Biochemistry Questions Biochemistry Questions


This website has a collection of notes from my biochemistry degree. They may be useful.

These notes are unreferenced. This is also not a textbook. When you buy a textbook, you expect the text within to be correct. Extend no such expectation here.

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Analyse the DNA replication initiation process in bacterial cell division, detailing the role of DnaA, hemi-methylated DNA, and the eclipse period.
Analyse the implications of elevated telomerase activity in cancer cells.
Analyse the pathogenesis of Helicobacter pylori infections, detailing its unique properties and the mechanisms it employs to cause disease.
Analyse the potential of cyanobacteria in biotechnology, highlighting their advantages as a chassis organism and their ability to synthesize various products. What are the current limitations in commercializing cyanobacterial products compared to traditional organisms like E. coli and yeasts?
Analyse the production of cyanotoxins and cyanobactins by certain cyanobacteria species. How can these compounds be potentially utilized in pharmaceutical applications?
Analyse the relationship between body fat percentage and drug distribution in the body.
Analyse the role of NAD(P)H cofactors in fatty acid biosynthesis, specifically focusing on the enzymes involved in removing and adding functional groups. How do these enzymatic reactions contribute to the elongation of fatty acid chains?
Analyse the role of spectroscopies like absorbance spectrometry and NMR in assay design, highlighting their strengths and limitations.
Analyse the significance of barriers in the innate immune system, focusing on the role of epithelial cells, skin, and mucosal surfaces. How do these barriers prevent pathogen entry and infection? Provide examples of infections that breach these barriers.
Analyse the significance of genetic variations in drug efficacy, using metoprolol's activity changes based on beta-1-adrenergic receptor differences as an example. How can personalized medicine account for these variations in treatment?
Analyse the symptoms and long-term effects of syphilis infection, including the neurological manifestations and the concept of 'sleeper cells'. How does the unique biology of Treponema pallidum contribute to its pathogenicity?
Analyse the TGN1412 clinical trial incident and its impact on the safety of biological drug trials.
Analyse the unique characteristics of glycerol spores in Myxococcus, comparing their resistance levels to traditional fruiting body spores and explaining the structural differences.
Analyse the various causes of antibiotic resistance, including over-prescription, misuse by patients, and agricultural practices. How can healthcare professionals and policymakers collaborate to combat this global issue?
Briefly discuss how RNA thermometers work.
Briefly discuss the functions of sigma factors in E. coli.
Briefly discuss the organisation of the E. coli chromosome.
Briefly discuss the roles of accessory proteins in the operation of two-component systems.
Compare and contrast different sequencing technologies
Compare and contrast humoral immunity by B cells and cell-mediated immunity by T cells in adaptive immunity. Explain the process of antigen recognition and the differentiation of B and T lymphocytes.
Compare and contrast in vitro testing with in vivo testing in the context of receptor occupancy.
Compare and contrast photosystem I and photosystem II. What are their roles in photosynthesis?
Compare and contrast primary pathways and secondary pathways in terms of their functions, regulation, and metabolite products.
Compare and contrast Rho-dependent and Rho-independent transcription termination mechanisms in bacteria. Discuss the significance of these mechanisms in regulating gene expression.
Compare and contrast targeted mutagenesis methods with random mutagenesis methods in studying virulence factors. How do these methods help in understanding the function of specific genes in pathogens?
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 ATP synthesis processes in glycolysis, the Krebs cycle, and oxidative phosphorylation. How do these processes collectively contribute to the overall ATP yield in aerobic respiration?
Compare and contrast the Brønsted-Lowry theory and the Lewis theory of acids and bases, highlighting their key differences and applications in enzyme catalysis.
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.
Compare and contrast the fatty acid synthetase types I and II in terms of their catalytic mechanisms and distribution in different organisms. How do these two types differ in their approach to fatty acid biosynthesis?
Compare and contrast the first generation and second generation antipsychotic drugs.
Compare and contrast the functions of different prokaryotic DNA polymerases, highlighting their specialized roles in DNA replication.
Compare and contrast the functions of Gαs and Gαi in GPCR signalling.
Compare and contrast the mechanisms of action between monoclonal antibodies and ligand mimics in drug design. How do these different approaches impact the treatment of various diseases?
Compare and contrast the mechanisms of action of attenuated, killed pathogen, and subunit vaccines. Analyse the advantages and disadvantages of each type of vaccine.
Compare and contrast the mechanisms of action of methotrexate and sulfasalazine as DMARDs for rheumatoid arthritis.
Compare and contrast the mechanisms of action of triclosan and diazaborine inhibitors on ENR. How do these inhibitors differ in their approach to enzyme inhibition?
Compare and contrast the modulation of GABA_A receptors by benzodiazepines and barbiturates.
Compare and contrast the properties of full agonists and partial agonists.
Compare and contrast the sizer mechanism and adder mechanism in controlling cell division, providing examples of organisms where each mechanism is observed.
Compare and contrast the spore formation mechanisms in Bacillus and Myxococcus, highlighting the differences in cell types and genetic screening challenges.
Compare and contrast the storage of excess glucose as glycogen in muscle and its conversion to fat.
Compare and contrast the structure and selectivity of porins and α-helical membrane proteins.
Compare and contrast the structures and functions of rhodopsin and β2-adrenergic receptor (β2-AR) as GPCRs.
Compare and contrast the use of animal models, cell lines, and organoids in studying pathogenesis. Discuss the ethical, practical, and cost considerations associated with each method.
Compare and contrast the use of continuous flow and stopped flow methods in analysing enzyme-substrate reactions. Discuss the advantages and limitations of each approach.
Compare and contrast the use of different quenching agents in stopping reactions and quantifying compounds.
Compare and contrast the virulence factors of Neisseria gonorrhoeae and the strategies it employs to evade the immune response. How does this contribute to antibiotic resistance?
Compare and contrast Watson-Crick base pairing with Hoogsteen base pairing in the context of DNA polymerase accuracy. How does the active site of DNA polymerase favour Watson-Crick pairing over Hoogsteen pairing?
Compare passive, primary active, and secondary active transport across membranes. Give examples of each.
Compare the ATP synthesis efficiency of a 14 C-subunit ring and an 8 C-subunit ring in ATP synthase.
Compare the efficiency of ATP synthesis with 8 C ring subunits to that with 13 C ring subunits. What factors contribute to the difference in efficiency?
Compare the process of dehydrating K+ ions versus Na+ ions in ion channels, and explain why it requires more energy to remove water molecules from Na+.
Define and explain the concept of half-life in biochemical kinetics. How is it calculated, and what does it signify about the reaction process? Provide a real-life example to illustrate the concept.
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 animal models used to study depression and their relevance in assessing the efficacy of antidepressant drugs.
Describe the challenges in treating multi-drug resistant gonorrhoea and the potential implications of untreatable infections. What strategies can be implemented to combat this issue?
Describe the chemical modification studies conducted on RNase A, specifically focusing on the binding of iodoacetate to histidine residues and its implications on the enzyme's function.
Describe the concept of dead time in faster reactions and how it is determined. Provide examples of methods used to minimize dead time in reaction kinetics.
Describe the concept of sp3 and sp2 hybridization in carbon atoms. How does hybridization affect the geometry and bonding properties of carbon compounds?
Describe the cyanobacterial carbon concentrating mechanism.
Describe the difference between translational fusions and transcriptional fusions in reporter gene fusions.
Describe the differences between strict (professional) pathogens and opportunistic pathogens, highlighting their unique characteristics and modes of transmission. Provide examples to illustrate these distinctions.
Describe the different phases of clinical research in drug development and their respective purposes.
Describe the different types of protein-membrane interactions.
Describe the different ways bacteria develop resistance to antibiotics, such as efflux mechanisms and inactivation of drugs. Provide examples of specific enzymes involved in resistance and discuss their significance in the context of antibiotic efficacy.
Describe the function of biotin as a carrier and its role in metabolism.
Describe the function of natural killer (NK) cells in recognizing and killing infected cells. Discuss the role of MHC I in inhibiting NK cell killing and how cancerous cells evade this mechanism.
Describe the function of SAGA complexes and their role in transcriptional activation.
Describe the function of σ32 in controlling heat-shock response genes in bacteria. How does the secondary protein structure change at higher temperatures, and what are the consequences for the cell?
Describe the kindling model of epilepsy and how it is used in research.
Describe the mechanism by which DNA polymerase ensures fidelity during DNA replication. How does the steric gate, specifically the Phe residue, contribute to the accurate selection of nucleotides?
Describe the mechanism of action of peptide deformylase (PDF) in bacterial protein synthesis. How does the coordination of metal ions influence PDF's enzymatic activity?
Describe the mechanism of action of t-box riboswitches in sensing uncharged tRNAs. How do t-box riboswitches control the expression of enzymes for amino acid synthesis?
Describe the mechanism of receptor-tyrosine kinases and their significance in signalling.
Describe the mechanisms of action of defensins in the innate immune system. How do these peptides disrupt bacterial membranes and aid in controlling infections? Provide examples of infections where defensins are particularly effective.
Describe the mechanisms of action of selective serotonin reuptake inhibitors (SSRIs) and the reasons for their slow onset of efficacy.
Describe the mechanisms of antibiotic resistance in pathogens and how it impacts their spread, with relevant examples.
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 attenuating live vaccines and the potential risks associated with them. How do attenuated live vaccines differ from killed vaccines in terms of immune response stimulation?
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 cryo EM and its advantages over X-ray crystallography for protein structure determination.
Describe the process of enzyme activation by proteolysis and the role of inhibitor proteins in controlling protease activation. Use chymotrypsinogen as an example to illustrate the activation cascade.
Describe the process of FaRLiP in cyanobacteria and its adaptation to far-red light. How does the synthesis of chlorophyll d and f in response to far-red light enhance the organism's competitiveness?
Describe the process of identifying regulons using microarray assays.
Describe the process of lesion bypass using trans-lesion synthesis polymerases and its importance in DNA replication.
Describe the process of ligand-mediated endocytosis and how it is mediated by membrane rafts. Discuss the role of caveolin in this process.
Describe the process of methionine auxotrophy screening and why it can be challenging to interpret the results.
Describe the process of neurotransmitter diffusion and how it contributes to signal transmission between cells.
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 process of nutrient acquisition by bacteria as a virulence factor. How do siderophores and iron-binding proteins contribute to bacterial survival and pathogenicity?
Describe the process of primary active transport and how it is powered by ATPases.
Describe the process of protein trafficking in the endoplasmic reticulum and how proteins are tagged for their destination.
Describe the process of quenched flow and its application in studying reactions. Explain how temperature can be utilized as a quencher in this method.
Describe the process of RNA self-cleavage in alkaline conditions and why RNA is more susceptible to breakage in basic environments. Discuss the formation of pentaphosphate intermediates during this process.
Describe the process of structure-based drug design using HIV protease inhibitors as a case study. How can understanding the molecular structure of a target enzyme lead to the development of effective drugs?
Describe the process of supercoiling in bacterial DNA and its impact on gene expression. How do topoisomerases regulate supercoiling in bacteria?
Describe the process of supercoiling in bacterial DNA and its impact on transcription. Discuss the role of topoisomerases in regulating supercoiling and the potential consequences of antibiotic resistance.
Describe the process of β-oxidation and its significance in fatty acid catabolism.
Describe the processes of gene duplication, replication slippage, and unequal crossing over, and how they contribute to genetic variation.
Describe the properties that industrial microbes should possess for efficient product synthesis. How do these properties contribute to successful industrial fermentation processes?
Describe the relationship between the number of ion channels open and the voltage across the membrane. Discuss the role of voltage-gated Na+ channels and voltage-gated K+ channels in nerve cells.
Describe the reversible enzyme lactate dehydrogenase (LDH) and its role in converting pyruvate to lactate. How does endurance training affect the proportion of LDH subunits in muscle tissue?
Describe the role of antagonists and agonists in receptor signalling. How do these ligands interact with receptors at orthosteric and allosteric sites? Provide examples of how drugs can modulate receptor activity.
Describe the role of dipicolonic acid (DPA) in stabilizing bacterial spores, including its interactions with DNA and water molecules.
Describe the role of fluorine in modulating drug metabolism. How does fluorine substitution affect the bioavailability of a drug by decreasing its metabolism?
Describe the role of GABA in the treatment of anxiety and the pharmacology of GABA_A receptors.
Describe the role of heterocysts in filamentous cyanobacteria.
Describe the role of human serum albumin (HSA) in carrying hydrophobic molecules in the body. How does this process help in overcoming the issue of drug solubility in the blood? Provide a comprehensive explanation with relevant illustrations.
Describe the role of IC50 in enzyme inhibition. How does IC50 differ from EC50, and how is it used to determine the potency of an enzyme inhibitor?
Describe the role of membrane rafts in controlling the localisation of membrane proteins.
Describe the role of Mg2+ in the Calvin cycle and its importance for rubisco activity.
Describe the role of OPG (osmoregulated periplasmic glucans) in protecting spores during sporulation and how it differs from endospores.
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 signalling pathway involving GPCRs, cAMP, and protein kinase A (PKA), and explain how it leads to the activation of genes.
Describe the significance of studying pathogenesis in the development of antibiotics and therapeutics. How can anti-virulence factor therapeutics be utilized in treating bacterial infections?
Describe the stereospecific nature of hydride transfer in enzymatic reactions, focusing on the enzyme's ability to differentiate between hydrogen atoms. How does the distance and angle of transfer influence the efficiency of the reaction?
Describe the structural features of the 'hotdog' fold in FabA and FabZ reductases. How does this unique fold contribute to their catalytic activity?
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 a photosystem and the function of the antenna complex in capturing and concentrating light energy.
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 how phase variation allows bacteria to evade immune responses by changing the antigens they present. Provide examples of mechanisms used by bacteria for phase variation.
Discuss Jardetzky's allosteric model for membrane pumps and how it explains the alternating access mechanism.
Discuss Marcus theory and its relevance in explaining electron transfer reactions in Photosystem I.
Discuss the acetone-butanol-ethanol (ABE) fermentation process in Clostridium species. How does this pathway contribute to biofuel synthesis, and how can genetic engineering optimize product yields?
Discuss the advantage of having a greater number of C ring subunits in ATP synthesis. How does this allow for continual ATP production in changing environmental conditions?
Discuss the advantages and disadvantages of using direct assay methods versus quenching techniques in quantifying reactions.
Discuss the advantages of forming resting bacterial spores and how they increase resistance to physical and chemical stressors.
Discuss the advantages of using linear DNA as opposed to plasmids in homologous recombination.
Discuss the application of bio-photovoltaics using cyanobacteria to convert light into electricity. How does the process of transferring electrons from the photosynthesis electron transport chain to an electrode work, and what are the challenges in scaling up this technology for practical use?
Discuss the assumptions underlying the Michaelis-Menten model in enzyme kinetics. How does the assumption that k-1 is much greater than k+2 impact the interpretation of enzyme-substrate interactions? Provide examples to support your discussion.
Discuss the c-value paradox and its implications for genome size.
Discuss the challenges associated with culturing certain pathogens in the lab and how this limitation affects the study of infectious diseases. Provide examples of pathogens that are difficult to culture and explain the implications of this difficulty on research and treatment strategies.
Discuss the challenges associated with developing antibiotics targeting ENR due to the differences in structure between bacterial and human enzymes. How can these challenges be overcome in drug development?
Discuss the challenges of animal toxicology in the development of biopharmaceuticals and propose alternative methods for testing.
Discuss the charged patch hypothesis and its implications for chromatin structure and transcription.
Discuss the concept of combinatorial control in gene regulation.
Discuss the concept of desensitisation and its impact on drug addiction.
Discuss the concept of receptor reserve and its impact on agonist binding.
Discuss the current challenges posed by multi-drug resistant bacteria like MRSA and VRSA. How do these strains develop resistance, and what strategies can be implemented to prevent their spread in healthcare settings?
Discuss the difference between the associative and dissociative mechanisms in nuclease enzymes, and explain how the nature of R groups influences their occurrence. Provide examples to support your explanation.
Discuss the differences between alpha helix and beta sheets in protein secondary structure.
Discuss the differences between batch, continuous, and fed-batch fermentation methods in industrial microbiology. How do these methods impact bacterial growth and product synthesis?
Discuss the differences between innate and adaptive immunity, highlighting their specificities and response times. How do these two systems work together in defending the body against pathogens?
Discuss the differences between unipolar depression and bipolar disorder, including their genetic components and brain regions affected.
Discuss the different classes of anxiety disorders and the specific treatments for each.
Discuss the different types of COX enzymes and their role in the production of inflammatory mediators.
Discuss the different types of satellite DNA and their importance at centromeres.
Discuss the discovery and significance of DNA polymerase I. How does the structure of DNA polymerase resemble a right hand, and what are the roles of the finger, thumb, and palm domains in DNA replication?
Discuss the diversity of gene regulatory mechanisms involving changes in the secondary structure of the 5’ untranslated regions of mRNA.
Discuss the economic impact of antibiotic resistance on the global economy by 2050, considering the projected 10 million deaths annually. How can this issue be addressed?
Discuss the factors contributing to the increase in sexually transmitted infections (STIs) cases, including the impact of 'the pill' and online dating apps. How can these trends be addressed?
Discuss the factors contributing to the re-emergence of pathogens in the context of globalisation and urbanisation.
Discuss the factors that affect drug absorption through lipid membranes. How does lipid solubility impact pharmacokinetics?
Discuss the genetic and environmental factors that contribute to the development of schizophrenia.
Discuss the historical significance of opiates as some of the oldest known drugs from plant sources.
Discuss the historical significance of variolation and its impact on the development of vaccines. How did Lady Montagu contribute to popularizing this method in Europe?
Discuss the impact of allosteric modulators on enzyme activity, considering both positive and negative effects. Provide examples of how these modulators can affect substrate binding and catalysis.
Discuss the impact of fluorination on a drug's lipophilicity and metabolic stability. How does fluorine substitution affect the bioavailability of a drug?
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 implications of drug competition for plasma protein binding in patients taking multiple medications.
Discuss the importance of an antenna in photosynthesis and how it increases the excitation rate of the reaction centre.
Discuss the importance of antibodies in extracellular bacterial infections and intracellular pathogens, highlighting their role in antigen recognition and elimination. Provide examples to support your explanation.
Discuss the importance of bacterial differentiation in stress survival and its implications on the formation of spores and other dormant states.
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 different drug structures, such as rings, charged groups, hydrophobic residues, and H-bond forming groups, in interacting with target proteins. How do these interactions contribute to drug binding?
Discuss the importance of efficiency and flexibility in prokaryotes for their survival in competitive environments. Provide examples to support your explanation.
Discuss the importance of folate in the production of glycine and DNA synthesis.
Discuss the importance of gene expression regulation in eukaryotic and prokaryotic cells.
Discuss the importance of Lipinski's 'rule of 5' in drug discovery and how it applies to small molecule drugs. Provide examples to support your explanation.
Discuss the importance of preclinical development in determining the safety and toxicity of a potential drug.
Discuss the importance of rapid changes in gene expression for bacteria living in highly competitive environments. Provide examples of environmental changes that would require rapid gene regulation.
Discuss the importance of receptors as protein targets of drugs and how they can be manipulated by agonists and antagonists.
Discuss the importance of resonance structures in molecules like benzene and amino acids. How do resonance structures contribute to the stability and properties of these compounds?
Discuss the limitations of microarrays as a sequencing technology.
Discuss the limitations of using LD50 and ID50 as measures of pathogenicity, especially in comparing different strains of pathogens. How do these measures reflect the severity of infection inaccurately?
Discuss the mechanism by which Gα-GTP activates adenylyl cyclase and the role of cAMP as a second messenger.
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 naming conventions for enzymes and the significance of naming enzymes based on their catalytic reactions. How has the transition to EC numbers impacted enzyme classification?
Discuss the physiological effects of benzodiazepine agonists and their therapeutic uses.
Discuss the potential side effects of NSAIDs on the gastrointestinal tract and kidneys.
Discuss the principle behind flash photolysis and its application in triggering reactions. Provide examples of reactions that can be studied using this method.
Discuss the principle behind nanopore sequencing and its application in detecting methylated bases.
Discuss the process of affinity maturation in antibody production, explaining how B cells increase the affinity of antibodies for antigens. How does affinity maturation contribute to the effectiveness of the immune response? Provide examples to support your explanation.
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 relationship between catabolism and anabolism, and explain how insufficient catabolism can constrain biosynthesis.
Discuss the relationship between substrate concentration, enzyme affinity, and IC50 values. How does substrate concentration impact the observed IC50 value in enzyme inhibition studies?
Discuss the role of adaptor proteins in signalling and how they recognize phosphorylated receptors.
Discuss the role of allosteric modulators in enzyme activity regulation. How do allosteric modulators differ from competitive inhibitors in terms of binding sites and effects on enzyme function?
Discuss the role of arrestin in turning off GPCR signalling and the process of GPCR recycling.
Discuss the role of cas9 in the CRISPR-Cas system. How does it contribute to the degradation of phage DNA?
Discuss the role of chemiosmotic theory in bioenergetics and its impact on our understanding of cellular processes.
Discuss the role of cholesterol in membrane thickness and fluidity.
Discuss the role of chromatin remodelling complexes in transcription and how they are recruited to promoter regions.
Discuss the role of exonuclease activity in DNA Polymerase III and how it contributes to error detection and correction.
Discuss the role of fever in the innate immune response. How does fever help in combating infections and activating the immune system? What are the underlying mechanisms of fever induction?
Discuss the role of G proteins in signalling and how they are switched on and off.
Discuss the role of G-protein coupled receptors (GPCRs) in cell signalling and their significance in drug targeting.
Discuss the role of glycolysis in the production of energy in cells.
Discuss the role of group carriers in catalysis and genetic information storage.
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 hydride ions in oxidoreductases of fatty acid biosynthesis, comparing the use of borohydride and cofactors like NADH and NADPH. How do these reducing agents differ in terms of effectiveness and biological applicability?
Discuss the role of ion channels in the development of epilepsy.
Discuss the role of isozymes in controlling amino acid synthesis. How do they allow for better control of the amino acids present?
Discuss the role of membrane channels in allowing the movement of nutrients and waste in and out of a cell.
Discuss the role of microtubules in membrane trafficking and how disruption of microtubules can affect organelle movement.
Discuss the role of monoamines in depression and how they are targeted by different categories of antidepressant drugs.
Discuss the role of nuclear pore complexes in the transport of proteins and RNA across the nuclear membrane.
Discuss the role of pattern recognition receptors (PRRs) in innate immunity and how they contribute to the immune response. Provide examples of microbe-associated molecular patterns (MAMPs) and their significance in pathogen recognition.
Discuss the role of pigment environment in altering the excited state properties of chlorophyll and carotenoids.
Discuss the role of polar amino acids in protein structures. How does the environment's pH affect the polarity of amino acids like aspartate and glutamate?
Discuss the role of recombinational repair in DNA strand replication and its catalysing enzyme.
Discuss the role of retinal in the colour change of bacteriorhodopsin.
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 rubisco in the Calvin cycle and its significance in plant metabolism.
Discuss the role of SecB and SecY in the translocation of membrane proteins.
Discuss the role of serendipity in drug development, using penicillin as an example. How can unexpected discoveries like this shape the field of medicine?
Discuss the role of sigma factors in bacterial gene regulation and how they allow for the transcription of different sets of genes. Provide examples of different sigma factors and their specific functions.
Discuss the role of site-specific recombination phages in inserting DNA into the host chromosome.
Discuss the role of T Helper cells in the immune response, including their interactions with B cells, macrophages, and NK cells. How do they contribute to the development of T Cytotoxic cells?
Discuss the role of telomeres in aging-related diseases.
Discuss the role of the blood-brain barrier in limiting drug distribution to the central nervous system.
Discuss the role of the H+ gradient in ATP synthesis. How does the pH difference between the inside and outside of the membrane affect ATP production?
Discuss the role of the S-state cycle in stabilizing charge separation in Photosystem II.
Discuss the role of transcription factories in gene expression and the localization of active transcription within the nucleus.
Discuss the role of transport proteins in allowing molecules and ions to cross the membrane.
Discuss the role of transposons in driving evolution.
Discuss the role of virulence factors in bacterial pathogenesis, providing examples of different types of virulence factors and their effects on the host. How do these factors contribute to the distinction between symptomatic and asymptomatic carriage?
Discuss the role of Zymomonas mobilis in alcohol fermentation. How does its ethanol tolerance compare to yeast? Explain the potential applications of engineering Z. mobilis for bioethanol synthesis.
Discuss the role of β-arrestin in GPCR deactivation and its impact on further G protein activation.
Discuss the roles of ppGpp production and A-signalling in Myxococcus during stress responses and starvation, highlighting their effects on protein expression and metabolism.
Discuss the significance of adhesins, fimbriae, and pili in bacterial virulence. How do these structures facilitate bacterial adherence to host tissues and surfaces?
Discuss the significance of C ring size in ATP synthase and how it relates to energy input and ATP synthesis.
Discuss the significance of CpG islands and methylation in the regulation of gene expression.
Discuss the significance of cyanobacteria in global nitrogen fixation and their impact on ocean ecosystems. How can the control of mass blooms potentially benefit agriculture?
Discuss the significance of cyanobacteria in the evolution of photosynthesis and the impact of the great oxygenic event on Earth. How do cyanobacteria contribute to global carbon fixation?
Discuss the significance of cytokines in regulating immune cell behaviour. Provide examples of different groups of cytokines and their effects on the immune response.
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 enterohepatic cycling in drug excretion. How does this process affect the metabolism and excretion of drugs in the body? Provide examples to support your discussion.
Discuss the significance of glycolysis in cellular respiration, highlighting its occurrence in almost all cells and its net synthesis of NADH and ATP. Why is glycolysis considered an ancient process?
Discuss the significance of group carriers in the synthesis of ethylene and plant ripening.
Discuss the significance of having 2 copies of the chromosome in myxospore formation and how it aids in faster germination.
Discuss the significance of Legionnaire's disease as an emerging infection, including its origins, transmission, and control measures.
Discuss the significance of myelin sheaths in increasing the speed of nervous transmission.
Discuss the significance of pH in the reaction of RNase A and how it affects the formation of intermediate molecules.
Discuss the significance of regulatory T cells in immune regulation, including their synthesis of IL-10 and TGF-beta. How do these cells contribute to preventing autoimmune responses and downregulating inflammation?
Discuss the significance of riboswitches in gene expression regulation and tRNA function. How do riboswitches interact with small molecules to induce changes in protein expression?
Discuss the significance of screening programs for Chlamydia trachomatis, considering the asymptomatic nature of the infection in many individuals. What are the challenges in treating Chlamydia due to its unique characteristics?
Discuss the significance of the catalytic triad in chymotrypsin and how its protonation affects enzymatic activity. Provide examples of inhibitors that target specific residues in the triad.
Discuss the significance of the catalytic triad in trypsin, chymotrypsin, and elastase, and how different amino acids in the active site influence substrate binding. _Provide examples of specific amino acids in each enzyme._
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 significance of the NPA motif in aquaporins.
Discuss the significance of the Stokes shift in light harvesting.
Discuss the significance of two-component systems in bacterial gene regulation, emphasizing their role in responding to changing environments. Provide examples to support your explanation.
Discuss the significance of using alternative electron acceptors and donors in anaerobic respiration compared to aerobic respiration, focusing on the metabolic versatility of E. coli.
Discuss the steps involved in the protein import mechanism through nuclear pore complexes.
Discuss the structural features of nuclease enzymes, including the 'cup' shaped active site and the conserved motifs found in homodimers. Explain how these features contribute to the specificity and function of nuclease enzymes.
Discuss the structure and function of RNA polymerase in bacterial transcription. Explain the role of sigma factors in initiating transcription and the formation of closed and open complexes.
Discuss the three parts of DNA polymerase I and their functions in DNA replication. How does the formation of a double helix impact entropy?
Discuss the various methods by which mutations can be induced in DNA.
Discuss the various methods of protein attachment to the membrane.
Evaluate the role of immunotherapies, such as check-point inhibitors and CAR-T therapy, in the treatment of cancer.
Evaluate the role of Ndh and Cyd in the bacterial electron transport chain during aerobic respiration. Why are these complexes essential for pathogenesis, and how could they be targeted for antimicrobial drug development?
Examine the concept of immunotoxicology and its implications in drug development.
Examine the concept of receptor recycling and its impact on allosteric modulation. How does receptor recycling complicate the modulation process? Discuss the implications of receptor recycling in drug development and targeting specific receptors.
Examine the controversy surrounding the drug VIOXX and its withdrawal from the market.
Examine the functions of telomere-binding proteins in protecting telomeres.
Examine the impact of protein binding on drug concentration and therapeutic effect.
Examine the significance of metal ions in nuclease enzymes, particularly focusing on the coordination and positioning roles of metal ions in the cleavage of phosphodiester bonds. Compare the functions of different metal ions commonly used in nuclease mechanisms.
Examine the significance of operons in bacterial gene regulation. How do operons contribute to the efficiency of transcription in prokaryotes?
Explain forward and reverse genetics approaches
Explain how allosteric feedback inhibition can be overcome with anti-metabolites using LysC as an example.
Explain how amphetamines and cocaine affect dopamine and noradrenaline levels in the CNS.
Explain how bacteriorhodopsin uses light as a direct energy input to transport H+ across the membrane.
Explain how carrier proteins facilitate the transport of glucose across the membrane.
Explain how cells control membrane curvature through lipid composition.
Explain how changes in substrate concentration can affect the rate of a metabolic pathway. How does metabolic flux analysis help determine the impact of substrate concentration?
Explain how cholera toxin and the Bordetella pertussis toxin disrupt GPCR signalling and the consequences of these disruptions.
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 Förster resonance energy transfer (FRET) allows for the transfer of energy in photosynthesis.
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 lysine production in Corynebacterium glutamicum was improved by: (a) branchpoint engineering; (b) optimising cofactor supply; and (c) increasing product efflux.
Explain how microarrays work and how they can be used to determine the transcriptome of whole genomes.
Explain how multiple sclerosis (MS) is caused by a loss of myelin and its impact on nervous transmission.
Explain how natural disasters and decreased public health measures can lead to the spread of infectious diseases, using specific examples.
Explain how reduced representation bisulfite sequencing (RRBS) works and its advantages.
Explain how sugar molecules formed through photosynthesis contribute to various metabolic pathways in plants.
Explain how the Nernst equation can be used to calculate the membrane resting potential. What factors contribute to the membrane potential?
Explain how voltage-gated Na+ channels and voltage-gated K+ channels open and close in response to changes in membrane potential. Discuss the concept of refractory period.
Explain Koch's postulates and their significance in identifying the causative agent of a disease. Discuss situations where these postulates may not be applicable in determining the pathogen responsible for a disease.
Explain the chemiosmotic theory and discuss an experiment that provides evidence for this theory.
Explain the concept of anaplerotic reactions and their role in the Krebs cycle.
Explain the concept of attenuation in RNA riboswitches. How does the antitermination conformation allow for transcription to occur?
Explain the concept of clonal selection in adaptive immunity. Describe the role of memory cells in mounting a faster and stronger immune response upon subsequent exposure to the same pathogen.
Explain the concept of competitive enzyme inhibition and how it affects the enzyme-substrate complex formation. Provide examples of competitive inhibitors and their impact on enzyme activity.
Explain the concept of competitive inhibition using the Michaelis-Menten curve. How does this type of inhibitor affect binding efficiency and the maximal rate of the reaction? Discuss the necessity of mutational analysis in identifying non-competitive inhibitors.
Explain the concept of cumulative control of a single enzyme. Provide an example of an enzyme that can be inhibited independently by multiple different products.
Explain the concept of drug screening and how it is utilized in the development of medications like aspirin and heroin. What are the advantages and limitations of this approach?
Explain the concept of drug selectivity and the importance of off-target binding in drug development. How does a low off-target Kd value contribute to the selectivity of a drug?
Explain the concept of feedback inhibition in metabolic pathways and how it helps prevent wasteful reactions. Provide examples.
Explain the concept of general acid-base catalysis and provide examples of how it applies to the action of RNase A.
Explain the concept of herd immunity and its importance in preventing the spread of diseases. Provide examples of diseases where herd immunity plays a crucial role.
Explain the concept of hydropathy and its significance in determining transmembrane regions.
Explain the concept of kinetic proofreading in pre-mRNA splicing.
Explain the concept of ligand binding and the significance of the dissociation constant (Kd) in drug-target interactions. How does a lower Kd value indicate stronger interactions between a drug and its target?
Explain the concept of lipid composition in membranes and how it contributes to the formation of bilayers and the fluid mosaic structure.
Explain the concept of membrane trafficking via vesicles and how it allows for the control of molecule movement in eukaryotic cells.
Explain the concept of metabolic engineering in bacterial product synthesis. How can metabolic engineering techniques be utilized to enhance product yield and quality?
Explain the concept of negative entropy and its importance in sustaining life.
Explain the concept of operons in bacterial gene regulation and their significance in coordinating the expression of multiple genes. Provide examples of operons and their role in bacterial adaptation.
Explain the concept of pharmacogenomics and its role in personalizing medicine for more effective treatment strategies.
Explain the concept of potency and how it is measured in relation to a standard drug.
Explain the concept of pseudo-first order conditions in kinetics. How does the approximation of [A] ≪ [B] simplify the rate equation? Discuss the implications of this simplification in experimental data analysis.
Explain the concept of quaternary structure in proteins and provide examples of homo-oligomers and hetero-oligomers.
Explain the concept of RNA thermometers and their role in modulating protein expression levels. Provide examples of conditions that trigger changes in RNA secondary structures.
Explain the concept of specificity pockets in proteases and how they contribute to substrate recognition. Compare the specificity of TEV and thrombin, _providing examples of their specific cleavage sites_.
Explain the concept of the histone code and its correlation with chromatin structure.
Explain the concept of therapeutic index in drug development. How is it calculated and why is it important in determining the safety and efficacy of a drug? Provide real-world examples to illustrate your points.
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 concept of virulence factors in bacteria and how they contribute to pathogenicity. Provide examples of virulence factors and their roles in causing disease.
Explain the concept of voltage-gating in K+ channels and how it allows for the control of ion transport.
Explain the concept of volume of distribution and how it influences drug distribution in the body.
Explain the concepts of orthologous and paralogous genes and how they contribute to gene evolution.
Explain the diagnostic criteria for depression and the role of genetic risk in its development.
Explain the difference between a partial seizure and a generalised seizure.
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 passive (facilitated) transport and active transport. Give examples of each.
Explain the difference between primary and secondary membrane lipids.
Explain the difference between promoter-proximal elements and distal enhancers in mammalian genes.
Explain the differences between antiseptics, disinfectants, and antibiotics in terms of their applications and toxicity levels. Discuss the requirements for an effective antibiotic, including selective toxicity and pharmacokinetics.
Explain the different methods of bacterial cell division, focusing on synchronous septation and vivipary.
Explain the different pathways of dopamine and their functions in the brain.
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 different types of signal anchors and their role in determining the orientation of membrane proteins.
Explain the ENCODE / HGP projects
Explain the function and composition of the λ red recombination system.
Explain the function of plastoquinone in the electron transport chain of Photosystem II.
Explain the importance of choosing the right assay method based on sensitivity and availability when designing an experiment.
Explain the importance of CO2 in metabolic reactions and why reactions producing CO2 are energetically favourable.
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 importance of glucose as the main source of energy in cells.
Explain the importance of membranes in biological systems and how they act as a barrier between the interior and exterior of a cell.
Explain the importance of transamination reactions in amino acid metabolism.
Explain the increasing complexity of biological molecules and provide examples of different forms of biologics.
Explain the main uses of acetyl CoA and how it is produced.
Explain the major side effects associated with monoamine oxidase inhibitors (MAOIs) and the potential risks of combining them with certain foods.
Explain the mechanism of action of aspirin as an anti-inflammatory drug and how it differs from other NSAIDs.
Explain the mechanism of action of benzodiazepines as antiepileptic drugs.
Explain the mechanisms of antibiotic resistance, focusing on innate and acquired resistance types. Provide examples of each type and discuss their implications in healthcare settings.
Explain the mechanisms of transmission and symptoms of gonorrhoea in males and females. How can asymptomatic cases lead to severe complications?
Explain the metabolic flexibility of E. coli in aerobic conditions, emphasizing the role of Ndh and Cyd in respiration. How does the presence of these complexes enhance the survival and infection chances of pathogenic bacteria?
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 motility mechanisms of cyanobacteria, including the role of pili and nozzles in different species. How do filamentous cyanobacteria move without flagella?
Explain the pharmacokinetics of benzodiazepines and the potential side effects of their use.
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 action potential propagation along an axon and the role of voltage-gated channels.
Explain the process of canonical signalling by GPCRs and how it leads to downstream effector molecule interaction.
Explain the process of class switching in antibody synthesis and its significance in the immune response. How does class switching enhance the flexibility of the immune system? Provide a detailed explanation with relevant examples.
Explain the process of cytotoxic T cell activation and their role in inducing apoptosis in infected target cells. How do viruses evade cytotoxic T cell responses, and what implications does this have for the immune system?
Explain the process of DNA packaging in eukaryotic chromosomes and the role of histones and non-histone proteins.
Explain the process of drug metabolism, including the roles of oxidation and conjugation. How does xenobiotic metabolism impact drug compounds? Provide a detailed analysis with examples.
Explain the process of endospore formation in Bacillus subtilis, detailing the key steps involved in spore development and release.
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 injecting a virus into the brain to control epilepsy in animal models.
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 phagocytosis in killing pathogens. Describe the formation of phagolysosomes and the role of bactericidal agents in destroying pathogens.
Explain the process of pre-mRNA splicing
Explain the process of protein translocation in bacteria and its conservation in eukaryotes.
Explain the process of replication slippage and its role in generating different alleles of satellite DNA.
Explain the process of surface plasmon resonance (SPR) and how it is used to determine drug binding relationships. Discuss its limitations in representing real-world binding interactions.
Explain the process of target selection in drug discovery and the importance of finding the correct receptor, enzyme, or transport protein.
Explain the process of template-directed DNA synthesis catalysed by DNA polymerase. What are the different precursor molecules used in DNA replication?
Explain the process of vibrational relaxation and its role in the fate of the S2 excited state.
Explain the process of X-ray crystallography and how it is used to determine protein structure.
Explain the purpose of using positive and negative controls in a PCR-based genotype screen.
Explain the regulatory mechanisms involved in the transition from σ70 to σ38 in bacterial gene regulation. How do anti-sigma factors like Rsd and HscC play a role in this transition?
Explain the relationship between drug affinity for receptors and the dose required to obtain 50% occupancy of receptors.
Explain the relationship between drug affinity for receptors and the dose required to obtain 50% occupancy of receptors.
Explain the relationship between group carriers and the RNA world hypothesis.
Explain the relationship between mRNA turnover and translational efficiency in eukaryotic cells.
Explain the role of a pH-stat in maintaining a constant pH during a reaction. How does it work, and why is it important in certain experiments?
Explain the role of acetyl CoA in carrying carbon units and its significance in the link reaction and fatty acid biosynthesis.
Explain the role of carboxysomes in cyanobacteria and how they enhance CO2 fixation efficiency. How could introducing carboxysomes to plant chloroplasts potentially improve crop yields?
Explain the role of chlorophyll in photosynthesis and how it is involved in the light reactions.
Explain the role of cytochrome b6f as an electrical connection between PSII and PSI in photosynthesis.
Explain the role of cytokines and chemokines in the pathogenesis of asthma and how they contribute to the late phase response.
Explain the role of enzymes in pharmacology and how inhibitors and prodrugs can affect drug activity.
Explain the role of G-quadruplexes and OGREs in the regulation of origins of replication.
Explain the role of GPCRs in signal transduction and how ligand binding leads to the activation of G proteins.
Explain the role of histone variants in specific molecular processes and DNA repair.
Explain the role of inflammatory mediators in the degradation of joints in rheumatoid arthritis.
Explain the role of metal ions in nuclease enzymes' mechanisms, focusing on how they assist in the cleavage of phosphodiester bonds. Provide specific examples of metal ions and their functions in this process.
Explain the role of microRNAs in regulated mRNA turnover.
Explain the role of Myxococcus xanthus as a model organism in studying bacterial differentiation, highlighting its unique genetic features and social behaviour.
Explain the role of nucleoid-associated proteins (NAPs) in organizing and condensing bacterial DNA. How does this organization contribute to bacterial gene regulation?
Explain the role of nucleoid-associated proteins (NAPs) in organizing bacterial DNA. How do different NAPs contribute to gene regulation in bacteria?
Explain the role of Pattern Recognition Receptors (PRRs) in the innate immune system and how they contribute to the recognition of pathogens. Provide examples of microbe-associated molecular patterns (MAMPs) recognized by PRRs.
Explain the role of phagocytes in the innate immune response. How do neutrophils and macrophages contribute to combating infections? Provide examples of infections where phagocytes play a crucial role.
Explain the role of plastocyanin and ferredoxin in electron transfer in Photosystem I.
Explain the role of rhodopsin in detecting light in the eye and how it is able to detect different wavelengths.
Explain the role of S-adenosylmethionine (SAM) as a carrier in methylation reactions.
Explain the role of slip-strand mispairing in phase variation. How does slip-strand mispairing differ from epigenetic control of gene expression?
Explain the role of specificity pockets in serine proteases like trypsin and subtilisin. How do these pockets contribute to substrate selectivity and enzyme function?
Explain the role of the link reaction in aerobic respiration, detailing the conversion of pyruvate to acetyl coenzyme A and the production of NADH. How does the link reaction connect glycolysis to the Krebs cycle?
Explain the role of the manganese cluster in the oxidation of H2O to O2 in Photosystem II.
Explain the role of the neutral zone around the reaction centre in preventing electron escape in Photosystem I.
Explain the role of threshold enzymes in biosynthetic pathways and why they are tightly controlled and non-constitutive.
Explain the role of transcriptional repressors in fine-tuning gene expression.
Explain the significance of fermentation in the absence of aerobic and anaerobic respiration. How does the use of endogenous organic molecules impact ATP synthesis?
Explain the significance of p elements in drosophila and how they have evolved in wild populations.
Explain the significance of post-market surveillance in ensuring drug safety and detecting rare or long-term side effects.
Explain the significance of stable ADP and Pi concentrations for ATP synthesis. How can changes in these concentrations impact the energy required for ATP synthesis?
Explain the significance of the active site structure in high fidelity DNA polymerases and how it impacts replication fidelity.
Explain the significance of the conserved residues and structural similarities between E. coli ENR and B. napus ENR. How do these similarities impact their functionality?
Explain the significance of the PAM sequence in the search for a DNA sequence complementary to the sgRNA sequence.
Explain the significance of the quench flow apparatus in studying fast reactions in biochemical kinetics. How does it differ from traditional methods? Discuss the advantages and limitations of using this apparatus.
Explain the significance of the third metal ion in DNA polymerase activity and its potential impact on polymerase fidelity. How does the presence of this ion affect the stability of PPi during nucleotide incorporation?
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 changes in the nicotinamide ring of NAD(P)H during oxidation and reduction processes. How do these changes impact the efficiency of hydride transfer in enzymatic reactions?
Explain the structural components and activation process of histidine kinases in two-component systems. How does this activation lead to changes in bacterial cell physiology? Provide a detailed description with examples.
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 structure and function of membrane channels.
Explain the technique of patch clamping and how it is used to measure the current across a membrane. Discuss the different geometries that can be studied using patch clamping.
Explain the three mechanisms by which mRNAs are localized to specific subcellular regions.
Explain the three stages of the Calvin cycle (carboxylation, reduction, regeneration). What is the overall purpose of the Calvin cycle?
Explain the three stages of the Calvin cycle and their respective inputs and outputs.
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 the use of animal models in studying anxiety and how behavioural experiments can elicit fear responses.
Explain why animals are more mobile than plants due to the difference in energy storage.
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.
Explain why the electron transfer rate in Photosystem I is optimal when the driving force ΔG is equal to the reorganisation energy.
Explore the activation pathways of the complement system in response to pathogens. How do the classical, alternative, and lectin pathways contribute to pathogen killing and inflammatory responses?
Explore the concept of facultative pathogens and their adaptability to different lifestyles. How does the flexibility of facultative pathogens impact their pathogenicity compared to other types of pathogens?
Explore the concept of heterocysts in cyanobacteria, detailing their differentiation process and role in nitrogen fixation. How do heterocysts create a microoxic environment and facilitate the exchange of nutrients within the filamentous cyanobacteria?
Explore the concept of kin recognition in Myxococcus and how the expression of TraA alleles influences outer membrane protein exchange and the formation of fruiting bodies.
Explore the evolutionary aspects of two-component systems in bacteria, detailing how gene duplication events and mutations have led to the formation of diverse TCS. Provide examples to illustrate the evolutionary process of TCS in bacteria.
Explore the genetic regulation of heterocyst formation in cyanobacteria. How do NtcA and HetR play key roles in the development of heterocysts?
Explore the mechanism of polymerase translocation in DNA Polymerase I and its role in nucleotide addition during replication.
Explore the process of enhancing yields in industrial bacterial product synthesis. Discuss the various approaches, such as mutation and selection, metabolic engineering, and optimization of fermentation conditions.
Explore the process of error correction by the exonuclease domain of DNA polymerase. How does the polymerase recognize and remove incorrect nucleotides? Discuss the challenges associated with the distance between the synthetic and exonuclease domains.
Explore the role of peptide bonds in proteins. Why are peptide bonds considered planar, and how does the hybridization of Cα affect the flexibility of the peptide backbone?
Explore the role of prophylactic antibiotic use in agriculture in contributing to antibiotic resistance. How does this practice impact human health and what measures can be taken to mitigate its effects?
Explore the role of zoonotic transfer in the emergence of new pathogens, providing instances where this has occurred.
Explore the significance of Lipinski’s ‘rule of 5’ in drug absorption. What are the key criteria outlined in this rule, and how do they influence the absorption of small molecule drugs?
Explore the significance of sigma factors in spore formation, focusing on their roles in regulating gene expression during different stages of spore development.
Explore the significance of the release of PPi during nucleotide incorporation by DNA polymerase. How does the presence of Mg2+ ions aid in arranging DNA correctly during replication?
Explore the significance of the sigma factor cascade involving σ28 in ensuring the correct assembly of flagella in bacteria. How does this cascade maintain the temporal control of gene expression?
Explore the structural differences between subtilisin and chymotrypsin despite having the same catalytic triad arrangement. Discuss the implications of faults in threonine peptidases in cancers.
Give some examples of products produced by microorganisms and the microbes that produce them.
How can transposon insertion mutants be selected and identified?
How do beta-lactam antibiotics work?
How does continuous culture differ to batch culture? Explain what is meant by a fed-batch culture and why this is often the preferred growth setup in industrial fermentations.
How does fluorine substitution next to an oxygen atom impact a drug's polarity and solubility in water? Discuss the implications of fluorine's effect on the distribution and bioavailability of the drug.
How does the light reaction of photosynthesis regulate the Calvin cycle? Explain the role of thioredoxin in this regulation.
How does the lipid composition of a membrane affect its fluidity?
How does the presence of competitive inhibitors affect the Michaelis-Menten plots of enzyme-catalysed reactions? Explain the changes in Km and Vmax with increasing inhibitor concentrations.
Investigate the differences in the polymerase fidelity between DNA polymerases and the factors that influence error rates. How does the exonuclease domain contribute to maintaining the accuracy of DNA replication despite potential errors?
Investigate the impact of damaged bases on replication fidelity and the role of trans-lesion synthesis polymerases in overcoming this challenge.
Investigate the mechanism of action of bortezomib as a protease inhibitor, emphasizing its transition between trigonal and tetrahedral geometries. Explain why bortezomib is considered a suicide inhibitor.
Investigate the mechanisms that control the rate of DNA replication in bacterial cells, including the influence of RNR, primase, and nutritional status.
Propose potential strategies for designing inhibitors targeting peptide deformylase (PDF) based on its mechanism of action. Discuss the importance of substrate mimics and non-hydrolysable molecules in inhibitor design for PDF.
What are the characteristics of a good antibiotic?
What are the main sources of antibiotic resistance in the Western World?
What is metabolic engineering? List some general ways that product yield can be enhanced using metabolic engineering approaches.
What is the FaRLiP response? How does this benefit some species of cyanobacteria?
What is the nonsense-mediated decay pathway and how does it contribute to mRNA turnover?
What is the origin of antibiotic resistance?
What is the phase problem in structure determination and how is it solved?
What is the purpose of atomic force microscopy in studying membrane components?
What is the purpose of phase variation?
What is the Z-scheme and how does it describe changes in redox potential during photosynthesis?
What mechanisms help control metabolic pathway activity? Give examples to illustrate different mechanisms.
What methods can be employed to reduce the misuse of antibiotics?
What properties make a microorganism well suited to use in commercial applications. 
Why are antiseptics and disinfectants not be used as antibiotics?
Why is it important for bacteria to be invasive in order to cause disease? Discuss the factors that contribute to a bacteria's invasiveness and ability to damage the host.
Why is the incorporation of U (uracil) into DNA or T (thymine) into RNA uncommon during natural synthesis? Discuss the role of phosphodiester bonds in DNA structure.
Write brief notes on how a T-box riboswitch works.