| Analyse the implications of elevated telomerase activity in cancer cells. |
|
| Compare and contrast different sequencing technologies |
|
| Compare and contrast the advantages and disadvantages of second generation sequencing (e.g. Illumina) and third generation sequencing (e.g. PacBio and Oxford Nanopore). Which technology would you recommend for sequencing repetitive regions and identifying structural variants? Justify your answer. |
|
| Compare and contrast the different approaches used by the IHGSC and Celera to sequence the human genome. |
|
| Compare and contrast the different generations of sequencing technologies, including Sanger sequencing, Next Generation sequencing, and current generation sequencing. Discuss the advantages and disadvantages of each. |
|
| Describe how DNA fingerprinting using minisatellite DNA lengths can be used in paternity tests and forensics. |
|
| Describe how mRNA transcripts are localised in a cell |
|
| Describe the difference between translational fusions and transcriptional fusions in reporter gene fusions. |
|
| Describe the function of SAGA complexes and their role in transcriptional activation. |
|
| Describe the principle of Oxford Nanopore sequencing and the role of pore proteins in the process. How does Oxford Nanopore sequencing differ from PacBio sequencing in terms of read lengths and library preparation? Provide examples of studies that have utilized Oxford Nanopore sequencing and discuss the potential applications and challenges of this technology. |
|
| Describe the process of adaptation in the CRISPR-Cas system. How does it provide immunity to phage infection? |
|
| Describe the process of bisulfite sequencing and its application in identifying methylation. |
|
| Describe the process of creating synthetic bacteria and why genetic manipulation is easy in bacteria. |
|
| Describe the process of identifying regulons using microarray assays. |
|
| Describe the process of methionine auxotrophy screening and why it can be challenging to interpret the results. |
|
| Describe the process of northern blotting and how it can be used to determine gene expression. |
|
| Describe the process of nucleotide excision repair and its role in repairing thymine dimers. |
|
| Describe the processes of gene duplication, replication slippage, and unequal crossing over, and how they contribute to genetic variation. |
|
| Describe the role of promoter proximal elements in regulating gene expression. |
|
| Describe the role of sTFs in coordinating the expression of functionally linked genes. |
|
| Describe the role of the 'TATA' box in eukaryotic gene promoters and its importance in targeting the RNA polymerase. |
|
| Describe the role of zip code binding proteins (ZCBPs) in the transport of mRNAs within a cell. |
|
| Describe the shotgun sequencing approach used by Celera and its advantages and disadvantages compared to the clone-by-clone approach used by the IHGSC. |
|
| Describe the structure and function of leucine zipper domains in transcription factors. |
|
| Describe the structure and function of nucleosomes in DNA packaging. |
|
| Describe the structure and function of the RNA recognition motif (RRM) and its role in RNA binding. |
|
| Describe the structure of the spliceosome and its role in nuclear pre-mRNA splicing. |
|
| Describe the TMDH technique and its applications in identifying genes required for infection. |
|
| Describe the two main mechanisms for repairing Double Strand Breaks (DSBs) and their implications in gene editing. |
|
| Design a single guide RNA (sgRNA) |
|
| Discuss the advantages of using linear DNA as opposed to plasmids in homologous recombination. |
|
| Discuss the c-value paradox and its implications for genome size. |
|
| Discuss the charged patch hypothesis and its implications for chromatin structure and transcription. |
|
| Discuss the concept of combinatorial control in gene regulation. |
|
| Discuss the different types of satellite DNA and their importance at centromeres. |
|
| Discuss the impact of Next Generation sequencing on the field of genomics and personalized medicine. Explain how the cost reduction of sequencing a human genome has made personalized medicine more feasible. Provide examples of how genome sequencing can be used in diagnosis and treatment. |
|
| Discuss the importance of centromeres in ensuring equal segregation of chromosomes during mitosis and meiosis. |
|
| Discuss the importance of CpG islands in gene expression regulation. |
|
| Discuss the importance of gene expression regulation in eukaryotic and prokaryotic cells. |
|
| Discuss the limitations of microarrays as a sequencing technology. |
|
| Discuss the mechanisms by which transposons can cause gene duplication and the formation of pseudogenes. |
|
| Discuss the methods used to identify and map transcriptional start sites in genomes. |
|
| Discuss the principle behind nanopore sequencing and its application in detecting methylated bases. |
|
| Discuss the process of translational control and the role of eIF4E, eIF4G, and PABP in translation initiation. |
|
| Discuss the regulation of galactose metabolism in yeast cells. |
|
| Discuss the regulatory mechanisms involved in the yeast Gal gene switch. |
|
| Discuss the role of cas9 in the CRISPR-Cas system. How does it contribute to the degradation of phage DNA? |
|
| Discuss the role of chromatin remodelling complexes in transcription and how they are recruited to promoter regions. |
|
| Discuss the role of histone deacetylases in transcriptional repression. |
|
| Discuss the role of HOX genes in anterior-posterior development and how they are organized in the genome. |
|
| Discuss the role of nuclear pore complexes in the transport of proteins and RNA across the nuclear membrane. |
|
| Discuss the role of recombinational repair in DNA strand replication and its catalysing enzyme. |
|
| Discuss the role of RNA-binding proteins (RBPs) in gene expression and their impact on all steps of gene expression. |
|
| Discuss the role of RNA-binding proteins in gene expression. |
|
| Discuss the role of site-specific recombination phages in inserting DNA into the host chromosome. |
|
| Discuss the role of telomeres in aging-related diseases. |
|
| Discuss the role of transcription factories in gene expression and the localization of active transcription within the nucleus. |
|
| Discuss the role of transposons in driving evolution. |
|
| Discuss the significance of CpG islands and methylation in the regulation of gene expression. |
|
| Discuss the significance of designing primers with a melting temperature (Tm) of 58-66°C in a PCR-based genotype screen. |
|
| Discuss the significance of the ENCODE project and its contribution to our understanding of the human genome. How did it challenge previous assumptions? |
|
| Discuss the steps involved in the protein import mechanism through nuclear pore complexes. |
|
| Discuss the various methods by which mutations can be induced in DNA. |
|
| Examine the functions of telomere-binding proteins in protecting telomeres. |
|
| Explain forward and reverse genetics approaches |
|
| Explain how chromatin remodelling machines contribute to the stimulation of transcription. |
|
| Explain how CRISPR-Cas nucleases can be used as sequence-specific antimicrobials. What advantages does this approach have over traditional antibiotics? |
|
| Explain how enhancers and silencers contribute to the three-dimensional organisation of the transcription unit. |
|
| Explain how gel shift assays are used to assay DNA and RNA binding activity. |
|
| Explain how homologous recombination can be used to create gene replacements and knockouts in bacteria. |
|
| Explain how microarrays work and how they can be used to determine the transcriptome of whole genomes. |
|
| Explain how reduced representation bisulfite sequencing (RRBS) works and its advantages. |
|
| Explain the concept of kinetic proofreading in pre-mRNA splicing. |
|
| Explain the concept of the histone code and its correlation with chromatin structure. |
|
| Explain the concept of topologically associated domains (TADs) and their regulation by CTFC and cohesin. |
|
| Explain the concept of transformation efficiency and how it is calculated. |
|
| Explain the concepts of orthologous and paralogous genes and how they contribute to gene evolution. |
|
| Explain the difference between autonomous and non-autonomous transposons and how they contribute to the evolution of genomes. |
|
| Explain the difference between forward genetics and reverse genetics and provide examples of how each approach is used. |
|
| Explain the difference between heterochromatin and euchromatin and how their structures affect transcription. |
|
| Explain the difference between heterochromatin and euchromatin and how they are observed in interphase cells. |
|
| Explain the difference between promoter-proximal elements and distal enhancers in mammalian genes. |
|
| Explain the different types of DNA-binding domains and their functions. |
|
| Explain the different types of mutations and their effects on the final protein product. |
|
| Explain the ENCODE / HGP projects |
|
| Explain the function and composition of the λ red recombination system. |
|
| Explain the importance of designing primers that amplify a PCR product of approximately 400-600 bp in size in a PCR-based genotype screen. |
|
| Explain the modular structure of transcription factors and how it was discovered. |
|
| Explain the modular structure of transcription factors and its significance in the yeast two-hybrid assay. |
|
| Explain the principle of PacBio sequencing using Zero-Mode Waveguides (ZMWs) and SMRT-bell adapters. How does PacBio sequencing differ from Illumina sequencing in terms of library preparation, read lengths, and error rates? Discuss the applications and limitations of PacBio sequencing. |
|
| Explain the principle of Sanger dideoxy sequencing and its significance in the Human Genome Project. |
|
| Explain the process of DNA packaging in eukaryotic chromosomes and the role of histones and non-histone proteins. |
|
| Explain the process of fusing a reporter gene to the gene of interest and measuring the output from the reporter. |
|
| Explain the process of heterochromatin spreading and the role of gene insulators in blocking its spread. |
|
| Explain the process of Illumina sequencing, including library preparation, cluster generation, and sequencing by synthesis. Discuss the key features and innovations of Illumina sequencing. |
|
| Explain the process of interference in the CRISPR-Cas system. How does it prevent phage DNA from being replicated? |
|
| Explain the process of methyl-mismatch DNA repair and how it differs from nucleotide excision repair. |
|
| Explain the process of mRNA degradation in eukaryotes, including the role of deadenylases and decapping enzymes. |
|
| Explain the process of mRNA export and the role of NXF1 and Ref in mediating this process. |
|
| Explain the process of non-replicative transposition and its significance. |
|
| Explain the process of pre-mRNA splicing |
|
| Explain the process of replication slippage and its role in generating different alleles of satellite DNA. |
|
| Explain the purpose of using positive and negative controls in a PCR-based genotype screen. |
|
| Explain the relationship between mRNA turnover and translational efficiency in eukaryotic cells. |
|
| Explain the role of G-quadruplexes and OGREs in the regulation of origins of replication. |
|
| Explain the role of histone variants in specific molecular processes and DNA repair. |
|
| Explain the role of microRNAs in regulated mRNA turnover. |
|
| Explain the role of transcriptional repressors in fine-tuning gene expression. |
|
| Explain the significance of p elements in drosophila and how they have evolved in wild populations. |
|
| Explain the significance of the PAM sequence in the search for a DNA sequence complementary to the sgRNA sequence. |
|
| Explain the significance of U1 and U2 snRNAs in pre-mRNA splicing. |
|
| Explain the steps involved in chromatin immunoprecipitation (ChIP) and its use in isolating DNA bound by specific proteins. |
|
| Explain the structural differences between nucleosomes extracted under low salt conditions and physiological conditions. |
|
| Explain the structure and binding specificity of zinc finger domains. |
|
| Explain the structure and function of a single guide RNA (sgRNA) in the CRISPR-Cas9 system. |
|
| Explain the three mechanisms by which mRNAs are localized to specific subcellular regions. |
|
| Explain the two proposed models for the structural organization of the 30 nm fibre. |
|
| Explain the two ways in which S. cerevisiae transformants are screened for successful gene editing. |
|
| Explain why bacteria are useful model organisms for studying fundamental biological processes. |
|
| Explain why it is important to predict the expected screening results before analysing the actual results. |
|
| How can transposon insertion mutants be selected and identified? |
|
| What is the nonsense-mediated decay pathway and how does it contribute to mRNA turnover? |
|
Biochemistry Questions
/
Genes, Genomes, and Chromosomes