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Hey-hey-hoo, science nerds and fellow H. sapiens!

Heheh. I had to go geek here.

Not science papers!

As a result of some trouble in one of my courses this semester, I have put on my TA cap and have typed up how I read a scientific paper.  Its nitty gritty, stepwise and colloquial.  Exactly the opposite of a scientific paper.  But hopefully, it will give you a bit of a better insight on what you shouldbe looking for when it comes time to sit down and read it.  Its much better than having it in one eye and out the other. So, without further adieu, lets delve into it!

  • Step 1: The Title.  Why yes, you should start with the title, where else?  The title is going to tell you exactly, in no uncertain terms, what it is you’re going to be attempting to plug through in the next few pages.  Wait, but oh no, big words!  If you encounter a word you don’t know or an organism  you’re not familiar with, google it.  Why?  Because although the internet’s information should never be trusted for stringent details, it can give you the overall gist of what it means or what it is.  Also, pictures can be a boon here.
  • Step 2: The Abstract.  What is this bold paragraph that sits directly beneath the authors’ names?  The abstract is a concise, to the point paragraph that gives you (in general terms): 1) what they did. 2) what happened 3) a small summary of why they think its important.  This is another great way to check to be sure you’re going to at least understand what the heck is going to be said in this paper.  Don’t skip these two.  Knowing ahead of time what you’re going to be reading is an important part of reading scientific literature.  This isn’t like reading your novel of choice and not reading the end because it would spoil it for you.  Trust me, you want to know what the authors are going to say.  We, as scientists, must critically analyze what is being said, not just believe it.  Knowing what they think beforehand allows us to process what they are saying in the meat of the paper and compare it to what they asserted in the title and abstract.

Just to give you a recap of what we’ve done so far, my thought process once I’ve read both the title and the abstract should be: “Okay, the title said kryptonite turns on randomgeneX which causes atomic powers in mice and the abstract says they think kryptonite activates randomgeneX by…  It is important because…”  What I am saying here is after you’ve read the title and abstract, check to be sure you know what is being studied, what the basic result was and its purpose.  If you can’t quite figure it out, google the words and ideas you don’t know.  If you can, excellent, lets move on!

  • Step 3: The Introduction.  Now, the introduction is solely in the paper to give the reader background knowledge on randomgeneX that activates mouse atomic powers when upregulated by kryptonite.  The authors know that only a small percentage of the scientific community have had any sort of experience with atomic mouse powers and therefore provide background information; leading their readers in a small history lesson.  This information should bring you some semblance of an idea of where the authors started and got their hypothesis from.  Science, like all literature, is built upon the lessons and works of others.  Just like every author cites inspiration and every idea is never truly novel, each experiment in science has some basis in past research and discoveries.  Sure, there are a few “avant-garde” experiments here and there, but it is hardly ever the case that someone’s work is not built upon a foundation of those who came before them.  Once you’ve read, and googled if need be, the introduction, you should be able to answer why the authors did their research in the first place.
  • Step 4: The Materials and Methods. Reading the M&M can be a daunting task for anyone, especially those who have not been in or around a wet lab.  However, you all may sigh in relief because all I ever do in my first pass through a paper is skim the techniques.  Why?  Truly, because all you need to know is a general idea of what was done.  In more modern papers, kits (like from Invitrogen) are often sourced for their methods and if need be, their websites contain detailed information of how things are done.  But for our purposes, we just need the bare bones.  Read the M&M to find gene names, clone names, what techniques were done and any other information that might be beneficial to the rest of the read.  Don’t try to get every detail down, its not worth it at this point.
  • Step 5: The Results.  Alright, here we are.  The bulkiest and most important part of the paper.  How on earth do we tackle this?!?  Easily and stepwise.  Unlike in a textbook where you can look at figures ahead of time to get an idea of the things you will be reading about, the figures in a scientific paper are often best not looked at until they are needed.  Scientists are notorious (in my experience) for writing bad figure legends and captions.  So, instead, start reading.  Take it slow, take each point they are trying to make bit by bit.  Stop after every major point (usually each paragraph) and summarize it to yourself.  Did what they just say make sense, considering the background information?  When you reach a citation for a figure, stop and look at the figure.  Use the first few sentences of the image caption to orient yourself and find out what is being displayed.  Is it a blot?  A gel?  A phylogenetic tree?   Here is the point where, if need be, go back to the M&M and familiarize yourself with the technique if you do not understand it.  Now that you know what the figure is, think of what you expect it to tell you. Then, look at the image, given what you know, and ask “Does this make sense with what the authors’ said?”.  Usually, it is yes.  If you’re still not clear, read it again, look at it again; step yourself through what the figure is supposed to tell you.
His weakness is cheese.

His weakness is cheese.

Lets stop here and do an thought game.  Say that the authors of the atomic mouse paper show an agarose gel in which a reverse transcriptase-PCR was performed with primers targeting the mRNA of the randomgeneX in two conditions: kryptonite+ and kryptonite-.  Before we even think about the author’s exertion of kryptonite causing expression of randomgeneX, think about what the agarose gel should show us.  An agarose gel stained with EtBr would show bands of DNA that have been amplified by the PCR.  We would expect to see no bands in the lane in which the kryptonite- was run, while the lane with kryptonite+ should have a band at whatever size randomgeneX is.  Then, we examine the figure itself and find, lo and behold, that yes, there is a bright band in the + lane, but none in the -.  Therefore, the authors are right in asserting that randomgeneX is transcribed when kryptonite is present.

Once you’ve done this for all points made in the results, go back and summarize it for yourself.  Get a good idea of what exactly was done–what were the exact results?  Knowing these things will help you critically analyze the authors’ opinions in the next section.

  • Step 6: The Discussion.  It is in this section that our authors attempt to correlate what they’ve learned in their study to other research done in a similar fashion.  They will make points about the importance of their discovery in relation to other systems/organisms/fields.  It is up to you, who now knows what the authors know, to look at what they say and see if you agree.  Remember the introduction, as the information stored there often plays a role in the discussion.  Ask yourself, given what you know about the study, what conclusions you would make and would they match the authors’.
  • Step 7: Wrapping It Up. Once you feel you’ve got a good idea of the paper, tie it all together as a whole picture in your mind.  Write yourself your own abstract, detailing briefly what the meat of the paper was all about, as well as its implications for the field of science as a whole.  Bullet points are excellent for this.
Post-paper understanding...

Post-paper understanding...

I hope that this guide will help you begin to understand how to address scientific papers.  They are a tough bunch to read and must be approached differently than any other type of written work.  Remember that these papers are a presentation of evidence as a defense for an “idea” in which the authors have about atomic mouse powers and their regulatory systems, to use our running example.  Once you begin to examine them as something to be critiqued and analyzed, rather than something to be read and understood, scientific papers become almost second nature to read.

Best of luck and happy reading!

The Alchemist Kitten

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Alrighty, round two of sugar metabolism: the Citric Acid Cycle, also known as the Krebs Cycle or the Tricarboxilic Acid Cycle.  Just like my previous post, we’ll run through the cycle stepwise, indicating enzymes and reversibility as well as any other notable information.  Lets get crackin’!

The TCA Cycle: An Overview!

Its a lovely circle!

Big sucker, yeah?Step 0: First, before the cycle can begin, we must take pyruvate (from the results of our glycolysis) and transform it into acetyl-CoA in order for the cycle to legitimately begin.  To do so, pyruvate dehydrogenase takes CoASH and NAD+ (with the help of the coenzyme TTP) and binds CoASH as acetyl-CoA, while giving off NADH and H+. (The NAD+ is used as a cofactor to return the enzyme to its original state) Now we can begin the TCA cycle.

Citrate Synthase in action!Step 1: Acetyl-CoA is added to oxaloactetate to make citrate, which adds a carbon to the chain, making it 5 carbons (instead of oxaloacetate’s 4), as well as transforming several of the groups on the carbons.  I will not go into detail here to spare you all the pain, but instead provided an image of the transformation. CoAsH is removed. This is irreversible.

Step 2: Citrate is then transformed into isocitrate by moving the OH group on C3 to C4.  Aconitase catalyzes the reaction and it is reversible.

Step 3: Isocitrate then has the newly moved OH group dehydrogenated to a carbonyl group, as well as has the COO- group from C3 removed entirely (with two H’s added in its place).  This compound is called a-ketoglutarate and it is catalyzed via isocitrate dehydrogenase.  The reaction is not reversible as NAD+ is reduced to NADH and CO2 is formed.

Step 4: A-ketoglutarate then has CoASH added yet again, this time to replace the COO group at C5 to form an SCoA group (Succinyl CoA the whole compound is called).  A-ketoglutarate dehydrogenase catalyzes the reaction, which is irreversible.  It takes NAD+ and CoASH and releases NADH and CO2.

Step 5: Succinyl CoA then passes through Succinyl CoA synthase, which removes the CoA group, while adding an O(H) group to the C4 carbon, making Succinate.  GDP and Pi are used, while GTP and CoASH are products.  This reaction is reversible (hence the misleading name “Succinyl CoA synthase”!)

Step 6: Succinate is then dehydrogenated via succinate dehydrogenase (duh) to form fumarate.  H2 is eliminated (one from C2 and one from C3) to form a double bond between the two carbons.  The H2 (and its subsequent electrons) are transfered to Q to make Q2(in the ETC) or FAD to FADH2. This enzyme is the only membrane bound enzyme in the cycle and is also known as Complex II of the electron transport chain and the reaction is reversible.

Step 7: Fumarate is then hydrated into malate. The double bond formed in the last step then gains an OH group and a hydrogen (C2 gets OH C3 gets H, though it doesn’t matter, since the molecule is not chiral and either addition would produce the same product.)  Fumarase catalyzes the reaction and water is consumed; the reaction is reversible.

Cute lil fellaStep 8: Malate is then dehydrogenated such that the OH group becomes a =O group, while NAD+ is reduced to NADH and H+ via malate dehydrogenase.  Oxaloacetate is formed and thus the circle is complete.  The reaction is reversible.

Overall, the TCA cycle produces 4 NADH, 1 FADH2 (or QH2) and 1 GTP.  If we take into account that two pyruvates are formed via glycolysis, the total comes to 8 NADH, 2 FADH2 and 2 GTP.  Granted, this isn’t alot of energy, but the payoff from both of these cycles comes as we enter the electron transport chain, our next topic.

Stay tuned, as this study session crams forward!

The Alchemist Kitten

 

Hey you masses of scientists!  Today, since I feel rather prepared for my biochemistry exam tomorrow, I felt like reviewing what I learned with you all.  This post (and the *hopefully* two subsequent) will overview the topics of my exam and help both myself and you!  Ah, what a symbiotic relationship we have!  Anyways, lets get down to buisness.

Glycolysis–The cycle in overview!

In Overview.

Ahhh, sugar. <3Step 1: Phosphate (-OPO3-2 in our case) is added onto the sixth carbon of glucose to form Glucose-6-Phosphate.  This reaction occurs via the O- (formerly OH) group of C6’s nucleophilic attack on ATP’s third phosphoryll group.  Hexokinase aids the reaction (via a Lys group) and thusly ADP and H+ (from the -OH group) are formed as products.

**Gluconeogenesis–glucose-6-phosphatase catalyzes the reverse reaction, since this step is IRREVERSIBLE**

Step 2: Glucose-6-Phosphate is then isomerized to fructose-6-phosphate.  Via two His groups from phosphoglucose isomerase, the 6 membered ring of G6P is opened up and then reclosed as a 5 membered fructose ring; the phosphate group remains unchanged.  This reaction is reversible (and works backwards for gluconeogenesis).

Step 3: Fructose-6-phosphate picks up another phosphate group via the same mechanism as step 1.  The C1 carbon of F6P then picks up a phosphate group via nucleophilic attack on ATP.  Phosphofructokinase catalyzes the reaction to form Fructose 1,6 bisphosphate.  ADP and H+ are released as side products.

**Gluconeogenesis–The reverse is catalyzed by fructose bisphosphate since this reaction is IRREVERSIBLE!**

Note the action center in the center of the enzyme.Step 4: Fructose 1,6 bisphosphate is then cleaved at the third carbon to produce D-glyceraldehyde 3-phosphate and dihydroxyacetone phosphate. Fructose bisphosphate aldolase catalyzes the reaction.  It leaves two, three carbon chains–one aldehyde and one keytone.  The reaction is reversible.

Step 5: The keytone (C1) in Dihydroxyacetone phosphate is reduced to an alcohol, while the alcohol (C2) is oxidized into a keytone, thusly making a second glyceraldehyde-3-phosphate.  Triosephosphate isomerase catalyzes the reaction and it is reversible.

Step 6: (From here on out, there are two equivalents of each molecule *i.e. G3P). The two glyceraldehyde-3-phosphates then pick up a second phosphate group (from Pi, not ATP) onto C3.  The aldehyde (=O) is moved to C1 and the OH on C2 becomes out instead of in (to the page).  This forms 1,3-bisphosphoglycerate and is catalyzed by glyceraldehyde phosphate dehydrogenase (GAPDH).  NAD+ is reduced to NADH and H+.  This reaction is reversible.

Step 7: 1,3 Bisphosphoglycerate then has its C1 phosphate group removed leaving just the oxygen (O-).  3-phosphoglycerate is formed as is ATP via the catalyst phosphoglycerate kinase.  This reaction is reversible.

Step 8: 3-phosphoglycerate then has its C3 phosphate group moved to C2, forming 2-phosphoglycerate.  Phosphoglycerate mutase is the catalyst and the reaction is reversible.

Step 9: 2-phosphoglycerate is then dehydrogenated at the C3 carbon to form a double bond between C3 and C2, forming phosphoenolpyruvate. The OH group on C3 is removed and pulls a proton off of C2 in the process, forming the double bond.  Enolase catalyzes the reaction, which is reversible.  Water is formed.

Pyruvate with its Na ion, balancing the negative charge on O.Step 10: Phosphoenolpyruvate then has its phosphate group (C2) removed to form ATP via pyruvate kinase. This leaves a keytone group on C2 while fully hydrogenating C3 (methyl group) called Pyruvate. ADP and H+ are consumed, while ATP is produced.

**Gluconeogenesis–this step is catalyzed via two enzymes, pyruvate carboxylase and phosphoenolpyruvase.  Pyruvate carboxylase turns pyruvate to oxaloacetate which is then transformed into phosphoenolpyruvate by phosphoenolpyruvase.  This reaction, obviously, is IRREVERSIBLE!**

The net gain of glycolysis is 2 ATP (4ATP were formed but 2 were consumed initially) and 2 NADH.

That’s glycolysis in a nutshell.  Hopefully, the step wise explanation of the reactions (minus mechanisms, sorry!) will aid you all in your studies of biochemistry.  NOW! On to the Citric Acid Cycle!

Cheers,

The Alchemist Kitten

Alrighty, so even though this is going to be several days late, *hides in shame*, I finally found some downtime to type up some of the most fundamental rules to naming organic compounds.  To be honest, the entire idea of nomenclature wouldn’t be so bad, since IUPAC (International Union of Pure and Applied Chemistry) did a mighty fine job-ish of coming up with a good systematic way to name compounds.  Unfortunately, as it is with everything in chemistry, it is never that easy.  To put it the way Professor Glatzhofer did: “The first three pages of the IUPAC text, which is about three times your text book, is all you’ll ever really need to know about nomenclature.  The rest is the exceptions.”  Gee, thanks.

Yes, so not only does the IUPAC naming system have its own little twists and turns on the rules, we also have common names.  Obviously, these are the names that we used for compounds before IUPAC came along and created a giant rule book.  Nevertheless, the simpler compounds are rather easy to name and follow a comfortable step-by-step process.  Yay! (Right?)

The Carbon Chain–First and foremost, we must identify what the base chain of the compound is.  Usually, this can be a 12 membered carbon.relatively easy as it just entails counting up how many carbons we’ve got.  Of course, it will get difficult when the chain branches into several units.  Just remember, the longest chain may NOT be the one that looks like a straight (if zig-zaggedy) line across the page.  Quite often, if the chain is branched, the longest chain will follow a branch.  Also, you can only number two ways: left to right and right to left.  For now, just number it left to right.  Now, how many carbons do you have?  The nomenclature goes as follows: methane, ethane, propane, butane, pentane, hexane, heptane, octane, nonane, decane and so forth.

A derivative of this compound will become very useful to you in the future!There are two exceptions to this:  Is there a ring in your compound?  If yes, then you must use the ring as your base compound.  If there is more than one ring, use the largest one.  The naming follows the above pattern, just with a cyclo- prefix.  Does your compound contain a double or triple bond?  Then drop the -ane and add -ene or -yne respectively.  Are there branches of C chains coming off your main chain?  Then count the number of carbons and name it, then remove -ane and add -yl (i.e. methyl, ethyl, butyl…)

Easy, yes?  Great.  It gets better!

Simple Substituents on the Chain–Now of course, we would all love if everything was just a saturated carbon chain.  It never works out as such since substituents are the atoms we rely on to react organic compounds!  Let’s just do alcohols and halides for time’s sake, though I do plan to go into much further detail at some point in time (ketones, aldehydes, carboxylic acids, esters, ethers etc).  However, today is supposed to be a breif overview.  The rest will require their own topic…

Of course, an alcohol is an organic compound that contains an -OH group.  You, dear reader, will probably be quite familiar with ethanol, since that is the culprit in alcoholic beverages.  As you just saw, to name an alcohol, you drop the -ane, (-ene, or -yne) and add an -ol.  Simple, yes?

Halides are a bit different, as their nomenclature involves a prefix instead of a suffix.  We typically call them alkyl-halides and they are quite simple to name.  If there is a chlorine on your chain, you’d name it chloro-name (or boro, floro or iodo).

Putting it together–Alright, now you didn’t think you could just slap some -ol’s and boro-‘s on the name of your chain and get away with it scott-clean, did you?  Of course not, chemistry is never that nice.  You counted the number of substituents on your carbon chain for a reason, remember?

Now, in order to give someone who is reading the name of your compound enough information to actually draw/identify the Name that Molecule!compound, we must number its substituents.  Here it gets a tad tricky.  You want to number your carbon chain in the direction in which you get the smallest numbers. Ex: If I had this compound, the first thing I would do is count the number of carbons; the base chain is pentane.  Then, I would identify the fact that there is a chlorine group on the carbon chain, so I need to number as such that Cl gets the lowest number possible.  As it turns out, it is in the middle of the carbon and should be numbered as 3.  So, to put this together, the compound is named 3-Chloropentane.

If there is an alcohol somewhere on the compound, it gets numbering priority and you should number your base chain in the direThis one is trickier!ction that gives the OH group the smallest number.  So!  If we have this compound, we should first note that the carbon chain branches!  Lucky for you, however, the branches are the equivalent.  The only difference is that one methyl group comes out of the plane of the page, where as one goes into the plane of the page. So, when counting, we get 4 carbons, so our main chain is butane.  We have two functional groups here, an OH and a CH3 group.  The OH group has numbering priority so we must number such that OH gets the lowest number possible.  That gives us 2.  So we have 2-butanol so far.  Now, we must add the methyl group in.  It is on the same carbon as the OH group; therefore, we get 2-methyl-2-butanol!

Lets do one last example, one that takes into account what happens if we have two of one substituent.Name this Compound! Obviously, we only have one carbon, so this is a methyl compound.  Now, we have two Chlorines and and two Flourines.  I said that things need to go alphabetically, right?  Well, what happens when we have two functional groups that start with the same letter? (Dichloro and Difluoro)  Well, we remove the di- and we alphabetize that way. So, here we have dichloro-difluoromethane.

So, how was that for a brief overview of nomenclature?  Not very brief, eh?  Well, I hoped you all enjoyed this and you have a better understanding of the basic ways in which we name organic compounds.

Happy Chemistry!

The Alchemist Kitten

Unfortunately, life has been kicking my ass. With my new position as “lackey” in a micro-biology lab and the giant biochem test last week, i’ve been a tad bit swamped. However, I did get a rather pleasing comment this week and decided since I do have a bit of down time, I ought to comment on it.

Mohab R wrote “…if we have , Chlorine And Florine … what’s higher in eNeg ? and Why ? What’s the rule controlling that ? ”

Its rather simple, actually. It does have almost everything to do with atom size.  Chemistry is a subject that relies heavily on the student assuming that things just work.  I went through most of my baby-chem/AP chem years just knowing that electronegativity trends ran left and up and never really questioned why, as long as I could get the damned problems right.  However, eventually we all need to learn the rules and I’m glad you asked!

Chlorine, as you’ll learn, Mohab (et all), is a rather non-picky molecule in comparison to its other column mates.  It will preferentially react in organic chemistry to make several isomers, where as its brethren, Bromine, will not.  Flourine, unlike Chlorine, is like the whore of column 17.  She’ll react with just about anything and with explosive results I must add.  A prime example will come when you study Organic and you’ll find that though Cl and Br will react and bond to organic molecules and are incredibly useful when it comes to the plethora of reactions that you’ll inevitably memorize, I and F will not (for different reasons, mind you–F’s being that is damn reactive and is nigh uncontrollable in laboratory settings.  I is just so damn slow that its not worth the time usually).  It all boils down to, whether you like it or not, molecule size.

Remember, the only electrons that truly matter when determining electronegativity (or almost anything else in chemistry for that matter: bonding, ionizing etc) are the valence shell electrons.  The other shells play absolutely no role in determining eNeg except for this:  the more shells you have on a molecule, the bigger and bulkier it is.  If you’ll notice when you determine orbital shells, that F has an electron hybridization of (1s2, 2s2, 2p5), where as Cl has a hybridization of (1s2, 2s2, 2p6, 3s2, 3p).  There’s a vast difference, you’ll notice.  Cl has two shells (1 with 2 e’s, 1 with 8 e’s) separating its nucleus from its valence electrons, thus making it harder for the protons in the middle to keep a good hold on the 7 e’s, as well as attract more.  (This is in comparison to Flourine, not the rest of the periodic table, in which Cl trumps most other elements in electronegativity).  F, on the other hand, has only one shell separating its protons and its electrons and this shell, you’ll remember, is made of only 2 e’s.  (The first valence shell is made of only 2 electrons, the subsequent ones are made of 8).  Thusly, F has a much much stronger hold on its valence electrons and can easily attract the final electron needed to fill its shell.

Hopefully, this explains why F is considered the most electronegative element and makes the differences between the halogens’ electronegativity a bit more apparent.

Thank you, Mohab, for your great question!

The Alchemist Kitten

This past weekend, I had a rather full discussion with my boyfriend, Justin, about the rather gray line between chemistry and its adjacent fields (such as biology).  Recently, I acquired a job working in the medical buildings with a microbiology lab and have found myself at a loss of words in awe at how beautifully my education and past lab experiences will fit smoothly into my upcoming ones.  As we come flying hard and fast out of high school, our minds bewildered with the idea of adulthood, we often only glance at the possibilities before us with bemusement before diving headlong into majors, minors and the livelyhood that comes with the title “college student”.

Now that I sit happily in my last few semesters, I feel that “the earth is getting rather large in the window”, as my mom likes to quote to me from my favorite movie.  Today marks the last week of my time as a student working with an あるばと, or part-time job.  Next week, I shall blast forward into what will hopefully be the rest of my life.  That being as it may, I was considering how closely related all the mechanisms of science really are.

Membrane pump like this!  It should move too!Take, as Justin and I did, chemistry in relation to biology.  Truely, the focus is rather similar.  Some chemists (and especially biochemists, whom I feel stand directly on the line between the two fields and wave their hands like only a mad chemist could) study on the mechanisms that cause life to function.  An example could be: what chemical mechanism drives that ion pump in the cell’s membrane?  Some biologists, on the other hand, could look at that same ion pump and wonder what effect it has on the organism as a whole.

As chemists, we work with the building blocks of everything on earth.  The keys I’m typing with, the board my professor isHoly Shit!  Yep, that's Chemistry for you.  Big Booms.  Always. writing on, the chalk, my lab partner next to me.  All of these are made up of the chemicals that we, via definition, focus on.  I find this staggering.  There is so much I could do and see, learn and discover but only so many years in which to do so.  It is rather unfortunate and yet at least I know I shall always be employed!  Of course, my field is narrowed by a driven need to improve the human race and my love for medicinal chemistry.  (The internship I had a few years ago solidified that for me!)

I just find it phenomenal that each and every object about us all is made of tiny particles fluctuating with tiny bonds through minuscule electrons.

Anyways!  Since that was my second rant in a row, I promise to have a lesson of some sort ready for later this week.  Tune back in on Thursday for some good, ol’e fashioned, IUPAC organic nomenclature.  That’ll be fun, right?

Happy Chemistry,

The Alchemist Kitten

Greetings, fellow chemistry aficionados.

Kitty is tired...*sigh*First of all, I want to extend a sincere apology for my lack of updates over the past few weeks.  Last week was a “test-block” for me–in which all of my classes decided to dump tests on me within a 3 day radius.  Needless to say, I was rather swamped.  Following that, mother nature, aided via stress and supplemental hormones, decided to strike me this week.  So, I sit here today on this beautiful Autumn Friday, I figure I ought to give you all a glimpse into the Kitten’s mind.  Lots of things have been flowing there recently and I plan just to let them out.

This semester has me taking the organic laboratory over again because OU, great school as it is, has required me to take their lab–apparently, SMU’s lab was not sufficient.  Initially, I had no problem with this, fully intending to make the most of a nice lab and previous knowledge of the experiments to be run.  Unfortunately, I’ve been sorely dissapointed.

Not only does the organic chemistry lab lack in luster, it lacks in teaching ability as well.  Besides spending two 3-and-a-half hour periods in the lab with a TA (whom I actually love and who is just as fed up as I am), I have to take time on Tuesdays to return to school at 5pm in order to sit through a lecture class.  Right, not so bad, really?  Wrong.  Though I hear that the lab professor isn’t half-bad when actually teaching Organic, he has only half-a-clue of what’s going on in the actual labs.

How so?  Our first real lab included distilling two compounds from each other using a Hickman still.  Ah, no biggie.  Distillations are easy, I thought, rather naively I might add.  The two compounds, had relative boiling temperatures of 90C and 120C respectively and thusly one can heat the compounds up to about 90, let it reflux until a reasonable amount of distillate forms, collect, then continue to heat up to 120 to collect the next sample.  Well, lo and behold, here I sit with my hotplate at 90C and nothing is happening.  Okay, I think. Maybe I should let it go for ten minutes or so.  It will boil.

Nope.  Never refluxed at 90C.  So, shrugging my shoulders, I cranked my hotplate up to 120C.  Again, I waited ten minutes.  No reflux.  Sighing with disdain, I crank the plate up even further and finally, the compounds begin to reflux at 150C.  Please, dear readers, note that I was using toluene, which should be on FIRE at this point in time.  (Okay, maybe not fire, but it should be burnt and crispy at this temperature.)  Incredibly frustrated as I was, I collected my distillates and submitted them.

My spectra came back the following lab period and specifically read two unknown chemicals that were NOT what we were supposed to be using.  So, not only did this lab fail incredibly, the manual or the prep-man in the chem stock room royally fucked up.  I am frustrated with this lab.  Very, very frustrated.

But, what can you do?  Unfortunately, I have no control over anything that happens in the lab (thankfully, that will change one Damn, I've never been so proud of ethanol!day).  I, like many of my fellow chemists in the lab, have to persevere through this bullshit for the rest of the semester.  Thankfully, not all is lost, as I have found that if I tweak the labs to make them more like SMU’s effective labs, I tend to get better results.  A prime example is my partner, Russ, and I’s perfect 95% Ethanol distillation and purification.  We’re quite proud of that moonshine! xP

This weekend looks to be full as I need to analyze and complete two long labs that I have done recently.  I’ll post more about my incredible disappointment with this lab as time moves on.  Hopefully, these complaints will bring clarity to my own work and perhaps to yours.

Cheers!

The Alchemist Kitten

(note: to see image captions, place mouse on image!)

Happy late update!  My week became something along the lines of “fucked” and so unfortunately, I am writing this during my D&D session.

So, today I shall be teaching a lesson on ionic bonding.  It is the most commonly known style of bonding and probably the most important style of bonding to baby-chem students who are studying solubility and other various aspects of compounds in solution.  (Both topics that I shall talk on at some point in time.)

Ionic bonds typically couple a metal from the right side of the periodic table to a non-metal to the left side of the periodic table.*  Since the right-side elements (such as Na, Li and K) typically have outer shells with either one or two electrons, they are much more capable of ionizing down to their cationic state.  Due to this property, a much more electronegative element (such as Cl, O or Br) can come right along and pluck off the “loosely” held electrons for themselves. (It should be noted that non-metals are usually greedy little bitches.  If someone lost an electron, it likely went to them.)

Now, this leaves us with a cation and an anion, which, as anyone who has ever played with a magnet would know, attract each other.  Thusly, we have an ionic bond.  It’s easiest to understand the ionic bond as occurring when opposite attract, but technically there is another force at play–energy. (It should also be noted that usually, energy plays a huge role in anything chemistry related).

I really gotta get a tablet...

I really gotta get a tablet...

Let’s use table salt as an example, seeing as it is the most commonly demonstrated ionic compound.  Energetically, it is more favorable for Na to lose its valence electron to Cl.  On the flip side, it is also favorable for Cl to pick up the extra electron.  Once this electron trade is done, both Na and Cl have fully filled valence electron shells. (Remember, all atoms are looking for a full eight electrons to fill their shells.  Except for H and He of course.)  Thusly, the bonding of the two atoms into a molecule produces a decrease in energy that is thermodynamically favorable.**

Since the bond is mainly a connection due to the polarized atoms, the Na region of the molecule is partially positive (little delta +) and the Cl region of the molecule, obviously, is partially negative (little delta -).  This effect makes ionic compounds break down easily in water, which is also ionic (with the H being + and the O being -).  With the ionic compound broken into its cation and anion, it is quite easy to add another compound (ionic or no) and induce a chemical reaction.  This is one of the prime reasons that ionic bonding is important to solubility rules.***

*It should be noted now that many of the common anions that baby-chemistry typically memorizes can also participate in ionic bonding and will often do so.  (Such as NO3-, which commonly bonds with Na to create an incredibly un-reactive compound that once drove me incredibly mad.  Due to its inert nature, it also is a commonly used salt-bridge in electro-voltaic cells–we use this for oxidation-reduction reactions and one will likely encounter them in all introductory chemistry levels.)

Hopefully this has made the idea of Ionic bonding a little bit clearer!

Happy Chemistry,

The Alchemist Kitten

**This concept is easily explained by the Gibbs Free Energy Equation.  It is an incredibly important topic to cover, and I shall do so once I talk of…

***Solubility rules, which is what I plan to teach on next, since I have covered-albeit briefly-ionization in water.

Fondest greetings to you all on this fine Tuesday!  I hope that your Labor Day weekend was relaxing and fulfilling.  Unfortunately, its back to the old grind for most of us and in lieu of a lecture, I bring you something more interesting—a brief history of our knowledge of DNA!

So, without further adieu, lets take a step back in time and discover the initial unearthing of the “molecule of life”…

Any high-school biology class will tell you about Gregor Mendel’s description of a predictable pattern of inheritance through his pea plants.  Four years later, in 1869, Friedrich Miescher isolated nucleic acids from white blood cells taken out of pus on surgical bandages (ew!).  Little did these two men know that their findings were intimately related—we wouldn’t make this connection until the mid-1900’s.

I’m not here to talk about Mendel or Miescher, however.  They are topics for another post at another time.  Today, our subjects are Oswald Avery, Colin MacLeod and Maclyn McCarty and their groundbreaking experiment from 1944.

Rough-Left, Smooth-Right

Rough-Left, Smooth-Right

The Avery-MacLeod-McCarty experiment took two strands of the bacteria pneumococci (one non-virulent and one virulent) and injected them into mice in order to determine that DNA was the key component in information transfer.  It was already known that the smooth strain (virulent) could transform the rough strain (non-virulent) into itself via a “transformation principle” (see Frederick Griffith’s work).

Ah the joys of clean experimentation...

Ah the joys of clean experimentation...

As seen in the image, the heat-killed smooth strain transformed the rough strain into its own type using a “transformation principle” that had, up until this point, remained an unknown substance.  Avery et. al. went on to extract the “transformation principle” from the cells and apply tests to identify the substance.

First, they heat killed the bacteria and extracted its components with a saline-solution (since the “transformation principle” was saline-soluble.)  Next, they removed excess proteins and polysaccharides via precipitate using chloroform or enzymes respectively.  Finally, through alcohol fractionation (a subject I will touch on at a later date), the single strands of DNA were removed from the remaining solution into long whispy strands.

Since testing proved that proteases and lipases had no effect on the substance, Avery et. al. was able to rule out proteins and lipids as the substance in question.  They found that the “principle” precipitated in alcohols, unlike carbohydrates.  Finally, through the use of ribonuclease and the Dische-diphenylamine test, it was deduced that the substance must contain dioxyribose nucleic acids.

Hurray!  We’ve discovered that DNA is the substance that carries genetic information, right? Wrong!

Unfortunately, it was a commonly believed principle in those days that proteins, not nucleic acids, were the “molecule of life”.  You might be feeling a double-take here, but bear with me.  Proteins use twenty-two amino acids to build themselves into incredibly complex polypeptides.  Nucleic acids only have five base pairs (remember RNA’s uracil!) and had been deemed with no viable purpose as of yet.  So, with logic us towards the more complex molecule as the substance that carries genetic information, nucleic acids were looked over as something irrelevant.  Yet again, however, it was proved that the most complex solution can be found in the simplest answers.

Not only were Avery, MacLeod and McCarty challenging common belief, they were doing so well!  Biochemically, theAvery Oswald experiments and procedures used on the pneumococci bacterium were incredibly sound and the techniques were clean.  Common contemporaries were baffled at the results and some even threw the report out the window as “rubbish”.  Due to this disbelief, the Nobel Prize that year went to another chemist in what is now believed to be one of the darkest marks on the Nobel Prize’s history.

Eventually, Alfred Hershey and Martha Chase confirmed DNA’s role as a genetic carrier with their (much less biochemically sound in my honest opinion*) T2-Phage experiment.  Right on thier heels was Watson and Crick, who through the use of Rosalind Franklin’s x-ray diffractions, discovered DNA’s trademark double-helix structure and thus cemented DNA into the public eye as the “molecule of life”.

This is where I shall stop our historical journey today and bring us back to the present.  When I was first presented with the knowledge that DNA had been found several years earlier than Hershey-Chase and Watson-Crick, I was shocked!  The scientific community was a place where I felt any and all ideas were given the time deserved.  (Granted, they should be well researched and well documented, as Avery et. al.’s was.)  In the end, I suppose that even the most well-thought out, well organized research can be ignored if too premature.  Nevertheless, this blog post today was to bring Avery-MacLeod-McCarty’s work to the light again and remind the community who it was who discovered DNA’s actual purpose.

Cheers!

The Alchemical Kitten

*I wish to expand upon the unsound T2 experiment in comparison to the pneumococci experiment and will do so at another time.  However, this post was for history only.  A commentary will come in due time.

You guys have my sincerest apologies for my lack-of-update on Thursday!  I completely forgot!  However, as a treat, I decided to explain one of the more complicated concepts from general chemistry…

That’s right!  Today we’re going to talk about the seemingly complex topic of electronegativity.  A lot of general chemistry and baby/AP chemistry students struggle with this concept and how it applies to reactions and molecules.  For now, I’ll cover the general basics and trends of the subject.

First, let’s define electronegativity.

An atom is considered “electronegative” depending on its ability to attract electrons towards itself.  In this sense, electronegativity is a chemical property of a particular element.  Unfortunately, like most subjects in chemistry, this simple explanation, though sufficient, doesn’t completely grasp the entire subject.  For now, we will stick with this simple definition for our purposes today.

Since electronegativity is a chemical property, we should be able to map its trend across the periodic table.  Indeed we can.  Let’s think about some atoms for a moment and deduce whether they would prefer to have electrons or not.

Lithium—Li has three electrons in two valence shells.  Two electrons are on the inner shell closest to the nucleus and the last one is on the next shell alone and unpaired.  With this idea in our heads, lets ponder whether Li would want another electron or not.  The outer shell of Li requires seven more electrons to make the atom “happy”.  Finding seven electrons could be quite an impossible feat, and thusly Li tends to lose that electron rather than keep it.  This means that according to our definition of electronegativity, Li has low eNeg.

Oxygen—O has eight electrons in two valence shells.  Unlike Li, O’s outer shell electrons fill six of the eight electrons needed to fill up the second shell.  Again, let’s consider O ability to pick up electrons.  Those six outer electrons are not going to go away easily and thusly it is much more energetically favorable for O to pick up two extra electrons than to give away six.  Therefore, O has a high eNeg.

From looking at Li and O, we can define a trend of increasing eNeg going from left to right across the periodic table.  We’re not done yet, however!  Does the trend go up or down on the table?

Well, to describe this, we must think about atom size.  Let’s compare two right-side elements, say, F and I, both having a similar eNeg.  Comparatively, F is incredibly small—I having 44 more electrons than F—and therefore I’s outer seven electrons are much further away from the positive nucleus than F’s.  Due to this distance from the nucleus, I is less capable of attracting electrons than F.

So, our trend must increase in eNeg from left to right and from bottom to top! (A good way to remember this is “Up and to the Right”.)

Paint ftw!  I've got to get a tablet...

Paint ftw! I've got to get a tablet...

Hopefully, this little explanation helps you all understand the basic idea of eNeg and how to identify which atoms are more electronegative than others.

Happy Chemistry!

The Alchemist Kitten