Biochemistry: Biomolecules, Methods, and Mechanisms

Massachusetts Institute of Technology via edX

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Provider

edX
Pricing

Free Online Course (Audit)
Languages

English
Certificate

$150.00 Certificate Available
Duration & workload

12 weeks, 3-6 hours a week
Sessions

On-Demand
Level

Intermediate
Subtitles

English

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Do you want to prepare for medical school, study a STEM field, become a research scientist, or transition to a career in the booming biotechnology industry? Or maybe you just want to understand the chemical reactions that govern life itself. Join Professor Yaffe, an MIT professor and practicing surgeon, as he guides you through the science that inspires countless doctors, researchers, and students alike.

We developed 7.05x Biochemistry with an emphasis on:

Developing your scientific thinking skills including articulating hypotheses, performing thought experiments, interpreting data, and designing experiments.
Using data based on real scientific experiments and highlighting the scientific process.
Asserting that biology is an active field that changes daily through examples of MIT (and other current) research, not static information in a textbook.
Visualizing real molecular structures with PyMOL to better understand function and mechanism.
Appreciating the quantitative aspects of biochemistry and practicing this quantitation with MATLAB.
Translating topics in biochemistry to diseases and medicine.
Conveying the authentic MIT firehose experience.
Implementing the science of learning in the course design.

We offer a thorough and robust means of certifying edX learners in their mastery of the MITx biochemistry content, through the MITx 7.05x Biochemistry Competency Exam. This challenging option is available only to those who register for the verified-certificate track, and successful completion of this exam is the majority of the assessment grade that counts toward a certificate. The Competency Exam will be open during the final week of the course.

Syllabus

The course includes the following learning sequences:

Introduction to Biochemistry; pH and Buffers
Amino Acids and Proteins
Protein Purification
Protein Structure
Protein Folding
Hemoglobin and Allostery
Hemoglobin and the Bohr Effect
Enzyme Chemistry
Enzyme as Catalysts
Enzyme Kinetics
Membranes, Channels, Transporters, and Pumps
Blood Clotting
Signal Transduction

Taught by

Michael Yaffe, Mary Ellen Wiltrout, Darcy Gordon and Monika Avello

Reviews

4.5 rating, based on 35 Class Central reviews

4.1 rating at edX based on 17 ratings

Start your review of Biochemistry: Biomolecules, Methods, and Mechanisms

Karen Carlson @sloopie72

MIT’s biology department emphasis is always on the lab approach. That is, they go through a pathway or a process in detail, give you a couple of general questions to see if you’ve got the idea, then throw you into a story set in a lab and make you f…

MIT’s biology department emphasis is always on the lab approach. That is, they go through a pathway or a process in detail, give you a couple of general questions to see if you’ve got the idea, then throw you into a story set in a lab and make you figure out the setup: what assay do you need, what product are you looking for, what reactants do you need, what would you expect to see, what does this result – graph, gel image, whatever – mean. This is, after all, what biochemists are training for, not memorizing reactions. I really enjoy this approach. It doesn't compensate for the lack of lab component, but it does give some idea of what might be included in a lab session.
The course also includes some Matlab and Pymol work. For anyone planning university work in Bio, they're both important and their inclusion is a big plus; I just like taking these courses for information, so I skipped them. Pymol is completely optional; I skipped Matlab and didn't find it fatal to my overall score.
Like the original MIT Bio course, there's plenty of testing to make sure you're getting it, but no matter how well you do you'll only end up with about 30% unless you pay for the Verified Certificate and take the (timed, proctored) Competency Exam as a final. Whether or not this is necessary depends on your own goals.
I spent way more than the recommended 6 hours a week. Take the prereqs seriously; there is some review of organic chem principles, but my lack of prior coursework often showed.
FMI see my personal blog post at https://sloopie72.wordpress.com/2020/06/03/another-biochem-mooc-mit-version/
BL C

The course overall has good coverage of the subject and engaging supplementary materials through PyMOL, MATLAB, and database usage, but the interface, assessments, discussion environment seem half-baked. Content-wise the lectures are very informati…

The course overall has good coverage of the subject and engaging supplementary materials through PyMOL, MATLAB, and database usage, but the interface, assessments, discussion environment seem half-baked.

Content-wise the lectures are very informative at a good pace. Prof. Yaffe discusses the topics with great economy of words to the point that the lecture transcriptions are enough to understand the topics discussed. A simple listing of goals and objectives at the beginning of every learning sequence gives an idea of the scope.

Some of the test-yourself questions in the learning sequence do not inspire thinking about the lectures but others are rather decent. The first three problem sets are comprehensive enough with thought-provoking questions and with only minor issues about clarity. Problem sets are based on real-world examples, adding to student motivation.

The user interface of the course is quite finicky with issues tracking progress and occasional simply poor design. The integrated mobile app is practically useless except for viewing the lecture videos, and it does not track your progress as with the desktop course. However, the content of the lectures is still good and the same as that of the desktop course.

Note that if you do not pursue the verified track you will not be able to access all of the problem sets as per edX's change in policy about "free online courses". This is not indicated anywhere on the course page before you enroll (it appears completely free), and so you might be surprised that suddenly your access to assessments is restricted.
Kazuma Arino @karino2

karino2 completed this course, spending more than 15 hours a week on it and found the course difficulty to be hard. Great course! I learn quite a lot from this course. In my personal opinion, Biochemistry itself is not so interesting subject. It's…

karino2 completed this course, spending more than 15 hours a week on it and found the course difficulty to be hard.

Great course! I learn quite a lot from this course.

In my personal opinion, Biochemistry itself is not so interesting subject. It's too easy to become a list of bland chemical reactions.

But Prof. Yaffe does a great job making this subject very interesting.

Topics are well-chosen. Each topic is interesting on its own. And all topics put together to become a bigger story at last. It's amazing.

For me, as a professional software developer, the MATLAB part is very easy. I have no difficulty. I'm surprised that many people here say it becomes their hurdle. The prerequisite of organic chemistry is much much harder.

This course gives me a deep understanding of a few topics of biology. I can build a solid foundation for further learning.
Javier Pizarro @jpizarrob

The biggest hurdle for me, being rather familiar with the subject, have been the MATLAB modules, since I have little familiarity with coding and even though they have directions that have been enough for me, I feel they might be a bit non-intuitive for someone not too keen for computers, and it's a bit frustrating to feel that sometimes I'm just copying the reference solutions.

Aside from that, an amazing course so far, quite enjoy the teaching style of Prof. Yaffe, all the interesting tidbits he throws here and there, and the animations are probably among the best I've seen for the subject.
Anonymous

This is a fitting addition to the edX/MIT biology offerings (including 7.00x and the 3 7.28x courses). It is extremely comprehensive with respect to both the lectures and the testing, but one thing is always certain in these courses: if you dedicat…

This is a fitting addition to the edX/MIT biology offerings (including 7.00x and the 3 7.28x courses). It is extremely comprehensive with respect to both the lectures and the testing, but one thing is always certain in these courses: if you dedicate the amount of time required, which will vary widely depending on prior knowledge, you *will* come away knowing the material. For some, this may include more detail than they want, if a high level overview is desired, but however well one does on the testing, it is a real treat to have access to a professor like Michael Yaffe, who is extraordinarily knowledgeable and a very fine lecturer. Likewise, the associated faculty and staff do an excellent job preparing the support materials and illustrations that are incorporated into the lectures or are available as handouts. Access to PYMOL and MatLAB is definitely an added benefit of participation.

In short, if you enjoy the opportunity to 'virtually' study at a very high level with some of the finest practitioners in their field, this is among the very best courses available to engage that passion.
Anonymous

I am 2/3 through this course and am thoroughly enjoying it. The lecture content is presented by Professor Yaffe in a clear and easy to follow format. The interspersed 'test yourself questions' break up the lectures nicely and help make sure I have u…

I am 2/3 through this course and am thoroughly enjoying it. The lecture content is presented by Professor Yaffe in a clear and easy to follow format. The interspersed 'test yourself questions' break up the lectures nicely and help make sure I have understood topics before moving on. The problem sets are written in a fun, anecdotal way that is very engaging and helps me imagine what it would be like attending labs with students. The problem sets are not a simple regurgitation of facts, but challenge you to think critically and truly test understanding of the material. I am concurrently studying to write the MCAT and am finding the knowledge I'm learning here is definitely improving my practice testing in the Bio/Biochem section. Thanks for the opportunity!
Anonymous

I started this course after taking already MITx-7.00x and MITx-7.28 1-3x and to see whether/how this course fills gaps between the other two excellent course . I appreciate the mixture of chalkboard lectures, animations, and test yourself questions. In particular, I like the introduction to PyMOL and MATLAB.
The problem sets with the characters and storyline comes close to real life situations in the lab and are challenging but doable at the same time.
Anonymous

First, the bad news: gotta agree with the MATLAB comments. Longest so-called "help" video is less than 4 minutes and even less useful. It's become a guessing game and I'm not going to keep playing it. Feedback/question answers are not timely, and…

First, the bad news: gotta agree with the MATLAB comments. Longest so-called "help" video is less than 4 minutes and even less useful. It's become a guessing game and I'm not going to keep playing it. Feedback/question answers are not timely, and typically not particularly helpful in deciphering. If it's going to be part of the course, they really should say so up front. And MIT ought to offer a MATLAB course to get people going using it. NOTE: not referring people to MATLAB's idea of educating (wanting, at best), but offering the course in a detailed way, specifically targeted in a biological direction.

Problem set questions are either very good or they're very bad: if MATLAB, count on very bad and you won't be disappointed if you're unfamiliar with the language. If selected images of peptides, usually pretty bad--it would invariably be better to be able to interact with them to get different viewpoints to answer questions. The ones chosen are never optimal, at least for me.

Now the good: All that said, the biochem lectures themselves are excellent. Yaffe is a truly outstanding educator. He's intense, which I like, and a one-man show. He epitomizes the "drinking from a fire hose" education that is MIT, and is every bit its long suit. And it is this part of the educational experience that brings the eval up to 4 stars. It really is worth it, even if you have to do some cherry-picking about how to spend your time.
Anonymous

As someone with substantial chemistry and very little biology backgrounds, I can say that the course is tough yet rewarding. As others have mentioned, the course does assume a certain amount of background knowledge in organic chemistry and basic bio…

As someone with substantial chemistry and very little biology backgrounds, I can say that the course is tough yet rewarding. As others have mentioned, the course does assume a certain amount of background knowledge in organic chemistry and basic biology. However, even without meeting all the prerequisites, it is possible to work through this course and do well -- it just takes way longer. The problem sets truly test your understanding of the fundamentals being taught, they cannot be solved through mere regurgitation. Of course, this is painful at times, yet I find that it has really forced me to grasp the concepts (no pain no gain!).

The lectures are really well delivered and thorough. There were very few instances in which lecture content was not sufficient to perform well in the problem sets. Some just took a bit of re-visiting, but perhaps if you're smarter than I am then a first pass of the course content will suffice.

I would have to diverge from the other comments on MATLAB in that I found the supporting videos to be more than enough help for the problem sets. The only "coding" involved was only substituting 2-3 words from a pre-written script. Additionally, these count for very little of the total grade, so don't let that aspect intimidate you from taking the course.

In summary, the course is an excellent entry-way into the field of biochemistry. You will be challenged, but it's totally worth it.
Anna Tonkonogui

This is a very informative course, and I'm very glad to be taking it. However, it took me a while to get my bearings. When I signed up for this course, the only listed prereq was 7.00x, which I had just completed. However, it became immediately appa…

This is a very informative course, and I'm very glad to be taking it. However, it took me a while to get my bearings. When I signed up for this course, the only listed prereq was 7.00x, which I had just completed. However, it became immediately apparent that you were expected to have a background in organic chemistry and some amount of physics for this course. The first set of lectures were full of "as you remember from Ochem this" and "the buffers you use every day" that, and I found that somewhat frustrating. That said, once we got past the "review" and into the material Prof. Yaffe clearly considered to be new material for the class, everything went a lot more smoothly.

My recommendation for edX and MITx: since there is generally a substantial time gap between the end of one course (e.g. 7.00x) and the start of the next (e.g. 7.05x), it would be great to have the prerequisites more clearly identified and give students more time to consume them prior to starting the course. For example, one of the posted course resources was https://portlandpress.com/essaysbiochem/article/61/4/401/78233/Essential-chemistry-for-biochemists. It would have been great to have that posted in the course description, so that while students are waiting for the course to open, we can review.
Anonymous

This is one of the most challenging courses I've taken - but it has bar-none the best problem sets of any online course I've ever attempted. The problem sets build knowledge while you work through them, in a logical way. It's been a long time since…

This is one of the most challenging courses I've taken - but it has bar-none the best problem sets of any online course I've ever attempted. The problem sets build knowledge while you work through them, in a logical way. It's been a long time since high-school chemistry and algebra, but I've been able to catch up and enjoy the motivation to work through some of those topics again. I think I'm understanding this material much, much better than I did back then! Professor Yaffe is amazing and his love of learning is clear in this course. The first lecture was incredibly tough but that's mainly due to my lack of prerequisites/preparation beforehand. Don't give up there; it does get easier and passing the course is attainable (and a real accomplishment).
Danny Kim

I found this course to be challenging but very interesting! The instructor, Professor Yaffe, explained the most complex of concepts in a clear, easy-to-understand manner. The problem set questions were thought-provoking and useful in improving skill…

I found this course to be challenging but very interesting! The instructor, Professor Yaffe, explained the most complex of concepts in a clear, easy-to-understand manner. The problem set questions were thought-provoking and useful in improving skills such as data analyzation.

To elaborate on the course difficulty, this course will likely be quite difficult for anyone who hasn't taken freshman level courses in chemistry and biology. I'm taking this course after taking 7.016 and 5.111 on OCW, and I think I wouldn't have understood much of the material in this course if I hadn't completed those. (especially 5.111, the chemistry course)

Also, as for the recommended 6 hours a week, I don't think anyone could complete this course in time if they followed it. You'll likely have to spend more than 10 hours a week (personally, I spent 14 hours a week), so take that into consideration!

Overall, I highly recommend this course to anyone who has a fundamental grasp of biology/chemistry and wants to expand their knowledge of biological processes and molecules!
Anonymous

I am 2/3 through this course, and had only planned on browsing through some of the content, but it is presented in such an interesting way that it really got me hooked on to biochemistry. The presentation of the material is great, the length of videos and the intermediary test yourself questions are all spaced appropriately, so that the learner remains engaged in the course through out. It is also motivating to see yourself progress. Overall, I feel that I have already gained a better foundational knowledge of biochemistry and am motivated to learn more about various subjects in the field that interest me. Am extremely grateful to live in a time when such content is freely available.
Anonymous

It is super hard if you are an above-average student, but it challenges you to get into a very different league of understanding the concepts of Biochemistry. I personally believe that it brought me out of my comfort zone and has already helped me immensely in my PhD research as I work with proteins. I'd highly recommend this course to anyone who is currently pursuing research in any area related to biochemistry plus has a keen interest to level up their career. I hope I could receive the Verified Certificate, as it is proof that you are a lifelong learner and it adds some weightage on your CV if you have a degree already and/or are in a scientific field.
Anonymous

This is an in depth course requiring a thorough understanding of basic chemistry and biology. It starts with explaining the importance of buffers which becomes clear as the course progresses. The course builds on from the essential building blocks of amino acids to the complex structure of proteins.
The comprehensive cover of haemoglobin and myoglobin in relation to transporting oxygen and carbon dioxide to and from muscles is fascinating.
The demonstration of PYMOL is great.
Overall very happy to be taking this course but a word of warning to anyone not prepared to put in the hours of study. It is not a trivial undertaking.
Anonymous

This is an immersive course that requires a lot of time. To effectively follow and then make use of the material covered in the lectures it is necessary to take notes, just as though you were in the actual lecture hall. These notes are supported by some excellent handouts and by useful pyMol exercises.

The exercises are thorough and a valuable learning experience in their own right. They take the learner through a sequence of steps that allow you to mentally put the pieces together and come to a good understanding of the material.
Anonymous

I'm currently taking this course and was just asked for a review. Honestly, it's awesome! It's taught really well, and I highly enjoy it. The 'Test Yourself' questions are really helpful (and all of them explain the correct answer!). P-Sets are hard, but very nicely structured. Expect to spend more than 6 hours/week on this - what I can say for sure, though, is that it's a great course for those interested in biochem!
Anonymous

This is a fantastic course. Professor Yaffe is an engaging lecturer who is able to find just the right way to explain material so that students understand it. The "Test Yourself" questions after each lecture section are very helpful for increasing comprehension and cementing the knowledge in your mind. I'm also enjoying the thoughtfully written problem sets, which follow a narrative of doing different kinds of lab experiments. There is a lot of material, but it's really rewarding to see myself learning so much.
Anonymous

This is a fantastic course. Thanks to everybody for making it available. You may need to review the lectures and make your own research and experiments in order to achieve a good understanding. I hope I can complete this course, otherwise I will take it again on the next run. Not only the lectures, but also the exercises are very interesting. The exercises are not only validating your knowledge. Thanks to the exercises you learn and understand things not covered by the lectures.
Hannah Nguyen

I'm in the middle of the course. Prof Yaffe approaches teaching biochemistry subject from the multidisciplinary fields--chemistry, organic chem, physical chem, molecular biology...In addition, he often sprinkles into the lectures historical backgrounds and experimental data and laboratory practices. If I had had Prof Yaffe in undergrad, I would probably get the grade for grad school.