Development of a Certification Exam to Assess Undergraduate Students' Proficiency in Biochemistry and Molecular Biology Core Concepts.

With support from the American Society for Biochemistry and Molecular Biology (ASBMB), a community of biochemistry and molecular biology (BMB) scientist-educators has developed and administered an assessment instrument designed to evaluate student competence across four core concept and skill areas fundamental to BMB. The four areas encompass energy and metabolism; information storage and transfer; macromolecular structure, function, and assembly; and skills including analytical and quantitative reasoning. First offered in 2014, the exam has now been administered to nearly 4000 students in ASBMB-accredited programs at more than 70 colleges and universities. Here, we describe the development and continued maturation of the exam program, including the organic role of faculty volunteers as drivers and stewards of all facets: content and format selection, question development, and scoring.

Concept Inventories as a Complement to Learning Progressions.

Learning progressions (LPs) are descriptions of students' growing sophistication in the understanding of a particular construct through a curricular sequence. They are particularly useful for organizing complex constructs for which students do not necessarily connect concepts as taught in different courses. However, they are challenging to construct, because they attempt to linearize students' inherently nonlinear learning. As a result, it is essential to have methods to assess students' arrival at particular steps along the progression. One tool readily available to instructors is concept inventories (CIs). We have mapped published CIs to LPs for acid-base chemistry. The alignment not only provides an assessment that professors can use to pinpoint student learning, but also creates another tool to verify hypothetical LPs.  We have compared the types of questions asked on CIs in chemistry, biology, and biochemistry, as well as in some standardized test banks. The mapping of questions from CIs to steps on the LPs allows refinement of the LPs and reveals gaps in assessment tools for sophisticated concepts. This alignment is a novel addition to the cycle of validation of an LP.

Teaching progressions and learning progressions.

Just as students undergo "learning progressions" in moving from naivety to mastery of biochemical topics, faculty experience "teaching progressions" as they experiment with pedagogy, listen to students' feedback, and become members of a community of educators. An important element of both teaching and learning is assessment. Good assessment tools reflect the value we place on thoughtful instruction and in-depth thinking. © 2019 International Union of Biochemistry and Molecular Biology, 47(5):493-497, 2019.

Assessing stakeholder perceptions of the american society for biochemistry and molecular biology accreditation program for baccalaureate degrees.

The American Society for Biochemistry and Molecular Biology (ASBMB) began an accreditation program in 2013. The criteria for accreditation of undergraduate programs include sufficient infrastructure - number and expertise of faculty, physical space and equipment, support for faculty and students - and incorporation of core concepts in the curriculum - structure and function of biomolecules; information storage; energy transfer; and quantitative skills. Students in accredited programs are able to have their degrees ASBMB certified by taking an exam focused on knowledge or skills across the four core concept areas. Members of the accreditation committees administered a survey to key stakeholders in the BMB community: undergraduate programs, both those that have applied for accreditation and those that have not; alumni/ae of accredited programs; graduate and professional programs; and employers. The goals of the study were to gauge the success of the program and determine necessary areas of improvement. The results indicate that the major benefits of applying for accreditation are the impetus to gather data and analysis not generally collected, and access to assessment data via the exam. However, stakeholders outside of the undergraduate community showed little awareness of the accreditation program. Additionally, the application process itself was seen to be very time consuming. This feedback will be used to improve the process and engage in further outreach. © 2018 International Union of Biochemistry and Molecular Biology, 46(5):464-471, 2018.

Developing a conversation: A strategy to engage faculty in pedagogical change.

Personal interviews were conducted with biochemistry faculty during which they were presented with student performances on a content survey. From these interviews, four themes that reflect faculty responses to the surveys emerged: awareness of student understanding, self-reflection on teaching practice, planned collaboration with colleagues, and emotional reactions. Here, we discuss these themes and their implications for creating conversation designed to promote reflection on biochemistry teaching. © 2018 by The International Union of Biochemistry and Molecular Biology, 46:382-389, 2018.

Redesigning space for interdisciplinary connections: the Puget Sound Science Center.

Mindful design of learning spaces can provide an avenue for supporting student engagement in STEM subjects. Thoughtful planning and wide participation in the design process were key in shaping new and renovated spaces for the STEM community at the University of Puget Sound. The finished project incorporated Puget Sound's mission and goals as well as attention to pedagogical principles, and led to connections and integration throughout the learning environment, specifically at the biochemistry and molecular life sciences intersections.

Neuropeptidase activity is down-regulated by estradiol in steroid-sensitive regions of the hypothalamus in female mice.

Thimet oligopeptidase (TOP) and prolyl endopeptidase (PEP) are neuropeptidases involved in the hydrolysis of gonadotropin-releasing hormone, a key component of the hypothalamic-pituitary-gonadal axis. GnRH is regulated in part by feedback from steroid hormones such as estradiol. Previously, we demonstrated that TOP levels are down-regulated by estradiol in reproductively-relevant regions of the female rodent brain. The present study supports these findings by showing that TOP enzyme activity, as well as protein levels, in the ventromedial hypothalamic nucleus of female mice is controlled by estradiol. We further demonstrate that PEP levels in this same brain region are down-regulated by estradiol in parallel with those of TOP. These findings provide evidence that these neuropeptidases are part of the fine control of hormone levels in the HPG axis.

Hydrogen bond residue positioning in the 599-611 loop of thimet oligopeptidase is required for substrate selection.

Thimet oligopeptidase (EC 3.4.24.15) is a zinc(II) endopeptidase implicated in the processing of numerous physiological peptides. Although its role in selecting and processing peptides is not fully understood, it is believed that flexible loop regions lining the substrate-binding site allow the enzyme to conform to substrates of varying structure. This study describes mutant forms of thimet oligopeptidase in which Gly or Tyr residues in the 599-611 loop region were replaced, individually and in combination, to elucidate the mechanism of substrate selection by this enzyme. Decreases in k(cat) observed on mutation of Tyr605 and Tyr612 demonstrate that these residues contribute to the efficient cleavage of most substrates. Modeling studies showing that a hinge-bend movement brings both Tyr612 and Tyr605 within hydrogen bond distance of the cleaved peptide bond supports this role. Thus, molecular modeling studies support a key role in transition state stabilization of this enzyme by Tyr605. Interestingly, kinetic parameters show that a bradykinin derivative is processed distinctly from the other substrates tested, suggesting that an alternative catalytic mechanism may be employed for this particular substrate. The data demonstrate that neither Tyr605 nor Tyr612 is necessary for the hydrolysis of this substrate. Relative to other substrates, the bradykinin derivative is also unaffected by Gly mutations in the loop. This distinction suggests that the role of Gly residues in the loop is to properly orientate these Tyr residues in order to accommodate varying substrate structures. This also opens up the possibility that certain substrates may be cleaved by an open form of the enzyme.

Effect of nitrogen source on cyanophycin synthesis in Synechocystis sp. strain PCC 6308.

Experiments were carried out to examine the effects of nitrogen source on nitrogen incorporation into cyanophycin during nitrogen limitation and repletion, both with or without inhibition of protein synthesis, in cyanobacteria grown on either nitrate or ammonium. The use of nitrate and ammonium, 14N labeled in the growth medium and 15N labeled in the repletion medium, allows the determination of the source of nitrogen in cyanophycin using proton nuclear magnetic resonance spectroscopy. The data suggest that nitrogen from both the breakdown of cellular protein (14N) and directly from the medium (15N) is incorporated into cyanophycin. Nitrogen is incorporated into cyanophycin at different rates and to different extents, depending on the source of nitrogen (ammonium or nitrate) and whether the cells are first starved for nitrogen. These differences appear to be related to the activity of nitrate reductase in cells and to the possible expression of cyanophycin synthetase during nitrogen starvation.

One hundred years of American Women in biochemistry *.

The occasion of ASBMB's 100th anniversary provides an opportunity to consider the history and accomplishments of women biochemists over the past century. American women in biochemistry have ranged from the highly visible, such as Nobel Prize winners Gert Cori and Gertrude Elion, to those who contributed in relative obscurity to equally dramatic breakthroughs. Women with Ph.D.s in biochemistry established departments of public health, nutrition, and home economics when more prestigious academic departments were not open to them. As in all fields of science, women have made great progress in biochemistry in recent years, and ASBMB reflects that progress; the past, current, and incoming presidents of the Society are all women. The data and biographical information presented here should provide a basis for inclusion of more women in recounting the history of biochemistry.

Flexibility in substrate recognition by thimet oligopeptidase as revealed by denaturation studies.

Thimet oligopeptidase (TOP) is a soluble metalloendopeptidase belonging to a family of enzymes including neurolysin and neprilysin that utilize the HEXXH metal-binding motif. TOP is widely distributed among cell types and is able to cleave a number of structurally unrelated peptides. A recent focus of interest has been on structure-function relationships in substrate selectivity by TOP. The enzyme's structural fold comprises two domains that are linked at the bottom of a deep substrate-binding cleft via several flexible loop structures. In the present study, fluorescence spectroscopy has been used to probe structural changes in TOP induced by the chemical denaturant urea. Fluorescence emission, anisotropy and collisional quenching data support a two-step unfolding process for the enzyme in which complete loss of the tertiary structure occurs in the second step. Complete loss of activity and loss of catalytic Zn(II) from the active site, monitored by absorption changes of the metal chelator 4-(2-pyridylazo)-resorcinol, are also connected with the second step. In contrast, the first unfolding event, which is linked to changes in the non-catalytic domain, leads to a sharp increase in kcat towards a 9-residue substrate and a sharp decrease in kcat for a 5-residue substrate. Thus a conformational change in TOP has been directly correlated with a change in substrate selectivity. These results provide insight into how the enzyme can process the range of structurally unrelated peptides necessary for its many physiological roles.

Regulators of the neuropeptide-degrading enzyme, EC 3.4.24.15 (thimet oligopeptidase), in cerebrospinal fluid.

Endopeptidase EC 3.4.24.15 (EP 24.15; thimet oligopeptidase) is a soluble metalloendopeptidase implicated in the metabolism of a number of neuropeptides, including neurotensin, gonadotropin-releasing hormone, and opioid peptides. We have shown previously that thiol reducing agents, such as dithiothreitol, activate EP 24.15 by mediating the conversion of inactive multimeric forms to active monomers and that this conversion involves the disruption of intermolecular disulfide bonds involving cysteine residues 246, 248, and 253. We have identified two components of cerebrospinal fluid that activate recombinant EP 24.15, but have no effect on a thiol-independent cysteine mutant form of the enzyme. The low molecular weight (<10 kDa) component co-elutes with glutathione by reversed-phase HPLC, whereas the high molecular weight component (>50 kDa) is sensitive to digestion with trypsin, suggesting it is proteinaceous in nature. These results suggest that EP 24.15 activity in the brain may be modulated by factors released into cerebrospinal fluid.

pH dependence studies provide insight into the structure and mechanism of thimet oligopeptidase (EC 3.4.24.15).

Thimet oligopeptidase (EC 3.4.24.15; TOP) is a Zn(II) endopeptidase implicated in physiological regulation of processes involving neuropeptides. The present study clarifies the active site structure and mechanism of catalysis of TOP. The enzyme exhibited a bell-shaped pH dependence of activity having an acidic limb due to a protonation event with a pK(a) of 5.7 and a basic limb with pK(a) of 8.8. The acidic limb can be attributed to protonation of a residue affecting k(cat) while the alkaline limb may be due to conformational change. Mutation of Tyr612 to Phe resulted in more than 400-fold decrease in activity. This result, supported by modeling studies, implicates Tyr612 in transition state stabilization analogous to the role of His231 of thermolysin.