20.11: The Evolution of Biochemical Pathways
- Page ID
- 89050
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\(\newcommand{\avec}{\mathbf a}\) \(\newcommand{\bvec}{\mathbf b}\) \(\newcommand{\cvec}{\mathbf c}\) \(\newcommand{\dvec}{\mathbf d}\) \(\newcommand{\dtil}{\widetilde{\mathbf d}}\) \(\newcommand{\evec}{\mathbf e}\) \(\newcommand{\fvec}{\mathbf f}\) \(\newcommand{\nvec}{\mathbf n}\) \(\newcommand{\pvec}{\mathbf p}\) \(\newcommand{\qvec}{\mathbf q}\) \(\newcommand{\svec}{\mathbf s}\) \(\newcommand{\tvec}{\mathbf t}\) \(\newcommand{\uvec}{\mathbf u}\) \(\newcommand{\vvec}{\mathbf v}\) \(\newcommand{\wvec}{\mathbf w}\) \(\newcommand{\xvec}{\mathbf x}\) \(\newcommand{\yvec}{\mathbf y}\) \(\newcommand{\zvec}{\mathbf z}\) \(\newcommand{\rvec}{\mathbf r}\) \(\newcommand{\mvec}{\mathbf m}\) \(\newcommand{\zerovec}{\mathbf 0}\) \(\newcommand{\onevec}{\mathbf 1}\) \(\newcommand{\real}{\mathbb R}\) \(\newcommand{\twovec}[2]{\left[\begin{array}{r}#1 \\ #2 \end{array}\right]}\) \(\newcommand{\ctwovec}[2]{\left[\begin{array}{c}#1 \\ #2 \end{array}\right]}\) \(\newcommand{\threevec}[3]{\left[\begin{array}{r}#1 \\ #2 \\ #3 \end{array}\right]}\) \(\newcommand{\cthreevec}[3]{\left[\begin{array}{c}#1 \\ #2 \\ #3 \end{array}\right]}\) \(\newcommand{\fourvec}[4]{\left[\begin{array}{r}#1 \\ #2 \\ #3 \\ #4 \end{array}\right]}\) \(\newcommand{\cfourvec}[4]{\left[\begin{array}{c}#1 \\ #2 \\ #3 \\ #4 \end{array}\right]}\) \(\newcommand{\fivevec}[5]{\left[\begin{array}{r}#1 \\ #2 \\ #3 \\ #4 \\ #5 \\ \end{array}\right]}\) \(\newcommand{\cfivevec}[5]{\left[\begin{array}{c}#1 \\ #2 \\ #3 \\ #4 \\ #5 \\ \end{array}\right]}\) \(\newcommand{\mattwo}[4]{\left[\begin{array}{rr}#1 \amp #2 \\ #3 \amp #4 \\ \end{array}\right]}\) \(\newcommand{\laspan}[1]{\text{Span}\{#1\}}\) \(\newcommand{\bcal}{\cal B}\) \(\newcommand{\ccal}{\cal C}\) \(\newcommand{\scal}{\cal S}\) \(\newcommand{\wcal}{\cal W}\) \(\newcommand{\ecal}{\cal E}\) \(\newcommand{\coords}[2]{\left\{#1\right\}_{#2}}\) \(\newcommand{\gray}[1]{\color{gray}{#1}}\) \(\newcommand{\lgray}[1]{\color{lightgray}{#1}}\) \(\newcommand{\rank}{\operatorname{rank}}\) \(\newcommand{\row}{\text{Row}}\) \(\newcommand{\col}{\text{Col}}\) \(\renewcommand{\row}{\text{Row}}\) \(\newcommand{\nul}{\text{Nul}}\) \(\newcommand{\var}{\text{Var}}\) \(\newcommand{\corr}{\text{corr}}\) \(\newcommand{\len}[1]{\left|#1\right|}\) \(\newcommand{\bbar}{\overline{\bvec}}\) \(\newcommand{\bhat}{\widehat{\bvec}}\) \(\newcommand{\bperp}{\bvec^\perp}\) \(\newcommand{\xhat}{\widehat{\xvec}}\) \(\newcommand{\vhat}{\widehat{\vvec}}\) \(\newcommand{\uhat}{\widehat{\uvec}}\) \(\newcommand{\what}{\widehat{\wvec}}\) \(\newcommand{\Sighat}{\widehat{\Sigma}}\) \(\newcommand{\lt}{<}\) \(\newcommand{\gt}{>}\) \(\newcommand{\amp}{&}\) \(\definecolor{fillinmathshade}{gray}{0.9}\)The tale of the evolution of enzymes from ribozymes and of informational DNA from RNA, and the other metabolic chemistries behind prebiotic semipermeable boundaries is ongoing in cells today. Undoubtedly, early cellular metabolism involved only reactions crucial to life…, catalyzed by a limited number of enzymes. But, if evolution inexorably trends towards greater complexity of molecular communication and coordination—in other words, towards increasingly refined regulation of metabolism—how did the repertoire of enzymes get larger and how did biochemical pathways become more elaborate? We answered the first question elsewhere, when we discussed gene duplication (e.g., by unequal crossing over). Duplicated genes encoding the same enzyme could provide the raw material for new enzymes and new enzymatic functions.
Whether in cells or in prebiotic structures, we can hypothesize how a new chemical reaction could evolve. For example, assume that a cell usually gets molecule D required for an essential function, from an external, environmental source. What would happen if levels of D in the environment become limiting? Clearly, cells would die without enough D. That is, unless some cells in the population already have a duplicated, redundant gene that has mutated and now encodes an enzyme with the ability to make D in the cell. Such a cell might have coexisted with cells without the mutation, but a D-limited environment would select the mutant cell for survival and reproduction. Imagine the scenario illustrated in Fig 20.21.
Using the illustration in Figure 20.21 as a guide, draw the steps leading to the evolution of a biochemical pathway converting A to B and B to C. Explain what you assume in each step of your drawing.
358 Origins and Evolution of Biochemical Pathways
In a similar scenario, a mutation in a duplicated gene could result in a novel enzyme activity that can convert some molecule (e.g., C or D) in the cell into a new molecular product. If the new enzyme and molecular product do not kill or debilitate the cell, the cell might survive to be selected by some future exigency.
How did cells originating in thermal vents or warm tidal pools escape and survive in the oceans, especially as the planet cooled down? Based on a phylogenetic identification of a likely ‘ancient’ bacterial adenylate kinase (adk) enzyme, Dorothee Kern may have the answer. Click Enzyme Evolution on a Cooling Planet to read a summary of her research. Then suggest a hypothetical structure to explain the actual structure of the “transitional” adk that she synthesized!