Living organisms and individual cells continuously adapt to changes in their environment. Those changes are particularly sensitive to fluctuations in the availability of energy substrates. The cellular transcriptional machinery and its chromatin-associated proteins integrate environmental inputs to mediate homeostatic responses through gene regulation. Numerous connections between products of intermediary metabolism and chromatin proteins have recently been identified. Chromatin modifications that occur in response to metabolic signals are dynamic or stable and might even be inherited transgenerationally. These emerging concepts have biological relevance to tissue homeostasis, disease and ageing.The authors argue that, among other things, methylation of histones is regulated by changes in the concentrations of some citric acid cycle metabolites. I find it difficult to imagine that the concentrations of the citric acid cycle intermediates could change significantly enough to act as allosteric effectors but that's not what grabbed my attention.
The American Museum of Natural History is one of the world’s preeminent scientific, educational and cultural institutions. Since its founding in 1869, the Museum has advanced its global mission to discover, interpret, and disseminate information about human cultures, the natural world, and the universe through a wide-ranging program of scientific research, education, and exhibition.This is a course for educators and that's right up my alley. You may want to sign up as well. Here's the description and the video.
How are all of the species living on Earth today related? How does understanding evolutionary science contribute to our well-being? In this course, participants will learn about evolutionary relationships, population genetics, and natural and artificial selection. Participants will explore evolutionary science and learn how to integrate it into their classrooms.It's a bit disturbing that the Next Generation Science Standards don't mention random genetic drift, Neutral Theory, speciation, or population genetics [Natural Selection and Evolution] but the course promises to cover population genetics and I assume that it will also cover all mechanisms of evolution since it's being taught by an evolutionary biologist (Joel Cracraft).
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The AMNH course Evolution: A Course for Educators provides an overview of biological evolution for educators. Informed by the recently released Next Generation Science Standards, the course explores the history of evolutionary theory and the evidence that supports it. We will learn about patterns of human evolution and societal implications of modern evolutionary biology, and how scientists determine relatedness among living and extinct organisms. Course participants will bring their understanding of course themes - along with content resources, discussion questions, and assignments - into their own teaching.
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This collection is being developed for the revised MCAT® exam that will first be administered in spring 2015. Videos will be added to the collection through fall 2014. All content in this collection has been created under the direction of the Khan Academy and has been reviewed under the direction of the Association of American Medical Colleges (AAMC). All materials are categorized according to the pre-health competencies tested by the MCAT²⁰¹⁵ exam; however, the content in this collection is not intended to prescribe a program of study for the MCAT²⁰¹⁵ exam. The content is also included in the Pre-health Collection within MedEdPORTAL’s iCollaborative sponsored by the AAMC: www.mededportal.org/pre-health *MCAT® is a program of the AAMC and related trademarks owned by the Association include Medical College Admission Test, MCAT, and MCAT²⁰¹⁵. For more information about the MCAT exam visit : www.aamc.org/mcat2015.So, how did the Khan Academy prepare the videos? They set up an MCAT Video Competition and picked the best ones. You can read about the winners at MCAT Video Competition Winners. It's an eclectic mix of people but 11 out of 15 winners are medical school students or graduate students. Keep in mind that teaching introductory subjects like evolution and biochemistry is hard and Teachers Have to Know Their Subject.
One of the first things you learn when you start teaching is that you have to know the content inside and out — it’s simply not enough to know the bare minimum that you expect the students to master, because as a teacher, you need to push just a bit farther to get them up there. You need to be able to lead them to knowledge, and you need to be able to point off in the distance to all the cool stuff they can learn if they continue. How can you inspire if you’re not drinking deeply from the Pierian Spring yourself?Keep this in mind next time we discuss teaching evolution and biochemistry. Teachers have to be experts and it takes a lot of work to make sure you know your content. If what you're teaching is not correct then you are not a good teacher no matter what the student evaluations say. And it's not only a question of accuracy—as PZ points out, you need to be more than a few steps ahead of your students in order to inspire them to do better.
Image Credit: Moran, L.A., Horton, H.R., Scrimgeour, K.G., and Perry, M.D. (2012) Principles of Biochemistry 5th ed., Pearson Education Inc. page 568 [Pearson: Principles of Biochemistry 5/E] © 2012 Pearson Education Inc.The winner, for the second week in a row, is Jean-Marc Neuhaus. [Monday's Molecule #220]. Jean-Marc lives in Switzerland so I've made arrangements to fly over there to visit him and treat him to two fondues at the Pinte de Pierre-à-Bot in Neuchatel.
Jean-Marc was kind enough to send me a menu [PDF]. There are about 30 different fondues to choose from. If you would like to join us you can leave a comment on last week's post. 
Faces are sculpted by 'junk DNA'It's pretty clear that science correspondent Alok Jha doesn't understand what he's writing and it's about time we started publicizing the names of those science writers who mislead the public about science. The consensus among knowledgeable scientists is that at least 80-90% of our genome is junk. It's time for science writers to admit that the science favors junk.
Though everybody's face is unique, the actual differences are relatively subtle. What distinguishes us is the exact size and position of things like the nose, forehead or lips. Scientists know that our DNA contains instructions on how to build our faces, but until now they have not known exactly how it accomplishes this.
Visel's team was particularly interested in the portion of the genome that does not encode for proteins – until recently nicknamed "junk" DNA – but which comprises around 98% of our genomes. In experiments using embryonic tissue from mice, where the structures that make up the face are in active development, Visel's team identified more than 4,300 regions of the genome that regulate the behaviour of the specific genes that code for facial features.
Attanasio, C. et al. (2013) Fine Tuning of Craniofacial Morphology by Distant-Acting Enhancers. Science 342: Oct. 25, 2013 [doi: 10.1126/science.1241006]
Matter and Energy TransformationI think we can all agree that a basic understanding of thermodynamics is an important core concept. However, I would have worded this paragraph somewhat differently.
The Many Forms of Energy Involved in Biological Processes
The energetics of a biological system or process—be it an ecosystem, an organism, a cell, a biochemical reaction—conforms to and is understood in terms of the fundamental laws of thermodynamics. Biological systems capture and process energy from the environment in many forms including that emanating directly from the sun (photons through photosynthesis), heat from the environment (kinetic energy), and energy rich compounds produced by geothermal processes (e.g. sulfur compounds) or other organisms (e.g. carbohydrates). Energy from all sources is chemically converted into useful chemical and physical work in a controlled and regulated fashion. The potential
energy stored in chemical bonds can used to generate motion, light, heat, and electrochemical gradients; likewise, electrochemical gradients can be used to generate motion and new chemical bonds. The input of energy from the environment allows living systems to exist in a state of nonequilibrium with their environment. The discussion of energy and matter conversions in biological systems makes use of the physical concept of changes in Gibbs free energy, or ΔG.
CatalysisThis is pretty good. I would only add that there are some fundamental concepts of enzyme mechanisms that need to be covered. The idea of a transition state is important. I put a lot of emphasis on oxidation-reduction reactions as a core concept in biochemistry.
Biologically relevant energy and matter interconversions do not occur rapidly enough (often by many orders of magnitude) to support life. In living systems, biological catalysts called enzymes facilitate these reactions. Enzymes are macromolecules, usually proteins or RNA molecules with a catalytic function. Enzymes do not alter reaction equilibria; instead, they lower the activation barrier of a particular reaction so that reactions proceed much more rapidly. The presence of powerful enzymatic catalysts is one of the key conditions for life itself.
Description of the rates of enzymatic reactions represents the subdiscipline enzyme kinetics. Key concepts of kinetics, including the definitions of the terms vo, Vmax, Km, and kcat, constitute a common language for biochemists and molecular biologists in discussing the properties of enzymes.
Students should be able to apply their knowledge of basic chemical thermodynamics to biologically catalyzed systems, quantitatively model how these reactions occur, and calculate kinetic parameters from experimental data.
Coupling Exergonic and Endergonic ProcessesI have a problem with this section. I don't think that the concepts of "exergonic" and "endergonic" processes are very important in biochemistry and I don't use them in my textbook. They're not found in many other textbooks, either. Also, the idea of "coupled" reactions is very poorly taught in biochemistry courses. It's almost never true that enzymes simply link up two independent reactions, one of which is "favorable" and the other "unfavorable." What usually happens is that a completely new reaction is catalyzed. For example, ATP is not hydrolyzed but, instead, a group transfer reaction is created. This important concept is covered in the next section but the authors do not appear to have grasped its significance.
Biochemical systems couple energetically unfavorable reactions with energetically favorable reactions to allow for a wider variety of reactions to proceed.
Students should be able to discuss the concept of Gibbs free energy, and how to apply it to chemical transformations, be able to identify which steps of metabolic pathways are exergonic and which are endergonic and relate the energetics of the reactions to each other.
The Nature of Biological EnergyThe essence of these statements is correct but it is not explained very well. The important concept is not that you "couple" a "favorable" reaction like ATP hydrolysis to an "unfavorable" reaction like synthesis of glutamine from glutamate and ammonia (ΔG°′ = +14 kJ mol-1).
In biological systems, chemical energy is stored in molecules with high group transfer potential or strongly negative free energy of hydrolysis or decomposition. These molecules, particularly ATP, provide the free energy to drive otherwise unfavorable biochemical reactions or processes in tightly coupled and highly controlled fashion. Most frequently, the free energy needed for a process or metabolic pathway is provided by group transfer rather than by hydrolysis. In this way, efficient energy transfer is optimized, while inefficient energy transfer to the environment (in the form of heat for example) is minimized.
Students should be able to show how reactions that proceed with large negative changes in free energy can be used to render other biochemical processes more favorable.
1. I believe that all introductory biochemistry students should be able to explain where chemoautrophs get their energy. If they can't do it, they haven't been taught the fundamental concepts.
Tansey, J.T., Baird, T., Cox, M.M., Fox, K.M., Knight, J., Sears, D. and Bell, E. (2013) Foundational concepts and underlying theories for majors in “biochemistry and molecular biology”. Biochem. Mol. Biol. Educ., 41:289–296. [doi: 10.1002/bmb.20727]
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I would recommend citing examples from the numerous scientists who have integrated current science into their religious worldviews, scientists such as Kenneth Miller, Francis Collins, Robert Russell, and Father George Coyne.There's so much wrong with this advice that I hardly know where to begin.
Another tack would be to cite statements from theological figures, such as Pope Benedict’s statement in Communion and Stewardship (2002), when he was still Cardinal Ratzinger:Converging evidence from many studies in the physical and biological sciences furnishes mounting support for some theory of evolution to account for the development and diversification of life on earth, while controversy continues over the pace and mechanisms of evolution. While the story of human origins is complex and subject to revision, physical anthropology and molecular biology combine to make a convincing case for the origin of the human species in Africa about 150,000 years ago in a humanoid population of common genetic lineage.Let me be clear: I’m not suggesting that you cite the views of such scientists and theologians as authoritative. There’s a wide range of religious reactions to evolution, from rejection to embrace, and you may not feel comfortable in endorsing any of them. (Indeed, a teacher in the public schools is required not to endorse any of them in the classroom.) But many people who reject evolution for religious reasons are ignorant about, or have never been seriously exposed to, the range of religious reactions to evolution. It may come as a complete surprise to them that devout religious people—perhaps even people of the same faith—have no theological objection to evolution. And opening people’s horizons is part of what education is all about, isn’t it?
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