Systems Level Reasoning | Molecules to Pathways

Question

4.Question

Which of the following statements about the usage of bioinformatics databases is correct?Choose

(a.)The Ensembl database does not include information about transcripts.

(b).The OMIM database can be used to look for genes involved in a certain disease, e.g. rheumatoid arthritis.

(c).Swiss-Prot contains information about protein-coding DNA sequences.

(d).Experimental data is superior to information obtained from bioinformatic databases, so that any prior knowledge from bioinformatic databases can be ignored, once experimental data has been obtained.

(e).The FDA Adverse Event Reporting System database summarizes unexpected events observed after knocking out genes in mice.

5.Question

What are the key characteristics of systems biology?

(a).Systems biology focuses on development of mathematical descriptions of organ function such as the calculation of the glomerular filtration rate (GFR) for kidney function.

(b).Systems biology is a subtype of botany.

(c).Systems biology describes how the human or animal phenotypes change due to disease, mutation and environment (for example, as outlined for gene mutations in the Mouse Genome Informatics Phenotypes, Alleles & Disease Model database).

(d).Systems biology describes the interface between brains and machines.

(e).Systems biology integrates gene products, other molecules and their interactions into quantitative descriptions of physiological functions.

6.Question

Different types of radiation increase the cellular protein p53 to produce variable responses to cell proliferation. What can you conclude from the schematic below?Choose

(a).p53 oscillations are detrimental for cell function under UV light.

(b).The response of a cellular system to a given input only depends on the activated pathway.

(c).p53 expression is proportional to the wavelengths of the light.

(d).Although different inputs activate the same protein, different activation dynamics could explain different cellular responses.

(e.)Gamma radiation would be healthier than UV light if p53 dynamics are regulated properly.

7.Question

Given the below reaction scheme, which statement about enzyme kinetics is correct?Choose

(a.)cAMP production rate increases with increasing k-1.

(b.)cAMP production rate increases with increasing k1.

(c).cAMP production rate decreases with increasing k2.

(d).cAMP production rate increases with increasing k2.

(e).cAMP production rate increases with decreasing ATP concentration.

8.Question

The value of the Hill coefficient indicates...?Choose

(a).the difference between cooperative binding and competitive binding of different substrates to an enzyme.

(b).the quotient of the activation energy (energy barrier) for an enzymatic reaction divided by the activation

energy of the same reaction without enzymatic catalysis.

(c).the number of intermediates which are generated but not released during the enzymatic processing of a substrate to its final product.

(d).the number of reactions required for non-linear enzymatic processes.

(e)the influence of ligand binding to the first binding site on the affinity for the second binding site.

9.Question 9

Which statement is true for partial agonist?choose

(a). .Addition of a partial agonist requires less agonist for receptor activation.

(b). A partial agonist acts as a competitive antagonist to a full agonist.

(c). A partial agonist does not activate the receptor.

(d). Partial agonists only activate extracellular domains of the receptor.

(e). A partial agonist is a chemical that is defined by a partial structural overlap with the agonist.

10.Question

A competitive inhibitor competes with the substrate for the catalytic site. An uncompetitive inhibitor binds to a separate site, which reduces substrate conversion to the product. In the reactions below, which interaction depicts competitive inhibition only?Choose

(a). E

(b). D

(c). C

(d). B

(e). A

11.Question

What is kcat?choose

(a).kcat is the Michaelis constant divided by the free enzyme concentration.

(b).kcat is the maximum reaction velocity (Vmax) divided by the total enzyme concentration.

(c).kcat is the Michaelis constant (Km) divided by the total enzyme concentration.

(d).kcat is the reaction velocity divided by the free enzyme concentration.

(e).kcat is the Michaelis constant divided by the reaction velocity.

Answer 1

4. Bioinformatics Databases

Correct answer: (b). The OMIM database can be used to look for genes involved in a certain disease, e.g. rheumatoid arthritis.

Explanation: OMIM (Online Mendelian Inheritance in Man) specifically focuses on genetic disorders and genes, providing information about genes related to diseases.

5. Key Characteristics of Systems Biology

Correct answer: (c). Systems biology describes how the human or animal phenotypes change due to disease, mutation and environment.

Explanation: This option captures the essence of systems biology, which examines complex interactions within biological systems and how they affect phenotypes.

6. p53 Response to Radiation

Correct answer: (d). Although different inputs activate the same protein, different activation dynamics could explain different cellular responses.

Explanation: This recognizes that different radiation types may lead to varying levels or patterns of p53 activation, which can result in different cellular responses.

7. Enzyme Kinetics

Correct answer: (c). cAMP production rate decreases with increasing k2.

Explanation: In enzyme kinetics, an increase in the rate constant k2 (which often represents the conversion of the enzyme-substrate complex to product) typically means that less substrate might be converted to cAMP if inhibition is at play.

8. Hill Coefficient

Correct answer: (e). the influence of ligand binding to the first binding site on the affinity for the second binding site.

Explanation: The Hill coefficient is often used to describe cooperative binding, where the binding of one ligand affects the binding affinity of additional ligands.

9. Partial Agonist

Correct answer: (b). A partial agonist acts as a competitive antagonist to a full agonist.

Explanation: A partial agonist can activate the receptor but to a lesser extent than a full agonist, and its presence can inhibit the effect of a full agonist.

10. Competitive Inhibition

Correct answer: (a). E

Explanation: The interaction that depicts competitive inhibition is characterized by a substrate and inhibitor competing for the same active site on the enzyme.

11. kcat

Correct answer: (b). kcat is the maximum reaction velocity (Vmax) divided by the total enzyme concentration.

Explanation: kcat (turnover number) indicates how many substrate molecules one enzyme active site converts to product per unit time when the enzyme is fully saturated with substrate.

Feel free to ask if you need further details or explanations on any of the concepts!