Download Biochemistry Biochemistry is a science concerning the chemical

Biochemistry
Biochemistry is a science concerning the chemical reactions occuring in living cells and organisms.
Biochemistry in the medicine is mainly concerned with balance of biochemical reactions occuring in
the body, both in physiological state as in pathology.
The program of teaching biochemistry for medical students consists of lectures, seminars and
laboratory classes.
The main object comprises five sections: Structure and Function of Proteins and Enzymes,
Metabolism of Carbohydrates, Lipids of Physiological Significance, Nulceic Acids and special topics
(Nutrition, Digestion, Vitamins, Plasma Proteins, Immunoglobulins, Haemostasis, Xenobiotics). At the
end of the course students must take the final examination prepared by Board of Medical Examiners.
Teachers:
Prof. dr hab. med. Józef Kędziora
Dr Jolanta Czuczejko
Dr Karolina Szewczyk-Golec
Dr Mariusz Kozakiewicz
Contact: Jolanta Czuczejko [email protected], Karolina Szewczyk-Golec [email protected], Mariusz
Kozakiewicz [email protected]
Syllabus
I. Department of Biochemistry
II. Head of the Unit: prof. dr hab. med. Józef Kędziora
III. Faculty of Medicine, Medical Program, for:
- second semester (summer) of the first year
- first semester (winter) of the second year
IV. Course coordinator – prof. dr hab. Józef Kędziora
V. Form of the classes - lectures, tutorials, seminars
VI. Assessment - examination
VII. Subject hours:
-
second semester (summer) of the first year - 30 hours of lectures, 30 hours of practicals
and seminars
-
first semester (winter) of the second year - 30 hours of lectures, 30 hours of practicals
and seminars
VIII. Aim of the course:
Acquiring knowledge of the chemical processes occuring in human cells. Studying the
chemical constituents of human cells: structure, properties and function of proteins,
saccharydes, lipids, nucleic acids, vitamins and coenzymes. Studying biochemical aspects of
metabolic disorders. Analysis of the compartmentation, integration and regulation of
metabolic pathways. Learning about the metabolism of the main human organs.
Emphasising the relationships between medicine and biochemistry and the role of
biochemical knowledge in medical diagnostics.
Amino acids, peptides, proteins.
1. Nature of Proteins
-
Function: Enzymatic catalysis, transport and storage of small molecules, structural
elements of cytoskeleton, immunity (immune defense system)
2. Amino Acids – fundamental units of proteins
-
Composition
-
Optical activity
-
Amphoteric properties
3. Peptides and polypeptides
-
Formation
-
Amphoteric properties
4. Purification of proteins
5. Conformation of proteins - primary, secondary, tertiary, quaternary structure
6. Protein Structure – Function Relationship
Oxygen transport proteins
A. Myoglobin and Hemoglobin Structure and Function
B. Hemoglobinopathies (HbS, HbC, HbM, thalassemias)
C. Humoral Immunity - five basic classes of immunoglobulin (structure and
function): IgM, IgD, IgG, IgE, IgA
D. Fibrous proteins - collagen
Enzymes, co-enzymes, vitamins.
1. General characteristics of enzyme
Differences between enzymes and chemical catalysts
-
Measures of enzyme activity
-
Enzymes nomenclature
2. Enzyme Kinetics
A.
Quantification of enzyme activity
B.
Quantification of chemical reaction by kinetic order
C
Michaelis – Menten kinetic theory of enzyme action
-significance of the Michaelis constant
-Lineweaver Burk transform
3. Enzyme Inhibition
A.
Competitive
B.
Uncompetitive
C.
Medical relevance of enzyme inhibitor
D.
Regulation of enzymes
4. Enzymes in clinical diagnosis
5. Nomenclature of vitamins - water soluble and fat soluble.
6. Coenzymes:
Nicotinamide-adenine dinukleotide (NAD+)
Nicotinamide – adenine dinukleotide phosphate (NADP+)
Flavin mononucleotide (FMN)
Flavin adenine dinukleotide (FAD)
CoA-SH, ACP
Folic acid
Pyridoxal phosphate (PLP)
Thiamin pyrophosphate (TPP)
Biotin
Cobalamine
Ascorbic acid
7. Cofactors: metal ions of Co, Cu, Mg, Mn, Se, Zn, Fe.
Saccharides, glycolysis pathway, tricarboxylic acid cycle, pentose phosphate pathway.
1. Structures of saccharides
A. Open chain form (asymmetric carbon, isomers, epimers, enantiomers, hemiacetals)
B. Cyclic form (acetals, glycosialles) polysacharydes
2. Carbohydrate derivates
A. Phosphoric acid esters of monosacharides
B. Amino sugars
C. Sugar acids
D. Deoxy sugars
3. Glycoproteins - physiologic functions
A. Glycosaminoglycans (heparin, chondroitin sulfate, dermatan sulfate, heparin
sulfate, keratin sulfate, hyaluronic acid)
4. Glycolysis - anaerobic glycolysis, aerobic glycolisys.
5. The pyruvate dehydrogenase (PDH) enzyme complex, PDH regulation
5. Pentose phosphate pathway
6. Uronic acid pathway (glucuronic acid cycle)
7. Citric acid cycle
Oxidative phosphorylation and biologic oxidation.
Mitochondrial Electron Transport
Localization of electron transport chain
1. The outer membrane
2. The itermembrane space present
3. The inner membrane
4. Organization of the electron transport chain - Complex I, II, III, IV
Lipids
1. Nomenclature of lipids and physiologic significance
2. Phospholipids and glycosphingolipids – structure, function and biosynthesis
3. Fatty acids chain biosynthesis
4. Desaturase & elongase enzyme systems
5. Eicosanoids biosynthesis and their physiologic role
6. Cholesterol biosynthesis (regulation of HMG-CoA reductase activity)
7. Cholesterol as a precursor of steroids (corticosteroids, sex hormones, bile acids,
vitamin D)
8. Lipid and cholesterol transport and storage – plasma lipoproteins
9. β-oxidation of saturated, unsaturated and odd number of carbon atoms fatty acids
10. Ketogenesis
11. Lipid peroxidation
12. Interrelationships among carbohydrates and lipids metabolism
Nucleic acids – structure, function, organization. Molecular genetics.
1. Human genome – definition and structure. Nucleosome and chromatin package.
Hetero – and euchromatin. Structure of nucleic acids. Genetic information and genetic
code. Organization of genes, promoters, microsatellite DNA, pseudogenes.
2. DNA replication – DNA polymerases, start of replication, role of starters in DNA
synthesis, Okazaki fragments. Topology of DNA associated with replication and role of
helicases.
3. Transcription of genetic information. RNA synthesis by DNA-dependent RNA
polymerase. Types of RNA and their function. Reverse transcriptase.
4. Translation of genetic information. Components of the translation apparatus. Protein
biosynthesis. Protein maturation and posttranslational modifications. Protein degradation
and turnover.
5. Epigenetics – DNA modifications, DNA methylation. Modulation of genes expression.
Epigenetics and cancer.
6. DNA damage and repair. DNA damage in the way of health & on the way to ageing.
Oxidative DNA damage and repair. Measurement of DNA damage. Biological
consequences of oxidative DNA damage. DNA repair pathways. Mutagenesis. Mutations
and polymorphisms in genes encoding DNA repair enzymes.
7. Mitochondrial genome and its metabolism. Organisation of the human mitochondrial
genome.
Maternal
inheritance.
High
mutation
rate.
Mutations
in
mtDNA.
Nutrition, digestion & absorption.
1. Macro- and micronutrients. Digestion and absorption of proteins, carbohydrates and
lipids. Vitamins. Bile acids metabolism.
2. Energy metabolism. Protein-energy intake. Malnutrition. Obesity. Assessment of
nutritional status.
Blood, hemostasis & thrombosis.
1. The composition of blood. Blood cells and plasma. Oxygenation of blood.
2. Mechanism of blood coagulation.
Excretory system.
1. Organs of the excretory system. Removal of carbon dioxide excess by lungs. Skin
functions. Break-down of proteins and urea production in liver. Urea cycle.
2. Kidney function. Hormonal control of water and salt
Detoxification processes – liver functions
1. The metabolism of the liver - amino acids, urea cycle, proteins, carbohydrates, lipids
2. Steps of detoxification – cytochrome P450, conjugation (role of reduced glutathione
GSH – biosynthesis of mercapturic acids)
3. Other role of GSH – peroxidase glutathione (GSH-Px), reductase glutathione (GR),
transport of amino acids
Metabolism of amino acids.
Deamination (role of Glu), transamination, decarboxylation, glucogenic and ketogenic
aminoacids, role of aminoacids on biosynthesis, essential and non-essential amino acids
Hormones and hormonal regulation.
Hormones and the hormonal cascade system. Major polypeptide hormones and their
action. Steroid hormones. Hormone receptors and intracellular hormone signalling.
Practical 1 Chemical properties of amino acids
The aim of the class: studies on selected properties of amino acids
Theoretical basis: general structure of amino acids, the names (full names and their threeletter abbrevations) and structures of protein amino acids, characteristics of the chemical
groups attached to amino acid chain (like carboxylic, amino, imino, sulphydryl, imidazol,
guanidine, hydroxyl groups), amphoteric properties of amino acids, classification of amino
acids according to the chemical properties of their side chains (charged, nonpolar
hydrophobic, uncharged polar; aliphatic, cyclic, aromatic; acidic, basic)
Practical 2 Some properties of peptides and proteins
The aim of the class: Some physical and chemical properties of peptides and proteins
Theoretical basis: structure and characteristics of the peptide bond, classification of peptides
according to their structures, the physiologic significance of some peptides in human body,
the characteristics of primary, secondary, tertiary and quaternary structures of proteins,
classification of proteins according to their structures, properties and functions, the
amphoteric properties of proteins (the isoelectric point of proteins)
Practical 3 Blood proteins
The aim of the class: Some properties of blood proteins
Theoretical basis: the constituents of the blood, the compositions of blood plasma and blood
serum, characteristics of main blood plasma proteins: albumins, globulins and fibrinogen,
electrophoresis as an important method of plasma (or serum) protein fractionation, the
characteristics of individual protein fractions,
Practical 4 Quantitative methods for determination of proteins
The aim of the class: Assessment of some quantitative methods for determination of
total protein concentration.
Theoretical basis: The physiologic and pathological concentrations of blood plasma protein,
the diagnostic role of alterations in the amount of total proteins and in mutual quantitative
relationships between individual fractions, examples of methods for protein concentration
determination (biuret protein assay, Lowry protein assay, Bradford protein assay)
SEMINAR / TEST I Amino acids, peptides, proteins
The key problems: The structure of protein amino acids. The classification of amino acids
according to both the polarity and the structural features of their side chains (e. g. polar,
nonpolar; aliphatic, aromatic; sulfur-containing; charged, uncharged; acidic, basic). The
amphoteric properties of amino acids, zwitterions. The structure of some modified amino
acids (as selenocysteine, 4-hydroxyproline, 5-hydroxylysine). The structure of some
physiologically important nonprotein amino acids.
The formation, structure and properties of the peptide bond. Some important peptides
in the human organism (glutathione, peptide hormones). The insulin synthesis.
The classification of proteins according to their structure, properties and functions. The
characteristics of primary, secondary, tertiary and quaternary structures of proteins. The
interactions involved in a protein folding into its final conformation (e. g. the attraction
between positively and negatively charged molecules, the hydrophobic effect, hydrogen
bonding, and van der Waals interactions). Posttranslational modifications of amino acids in
proteins. Structure – function relationships in myoglobin, hemoglobin and immunoglobulins.
The structure and synthesis of collagen. Rybonuclease renaturation as an example of the
importance of primary protein structure. The prions as an example of medical importance of
proper protein folding.
Practical 5 Preparation and purification of saccharase.
The aim of the class: the isolation and purification of yeast saccharase
Theoretical basis: the structure of enzymes, classification of enzymes, the enzymes names, the
methods of isolation and purification of enzymes from biological materials.
Practical 6 The kinetics of the enzymatic reaction
The aim of the class: the determination of the initial velocity and Michaelis constant in
reaction catalysed by saccharase
Theoretical basis: the enzyme-catalyzed reaction, the definitions of initial velocity, maximal
velocity and Michaelis constant, the Michaelis-Menten equation, the standard units of
enzymatic activity (katal, international unit), the influence of some factors on the enzyme
activity (e. g. temperature, pH, the concentration of substrate and enzyme, competitive and
noncompetitive inhibitors).
Practical 7 Properties of vitamins A, C, D in biological materials
The aim of the class: Properties of retinol, ascorbic acid and cholecalciferol in different
biological materials
Theoretical basis: classification, structure and functions of water and fat soluble vitamins,
classification, structure and functions of coenzymes.
SEMINAR / TEST II Enzymes and coenzymes
The key problems: The definitions: enzyme, coenzyme, cofactor. The isoenzymes of the
diagnostic importance (lactate dehydrogenase (LDH), creatine phosphokinase (CPK)). The
structure of the active site and models for substrate binding. The specificity of enzymes to the
substrates and the catalysed reaction.
The catalytic mechanisms of the enzymatic reactions. The influence of physical and chemical
factors on the enzyme activity (temperature, pH, the enzyme concentration, the substrate
concentration, the product concentration).
The kinetics of enzymatic reaction: the
initial and maximal velocities, Michaelis constant, the Michaelis-Menten equation, the
Lineweaver-Burk plot.
Regulation of enzyme activity: allosteric enzymes (allosteric activators and inhibitors,
the examples of allosteric enzymes, the sequential and concerted models for an allosteric
enzyme, the kinetics of allosteric enzyme reaction), feedback regulation and its examples in
the human organism, covalent modification of enzymes (phosphorylation), proteolytic
cleavage (proenzymes, zymogens, autocatalysis), reversible inhibition (competitive and
noncompetitive inhibitors, the mechanism of the inhibition, the kinetics of competitive and
noncompetitive inhibitions, medical significance of inhibition: acetylsalicylic acid, Fluorouracil,
methotrexate, penicillin, allopurinol).
The standard units of enzymatic activity (katal, the international unit, the specific activity of an
enzyme). The classes of enzymes (oxidoreductases, transferases, hydrolases, lyases,
isomerases, ligases).
Coenzymes: their structrures and functions in the reactions. Water-soluble and fat-soluble
vitamins: their structures and functions. The trace elements: some enzymatic reactions that
involve the iron, cobalt, zinc, or copper ions.
Practical 8 Some properties of monosaccharides
The aim of the class: some chemical properties of monosaccharides
Theoretical basis: nomenclature of monosaccharides and their isomerism, the structure of
monosaccharides (Fischer projection and cyclic structure), the chemical properties of
monosaccharides, the examples of biologically important monosaccharides.
Practical 9 Some properties of di- and polysaccharides
The aim of the class: some properties of biologically important disaccharides and
polysaccharides
Theoretical basis: nomenclature of disaccharides and polysaccharides, their structure and
properties, the examples of biologically important di- and polysaccharides, physiologically
significant saccharide derivatives (e. g. heparine) and glycoproteins
1. Iodine test – the detection of starch.
Practical 10 Saccharides of physiological importance
The aim of the class: preparation of glucose tolerance curve, the estimation of sialic
acids concentration in the blood serum
Theoretical basis: the glucose concentration in the blood, the maintenance of blood glucose
levels, regulation of blood glucose level by hormones, the glucose levels in diabetes mellitus,
glucose tolerance test in healthy persons and diabetes mellitus patients, the physiologic role
of sialic acid
SEMINAR / TEST III Saccharides
The key problems: Classification of monosaccharides by both the number of contained carbon
atoms (e. g. triose, tetrose etc.) and the type of contained carbonyl group (aldose, ketose),
and their isomerism. Common disaccharides. The structure of important polysaccharides
(starch and glycogen). Physiologically significant saccharide derivatives (especially amino
sugars). Synthesis and functions of sialic acids.
Generation of ATP from glucose: glycolysis (reactions of glycolytic pathway, substrate-level
phosphorylation, regulation of glycolysis). Synthesis of 2,3-bis-phosphoglycerate in a “side
reaction” of the glycolytic pathway. Anaerobic glycolysis – (lactate fermentation, tissues
dependent on anaerobic glycolysis, fate of lactate – Cori cycle, lactic acidemia, ethanol
fermentation). Fructose and galactose metabolisms. Synthesis and degradation of lactose.
Formation and degradation of glycogen. Disorders of metabolisms of fructose, galactose and
glycogen. The pentose phosphate pathway. The directions of the pentose phosphate pathway
reactions due to the cellular needs. Hemolysis caused by reactive oxygen species in the
conditions of glucose-6-phosphate dehydrogenase deficiency. Gluconeogenesis. The
maintenance of blood glucose levels by hormones (regulation of glycolysis and
gluconeogenesis, as well as formation and degradation of glycogen by insulin, glucagon and
noradrenaline).
Practical 11 The electron-transport chain.
The aim of the class: studies on selected enzymes of the electron-transport chain and
some enzymes of antioxidative properties.
Theoretical basis: the oxidative-reduction components of the electron-transport chain and
their structures, the electron-transport chain as a major source of the free radicals in the cell,
the antioxidative defense in the human organism, the enzymatic and non-enzymatic
components of the antioxidative defense
SEMINAR / TEST IV Oxidative phosphorylation and tricarboxylic acid cycle
The key problems: Oxidative fates of pyruvate – oxidation of pyruvate to acetyl CoA by
pyruvate dehydrogenase. The tricarboxylic acid (TCA) cycle (reaction, enzymes, coenzymes,
regulation of this cycle). The energetics of the TCA cycle. Cellular bioenergetics: the
compounds containing high-energy bonds (ATP and the others nucleoside triphosphates,
creatine phosphate, 1,3-bis-phosphoglycerate, acetyl CoA). Oxidative fates of NADH,
produced from glycolysis (glycerol 3-phosphate shuttle and malate-aspartate shuttle).
Transfer of compounds through the inner and outer mitochondrial membranes. The
generation of ATP from glucose (complete aerobic oxidation of glucose, anaerobic glycolysis).
Oxidative phosphorylation. The electron-transport chain. Chemiosmotic model of ATP
synthesis. The structure of protein complexes of the electron-transport chain. Respiratory
chain inhibitors, chemical uncouplers of oxidative phosphorylation. The generation of reactive
oxygen species (ROS) in the cell (the mitochondrial electron-transport chain and other
sources). ROS-mediated cellular injury. Formation of free radicals during phagocytosis and
inflammation. Cellular defences against oxygen toxicity.
Practical 1 Some properties of lipids.
The aim of the class: some chemical properties of lipids, lipids of physiologic
significance.
Theoretical basis: categories of lipids, the nomenclature of both saturated and unsaturated
fatty acids, examples of biologically important fatty acids, the structure of glycerolipids, the
structure of sphingolipids, the role of some important lipids in the human organism, the lipid
peroxidation, the structure of cholesterol, the physiological blood concentrations of both
cholesterol and triacylglycerols, the diagnostic significance of cholesterol, triacylglycerols and
lipoproteins levels in the blood.
SEMINAR / TEST I Lipids
The key problems: Saturated and unsaturated fatty acids, their nomenclature and structure.
Acylglycerols, phosphoacylglycerols, sphingolipids, steroids, eicosanoids. Structure and
functions of cholesterol. The cholesterol derivatives (vitamin D, steroid hormones, the bile
acids) and their role in the organism. Transport of cholesterol by the blood lipoproteins. The
cholesterol synthesis and its regulation. Medical significance of elevated cholesterol blood
levels. Dyslipoproteinemias.
Activation of long-chain fatty acids and their transport into mitochondria. β-oxidation of longchain fatty acids, oxidation of unsaturated fatty acids. Energy yield of β-oxidation. Odd-chain-
lenght fatty acids oxidation. Conversion of propionyl CoA to succinyl CoA. Metabolism of
ketone bodies.
The acetyl CoA transport from mitochondria into cytosol (role of citrate). The sources of
NADPH for fatty acid synthesis. Fatty acid synthesis. Elongation of fatty acids. Desaturation of
fatty acids. Conversion of linoleic acid to arachidonic acid. The synthesis of eicosanoids and
their physiologic significance. Synthesis of triacylglycerols. Synthesis of glycerophospholipids
and sphingolipids. Integration of carbohydrate and lipid metabolism.
Practical 2 Nucleic acids extraction from yeast
The aim of the class: isolation of nucleic acids from yeast.
Theoretical basis: the structure and nomenclature of nucletides, the structure of nucleic acids:
DNA and RNA, the conditions of nucleic acid separation from yeast
Practical 3 Some properties of nucleic acids
The aim of the class: studies on the composition and some properties of nucleic acids
Theoretical basis: characteristics of nucleic acids, their structure, metabolism and functions in
the human body
SEMINAR / TEST II Nucleic acids and their metabolism
The key problems: The nomenclature and structure of purine and pirymidine bases. The
structure of nucleotides. Purine and pyrimidine synthesis and its regulation. The purine
nucleotide salvage pathway. The formation of deoxyribonucleotides. Degradation of purine
and pyrimidine bases. Lesch-Nyhan syndrome, sever combined immunodeficiency disease
(SCID), hyperuricemia.
The structure of the nucleic acids. Synthesis of DNA. Transcription: synthesis of RNA.
Translation: synthesis of proteins. Regulation of gene expression. Use of recombinant DNA
techniques in medicine. The molecular biology of cancer.
Practical 4 Enzymes of digestive tract
The aim of the class: studies on some properties of digestive juices
Theoretical basis: the composition of digestive juices, the physical and chemical properties of
digestive juices, the role of the components of digestive juices in the digestion process. The
characteristics of digestive enzymes.
Practical 5 The constituents of the blood
The aim of the class: studies on some properties of some constituents of the blood
Theoretical basis: the constituents of both cellular and noncellular fractions of the blood,
major functions of the blood, the structure of hemoglobin and its role in the respiration
(oxygen and carbon dioxide transport), the oxygen-binding curve of hemoglobin, the allosteric
effectors for oxygen binding to hemoglobin (pH, carbon dioxide, 2,3-bisphosphoglycerate),
the Bohr effect, some examples of hemoglobinopathies (hemoglobin M, hemoglobin S,
thalassemias), the role of the blood proteins in the maintenance of homeostasis, the functions
of inorganic compounds in the blood
Practical 6 The blood serum enzymes used in clinical diagnosis
The aim of the class: the analysis of some serum enzymes activities and its role in the
diagnosis of disease processes
Theoretical basis: classification of blood diagnostic enzymes, the major enzymes used in
clinical diagnosis, the role of diagnostic enzymology in diagnosis of myocardial infarction and
some liver diseases, absorption spectra of NAD+ and NADH, the usage of these spectra for the
assays of dehydrogenases activities, the coupled enzyme assays
Laboratory tests:
SEMINAR / TEST III The blood. Nutrition, digestion, and absorption
The key problems: The composition of digestive juices, the enzymes of digestive tract.
Digestion and absorption of carbohydrates, lipids, proteins, vitamins and minerals. The role of
hydrochloric acid and the bile salts in digestion processes. The production of hydrochloric acid
by parietal cell of the stomach. The biosynthesis and degradation of bile salts. The
enterohepatic bile salts circulation.
Synthesis of heme and regulation of this process. Catabolism of heme. The fates of
bilirubin: transport to the liver, conjugation with glukuronic acid, secretion into bile, reduction
to urobilinogen. The enterohepatic urobilinogen cycle. Hyperbilirubinemias, different causes
of jaundice (hemolytic anemia, hepatitis, obstructive jaundice), the laboratory tests important
in helping to distinguish between prehepatic, hepatic and posthepatic causes of jaundice.
The major functions of the blood, the constituents of the blood. The organic and
inorganic constituents of the blood plasma. The characteristics and functions of plasma
proteins. Structure and functions of red blood cells. Metabolism of the red cell. Reaction of
importance in relation to oxidative stress in blood cells. System for reducing heme Fe3+ back to
the Fe2+ state in the red blood cell. Physiologic roles of hemoglobin and mioglobin, the oxygen
dissociation curves for myoglobin and hemoglobin. The mechanism of binding O2 to
myoglobin and hemoglobin. The cooperative interactions infuencing the binding O2 to
hemoglobing, the changes of oxygen-binding curve of hemoglobin (effect of temperature, pH,
carbon dioxide concentration, 2,3-bis-phosphoglycerate concentration). The Bohr effect. The
carbon dioxide transport in the blood. Binding CO to hemoglobin. Changes of the subunit
composition of hemoglobin tetramers during development (embryonic, fetal and adult
subunits). Abnormal hemoglobines. Anemia. The classification of the causes of anemia.
Practical 7 Urine physiologic parameters
The aim of the class: the analysis of some substances extreted by the kidney from the
body via the urine during physiologic conditions
Theoretical basis: the functions of the kidney (excretion of waste products produced by
metabolism, acid-base homeostasis, osmolality regulation, the blood pressure regulation,
hormone secretion), the production of urine, characteristics and composition of the urine,
glomerular filtration rate (GFR), creatinine clearance as a creatinine-based approximation of
GFR
Practical 8 Diagnostic chemical markers in human urine
The aim of the class: the analysis of some substances excreted by the kidney from the
body via the urine during pathologic conditions
Theoretical basis: the role of the urine analysis in the medical examination, the substances
excreted by the kidney via the urine in selected disease processes, diagnostic urine stripes as a
rapid method of urine analysis.
SEMINAR / TEST IV Metabolism of amino acids.
The key problems: Fate of amino acid nitrogen. Enzymes important in the process of
interconverting amino acids and in removing nitrogen (dehydratases, transaminases,
glutamate dehydrogenase, glutaminase, deaminases). The convertion of amino acid nitrogen
to urea – the urea cycle.
Degradation of amino acid: fate of amino acid carbon skeletons. Glucogenic and
ketogenic amino acids. The role of pyridoxal phosphate, tetrahydrofolate and
tetrahydrobiopterin coenzymes in amino acid metabolism. Some disorders of amino acid
catabolism: alkaptonuria, phenylketonuria, maple syrup urine disease.
The biosyntheses of biologically important compounds from amino acids (sphingosine,
choline, taurine, creatine, catecholamines, hippuric acid, nitric oxide, glutathione,
glycerophospholipids, purines, pirymidines, carnosine, anserine, bile salts, hem, serotonin,
melatonin, nicotinin acid, coenzyme A). Biosynthetic decarboxylations of amino acids to
amines – the biogenic amines and their biological functions.
The one-carbon carriers in the body: tetrahydrofolate (FH4), vitamin B12, Sadenosylmethionine (SAM). Sources and recipients of one-carbon FH4 pool.The methyl-trap
hypothesis. The role of SAM in the biosynthesis of the compounds of biological importance
(creatine, phosphatidylcholine, adrenaline, melatonin, methylated nucleotides, methylated
DNA).
Essential and nonessential amino acids. The synthesis of nonessential amino acids in the
human organism.
SEMINAR / TEST V Integrative seminar 1 – Metabolism of tissues and organs.
The key problems: Carbohydrate, lipid and amino acid metabolism of liver, brain, skeletal
muscle, cardiac muscle cells, and kidney. The sources of ATP for skeletal muscle cells (e. g.
creatine phosphate, purine nucleotide cycle). Major functions of the kidney (excretion of
waste products produced by metabolism, acid-base homeostasis, osmolality regulation, the
blood pressure regulation, hormone secretion, γ-glutamyl cycle). The substances excreted via
the urine in normal and pathologic conditions. The metabolism of liver (detoxification of drugs
and metabolites, glutathione S-transferases, metabolism of ethanol). The functions of
glutathione in the organism. Intertissue relationships in the metabolism of carbohydrates,
lipids and amino acids.
Classification of hormones according to their structure, a type of hormone receptor, and
a second messenger. The synthesis of thyroid hormones. The hormones involved in the
glucose maintenance in the blood. The major hormones influencing nutrient metabolism and
their actions on muscle, liver, and adipose tissue. The changes in the fuel metabolism during
fasting state and starvation. The metabolism of carbohydrates, lipids, and amino acids in the
diabetes mellitus type I and type II.
Practical 20 End-of-year practical
Booklist:
1. Lieberman M, Marks AD "Marks` Basic Medical Biochemistry a Clinical Approach". 3rd
edition
2. Murray RK, Bender DA et al. "Harper`s Illustrated Biochemistry" 28th edition
3. Devlin Thomas M. Textbook of Biochemistry with Clinical Correlations, Seventh
Edition Wiley-Blackwell 2010
Rules and regulations
The main objective of the course is to provide an understanding of biochemical processes
and to gain relevant basic laboratory skills according to the educational requirement defined in the
program of teaching biochemistry for medical students.
The program (120 hrs) consists of lectures (60 hrs), practical classes (60 hrs), and a closing
test. All classes are compulsory. Students should check the schedule carefully and be on time. If
students cannot attend class they must have sick note and arrange for an alternative date to carry
out the lab/seminar.
The performance during each laboratory class will be evaluated by the quality of theoretical
preparation, laboratory skills and written protocol from the experiments.
Seminars: Students must be prepared to give a short presentations of topics which will be
given to them by the teacher after each part of material.
Tests: One-choice tests (50 questions, graded 1 point for a correct answer) will be held at the
end of the each part of the material.
Final examination: Students who has earned credit must take the final examination (100
questions, one-choice questions test, graded 1 point for a correct answer).
The final examination and partial tests can be retaken according to the schedule and the
percentage of the points according to the following system:
60-67 % - satisfactory
68-75 % - fairly good
76 - 83 % - good
84 - 90% - better than good
90 - 100 % - very good