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Students learn about rate laws and reaction order in general chemistry; in biochemistry, connections should be drawn between these ideas and enzyme kinetics.
Enzyme inhibition can be framed as a spectrum with competitive, noncompetitive, and uncompetitive being special points on this continuum; figure reproduced from Rodriguez and Towns (69) with permission from the Royal Society of Chemistry.
Papain secondary structure examples presented in presurvey lecture. (A) All α-helices (red) displayed as ribbons. (B) One α-helix (red) displayed with all atoms shown as stick models. (C) All β-strands (blue) displayed as ribbons. (D) Two β-strands (blue) displayed with all atoms shown as stick models.
Comparison of the reference papain structure to a molecular model of a new protein, DCAP_4793. (A) The papain structure is shown in red. Circled areas (cyan) highlight differences in compared with DCAP_4793. (B) The molecular model for DCAP_4793, generated with Rosetta, is shown in blue. (C) An overlay of the 2 proteins in panels A and B highlights similarities and differences described in the main text. The active site residues in both proteins are shown as space-filling models with color codes as follows: cysteine, gold/yellow; histidine. purple/magenta; asparagine, dark/lime green for papain and DCAP_4793, respectively.
Example cysteine proteases, aligned with papain (red), presented to students before taking the in-class survey. (A) Aspain: DCAP_3968 (orange). Aspain's unusual active site (top inset) replaces the typical asparagine (dark green) of papain (bottom inset) with aspartic acid (lime green). Its occluding loop, which partially blocks the active site, is indicated by an arrow. Other active site residues: cysteine, gold/yellow; histidine, purple/magenta for papain and aspain, respectively. (B) DCAP_6097 (dark grey). DCAP_6097's C-terminal granulin domain, indicated by an arrow, extends well beyond the rest of the papain-aligned structure.
Example survey questions and student responses using proteins aligned to papain (red). (A) Examples of accurate and informative student responses using DCAP_5945 (light grey). (B) Example of ambiguity in student responses with DCAP_6547 (black). (C) Example of inaccuracy in student responses with C. follicularis protein A0A1Q3AYB2 (dark grey). (D) Accuracy of all student responses to Q3, Q4.5, and Q13. All 34 proteins are shown in each panel, and those whose examples appear in panels A, B, and C are indicated by colored stars (DCAP_5945, light grey; DCAP_6547, black; A0A1Q3AYB2, dark grey). Black brackets below each graph show which subsets of proteins contain the feature in question.
Principles of enzyme and ion channel function. In (A) the cartoon depicts the reaction steps of a hypothetical enzyme that binds a substrate, cuts it, and then releases 2 products. (B) Single-channel traces of an acetylcholine receptor at various voltages are shown (4). (C) This illustrates the typical dwell-time distributions of a 3-state system with 2 closed states and 1 open state, in which the open dwell-time distribution is well fitted by a single exponential function (left, pink line), while the closed state histogram requires the sum of 2 exponential functions (right, pink line). The histograms were generated by MarkovEditor and a simple 3-state system. (D) All examples of Markov models are explained in more detail in the present article.