0.5 End-of-topic assignments

Topic 1. chemistry of the cell

1. What are the main chemical components of a cell?
2. What are the structure levels of a protein?
3. Give an example of the modular characteristic of a protein.
4. What is a “Watson-Crick basepairing”?
5. What are the differences between a DNA and an RNA molecules
6. What are the main weak chemical bonds existing in living organisms?
7. What are the characteristics of these bonds which determine their functions?
8. What is the chromatin? the chromosome?
9. Why is the eukaryotic genome much more compact than prokaryotic genome?

Topic 2. constancy of dna

1. Describe some experiences showing that DNA is the genetic material.
2. What is the Central Dogma of Molecular Biology?
3. Describe Meselson&Stahl’s experience about DNA replication in E. coli; what is the meaning of this experience?
4. What is a replicon?
5. What are the factors needed for the initiation of DNA replication in E. coli
6. How are the two strands of DNA molecule being copied from an origin of replication?
7. What are the problems encountered by the replication machinery at the replication fork ? How are these problems resolved
8. What are the roles of Helicase, Topoisomerase, Primase, SSB proteins, DNA polymerase III, RNase H, DNA polymerase I?
9. What are the problems of finishing DNA replication in prokaryotes? eukaryotes? How are they resolved?

Topic 3. variations of dna

1. What are the main causes of DNA variation? What are their roles in the living world?
2. How are the mutations being repaired during and shortly after the end of the replication process?
3. What are the main repair systems used by the cell to repair DNA damages between two replication processes?
4. What are the differences between homologous and site-specific DNA recombination?
5. What are the biological roles of homologous recombination? site-specific recombination?
6. Describe the Holliday model used to explain DNA homologous recombination.
7. Compare the Holliday model and the Double-Stranded Break (DSB) model of recombination.
8. What are the functions of RecBCD complex, RecA, RuvAB and RuvC in the homologous recombination in E. coli?
9. What are the functions of SSR recombinases in site-specific recombination?
10. What are transposons? How are they being classified?
11. What are the differences between replicative and non-replicative transposition?
12. How does a polyA retrotransposon transpose?
13. How is a retroviral-like retrotransposon transpose?

Topic 4. gene expression – transcription

1. What are the characteristics of transcriptional process that distinguish it from DNA replication?
2. What are the components of prokaryotic RNA polymerase? What are their functions?
3. What are the structure and functions of a promoter?
4. How does the RNA polymerase initiate the transcription?
5. How is the RNA molecule being elongated?
6. What are the mechanisms of transcription termination?
7. What are the eukaryotic RNA polymerases? What are their functions?
8. What are the DNA sequences involved in transcription initiation by RNA polymerase II?
9. How does RNA polymerase II function during transcription?
10. What are the post-transcriptional mRNA processing’s?
11. Why is RNA splicing a crucial step in gene expression in eukaryotes?
12. What is a spliceosome? How does it function during splicing process?

Topic 5. protein synthesis

1. What are the characteristics of the Genetic Code?
2. What is the Wobble concept?
3. What are the disadvantages of translational compared to replicational and transcriptional processes?
4. What are the roles of tRNA, rRNA, mRNA?
5. What is an ORF? What are the criteria used to define it?
6. What is the 5’ end structure of a prokaryotic (and eukaryotic) mRNA necessary to its translation?
7. What are the functions of a ribosome?
8. What are the structural characteristics of a tRNA?
9. How is an amino acid attached to a tRNA? What determines the specificity of the reaction?
10. How is the translational process initiated in prokaryote? in eukaryote?
11. What are the main steps of translational elongation?
12. How is the translational process terminated?

Topic 6. regulation of gene expression in prokaryotes

1. What are the purposes of the regulation of gene expression in prokaryotes? in eukaryotes ?
2. What are the main mechanisms of gene expression regulation in prokaryotes? in eukaryotes ?
3. What do you think which determine the differences in the regulation of gene expression between these two groups?
4. What is a positive control of gene expression? a negative control
5. What are the structural and functional characteristics of an operon?
6. What is a catabolite repression?
7. What is “attenuation” in terms of regulation of gene expression?
8. How does the alternative use of σ factors fit the purpose of the regulation of gene expression in prokaryote?

Topic 7. regulation of gene expression in eukaryotes

1. What are the structural characteristics that determine different levels of the control of gene expression in eukaryotes?
2. What is an epigenetic inheritance? What are the basic mechanisms underlying epigenetic in heritance
3. Give an example for epigenetic inheritance through histone modifications and DNA methylation?
4. What are the roles of TRANS proteins and CIS sequences in the control of transcriptional initiation?
5. What are the respective roles of general and specific transcription factors in initiating the transcription process?
6. What are the common modules of transcription factors?
7. How can alternative splicing generate more than one transcript from one gene?
8. How can transcription factors act at distance?
9. What are the determinants of mRNA stability?
10. What are the main mechanisms of post-translational control?
11. What are siRNAs? miRNAs? What are their roles in the control of gene expression?

Topic 8. methods

1. What are the main steps of a nucleic acid extraction protocol?
2. What is electrophoresis used for?
3. How can one determine the concentration of a double-stranded DNA by spectrophotometric analysis?
4. What are the enzymes used for PCR technique? What are their characteristics?
5. What are the principles of quantitative PCR based on the use of Taqman probe?
6. What are Molecular cloning techniques used for?
7. What is a vector? What are its characteristics?
8. What are the main steps of Molecular cloning protocols?
9. How is a PCR performed?
10. What are the main steps of Southern blotting?
11. What is the principle of Dideoxy sequencing? How is it applied in automatic sequencing?
12. Give a definition for Genomics? Transcriptomics? Proteomics? Metabolomics? Phenomics?
13. How can Bioinformatics be used to predict gene function from their structures?
14. What are microarrays used for?
15. What is the principle of the Yeast Two-hybrid system?