Download Biochemistry with Elements of Chemistry - Collegium Medicum

BIOCHEMISTRY WITH ELEMENTS OF CHEMISTRY
Biochemistry is a science concerning the chemical reactions occurring in living cells and organisms.
Biochemistry in the medicine is mainly concerned with balance of biochemical reactions occurring 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 purpose of teaching "Biochemistry" in the direction of Medicine is to deepen the knowledge of the
chemical processes occurring in the surrounding world. Understanding the importance of chemistry in
biological and medical sciences to the extent necessary for further medical studies. The aim is also to
prepare students for teaching clinical subjects, as well as to work in the profession. Allow you to see the
contents transferred to pathological changes in the structure and functioning of the most important
biomolecules (proteins, nucleic acids, carbohydrates, lipids), allow you to understand the basic pathways of
catabolic and anabolic explain the mechanisms of metabolic diseases.
TEACHERS:

dr Aleksandra Karczmarska-Wódzka

mgr Joanna Sikora
CONTACT: dr Aleksandra Karczmarska-Wódzka, [email protected],
SYLABUS
I. Name of the unit offering the course: Department of Biochemistry
II. Head of the Unit/Course coordinator: dr hab. Beata Augustyńska/dr Aleksandra KaczmarskaWódzka
III. 1st year, number of hours: 90
IV. Form of the classes – lectures: 50, tutorials: 40 (first year), lectures: 30, tutorials: 30 (second
year)
V. Form of crediting:
a) second semester (summer) of the first year - credit with grade
b) third semester (winter) of the second year – exam
VI. Number of ECTS points: 6.5 (first year), 3 (second year)
VII. Topic of classes:
Lectures
1.
2.
3.
4.
5.
6.
7.
8.
REVISION OF BASIC CHEMICAL AND BIOCHEMICAL REACTIONS
PROPERTIES OF SOLUTIONS AND BUFFERS
REACTIONS RATES AND CHEMICAL EQUILIBRIUM. DIALYSIS
CHEMICAL PROPERTIES OF MONOFUNCTIONAL ORGANIC COMPOUNDS
CHEMICAL PROPERTIES OF AMINO ACIDS, PEPTIDES AND PROTEINS
THE THREE-DIMENSIONAL STRUCTURE OF PROTEINS
PROTEIN FUNCTION
ENZYMES
9.
10.
11.
12.
13.
14.
15.
SOME PROPERTIES OF MONOSACCHARIDES
SOME PROPERTIES OF DISACCHARIDES AND POLYSACCHARIDES
SACCHARIDES OF PHYSIOLOGICAL IMPORTANCE
CARBOHYDRATES AND GLYCOBIOLOGY
THE PENTOSE PHOSPHATE PATHWAY
THE ROLE OF VITAMINS IN METABOLIC REACTIONS
REVIEW OF BIOCHEMISTRY
Tutorials
Summer semester of the first year
1. Tutorial 1 REVISION OF BASIC CHEMICAL REACTIONS
Basic chemical reactions. Regulations in the laboratory. Basic laboratory activities. Aqueous solutions as an
environment of the cell - the reactions of precipitation, complexation, redox. Conversion of units. The role
of micro- and macroelements in the human body. The reactions of selected cations and anions.
2. Tutorial 2 PREPARATION OF BUFFER SOLUTIONS – DETERMINATION OF BUFFER CAPACITY
1. Electrolytes and nonelectrolytes
2. Key terms: dissociation degree, dissociation constant, Ostwald's dilution law
3. Dissociation and hydrolysis reactions
4. Solution concentration - calculations
5. Strengths of acids and bases
6. The buffer solutions, buffer capacity, mechanism of buffer action
7. Buffers in the blood
8. pH, pOH, ionization of water
3. Tutorial 3 DIALYSIS OF CONGO RED SOLUTION CONTAMINATED WITH POTASSIUM THIOCYANATE
1. Structure of complex compounds
2. Redox reactions
3. Dilution of solutions, solubility equilibrium
4. Diffusion, osmosis, osmotic pressure
5. Dialysis
6. Tonicity and osmolarity of solutions
4. Tutorial 4 ELEMENTAL ANALYSIS OF ORGANIC COMPOUNDS. CHEMICAL PROPERTIES OF MONOFUNCTIONAL ORGANIC
COMPOUNDS
1. Organic compounds –classification of organic compounds, functional groups
2. Hydrocarbons – nomenclature. Characteristic reactions of: alkanes and cycloalkanes – combustion
reaction, free radical halogenation reaction; alkenes and alkynes – electrophilic addition reactions; arenes–
Hückel's rule, electrophilic substitution (ortho/para directors, meta directors)
3. Haloalkanes – nucleophilic substitution reactions, elimination reaction, Würtz’s reaction
4. Alcohols and phenols – synthesis reactions
5. Alcohol reactions – dehydration, oxidation, haloform reaction, reactions with: acids, metals
6. Phenol reactions – with bases, esterification, electrofilic aromatic substitution
7. Amines – nomenclature, a basicity of amines, reactions with acids, alkylation, acylation
8. Aldehydes and ketones – nomenclature, characteristic reactions: oxidation (acidic and basic conditions),
reduction, nucleophilic addition reactions (addition of H2O, alcohols, amines)
9. Carboxylic acids – nomenclature, acidity of carboxylic acids, reactions: with metals, with bases,
esterification, synthesis of acid chloride, decarboxylation
5. Test 1
1. Composition of complex compounds.
2. Redox reactions. Solubility products. Electrolytes solutions (weak, strong). Degree of dissociation,
dissociation constant. Ostwald’s dilution law. Dissociation and hydrolysis reactions. Calculations of solution
concentrations. Acid-base theory. Buffer solutions. Strong/weak acids. Strength in terms of pH.
3. Diffusion, osmosis, osmotic pressure, dialysis, tonicity and osmolarity of solutions
4. Hydrocarbons – nomenclature. Characteristic reactions of: alkanes and cycloalkanes – combustion
reaction, free radical halogenation reaction; alkenes and alkynes – electrophilic addition reactions; arenes–
Hückel's rule, electrophilic substitution (ortho/para directors, meta directors)
5. Haloalkanes – nucleophilic substitution reactions, elimination reaction, Würtz’s reaction
6. Alcohols and phenols – synthesis reactions; alcohol reactions – dehydration, oxidation, haloform
reaction, reactions with: acids, metals; phenol reactions – with bases, esterification, electrofilic aromatic
substitution.
7. Amines – nomenclature, a basicity of amines, reactions with acids, alkylation, acylation
8. Aldehydes and ketones – nomenclature, characteristic reactions: oxidation (acidic and basic conditions),
reduction, nucleophilic addition reactions (addition of H2O, alcohols, amines)
9. Carboxylic acids – nomenclature, acidity of carboxylic acids, reactions: with metals, with bases,
esterification, synthesis of acid chloride, decarboxylation
10. Carboxylic acid derivatives – acid chloride, acid anhydride, amides, hydroxy acids
11. Isomerization of organic compounds (configuration, conformation).
6. Tutorial 6 CHEMICAL PROPERTIES OF AMINO ACIDS, SOME PROPERTIES OF PEPTIDES AND PROTEINS
1. General structure of amino acids, the names (full names and their three-letter abbrevations) and
structures of protein amino acids.
2. Characteristics of the chemical groups attached to amino acid chain (carboxylic, amino, imino, sulphydryl,
imidazol, guanidine, hydroxyl groups).
3. Amphoteric properties of amino acids.
4. Classification of amino acids according to the chemical properties of their side chains (charged, nonpolar
hydrophobic, uncharged polar; aliphatic, cyclic, aromatic; acidic, basic)
7. Tutorial 7 PREPARATION AND PURIFICATION OF INVERTASE ( -FRUKTOSIDASE)
1. Structure and characteristics of the peptide bond
2. The physiologic significance of some peptides in human body
3. Classification of proteins according to their structures, properties and functions
4. Amino acids which stabilized and destabilized α-helix
5. Types of bonds according to protein structure (hydrogen, ionic, electrostatic, van der Waals bonds)
6. Posttranslational modifications of amino acids
7. Correlation between protein structure and function (myoglobin, hemoglobin, immunoglobulin)
8. Tutorial 8 THE KINETICS OF THE ENZYMATIC REACTION
1.Definitions: enzyme, coenzyme, cofactor.
2. Izoenzymes important in diagnostic: lactate dehydrogenase-LDH, creatine kinase-CK.
3. The structure of active site. Models of substrate binding: “lock and key model” and “induced fit model”.
Specificity of enzyme to substrate and type of the catalysis.
4. The mechanism of enzymatic reaction. The influence of physical and chemical factor on the enzyme
activity (temperature, pH, concentration of enzyme, substrate and product)
5. Kinetic of enzymatic reaction: the initial and maximum speed of enzymatic reaction, Michaelis-Menten
constant, Michaelis-Mentenequation, Lineweaver-Burke plot.
6. Regulation of enzyme activity: allosteric enzymes (activators and inhibitors, examples of allosteric
enzymes, concerted model and sequential model, kinetic of allosteric reaction); regulation by feedback and
its examples in human organism; modification of enzymes: phosphorylation and specific limited
proteolysis(proenzymes,
zymogens,
autocatalysis);
competitive
and
non-competitive
inhibition
(competitive and non-competitive inhibitors, application of enzymes in medicine: acetylsalicylic acid,
penicillin, fluorouracil, methotrexate, allopurinol)
7. Units of enzymatic activity (katal, enzyme unit, activity of enzymatic preparation)
8. Classification of enzyme (oxidoreductases, transferases, hydrolases, lyases, isomerases, ligases)
9. Coenzymes: their structure and functions.
9. Test 2
1. The structure of protein amino acids.
2. Reactions with amino and carboxyl group. Dehydratation of amino acids.
3. 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).
4. 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(homocysteine, homoserine, ornithine, cytrulline, β-alanine, γ-aminobutyric acid, βaminoizobutyric acid)
5. The formation, structure and properties of the peptide bond. Some important peptides in the human
organism (glutathione, peptide hormones, peptide antibiotics). The insulin synthesis.
6.The classification of proteins according to their structure, properties and functions.
7.The characteristics of primary, secondary, tertiary and quaternary structures of proteins.
8.Structure of alpha helix and beta sheet.
9.Amino acids which stabilized and destabilized α-helix
10.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).
11.Posttranslational modifications of amino acids in proteins.
12. Correlation between protein structure and function (myoglobin, hemoglobin, immunoglobulin)
13. The structure and synthesis of collagen.
14. Rybonucleaserenaturation as an example of the importance of primary protein structure.
15. The prions as an example of medical importance of proper protein folding.
16. The definitions: enzyme, coenzyme, cofactor.
17. The isoenzymes of the diagnostic importance (lactate dehydrogenase (LDH), creatine phosphokinase
(CPK)).
18. The structure of the active site and models for substrate binding. The specificity of enzymes to the
substrates and the catalysed reaction.
19. The catalytic mechanisms of the enzymatic reactions.
20. The influence of physical and chemical factors on the enzyme activity (temperature, pH, the enzyme
concentration, the substrate concentration, the product concentration).
21. The kinetics of enzymatic reaction: the initial and maximal velocities, Michaelis-Menten constant, the
Michaelis-Menten equation, the Lineweaver-Burk plot.
22. Regulation of enzyme activity: allosteric enzymes (activators and inhibitors, examples of allosteric
enzymes, concerted model and sequential model, kinetic of allosteric reaction); regulation by feedback and
its examples in human organism; modification of enzymes: phosphorylation and specific limited
proteolysis(proenzymes,
zymogens,
autocatalysis);
competitive
and
non-competitive
inhibition
(competitive and non-competitive inhibitors, application of enzymes in medicine: acetylsalicylic acid,
penicillin, fluorouracil, methotrexate, allopurinol)
23. Units of enzymatic activity (katal, enzyme unit, activity of enzymatic preparation)
24. Classification of enzyme (oxidoreductases, transferases, hydrolases, lyases, isomerases, ligases)
25. Coenzymes: their structure and functions.
10. Tutorial 10 SOME PROPERTIES OF MONOSACCHARIDES
1. Nomenclature of monosaccharides according to the carbon atom e. g. triose, tetrose etc.) and functional
group (aldose, ketose)
2. The isomerism of monosaccharides (Fischer projection and cyclic structure)
3. Oxidation and reduction of monosaccharides
4. Cyclic form of monosaccharides
5. Metabolism of fructose and glucose
6. Synthesis of 2,3-bisphosphoglyceric acid - 2,3-bisphosphoglyceric acid pathway
7. Derivatives of biologically important monosaccharides.
the chemical properties of monosaccharides, the examples of biologically important monosaccharides.
8. Synthesis and functions of sialic acids
11. Tutorial 11 SOME PROPERTIES OF DI- AND POLYSACCHARIDES
1. Basic disaccharides
2. Structure of polysaccharides
3. Synthesis and functions of sialic acids
4. Generation of ATP from glucose: glycolysis (reactions of glycolytic pathway, substrate-level
phosphorylation, regulation of glycolysis)
5. Structure and properties, the examples of biologically important di- and polysaccharides, physiologically
significant saccharide derivatives (e. g. heparine) and glycoproteins
6. Anaerobic glycolysis – (lactate fermentation, tissues dependent on anaerobic glycolysis, fate of lactate –
Cori cycle, lactic acidemia, ethanol fermentation).
7. Synthesis and degradation of lactose
12. Tutorial 12 SACCHARIDES OF PHYSIOLOGICAL IMPORTANCE
1. Synthesis and degradation of glycogen
2. Disorders of metabolisms of fructose, galactose and glycogen.
3.The pentose phosphate pathway. The directions of the pentose phosphate pathway reactions due to the
cellular needs.
4. Hemolysis caused by reactive oxygen species in the conditions of glucose-6-phosphate dehydrogenase
deficiency.
5. 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).
6. Oxidative fates of pyruvate – oxidation of pyruvate to acetyl CoA by pyruvate dehydrogenase. The citric
acid cycle. The energetic efficiency of citric acid cycle.
7. Bioenergetics of cell: ATP, AMP, ADP, 1,3-bisphosphoglyceric acid, acetyl-CoA, phosphocreatine. NADH
after glycolysis in aerobic conditions. Transfer of compounds through the inner and outer mitochondrial
membranes.The generation of ATP from glucose (complete aerobic oxidation of glucose, anaerobic
glycolysis).
13. Test 3
1. 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
2. Oxidation and reduction of monosaccharides
3. Cyclic form of monosaccharides
4. Basic disaccharides
5. Structure of polysaccharides
6. Derivatives of biologically important saccharides
7. Synthesis and functions of sialic acids
8. Generation of ATP from glucose: glycolysis (reactions of glycolytic pathway, substrate-level
phosphorylation, regulation of glycolysis)
9. Synthesis of 2,3-bisphosphoglyceric acid - 2,3-bisphosphoglyceric acid pathway
10. Anaerobic glycolysis – (lactate fermentation, tissues dependent on anaerobic glycolysis, fate of lactate –
Cori cycle, lactic acidemia, ethanol fermentation).
11. Metabolism of fructose and glucose
12. Synthesis and degradation of lactose
13. Synthesis and degradation of glycogen
14. Disorders of metabolisms of fructose, galactose and glycogen.
15. The pentose phosphate pathway. The directions of the pentose phosphate pathway reactions due to
the cellular needs.
16. Hemolysis caused by reactive oxygen species in the conditions of glucose-6-phosphate dehydrogenase
deficiency.
17. 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).
18. Oxidative fates of pyruvate – oxidation of pyruvate to acetyl CoA by pyruvate dehydrogenase. The citric
acid cycle. The energetic efficiency of citric acid cycle.
19. Bioenergetics of cell: ATP, AMP, ADP, 1,3-bisphosphoglyceric acid, acetyl-CoA, phosphocreatine. NADH
after glycolysis in aerobic conditions. Transfer of compounds through the inner and outer mitochondrial
membranes.The generation of ATP from glucose (complete aerobic oxidation of glucose, anaerobic
glycolysis).
14. Tutorial 14 THE ROLE OF VITAMINS IN METABOLIC REACTIONS
1. Structure and functions of water-soluble and fat-soluble vitamins
2. Microelements: examples of enzymatic reaction with iron, cobalt, zinc and cooper.
16. Tutorial 15 THE COMPLETION OF THE BIOCHEMISTRY LABORATORY
VIII. Booklist:

Timberlake KC "General, Organic, and Biological Chemistry"

Lieberman M, Marks AD "Marks` Basic Medical Biochemistry a Clinical Approach". 3rd
edition

Murray RK, Bender DA et al. "Harper`s Illustrated Biochemistry" 28th edition

Devlin Thomas M. Textbook of Biochemistry with Clinical Correlations, Seventh Edition
Wiley-Blackwell 2010
RULES AND REGULATIONS
I.
II.
III.
IV.
V.
Assessment form and regulations
Assessment is based on the presence at the lectures, passing all tests as well as completing
and passing all tutorials.
Assessment form and regulations of tutorials
1. Students should attend all classes and be prepared for every practical task based on an
programme posted on the notice board of the Chair and Department of Biochemistry.
Completing the practical task is based on obtaining the positive assessment of the current
material and passing the report.
Assessment form and regulations of passing tests
1. The dates of the tests are listed on the notice board of the Chair and Department of
Biochemistry, prior to the start of the semester.
2. The retake of a failed test has to be in the same form as the original test. The first retake
must take place before the next test. The second retake, called additional test, takes place
right before the admission to the exam. If a student fails more than one test as a first
retake, they need to pass an additional test covering the whole material.
3. Obtaining the average assessment of all tests above 4.0, can be the basis for the admission
to taking the exam before the beginning of examination session.
4. The material included in the test cannot exceed the predetermined material based on the
listed literature.
Examination form
1. Each exam date (I, II, first and second condition) must be conducted in a form of a test with
one positive answer. Evaluation criteria must be announced and cannot be altered.
2. Every student has the right to access tests and exams materials (question & answer sheet).
3. The term of each examination should be announced at least two weeks in advance, by prior
arrangement between the Head of the Department, and the governor of the year.
The regulations concerning passing missed tutorials due to authorized or unauthorized absence
1. Every student is required to attend all lectures and practical tutorials.
2. In case of absence or failing practical classes every student is allowed to make up for them
on a date consulted and agreed with the teacher assistant. Students can maximally miss
two tutorials during a semester.
3. Absence due to medical conditions requires a sick leave. Students must justify the absence
during the first class after the period of absence.
VI. General and specific health and safety regulations required during tutorials
1. Tutorials take place in the Chair and Department of Biochemistry.
2. Students’ outerwear and bags must be left in the coatroom before entering the Chair and
Department of Biochemistry,
3. The access to a laboratory is only given to UMK Collegium Medicum Students equipped
with protective lab coats and disposable latex gloves.
4. Protective lab coat should be put on and taken off outside the laboratory.
5. At the first class students will be familiarized with the organization of classes, teaching and
safety rules, and the assessment criteria.
6. Due to the fact that students might be exposed to harmful chemicals, they are required to
familiarize themselves with the characteristics of these harmful chemicals (which are
available in the Chair and Department of Biochemistry).
7. It is recommended that students wash their hands every time they leave the laboratory.
8. Students are not allowed to replace corks in the bottles of reagents, transfer reagents to
other tables, apply or pour chemicals into bottles or jars.
9. It is strictly forbidden for students to perform experiments other than those established by
the assistant.
10. It is strictly forbidden for students to taste or smell testing any substances and solutions.
11. Students should be careful while working to prevent putting at risk themselves or others,
and to prevent damaging the equipment.
12. Students should always work with respiratory irritants under the digesters.
13. Due to the threat of biological virus (HCV, HBV, and HIV) contamination, all operations
while working with biological material should be done in disposable protective gloves.
14. Students are forbidden to move around the grounds of the Chair and Department of
Biochemistry with protective gloves on, because it is absolutely forbidden to touch door
handles and other equipment with the gloves used during practical tasks.
15. After completing the tasks, students are required to clean and wash their workplace as well
as used laboratory equipment.
16. Students are forbidden to stay in a laboratory at times other than tutorials and consultation
hours.
17. Eating, smoking and using fire are totally prohibited in a laboratory.
18. Students are responsible for any damage done to the property, caused by the ignorance of
health, safety and fire regulations.
19. The lectures and multimedia presentations used during the course of biochemistry with
elements of chemistry are the intellectual property and thus are subject to copyright.
Copying, processing and dissemination of these materials in whole or in part without
permission are prohibited.