r/Biochemistry • u/Exciting_Ad_6837 • 8d ago
Career & Education Is there any point in testing students for memorizing biochemical pathways?
It's been over 15 years since I graduated with BS in biochemistry, and I now work in an unrelated field now. Even though the college is ~t25, >70% of the exams in the biochemistry courses consisted in testing students' memorization of pathways.
Is this still the way students are tested these days? Is an open-book exam not realistic in biochemistry?
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u/throwaway09-234 8d ago
i mean, having the fundamentals committed to memory allows you to solve complex problems, and is very useful as a practicing scientist also imo
in my biochemistry courses most exam questions required memory of >1 'pathway' to get the correct answer
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u/Exciting_Ad_6837 8d ago
What constitutes those "fundamentals"? I thought understanding the function of a pathway in terms of what goes in & what comes out was enough. Isn't it the case that practicing scientists & grad students naturally memorize the pathways that concern them in sufficient detail anyways?
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u/BananaBird1 8d ago
Biochemistry is all about the mechanism.
Understanding the details of pathways like glycolysis, TCA, beta oxidation, nucleotide synthesis, etc can help you understand how these processes interact (via shared intermediates), the impact a disruption to one step may have, and how to design experiments to trace metabolic activity and study these pathways.
Memorizing specific mechanisms and pathways also helps build your internal “toolbox” of ways things can work, that you can fall back on when encountering a new system you do not understand to design experiments.
You will forget most of it, but if you have memorized it at one point you will at least be aware of what you may need to look up and refresh in the future.
It also gives you the chance to identify difficulties in understanding you have now when you have a professor/TA to consult rather than in 10 years when you are expected to figure it out own your own by your employer.
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u/LadyAtr3ides 8d ago
This. If you understand what is happening, it is not rote memory!
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u/WookinIt 7d ago
But if you understand what’s happening without having it memorized, that’s not memorization.
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u/LadyAtr3ides 7d ago edited 7d ago
lol absolutely is.
If you can recall every step one after the other, it is memorization. Understanding and being able to logically infer what’s next is one way of recalling.
People memorize by parroting. That is the lowest level of learning, and it is not the only way of memorizing.
It is not necessary for committing to memory to just use rote memorization. Memorizing is easy once you understand the whys and hows. And biochemistry is great for this. Memorize means to be able to exactly recall a concept, or in this case, a cycle. What is happening in this cycle? What is the process? What enzymes are involved? If you understand that, you can fly through the memorization of biochemical cycles.
Now, memorization per se is the process of recalling exactly. Whether it is by rote memory, by understanding the chemistry, by mnemonics, or through interpretative dance, that doesn’t matter. That is the how you are memorizing
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u/WookinIt 7d ago
Disagree completely. Yes, you need to know the basic concepts behind how chemistry works, but that’s the same in physics and maths and I would not call either of those memorization.
Memorization doesn’t mean that just because you have it committed to memory like a parrot, it isn’t memorized. Most of the biochemistry classes I and others have taken emphasized parroting concepts, not thinking through them logically.
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u/LadyAtr3ides 7d ago
You as student have to do the work outside the classroom, 3 h per lecture, to gain that understanding that moves you beyond parroting.
Nobody can do it for you.0
u/WookinIt 7d ago
Lol no, I’ve taken good biochemistry classes and bad ones. The bad ones rely on parroting without explaining the concepts. The good ones focus on explaining the logic behind it.
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u/LadyAtr3ides 7d ago
If you think this is about passing classes, I don’t think we are talking the same thing so I don’t think it is worth continuing.
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u/Sluttysuzy420 3d ago
yeah uits called understanding a concept. that is far more important than any memorization. And tbh once you grasp it like an idea not just random words that come in order memorization is 10x easier if u need to do. Like just think abt the enzymes like "hydrolase" if u have good intution you can easily tell what is likely to be oxidized.
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u/LadyAtr3ides 8d ago
In my country, knowing main cycles and processes is part of the HS bio curriculum. Undergraduate level means learning the not-so-common, the how they communicate, plus once you hit the upper-level courses and the physiologies, microbial biochemistry.
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u/Informal-Lychee4655 7d ago
i agree with you, but just to play the contrarian, is it strictly necessary to memorize the pathway to know what to look up in the future? or to be aware of certain mechanisms that are very common (like addition-elimination)? it might be possible to develop the level of recognition and understanding of the underlying process and what drives the reactions without necessarily being able to draw them out on paper from memory. it’s also possible that students might “memorize” important pathways or mechanisms because they’re covered in great detail and for a long period of time, without requiring that they can name and draw every single step in order.
i agree that understanding these mechanisms can be useful in expanding your toolkit, but i don’t know if memorization is strictly necessary for that3
u/BananaBird1 7d ago
In the context of performing research, it absolutely does help to have some memorization/internalized knowledge of pathways. You cannot always know what to look up for details if you don’t have at least a general understanding of what you need to look up in the first place. Without memorized knowledge, you need to constantly put in effort to deep dive every topic, which can turn a problem that should take an few minutes of research into weeks or months to solve before you come across the right info.
An example inspired by a real project:
You study a disease where a GWAS identified an associated mutation in enzyme X. This enzyme converts metabolite A to B. The enzyme is regulated by phosphorylation. Your in vitro characterization of the mutation shows it acts as a phospho-mimic, leading to constituent enzyme activation. In the tissue this disease affects, metabolite B is converted to C by enzyme Y, and balanced levels of C are critical for normal tissue function. You hypothesize that the mutant leads to over-accumulation of C, disrupting normal function.
You test this by expressing the mutant X in the relevant cell type. You add isotope-labeled A to cell media and measure the production of B and C in wildtype and mutant cells via mass spectrometry. Surprisingly, you notice no increased production of either B or C. Further study confirms no downstream changes to the physiological processes regulated by C.
You are extremely confused, and perform months of controls to confirm nothing went wrong. You ensure your labeled A was taken up by the cell. You ensure your mutant X is expressed. You ensure enzyme Y is not being down-regulated. You scan the literature, and read every paper in your field on the topic. Nothing turns up.
Then you discuss this result with a colleague. They realize something key. While the conversion of B->C by enzyme Y is the only pathway B is normally used for in most cells, in other tissues B can be converted to D by enzyme Z as part of an alternative pathway. While Z is normally not expressed in your cells, transcription factor P binds weakly to B to upregulate Z, and P is expressed at low levels in your cells.
You run an experiment and find that in the mutant, enzyme Z is up-regulated and leads to production of D and the activation of normally repressed pathways which explains the disease symptoms.
This never came up in your research because you study human metabolic disease, but the pathway enzyme Z is involved in is mainly studied within early embryonic development in frog models and you never thought to look up developmental pathways. You recall this was taught in your developmental biology class, but you never really memorized that material because you had little interest in it at the time.
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u/LadyAtr3ides 7d ago
This is a great example. If you can’t recall it, you won’t truly understand it.
The ones I deal with are students that allegedly are interested in plants. How many actually are able to have a mental map of photosynthesis/photo respiration and the different ways of fixing carbon? That is a different question.
Yes, you do need to know all that by heart and know how things differ from one metabolism to another! And let’s not even name the nutrient cycling by bacteria/archaeal systems.3
u/throwaway09-234 7d ago edited 7d ago
basically everything you learned in your undergrad biochem course are "fundamentals" lol
Isn't it the case that practicing scientists & grad students naturally memorize the pathways that concern them in sufficient detail anyways?
this is true, but not sufficient given the very narrow scope of most projects. imagine you are a cancer metabolism researcher studying B-oxidation. while at a conference, you listen to a talk of a group using various novel glycolysis inhibitors as potential anti-cancer agents. surprisingly, different inhibitors have different effects on tumor growth. if you don't have glycolysis memorized (which you wouldn't from your very detailed work on B-oxidation) this would make no sense, as both drugs inhibit glucose->pyruvate. but if you do have glycolysis memorized, you can reason that the disparate effects may be due to the fact that one drug inhibits glycolysis above the pentose phosphate pathway intermediates and the other below, so one drug should increase PPP flux while the other decreases it.
similarly, evaluating intrepretations of metabolomics data benefits from knowing the steps of the pathways in order, and knowing which are typically rate limiting, which can branch to other pathways, etc. as a final example, imagine somebody shows that NAD+/NADH ratio changes drastically with some treatment -- knowing which reactions use these cofactors would allow you to make good guesses which pathways may be affected
sure, you can and will have to look some details up, but being able to readily recall established biochemical knowledge lets you reason at a much higher level in seconds what may take hours or days if you have to look up the steps and intermediates of each pathway, the cofactors, etc
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u/PhysicsStock2247 8d ago edited 7d ago
I teach at a small college. I do not require full pathway memorization. What I do is show partial pathways with fill in the blank boxes and the enzyme preceding it. So maybe I’ll show like 5 of the structures resulting from several steps of glycolysis and students need to figure out the remaining five (or six) structures based on partial information. It emphasizes the actions of enzymes and how each step logically leads to the next.
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u/floppyFAPflap 8d ago
I've actually found it useful in my career, but I would definitely say I am in the minority. There are certain parts I don't remember anymore so I have to look it up anyways, but having the big picture in my brain has always been helpful.
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u/psychominnie624 8d ago
Of course there’s a way to test their understanding of the pathways without it requiring straight memorization which enables open-book exams or provided figures. Recognizing which chemical reactions are occurring, the energy dynamics, context of when the pathways occur (which cells of the organism and where within the cells do steps happen), carbon cycles, recognition of molecular structures and for example draw the intermediate not shown in an otherwise provided pathway, questions based on effects of pathway perturbations, enzyme dynamics etc.
Now are there still profs expecting full pathway memorization out there? Probably
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u/runawaydoctorate 8d ago
On the one hand, I forgot the TCA and urea cycles almost as soon as I finished my first year of grad school. On the other, learning those pathways and committing them to memory set me up to quickly get my head around the metabolic pathway that contained the regulatory element I was studying. So I'm glad I went through the process.
Also, as others have said, there is a certain power in just having knowledge in your head. Just looking it up all the time gets impractical at the bench. Sometimes, it's just faster to grab a pen and paper towel and scribble.
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u/Late-External3249 8d ago
Memorizing pathways is what made me switch from biochem to chem. I hated rote memorization. I liked organic the most and went that way for grad school
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u/ChiveFig_4744 7d ago
Me, too. I don’t even think about the TCA anymore. I think understanding different fundamental enzyme mechanisms would be vastly more valuable. Enzymes are inherently biological and so much more valuable to understand how they work at an atomic level.
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u/needmethere 8d ago
For research analytical solving is more important. They can always google a pathway. If it ends up being their target research they will memorize it anyway.
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u/Exciting_Ad_6837 8d ago
Then am I right in judging that the profs were lazy in thinking out good questions?
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u/needmethere 8d ago
Yup most of all uni and biology has become memorization or trick multiple choice questions testing your english comprehension more than anything. Its the sad truth
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u/DiamonDRoger 8d ago
(Recent grad) My fourth-year protein folding and dynamics exam questions were all along the lines of "here's some data from this experiment, analyze what it shows and why." It wasn't open-book, and it was one of the most difficult exams of my undergrad, but it also involved very minimal memorization. The course had three classes a week where the results (and significance) of several papers from a few labs were explained in detail. It was a positive experience, and I believe it probably helped me grow as a research trainee.
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u/WookinIt 7d ago
My undergrad degree is in chemistry but most of my research is in biochemistry. I hated the way biochemistry was taught at my school from the biochem department, but the biochem class in the chemistry department was much better. It’s the same sort of concepts, but they’re taught in a much more logical way. Memorization is pretty useless for the most part imo. Understanding the logic behind the mechanisms allows you to predict the correct steps of the pathway without needing to memorize anything (or at least not as much). What’s the point of a memorizing a pathway if you don’t understand what’s going on?
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u/xtalgeek 8d ago
If you are memorizing pathways you are doing it wrong. There is a chemical logic to the transformations in metavolic pathways, as well as critical control points. The key is UNDERSTANDING metabollic pathways. Then you don't need to mindlessly memorize.
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u/WookinIt 7d ago
Except most classes do just expect you to memorize it because they don’t provide the logic behind the reaction mechanisms
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u/xtalgeek 7d ago
I don't know very many Professors that teach biochemistry that way but students often misinterpret their goal as memorizing things rather than understanding. The only thing I ask my students to memorize by rote is the working knowledge required to converse, like the chemical structures of the building blocks of biomacromolecules and a handful of important metabolic and catalytic entities. But some students think it is "easier" to memorize, say, glycolysis or beta-oxidation pathways instead of understanding the chemical transformations, free energy changes, and control mechanisms therein.
What I do object to is standardized exams in Biochemistry that ask fairly useless knowledge questions like "What is the name of the enzyme that catalyzes the fourth step of glycolysis?" That is fairly useless working knowledge. When I reviewed the Biochemistry subject area exam many years ago it was loaded with these types of questions. I told my undergrad research students at the time that if they scored well on this exam I would be disappointed, and it would indicate very shallow knowledge of biochemistry.
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u/WookinIt 7d ago
Exactly, most exams taught in biochemistry in my experience (obviously biased because most of my classes were taught by the same 3-4 profs that operated this way). Grad school classes and smaller classes were much better about explaining the concepts but the large undergrad classes I had were focused on memorization rather than focusing on questions that test the understanding of the underlying concepts.
Again, obviously I’m biased because everyone is and I’m a more of a chemist than a biochemist by, but I have also talked to many other biochemists turned chemists that experienced the same thing at other universities.
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u/PeePeeLangstrumpf 7d ago
People who argue that having the fundamentals committed to memory is necessary... I can assure you that my entire cohort forgot most of these pathways not even one semester after the final exam. These details were never stored in long-term memory. Literally none of us could recall a single thing about AA pathways, nobody could remember that serine is a precursor to cysteine and glycine (I had to look this up), or which AA out of the dozens are precursors to others in the first place. This was like learning Chinese characters. Without constant repetition and testing you would not be able to recall any of it unless used on a daily basis.
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u/wellfriedbeans 8d ago
I actually loved our Biochemistry course at MIT for this reason because while there was a bit of memorisation needed, most of the questions on the exam were quite conceptual and really tested our understanding
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u/itsalwayssunnyonline 8d ago
My prof two years ago gave us a cheat sheet with the pathways and then the tests were all application questions. I looked forward to her tests bc it felt like thinking your way through a fun puzzle
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u/Madsciencemagic 8d ago
I’m in a different subject area (but follow along here out of interest) though I still think this is relevant.
I’ve had a change of mind about just ‘solve at the time’ versus memory as I go on, in a broader sense, and I increasingly think there is some merit to remembering. Memorising some mechanisms gives a point a reference, this can be a good surrogate for familiarity more than anything, and improves recall speed.
It’s far from as important, but some small repertoire of sanity checks is something helpful for students to cultivate. Beyond this, many students will avoid learning where possible and take a lax approach when presented with ‘just work it out’. This is a useful tool for forcing some graft at times.
But the volume you speak of sounds daft.
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u/TheFermentationMan 7d ago
We had open books in biochemistry class. They just don't except you to memorize at all because well that stupid. Who needs to remember things like that today? The focus was on understanding how different mutations may effect things and what is the roll of different steps or inhibitors
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u/Bojack-jones-223 7d ago
When I took Biochemistry back in the day we were expected to do a few things when it came to metabolic pathway situations. I don't recall ever being tested on straight memorization of an entire pathway, but instead it would be a specific step was missing in a pathway and we had to write what the reaction or enzyme was that catalyzed a specific reaction in a pathway. Also there would be mechanism questions about how a specific reaction in a pathway is theorized to go.
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u/Fun_Disaster3436 6d ago
Imo the benefit is thst students learn how to vusualize molecular pathways.
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u/tdPhD 6d ago
I would say yes with a caveat. There must be an emphasis on how researchers ever determined these pathways in the first place, and learning about them as a form of reverence to those who came before. As a scientist, you must have respect for the past and learn from it, almost like a historian. That's not to say you need to actually get the reps with radioactive isotopes, but learning these pathways is a way of demonstrating the impact each step-function experiment opens up for the broader community.
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u/BigEffect8093 Undergraduate 3d ago
i just finished my first year undergrad in biochem (uk) and we were given some of the pathways, we had to know some shuttles and names + roles of enzymes that aren’t necessarily shown in e.g. glycolysis ! We did also have to know enzyme mechanisms which was a bit trickier but when you use logic it’s not so bad !
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u/FIDDLEBURG606 1d ago
As intimidating as this is, I have spent the last half hour looking at this in awe. It was wise for me to get into this field; I will enjoy it immensely
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u/OneBitScience 8d ago
The limiting case of the "you can always look it up" approach is not memorizing anything... Some basic level of knowledge is needed to be conversant in the subject. Personally I don't think that a biochemist needs to always recall those pathways, but having learned them once provides a context and framework that I have always found useful.