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:

1. Prof. dr hab. med. Józef Kędziora

2. Dr Jolanta Czuczejko

3. Dr Karolina Szewczyk-Golec

4. Dr Mariusz Kozakiewicz

Contact: Jolanta Czuczejko joczu@wp.pl, Karolina Szewczyk-Golec karosz3@wp.pl, Mariusz

Kozakiewicz markozx@wp.pl

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 three-letter

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 long-chain

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, S-adenosylmethionine

(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