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General biochemistry

Code: 72922
ECTS: 7.0
Lecturers in charge: doc. dr. sc. Aleksandra Maršavelski - Lectures
doc. dr. sc. Marko Močibob - Lectures
Lecturers: Igor Živković - Seminar
Take exam: Studomat
Load:

1. komponenta

Lecture typeTotal
Lectures 60
Seminar 30
* Load is given in academic hour (1 academic hour = 45 minutes)
Description:
COURSE CONTENT:
1. INTRODUCTION. The molecular logic of life. The hierarchy in the molecular organization of cells. Macromolecules and their monomeric subunits. Chemical composition and bonding. Weak interactions in aqueous systems: hydrogen bonds, ionic interactions, van der Waals interactions.
2. NUCLEIC ACID STRUCTURE. Chemical structure and base composition. Forces stabilizing nucleic acids structure. Basic concepts in the transmission of genetic information.
3. PROTEIN STRUCTURE. Properties of amino acids. Peptide bonds. Simple and conjugated proteins. Levels of structure in proteins. The sequence of amino acid residues define primary structure of a polypeptide chain. Common secondary structures: alpha-helix and beta-conformation. Turns and loops in polypeptides. Structure of collagen. Protein tertiary structure. Quaternary structures of oligomeric proteins.
4. PROTEIN FOLDING AND NATIVE CONFORMATION. Structural diversity reflects functional diversity in globular proteins. Stable folding patterns in proteins. Ramachandran diagram. Protein motifs. Conformational changes and native conformation. Protein denaturation.
5. PROTEIN FUNCTION: MYOGLOBIN AND HEMOGLOBIN. Protein-ligand interactions. Protein structure affects how ligand bind. Quaternary structure and structural changes of hemoglobin caused by oxygen binding. Mechanisms for cooperative ligand binding. Hemoglobin also transports H+ and CO2: the Bohr effect. The role of 2,3,-bisphosphoglycerate. Sickle-cell anemia as a molecular disease of hemoglobin.
6. EXPLORING PROTEINS. Methods of protein purification: according to solubility, size, charge, binding affinity. Determination of the mass of the protein. Separation of proteins by gel-ectrophoresis. Immuno-techniques. Determination of amino acid sequence. Methods for three-dimensional structure determination. Peptide synthesis.
7. ENZYMES: BASIC CONCEPTS AND KINETICS. Enzymes are powerful and highly specific catalysts. Free energy is a useful thermodynamic function for understanding enzymes. Enzymes accelerate reactions by facilitating the formation of the transition state. Kinetic properties: the Michaelis-Menten model. Allosteric enzymes do not obey Michaelis-Menten kinetics. Enzyme inhibition: competitive and noncompetitive.
8. CATALITIC STRATEGIES (of hydrolytic enzymes): lysozyme, ribonuclease A, carboxypeptidase A, chymotrypsin.
9. REGULATORY STRATEGIES. Aspartate transcarbamoilase (separable catalytic and regulatory subunits; allosteric interactions); switching the activity of target proteins by phosphorylation; activation by specific proteolitic cleavage (chymotrypsinogen and trypsinogen); cascade regulation of zymogen activity (clotting and hemophilia)
10. PROTEIN DEGRADATION. Ubiquitin-labeling and destruction in proteasome.
11. STRUCTURE AND DYNAMICS OF BIOLOGICAL MEMBRANES. Molecular constituents of membranes. Structural lipids in membranes (phospholipids, glycolipids, sphingolipids, glycolipids, cholesterol). Supramolecular architecture of membranes - a lipid bilayer as the basic structural element of membranes. Membrane proteins, peripheral and integral. Membranes are asymmetric. Membrane fusion and reconstitution. Basic concepts of solute transport across the membrane.
12. INTRODUCTION TO METABOLISM. Principles of bioenergetics. Free-energy changes. Phosphoryl group transfers and ATP. Biological oxidation-reduction reactions. Coenzymes. Vitamins as precursors to coenzymes. Three stages of metabolism and generation of energy.
13. STRUCTURE AND FUNCTION OF CARBOHYDRATES. Monosaccharides. Glycosidic bonds. Common disaccharides: sucrose, lactose, maltose. Polysaccharides: glycogen, starch, cellulose. Glycolysis: reactions, enzyme mechanisms, regulation.
14. PENTOSE PHOSPHATE PATHWAY AND GLUCONEOGENESIS. NADPH generation and five-carbon sugars synthesis in the pentose phosphate pathway. Role of transketolase and transaldolese catalyzed reactions; mechanisms, the link to glycolysis. Regulation of the pathway. Synthesis of glucose from noncarbohydrate precursors. Gluconeogenesis is not a reversal of glycolysis. These two pathways are reciprocally regulated. Enzyme catalyzed reactions and mechanisms; pyruvate carboxylase and the role of biotine.
15. CITRIC ACID CYCLE. Formation of acetyl coenzyme A from pyruvate. Reactions, enzymes and mechanisms of the citric acid cycle. Stoichiometry and regulation of the cycle. The pyruvate dehydrogenase complex and its regulation. Asymmetric reactions of symmetric molecules. The citric acid cycle as a source of biosynthetic precursors. The glyoxylate cycle.
16. OXIDATIVE PHOSPHORYLATION. Redox potentials and free-energy changes. Electron-transfer reactions in mitochondria. Electron carriers and the respiratory chain. Proton gradient. Structure and function of ATP-synthase. Shuttles and translocases. Regulation of oxidative phosphorylation.
17. GLYCOGEN BIOSYNTHESIS AND BREAKDOWN. Synthesis of UDP-glucose. Inactivation of glycogen synthase by phosphorylation. Coordinated control of glycogen metabolism by a cyclic AMP cascade. Role of insulin in stimulating phosphatases. Regulation of blood glucose level. Glycogen and starch are degraded by phosphorolysis. Glycogen phosphorylase is regulated allosterically and hormonally. The role and mechanisms of other enzymes. Reactions, enzymes, activated precursors.
18. DEGRADATION OF LIPIDS AND FATTY ACIDS. Triacylglycerols as highly concentrated energy stores. Hydrolysis of triacylglycerols by cyclic AMP-regulated lipases. Degradation of fatty acids by the sequential removal of two carbon units. Fatty acid activation and linking to coenzyme A. The role of carnitine in transport to mitochondrial matrix. Oxidation of unsaturated and odd-chain fatty acids. Formation and utilization of ketone bodies.
19. AMINO ACID DEGRADATION AND UREA CYCLE. Conversion of alpha-amino groups into ammonium ion. Aminotransferases. Pyridoxal phosphate as a highly versatile coenzyme. Conversion of NH4+ into urea. Reactions of the urea cycle. The linkage to the citric cycle. The fate of the carbon atoms of degraded amino acids. Some degradation pathways. Coenzyme B12.
20. PHOTOSYNTHESIS. Structure of chloroplasts. Chlorophylls trap solar energy. Light reactions. Complementary role of two photosystems. Transfer of electrons from water to NADP+. Proton gradient and ATP synthesis. Cyclic electron flow. Structure of a bacterial photosynthetic reaction center. Calvin cycle. Role and catalytic imperfection of rubisco enzyme. C4-pathway in tropical plants. Coordination of light and dark reactions by thioredoxine.
21. BIOSYNTHESIS OF FATTY ACIDS. Synthesis and degradation occur in different pathways. Formation of malonyl coenzyme A as committed step in fatty acid synthesis. ACP. Fatty acid synthesis by a multifunctional enzyme complex. Source of NADPH and acetyl groups for fatty acid synthesis.
22. BIOSYNTHESIS OF MEMBRANE LIPIDS. Phosphatidate as an intermediate in the synthesis of phosphoglycerides and triacylglycerols. Activation reactions: CDP-diacylglycerol and CDP-alcohol intermediates. Sphingolipid biosynthesis. Synthesis of cholesterol from acetyl coenzyme A and its regulation. Lipoproteins.
23. BIOSYNTHESIS OF AMINO ACIDS. Nitrogen fixation. The iron-molybdenum cofactor of nitrogenase. NH4+ assimilation into amino acids by way of glutamate and glutamine. Essential and nonessential amino acids. Some biosynthetic pathways. Tetrahydrofolate as one carbon unit carrier. S-adenosylmethionine as methyl group donor. Regulation. Inherited disorders of amino acid metabolism.
24. BIOSYNTHESIS OF NUCLEOTIDES. Purine ring synthesis. PRPP as activated ribose phosphate donor. Synthesis of AMP and GMP from IMP. Feedback inhibition of purine nucleotide biosynthesis. Pyrimidine ring synthesis. Formation of CTP by amination of UTP. Synthesis of deoxyribonucleotides. Formation of deoxythymidylate. Regulation of biosynthetic pathways.
25. INTEGRATION OF METABOLISM. Metabolic strategies and metabolic regulation. . Metabolic profiles of the major organs. Recapitulation of hormonal regulation.
26. DNA AND RNA - MOLECULES OF HEREDITY. DNA sequence. DNA double helix. Denaturation and renaturation of DNA. A-, B- and Z-conformation. Topological properties. Negative supercoiling in naturally occurring DNAs. Topoisomerases.
27. REPLICATION OF DNA. DNA replication is semi-conservative. DNA is synthesized by DNA-polymerases. Other enzymes and proteins are involved in DNA replication. Enzymes structure and reaction mechanisms. DNA proofreading. The leading and lagging strands are synthesized in a coordinated fashion.
28. TRANSCRIPTION AND TRANSCRIPTIONAL CONTROL. In bacteria, all RNAs are made by a single RNA-polymerase. RNA synthesis is DNA-dependent. It proceeds in several stages: initiation, elongation, termination. RNA synthesis is initiated at promoters; specific sequences signal termination of RNA synthesis. Posttranscriptional editing and modifications of tRNA and rRNA transcripts in bacteria. RNase P as an example of the enzyme with RNA component. Structure, function and regulation of operons. Positive and negative regulation - operators and represors; CAP-cAMP regulation.
29. TRANSLATION OF mRNA INTO PROTEINS. The genetic code was cracked using artificial mRNA templates. The ribosome: structure and function. tRNAs and rRNAs: structure and function. Aminoacyl-tRNA synthetases attach the correct amino acids to their tRNAs. Wobble allows some tRNAs to recognize more than one codon. A specific amino acid initiates protein synthesis. Peptide bonds are formed in the elongation stage. Termination of polypeptide synthesis requires a special signal. Errors in protein synthesis: the quality control (editing by aminoacyl-tRNA synthetases; the role of translation factors). Protein synthesis is inhibited by many antibiotics and toxins. Nonsense suppression. Selenoprotein biosynthesis - the incorporation of 21st amino acid.
30. EUKARYOTIC CHROMOSOMES AND GENE EXPRESSION. Eukaryotic DNA is highly organized. Nucleosomes are the fundamental organizational units of the chromatin. Nucleosomes are packed into successively higher order structures. Eukaryotic genes contain introns. Eukaryotic genomes contain many repetitive DNA sequences. The differences in the transmission of genetic information in prokaryotic and eukaryotic organisms.
31. EUKARYOTIC TRANSCRIPTION AND RNA PROCESSING. Eukaryotic cells have three kinds of nuclear RNA polymerases. The introns transcribed into RNA are removed by splicing. Spliceosome and RNA catalyzed splicing. Eukaryotic mRNAs undergo additional processing. Multiple products are derived from one gene by differential RNA processing. Some events in RNA metabolism are catalyzed by RNA enzymes.
32. VIRUSES. Structure and flow of genetic information.
33. INTRODUCTION TO GENETIC ENGINEERING. DNA fragmentation; restriction enzymes. DNA sequencing. Vectors in genetic engineering. Recombinant DNA molecules.

LEARNING OUTCOMES:
1. Explain the basics of protein structure, correlate the interrelations between various levels of their structure and demonstrate the understanding of the linkage between protein structure and function.
2. Conclude about requirement for catalysis in cellular processes 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, differentiate and compare the various solute transport systems across membranes.
5. 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.
6. 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.
7. Provide an overview of the metabolic pathways for ATP formation. Explain the energy transduction mechanisms and the role of cellular membranes in that process.
8. Recognize and explain biochemical principles characteristic for the photosynthetic organisms.
9. 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.
10. Interpret the species-specific (bacteria, plants, mammals) and tissue-specific (liver, muscle, brain) features of the metabolic pathways.
11. Describe the structure of nucleic acids and demonstrate the knowledge and understanding of the biochemical principles governing flow of genetic information from nucleic acids to proteins.
12. Explain the mechanism of the template-based synthesis of biological polymers and comment on the structure and mechanisms of the enzymes participating in these processes.
13. Express similarities and differences between prokaryotes and eukaryotes in the structure and organization of the genom, and in the mechanisms maintaining flow of genetic information.
14. Explain the basic principles of genetic engineering and conclude about the relevance of recombinant DNA methodology for modern biochemistry.
Literature:
  1. Dovoljno je rabiti jedan od sljedećih udžbenika:
    D. L. Nelson and M. M. Cox, LEHNINGER PRINCIPLES OF BIOCHEMISTRY (6th Edition), W. H. Freeman and Co, New York, 2013.
    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.
  2. DOPUNSKA LITERATURA:
    zbirke zadataka i problema koje prate gore navedene udžbenike
Prerequisit for:
Enrollment :
Attended : General biochemistry
6. semester
Mandatory course - Mandatory studij - Chemistry
Consultations schedule: