I’ve been home for a couple of weeks for the holidays – and it’s been great seeing family – but I also miss the lab. Instead of dreaming of sugar plum fairies I’ve been dreaming about some of this lab equipment I’m headed back to (many a time I’ve woken up to realize I was just dreaming and hadn’t really just done the experiment I thought I had). If you spend lots of time in the lab, it becomes like your second home. But most people have (sadly) never been in a biochemistry lab & our “furniture” & “appliances” may seem foreign, so this post will be a “glossary” of some equipment we use
This GLASSWARE’s really cool, I swear! Instead of vases and jars, biochemists use Erlenmeyer flasks and Pyrex bottles (in lots of different sizes). Here’s a look into our glassware cabinets.
Erlenmeyer flasks are a classic go-to “science icon” – they’re wider at the bottom & narrower at the top, which makes them good for swirling liquids & their narrow top helps prevent gas escape (especially if you put in a stopper!) Our normal beakers don’t have a skinny top – they’re more like glass tumblers – But they do usually have a lip to help you pour & wide top makes them easier to get in & out of. We use beakers for preparing solutions or temporarily holding them. If we want to store liquids longer-term, we usually put them in Pyrex bottles. These are made of a very strong glass that can withstand the super hot temperatures & pressure of our autoclave (like a dishwasher but much much hotter)
Flasks, beakers, & bottles all have measurement lines, but they’re more of “estimates.” If you want accurate measurements you’ll need to go elsewhere & that elsewhere depends on how much you need to measure & how accurate you need to be (does your 50mL really need to be exactly 50mL or is 50.5mL ok?
So what are the biochemist’s “measuring cups”? When you want to measure ~50mL – 2L reasonably accurately, the graduated cylinders are your friends. Graduated cylinders are similar to the beakers except they’re skinnier and have more measurement lines (graduations) (being narrower allows these lines to be more spread out). For our purposes, graduated cylinders are usually plenty accurate for these larger volumes (when you have larger volumes, slight measurement error is “diluted out” like a drop in a pool) but there are more accurate types of glassware – volumetric flasks are very accurate, but each is accurate for 1 specific volume – each size has a “fill to” line for that 1 volume. And this fill to line is on the long skinny neck where you get a nice meniscus you can clearly see the bottom of (the meniscus is the smiley shape that liquid takes when it starts crawling up the sides of the container & you want to measure from the bottom of it). They’re more accurate than a graduated cylinder but less multi-functional.
We’re mostly concerned about accuracy when measuring smaller volumes and for that, we use pipettes. Getting from tube A to tube B (the Biochemistry Transit System) by transferring liquid from one place to another is probably ~70% of what my lab life entails, so it’s about time we talk about Picking Pipettes
A pipette is a piece of lab equipment that you use to draw up and dispense liquid. They come in many sizes and types. The “classic” Pasteur pipette is basically as simple as pipettes get – glass tubes w/a narrowed tip – you attach a rubber bulb to the top & squeeze it to create suction to suck up liquid (people used to do this with their mouth – DON’T!) I don’t use Pasteur pipettes often because you can’t measure with them, but they’re good for adding liquid drop by drop, like when you’re trying to adjust the pH of a solution & have to add drops of acid or base until it settles on the pH you want. We also have plastic transfer pipettes (“eyedroppers”) that are similar to the Pasteur pipettes but they’re plastic and all-in-one (no bulb required)
If I want to transfer volumes ranging from ~2mL-25mL, I use serological pipettes. These pipettes have measurement lines so you can move around measured volumes of liquid. You can use rubber bulbs (bigger ones) with serological pipettes, but (thankfully) we have electric “Pipet-Aids” to help. The top button draws up fluid and the bottom button releases it. The Pipet-Aid is powerful, so thankfully these serological pipettes have cotton plugs to prevent you from drawing up liquid too far and damaging the Pipet-Aid.
For transferring volumes 1mL or less, we use micropipettes. These are probably our most-used pieces of equipment. They come in multiple volume ranges. When possible, you want to choose a range the volume you want is in the middle of, as that’s where it’s most accurate.
We refer to these micropipettes in terms of the largest volume they can transfer – for example, a “P20” is a pipette which can transfer volumes from 2-20µL“P20” is a pipette which can transfer volumes from 2-20µL (a microliter (µL) is 1000X smaller than a mL). To use a micropipette, you push down the top button, place the pipette in liquid then release the button. Then move it to where you want it and push back down to dispense. Once you’re done, you push the ejection lever to eject the tip into a waste container (old salts containers work great – and I got really excited when, in the early days of my PhD work, we finally finished a good one…)
Speaking of tips, different size micropipettes use different size tips. We buy them in “racks” that we refill our tip boxes with (so much more convenient than filling them one tip at a time like I did in undergrad). We also have filter tips that we use when we’re pipetting sensitive samples (like RNA) to prevent the pipette from dirty-ing the sample, or radioactive samples – to prevent the sample from dirty-ing the pipette. Pipetting the same volume over and over can be hard on the thumb, so we have a repeater pipette. It has different size tips and you can pull up more liquid than you need and have it eject a set amount every time you push down.
So far, I’ve told you about single-channel micropipettes, but they also make multi-channel micropipettes that are thumb-savers when you have to pipette into multi-well plates. We have 8-channel and 12-channel ones in multiple volumes. And if we need to pipette a whole 96-well plate at once, we have a liquidator pipetter thing that can do that. And if we need to pipette really really tiny volumes onto crystallization trays, we have a “Mosquito” robot.
Before, I showed you some of our glassware, now for a tour of our not-so-glass-ware. Here’s a look at some of the disposable “tupperware” we use to store our samples and solutions.
Like “Tupperware,” some of the plastic tubes we use we tend to call by their brand name (or what was once their brand name – generics usually work fine!). For example, the Falcon tube (aka conical). Conical (“Falcon”) tubes come in multiple sizes (e.g. 50mL & 15mL) & like their name implies, have cone-shaped bottoms. That’s great for some things (like mixing by finger flicking to create a mini-tornado) but not-so-great for other things (like standing)
Another example of the “Kleenex 4 tissue” generic trademark phenomenon: the “eppendorf” tube. (Did you “Google” it?) More properly called “microcentrifuge tubes,” eppendorfs are like mini versions of the conical tubes that have hinged lids, hold ~1.5mL & (no surprise) are sized to fit in microcentrifuges (or microcentrifuges were designed to fit them…) Eppendorf tubes are probably one of our lab’s most used item because we usually work with (relatively) small volumes.
Sometime we need to hold even smaller amounts of liquid, so we have even smaller tubes, PCR tubes – these are like mini eppendorfs (hold ~0.2mL). Some have attached caps & some caps come separately. They often come in strips.
All these tubes with cone-shaped bottoms need help standing up, so we have racks to hold them while we work – for the PCR tubes, we make our own racks by taping together empty tip racks. We also have “freezer boxes” to hold tubes for longer-term storage.
Some other random plastic-y stuff…
Need to squirt? No problem. We have squirt bottles for that – they’re great for holding water, ethanol for cleaning, soap etc. And can’t forget the Petri dish! We pour agar plates in these (gel-like beds for growing bacteria). Speaking of growing bacteria, we also have culture tubes that are like the Falcon tubes but they have vented lids so the bacteria can breathe. We also have sandwich-box-like gel boxes for staining (and de-staining) gels. And sometimes we really do use Tupperware (or Rubbermaid) for this!
Some of the “furniture” & “appliances” I’ve shown you/will show you may seem foreign, but there are many things in my lab home you might have in your own home (though we might not always use them in the same way as you do)
Does your house have a microwave? So does my lab home! But we’d never heat food in it! Instead, we mainly use it to “cook” agarose gels to look at DNA. Agarose is a type of sugar & we boil it into a solution we pour into a tray & let harden
We also probably both have refrigerators. We often refer to them as “4C’s” (their temperature in degrees Celsius) and we have little ones & big ones. Our lab home also has “deli fridges” like you might find in a grocery store (we house our protein purification systems in them) and a walk-in “cold room” like you might find in a warehouse store (my least favorite room in my lab home) .
We also have freezers. LOTS of freezers. Many of them are “normal” freezers like you might have – we have big & little ones scattered around our lab home. We call these “-20’s” because we keep them at -20°C. We also have a row of freezers which are probably MUCH colder than freezers you have in your home. These “-80’s” are set to -80°C and we use them for long-term storage and storing sensitive samples.
Probably unlike your freezers, ours have alarms on them that go off when the temperature gets too high (usually because people are going in & out of it too much and/or leaving the door open when trying to find something). These alarms are really sensitive so our lab is often cacophonous…
Another “kitchen-like” appliance – the sink! Most of our sinks have three faucet handles – hot and cold like a usual sink, and then an extra faucet for de-ionized (DI) water that has most of its salts taken out. If we need even purer water, we have “milliQ” water that goes through an additional set of filters and then our media maker puts containers of it in our lab. And if “milliQ” isn’t pure enough, we have water that comes in small bottles and is guaranteed to be free of RNAse & DNAses (proteins that can chew up RNA and DNA). (At least until you open it…)
A couple other things you might have in your kitchen: aluminum foil’s great for keeping light away from light-sensitive solutions & temporarily sealing bottles that go into our autoclave (like a really hot dishwasher for sterilization). You also might have cling wrap. It’s great for keeping the gels we pour and wrap in wet paper towels from drying out. We also have a thing called Parafilm that is like cling wrap but thicker, stretchier, and less cling-y. It’s AWESOME (one of my favorite things in my lab home) and we use it to seal Petri dishes, etc. You might also have funnels like we do. You probably have table salt in your kitchen – we have it too – but we have to keep it under the bench instead of on the table because we buy big buckets of this sodium chloride (NaCl) – hopefully you don’t go through as much of it as we do…
We try to keep our lab home clean, but we make a lot of messes! Fantastik cleaner is fantastic at cleaning up many of them. And when we need to disinfect, we have bleach. We express our proteins in bacteria and insect cells and, once we remove the cells, we disinfect the media they grew in with bleach in a giant graduated cylinder.
Many of the things I’ve shown so far you might have in in your kitchen. One that might be in your garage – RainX! It’s good for keeping raindrops off windshields & polyacrylamide gels from sticking to the glass plates we pour them between. Normally we don’t bother with RainX-ing the normal, mini SDS-PAGE gels we make, but it’s helpful for when you’re pouring the big ones.
Now to your office – we use normal office supplies – especially sharpies – we have to label LOTS! We mostly use regular sharpies but we also have special lab markers that are alcohol-resistant & multiple colors for color-coding. And speaking of color coding, we also have colored labeling tape in addition to traditional scotch tape (good for taping printouts into lab notebooks) and packing tape (good for temporarily sealing plates (and packages)). And while we’re getting sticky… we have epoxy glue that we use when preparing pins for crystal collecting
Now I want to show you some our Biochemical Blenders – and hopefully not blunders! Centrifuges, vortexers, shaker platforms, & more!
Our main “blender” is the centrifuge. A centrifuge is a piece of equipment that spins really fast, pulling heavier molecules out of solutions and leaving you with a solid pellet and liquid (supernatant) on top. The amount of separation you get depends on how fast you spin, and we have lots of types of centrifuges for different purposes. Centrifuges come in lots of different sizes, and within those different sizes, you can use different inserts to hold different size tubes, bottles, or even plates. We use the bigger ones for things like separating insect cells expressing our protein from the media we grow them in (we call this harvesting). We use the medium ones 4 things like concentrating proteins and pelleting small bacterial cultures. We also have microcentrifuges that we use with, you guessed it – microcentrifuge tubes!
Centrifuges can be “fixed angle” or “swinging bucket.” You can think of swinging bucket as kinda like swing rides at amusement parks where the seat can move & fixed rotor would be more like the teacups where the “seat” can’t move. Some of our centrifuges have coolers so we can control the temperature. This is important when working with temperature-sensitive things like proteins.
So far, I’ve shown you “regular” centrifuges, but we also have “ultracentrifuges” that go even faster. We use these during protein preparation to separate soluble proteins from “cell gunk.” We also have centrifuges that go slower. Why would you want that? Sometimes, you just need to draw liquid drops off the sides of small tubes -> just want something quick & gentle. Mini “pulse” centrifuges are great for this. They only have one set speed but you can let it spin as long as you need & quickly get your samples in & out (centrifuges that spin faster take longer to wind down)
I often use the pulse centrifuge after “finger vortexing” – basically I just flick the bottom of a microcentrifuge tube to create a mini tornado-like vortex in the liquid that mixes it nicely (but also leaves drops on tube walls). If I want a “real” vortex, we have vortexers that vibrate really fast when you push on them. They’re great for resuspending pellets in a new liquid after you’ve centrifuged them out of their old liquid (also “great” for making your arm go numb)
Need to spin yourself? We have swivel chairs for that 🙂 (and my feet even reach the floor with some of them). But remember Officer Buckle’s words of wisdom – never stand on a swivel chair! Use a step stool instead (The Bumbling Biochemist’s sidekick Steppy the Stepstool often comes to her rescue). Another option – find someone tall… I have frequently been heard asking labmates if they could “be tall for a second” for me.
Sometimes you want to roll, not spin, and for this we have a “hotdog roller” – I use it when binding proteins to resin to make sure all the protein and resin have a chance to meet. If you want to somersault not hot dog roll, we have an end-over-end rotator for microcentrifuge tubes. And if you want to rock, not roll, we have a rocking platform we use when staining & de-staining gels that we use to separate our proteins.
We make lots of solutions and need to make sure that they get thoroughly mixed, so we use magnetic stir bars that get spun by magnetic stir plates
For those who like things shaken, not stirred, we have shaking incubators in many sizes. We use these when growing bacterial cultures & insect cell cultures (NOT the same ones) to keep the temperature constant and the cells aerated. If you want more gentle orbital motion, we have orbital shaker platforms that move in circles (and we use heavy weights to keep our plates from flying off!)
And, just like we really do have regular microwaves, fridges, freezers, and tupperware, we also have a regular blender! I don’t think this blender’s been used in decades but I like to think it was used for something exciting like the Hershey-Chase experiment showing DNA to be the source of genetic information! I am at CSHL…
This post is part of my weekly “broadcasts from the bench” for The International Union of Biochemistry and Molecular Biology (@theIUBMB), whose president-elect Dr. Alexandra Newton agrees with me that it’s perfectly normal to dream that you’re a protein. Be sure to follow the IUBMB if you’re interested in biochemistry! They’re a really great international organization for biochemistry.