Biochemistry Becomes Us All

Pair of helix structures, showing one with missing H bond.

An illustration from the notes for Session 2 of 5.07SC Biological Chemistry I, describing the hierarchy in protein structure, with hemoglobin as an example. (Figure by O’Reilly Science Art for MIT OpenCourseWare.)

By Joe Pickett, OCW Publication Director

Did you know that life, in all its mindboggling diversity, from single-celled bacteria to reptiles, birds, and mammals, is made possible by ten simple chemical reactions?

These reactions, and their interconversions in our primary metabolic pathways, are the focus of 5.07SC Biological Chemistry I, just published on OCW.

It’s amazing, really. The basic reactions, their metabolic pathways, and the vitamins that are modified to make catalysts boosting still more reactions, are conserved across organisms.  “It doesn’t matter whether you study a bacteria or a human, the central metabolism is pretty much the same,” says star researcher Professor JoAnne Stubbe, one of the 5.07SC instructors. “The thing that’s different is the detailed regulation and the complexity of the regulation.”

So if you can understand the basics of biochemistry, you have the keys to understanding the living universe.

And the keys to understanding most diseases, since most diseases involve some sort of dysfunction in the regulation of metabolic reactions.

Co-Teaching with Varied Resources

A recipient of the National Medal of Science, Stubbe has devoted much of her career to elucidating the workings of nucleotide reductases, the enzymes involved in the chemical reactions essential to the biosynthesis of DNA and RNA. Professor Stubbe’s co-instructors are Professor John Essigmann and Dr. Bogdan Fedeles. Essigmann leads a lab that investigates how chemicals in the environment can damage DNA in cells and how cells respond to and sometimes repair the damage. Working in that lab, Fedeles and Essigmann have shown how chronic inflammation in the body can lead to cancer and how the HIV virus can be induced to deactivate itself after invading a cell.

As another of OCW’s Scholar courses, 5.07SC Biological Chemistry I abounds in learning resources. The course is arranged in a linear structure through three modules that reflect the shared teaching of the professors. Stubbe teaches the first part of the course, introducing fundamental reactions in her four Lexicon videos, and detailing further biochemical reactions through seven sessions in her illustrated lecture notes.

Starting in session 8, Professor Essigmann narrates a series of storyboard videos, showing how energy is produced in the cell and how that energy is used to make macromolecules like proteins.

In his own series of videos, Fedeles guides learners through carbonyl chemistry, pyridoxal phosphate (PLP) chemistry, and ten key problems sets distributed throughout the site.

All the learning resources are assembled on a single Resource Index page for convenient reference.

Envisioning Future Pathways for Students

The course site also features a series of video interview clips on its This Course at MIT page (“Meet the Educators” and “Instructor Insights”), in which Professors Stubbe and Essigmann share their reflections about how they teach biochemistry, what turned them on to biochemistry in the first place, what their research focuses on, and where they think biochemical research is headed. Topics include “Using the Vitamin Bottle as a Teaching Tool,” “How Can You Not Think Enzymes Are Cool?,” and “Motivating Students to Study Metabolic Biochemistry with Oncology Applications.”

So take a look at 5.07SC. Like the cell itself, it’s packed with material delivered with lots of energy.

Innovating Dirt Cheap: What Sadoway Can Teach Us About The Future Of Clean Energy (Huffington Post)

Screenshot of video with tuxedo-clad professor at the front of lecture hall, holding up a glass of champagne.

Professor Donald Sadoway toasts the students at end of his class 3.091 Introduction to Solid State Chemistry.

Professor Donald Sadoway is the charismatic and insightful instructor of one of OCW’s most popular courses, 3.091SC Introduction to Solid State Chemistry. With legions of fans around the world, his video lectures reveal frequent pearls of general wisdom among the clear explanations of chemistry fundamentals and applications.

Sadoway’s research on grid-scale energy storage also has legions of fans. Louika Papadopoulos recently wrote on five favorite Sadoway quotes springing from his clean energy work.

When it comes to alternate power sources and batteries, Donald R. Sadoway, John F. Elliott Professor of Materials Chemistry at the Massachusetts Institute of Technology (MIT) is the man to turn to. Voted one of Time magazine’s 100 most influential people in the world in 2012, Sadoway is not only known for his packed classes, despite being one of the largest in the history of the institute, but for the pieces of wisdom he imparts when simply speaking about batteries. Here are a few of my favorite Sadoway quotes and what I believe they can teach us about the future of clean energy.

My personal favorites are these two:

2. “The liquid metal battery story is more than an account of inventing technology. It’s a blueprint for inventing inventors.”
This is an often overlooked and yet ubiquitous truth. Whenever dealing with innovation it is important to remember it’s not just about the technology, it is about nurturing a culture of innovation. It’s about investing in people who can maximize any technology’s potential, adapt it efficiently to current circumstances and ensure its appropriate future development. It’s about creating inventors of technology who can use what they have learned to tackle new problems and develop new technologies. The bottom line is: more energy inventors moulded, more energy inventions made…

4. “If you want to make something dirt cheap, make it out of dirt. Preferably dirt that’s locally sourced.”
If we want innovation in energy to truly benefit humanity we have to make sure it is available to all. What better way to do that than to make it cheap and locally sourced? This quote is also the inspiration for the title of this piece as it also represents a key element of Sadoway’s work. Instead of trying to invent a product and then struggle to make it economically viable, Sadoway opted instead to develop a battery that would meet the pricing point of the electricity market upon creation. This is the reason why he looked only at earth-abundant materials that would work well with cheap manufacturing techniques. Dirt-cheap innovation indeed!

Read the complete story.

4 Fun Facts from “Fundamentals of Biology”

Magnolia petals stained with methylene blue and shown at 100 times magnification.

(Original image courtesy of kaibara on Flickr.)

Fundamentals of Biology is an OCW Scholar course that’s designed to help you learn the principles of the basic mechanisms of life. Our Digital Publication Specialist Alicia Franke, who works with the Biology Department, has collected a few interesting tidbits from this rich course.

#1: Your genome (assuming you’re human) contains 3 billion base pairs of DNA, and about 20,000-25,000 genes.

Learn about nucleic acids and the structure of DNA, and click over to the Human Genome Project to learn about how the sequence of these 3 billion bases were determined.

#2: van der Waals forces in action: These geckos are able to stick to any surface, even climb up walls. How? Their toe pads contain millions of tiny hairs (known as setae), so tiny that they can interact with surfaces on a molecular level. No glue required.

Learn about van der Waals forces in the video lecture: Proteins, Levels of Structure, Non-Covalent Forces, Excerpt 2. (Skip forward to 25:40.)

#3: Another reptile fact! A species of lizard, known as the Jesus Christ lizard, can actually walk on water. They are able to do this because of the structure of their feet, combined with a very important property of water known as surface tension.

Watch this video of the lizard in action, and then learn about surface tension in the video lecture Covalent Bonds, Hydrogen Bonds. (Start at 20:45.)

#4. You already know donuts are delicious. You also know that fats can be both good and bad for us. Why, exactly, are some fats (like cis-unsaturated) good for us, while other fats like trans-unsaturated (or “trans fats”) are bad for us?

Learn the details of the answer in the video lecture Macromolecules: Lipids, Carbohydrates, Nucleic Acid, Excerpt 1. Prof. Havel Sive gets into saturated fats at 14:45, unsaturated fats at 17:00, and trans fats at 18:25.

A step ahead for liquid metal batteries and renewable energy

Image showing three vertical layers of material in a glass container.

A physical model of the liquid metal battery at room temperature, in a glass container. (Image: Felice Frankel)

One of the challenges facing some renewable energy sources — such as solar or wind power — is that our demand for electricity stays high when the sun’s not shining or the wind’s not blowing.

MIT’s Donald Sadoway — instructor for our popular OCW Scholar course 3.091SC Introduction to Solid State Chemistry — has been working for several years on a high-tech liquid metal battery system to help bridge between electricity supply and demand. Such batteries could store excess generated energy when it’s available, and pump it back into the electric grid when it’s needed. The promise of this research landed Prof. Sadoway on Time magazine’s 2012 list of “the 100 most influential people in the world.”

The technology continues to progress. This month, Prof. Sadoway and colleagues announced a substantially improved battery formulation, which could make the cost of battery-backed renewable energy more competitive with fossil-fuel sources. MIT News reports:

Donald Sadoway and colleagues have already started a company to produce electrical-grid-scale liquid batteries, whose layers of molten material automatically separate due to their differing densities. But the new formula — published in the journal Nature by Sadoway, former postdocs Kangli Wang and Kai Jiang, and seven others — substitutes different metals for the molten layers used in a battery previously developed by the team.

Sadoway, the John F. Elliott Professor of Materials Chemistry, says the new formula allows the battery to work at a temperature more than 200 degrees Celsius lower than the previous formulation. In addition to the lower operating temperature, which should simplify the battery’s design and extend its working life, the new formulation will be less expensive to make, he says.

The battery uses two layers of molten metal, separated by a layer of molten salt that acts as the battery’s electrolyte (the layer that charged particles pass through as the battery is charged or discharged). Because each of the three materials has a different density, they naturally separate into layers, like oil floating on water.

The original system, using magnesium for one of the battery’s electrodes and antimony for the other, required an operating temperature of 700 C. But with the new formulation, with one electrode made of lithium and the other a mixture of lead and antimony, the battery can operate at temperatures of 450 to 500 C. Read more.

Prof. Sadoway’s innovative work on one of today’s most pressing needs will come as no surprise to anyone that’s watched his lectures in 3.091SC Introduction to Solid State Chemistry. Bill Gates called them “the best chemistry lessons anywhere.”

The MIT freshman year, all in OCW Scholar

Graphic introducing OCW Scholar

What’s it like to be a freshman at MIT? Dorms, roommates, late-night pizza…new opportunities for hands-on learning, collaboration, and rich personal connections…and a rigorous and fascinating set of courses.

OCW can’t give you campus living or discover your new favorite lab partner. But with our OCW Scholar collection, you can explore all of the courses in a typical MIT freshman year: six core classes in calculus, physics, chemistry, and biology, and a couple of electives. Each OCW Scholar course has everything you need for self-study: lecture videos with some of MIT’s best faculty, notes, assignments and exams with solutions, and supplemental problem solving or study materials.

You might follow the example of new MIT freshman Monica Valcourt, recently profiled in MIT News. While a high school sophomore, Monica used the OCW Scholar course 9.00SC Introduction to Psychology for independent study, since her school didn’t offer a psychology course. She got her school to grade her work and provide credit for this course. Watching the videos, reading the books, and doing the homework ultimately earned her an A in the course. Monica continued on with other OCW courses, including computer programming — which she hopes will become her MIT major.

Here’s what a typical MIT freshman might take, assuming no AP credits for physics or calculus:

Semester 1

Semester 2

The OCW Scholar collection continues with several more STEM subjects taken by many MIT sophomores: differential equations, linear algebra, physics of vibrations and waves, probabilityintroduction to electrical engineering, and engineering dynamics.

With fifteen courses in all, OCW Scholar gives you a hearty slice of the MIT undergraduate experience. But you’ll need to supply the pizza.

6.041 Probabilistic Systems: The educational resource trifecta

We’ve done it again.  As we did with Dynamics a while back, we now offer MIT probabilistic systems curriculum in three delicious flavors.  A standard OCW publication, an OCW Scholar version intended for independent and self-paced learning, and an MITx MOOC supporting the complete online learning experience.

Visually, you can see the difference.  First the standard OCW course:

Screen Shot 2014-03-04 at 8.25.25 AM

Note how the sections of the site are organized by content type.  The standard OCW publication is a general resource for educators and students, providing materials that can be easily downloaded and shared offline for a variety of purposes, including independent learning.

Now the OCW Scholar version:

Screen Shot 2014-02-28 at 3.11.00 PMHere, we’ve taken the extra effort to organize the content into logical units (and to ensure it’s complete), but now it more explicitly supports independent learning at the expense of resource sharing, since it’s a more integrated and online offering.  Still OCW, though, with no interaction with faculty or other students, and no recognition for learning, but persistently available so you can move at your own pace. The OCW Scholar course combines content previously published on the standard OCW site above with 51 new videos recorded in 2013 by MIT Teaching Assistants.

Now the MITx MOOC:

Screen Shot 2014-02-28 at 3.12.14 PMOrganized for study, linked to discussion forums, some access to faculty, a lovely certificate at the end.  To earn the certificate, though, you commit to moving at the pace of the course when it’s offered.

There you have it.  However you like your learning, we gotcha covered.