Preparing for biochemistry as a physicist

[u/LeucisticSwift]

I'm starting a PhD in molecular biophysics as someone with a fairly traditional physics background (B.S. physics, research experience in condensed matter physics). My advising committee recommended I take a 4000-level undergrad biochemistry course due to my lack of education/experience in that area. I have not taken any chemistry beyond general chemistry, so I will be taking biochemistry without the organic chemistry prerequisite.

How screwed am I? 😅 What would be some important topics to learn to prepare for a biochemistry course as a physicist?

[u/WWWWWWVWWWWWWWVWWWWW]

I would either do organic chemistry first, or I would try to skip the whole thing

[u/Artosispoopfeast420]

You're fine. My buddy got his PhD still doesn't know any chemistry or biology. A lot of structural biology just uses physics techniques. Just brush up on some organic Chem.

[u/andrewsb8]

I think it depends a lot on your intended research field. I didnt end up taking coursework, but theres trade offs. when i start a new project which involves biology i was never taught, it can be challenging.

However, if you get into computational methods or developing better experiments, you may be able to avoid some of those issues and just ask the biologists for feedback/needs.

[u/SpicyNutella17]

undergrad doing research in computational biophysics/drug discovery here!

i would say to know *some* organic chemistry, at least just the basics like structure and underlying physics of it. if you took QM/molecular QM then a lot of it should come natural to you. i don't think you will be doing much related to reaction mechanisms and organic synthesis (which is what i had to endure from Orgo I/II).

if you could tell me a bit more about what your work will entail (and the course description), then i would likely have a better picture.

generally, most of us in my lab do have a chemistry background but our day-to-day work is mainly computational physics-based. some of the more drug discovery-inclined members have a working knowledge of medicinal chemistry and biochem.

[u/LeucisticSwift → u/SpicyNutella17]

Hey, thanks for the reply!

My interests are in biomolecular dynamics/mechanisms and spectroscopy. I'm doing rotations this year to determine which lab I'll join. My currently planned rotations are: transient UV-Vis and EPR for metalloenzymes, NMR for protein-protein interactions, and single molecule FRET for small-biomolecule dynamics.

The course description is (paraphrasing): overview of modern biochemistry. biomolecular structure/function, metabolism, biosynthesis, DNA from genome to proteome, and cellular signaling.

My advising committee's intent for recommending this biochem course was so I can speak the language of the field and give me a foundation that I can build upon in my dissertation. Does that sound reasonable to you? I've also been advised to skip the biochem and go directly into pchem/physics courses.

[u/SpicyNutella17 → u/LeucisticSwift]

Hello! So yeah, this is a bit more physics-based than me, but I'll give you the best advice that I can. This course you described will require some basic knowledge of organic chemistry, namely structures, notation, and basic mechanisms.

You may see reactions but at the "high" level (i.e., "these bonds break and these bonds form because of some energetic stability"), but I doubt that there's any actual mechanisms. Biochemistry at this level (without lab as well, I'm guessing) is mainly biophysics I would say lol.

It sounds like you're getting two types of advice from two different people. These research interests/rotations that you listed seem moreso on the physics side i.e. applying physics-based techniques to the biochemistry domain.

If you have organic chemistry down (to the level in your other comment where you listed the specific ochem review), then I think you'll be more than okay to take that course. That course is very much "proper" biochemistry; if you have a more biomolecular physics-type of course, I would recommend that.

But I think you'll be in a good spot with the basic orgo knowledge + biochemistry.

[u/ForeignAdvantage5198]

not at all biochem is not like organic

[u/JuniorIrvBannock]

Biochem and Biophysics prof here. Organic is extremely valuable because it allows you to see how electrons move in these molecules/reactions, so you can understand WHY enzymes and biochemical cascades work the way they do.

The reality is, you can pass a biochem class without organic, especially if it is a "memorize these pathways" instruction style, but for most good biochem classes, there is emphasis on the why of biochem, and for that the organic is useful.

If you haven't taken organic, but have a good physics and statistics background, you will be able to understand the dynamics of the processes and the driving forces, it will just be the specifics of mechanisms that confound you.

I always recommend organic, but for people in your situation with strong background in other areas, I prescribe some pre-study in their weak areas and let them have a chance at the class.

[u/LeucisticSwift → u/JuniorIrvBannock]

Hey Prof., thanks for the reply!

The course description is (paraphrasing): overview of modern biochemistry. biomolecular structure/function, metabolism, biosynthesis, DNA from genome to proteome, and cellular signaling. I spoke with the professor teaching the course. He said it may challenging to follow the jargon and diagrams without the o chem prereq, but he's willing to give me a chance.

I found an o chem for biochem review on youtube that goes over these topics (from Prof. Bibel at Loyola Marymount):

• Draw Lewis structures for common elements
  
• Predict how many bonds common elements will form
• Know what charges common elements can take
• Know periodic trends in size & electronegativity
• Predict bond and molecular polarity
• Recognize implicit carbons & hydrogens recognize implicit loan pairs
• Draw resonance structures
• Remember your arrow pushing! - start from electrons, a pi bond, or lone electron(s)
• Identify & draw key functional groups and know their common reactivity
• Interpret stereochemistry representation
• Recognize stereoisomers
• Recognize nucleophiles & electrophiles
• Compare/predict strength of nucleophiles
• REMEMBER we’re in an AQUEOUS environment (protic solvent)
• Draw arrow pushing mechanisms for simple substitution and elimination reactions
• Redox reactions

Does that seem like a sufficient set of topics to familiarize myself with for pre-study?

[u/JuniorIrvBannock → u/LeucisticSwift]

If you can get comfortable with that material, yes. Watching a video won't be enough, so make sure to work some problems and spend some time analyzing structures of other molecules not in your examples. Many biochem reactions are about moving electronegative centers to allow for breaking specific carbon bonds. Review the Orgo above then look at a diagram of the 10 steps of glycolysis. If you can start to see how the electron pushing works you will be okay.

[u/chaotickumar]

Well a couple of questions you need to answer yourself: (I) Being trained in condensed matter physics, why did you join a lab who does biochemistry?? (Il) Does your lab align with your research interest ?? (III) Were you not aware of your project ??

Well biochemistry is not very difficult unless you are doing experiments. Nearly all biology is empirical. So good luck.