How to Read a Scientific Paper (and Actually Understand It!)

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

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.

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...

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

Retrogaming co-op post!

Hey hey hoo!

All, I am working on a bit of a biographical post for you all.  But, while you wait ever so patiently on bated breath, my darling readers, here’s a bit of a co-op I did with a friend!

Retrogaming 101–Legend of Zelda: Ocarina of Time

I really like to play older video games and this is the first of a few that we will be co-authoring.  GASP! No, no, my life does not consist wholly of science and study.  In fact, I’ve done nothing this summer but read, drink and play WoW. So, enjoy another bit of my awesome life, readers.  And give Cluttered Mind a bit of your patronage!

Cheers!

Update from the Road: The epic DNA analogy.

Hey-hey-hoo, fellow science nerds and blog-o-philes.

Today, unfortunately, will not be filled with the gooey sciencey goodness you are hoping for! I just made the long haul journey from Oklahoma to Baltimore and unfortunately will not have internet until Tuesday!  As such, I do not have the resources (though not for a lack of time) to create a informed, well-researched post about something good and magical! Starbucks internet, though glorious, has been put to use periodically these past few weeks answering emails and ensuring that everything in the adult folder of my life has been filed correctly.  (Adult as in money and mortgages, you naughty readers!)

dsDNA denatured to ssDNA by the breaking of hydrogen bonding. There, you got some science today!

However, I did come across an excellent speech from Christopher Hitchens on the Catholic Church that I thought I should share.  In no way am I attempting to pass judgement on the Church or spout my opinion on religion in any sense.  But, what I do plan on doing is inspiring conversations about how religion and science are not separated by a solid black line, as many would like it to be.  That would be far too comfortable.  Instead, these two polar opposite systems of reality aren’t truly separated at all, but rather merge and flow with one another.  They are like the phosphodiester backbones of dsDNA–Apart from one another, and yet conjoined by the hydrogen bonding of the nitrogenous bases.  Sure, they can be separated and function well on their own, but without each other, they are not as stable and the message is not complete.

Unfortunately, as humankind is wont to do, we often forget how integrally important religion is to science.  Religion was the initial way in which we questioned and found answers to the world.  Astrology and alchemy have long since been outdated and forgotten as ‘primitive’ forms of interpretation, but they were, at one point, methods in which the philosopher in each human could formulate questions and find a subsequent response towards the inner machinations of the world.  The arts of astronomy and chemistry (and subsequently biology, physics, nasa etc…) evolved from these initial surveys of the world to form what we see today as “Science”.

The Vatican

Religion, like the Catholic Church, was created much like my examples above to be an answer to the things in life that we cannot explain.  The only real difference is that most religions do not change.  They aren’t stagnant, so to speak, but they do not follow a natural, Darwinian path of adaptation to the changing times.  And if they do, as some have, accept changes, they are slow to do so and even slower to enact them.  This, my readers, might be the crux of the issue.

H. sapiens, like most other higher evolutions of life, struggle to deal with changing situations.  We are not, by nature, open-minded to things that will affect how we live, work, strive and believe.  We prefer, in general, for things to be stagnant and slow, like a river in the heat of summer.  Earth, on the other hand, does not sit in a continual state of apathy and the environment in which we live is constantly flitting faster and faster.  It is because of this perpetual motion that religions have stayed the same.  They provide a sense of stability to our species as a whole.  They are always something that we can go back to and rely on.

It is this clash of evolution and rock-steady sameness that causes the inevitable arguments we see every day on TV.  Is it the universe or is it God?  Were we made out of randomness or was entropy not a factor in the least?  Curious arguments to say the least.  Perhaps, in this new age of twitter, facebook and the internet, where people are melding ideas faster than I can type, we might see, at long last, the melding of the stability of religion with the truth seeking of science.

Alas, the price for Internet...

Or I could be too hyped up on coffee.

Cheers,

Kat

How to Wine and Dine your Bacteria: Basic Agar

Howdy all! Why yes, I did post again…

Today’s topic spawns off of a discussion I had with a friend a while back about agar plates, as they had never really heard the basics of what a petri plate is and why it is so crucial to a modern microbiologist’s work (despite being “low tech”).  As such, lets take a brief run through of agar plates.

Of course, when I was in grade-school, this is what I thought of when I heard Petri plate.

Example of agar agar in food stuffs.

So, first lets hit the history of agar plates in true Alton Brown style.  Agar, or if you’re being picky “agar-agar”, is a substance isolated from red algae, aka: seaweed.  This polysaccharide (a polymer of galactose, I believe) provides stability to the algae’s cellular walls and just happens to make a very firm structure.  As such, we humans found the texture and structure of this gelatinous seaweed appealing and most asian cultures have adapted it to suit their fancy.  (Americans, on the other hand, are a bit more slow on the uptake.  Weird textures freak us out it seems!).  Agar-agar is also used in jellies, jams, soups and other various food-stuffs that need to be thickened or solidified, as it produces a smooth texture and has a melting point that is easy to reach in the kitchen without burning. (85C is the common temp we lab rats give).

Sciency-food-fact! Often, myself and my peers refer to agar plates as “similar to Jell-O”. (In fact, in lieu of a proper plate, I demonstrated an experiment once using Jell-O as a growth substrate!).  Unfortunately, this is a bit of a misnomer…Jell-O also contains a giggly food thickener, like agar-agar, called gelatin. However, it is a collagen polymer derived from animal tissue, not a sugar polymer from plants.  The collagen is a much more loose mesh, molecularly, and does not give as firm of a structure as the plant cell polymer does.  (Play with your upper ear for a good example of collagen).  A plant polymer, like agar-agar, affords more stability and more rigidity to the cells. (Try bending a leaf, it doesn’t work quite so well as your ear…) Therefore, if you were to compare a treat solidified by agar-agar to one solidified by gelatin, the agar-agar product would be more solid and have a thicker, smoother texture than that of the gelatin product.  And now you know!

Anyway, back to science.

A lab tech in Robert Koch’s lab, clearly enjoying her jelly tea, realizes that this agar-agar stuff would be a great solidification substance to grow bacteria on.  Thus, agar plates were born.

MacConkey agar. The growth in pink indicates lactose utilization, while the yellow does not.

We use agar-agar to solidify damn near all sorts of media into small, compact little circles that allow us to more easily quantify and isolate the microscopic lifeforms we work with.  From LB and minimal medias to MacConkey and blood agar, we use this white powder for damn near everything.  Its relatively simple, toss an amount into the liquid media (i.e. 15g for 1L of LB in most labs), autoclave it up, let it cool and pour. Simple as that.

Agar has numerous practical uses.  We can identify enviromental isolates (or at least start to) using several selective medias in agar.  For example, MacConkey agar grows only Gram negative bacteria and will change color depending on the isolate’s ability to ferment lactose.  Blood agar plates demonstrate whether a species can lyse bloodcells (either beta or alpha) and often help to differentiate between Strep and Staph isolates.  Hektoen enteric agar is used to identify organisms from, as the name states, the Enterobacteriaceae family.  I’ve used HEA before to identify a Shigella species in particular, but it is often used for any fecal MO’s (like Salmonella).

A fine example of a quadrant streak that shows the isolation of several distinct colonies, as indicated by color.

We also modify agar in order to isolate a pure culture: a colony in which the cells came from ONE lone parent organism via the quadrant or enviromental streak.  We can also identify microorganisms by their resistance to an antibiotic impregnated into the media.  For example, alot of plasmids that we use commercially have an antibiotic resistance cassette placed within the DNA.  This provides us researchers an easy form of identification of clones who had the correct plasmid shoved into their membranes as they will grow on, say, LB with Amp.

Of course, this technique and the other plates I’ve mentioned will have to wait for another day.  This post is getting long and my intentions were only to give a brief explanation of agar and why we use it!  Clearly I got carried away!  So stay tuned for my next post and perhaps the next in my series of HTWADYB!

Cheers!

Kitty

Graduate School Admissions: The Good, the Bad and the Epic.

Hello world!

Apollo, my new Shiba Inu pup.

As it turns out, applying to graduate school and attempting to survive your last year of college takes alot more out of a student than I expected.  Who knew?  Well, I made it!  Graduate school at UMBC is on the horizon and I will be packing up to move to Baltimore within the next few weeks.  In the interim between now and when my course work starts, it is my utmost goal to get a few blog posts out per week on an assortment of information biological or scientific that I find interesting.

So, what shall we do for today?  Well, for starters, lets talk about graduate school admissions.  The decision to go to graduate school is not one that should be taken lightly in today’s economy.  Below are the tips I received or learned on my own about the graduate admissions fiasco process.  Take my advice as you see fit.  Note: I am NOT part of any graduate admissions board–this is just the process I went through and my thoughts on the matter.  Anything I say does not reflect my school or any other school’s opinion on the matter.

The Good:

Formalities aside, applying to graduate school is a very big step forward in your career as a scientist.  For most college juniors and seniors, there are three major choices that they can make towards their future.  They can go to medical school, to graduate school or they can attempt to work for a few years to fill in their resume.  Having a higher education in this field is incredibly important in moving up on (not only the pay-scale) but in the research community.

This being said, make friends with the graduate admissions secretary at each school you are applying to.  Typically, I received an email within a week of submitting my online application from the secretary stating that everything (or not) was in her office and she was avaliable for questions.  I followed up almost instantaneously, making sure that transcripts, letters of reference and my own cover statement made it to the school in a timely fashion.  They were usually super helpful, provided you were chipper and polite, and were prompt in letting me know if something was askew.

The Bad:

Does this need a caption?

As thankful as you may be for your professor/boss/co-worker to write your LoR for you, recommendations do get lost in the mail/translation/minds of the recommender, so you must keep on your three people to ensure that everything was put in on their end.  Each school wants something different from your recommender and it is up to you, not them, to keep it straight.  Give them a list that includes: each school’s name, address, form or format wanted as well as the dates in which your application is due.  Hand it to them with lots of praise (and treats, like cookies, always help!) and then ride their ass until you get confirmation from them and the admissions office that the recommendation has been accepted.

(As it turns out, I had to chase down one of my people for over a week to get him to submit the recommendation. As it turns out, he forgot. -_-;)

Again, is a caption really needed here?!?

Another glorious /sarcasm aspect to the admissions process, while we’re on the topic, is the vast differences each school wants out of you, the applicant.  Some schools want everything online, some want it in paper, some want half and half.  Its truly a PITA process and again, it is up to you to keep it straight.  I kept a running list of my usernames, passwords and current application status going on my desktop, as well as on my bathroom mirror.  And I still struggled to keep it straight.

The absolute worst part about the graduate admissions process, unfortunately, is the waiting game.  I submitted all of my applications by December 15th and waited for close to three months before I got my first letter.  Oh! And speaking of letters…Rejection letters are the worst, most horrible feeling an applicant can ever get.  Quite honestly, its like taking a bit of your soul, crumpling it into little bits and then feeding it to rabid hyenas (which is exactly what you did during the application process) and then finding out that you gave the hyenas E. coli and they don’t want to see you again.

All I can tell you is chin up.  It may be the absolute worst feeling in the world, but it does, indeed get better…

The Epic:

The feeling you get when you finally get a “We LOVE you, come to our school.”  There’s no other thing I need to say but that.

Seriously.  That’s it.  I expect all of my readers to be intelligent enough to know how to handle an interview/wine-and-dine date with your school.  If you don’t GTFO ask me!

That, ladies and gentlemen, was my experience with graduate school admissions as a helpless undergrad.  I sincerely hope that it will help you find a bit of clarity, or at least a smile, as you read it.  Especially to those of you out there who will be applying this upcoming fall.  Start early, stay positive and good luck!

I should have another update to you all within the week.  This time, hopefully about something much more sciencey and gooey. Well, maybe not gooey…

Cheers,

The Alchemist Kitten

My Reboot, with a Change of Style and Situation.

It is well known that I had a rough first year of college. I initially started this blog long ago to help me study towards bettering my grades. Well, since then I have switched majors (Microbiology, ftw) and have found myself in a very happy internship.

Regardless, I still find myself trying to come to ease with college in a hurry (two years down, one to go). There isn’t alot of help out there for science majors who struggle to balance everything that is important to them in life. Unfortunately, we have to make a lot of cuts in order to make our dreams come true.

I am having to quit my DnD group of close to two years because I have found that despite my incredible efforts towards garnering an A in my most difficult courses, I still fell short and I think the extra time Saturday evening for review (which I did loyally every Saturday in high school after a day of play and relaxation) is what I really need back.

So, here’s to a new start on education and a restarted blog to go along with it.

What to expect to see:
Lessons on Microbiology, Chemistry and college in general
Tips for the GRE
Tips for Graduate School
Occasional rants

Here’s to a good semester of summer courses!
Cheers,
Kitty

The Citric Acid Cycle (aka, Krebs or TCA cycle)

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!

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.

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.

Step 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

 

Glycolysis (and Gluconeogenesis)

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!

Step 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!**

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.

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

Star-Treky-Dungeon-Dragonie rant.

I feel that I must write an entry on Star Trek—it is an obligation that my geeky innards require me to speak on.  It is hardly a secret that I am a huge gamer and sci-fi nerd, so I suppose it is almost my specialty to speak on sci-fi and fantasy in general.

The one particular thing I found interesting in my travels through the universe was that of the “god-like” figures that appear frequently in Star Trek.  Having watched every movie, seen part of the original tv series, most of The Next Generation, all of Voyager and a majority of Enterprise, I must say that these god-like figures can be found in every which direction and in every shape and size.  Each and every one of them is inherently flawed in some way.

For example, the Caretaker, a god-like entity who is the catalyst for the entire plot of Voyager, finds himself at the end of his life.  Granted, it is implied that his life has lasted millennia and shouldn’t be ending, he is, nevertheless, dying.  The reason?  His “life” partner had left him in some sort of relationship-trauma huff and never returned.  Unable to return to his home and unable to continue living, the Caretaker has been searching the galaxy for a means of power to keep his subjects alive.  Oh yes, did I mention that he created a race, placed them on the planet, and provided for their every whim?  Now that he is dying, the Caretaker belatedly realizes that his little race will soon die after him, since he had been their only source of sustenance.

Flawed?  Totally.  Almost human?  Yep.  Are the writers of Star Trek attempting to make an underhanded comment?  Oh yeah.

What?  I have no idea.

Whether they are just reinforcing the idea that the God on earth is supreme or making a comment on evangelist Christianity is beyond me.  What is apparent is that flawed god-like figures has become a staple in Star Trek lore.

Another interesting point, while on the topic of flawed gods, is that of the deities in the popular role-playing game Dungeons and Dragons.  Each and every one, like the Greek or Roman pantheon, has a specific realm of worshipers and jurisdiction.  They also have their stories about how they rose to god-hood.  Some fell through the depths of hell and emerged the glorious victor.  Others corrupted nations and defeated lich empires to steal the throne.  Each have their own story of failures and triumphs.

In fact, that’s the whole point of the “game” called D&D!  You, as a player, must conquer your enemies and your own personal issues in order to rise above and become whatever you (or your alignment, at least) are destined to be come.  A very fine example comes from the last campaign that I played with the guys.  In order to flesh out our DM’s homespun setting, we aspired to play fully in the “asian” empire, whose name I cannot spell for the life of me at the moment.  The entire game started out with the emperor slain at the feet of a once player character, Malek.  We then found ourselves running from the rather corrupt law and joining forces with the once-Shogun to take back what was our country.

After many battles and negotiations with other nations, we defeat Malek and his minions and take back the country that rightfully belongs to the people.  Kero Kuma, our silently designated leader, was then vocally promoted to the position of Emperor, after proving his worth as an apt and competent “Commander In Chief”.  It was perfect for a character that rose from nothing and became one of the most powerful men in the nation.

As it turns out, most of the deities in the current D&D pantheon weren’t even gods to begin with, but were raised to the title after their death (Even though Kuma-sama may never reach god-hood, we have several past player characters who have at least achieved sainthood.  My own character, Rosalynd, is quite on her way to being a god.  It all depends on who you become when you don the dice.).  Hence, one must redefine what they consider god/god-like.  If our flawed gods in Star Trek were placed in the D&D realms, would they have been given deity-hood?  I have to wonder.

My apologies for the rambling rant, I just wanted to examine the differences in god-like figures while waiting for my electrophoresis DNA run to be done.  And it is!

Cheers!

The Alchemist Kitten

IUPAC–The Baby-Name Book for Chemists

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 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.

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 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 direction 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. 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