AP Biology Exam: Last Minute Cramming!

If you are reading this, then you are probably in an AP Biology class.  By this point, you have probably already taken the AP Biology Exam as well.  For those who have – I hope you did well!  For those reading this at another time, possibly before the test –  good luck!  It’s a league of a test all in its own!  What makes the AP Biology test so challenging is that biology is such a wide field of study.  Virtually anything from the natural world can find its way into a question.  As a student taking it, you have to be prepared to answer whatever is given to you!  My science professor did a spectacular job of preparing my class for such a critical test.  However, even the best laid plans can go astray.  Point being, even though we were productive all year, my class didn’t achieve everything we were hoping.  So, the last week leading up to the test was nothing but a “cramming phase”.  This post, a tribute to our last study sessions, is a compilation of the various topics we covered in that time.  Pay attention, because it’s about to get very random!

________________________________________________________________________

First up on our list of discussion topics is Developmental Biology.  We spent most of our time going over a lot of terms and vocabulary that apply to this category of science.  As a result, we did not spend much time going over individual steps or components in-depth.  As far as embryonic development, we talked about some of the initial terminology used during early development.  The blastula, for example, is a sphere full of cells.  The embryo, as it develops further, will create what is known as a blastula pore.  This is the first instance in which a fold occurs toward the center of the blastula sphere.  The process of Gastrulation is when the tissue truly folds inward on itself.  The end result is a ball with 3 layers.  Each layer is important as it creates a different structure of the developing organism.  The outermost layer is known as the ectoderm, and is responsible for skin and nervous system.  The middle layer is the mesoderm, creating tissues, organs, muscles, and the skeleton.  The endoderm is responsible for creating glands and inner organ linings.  The interesting part of this is that most creatures, whether it be a fish or a chicken, develop in this three layer fashion.

The layers become important because they very based on the complexity of the creature.  Humans, for example, are known as Deuterostomes.  Under a category known as Triploblasts (meaning to have three layers in the embryo), we form a separate mouth that is distinct from our anus (the latter being formed from the blastula pore).  A step below us, but still in the Triploblast category, are Protostomes.  They have a unified mouth and anus, which is formed from the blastula pore.  An example of such a creature would be a squid or jellyfish.  Finally, less complex creatures are under a category known as Diploblasts (they only have two layers – the ectoderm and endoderm).  To put it simply, think about cnidarians.  Their primary feature is that they have radial symmetry.

The main point of learning about these embryonic features is to understand that many animals develop differently.  We can use this knowledge to help further our research of cell development, as well as in experiments involving the moving/affecting of cells.  When it comes to comparing the developmental biology of animals, there are two terms that come to mind: homologous and analogous.  They both refer to structures that are found on animals.  Homologous structures are things that animals have that come from a common ancestor.  An example would be the forearm in the skeletal system of bats and humans.  They are particularly similar in their structure and appearance.  An analogous structure, on the other hand, is a feature with similar functions, but no common ancestor.  The best example of this would be a bird wing and an insect wing.  Both are used for flight, but they are developed drastically different.

One other term we learned about within Developmental Biology is apoptosis.  This is when the organism’s body intentionally tells certain cells to die.  An example would be human hands.  In the embryo, there is a webbing that connects the fingers together.  Apoptosis is the process that tells the web cells to die, removing the webbing, and giving us defined fingers.  Another example is a tadpole’s tale.  As the tadpole develops into a frog, the tail undergoes apoptosis.  The cells are reabsorbed into the frog after they are killed.

________________________________________________________________________

Now on to the second piece of information that we covered during our final week.  Understand that this information does not in any way, shape, or form relate to the previous topic or potentially the next one.  Think of this post as a “grab bag” that is comprised of many smaller, separate potential posts.  Next we discussed the Gibbs Free Energy equation.  This equation is as follows:
The change in free energy = change in enthalpy – temperature x change in entropy.

This equation is used to find the total amount of energy that can be used to do work.  Enthalpy is the measure of the total energy within any given situation/system.  Entropy is the number of “combinations”/the energy that is already used in a system.  Entropy is multiplied by temperature because as the temperature increases, the amount of energy used also increases.

This is a basic formula that, greatly simplified, shows:
usable energy = total energy – temperature x used energy.

________________________________________________________________________

While we are on the topic of equations, there is another equation that we learned that was almost guaranteed to show up on the AP Exam: the Chi Square Test.  While this test is somewhat elaborate, it provides some useful information that determines whether a series of data fits/correlates to Mendel’s laws.  His laws were that a monohybrid cross (cross breeding one trait) would have a 3:1 ratio of traits, while a dihybrid cross (cross breeding two traits) would have a 9:3:3:1 ratio of traits.  Let’s use an example problem to understand the processes behind Chi Square:

Example: A plant heterozygous for color undergoes self pollination.  There are 27 total offspring.  23 of the offspring are purple, and only 4 are white.  Do a Chi Square Test to see if the results match a Mendelian Ratio.

The equation for a Chi Square Test is as follows:

Using such an equation is relatively simple!  We know the observed numbers: 23 purple plants, and 4 white plants.  Now, to find the expected, we have to see what a 3:1 ratio would look like with 27 plants.  (This involves dividing 27 by 4, giving you about 6 plants, then multiplying by three to get 20.)  This means our expected ratio should be 20:7.  Is this close enough to fit Mendelian’s theory?

To find out, we have to plug in our data to the equation.  We must do this twice, once for each phenotype of plant.

The purple plants would be the following: (23-20) squared / 20 = (9/20)
The white plants would be the following: (4-7) squared / 7 = (9/7)

Since you are finding the sum, you must add these two numbers together.  After you simplify, you get 1.74.  This is our chi squared value.  Now we must see if the results match the 3:1 ratio.

To do this, we must compare it to a Chi Square Table.  The table works off of degrees of freedom and probability.  Degrees of freedom is found by taking the number of offspring minus 1 (purple and white make 2.  So 2-1 = 1).  Probability, as a rule of thumb, is accurate if the 0.05 value is used.  Use the table below to find the point where there is 0.05 probability and 1 degree of freedom.

The number you found is 3.84.  You know that you have found an accurate test group if your results from the chi square test fall below the probability number.  As our number 1.74 is below 3.84, then we know we have a proper 3:1 ratio.  Mendel’s laws work for this population!

________________________________________________________________________

And that concludes today’s programming!  What you just saw were the three big topics that we talked about as last minute preparations for the AP Biology Exam.  These concepts are good things to know in this field of science, I will say.  I hope you learned something, and enjoyed this very informal blog post!

The Central Dogma

There are certain topics in science that do not allow you to know “basics”. These are the topics that you either have vast knowledge about, or have no knowledge at all. Typically, these are the topics that are categorized as complicated and difficult. I’m not going to lie, this post will divulge into one of these topics – and it won’t be easy. But rest assured that, if you hang in there, and concentrate, this will be comprehendible. As I’m sure you are well aware by now, this post is on the Central Dogma.

What exactly is the Central Dogma, might you ask? For those who are unfamiliar, the Central Dogma is – basically – the processes involving genetic information. These processes are known as transcription and translation. The goal of the Central Dogma is to go from DNA, to Protein. This requires an intermediate step of turning into RNA. While this seems basic now, there is a lot more to it than meets the eye. Shall we begin?

The entire process starts with DNA. As you know, DNA is located in the nucleus of a cell, and permanently contains genetic material. It is comprised of nucleotides that form the pairs A-T, and G-C. The first step in Central Dogma is transcription. This is, basically, the process that forms RNA. Transcription occurs in three major steps: Initiation, Elongation, Termination. The former step, Initiation, is when an RNA Polymerase – an enzyme that specializes in creating RNA polymers – is attracted to what is known as a TATA box. The TATA box is a location on the DNA where there is a pattern of T-A-T-A nucleotides. This is where the new strand of genetic material will start to be copied from. Initiation continues when other factors are assembled around the DNA. These other factors include an RNA transcript, which temporarily separate the hydrogen bonds that run down the middle of DNA’s double helix.

The secondary step of transcription is Elongation. This is when the RNA polymerase slides down the DNA, using RNA nucleotides to “match” the DNA strand being replicated. The RNA nucleotides still follow the A-T and G-C pattern of pairing together. However, in RNA, the T nucleotide (Thymine) is replaced with a U (Uracil) nucleotide. A diagram of elongation can be seen below. Take notice of how the RNA nucleotides (which are red in picture) match with the blue DNA nucleotides (which are blue in picture) inside of the RNA Polymerase structure (the white “bubble” looking figure).

The final step of transcription is known as Termination. The process of Elongation creates what is known as Pre-mRNA. In termination, the elongation process ceases (the RNA polymerase received a message from a codon to stop replicating the DNA). Then, the Pre-mRNA is given a 5′ cap and a 3′ tail. The 5′ cap goes at the “head”/”front” of the RNA strand. The purpose of this cap is to ensure that nothing can be added to this side of the genetic strand. The 3′ tail, known as a Poly-A tail as it is primarily comprised of the nucleotide A (Adenine), is where any additions to the strand are made. Termination is also the process where splicing happens. Splicing is when any unneeded segments are removed from the strand (we will touch on that a little later). After the Termination process is complete, Pre-mRNA becomes mRNA, otherwise referred to as messenger RNA.

Ok wow! That is a lot of steps! Here’s what we’ve done so far: we’ve taken DNA in the nucleus, undergone the process of Transcription, and made RNA. The next step is that of Translation (which occurs in the cytoplasm of a cell). This is the step that actually creates the proteins that will be used throughout the body. The process uses what is known as a tRNA to create proteins. The tRNA is an entity that contains an amino acid (which is used to make proteins) on one side. The other side has what is known as an anticodon. An anticodon is the exact opposite of a codon. So what then is a codon? A codon is a segment of three nucleotide codes.

(Time for a mini lesson on codons! Pretend you have an mRNA with the following nucleotides: AGUCCAGUG. The codons for this selection would be AGU, CCA, and GUG. A codon is a segment of three nucleotides. Understand? Good!)

Going back to translation, now: tRNA is comprised of an amino acid on one side and an anticodon on the other (see the picture above). The anticodon is the “opposite” of the codon. This is the case so that the codon and anti-codon are able to pair together. (If a codon was CAC, then the anti-codon would be GTG). This process of pairing occurs inside of a Ribosome, which slides down the strip of RNA. The Ribosome, for purposes of this post only, has the same “job” as the RNA polymerase – it “houses” the process as it occurs (if that helps you any in visualizing what is happening). As tRNA pair up with the mRNA, long strips of amino acids start to form. These strips are known as polypeptides, and are what make up proteins. The picture below demonstrates this process of Translation. Take special notice of the tRNA (light blue) and the Ribosome (brown).

There you have it! That’s the Central Dogma! We’ve gone from DNA, through transcription to RNA, through translation to a Protein! That about does it for this blog post. I hope you lear-…

…just kidding! We aren’t done yet! Absolutely not! There is still so much more of the Central Dogma to discuss! The next topic on the table is that of alternate splicing. As we just talked about above, DNA makes RNA, which makes protein. The concept of alternate splicing is relatively simple. This process says that DNA makes RNA, and RNA is capable of producing multiple types of protein. As a result, one gene is able to make multiple proteins!

First thing’s first, however: we need to learn what exactly is splicing? Splicing is the process of removing a “segment” of RNA that is not needed for a specific protein synthesis. The removed segment, known as an intron, is recycled for its nucleotides. The pieces that are then joined together are known as exons. The process of splicing occurs by a splicesome – which is comprised of RNA and protein. The diagram below most accurately represents splicing.

So now we know how splicing works. Take the same general concept and apply it to the transcription process we talked about earlier. By using the process of alternate splicing, each piece of mRNA can end up with different combinations of exons. These different combinations will lead to different proteins. Check out the diagram. Take notice of how the transcription process occurs the same regardless of which exons are selected.

Still with me, so far? Like I said, this was not going to be an easy blog post! If you have made it this far, though, then you definitely deserve some credit! You are doing really well! Hang in there, because we are almost done! The final part of the Central Dogma that we are going to discuss is the idea that transcription is not a one way street. That’s right, we’re now going to talk about reverse transcription!

The process of reverse transcription is exactly how you picture it to be: starting with an mRNA, and ending with DNA. The process is virtually the same as normal transcription. This time, however, the enzyme reverse transcriptase starts at the Poly A tail and moves “up” the strand of mRNA. As it goes, it uses DNA nucleotides to make pairs with the mRNA nucleotides. The end result is a cDNA strand (complimentary DNA).

What exactly is the purpose of reverse transcription? The most common use is that of viruses. A normal virus works by implanting its genetic material into a cell’s DNA. The cell then copies the genetic material of the virus, turning it into mRNA, which in turn makes more of the virus. The virus then spreads to other cells, which also copy and duplicate the virus. Sometimes, however, the virus starts with RNA. Known as a retrovirus, these viruses have to use reverse transcription, using the cell’s genetic material as a template, to create DNA. This viral cDNA is then used to make more viruses within the cell. A common retrovirus, by the way, is the HIV/AIDS virus.

Well there you go! Now we are done with Central Dogma! And I mean it this time too! We have covered a lot. I hope that you have been paying attention, and have learned a lot about the processes of our genetic material. Now, at least, you can say that the Central Dogma is a topic in science that you really understand!

My Dog Is Broken!

You may not realize it, but you are in for a different type of blog post!  You may already have suspicion, as the title involves a broken dog.  That’s right – a broken dog.  Wait, a broken dog?  No need to call animal services, the animal in question is only hypothetical.  It is the subject of a digital case study that focuses on cell signaling within organisms.  So that isn’t too bad, is it?  The dog, by the way, is broken because it is experiencing erectile dysfunction (ED).

Like I said, there is no way this will be a normal post.

Please quit your laughing, and stop with the inappropriate jokes to the people around you.  (Ok, we did it in our class too.  Keep reading only after you’ve composed yourself.  There is serious science in this, after all).  The case study involves looking at the cell signaling pathway of the animal.  Then, we have to determine what is probably defective, and what the best course of treatment would be.  The case study, if you care to see it for yourself, is linked here.

The important information for figuring out a solution to our little pooch’s problem is all within the cell signal pathway.  Obviously, there is a protein that is not activating, and not letting the signal for the erection to get through.  Let’s first look at a simple pathway, and identify some of the major components:

The first thing to do when looking at a cell signal pathway is to identify what substance is starting the signal.  By looking at the top of the chart, we can clearly see that nitric oxide is the first messenger.  The presence of nitric oxide in the cell (whether it comes from nitroglycerin or a neuronal cell in the body)  will cause a minor reaction that will, in turn, effect the secondary messenger: cGMP.  Now the technical name for cGMP is cyclic guanosine monophosphate.  For simplicity, we will stick with cGMP.  The cGMP then acts upon PKG (which is a cGMP reliant protein kinase – meaning a protein that adds phosphate groups to other proteins – that effects the turning on and off of enzymes), and that ultimately creates phospho-proteins.  These phospho-proteins reduce the amount of calcium within the cell.  The lack of calcium, which normally is restrictive, allows the cells to  relax.  Relaxation in the smooth muscle cell is what allows blood to flow through; thus achieving an erection.

So now we know how the signal works.  Are we done?  In a word, no.  It is important to know that the more reactions occur, the greater the result becomes.  This can be seen through the arrows in the pathway, as they start small and get bigger as more reactions occur at each step.  Now we know how it all works.  It’s time to step it up a notch and try to help our little dog friend.  Below is a more complicated cell signal pathway.  See what you think:

A lot more complicated than the first, isn’t it?  Well don’t panic, it really isn’t too bad once you get started with it.  At this point in the case study, the doctor is recommending that the dog be given one of two substances.  The first, the well known Viagra.  Viagra works on PDE, which may help the dog overcome erectile dysfunction.  The second is ginseng, a substance found in tea that affects the nitric oxide that is entering the cell.  What will each substance do to the dog?  That’s what we are going to find out!

Let’s start with the more simple of the two explanations and talk about ginseng.  If we were to give the dog ginseng, then the amount of nitric oxide that it would produce would increase.  More nitric oxide means that there would be an increase in the creation of cGMP, which in turns means more PKG, which means a more relaxed collection of cells.  This solution is relatively simple, and would solve the dog’s problems by increasing the amount of the first messenger.

The second substance to consider would be Viagra.  Viagra is what is known as a PDE 5 inhibitor.  That means that Viagra negatively impacts the reactions that occur with PDE 5.  Now PDE 5 itself is also an inhibitor, but an inhibitor to cGMP.  Normally, the dog has PDE 5 causing a decrease in the amount of cGMP production, which in turn lowers the PKG production, which leads to less relaxation (basically erectile dysfunction).  But with Viagra, the work of the PDE 5 inhibitor is decreased, allowing more cGMP to be made (which, following the pathway, leads to greater relaxation).  Basically, assuming it doesn’t confuse anyone, you could say that Viagra is an inhibitor to the inhibitor!

As ginseng and Viagra show, fixing a cell signal pathway can be done by either increasing a positive response (in this case, producing more nitric oxide via ginseng), or decreasing a negative response (using Viagra to minimize the inhibitor).

One final thought to consider: what happens if neither the ginseng or the Viagra fixes the dog’s ED problem?  Any clue?  If neither substance had any positive result, then the “broken” part of the dog would probably be the PKG protein.  This is because both the Viagra and ginseng work to increase the amount of cGMP in an organism.  If that cGMP is unable to travel down the pathway because of a defective PKG, then the end result of erectile dysfunction would be the same.

Well there you go!  You can now say that you helped a dog fix its erectile dysfunction problem!  I bet you weren’t expecting that when you woke up today, were you?  And while you can go boast to all your friends about what you just accomplished, there is something more relevant to be gained from all this.  This case study, regardless of how humorous the subject is, was a great way to understand how cell signal pathways work.  It is easy to see how one simple defect can cause an entire process to stop working!  I hope you leave this post happy about what you learned (I guarantee the dog is!).

Gaining Immunity

What would you say if you were asked to name the most vital system in the human body?  Would it be the nervous system, which controls everything?  Or the digestive system, which provides energy for your body?  What about the cardiovascular system, which transports blood and oxygen so that your body can survive?  While it is impossible to truly identify which system is “most” important, there are some that are more specialized than others.  In particular, there is one body system that has to be more prepared and ready to act – mainly because it has to handle an extremely large variety of unpredictable things.  This is the Immune System; the system responsible for combating foreign diseases as they attempt to infect the body.  As you are about to see, how the Immune System works is quite the spectacle!

The first step to understanding the Immune System is to understand what it is trying to fight.  While the range of foreign entities that harm the body far exceed the capacity of this blog post, it is worth mentioning one of the most potent: the virus.  The virus is comprised of numerous protrusions (they look like spikes) on its external surface.  These protrusions are named H or N, and in different combinations can lead to different sicknesses (thus how the H1N1 virus received its name).  Viruses are incredibly effective because they hijack the cells within the body, and use the cells own replication processes to create more virus cells.  Of course, this is only the case if the cell can enter the body…

There are two types of defense that your immune system has to resisting infection.  The first is known as your non-specific, otherwise known as innate, immune system.  This is the type of protection that occurs all the time, without needing to be “activated”.  Such examples include the skin as a natural barrier, nose hairs which capture foreign particles that are breathed in, or the natural production of mucus.  The non-specific immune system is also the category for what are known as phagocytic cells.  These are cells that consume any foreign entity that is not native in the body (an example would be white blood cells).  These cells are innate because they are always patrolling throughout the body.

The other type of defense is known as the specific or adaptive immune system.  This involves the specific reactionary measures that occur with the presence of certain viruses.  The specific immune system is activated by the presence of an antigen; a substance such as a toxin that the body produces antibodies against.  Viruses have antigens on them.  When the body detects the substance, then antibodies are created to target the infection.

The specific immune system is where most of the “action” takes place, as your body tries to fight off a disease.  There are many different types of cells that play very important roles within the system.  To start, there is the T Cell.  There are two types of T Cells: Helper T Cells (known as CD4) and Killer T Cells (known as CD8).  We shall start with the former- the Helper T Cells.  These are the cells that are responsible for recognizing specific antigen receptors found on viruses.  They get their information from an APC (antigen presenting cell).  These cells are responsible for consuming bacteria, receiving the antigen, and then presenting it to the Helper T cell to be “read” and identified.  The Helper T cell then uses the information to distribute TH1 and TH2 cells.  TH1 cells and TH2 cells are types of Helper T cells.  The former are the cells that send a message to another type of cell (which we will get to in a little while) to go eat the virus.  The TH2 cells are also known as B cells, which is mentioned later.

The other type of T Cell is the Killer T Cell.  These cells are also commonly called cytotoxic cells.  The reason is that these cells identify the virus, and then spray a poison over it to try and kill the specific region that the virus is located on (resulting in the death of both virus cells and normal body cells).  While this may not completely stop an infection, it can slow it down and buy the body some time while the immune system continues to react.  Interestingly enough, it is these Killer T Cells that are the cause of many uncomfortable symptoms.  Sore throat for example is the result of Killer T cells killing the naturally occurring throat cells.  The virus cells, except by activating the Killer T Cells, have no part in the discomfort the individual feels when sick.

Another type of important cell in the Immune System is the B Cell.  There is a series of lymph nodes that traverse everywhere in the body.  These lymph nodes, as part of the lymphatic system, are brimming full of what are known as B Cells.  (By the way, both T Cells and B Cells are known as lymphocytes, because they are created in the lymphatic system.  Just some extra information for you!)  B cells are specialized in the sense that each one is only able to detect one individual type of disease.  When the disease is detected, that individual cell undergoes what is known as clonal selection.  This is when the cell, which is capable of resisting the chosen disease, clones itself millions of times.  It is these B cells that make antibodies, which go attach to the virus.  The B cells also create what are known as memory B cells, during the proces of clonal selection.  These cells stay in the body after the disease has passed, and “remembers” that specific disease.  If it ever comes back, it will be able to immediately respond.

The last major component of the immune system is the macrophage cell.  Macrophage is a collective term for the cells that go and consume the virus.  They normally are used to “eat” the debris that is found around the body (sometimes created by Killer T cells).  However, when they receive a signal from a TH1 Helper Cell, they then try to consume the bad virus cell.  Remember how I mentioned earlier that the antibodies go and attach to the virus, after the B cells detect the antigen?  Well, the antibodies are the cells that “mark” the virus, making it distinct for the macrophage cells (which include phagocytes) to go and consume it.

Below is a diagram that outlines the relations between the cells in the immune system:

Pretty interesting, don’t you think?  Well, before we call it quits for this blog post, there is one more very intriguing part that needs to be mentioned.  The AIDS disease is that part, because it manages to impact the Immune System in a very unique way.  When someone gets the HIV virus, the T cells within their immune system are being targeted.   The T cells are ultimately destroyed to the point where they cannot do their job.  As a result, the body cannot identify any antigens/viruses that enter the body.  This in turn means that the immune system cannot fight any infections, because it does not recognize having any!  It is this concept that makes AIDS such a potent condition.  The HIV/AIDS virus itself cannot kill you, no!  But its presence disables your immune system, leaving the body vulnerable to being infected by any other disease.

That about does it!  You have seen how the immune system works, and what can happen in the most severe cases where something goes wrong.  When you really dive into the workings of the Immune System, it is really easy to see why it is such a spectacular system!  It is extremely prepared to handle even the worst types of diseases.  Don’t you feel safe now, knowing you have such an elite protection force working inside you?

Becoming One With an Enzyme!

Often times in science, you get to read about the topic that you are learning about.  Sometimes, depending on the resources available to you, you may even get the chance to see your current study topic – such as through a video or lab experiment.  But how many times in science do you get to BE your topic of study?  Not nearly as often, I’m sure!  In AP Biology, we have recently been studying enzymes and their significance.  Of course, where’s the fun in only learning about them?  My classmates and I went one step further and actually became enzymes!  To do this, we had to balance our yin and yang, center our chi, and become one with the enzyme!  Let me explain:

To become an enzyme involves participating in a simple yet effective lab.  This lab requires 60 toothpicks to be placed into a bowl.  These toothpicks represent the substrate that the enzyme (a student) would be acting upon.  For those who are unfamiliar, that is exactly what a substrate it; a substance that is acted upon by an enzyme.  Now, just for clarification, an enzyme itself is a sort of catalyst that speeds up and/or triggers many of the chemical reactions that occur in living organisms.  The purpose of this lab would be to see how they work.

To do so, the two students (who are blindfolded, to ensure the task isn’t too easy) has to break as many toothpicks as they can in two minutes.  The toothpick must be completely snapped in half, and only complete toothpicks can be counted when broken.  The studen-ehhh enzymes, cannot break a toothpick that is already broken (it won’t be counted).  Every 30 seconds, a counter would report the number of toothpicks broken.  We ran two trials at the same time: one with Enzyme Mandi, and another with Enzyme Henry.  These initial trials are represented in the graphs below as the baseline (the blue line).

The next step was to have the enzymes undergo denaturation.  To simplify a complex term, denaturation is when an enzyme “breaks down” and loses its normal shape.  This process makes it more difficult for the enzyme to do its job.  So, to test the effects that such a process would have on a reaction, our enzymes were forced to tape their thumb and forefinger together.  Then, with 60 new pieces of substrate (toothpicks), they had to undergo a second trial.  Obviously much slower, the results can be seen as the red line in the below graphs.

The final step for this lab would be to add an inhibitor.  Inhibitors are responsible for slowing down the chemical reactions that occur within living organisms.  Think of them as the arch nemesis to an enzyme.  To demonstrate an inhibitor’s impact, 20 plastic toothpicks were added to the bowl.  These toothpicks cannot be broken by enzymes, and would not be counted in the total number.  Another two minutes, and our results with the inhibitors can be seen with the yellow line down below.  Clearly the inhibitor has an adverse effect on an enzyme’s performance.  That said, the effect is not nearly as drastic as that of denaturation.

So what did we learn from this lab?  We learned that enzymes are responsible for catalyzing the chemical reactions that occur within organisms.  We learned that denaturation occurs, which causes a decrease in the productivity of the enzyme, as its overall shape is altered.  We learned that inhibitors decrease the speed at which enzymes work.  The important thing to realize is that there are many factors that can alter the overall efficiency of a chemical reaction (another concept not mentioned above, but represented in the lab, is that of concentration.  The bowl with the toothpicks acted as a certain degree of concentration.  This factor plays a role in enzyme speed, as the more spread out the substrate is, the longer it takes to react with them).  But most importantly, we learned what it is like to be an enzyme!

Declaration of Respiration

Ok!  Before we get this blog post going, let’s do a quick exercise:  Ready?  Now breath!  In!  Out!  In!  Out!  Deep breaths!

Good!  Do you realize what you just did (other than, probably, making the noises of a certain Star Wars villain)?  The entire breathing process, compacted into one word, is: respiration.  That’s right- you were respiring at the beginning of this post.  In fact, you are still respiring now!  To breathe is one of the most crucial parts to staying alive!  (Obvious, but true.  After all, I want to see how long you would try to last without oxygen).  However, do not think that this is a topic not worth studying.  In fact, it is quite the opposite!  My AP Biology class has performed numerous experiments, as well as doing some extensive research, for our study of respiration.  What we found and accomplished are the components to this blog post!

How Does Respiration Work?

If I were to ask you how does respiration work, could you tell me?  You would probably say air enters the lungs and carbon dioxide exhales.  While that is true, it is not what I’m looking for!  How does that provide energy? Being an advanced class, we are going three steps deeper into the inner workings of the respiration system.  This understanding, on the most molecular of levels, is what is going to aid the experiment later in the post.

The first step of respiration occurs in the cytoplasm of the cell.  In this area, glucose undergoes a process known as Glycolosis.  This process consumes 2 ATP energy molecules, but expels 4 ATP energy and 2 reduced NAD molecules (NAD molecules are carriers that transport electrons around the cell.  To be reduced means that they have gained extra electrons, giving a negative charge).  The end result of Glycolosis are two pyruvates.  One pyruvate enters the lumen; a fluid filled space in the middle of the cell.  By doing so, it loses two carbon dioxide molecules and a reduced NAD molecule.  This leads to a reaction with the pyruvate and a substance known as COA that creates Acetyl COA.

The next step in respiration is known as the Kreb’s Cycle (or Citric Acid Cycle).  The Acetyl COA interacts with a substance known as oxaloacetate, within the lumen, and breaks apart.  The second pyruvate, from the Glycolosis step, will do the same thing.  By the end of this step, for both pyruvates, there would be an expulsion of 6 reduced NAD carriers, 2 reduced FAD molecules (a different type of electron carrier), 4 carbon dioxide molecules, and ATP. All of these products go into the Mitochondria’s Electron Transport Cell.  Recall that the Mitochondria’s job is to provide energy for the cell.  Providing the products of the Kreb’s Cycle to it leads to an extremely large number of ATP energy!

But hold on!  We’re not done yet!  We’re going to take a moment and expand upon what happens inside the mitochondria to produce that ATP energy.  In short, it is known as the Electron Transfer Chain.  Please refer to the diagram below for a visual aid:

The circles in the center of the screen are energy carriers, which are carrying hydrogen molecules.  The reduced NAD and FAD carriers come to these energy carriers, and dispense their electrons.  Oxygen will then join the system (when someone takes a breath) and remove the electrons in the energy carriers.  This will not only produce water, but also will make room for new electrons and hydrogen molecules to move down the chain.  A gradient is created from the empty space that the oxygen created.  The hydrogen, moving across energy carriers to fill that space, creates energy.  That’s how it all works!

(As a side note, the process is different in muscles.  After Glycolosis, the pyruvates go to the muscles, where reduced NAD carriers drop of electrons and hydrogen.  This leads to the creation of lactate, which is what makes you sore after exercising.  However, minor ATP is created by this process).

Respiration Lab

So now that we know about how respiration works, it is time to put that knowledge to use with a lab that was recently completed by my AP Biology class.  The goal of the lab was relatively simple: we were going to analyze the respiration rates of three different organisms.  These organisms would be crickets, fish, and peas (yes, I did say peas.  I’ll explain in a little bit).  Going one step further, we decided it would be best to see if respiration would be effected by different temperatures.

The first step was finding a way to measure respiration.  Obviously, this would be slightly tricky, as two of our organisms thrive on land, and one in water.  The answer is much more simple than you think.  The crickets and peas would be placed into a plastic container, which would be sealed at the top by a carbon dioxide sensor.  This sensor would detect the amount of carbon dioxide in the bottle.  As the crickets and peas respire, that number should increase.  This is how we would record the respiration levels of these organisms.  See below:

The fish, on the other hand, would have water that is mixed in with a BTB solution (which is blue until carbon dioxide is entered into it.  Then it becomes yellow).  The fish in theory, as they respired, would introduce more carbon dioxide into the water and turn it yellow.  We performed a miniature experiment to see if this is even a possible option for measuring fish respiration.  To put it simply, yes it can work!  Take a look at what we found:

Before:

After about an hour:

However, as sad as I am to admit, this is about as far as we made it with the fish.  Complications with time and health restricted us from being able to get logistical information about the respiration of fish.  Though we did get the mini experiment- which beats nothing!  (If you have done this lab with fish, and completed it, please message me!  I’d like to hear your results!).  This did not stop us from continuing our studies with crickets and peas however!

To start with the former, we placed 4 crickets into a bottle, and subjected them for 5 minutes to different conditions.  For each condition change, we switched crickets and containers (to ensure the last trial wouldn’t be impacting the next one).  The conditions were an ice bath at 0 degrees, 45 degrees C water, and 80 degrees C water.  The results, to start and end the time period, are below.  Remember, we are measuring the rise in carbon dioxide.

Ice bath:

start- 1500 ppm

End- 1700 ppm

45 Degrees Warm:

Start- 2100 ppm

End- 4100 ppm

80 Degrees Warm:

Start- 1450 ppm

End- 3450 ppm

But wait!  As with countless science experiments, we ran into an issue with this data.  In the middle of the two trials with warm water, all 5 crickets died.  They were unable to withstand the temperatures.  So, while this information looks beneficial, it really cannot be taken at full value as being accurate (as we don’t know when the crickets died).

So now we were out of luck with fish and crickets.  There was only one option left: peas!  The experiment would be set up exactly the same with peas as with crickets.  The only differences would be minor tweaks to the time, temperature and the addition of a control.  The time is now 10 minutes per condition, with the condition temperatures being an ice bath at 0 degrees C, warm water at 37 degrees C (body temperature), and hot water at 55 degrees C.  The control would be using non-germinating peas (as they do not respire like the germinating ones do, seen below).

Once again, we were looking to measure the change in carbon dioxide levels (though this was slightly skewed as the peas started respiring before their testing time, as they were left out).  The results, which were still valid, of this second trial are seen in the graph below:

What this graph shows is that there is an extreme change in the carbon dioxide levels of respiring organisms at different temperatures.  Respiration seems to slow down with cooler temperatures (similar to the Mammalian Diving Reflex.  If you don’t know what that is, look it up!  It is quite neat).  Warmest temperatures also negatively impact respiration rates.  It appears that there is a happy “middle ground” for respiring peas.

Despite all of the complications among the experiment, you can’t deny that it was a pretty cool concept!  The entire focus of this post was to enlighten you with the process of Respiration.  How does it work?  What affects it?  How much heat can crickets stand before dying? (Just kidding on the last one!).  These are all questions that you should be able to answer now!  Respiration is an important quality that is often times overlooked and under appreciated!  I hope you now realize just how important it is for all organisms!

Shining Light on Photosynthesis

In AP Bio, we have spent a large portion of our time working with the concept of Photosynthesis.  All of our studies into this topic – which range everywhere from the components that absorb sunlight, to the ways energy is made, to even labs involving the study of Photosynthesis – can all be found by clicking the Prezi Presentation here.

I do warn you, however, that the presentation is quite large.  I apologize for any long loading periods, or lagging display.  Thank you for your patience!

Enjoy!