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  • a
  • acids and bases
    Acids are (in one definition) molecules that can donate a proton (H⁺ ) and bases are (in one definition) molecules that can accept a proton. We talk about “acids” and “bases” but these are just temporary roles that molecules take on - it’s their “job” not their “identity” and they go back and(...) Read More
  • active site
    the part of an enzyme where the action happens! So, for example, the active site of a serine protease (a protein that cuts other proteins or peptides) is the pocket in the protease where the catalytic serine sticks out and attacks a peptide bond to break it. Drugs that inhibit enzymes often(...) Read More
  • affinity
    binding strength. The ability of a molecule to stick to a particular binding partner and stay stuck. It's often measured/reported with a value called the equilibrium dissociation constant, Kd. Ultimately it's the result of energetically-favorable interactions between the binding partners (you(...) Read More
  • Affinity chromatography
    a protein purification technique to "capture" your protein of interest based on something unique about it, such as an affinity tag you added to the end of the protein when you were doing the cloning. When you flow a mixture of proteins containing that unique-thing-having protein through a(...) Read More
  • agarose gel electrophoresis
    a technique used to separate pieces of DNA by length using electricity to entice the (naturally negatively-charged) DNA through a slab of gel made of the sugar agarose towards a positive charge. The DNA strands get tangled up in the mesh as they go (kinda like if you were to try to pull(...) Read More
  • aliquot
    "snack-size/single-use portions" of something (typically something you're saving for later use or giving to someone). For example, after you make a ton of some solution, like an antibiotic solution, and you need to freeze it for storage, you don't want to have to freeze-thaw the whole 50mL or(...) Read More
  • allosteric effect
    an allosteric effect is when something happens in one part of a molecule (such as binding of another molecule or phosphorylation) and that causes a change somewhere else in the molecule. So, for example, some enzyme inhibitors bind someplace distant from the active site and still inactivate(...) Read More
  • amino acid
    a protein letter - but not always... When we talk about amino acids, we're usually referring to one of the 20 (common) proteinogenic amino acids - that is to say one of the amino acids that gets incorporated into a protein during the protein-making process called translation. There are also(...) Read More
  • anion
    a negatively-charged particle. It is a type of ion (charged particle), and it's "opposite" is the cation, which is positively-charged. The charge comes from having more electrons (-) than protons (+) and can be associated with a single atom (such as Cl⁻) or a larger molecule (polyatomic(...) Read More
  • apo-
    a term used to describe the form of a molecule without its binding partner. So, for example, an enzyme that requires a cofactor (helper molecule such as a metal or vitamin-based molecule) to function is called an apoenzyme without its cofactor and an holoenzyme when it's bound to that(...) Read More
  • assay
    this is basically just a word for an experiment where you're measuring the "amount" of something, such as the activity of an enzyme or the "binding" of a molecule. Typically, the measurements are taken over time and/or while changing some reaction component in order to determine the inherent(...) Read More
  • atom
    the basic unit of an element (things like carbon, hydrogen, nitrogen, etc.). It's the smallest bit of that element that's still that element (i.e. if you took a hunk of carbon and cut it up into clumps of carbon and kept cutting those clumps in half and in half and in half, the level at(...) Read More
  • autoclave
    a steam sterilizer. A bit like a big really really hot really really high pressure oven. We use it to sterilize things like bacterial growth media and flasks and tools we want sterile. It doesn't do the scrubbing for you though - you still have to wash all those flasks first! Read More
  • avidity
    the "bonus binding strength" that comes when a binding partner binds with multiple binding sites (is multivalent). Basically, avidity makes it so that the strength you measure (the effective or apparent affinity) is greater than if you were to add up the individual affinities of each(...) Read More
  • b
  • biologic
    a "biologic" or "biological drug" is a pharmaceutical drug that something living helped make. These days, biologics are often made using biotechnology, such as genetically engineered and recombinantly-produced proteins (such as antibodies - all those drug names ending in -ab are antibodies(...) Read More
  • c
  • catalyst
    a catalyst is a molecule that speeds-up (catalyzes) reactions without getting used up or permanently changed in the process. Biological catalysts are called enzymes and they're typically proteins, RNA, or protein/RNA combos. An important feature of catalysts is that they can't change what(...) Read More
  • cation
    a positively-charged particle. It is a type of ion (charged particle), and it's "opposite" is the anion, which is negatively-charged. The charge comes from having fewer electrons (-) than protons (+) and can be associated with a single atom (such as Na⁺) or a larger molecule (polyatomic(...) Read More
  • centrifuge
    a piece of equipment that spins tubes really fast, pulling heavier molecules out of solutions and leaving you with a solid pellet and liquid (supernatant) on top. (or, as a verb, the process of using a centrifuge). The amount of separation you get depends on how fast you spin, and we have(...) Read More
  • chromatography
    Chromatography is a way to separate components of a mixture (like different proteins) based on how they interact differently with a material. We take a mixture of things in a “mobile phase” (like a mix of proteins in a buffer (pH-stabilized salt water) and get it to travel through some(...) Read More
  • cofactor
    a co-factor is a non-protein "helper molecule" that a protein needs in order to be functional. Cofactors can be inorganic (non-hydrocarbon-based) such as metal ions or organic (carbohydron-based). When the cofactor is a metal, we call the metal-protein combo a metalloprotein - or a(...) Read More
  • cold room
    the bumbling biochemist's nemesis... basically like a walk-in fridge with lab benches inside. I try to avoid it whenever possible because it's really cold (~4°C (~40°F)) but I have to work in there for some protein purification steps to protect my protein from getting degraded at higher(...) Read More
  • conformation
    shape. "Conformation" is often used to refer to one of several alternative shapes a protein can take. So, for example, a protein might exist in one shape when it's not bound to a partner and then, upon binding to a partner it can undergo a conformational change (maybe clamping around the(...) Read More
  • conformational change
    shape-shift. "Conformation" is often used to refer to one of several alternative shapes a protein can take. So, for example, a protein might exist in one shape when it's not bound to a partner and then, upon binding to a partner it can undergo a conformational change (maybe clamping around(...) Read More
  • covalent bond
    a strong bond formed between atoms by sharing pairs of electrons (1 pair for a single bond and 2 pairs for a double bond). If the sharing is unfair, and 1 of the atoms (the more electronegative one) hogs the shared electrons, we call it a polar covalent bond. Covalent bonds are(...) Read More
  • cytoplasm
    the general interior of a cell - outside of any membrane-bound "rooms" (organelles like nuclei and mitochondria) Read More
  • d
  • domain
    domain” is just a fancy word for a part of a protein that has some function or structure or something and you need a way in which to refer to it. Structural domains are parts of the protein that have distinct, stable, 3D shapes. Often structural domains can fold into that shape even when(...) Read More
  • e
  • electron
    redox A negatively-charged subatomic particle. One of 3 main subatomic particles (parts of an atom). Electrons are negatively-charged and they hang out in an "electron cloud" around the dense central nucleus where the protons and neutrons live. Electrons move around a lot so you never know(...) Read More
  • enzyme
    a biochemical reaction mediator/speed-upper (catalyst). Enzymes are usually proteins (e.g. DNA polymerase), sometimes protein/RNA complexes (e.g. ribosomes), and sometimes RNA alone (ribozymes) and there are lots of different enzymes with different jobs & specificities. They bind to specific(...) Read More
  • equilibrium
    a reversible reaction or mixture's "happy place." Dynamic equilibrium occurs when the forward and backward reaction rates equalize so that the amount of the forward reaction equals the amount of the backward and the overall proportions of reactants vs products doesn't change over time (even(...) Read More
  • g
  • glycoconjugates
    Molecules which have sugar chain(s) (aka glycans) attached to something else - like a protein or a lipid. This teamwork is accompanied by team names that can be confusing…⠀The order of the names of these “hybrids” indicates which is dominant - the first one is the minor component and the last(...) Read More
  • glycolipid
    a lypid with sugar chain(s) (glycans) attached. Aype of glycoconjugate (molecule with sugar attached to something). There are several different subclasses of them  with different names (of course…) These include lipopolysaccharides, glycosylphosphatidylinositol (GPI), cerebrosides, &(...) Read More
  • glycoprotein
    a protein with sugars attached. ~1/2 of all proteins have at least one glycan (sugar chain) & some glycoproteins are up to 60% carb by mass. Glycoproteins are often found in the outer leaflet of the plasma membrane, facing the cellular exterior, or secreted into the extracellular matrix. The(...) Read More
  • h
  • H-bond
    aka H-bond. a noncovalent (no-electrons shared) attraction between molecules. It can be more helpful to think of them more as attractions than "bonds" because they're "easily" reversible. The attraction comes from oppositely-charged partial charges liking each other and "hydrogen bond" is(...) Read More
  • holo-
    a term used to describe the form of a molecule with its binding partner. So, for example, an enzyme that requires a cofactor (helper molecule such as a metal or vitamin-based molecule) to function is called an apoenzyme without its cofactor and an holoenzyme when it's bound to that cofactor. Read More
  • hydrogen bond
    aka H-bond. a noncovalent (no-electrons shared) attraction between molecules. It can be more helpful to think of them more as attractions than "bonds" because they're "easily" reversible. The attraction comes from oppositely-charged partial charges liking each other and "hydrogen bond" is(...) Read More
  • hyper-
    a prefix used to mean "over" or "more than." I remember it as "hyper -> over" (as opposed to its opposite, "hypo-" ("hypo-below"). Another way to remember is that hyper people have a lot of energy! We can stick hyper- in front of a lot of different terms (e.g. hypertonic, hyperosmotic). Read More
  • hypo-
    a prefix used to mean "under" or "less than." I remember it as "hypo - below" (as opposed to its opposite, "hyper-" ("hyper-over"). We can stick hypo- in front of a lot of different terms (e.g. hypotonic, hypoosmotic). You might have heard it in more "normal talk" in the context of(...) Read More
  • i
  • ion
    a charged particle. This umbrella term can refer to a positively-charged particle (cation) or a negatively-charged particle (anion). The charge comes from having an unequal number of protons (+) & electrons (-) and can be associated with a single atom (such as Na⁺ or Cl⁻) or a larger(...) Read More
  • ion exchange chromatography
    ion exchange chromatography (IEX) is a common protein purification technique in which we separate proteins based on charge. Proteins are made up of amino acid letters, some of which are sometimes charged (depending on pH). Different proteins have different amino acid spellings and thus(...) Read More
  • ionic bond
    aka salt bridge, a strong noncovalent attraction between 2 charged molecules (ions), a negatively-charged on (anion) and a positively-charged one (cation). There is no electron sharing involved, but they stick together because they like each other's opposite charge. Because ionic bonds(...) Read More
  • iso-
    a prefix used to mean "same." We can stick iso- in front of a lot of different terms that we also stick hypo- (below) and hyper- (over) in front of (e.g. isotonic, isoosmotic). But iso- can be put in front of a lot of other words too. For example, "nuclear isotopes" refers to versions of the(...) Read More
  • k
  • Kd
    equilibrium dissociation constant. A measure of binding affinity (binding strength) - the tendency of a molecule to stick to a particular binding partner and stay stuck. tells you how much of one binding partner (in terms of concentration, often in some form of molarity) you need to add(...) Read More
  • l
  • ligand
    a binding partner. This term is often used when talking about receptor proteins. So, for example, insulin is the ligand for the insulin receptor and opioids are the the ligands for opioid receptors. Ligand is similar to the word "substrate" but substrate refers specifically to ligands of(...) Read More
  • m
  • macromolecules
    "big molecules" - this term is commonly used to refer to proteins, lipids, nucleic acids, and carbohydrates which can have thousands of atoms connected through strong covalent bonds. Apart from lipids, macromolecules are typically "polymers" - chains made up of similar units (monomers). So,(...) Read More
  • mole
    a mole is the biochemist's dozen - it just means 6.02 x 10²³ of something - anything. That number might seem random, but it's Avogadro's number and it's defined as the number of atoms in 12 grams of carbon-12 (the main isotope (version) of carbon). But normally we don’t really care about that(...) Read More
  • molecule
    a group of atoms held together with covalent bonds (strong bonds that involve electron sharing). Molecules can be small (like water or carbon dioxide which only involve a few atoms) or large (like proteins with thousands of atoms). They don't break apart into their component atoms easily (so(...) Read More
  • monomer
    a protein made up of a single polypeptide chain is called monomeric. Monomeric proteins do not have quaternary structure. Contrast with multimeric proteins (multimers) which have more than one chain. For example, dimers contain two polypeptide chains stuck together. Read More
  • multimer
    a multimer (aka oligomeric protein) is a protein that's made up of more than one polypeptide chain stuck together is called multimeric. Some proteins are only multimeric are always stuck together but other proteins can exist alone (as a monomer) or as part of a multimer. Multimers can(...) Read More
  • n
  • neutron
    radioactive; isotopes a neutral (non-charged) subatomic particle (atom part). It hangs out with positively-charged protons in an atom's dense central nucleus, surrounded by a sea of negatively-charged electrons. Neutrons contribute to an atom's mass, but not an atom's charge. Elements are(...) Read More
  • noncovalent bond
    a relatively weak bond formed between molecules without sharing electrons. It can be more helpful to think of them more as attractions than "bonds" because they're "easily" reversible. Just how easy depends on the strength of the attraction. The attraction comes from charges and/or partial(...) Read More
  • nuclease
    a nuclease is a DNA or RNA cutter (endonuclease) or chewer (exonuclease). "Nuclease" is an umbrella term for protein enzymes (reaction mediators/speed uppers) that cleave the phosphodiester bond connecting DNA or RNA letters (nucleotides). Endonucleases cut somewhere in the middle of the(...) Read More
  • nucleus
    refers either to: 1) the atomic nucleus which is the dense central part of an atom where protons and electrons hang out OR 2) the cellular nucleus which is the membrane-bound room (organelle) in cells where DNA is stored as chromosomes Read More
  • o
  • open access
    free for anyone to access and read (not paywalled) Read More
  • p
  • pellet
    as a verb this is biochem "slang" for using a centrifuge to spin a sample really fast so that undissolved things separate from the liquid . As a noun, it refers to the solid part (consisting of the undissolved things) that has "pelleted out". For example, when you purify proteins, you break(...) Read More
  • peptidoglycan
    a type of glycoconjugate (sugar attached to something) in which peptides play supporting roles (literally) to the sugars - short chains of amino acids serve as bridges between carbohydrate chains for extra sturdiness. These are seen in bacterial cell walls, and many antibiotics target them. Read More
  • pH
    pH is a measure of acidity (proton (H⁺) concentration). The lower the pH, the higher the proton concentration, [H⁺], and the more acidic. The higher the pH, the lower the proton concentration, [H⁺], and therefore the less acidic (more basic/more alkaline). This inverse relationship can be(...) Read More
  • pKa
    pKa is a measure of the strength of an acid. pKa is the pH @ which 1/2 of the acid molecules have given up a H⁺. It’s a measure of “how extreme” (i.e. basic/alkaline) conditions must be in order for an acid to give up its H⁺  at any pH above an acid’s pKa, any particular molecule of that(...) Read More
  • postdoc
    a postdoctoral researcher - someone who has earned a PhD and wants more! Postdocs typically seek out more experience in a different lab than they did their PhD in and they often look to gain new, complementary, skills to what they learned in their PhD. They have more independence and less(...) Read More
  • preprint
    a scientific paper that has been published before being peer-reviewed. So it's gone through an initial "SPAM filter" type screen but it hasn't gone through the (hopefully) rigorous peer-review process that takes before articles are published in journals. Preprints can be great for getting(...) Read More
  • primary structure
    sequence of letters. When talking about proteins, it's the sequence of amino acids. When talking about nucleic acids (DNA or RNA), it's the sequence of nucleotides. Read More
  • proteoglycan
    a glycoconjugate (sugar/something else combo) where sugars get the starring role and protein serves to kinda hold them all together. These sugars are GlycosAminoGlycans - large polysaccharides with a lot of modifications. These modifications include lots of amino sugars (hence the A in GAG)(...) Read More
  • proton
    a positively-charged subatomic particle. One of 3 main types of subatomic particles (parts of atoms). Protons hang out with neutral neutrons in a dense central nucleus and are surrounded by a cloud of negatively-charged electrons. The number of protons an atom has determines what element(...) Read More
  • q
  • quaternary structure
    the structure of proteins that comes from interactions between different polypeptide chains or subunits. Only multimeric/oligomeric proteins have quaternary structure. Read More
  • r
  • recombinant
    used to describe DNA that has been "recombined" from more than 1 source through molecular cloning and/or the proteins expressed from such DNA. For example, you can take the gene for a protein you want to study out of one place (either cut it out with restriction enzymes or use PCR to make(...) Read More
  • residue
    a word for amino acids (protein letters) after they've been incorporated into proteins or peptides. Amino acids get their name because they have an amino group on one end and a carboxylic acid group on the other end. When amino acids join together through peptide bonds, they do so by joining(...) Read More
  • resin
    tiny beads with superpowers! Often they have a sugar (such as agarose or dextrose) or polyacrylamide core that's been "functionalized" with the addition of chemical groups that give them particular properties such as a + or - charge. Resin can be packed into chromatography columns and used to(...) Read More
  • s
  • SDS-PAGE
    Sodium DodecylSulfate- PolyAcrylamide Gel Electrophoresis is a technique used to separate samples of proteins by size by unfolding the proteins & coating them with a uniform negative charge and then using electricity to send them them traveling through a thin vertical slab of gel mesh.(...) Read More
  • secondary structure
    when talking about proteins, secondary structure is structure that comes from hydrogen bonding between oxygens and hydrogens in the generic part of the protein backbone. The peptide bonds linking amino acids are covalent bonds that form when the carboxyl (-(C=O)-O⁻) of one amino acid joins(...) Read More
  • Size Exclusion Chromatography (SEC), aka Gel Filtration
    column-based method used to separate proteins by size/shape - either for: purification (preparative SEC), often as a “polishing step” after you’ve done other separations (e.g. affinity and/or ion exchange) or to see if proteins interact (analytical SEC) It works by flowing a(...) Read More
  • small molecule
    "small molecule" is often used to refer to things like traditional pharmaceutical drugs, but "small molecules" are also naturally made & used in the body, such as ATP. It's basically just a classification for "low molecular weight" (i.e. small) molecules (typically organic (hydrocarbon-based)(...) Read More
  • solute
    a thing that's dissolved in a solution Read More
  • solution
    when you take (at least) 1 thing (the solute)(like a salt) and stick it in another thing (the solvent)(like water) and the solute molecules all give up their solute-solute interactions, replacing them with solute-solvent interactions, acquiring a full coat of the solvent. Dissolving does(...) Read More
  • solvent
    the dissolver in a solution - often, but not always, a liquid. When the solvent is water, we call the solution aqueous. Read More
  • spin down
    use a centrifuge to spin a sample really fast so that undissolved things separate from the liquid. After you spin something down you're left with a "pellet" - the solid part (consisting of the undissolved things) - and the liquid part which we call the supernatant. Read More
  • structural biology
    a field of biochemistry that studies how molecules' shapes contribute to their function (the so-called structure-function relationship). Structural biology uses techniques such as x-ray crystallography, cryo-electron microscopy (cryo-EM) and nuclear magnetic resonance (NMR) to figure out what(...) Read More
  • substrate
    something that an enzyme binds & transforms into "product." remember Substrate-Start. It's the "S" in E + S - [ES] - P (where E is enzyme, S is substrate, and P is product) For example, in our stick-snapper enzyme example (where an enzyme binds and snaps sticks), the stick-snapper is the(...) Read More
  • t
  • tertiary structure
    the tertiary structure of a protein is structure that comes from interactions between the unique side chains (R groups) of different amino acids within a single protein chain. These interactions can be from one side chain to another sidechain or from one sidechain to the backbone of(...) Read More
  • transfection
    when you stick foreign (exogenous) genetic information (like DNA) into eukaryotic cells (cells with membrane-bound “rooms” like nuclei inside) - things like animal cells). It's a form of transformation, but we call it transfection so it doesn’t get confused with tumor transformation (just(...) Read More
  • transformation
    when you stick foreign (exogenous) genetic information (like DNA) into a cell. Typically used to refer to sticking DNA into bacteria - when we do the same put DNA into eukaryotic cells (cells with membrane-bound “rooms” like nuclei inside) - things like animal cells) we call it transfection(...) Read More
  • v
  • valency
    depends on context... If you're talking about ions (charged particles) valency refers to the "number of charges" (e.g. Na⁺ is monovalent whereas Ca²⁺ is bivalent). If you're talking about binding partners, it refers to the number of binding sites - monovalent binders have a single binding(...) Read More
  • vector
    a "vehicle" that provides a "backbone" for sticking a piece of genetic information (transgene or "insert") that you want in cells that you want. A few common types are plasmids, viral vectors, & artificial chromosomes. Vectors can differ in how much DNA they can hold, how they get into cells,(...) Read More
  • w
  • wild-type
    the "normal" naturally-occurring version of something (protein, gene, bacterial strain, etc.) (as compared to a mutated version of it and/or something derived from it). So, for example, if you're studying some protein and you make different versions (aka constructs) with different amino acid(...) Read More
  • x
  • x-ray crystallography
    a structural biology technique used to figure out the atomic or near-atomic structures of molecules and/or molecular complexes (groups of molecules bound to each other). Basically, the goal is to determine where molecules are located relative to one another in 3-D. It's often used to "solve"(...) Read More