Best products from r/Biochemistry

I'm an MSc Biology student doing pharmaceutical bioprospecting (lots of chemistry, toxicology, pharmacology, molecular bio, and microbio). I have an SP3 and I LOVE it. It is hands down my favourite piece of tech that I have ever bought. It makes my life as a grad student 100x easier. Also, mine is an SP3 i7, 8gb RAM, 256 gb SSD HD (with a 128gb SD card to expand my memory).

First off, I put an STM DUX Rugged Fit SP3 case on my SP3. It makes me much more comfortable about carrying it with me all the time. It doesn't affect the fuctionality of the kickstand, keyboard, cameras, or buttons, and has cooling vents. Hands down best one I found.

I also bought a miniDisplayPort to DVI/HDMI/VGA adapter so I can plug my SP3 into any projector or screen. Very handy.
I also bought an Anker 3-Port USB Hub w/ Gigabit Ethernet Port so that I can use Ethernet cables if need-be, and also gives me 3 USB ports to use instead of one.

Now for software! As expected, I also run the typical Microsoft Office Suite (Office 365 University).


I use Microsoft OneNote for most of my dry lab notes and for roughing out protocols/experimental designs. Its amazing for having a lot of different data together in one place. I can intermix pictures/figures of my results (such as TLC plates, mass spec readings from LC-MS, cell viability assays from TC culture, flow cytometry graphs from expression analysis, etc etc) with hand-written or typed notes. It's great for planning out experiments and designing protocols too, as I can just screen grab and insert diagrams of 96 well plates, assay layouts, etc. It makes things much faster than writing it all out. I then just print out my protocols and keep them in a binder in the wet lab. I then reference those protocols in my wet lab hand-written book. I bring my SP3 into the wet lab on occasion, but not too often as I have to decontaminate it and I'm not a fan of getting it covered in ethanol.

The screen grab feature (double clicking the top of the pen, then selecting the area you want to "grab") is incredibly handy for quickly grabbing and inserting a figure or something from a publication into your notes. It's very well implemented.

For PDF reading, annotation, and analysis I use Drawboard PDF. You have to pay for it ($12 CAD I think it was?) but it's unbelievable. The user interface is amazing with the pen and touch input. I used to print out papers to read them but now I just read, highlight, and annotate them in Drawboard. Awesome program. You can also create PDF's in it which is nice. All in all it's a very full-featured program and worth the money.

I also run GraphPad Prism 6 with no issues whatsoever. The SP3 can handle it without breaking a sweat.

I run R Statistical Analysis and R Studio for my stats, again handles it no problem.

I also run WinMDI and FlowingSoftware (flow cytometry data analysis) and it runs those without even having the fan come on.

I have Zotero and EndNote X7, both of them run great and work very very well with all of the microsoft suite of programs.

Edit: I've also used BioEdit and MEGA6 for a bit of sequence editing, aligning, and BLASTing. Nothing too intense though. The only drawback is that doing sequence work on a small screen can get tedious. A nice 20"+ monitor is way easier.

I use it for teaching a lot too, as I can walk students through problems in either OneNote or Plumbago, then save my rough work and email it to them, post it to D2L, etc etc.

For a more performance-oriented comparison, I'll point out that I also heavily run Adobe Photoshop CS6, Adobe Lightroom 5, and Sony Vegas Pro 13 for my photography and video hobbies. It can run these programs flawlessly too. My other computer is a Dell Precision w/ Intel i7 vPro and my SP3 does very well in comparison to that beast. Obviously if you're doing something very intense for 4 hours the fan will be on and it'll get warm, but it has handled everything I've thrown at it so far.

Also, the battery life is pretty good. I can't complain. In an average day of in-lab work, attending seminars, and teaching with it, I can get 6-7 hours of battery life out of it. If I'm not multi-tasking as much I can get more than that, and if I'm working it really hard with high brightness I get 5ish hours. All in all pretty impressive for such a powerful little device though. It also charges pretty fast.

Edit: spelling.

I would go look on Amazon and buy a cheap, old edition of a biochemistry textbook (you can find one usually for <$25). You can even buy a used copy, who cares? In undergraduate I used Garrett & Grisham's "Biochemistry" and I loved it. That link has the book for $19 plus shipping - not a bad deal. That's the exact edition I used. Mark's "Basic Medical Biochemistry: A Clinical Approach" is a good book, but I do not think it is appropriate for undergraduate classes.

It is true that you do not need biology courses to take a biochemistry course. However, if you are not willing to peruse a biochemistry book, you then NEED to read the first few chapters of a general biology textbook. The material is not impossible to comprehend without a background, but you'll be wasting your time learning super simple biology concepts like "what is a protein" rather than focusing on the intricacies that you will be tested on.


As for your classes below, I've taken them all except "Biometry" (do you mean Biostatistics?), so I'll add a quick word.

• Molecular and Cellular Biology: You will need General Biology, and you should first take Genetics if possible. Biochemistry will help a little bit. This will probably be the hardest class of all of these.
  
• Plant Biology: Probably the easiest of all of these. You will need General Biology, and probably nothing else.
  
• Genetics: You will need General Biology. It will be a hard class, but it is certainly manageable, and can even be fun.
  
• Microbiology: You will need General Biology and probably Genetics. This is a great course.
  
• Animal Diversity: You will probably need General Biology. That's it.
  
  Again, it's not that you will absolutely fail if you do not first learn some basic biological concepts. The point is that you will spend too much time learning basic concepts during the semester that you will run out of time to study the big broad concepts. For example, you cannot understand bacteriophage-mediated transduction (microbiology topic) if you do not understand anything about DNA or a cell membrane. Also, most of these classes are not even remotely math-intensive, so do not worry about it. At my school, none of these courses required anything passed Calculus 1.
  
  
  Let us know what you decide to do!
  

Advanced Nutrition and Human Metabolism by Gropper is the book my university classes on nutritional biochemistry used. Difficult to comprehend for the lay person but great for those with a decent background in organic and biochemistry. I notice it is uber expensive on this link from Amazon but look up and get an old edition or even look around for a PDF or something.

http://www.amazon.com/Advanced-Nutrition-Metabolism-Sareen-Gropper/dp/1133104053

Also, pages like this may be of interest.

https://ods.od.nih.gov/factsheets/VitaminK-HealthProfessional/

Lastly, I believe you can find and read the Dietary Reference Intakes as PDF online but that doesn't focus too much on biochemistry.

Good luck and hope that helps!

• This website for some software that I use (Scaffold by Proteome Software) has some good information about proteomics.
  
  
• Also, the website for the American Society for Mass Spectrometry has some good information about mass spectrometers. Start with the video about Mass Analyzers (if you are new to mass spec, the other videos might be a bit over your head).
  
  
• This article is a bit dated but it's still pretty good if your school has access to the article:
  > Dunn, Warwick B. "Mass spectrometry in systems biology an introduction." Methods Enzymol 500 (2011): 15-35.
  
  
• This book (especially the first chapter) does a pretty good job of helping bridge mass spec concepts concepts with biology
  
  
  

Here are some resources/tips that I've found helpful in my time working in a crystallography lab.

• Crystallography made Crystal Clear - good overview https://www.amazon.com/Crystallography-Made-Crystal-Clear-Macromolecular/dp/0125870736/ref=sr_1_1?ie=UTF8&qid=1536938710&sr=8-1&keywords=Crystallography+made+crystal+clear
  
• Tererese Bergfors website: http://xray.bmc.uu.se/terese/tutorials.html Good tutorials
  
• Look for Studier 2002- his formulations for Auto-induction media. Of interest is the formulation for PASM-5052 should you need to do experimental phasing via Selenomet labeling. As a side note, always look up the percent sequence identity of your protein to its homologs in the PDB. If its below 40%, definitely plan to do experimental phasing. Even at that, some labs have started hopping straight to expressing and crystallizing Selenomethionine labeled protein and collecting on the selenium edge from the get-go so that they hedge their bets on phasing. If doing experimental phasing, always collect until your crystal is dead dead dead.
  
• Most common issue with crystallization in my experience is a sample prep issue. This paper was very helpful to me when troubleshooting protein prep quality issues. http://dx.doi.org/10.1016/j.febslet.2013.10.044 One of my proteins was aggregating on the hours-days timescale. Don't neglect the utility of SEC, even if you see a single band on an SDS gel, you may have a mixture of oligomeric states which can only be detected by looking at the chromatogram from an SEC run.
  
• Look at the drops that do crystallize, then look at the neighbors in the same tray that don't have crystals. These observations can make it easier to figure out when you're close to the right crystallization conditions.
  
• High purity reagents- It's 2 O'clock in the morning, what is the purity of your Tween 20? 40%....40 fucking %. This is from Sigma aldrich, not some po dunk little chemical firm. Document your manufacturer if you need to use a detergent or reagent with purity this low. Regardless, document your fucking manufacturers of your reagents. One of the grad students in my lab was using TCEP and even though the purity was fairly high, a change of manufacturer stopped his protein from crystallizing. We also had a similar incident with a syringe filter manufacturer change.
  
• Submit samples for High-throughput screening at multiple concentrations, also recommended is to document the buffer your protein is in and try multiple different buffers so long as you get a clean chromatogram from SEC. Sometimes one buffer system works better than another for getting good quality crystals.
  
• Generally if possible, avoid glycerol. If your protein is having aggregation issues due to hydrophobic interactions, use a high-purity detergent like CHAPS, or n-Octyl-β-D-Glucopyranoside, or even sometimes an organic solvent like DMSO or isopropanol. All of the above mentioned compounds are the most cost-effective in my experience.
  
• Don't neglect the role of ligands. Sometimes you need to add a ligand or product to lock down the conformation.
  
• Don't neglect activity assays to make sure your sample preps are producing active protein.
  
• Don't count on an NMR structure to phase a crystal structure. I made this mistake, same protein, identical sequence, unable to phase with molecular replacement. I ultimately had to do a SAD experiment to phase.
  
• If your protein is badly behaved, you can try to rescue it with a maltose binding protein tag or a SUMO tag, etc. Sometimes they're helpful.
  
• DNA-binding proteins are often unstable in low salt when not bound to their target DNA sequence. Try binding the protein to its target DNA sequence then buffer exchanging into a low salt buffer.
  
• Seeding can sometimes be helpful.
  
• Make sure your sample purity is very high, the higher the better. Heterogeneity will fuck you on diffraction.
  
• Don't judge a book by its cover. Some crystals are ugly and diffract beautifully, others look beautiful and diffract terribly. I had these beautiful hexagonal crystals- no diffraction. In contrast, I had these plates that I expected nothing of that diffracted out to 1.7Angstroms.
  
• Common issue that can stop you from phasing is processing in the incorrect space group.
  
• Don't bother with HKL-2000 or HKL-3000. I strongly prefer XDS for data processing as it doesn't fail silently. There was a crystal dataset I was working on that had strong space group ambiguity and HKL-2k just wouldn't process it. XDS gave me enough feedback I was able to correctly diagnose and correct the issue. XDS is command line based but it gives you a lot more control and feedback.
  
• Get cozy with Phenix and Coot.
  
  I hope this helps. Let me know if you have any questions.

Interesting:

Life on the Edge: The Coming age of Quantum Biology by Jim Al-Khalili
Great, easy read on a fascinating topic of quantum biology; topics from animal migrations and photosynthesis elegantly discussed.

The Viral Storm: The Dawn of a New Pandemic
by Nathan D. Wolfe
Seat-of your pants virology that explores the coming viral pandemic. Great reading in view of the Ebola crisis in West Africa.

Life's Greatest Secret: The Race to Crack the Genetic Code by Matthew Cobb

Lilting historical re-telling of a well-worn story of the discovery of DNA, the genetic code, and the winners and losers of the race.

Useful:

Bioenergetics Paperback – by David G. Nicholls

The go-to text on Bioenergetics, useful for every aspect of biochemistry in my humble opinion.

Based on your post, I think you need more knowledge of biology and chemistry before you can really approach pharmacology. Gotta walk before you can run, if you will. But you're taking organic this year and hopefully biochem and a biology class next year so that will come with time.

If you're really excited about PK though, check out this youtube primer on the subject (~30min total). I also suggest checking out Derek Lowe's blog (/u/dblowe) In the Pipeline. There are over a decade of posts and especially since it's become associated with Science Translational Medicine, he does a great job introducing topics for those not directly in the field. He's made 73 posts tagged PK, and it may also give you insight about what your future career will be like and controversies in medicinal chemistry.

My undergrad med chem professor sadly passed away shortly before the course began, so I bought Richard Silverman's "The Organic Chemistry of Drug Design and Drug Action." Amazon has the 2nd edition (the one I have) for $13 and you may enjoy flipping through it when you take organic. However, it's a pretty advanced book (probably for folks who have already taken a med chem class) so you can also consider the legend EJ Corey's short book "Molecules and Medicine" or Patrick (the standard med chem textbook) if you want to see medicinal applications of organic while you take the course.

My favorite science-related leisure reading is Derek Lowe's blog In The Pipeline. He covers new developments in chemistry/biology, the drug discovery industry, and occasionally some other stuff. He writes it in a way would be interesting to anyone that like chemistry and biology regardless of their level of education. I always look forward to reading it over lunch.

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If you are looking for a book, The Disappearing Spoon is a great set of true short stories about chemistry that is a really fun read.

I have pretty limited experience with more advanced enzyme kinetics, but the scenario you described seems pretty straightforward and I imagine it would be covered in pretty much any book on the subject. I've used Cornish-Bowden's Fundamentals of Enzyme Kinetics as a reference before and found it to be well written and clear. I know Segel is kind of an encyclopedia of enzyme kinetics and is certain to have the formulas you need, though might not be best as a text to actually learn the subject properly.

Crystallography Made Crystal Clear is a fantastic resource for learning the theory behind protein crystallography and structure solution. I used it to learn when I was starting out and I still consult it at times.

Crystallography Made Crystal Clear: A Guide for Users of Macromolecular Models (Complementary Science) https://www.amazon.com/dp/0125870736/ref=cm_sw_r_cp_api_Rp9MBb4PTEANT

Good luck!


Beyond this, I’ll add that there’s really no substitute for doing this hands on and learning from other students/postdocs in the lab. Crystallization feels like black magic a lot of the time, so the theory only gets you so far. Most of the learning really happens as you go along.

I took a chemical and synthetic biology class last semester, we used a textbook called The Organic Chemistry of Biological Pathways. It was pretty good but I feel like it relied on you having a pretty good organic background.

I agree with those mentioning to take a notebook. This is the one I use in my research.
Observe and listen. then ask. Write everything down.
Your homework for the first few days will be to google anything (technique, equipment, concepts, jargon etc.) that comes up you're not familiar with.
What a great opportunity, have fun!
http://www.amazon.com/gp/product/B00007LV4B?ref_=oh_aui_detailpage_o00_s00&redirect=true&psc=1&pldnSite=1

What is Life? By Erwin Shrodinger is a beautiful little book that was based on a series of public lectures given at the Dublin Institute for Advance Studies. It's only about 200 pages but it is full of great science and thinking. One of my favorites.

The Epigenetics Revolution. A book about genetics and molecular bio, rather than biochemistry, but this is a pretty good book.

You don't exactly sound like a complete layman though, so I say there's nothing wrong with picking up a textbook like Stryer and seeing which topics interest you!

In addition to Crystallography Made Crystal Clear, Biomolecular Crystallography by Bernhard Rupp is an excellent resource for new crystallographers: https://www.amazon.com/Biomolecular-Crystallography-Principles-Application-Structural/dp/0815340818/

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Also see this JoVE Article on which I am an author: https://www.jove.com/video/4225/multi-target-parallel-processing-approach-for-gene-to-structure

Goes through construct design, expression screening, large scale expression, purification, crystallization, data collection and structure solution.

If you have an organic chemistry and biochemistry understanding, I'd highly recommend Molecules and Medicine. It's a really interesting read about different drug molecules, the history of their discovery, their mechanism of action, and a bit about the diseases they treat. We used it for my Biology & Chemistry of Medicine course, but I ended up reading the whole book because of how interesting it was!

'power sex and suicide' by Nick Lane. Great book on the importance of mitochondria.

Statistical physics of biomolecules of Zuckeman is a good book. Also Ken Dill's Molecular Driving Forces is more thermodynamics. Both books are quite good.

Power Sex Suicide: Mitochondria and the meaning of life by Nick Lane is a good pick. It isn't entirely biochemistry, but does delve into the electron transport chain and metabolism. It is also packed with interesting stuff.