Assessment of Biochemistry/Molecular Biology (BMB) Foundational Concepts

Naphthoquinone-mediated Inhibition of Lysine Acetyltransferase KAT3B/p300

Henry Jakubowski, Ph.D., Professor, Chemistry Department, College of Saint Benedict/Saint John's University

 
05/18/2014

The questions below are based on data, graphs, and figures from the following article:

Naphthoquinone-mediated Inhibition of Lysine Acetyltransferase KAT3B/p300, Basis for Non-toxic Inhibitor Synthesis. Mohankrishna Dalvoy Vasudevarao et al. The Journal of Biological Chemistry, 289, 7702-7717. March 14, 2014 . doi: 10.1074/jbc.M113.486522 . 

These guidelines apply to the reuse of articles, figures, charts and photos in the Journal of Biological Chemistry, Molecular & Cellular Proteomics and the Journal of Lipid Research.

These questions may be used to help assess student mastery of key foundational concepts in BMB developed by the American Society for Biochemistry and Molecular Biology (ASBMB) and tested in the new MCAT2015 developed by the American Association of Medical Colleges.  The particular foundational concepts and learning objectives relevant for this particular assessment are listed below.

ASBMB Biochemistry and Molecular Biology Foundational Concepts  -   Detailed Learning Objectives (Excel)

Foundational Concept 2:  Macromolecular structure determines function and regulation.

  • 2. Given a list of macromolecules, students should be able to devise an experiment on how they interact or interpret results of experiments on their interactions
  • 4. Given experimental data, students should be able to assess how enzymes facilitate biochemical reactions.

Foundational Concept 3:  Information storage and flow are dynamics and interactive

  • 2. Given an understanding of common mechanisms of gene regulation, students will be able to explain or predict changes in transcription in response to biologic variables. 

Foundational Concept 4: . Discovery requires objective measurement, quantitative analysis, and clear communication. 

  •  2. Given a fundamental understanding of BMB concepts, students should be able to formulate experiments and assess the quality of experiments addressing molecular structure, assays of biological function, and isolation / separation of biomolecules.

MCAT 2015:  Foundational Concepts, Detailed Content and Topics (Excel)

Biological and Biochemical Foundations of Living Systems

Foundational Concept 1 : Biomolecules have unique properties that determine how they contribute to the structure and function of cells, and how they participate in the processes necessary to maintain life

  • 1A. Structure and function of proteins and their constituent amino acids

Chemical and Physical Foundations of Biological Systems

Foundational Concept 5: The principles that govern chemical interactions and reactions form the basis for a broader understanding of the molecular dynamics of living systems.

  • 5B. Nature of molecules and intermolecular interactions

  • 5D. Structure, function, and reactivity of biologically - relevant molecules

  • 5E. Principles of chemical thermodynamics and kinetics

Scientific Inquiry and Reasoning Skills

  • 1.  Knowledge of Scientific Concepts and Principles; 

  • 2.  Scientific Reasoning and Problem;

  • 3.  Reasoning about the Design and Execution of Research;

  • 4.  Data-based and Statistical Reasoning

Background

The article and these questions deal with the inhibition of an enzyme that is involved in DNA packing and epigenetic control of gene transcription.

Double-standed DNA is a polyanion as every phosphate in the backbone is negatively charged. To pack it into chromosome in the nucleus, DNA is complexed to a variety of proteins. In the first stage of packing, DNA is wound around a core of positively charged histones protein, forming a nucleosome. The size of the nucleosome is about the size of RNA polymerase.

Nucleosome:   Jmol14 (Java) |  JSMol  (HTML5) 

Background Reading:

Background Videos:

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