminoglycanes,
proteoglycanes, glycoproteins, reducting and non-reducting saccharides, O- and N- glycosidic bond,
glycosides, glycosidases and their specifity, Fischer´s, Tollens´s and Haworth´s formula, hemiacetal
structure, triose, tetrose, pentose, hexose, heptose, asymmetrical (chiral) carbon atom, izomerism of
saccharides: aldoses and ketoses, pyranoses and furanoses, epimers, D- and L- series of
saccharides, alfa and beta anomers, optical activity, mutarotation, racemic mixture, amino
saccharides, oxidation and reduction of saccharides, deoxysugars, aldonic, aldaric and alduronic
acids, sugar alcohols, esters with phosphoric acid.
(Detailed structure of lipids and proteins is a part of other questions.)
3. Catalysis - the principle and importance.
Enzymes – structure (apoenzyme, cofactor - coenzyme or inorganic ion, prosthetic group, active
centre, subunits, allosteric place, proenzymes, isoenzymes, isoforms), classification into six classes
(oxidoreductases, transferases, hydrolases, lyases, izomerases, ligases), nomenclature, chemical and
physical properties (chemical character of apoenzyme and cofactor, pH-optimum),
kinetics
(mechanism of enzyme catalysis, complex enzyme-substrate, enzyme activity, units of enzyme
activity, Michaelis-Menten´s equation, Michaelis´s constant, maximum rate, graph of dependence of
reaction rate on concentration of substrate, activation and inhibition of enzyme activity, competitive
and non-competitive, reversible and irreversible inhibition, allosteric regulation of enzyme activity,
induction of enzyme, influence of temperature and pH on the enzyme activity), reaction and substrate
specifity, biological function.
Coenzymes - structure, relation to vitamins, classification (redox coenzymes, coenzymes transfering
groups), function, examples of their use in biochemical reactions.
4. Chemical reactions – rate of chemical reactions, influence of concentration and temperature on
reaction rate, equilibrium of chemical reactions, the law of Guldberg-Waag, reversible and irreversible
reaction, exergonic and endergonic reactions, exothermic and endothermic reactions, Gibbs´s energy,
enthalpy, entropia, coupled reactions, the principle of action and reaction. Redox reactions - oxidation
(dehydrogenation), reduction (hydrogenation).
Energy-rich (macroergic) compounds – kinds, structure (phosphoric acid anhydrides, derivatives of
CoA, enolphosphates, phosphoguanidine), properties, importance, examples from metabolism (their
origin and utilization).
Importance of redox coenzymes in cell energetics - NAD+, NADH (versus NADP+ and NADPH), FAD,
FADH2
Production of ATP in a cell – oxidative (aerobic) phosphorylation and substrate level phosphorylation,
localization in the cell, description, importance; adenylates in the cell (the ratio of ATP / ADP + AMP),
uncoupling proteins (uncouplers of the respiratory chain from the aerobic phosphorylation).
5. Glucose and its transformation - transport of glucose through cellular membrane, phosphorylation of
glucose to glucose-6-phosphate, importance of reaction catalyzed by pyruvate dehydrogenase,
metabolic pathways of glucose utilization: glycolysis, synthesis of glykogen, pentose phosphate cycle;
pathways serving for supplying glucose into circulation: glycogenolysis, gluconeogenesis;
transformation of glucose-6-phosphate to glucose; important derivatives of glucose: glucuronic acid,
glucitol – their origin and utilization.
The importance of other saccharides and their derivatives in metabolism: fructose, galactose, ribose –
their utilization and metabolism.
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6. Lipids in metabolism – fatty acids as a source of energy: structure and source of fatty acids,
transport of fatty acids in blood, lipases, beta oxidation; ketone bodies: structure, synthesis and
degradation; store of energy in the form of lipids: synthesis of fatty acids, synthesis of triacylglycerols,
their structure (monoacylglycerols, diacylglycerols, triacylglycerols); cholesterol and its derivatives structure, synthesis, importance in organism; transport of lipids in plasma, metabolism of lipoproteins
(formation and fate of chylomicrons, VLDL, IDL, LDL and HDL).
7. Proteins in energy metabolism - enzymes degrading proteins to amino acids, removal of aminogroup: transamination and deamination, transport of amino-nitrogen in blood, synthesis of urea, ways
of excluding of amino-nitrogen from organism; fate of carbon sceleton of amino-acids (synthesis of
glucose or oxidation in Krebs cycle). Decarboxylation of amino acids: formation of monoamines (only
review, not their synthesis: histamine, catecholamines (adrenaline, noradrenaline, dopamine),
serotonin (5-hydroxytryptamine), ethanolamine, acetylcholine; GABA (gamma-aminobutyrate).
Amino acids - structure, classification, chemical and physical properties, biological importance,
occurence in the nature; important amino acids: glycine, alanine, serine, cysteine, methionine, valine,
leucine, isoleucine, threonine, tryptophan, tyrosine, phenylalanine, aspartic acid, glutamic acid,
arginine, histidine, lysine, proline; ornithine, citrulline, taurine; important terms: L- and D- amino acids,
asymmetric (chiral) carbon atom, alfa-amino acids, beta- and gama- amino acids, essential aminoacids, amino-nitrogen, side chain, polar and nonpolar structure, ampholyte ion (zwitterion), isoelectric
point, decarboxylation, transamination, dissociation.
Synthesis of amino acids - essential and nonessential amino acids, synthesis of Ala, Cys, Asp, Asn,
Glu, Gln, Tyr. Modified amino acids (3- and 4-hydroxyproline, 5-hydroxylyzine, 3-methylhistidine).
8. Structure of DNA - description, chemical and physical properties, biological importance, occurence
in the nature; important terms: phospho diester bond, N-glykosidic bond, purine and pyrimidine bases,
minority bases, nucleoside, nucleotide, oligonucleotide, polynucleotide, 5´- and 3´- end of
polynucleotid chain, hydrogen bridge, primary, secondary and tertiary structure of DNA, right-handed
and left-handed helix, double helix, parallel and antiparallel polynucleotid chains, nucleosom,
nucleoproteins, histones, 2´-deoxyribose, nucleases, nucleotidases, nucleosidases, gene, exone,
introne, triplets of bases (codons), anticodon, pairing of bases, replication, transcription.
9. Nucleic acids - structure, classification, chemical and physical properties, biological importance,
occurence in nature; important nucleic acids: DNA, RNA; important terms: phospho diester bond,
N-glykosidic bond, purine and pyrimidine bases, minority bases, nucleoside, nucleotide,
oligonucleotide, polynucleotide, 5´- and 3´- end of polynucleotid chain, hydrogen bridge, primary,
secondary and tertiary structure of DNA, right-handed and left-handed helix, double helix, parallel and
antiparallel polynucleotid chains, nucleosom, nucleoproteins, histones, ribose, 2´-deoxyribose, rRNA,
tRNA, mRNA, hnRNA, nucleases, nucleotidases, nucleosidases, gene, exone, introne, triplets of
bases (codons), anticodon, aminoacyl-tRNA, pairing of bases, replication, transcription.
10. Peptides and proteins - structure, classification, chemical and physical properties, biological
importance, occurence in the nature; important proteins: enzymes, structural and transport proteins,
immunoglobulins, complement, coagulation factors, signal molecules; important peptides: glutathione,
peptide hormones, neuromodulators; important terms: peptide bond, hydrogen bridge, hydrophobic
and ion interactions, disulfide bond, primary, secondary, tertiary and quaternary structure of protein,
beta pleated-sheet structure, beta-turns, domains, subunits, allosteric effect, random coil, C- and Nend of peptid chain, nomenclature of peptides, oligopeptides, polypeptides, alpha-helix, simple and
complex proteins, nucleoproteins, glycoproteins, phosphoproteins, hemoproteins, metalloproteins,
lipoproteins, globular and fibrous proteins (spheroproteins and scleroproteins), denaturation of
proteins, hydrolysis of peptid chain, peptidases, proteases, colloidal solution, swelling.
Post-translational modification of proteins - cleavage of the polypeptide chain (preprotein  protein),
hydroxylation, methylation, glycosylation - the difference between glycosylation and glycation;
oxidation of cysteine residues - formation of disulfide bridges. Formation of crosslinks between
polypeptide chains (e.g. in collagen).
11. Membranes - structure, properties, importance; important terms: semipermeability, amphipatic
structure, phospholipids, phospholipid bilayer, differences in composition of the cytosolic and
noncytosolic layer of the phospholipid bilayer, polar „head“ of phospholipid, hydrophobicity,
glycerolphospholipids, sphingophospholipids, glycolipids, cholesterol, saturated and unsaturated fatty
acids, membrane proteins (classification, anchoring the proteins in the membrane), peripheral and
integral proteins, glykoproteins, antigenic determinants, membrane receptors, fluidity, rigidity, fluid
mosaic model, cross-asymetry, micelles.
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Lipids - structure, classification, chemical and physical properties, biological importance, occurence in
the nature; important lipids: fatty acids, (lauric, myristic, palmitic, stearic, oleic, linoleic, linolenic,
arachidonic), triacylglycerols, phospholipids, cholesterol, esters of cholesterol; important terms:
saturated and unsaturated fatty acids, cis- and trans- fatty acids, omega-3 and omega-6 fatty acids,
essential fatty acids, glycerol, phosphatidic acid, ester bond, glycerolphospholipids,
sphingophospholipids, glycolipids (cerebrosides and ganglyosides), micelles, lipoproteins,
hydrophobic and hydrophylic properties, amphipathic structure, polar and nonpolar solvents, tensides,
hydrolysis of fats, hydrolysable and nonhydrolysable lipids, phospholipases.
12. Transport across membranes - general rules of difussion of substances through the phospholipid
bilayer of membranes; kinds of transport, importance and description of transport systems,
mechanisms of transport; important terms: primary and secondary active transport, simple and
facilitated diffusion, channels and pores, ion channels, the „pumps“, sodium-potassium pump, the
transporter (carrier), ligand, effect of saturation of the carrier, uniport, symport (cotransport), antiport,
shuttles, gradient, hydrofilic and hydrophobic compounds, endocytosis, exocytosis, fagocytosis,
pinocytosis, membrane potential.
13. Structure and function of cellular organels - review, description of their structure, metabolic
pathways localized in the organels and in the cytoplasm, interconnection of the pathways; importance
of the metabolic compartmentalization (regulation of metabolism, reactive molecules within discrete
organels - e.g. hydrolases and acidic pH in lysosomes, H2O2 in peroxisomes); transport of metabolites
among the compartments.
14. Metabolic pathways localized in the mitochondrion - general review, regulation.
Citrate cycle (Krebs cycle) – sources of acetyl-CoA, energetic balance, interconnection with the
respiratory chain, anaplerotic reactions, anabolic function of citrate cycle, transfer of citrate into the
cytoplasm and its importance for regulation of cytoplasmatic metabolic pathways.
Respiratory chain (electron transport chain) - localization in the cell, arrangement, description of
function, importance. Uncoupling proteins (uncouplers of the respiratory chain from the aerobic
phosphorylation).
15. Structure, properties and dynamics of microtubules, intermediate and actin filaments.
Molecular motors - actin/myosin, kinesin and dynein motors; sources of ATP, hydrolysis of ATP as an
energy power for movement (energy-rich bonds).
16. Synthesis of purine and pyrimidine nucleotides - localization within the cell, de novo synthesis and
salvage reactions: brief description of the reactions (important intermediates: 5-phosphoribosyl-1diphosphate = PRDP, inosine monophosphate, orotic acid, uridine monophosphate), substrates and
their origin, coenzymes (importance of the enzyme dihydrofolate reductase!), regulatory enzymes and
their regulation, products (nucleoside mono-, di- and triphosphates, deoxyribonucleotides); substrates
for synthesis of DNA (deoxynucleoside triphosphates).
17. Kinases and phosphatases - function of the enzymes, their substrates and products; importance of
the enzymes in a regulation of enzyme activity (protein kinases and protein phosphatases). Sources of
ATP within the cell (aerobic phosphorylation, substrate level phosphorylation, adenylate kinase).
18. Regulation on the cell level - in general: 1) regulation on the level of enzyme: modulation of activity
of the already existing enzyme (activators, inhibitors, covallent modification of enzyme); the change in
concentration of regulatory enzyme (influence of hormons on induction / suppression of the gene
expression, influence of substrates on expression of gene); change in concentration of substrate of the
regulatory enzyme; 2) compartmentation of metabolic pathways (different pathways in different parts
of the cell, transport of metabolites among the compartments).
Regulation of the particular metabolic pathways and the intermediary metabolism relationships
(interconnections of particular biochemical processes: shared intermediates and their fate, subsequent
reactions, regulation of one metabolic pathway by the compounds from another metabolic pathway).
19. Hydrolytic enzymes (hydrolases) - localization and function within the cell, classification. Examples
of their substrates, hydrolyzed bonds and products of the reactions (e.g. proteinases brake down
proteins: they hydrolyze peptide bonds).
Cytochrome c - its role during apoptosis; the other use of the cytochrome c within the cell (mobile
electron carrier in the electron transport chain).
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20. Signal transduction across the membrane – kinds of receptors and signal transduction into the cell;
important terms: receptors, G-proteins, effectors (e.g. adenylate cyclase, guanylate cyclase,
phospholipase C), signal molecules, second messanger, cAMP, cGMP, diacylglycerol, inositol
triphosphate, Ca2+.
21. Cells of immune system (metabolism of neutrofils, respiratory burst;
immunoglobulins).
structure of
22. Structure of membrane lipids - glycerolphospholipids, sphingophospholipids, glycolipids,
cholesterol.
Metabolism of nerve tissue - glycolysis, oxidation of ketone bodies, citrate cycle, respiratory chain,
aerobic phosphorylation; decarboxylation of amino acids: formation of monoamines (= biogenic
amines as neurotrasmitters; only examples of the substances, not their synthesis).
23. Muscle cell - energy metabolism: transport of glucose through the membrane, glycolysis,
metabolism of glycogen, -oxidation of fatty acids, oxidation of ketone bodies, citrate cycle, respiratory
chain, aerobic phosphorylation, other sources of ATP (substrate level phosphorylation, adenylate
kinase, creatine kinase); Cori cycle and glucose / alanine cycle.
24. Synthesis and degradation of heme - localization, substrates, important intermediates, products
and their fate; regulatory enzymes and their regulation. Structure of heme.
25. Connective tissue - structure of its components (collagen, elastin, glycoproteins and
proteoglycans); synthesis of collagen (preprocollagen, procollagen - hydroxylation, glycosylation,
formation of disulfide bridges; tropocollagen, formation of crosslinks; role of vitamin C in collagen
syntesis.)
26. Transport across membranes - kinds of transport, importance and description of transport
systems, mechanisms of transport; important terms: primary and secondary active transport, simple
and facilitated diffusion, channels and pores, ion channels, the „pumps“, sodium-potassium pump, the
transporter (carrier), ligand, effect of saturation of the carrier, uniport, symport (cotransport), antiport,
shuttles, gradient, hydrofilic and hydrophobic compounds, endocytosis, exocytosis, fagocytosis,
pinocytosis, membrane potential.
27. Primary structure of proteins - description, relationship between the primary structure and
properties of proteins (including biological activity).
Isoenzymes (isozymes) - definition, properties, examples from the metabolism.
28. Signal transduction from cellular surroundings to the nucleus of the cell - cytosolic and nuclear
receptors, signal transmission from the membrane to the nucleus (tyrosine kinase receptors and
serpentin receptors).
Isoprenoids (terpenoids and steroids) - general structure.
(Retinoids and steroid hormones are bound to ligand-dependent transcription factors in the cell).
29. Methylation in the metabolism - transfer of -CH3 group: examples of the reactions, coenzymes (Sadenosylmethionine = SAM, folate, vitamin B12). Cycle methionine-SAM-homocysteine.
30. Synthesis of purine and pyrimidine nucleotides - localization within the cell, de novo synthesis and
salvage reactions: brief description of the reactions (important intermediates: 5-phosphoribosyl-1diphosphate = PRDP, inosine monophosphate, orotic acid, uridine monophosphate), substrates and
their origin, coenzymes (importance of the enzyme dihydrofolate reductase!), regulatory enzymes and
their regulation, products (nucleoside mono-, di- and triphosphates, deoxyribonucleotides); substrates
for synthesis of DNA (deoxynucleoside triphosphates). The importance of glutamine for rapidly
dividing cells (it is a substrate of the nucleotide synthesis).
31. Biochemical principles of mutagenesis - examples of chemical mutagens, mechanisms of their
action (activation by biotransformation, the ability to transform bases of DNA).
32. Biotransformation of xenobiotics – 1st phase of the biotransformation as an activator of mutegens
(e.g. formation of epoxides).
Free radicals and antioxidants – definition, radical reaction, reactive species of oxygen and nitrogen:
examples, origin, importance (both physiological and pathological – possibilities of biomolecules
damage: peroxidation of membrane lipids, protein damage, DNA), antioxidant protective system
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(antioxidants, scavengers), enzymatic antioxidant systems (superoxide dismutase, glutathion
peroxidase, catalase), high molecular endogennic antioxidants (transferrin, ferritin, haptoglobin,
hemopexin, albumin), low molecular antioxidants (ascorbate, alpha-tocopherol, ubiquinone,
carotenoids, glutathione, lipoic acid, melatonin, uric acid, bilirubin, flavonoids).
33. Chemical carcinogens - examples, mechanisms of their action: direct carcinogens (alkylating and
arylating reagents, metals and their compounds) and indirect carcinogens (polyaromates, aromatic
amines and nitro-compounds, halogenated hydrocarbons, nitrosamines, azo-dyes), activation of
indirect carcinogens (see biotransformation of xenobiotics.
Degradation of nucleic acids - nucleases, nucleotidases, nucleosidases; description of the process;
products of degradation of purine nucleotides (uric acid! - it is formed in higher extent after cytostatics or radiation
therapy) and pyrimidine nucleotides.
34. Biotransformation of xenobiotics – explanation of this term, two steps of the conversion of
hydrophobic compounds: 1) reaction increasing the number of free functional groups of the xenobiotic
(e.g. hydroxylation, uncovering of polar functional group by hydrolysis) and 2) conjugation (reaction
with endogennic compounds); enzymes participating in biotransformational reactions, the ways of
excretion of reaction products from organism; examples of biotransformational products which can
damage organism.
35. General toxicology – entrance of xenobiotics into the organism, exposure time, connection of the
effect of xenobiotic with its structure, mechanisms of toxic effect (irritation, cauterization, narcotic
effect, influence on transport of oxygen, influence on respiratory chain, enzyme inhibition, induction of
enzymes, alkylation, radical reaction, mutagens, carcinogens, teratogens, allergens); chemical
mutagens (examples), biochemical principles of mutagenesis, direct carcinogens (alkylating and
arylating reagents, metals and their compounds) and indirect carcinogens (polyaromates, aromatic
amines and nitro-compounds, halogenated hydrocarbons, nitrosamines, azo-dyes), activation of
indirect carcinogens (see biotransformation of xenobiotics.)
36. Biochemical consequences of inherited metabolic diseases: phenylketonuria - defect of
phenylalanine hydroxylase, familiar hypercholesterolemia – defect of LDL receptors, hemolytic anemia
– defect of glucose-6-phosphate dehydrogenase (describe the metabolic function of the proteins).
37.X
38.Structure of DNA - description, chemical and physical properties, biological importance, occurence
in the nature; important terms: phospho diester bond, N-glykosidic bond, purine and pyrimidine bases,
minority bases, nucleoside, nucleotide, oligonucleotide, polynucleotide, 5´- and 3´- end of
polynucleotid chain, hydrogen bridge, primary, secondary and tertiary structure of DNA, right-handed
and left-handed helix, double helix, parallel and antiparallel polynucleotid chains, nucleosom,
nucleoproteins, histones, 2´-deoxyribose, nucleases, nucleotidases, nucleosidases, gene, exone,
introne, triplets of bases (codons), anticodon, pairing of bases, replication, transcription.
39.X
40. Structure of DNA and RNA - description, differences.
Nucleic acids - structure, classification, chemical and physical properties, biological importance,
occurence in nature; important nucleic acids: DNA, RNA; important terms: phospho diester bond,
N-glykosidic bond, purine and pyrimidine bases, minority bases, nucleoside, nucleotide,
oligonucleotide, polynucleotide, 5´- and 3´- end of polynucleotid chain, hydrogen bridge, primary,
secondary and tertiary structure of DNA, right-handed and left-handed helix, double helix, parallel and
antiparallel polynucleotid chains, nucleosom, nucleoproteins, histones, ribose, 2´-deoxyribose, rRNA,
tRNA, mRNA, hnRNA, nucleases, nucleotidases, nucleosidases, gene, exone, introne, triplets of
bases (codons), anticodon, aminoacyl-tRNA, pairing of bases, replication, transcription.
15.5. 2008
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