Department of...
 
Biochemistry 1
 
Biochemistry 1
 
Code: 40367
ECTS: 9.0
Lecturers in charge: prof. dr. sc. Ita Gruić Sovulj - Lectures
Lecturers: Marija Pranjić - Seminar

Alojzije Brkić - Practicum
Mario Kekez - Practicum
Aleksandra Maršavelski - Practicum
Vladimir Zanki - Practicum
Take exam: Studomat
English level:

0,0,0

The lecturer is not able to offer courses in English at this time.
Load:

1. komponenta

Lecture typeTotal
Lectures 60
Practicum 30
Seminar 30
* Load is given in academic hour (1 academic hour = 45 minutes)
Description:
LECTURES:
1. An introduction to biochemistry: water as a solvent
2. Principles of protein structure: amino acids, peptides and protein primary structure;
3. Principles of protein structure: secondary, tertiary and quaternary structures, protein denaturation and folding
4. Working with proteins: chromatography, electrophoresis, immunochemical methods, mass spectroscopy, X-ray diffraction and NMR
5. Protein function: hemoglobin and myoglobin
6. An introduction to enzymes: how enzymes work
7. The basic principles of enzyme kinetics: Michaelis-Menten model, the kcat and KM definition; irreversible inhibition, mechanisms of reversible inhibition
8. Enzyme mechanisms: covalent catalysis, acid-base catalysis, utilization of binding energy in catalysis
9. Regulatory enzymes: allosteric enzymes, reversible covalent modification, proteolytic activation
(1st partial test)
10. Carbohydrates and glycoproteins: monosaccharides and disaccharides, polysaccharides (starch, cellulose, glycogen, chitin), glycoconjugates (proteoglycans, glycoproteins, glycolipids), carbohydrates as informational molecules- the sugar code
11. Lipids: storage lipids, membrane lipids, lipids as signals, cofactors and pigments
12. Structure and function of biological membranes: membrane dynamics
13. Solute transport across membranes; passive (glucose transporter) and active transport (P-type ATP-ase), channels (K+ channel, aquaporins);
14. Biosignaling: second messengers; G-protein, receptor tyrosine kinase, gated ion channels
15. Bioenergetics and biochemical reaction types: bioenergetics and thermodynamics, phosphoryl group transfers and ATP
16. Glycolysis, gluconeogenesis, and the pentose phosphate pathway
17. Principles of metabolic regulation: regulation of metabolic pathways, coordinated regulation of glycolysis and gluconeogenesis, the metabolism of glycogen - regulation of the synthesis and degradation pathways
(2nd partial test)
18. The citric acid cycle and the glyoxylate cycle
19. Oxidative phosphorylation: electron-transfer reactions in mitochondria, ATP synthesis, regulation of oxidative phosphorylation
20. Photophosphorylation and carbohydrate biosynthesis in plants: light absorption, light-driven electron flow, ATP synthesis by photophosphorylation, the Calvin cycle, photorespiration and the C4 plants
21. Fatty acid catabolism; digestion, mobilization, and transport of fats, oxidation of fatty acids, ketone bodies
22. Amino acid oxidation and the production of urea; metabolism of amino groups, nitrogen excretion, pathways of amino acid degradation
23. Lipid biosynthesis: biosynthesis of fatty acids, triacylglycerols, and membrane phospholipids, metabolism of cholesterol
24. Biosynthesis of amino acids and nucleotides: overview of nitrogen metabolism, biosynthesis of amino acids
25. Metabolism of nucleotides: biosynthesis and degradation of nucleotides
26. Hormonal regulation and integration of metabolism
(3rd partial test)

EXERCISES:
Amino acid structures. Acid-base properties of amino acids and petides. Determination of protein primary structures. Secondary, tertiary and quaternary protein structures. Exploring proteins. Hemoglobin and myoglobin. Enzyme kinetics. Reversible enzyme inhibition. Enzyme mechanisms and control. Carbohydrates: structure and function, Lipids properties and structure of biological membranes. Solute transport across the membrane. Signal transduction. Introduction to metabolism. Glycolysis. Gluconeogenesis and pentose phosphate pathway. Glycogen: biosynthesis and biodegradation. The citric acid cycle and the glyoxylate cycle. Oxidative phosphorylation. Photophosphorylation. The Calvin cycle. Fatty acid catabolism. The urea cycle and amino acid degradation. Fatty acid biosynthesis. Biosynthesis of triacylglycerols and membrane lipids. Amino acid biosynthesis. Nucleotides metabolism.

LABORATORY:
Potentiometric titration of amino acids. Determination of alcohol-dehydrogenase kinetic parameters for NAD+. Determination of alcohol-dehydrogenase kinetic parameters for ethanol and inhibition of activity by 2,2,2-trifluoroethanol. Size-exclusion chromatography of biological macromolecules. Size-exclusion chromatography of hemoglobin. Polyacrylamide gel electrophoresis in the presence of SDS (SDS-PAGE).

LEARNING OUTCOMES:
1. Define the basics of protein architecture, correlate the interrelations between various levels of protein structure, demonstrate the understanding of the linkage between protein structure and function, and describe the methods for exploring proteins.
2. Explain the importance of biocatalysis and demonstrate the understanding of the catalytic mechanisms employed by enzymes.
3. Make a distinction between various enzyme regulatory strategies (from simple inhibition, over allosteric control and posttranslational modifications to inactivation by proteolysis), explain their mutual interrelations and display the ability to link these strategies with regulation of the metabolic pathways and the physiological status of cell.
4. Describe the structure and explain the function of cell membranes, draw the structures of the membrane basic structural elements.
5. Differentiate and compare active and passive solute transport across the membrane, describe the importance of electrochemical gradient, and demonstrate the understanding of mechanisms that govern specificity of the transport.
6. Differentiate and compare signal transduction pathways. Name and describe various signals and corresponding second messengers.
7. Explain the biological functions of carbohydrates and lipids. Draw the representative structures and write the anabolic and catabolic reactions of the carbohydrate and lipid metabolisms.
8. Explain the biological functions of amino acids and nucleotides. Draw the representative structures and write the anabolic and catabolic reactions of the amino acid and nucleotide metabolisms.
9. Provide an overview of the metabolic pathways for ATP formation. Explain the energy transduction mechanisms and the role of cellular membranes in that process.
10. Recognize and explain biochemical principles characteristic for the photosynthetic organisms.
11. Demonstrate the understanding of the basic metabolic principles. Compare catabolic and anabolic metabolism with the emphasis on the reciprocal metabolic pathways and their mutual regulation.
12. Interpret the species-specific (bacteria, plants, mammals) and tissue-specific (liver, muscle, brain) features of the metabolic pathways.
13. Summarize and explain the basic safety rules for the work in biochemical laboratory.
14. Carry out experiments by themselves using the standard biochemical methods, and operate the standard/basic equipment used in biochemical laboratory.
15. Be able to complete data analysis and results interpretations for the biochemical reactions of interest.
16. Apply numerical methods for the extraction of biochemical parameters related to enzyme catalysis.
Literature:
  1. D. L. Nelson and M. M. Cox, LEHNINGER PRINCIPLES OF BIOCHEMISTRY (6th Edition), W. H. Freeman and Co, New York, 2013.

    Moguće je rabiti i jedan od sljedećih udžbenika:
    L. Stryer, J. Berg i J. Tymoczko, BIOKEMIJA, Školska knjiga, 2013. (prijevod VI izdanja na hrvatski jezik)
    J. M. Berg, J. L. Tymoczko, and L. Stryer, BIOCHEMISTRY (7th Edition), W. H. Freeman and Co, New York, 2012.
    D. Voet and J.G. Voet, BIOCHEMISTRY (4th Edition), J. Wiley and Sons, New York, 2011.
Prerequisit for:
Enrollment :
Passed : Cell Biology
Passed : General and Inorganic Chemistry
Passed : Organic Chemistry
4. semester
Mandatory course - Mandatory studij - Molecular Biology
Consultations schedule:
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