Blatant Biology: Questions

Biochemistry 2

These are questions related to the module biochemistry 2

• Explain the concept of negative entropy and its importance in sustaining life.
• Discuss the role of chemiosmotic theory in bioenergetics and its impact on our understanding of cellular processes.
• Explain the role of chlorophyll in photosynthesis and how it is involved in the light reactions.
• Compare passive, primary active, and secondary active transport across membranes. Give examples of each.
• 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.
• Discuss the importance of an antenna in photosynthesis and how it increases the excitation rate of the reaction centre.
• Describe the structure of a photosystem and the function of the antenna complex in capturing and concentrating light energy.
• Explain the process of vibrational relaxation and its role in the fate of the S2 excited state.
• Discuss the significance of the Stokes shift in light harvesting.
• Explain how Förster resonance energy transfer (FRET) allows for the transfer of energy in photosynthesis.
• Discuss the role of pigment environment in altering the excited state properties of chlorophyll and carotenoids.
• Explain the role of the manganese cluster in the oxidation of H2O to O2 in Photosystem II.
• Explain the function of plastoquinone in the electron transport chain of Photosystem II.
• Discuss the role of the S-state cycle in stabilizing charge separation 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 plastocyanin and ferredoxin in electron transfer in Photosystem I.
• Discuss Marcus theory and its relevance in explaining electron transfer reactions in Photosystem I.
• Explain why the electron transfer rate in Photosystem I is optimal when the driving force ΔG is equal to the reorganisation energy.
• Explain the role of cytochrome b6f as an electrical connection between PSII and PSI in photosynthesis.
• Explain the chemiosmotic theory and discuss an experiment that provides evidence for this theory.
• Compare and contrast photosystem I and photosystem II. What are their roles in photosynthesis?
• Explain the three stages of the Calvin cycle (carboxylation, reduction, regeneration). What is the overall purpose of the Calvin cycle?
• Compare the ATP synthesis efficiency of a 14 C-subunit ring and an 8 C-subunit ring in ATP synthase.
• Discuss the significance of C ring size in ATP synthase and how it relates to energy input and ATP synthesis.
• Explain the three stages of the Calvin cycle and their respective inputs and outputs.
• Discuss the role of rubisco in the Calvin cycle and its significance in plant metabolism.
• How does the light reaction of photosynthesis regulate the Calvin cycle? Explain the role of thioredoxin in this regulation.
• Describe the role of Mg2+ in the Calvin cycle and its importance for rubisco activity.
• Explain how sugar molecules formed through photosynthesis contribute to various metabolic pathways in plants.
• Discuss the differences between alpha helix and beta sheets in protein secondary structure.
• Explain the concept of quaternary structure in proteins and provide examples of homo-oligomers and hetero-oligomers.
• Explain the importance of CO2 in metabolic reactions and why reactions producing CO2 are energetically favourable.
• Discuss the relationship between catabolism and anabolism, and explain how insufficient catabolism can constrain biosynthesis.
• Explain the role of threshold enzymes in biosynthetic pathways and why they are tightly controlled and non-constitutive.
• Discuss the role of group carriers in catalysis and genetic information storage.
• Describe the function of biotin as a carrier and its role in metabolism.
• Discuss the importance of folate in the production of glycine and DNA synthesis.
• Explain the role of S-adenosylmethionine (SAM) as a carrier in methylation reactions.
• Explain the relationship between group carriers and the RNA world hypothesis.
• Discuss the significance of group carriers in the synthesis of ethylene and plant ripening.
• Compare and contrast primary pathways and secondary pathways in terms of their functions, regulation, and metabolite products.
• Explain the role of acetyl CoA in carrying carbon units and its significance in the link reaction and fatty acid biosynthesis.
• Discuss the role of glycolysis in the production of energy in cells.
• Explain the importance of glucose as the main source of energy in cells.
• Compare and contrast the storage of excess glucose as glycogen in muscle and its conversion to fat.
• Explain why animals are more mobile than plants due to the difference in energy storage.
• Explain the concept of anaplerotic reactions and their role in the Krebs cycle.
• Explain the main uses of acetyl CoA and how it is produced.
• Describe the process of β-oxidation and its significance in fatty acid catabolism.
• Explain the importance of transamination reactions in amino acid metabolism.
• Explain the concept of feedback inhibition in metabolic pathways and how it helps prevent wasteful reactions. Provide examples.
• Discuss the role of isozymes in controlling amino acid synthesis. How do they allow for better control of the amino acids present?
• 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?
• 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.
• Discuss the role of membrane channels in allowing the movement of nutrients and waste in and out of a cell.
• 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 the importance of membranes in biological systems and how they act as a barrier between the interior and exterior of a cell.
• Describe the process of protein trafficking in the endoplasmic reticulum and how proteins are tagged for their destination.
• 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.
• Discuss the role of microtubules in membrane trafficking and how disruption of microtubules can affect organelle movement.
• Explain the difference between primary and secondary membrane lipids.
• How does the lipid composition of a membrane affect its fluidity?
• Discuss the role of cholesterol in membrane thickness and fluidity.
• Explain how cells control membrane curvature through lipid composition.
• Describe the role of membrane rafts in controlling the localisation of membrane proteins.
• What is the purpose of atomic force microscopy in studying membrane components?
• Describe the process of ligand-mediated endocytosis and how it is mediated by membrane rafts. Discuss the role of caveolin in this process.
• 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.
• 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.
• 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.
• Describe the process of neurotransmitter diffusion and how it contributes to signal transmission between cells.
• Explain the process of action potential propagation along an axon and the role of voltage-gated channels.
• Discuss the significance of myelin sheaths in increasing the speed of nervous transmission.
• Explain how multiple sclerosis (MS) is caused by a loss of myelin and its impact on nervous transmission.
• Explain how the Nernst equation can be used to calculate the membrane resting potential. What factors contribute to the membrane potential?
• 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?
• 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?
• 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?
• 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 role of G proteins in signalling and how they are switched on and off.
• Describe the mechanism of receptor-tyrosine kinases and their significance in signalling.
• Discuss the role of adaptor proteins in signalling and how they recognize phosphorylated receptors.
• Explain the role of GPCRs in signal transduction and how ligand binding leads to the activation of G proteins.
• Discuss the mechanism by which Gα-GTP activates adenylyl cyclase and the role of cAMP as a second messenger.
• Describe the signalling pathway involving GPCRs, cAMP, and protein kinase A (PKA), and explain how it leads to the activation of genes.
• Compare and contrast the functions of Gαs and Gαi in GPCR signalling.
• Explain how cholera toxin and the Bordetella pertussis toxin disrupt GPCR signalling and the consequences of these disruptions.
• Discuss the role of arrestin in turning off GPCR signalling and the process of GPCR recycling.
• Describe the different types of protein-membrane interactions.
• Discuss the various methods of protein attachment to the membrane.
• Explain the structure and function of membrane channels.
• Compare and contrast the structure and selectivity of porins and α-helical membrane proteins.
• Explain the concept of hydropathy and its significance in determining transmembrane regions.
• Discuss the role of transport proteins in allowing molecules and ions to cross the membrane.
• Discuss the significance of the NPA motif in aquaporins.
• Explain how carrier proteins facilitate the transport of glucose across the membrane.
• Explain the difference between passive (facilitated) transport and active transport. Give examples of each.
• Describe the process of primary active transport and how it is powered by ATPases.
• Discuss Jardetzky's allosteric model for membrane pumps and how it explains the alternating access mechanism.
• 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+.
• Explain the concept of voltage-gating in K+ channels and how it allows for the control of ion transport.
• Explain how bacteriorhodopsin uses light as a direct energy input to transport H+ across the membrane.
• Discuss the role of retinal in the colour change of bacteriorhodopsin.
• Discuss the role of G-protein coupled receptors (GPCRs) in cell signalling and their significance in drug targeting.
• Compare and contrast the structures and functions of rhodopsin and β2-adrenergic receptor (β2-AR) as GPCRs.
• Discuss the role of β-arrestin in GPCR deactivation and its impact on further G protein activation.
• Explain the role of rhodopsin in detecting light in the eye and how it is able to detect different wavelengths.
• Explain the process of X-ray crystallography and how it is used to determine protein structure.
• What is the phase problem in structure determination and how is it solved?
• Describe the process of cryo EM and its advantages over X-ray crystallography for protein structure determination.
• Explain the process of protein translocation in bacteria and its conservation in eukaryotes.
• Discuss the role of SecB and SecY in the translocation of membrane proteins.
• Explain the different types of signal anchors and their role in determining the orientation of membrane proteins.