Topic list - Molecular Biology

 

Nucleic acid synthesis (1-23)
Protein synthesis and regulation of gene expression (24-37 )
Biology of cancer. Methods in molecular biology and gene technology. (38-49)

  1. The properties of DNA polymerases (I-II-III) and the reactions catalyzed by these enzymes.
  2. The reaction catalyzed by DNA ligase, please mention several processes where this enzyme has an important role.
  3. The initiation of DNA replication in prokaryotes, the replication fork, please characterize the leading and lagging strand!
  4. Please describe the nascent Okazaki fragment, what kind of reactions (and enzymes) are necessary to form the final DNA strand from Okazaki fragments.
  5. The proteins participating in the replication of the prokaryotic genome, and their roles.
  6. The properties of the DNA polymerases present in eukaryotes. The time of DNA replication in the cell cycle.
  7. The replication bubbles (the movement of the replication forks: leading strand and lagging strand). The distribution of old and new histones
  8. The organization of the eukaryotic genome (nucleosome structure, packaged nucleosomes, extended chromatin, condensed chromatin, chromatids in the metaphase chromosome.) The number of DNA molecules in G2 phase of the human cell.
  9. The most frequent lesions of DNA and the agents resulting these lesions. The significance of the presence of thymine in the DNA instead of uracil.
  10. The enzymes and reactions in the repair of depurination and deamination
  11. The formation of thymine dimers and the enzymes and reactions in the repair of this lesion. The possibility of the correction of DNA lesions of both strands.
  12. Please, characterize the point mutations (substitutions and frame-shift mutations). What is the "nonsense-mutation"?
  13. Please, describe the mechanism of spontaneous mutation (for example the transition from T-A to C-G)
  14. What is a suppressor mutation? What is the principle of Ames' test?
  15. Fundamental differences between the transcription of prokaryotic cells and the transcription of eukaryotes.
  16. The properties of the DNA directed RNA polymerase of E. coli
  17. The promoter. The inhibition of transcription in prokaryotes. Strong and weak promoters. The elongation and termination of transcription in prokaryotes. The structure of polycistronic mRNA.
  18. Transcription of DNA in eukaryotic cells. The structure of the gene in eukaryotes, the eukaryotic promoter and the role of enhancers.
  19. Eukaryotic RNA polymerases. Modifications of the primary transcript at the 5' end and at the 3' end.
  20. The mechanism of splicing. The components participating in this mechanism. The mechanism of alternative splicing.
  21. Replication of bacteriophages. The lytic cycle of the replication of bacteriophages (T4 phage). The role of the restriction endonuclease-methylase pairs in the bacteria.
  22. The replication of the retroviruses. The reactions catalyzed by the reverse transcriptase,
  23. Viral oncogenes and cellular protooncogenes. Oncogenic DNA viruses.
  24. The structure and function of tRNA. The formation of aminoacyl-tRNA. The specificity of aminoacyl-tRNA synthetases.
  25. The structure, function, and assembly of ribosomes.
  26. The direction of protein synthesis and the mRNA reading. The recognition of initiation codon(s) in prokaryotes. The role of IF1, IF2, IF3.
  27. The recognition of translation start in eukaryotes. The role of eIF2, eIF3, eIF4.
  28. Steps of elongation. The function of elongation factors in prokaryotes and eukaryotes. The termination of protein synthesis in pro- and eukaryotes.
  29. The role and characteristics of signal sequences in direction of proteins. Transport of proteins across the endoplasmic reticulum membrane. The structure and role of the signal recognition particle.
  30. Retention signal for endoplasmic reticulum resident proteins, quality control in the endoplasmic reticulum.
  31. Anterograde and retrograde transport from ER to Golgi. Coat proteins, SNARES, Gproteins. Mechanism of exocytosis.
  32. Lysosomes at the intersection of protein trafficking pathways. Receptor-mediated endocytosis. Protein degradation pathways.
  33. Transport of proteins into the nucleus Nuclear import and export. Sorting of proteins into the mitochondria. The role of heat shock proteins in targeting proteins into different intracellular compartments.
  34. The lac operon. Induction of beta galactosidase activity. The function of lac operon. The role of CAP-protein and cAMP in dual control of lac operon.
  35. The control of gene expression in eukaryotes. Transcriptional control. The components (signal, level, mechanism) and purpose of gene control in eukaryotic organisms. Gene regulatory sequences (enhancer, upstream promoter element) and gene regulatory proteins.
  36. Processing control, Transport control, mRNA degradation conttol. Alternative RNA splicing, changes of poly-A addition. Control of mRNA degradation.
  37. Translational control in eukaryotes. Translational repressor protein. Translational enhancer. Translational frameshifting. Control by phosphorylation of eIF2.
  38. The molecular genetics of cancer. Mechanisms by which retroviruses can cause cancer. Major classes of protooncogenes in the intracellular control network
  39. Transformation of cells, detection of oncogenes. The conversion of protooncogenes to oncogenes. Tumor suppressor genes.
  40. General procedure for detecting and isolating DNA regulatory sequences. Gel retardation, footprinting. DNA binding proteins.
  41. Recombinant plasmids. Expression vectors, reporter genes (CAT, luciferase) Genomic and cDNA libraries. Screening of DNA libraries with colony hibridization. Southern, Northern and Western blotting. DNA chip technology.
  42. PCR as a new tool in medical diagnosis. Amplification of specific DNA fragments by PCR. Prenatal diagnosis of 21OH-ase deficiency by allele specific PCR. Prenatal diagnosis of DF508 deletion in cystic fibrosis by PCR
  43. The Human Genome Project. Mapping strategies (genetic and physical maps, markers, ordered chromosomal libraries). Automatic DNA sequencing, DNA and protein databases. The polymorphic nature of the human genome (SNP, STR, VNTR)
  44. Recombinant DNA technology in medical industry. Insulin production in bacteria and its regulation by IPTG. Production of secretory proteins in bacteria and in higher animals. Transgenic animals (the giant mouse)
  45. Cystic fibrosis (CF): Diagnosis and treatment by recombinant DNA technology. RFLP as a marker of genetic diseases. RFLP markers of CF. The structure and the function of CFTR protein.
  46. Human gene therapy. NeoR/TIL gene marking. ADA gene therapy. Cancer gene therapy. Prospects for CF gene therapy.
  47. Eukaryotic cell cycle I. Cyclins and cdk-s. Control of G1/S transition, restriction point. Control of G2/M transition.
  48. Proteolysis in the cell cycle. Oncogenes and cell cycle. The retinoblastoma protein (p105) cycle. p53 and the regulation of proliferation/apoptosis.
  49. Apoptosis. Function of apoptosis in tissue homeostasis. Morphological and biochemical characteristics of apoptosis. Different pathways for activating caspases.