Why no mechanisms in Biochem?

[Trayshawn]

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Whatever happened to arrow pushing in biochemistry?? Mechanisms are more intuitive, they describe what the electrons do and why.

I actually remember asking my biochem TA last year about a possible mechanism for some rxn and she said "forget about mechanisms, there are none in biochem" as if electrons just magically stop moving with a purpose because they react in the body. Is there some reason for the aversion to this approach?

Most biochem books explain reactions in a "just because" kinda way and encourage learning them in the very way we were taught not to in orgo - by rote memorization. This removes all the intuition behind it. Funny thing is that, for many of these reactions, it isn't very hard to use the more intuitive orgo way of analyzing the reactions. [Seeing why one nucleophile attacks instead of the other, or why such and such is unstable, why a particular carbon is attacked, etc]. I feel like using mechanisms would develop an intuitive way of figuring out the intermediates in many metabolic reactions without remembering what page blabla said. Back in orgo, this approach often equipped you to answer questions a few chapters ahead before having even read them.


I guess I should just take a bioorganic chem class and shutup lol.

 

[Charles Darwin]

You mustn't be taking a rigorous upper-level biochemistry course then. Or maybe your book sucks. Or both, I don't know. Besides, you should be able to intuit the mechanism yourself if you already know what's happening in the reaction.

 

[CuttingCorneas]

Your knowledge of organic chemistry should prepare you for the movement of electrons. Just because the books seem to encourage memorization doesn't mean that's all there is to it. Think of it this way: organic chemistry books are written for dummies who haven't yet grasped the concept of electron movement. By biochem, you should know and understand the basics enough to not need the arrow diagrams explicitly written out.

If you really want to challenge yourself, by all means, think about arrow diagrams and how they fit in to each reaction. Honestly, it doesn't matter in the long run. You're going for end products.

 

[Praefectus]

It's more important to see the reaction on a macro scale.

 

[Textbookversion]

The funny part is med school biochem = zero reaction mechanisms/arrow pushing/anything like undergrad biochem.

It's all memorizing pathways.

 

[angemon89]

I remember learning the mechanisms of trypsin and chymotrypsin in my class. Easy points on the exam.

 

[Arbor Vitae]

Whatever happened to arrow pushing in biochemistry?? Mechanisms are more intuitive, they describe what the electrons do and why.

I actually remember asking my biochem TA last year about a possible mechanism for some rxn and she said "forget about mechanisms, there are none in biochem" as if electrons just magically stop moving with a purpose because they react in the body. Is there some reason for the aversion to this approach?

Most biochem books explain reactions in a "just because" kinda way and encourage learning them in the very way we were taught not to in orgo - by rote memorization. This removes all the intuition behind it. Funny thing is that, for many of these reactions, it isn't very hard to use the more intuitive orgo way of analyzing the reactions. [Seeing why one nucleophile attacks instead of the other, or why such and such is unstable, why a particular carbon is attacked, etc]. I feel like using mechanisms would develop an intuitive way of figuring out the intermediates in many metabolic reactions without remembering what page blabla said. Back in orgo, this approach often equipped you to answer questions a few chapters ahead before having even read them.


I guess I should just take a bioorganic chem class and shutup lol.

The dynamics of proteins in solution are way too complex to map out with simple arrow pushing.

 

[weezynation]

The funny part is med school biochem = zero reaction mechanisms/arrow pushing/anything like undergrad biochem.

It's all memorizing pathways.

+1. Med school biochem could care less about arrow pushing. Maybe that's important for a PhD in biochem but for medicine it isn't important.

 

[NeuroLAX]

The funny part is med school biochem = zero reaction mechanisms/arrow pushing/anything like undergrad biochem.

It's all memorizing pathways.

I remember there being a few mechanisms in my medical biochem class this past semester. It certainly wasn't emphasized overall by any stretch of the imagination. We discussed interactions of certain drugs with proteins, which is fairly important regarding the mechanism of action of the drugs like methotrexate and fluorouracil.

There were definitely no arrows or electron tracking mechanisms.

 

[487806]

The funny part is med school biochem = zero reaction mechanisms/arrow pushing/anything like undergrad biochem.

It's all memorizing pathways.

Oddly, my undergrad biochem has nothing to do with mechanisms... but knowing pathways is crucial, not the mechanisms. Mechanisms weren't even focused that much in my organic chem class, except for common substitutions/elimination/additions. After that, it's all about knowing the reactions.

 

[Textbookversion]

I remember there being a few mechanisms in my medical biochem class this past semester. It certainly wasn't emphasized overall by any stretch of the imagination. We discussed interactions of certain drugs with proteins, which is fairly important regarding the mechanism of action of the drugs like methotrexate and fluorouracil.

There were definitely no arrows or electron tracking mechanisms.

To be fair it depends on the school, technically those phd wankers can teach whatever they want.

 

[NeuroLAX]

To be fair it depends on the school, technically those phd wankers can teach whatever they want.

Lol this is true. For better or for worse.

 

[cheesier]

So many of those reactions are 20 steps with huge molecules. 1 reaction would be your whole test.

 

[EnergyDrink]

As stated, you should be able to follow reactions on your own, since organic chemistry should be a pre-requisite.

 

[Drrrrrr. Celty]

Oddly, my undergrad biochem has nothing to do with mechanisms... but knowing pathways is crucial, not the mechanisms. Mechanisms weren't even focused that much in my organic chem class, except for common substitutions/elimination/additions. After that, it's all about knowing the reactions.

You didn't do mechanisms in organic chemistry? That sounds kinda chill.

 

[487806]

You didn't do mechanisms in organic chemistry? That sounds kinda chill.

Except for SN1/SN2/E1/E2/Markovnikov/EAS/acyl. I think when we did epoxidation and Diels-Alder sections, we stopped doing the mechanisms, because it was too confusing.

 

[dudeliness]

Except for SN1/SN2/E1/E2/Markovnikov/EAS/acyl. I think when we did epoxidation and Diels-Alder sections, we stopped doing the mechanisms, because it was too confusing.

The Diels-Alder rxns were some of my favorite ones to draw out. Those and radicals. Ah, I almost miss the joys of synthesis problems....almost.

 

[487806]

The Diels-Alder rxns were some of my favorite ones to draw out. Those and radicals. Ah, I almost miss the joys of synthesis problems....almost.

Meh. Synthesis is a pain, since it requires good knowledge of all possible reactions while working backwards. Very difficult for complicated compounds. I like radical reactions. Problem with diels-alder is drawing bicyclic compounds.

 

[NeuroLAX]

Meh. Synthesis is a pain, since it requires good knowledge of all possible reactions while working backwards. Very difficult for complicated compounds. I like radical reactions. Problem with diels-alder is drawing bicyclic compounds.

Synthesis was my favorite part of organic! For extra credit on exams my professor would give us the structure of a common drug and ask us to list the possible methods of synthesis for certain parts.

 

[487806]

Synthesis was my favorite part of organic! For extra credit on exams my professor would give us the structure of a common drug and ask us to list the possible methods of synthesis for certain parts.

I'll take that 😛. Guess I'm at the odds. The MIT website has a list of really complicated synthesis problems for undergrad orgo... I think that contributed to my fear 😱 (good thing I'm not at MIT)

 

[dudeliness]

Synthesis was my favorite part of organic! For extra credit on exams my professor would give us the structure of a common drug and ask us to list the possible methods of synthesis for certain parts.

Large portions of our entire exam was synthesis. I thought it was a fun challenge. Like a puzzle. Wicked hard though.

 

[Bangersandmash]

My biochem class had a book that explained the mechanisms of the pathways, but my professors did not emphasize them and detailed specifics of the mechanism were not required for exams, just the overall pathway.

I really don't see why you want to learn/memorize the detailed mechanism on top of the intermediates and the enzymes used. That would make an already difficult subject infinitely more difficult. For the purposes of basic biochemistry, why do we really care that Lysine or Histine residues are responsible for attacking the oxygen or carbon of a specific intermediate to stabilize it? That's more important for drug developers and biochemists researching how to alter a pathway or develop a chemical to inhibit it.

 

[dudeliness]

My biochem class had a book that explained the mechanisms of the pathways, but my professors did not emphasize them and detailed specifics of the mechanism were not required for exams, just the overall pathway.

I really don't see why you want to learn/memorize the detailed mechanism on top of the intermediates and the enzymes used. That would make an already difficult subject infinitely more difficult. For the purposes of basic biochemistry, why do we really care that Lysine or Histine residues are responsible for attacking the oxygen or carbon of a specific intermediate to stabilize it? That's more important for drug developers and biochemists researching how to alter a pathway or develop a chemical to inhibit it.

I agree with this.

My undergrad biochem class was in a summer block, so very condensed. Plus, our teacher who was a phd biochemist, believed in teaching about the forest instead of the trees, meaning teaching overarching concepts and principles instead of memorizing every little detail. It worked well for me, and I felt like I had a pretty good grasp on metabolic pathways by the end of the class. Granted, I couldn't tell you the specific pathway each enzyme in any metabolic pathway would follow, and I didn't have most of the enzymes memorized. I did know all the steps in each pathway, what goes into certain steps and what comes out, and what these pathways mean towards maintaining homeostasis.

 

[coyotelime]

I don't know why mechanisms aren't a big part of biochemistry, but looking back (just took it this semester) I couldn't imagine memorizing how each intermediate in metabolic pathways got to the next. Memorizing pathways plus stimulators/inhibitors and all the other stuff was time consuming and mentally taxing enough.

 

[Trayshawn]

From what I got, the main answer is "why memorize mechanisms in addition to all the other work?"

thats just it though, you DONT memorize mechanisms - that defeats the whole purpose. They should (theoretically) actually REDUCE the workload since you don't need to memorize all the intermediates in a pathway. You could always just figure them out with a little reasoning. This reduces workload by reducing memorization. And in the end, you finish the course much more satisfied since that reasoning will stay with you far longer than anything gained by rote memorization.

just like orgo.

 

[phunky]

My school offers two different Biochemistry series: one in the Chemistry department and one in Molecular Biology. The chemistry version is much more rigorous and mechanism based, while the biology version is more about how those reactions apply to biology (which sounds more like your school's course).

 

[roboflytrap]

The Diels-Alder rxns were some of my favorite ones to draw out. Those and radicals. Ah, I almost miss the joys of synthesis problems....almost.

Synthesis problems. 😍
Definitely found myself missing every aspect of organic during P-chem...

 

[Pattycake25]

Based on another thread from today, I guess JHU undergrad's approach in this was relatively uncommon, but when I was there Biochem was a bio department course that was wholly independent of Orgo. Since the nitty-gritty of the mechanisms is what Orgo is all about, emphasizing them in entry-level Biochem serves only to restrict who can take the course. There's always upper-level Biochem, as well as simply figuring out the mechanisms for yourself. Sounds like your TA is a little lazy.

Whatever happened to arrow pushing in biochemistry?? Mechanisms are more intuitive, they describe what the electrons do and why.

I actually remember asking my biochem TA last year about a possible mechanism for some rxn and she said "forget about mechanisms, there are none in biochem" as if electrons just magically stop moving with a purpose because they react in the body. Is there some reason for the aversion to this approach?

Most biochem books explain reactions in a "just because" kinda way and encourage learning them in the very way we were taught not to in orgo - by rote memorization. This removes all the intuition behind it. Funny thing is that, for many of these reactions, it isn't very hard to use the more intuitive orgo way of analyzing the reactions. [Seeing why one nucleophile attacks instead of the other, or why such and such is unstable, why a particular carbon is attacked, etc]. I feel like using mechanisms would develop an intuitive way of figuring out the intermediates in many metabolic reactions without remembering what page blabla said. Back in orgo, this approach often equipped you to answer questions a few chapters ahead before having even read them.


I guess I should just take a bioorganic chem class and shutup lol.

 

[dudeliness]

Synthesis problems. 😍
Definitely found myself missing every aspect of organic during P-chem...

Glad I didn't take p-chem. Or analytical chemistry either, although that was the last class I needed for a chemistry minor to go along with my Spanish major. Lol

 

[SilverCat]

What do you mean, there's no arrow pushing in Biochem?! I just took a whole semester of Biochem, and all we did was memorize the mechanisms of glycolysis, TCA, gluconeogenesis, fatty acid degradation, glycogenesis, ETC, etc. How I kept sane, I have no clue. Are you telling me all this won't help me in med school?!

 

[487806]

What do you mean, there's no arrow pushing in Biochem?! I just took a whole semester of Biochem, and all we did was memorize the mechanisms of glycolysis, TCA, gluconeogenesis, fatty acid degradation, glycogenesis, ETC, etc. How I kept sane, I have no clue. Are you telling me all this won't help me in med school?!

Simply put, knowing the steps in a pathway is the key. Memorizing mechanisms = waste of time and effort (unless colleges require it)

 

[Trayshawn]

Simply put, knowing the steps in a pathway is the key. Memorizing mechanisms = waste of time and effort (unless colleges require it)

Agreed, knowing intermediates is what you should really walk away with. But my point is that knowing the mechanisms make remembering those intermediates much easier, no? You should even be able to predict them as opposed to just remembering if you wanted.

 

[GadRads]

The funny part is med school biochem = zero reaction mechanisms/arrow pushing/anything like undergrad biochem.

It's all memorizing pathways.

Word.

OP, take a course in bio-organic mechanisms. I took a course like that in grad school. It was hardcore organic chemistry in biology. It was a lot of memorization AND electron pushing, but the exams required applications to new scenarios and experimental design so you couldn't just memorize your way to passing.

 

[487806]

Agreed, knowing intermediates is what you should really walk away with. But my point is that mechanisms make remembering those intermediates much easier, no?

meh, that's subjective. i found it harder because it requires me to know how each reaction takes place. that's good for few small pathways, but more complicated ones...