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,
laboratory classes, tests, presentations.
The main object in The First Semester comprises sections: Structure and Function of
Proteins and Enzymes, Coenzymes and Vitamins, Metabolism of: Carbohydrates,
Biologic Oxidation and ATP Synthesis. Hormonal Regulation of
Carbohydrtae
Metabolism.
Teachers:
1. Dr Jolanta Czuczejko
2. Dr Karolina Szewczyk-Golec
Contact: Jolanta Czuczejko: joczu@cm.umk.pl,
Karolina Szewczyk-Golec: karosz@cm.umk.pl
Syllabus - summer semester
I. Department of Biochemistry
II. Head of the Unit: dr hab. Beata Augustyńska
III. Faculty of Medicine, Medical Program, for:
- second semester (summer) of the first year
IV.
Course coordinator – dr Jolanta Czuczejko
V.
Form of the classes - lectures, laboratory classes, tests, presentations
VI. Form of crediting/assessment - credit with grade, 5 ECTS
VII. Subject hours:
-
second semester (summer) of the first year - 40 hours of lectures, 20 hours of
laboratory classes (with tests)
VIII. The aim of the course:
Acquiring knowledge of the chemical processes occuring in human cells. Studying the
chemical constituents of human cells: structures, properties and functions of proteins,
saccharides, vitamins and coenzymes. Studying the metabolic pathways of glucose
metabolism and biochemical aspects of metabolic disorders.
Amino acids, peptides, proteins.
Nature of Proteins
-
Function: Enzymatic catalysis, transport and storage of small molecules,
structural elements of cytoskeleton, immunity (immune defense system)
1. Amino Acids – fundamental units of proteins
-
Composition
-
Classification of amino acids
-
Optical activity
-
Amphoteric properties
2. Peptides and polypeptides
-
Formation
-
Amphoteric properties
-
Some important peptides in the human organism
-
The synthesis of insulin
3. Conformation of proteins - primary, secondary, tertiary, quaternary structure.
The prions as an example of medical importance of proper protein folding.
4. Protein Structure – Function Relationship
A. Oxygen binding proteins: Myoglobin and Hemoglobin. Structure and
Function.
B. Humoral Immunity - five basic classes of immunoglobulin (structure and
function): IgM, IgD, IgG, IgE, IgA
C. Fibrous proteins – collagen. Synthesis and structure of collagen.
Enzymes, co-enzymes, vitamins.
1. General characteristics of enzyme
Differences between enzymes and chemical catalysts
-
Measures of enzyme activity
-
Enzymes nomenclature and classification.
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 transformation
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 dinucleotide (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, Oxidative phosphorylation and biologic oxidation.
1. Structures of saccharides
A. Open chain form (asymmetric carbon, isomers, epimers, enantiomers,
hemiacetals)
B. Cyclic form (acetals, glycosialles)
C. 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 glycolysis.
5. The pyruvate dehydrogenase (PDH) enzyme complex, PDH regulation.
5. Pentose phosphate pathway.
6. Uronic acid pathway (glucuronic acid cycle).
7. Citric acid cycle.
8. Mitochondrial Electron Transport
9. Transfer of compounds through the inner and outer mitochondrial membranes
10. Organization of the electron transport chain - Complex I, II, III, IV
11. Respiratory chain inhibitors, chemical uncouplers of oxidative phosphorylation.
Practical 1 Some properties of peptides and proteins. Blood proteins.
The aim of the class: Some physical and chemical properties of peptides and
proteins. Some properties of blood proteins
Theoretical basis: structure and characteristics of the peptide bond, detection of
peptide bonds - thie biuret reaction, the characteristics of primary, secondary, tertiary
and quaternary structures of proteins - denaturation of proteins, the amphoteric
properties of proteins (the isoelectric point of proteins), 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, the physiologic and pathological concentrations of blood plasma
protein
Practical 2 Quantitative methods of blood protein determination.
The aim of the class: Some properties of blood proteins. Quantitative methods
for determination of proteins
Theoretical basis: 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).
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, 5hydroxylysine). 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 3 The isolation of enzymes from biological materials
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 4 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 5 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 fatsoluble vitamins: their structures and functions. The trace elements: some enzymatic
reactions that involve the iron, cobalt, zinc, or copper ions.
Practical 6 Saccharides of physiological importance
The aim of the class: preparation of glucose tolerance curve
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.
Practical 7 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 nonenzymatic components of the antioxidative defense
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, substratelevel 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 metabolism 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).
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 malateaspartate 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.
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 of Biochemistry classes
Department of Biochemistry
Head of Department: dr hab. Beata Augustyńska
Course coordinator: dr Jolanta Czuczejko
Subject: Biochemistry
Faculty of Medicine
Second and Third Semesters of MD Program in English
1. The program of the second semester (60 hrs) consists of lectures (40 hrs),
practical classes and tests (together 20 hrs).
The program of the third semester (60 hrs) consists of lectures (30 hours),
practical classes and tests (together 30 hours). All classes are compulsory.
2. The performance during each laboratory class will be evaluated by the short
entrance tests, laboratory skills and written protocol from the experiments.
 Students may obtain 5 points during each laboratory class – 3 points for
entrance test, 1 point for laboratory skills and 1 point for written protocol.
 There is no possibility to retake entrance test, students who fail entrance
test miss the opportunity to obtain 3 points.
 Taking into consideration the laboratory classes students may collect 35
points in the second semester (7 laboratory classes x 5 points = 35 points)
and 50 points (10 laboratory classes x 5 points) in the third semester.
 Students should check the schedule carefully and be on time.
3. Tests will be held at the end of the each part of the material. Tests will be
taken according to the schedule.
 Students may obtain 50 points for each test.
 Taking into consideration the tests students may obtain 150 points in the
second semester (3 tests x 50 points = 150 points) and 250 points in the third
semester (5 tests x 50 points = 250 points).
4. The sum of points that students may obtain after the second semester (7 lab
classes and 3 tests) is 185 (100%).
 Biochemistry course finishes after the second semester with a “credit with
grade”. The following scale of grades is binding:
Points/%
170-185/(92-100%)
Procent punktów
155-169/(84-91%)
141-154/(76-83%)
126-140/(68-75%)
110-125/(60-67%)
0-109/(0-59%)
Mark
Excellent (5.0)
Very good (4.5)
Good (4.0)
Satisfactory (3.5)
Acceptable (3.0)
Fail (2.0)
 If students obtain less than 60% of points (60% means the passing grade)
they will have no permission to continue the course of Biochemistry in the
third semester.
5. The sum of points that students may obtain after the third semester (10
laboratory classes and 5 tests) is 300 (100%). Students who obtain 60% of
points (180 points) may take the final exam. The best students may approach
the exam in the “zero” term, before the examination session. The course
coordinator will take a decision about qualification to “zero-term” exam.
6. The final exam will be held in the end of the third semester. Students may
obtain 100 points for the final test (100%).
 The following scale of grades is binding:
Points/%
Mark
92-100/(92-100%)
Excellent (5.0)
Procent
punktów
84-91/(84-91%)
Very good (4.5)
76-83/(76-83%)
Good (4.0)
68-75/(68-75%)
Satisfactory (3.5)
60-67/(60-67%)
Acceptable (3.0)
0-59/(0-59%)
Fail (2.0)
 In some cases the exam may also include the additional oral part. The course
coordinator will take a decision about qualification to the oral part of exam.
 Students who fail the final exam may resit it once in the resit examination
session (according to the Rules of Studies VIII, § 22, 34) in the form of test.
7. All classes are compulsory.
 If students can not attend the class they must have a sick-leave and arrange
for an alternative date to carry out the lab/test (only 1 class during each
semester). Students are obliged to do it immediately after the cause of
absence has ceased.
 Students who did not take part in the lab class without excuse miss the
opportunity to obtain 5 points for this lab class.
 The deadline to provide the completed laboratory protocol to the teacher is the
next lab class. Students who did not provide the protocol or provided the
protocol incorrectly completed, miss the opportunity to obtain 1 point.
 Students who did not parcitipate in the test without any reasonable excuse of
absence miss the opportunity to take the test in the additional term.
 Students who did not take an exam in a scheduled time may have, by the
approval of the Dean and the examiner, the additional date for the exam
settled, on the condition that the reasonable excuse of the absence is
proven. An application for setting the additional date for the exam must be
submitted within 7 days from the moment when the cause of absence has
ceased. (Rules of Studies, VIII, § 32).
8. Work safety regulations:
I. STUDENTS MUST:
1. Have a lab coat and protective gloves.
2. Leave their outer clothing in the cloakroom.
3. Keep quiet and tidiness in the lab class room.
4. Clean the tubes and their place of work after the lab class.
6. Be particularly careful when work with:
- concentrated acids
- concentrated bases
- toxic substances
- flammable substances
8. Use concentrated acids, bases, poisons and irritants of respiratory tract only under
the foom hood.
9. Be very careful when work with flame and keep the heated tube far away from
themselves and the other students.
13. Not smell vapour of substance directly.
14. Wash hands after lab class.
16. Inform the teacher about fire.
17. Inform the teacher about any accidents.
II. FOLLOWING ACTIVITIES ARE FORBIDDEN THROUGHOUT THE
LABORATORY CLASSES:
1. Smoking.
2. Eating and Drinking
3. Tasting of chemical substances.
4. Replacing of plugs that close the bottles with chemical substances.
5. Moving of chemical reagents from fume hood.
6. Performing of any lab experiments without the teacher agreement.
III. STUDENTS ARE OBLIGATED TO:
1. Introduce with properties of all chemical reagents.