Miss This!

Hey readers! I am really happy because I do get viewers on this blog! However, my AP Bio year is over! ūüė¶ I know sad day! But I really miss being able to do these blog posts! There won’t be anymore Inner Fish posts, because I no longer have the book on my iPad! I hope you enjoy reading what is here and thanks for visiting!


Development and Some Cool Plant Stuff :)

So, this my second to last blog! I SEE THE LIGHT! ūüôā Anyway, this is about embryonic development and also the cycle for plant reproduction in specific plants. ¬†It jumps around a little bit, but that is because these notes are straight from the discussion we had. ¬†So, bear with me.

So, we started our discussion with Mr. Ludwig by talking about Apoptosis. ¬†This is programmed cell death in your body; basically telling your cells to die. ¬†Why is this necessary? ¬†Well, for example, when you are an embryo, your hands are all webbed together. ¬†If your body didn’t do apoptosis than we would still have webbed fingers. ¬†Your body tells those cells to die so there isn’t a web.

Then we learned about the different stages of a developing embryo.  One of the stages we went over is when it is a Blastula.  This when the embryo is just a ball of cells.  Then you have gastrulation which is when your ball of cells starts to cave inwards to create multiple layers and one small opening.  This small opening is called the blastopore (which is important so remember it for later).  This is actually what will end up creating a lot of your guts and stuff.  More advanced embryos will have 3 layers.  The outer most is the Ectoderm which will end up creating the nervous and integumentary systems.  The middle layer is the Mesoderm, which brings forth muscles and bones.  And last is the Endoderm with your guts and schtuff.

Most experiments done on embryos involve removing or implanting in the embryo to see what happens. The other ways people study embryos is by marking a part of it and watching it as the embryo develops, using fluorescent dye and using genetic markers from a similar yet different species.

There are also cells in embryos call neural crest cells.  There are a dorsal root ganglions on either side of the spinal cord in the developing fetus.  They are a set of nerve cells and are mainly sensory nerves.  In order to be on your sides, where they are supposed to be, they have to migrate there.

So, remember how I talked earlier about the blastopore of an embryo.  Well this is important when you start talking about more advanced animals compared to less advanced animals.  The most advanced set of animals are called Deuterostomes.  In these animals the blastopore turns into the anus and the mouth is created in another area.

The next animals are Protostomes.  In these animals, the mouth comes from the blastopore and there is only one opening.  One example of this is a jellyfish. And the last animals are Diploblastic.  These animals only have 2 germ layers and have radial symmetry.

The next subject we brought up is the difference between Analogous and Homologous. ¬†Analogous means that similar characteristics didn’t come from the same ancestor, but they have a similar function. ¬†For example, bird wings and insect wings both have a similar function but are obviously not from the same ancestor. ¬†Homologous are characteristics that have a similar function and arise from a common ancestor.

SO, now we get to talk about plants.  I think most of our AP class agrees that plants are a pain the butt.  But here we go.

Today we are talking about Sporophytes and Gametophytes.  The first plants we talk about are Ferns.  Here is a little picture to help you out.

photo 2 (4)So, it is a little hard to see, but don’t worry I will explain it.

With these plants you have a diploid and a haploid generation.  Sporophyte is the diploid generation and in ferns, this is the generation you are used to seeing.  The Sporophyte creates the spores through meiosis.  They go to the Gametophyte and then, through mitosis you get female and male gametes. These then get fertilized and and turn into a Sporophyte again. Below is the picture for the moss.

photo 3 (5)

Now we get to learn about moss.  The moss that you see around is the gametophyte, which is the haploid.  The sporophyte in moss is a stalk that grows out of the top of the gametophyte.

In seeding plants the gametophyte is buried inside the sees.  It is more buried inside the plant but it is still there.  Almost all seeds have dual fertilization.  One part gets fertilized and becomes food for germinating seed and the other part becomes the  embryo.

Well, that was fun! I hope I didn’t confuse you too much.


The Central Dogma

Well, its late and I’m gonna jump right in.

The Central Dogma is the process where RNA is transcribe and then translated to make proteins.  Sounds pretty simple right? Well, like anything in AP Bio, its not.

So, lets start with Transcription.  This process happens in the nucleus of a cell.  The DNA that we need to transcribe is seen when you unfold the chromosomes and it has the information we need for protein synthesis.  Good? Great!

So, first you have to prepare for Transcription.  There are several transcription factors that are involved and they all gather around the transcription initiation site.  The most important of all these factors is the enzyme Polymerase.  This one does the biggest job.  It also has a tail like structure which is CTD and it processes RNA.  So, one of the transcription factors undoes the double helix structure of DNA so the work can be begin.

So, now that DNA has been unwound, the DNA opens up and Polymerase changes its shape to begin.  It reads the DNA info and with the nucleotides it is taking in, creates RNA.  Remember GATACA and how things like match up?  If the DNA has a C, then you match it a G.  Yes they have much more technical names.  Do I remember at 10 at night, no.  Same with A and T.  BUT, RNA is a little different.  Instead of having a T nucleotide, it has a U.  So just remember that it changes from DNA to RNA, or else they would be SUPER DUPER CRAZY similar, and it would be horrible.

As the DNA is being created it gets a 5′ cap attached to its head at the 5′ end. ¬†The reason the camp goes on this end and not the other is because nothing can be added onto the 5′ end. ¬†If something will be added to the RNA, it will be added on the other, 3′ end. ¬†Also, RNA gets spliced. ¬†There are different parts of the RNA called introns and exons. ¬†The introns are the information that is unnecessary for this certain protein. ¬†So, there areas get bent and cut off and broken down. ¬†However, the exons are the valuable part and they get stitched together to create the RNA. ¬†When the RNA is done, Polymerase leaves and Poly A Tail is added to the 3′ end. ¬†We believe a possible reason for the Poly A Tail is so you body can recognize that this RNA is natural and could help with that. ¬†It could be kind of like a defense. ¬†But, now, sense it has all the information for protein synthesis, it is taken out of the nucleus to get translated.

So, that RNA that we just made has a very specific name; mRNA.  This stands for messenger RNA because basically it is carrying the protein message.  So, translation happens outside of the nucleus and in cell.  Now the RNA we have consists of sets of 3 nucleotides, whether it be AUU or CGA or whatever.   These nucleotides are always recognized together and they are called a codon, like a secret code or something.  Pretty creative.  This is how it will be translated.  So, mRNA forms ring for translation and the big player for this process is the Ribosome.  It scans the mRNA until it finds the initiation site, which is a specific codon.

Then tRNAs (transfer RNA) arrive.  Each tRNA carries a different amino acid wit it.  tRNA match a certain codon on the mRNA and then drop their amino acid off.  The Ribosome takes the amino acid and starts linking them together.  All these amino acids create a protein that is based off the mRNA.  This process happens several times to make several proteins and then the RNA gets broken down and recycled.

Hope you learned.

And today I am feeling better and I realized I should show you the SWEET video we basically learned this cool stuff from.  Some stuff I mentioned came from class discussion but this basically covers it all.



OH NO! Doggy is Broken

So this is going to sound VERY strange but, the other day in AP Bio we did a little case study about cell signaling and strangely enough it was about a dog have ED (erectile¬†dysfunction¬†for those of you who don’t know!). ¬†YES, if was a very fun conversation to have with three teenage boys! ūüôā Just kidding, I should give them more credit than that! ¬†But basically I am going to take you through some of the questions we discussed and probably show you some of the diagrams we used to help us! Have fun!

So, erection is controlled by a cell signaling pathway that looks a little something like this….

dog broken simple

So our first “assignment” was to identify the first messenger that starts the signal transduction. ¬†As a class we decided that the first messenger is the nitric oxide. ¬†It starts the channel of messages. ¬†The next thing we had to find is the likely second messenger. ¬†We decided that the second messenger is the cGMP. ¬†This is because the phosphate is being acted on as it changes from GTP to cGMP. ¬†The next assignment is to identify the cellular response cause by the cell signaling cascade. ¬†The cellular response that is caused is relaxation (sometimes the easiest response is the right one). ¬†The next assignment was to explain why the arrows go from smaller to bigger. ¬†This is because the more reactions that happen then the more you accumulate and the more you move and that is why the arrows get bigger. ¬†Last for this is to identify whether the receptor that starts the cell signaling pathway ¬†is in the plasma membrane or intercellular. The answer to this is that it can be intercellular. ¬†When the particles coming in (nitric oxide) are small enough they can just slip through the membrane instead of having to use a receptor.

Now we can get onto the second (and a little more complex model).

dog broken 2

In this diagram you can see the PKG.  This is also known as Kinase.  Kinase adds phosphate groups to proteins and changes the function.  It creates phospho-proteins.

Now we get to answer the questions for the second assignment.  Here is the first question.

1. Melody said that ginseng enhances erection. What effect would you expect ginseng to have on nitric oxide? Why?

Ginseng can enhance erection because it will create more nitric oxide.  By creating more nitric oxide, you make a stronger signal, and it is more likely to work.

2. Knowing that Melody said Viagra also enhances erection, what effect would you expect it to have on PDE5? Why?

PDE 5 breaks down cGMP.  But there is a PDE 5 inhibitor that keeps it from doing that.  So, Viagra (wait for this) inhibits the inhibitor! That way cGMP can be broken.

3. If neither chemical works what protein(s) would you suspect is ‚Äúbroken‚ÄĚ?

If neither ginseng or Viagra work odds are that the PKG is the one having problems.


Inner Fish Update

Hey readers! Sorry to say, but Inner Fish may be officially over. ¬†At the moment, stuff has been so busy we haven’t been reading and I wont have the book over the summer! Sorry about that! I was actually having fun writing them and loved seeing views on them! Maybe next year I will finish it out! But thank you for reading them!


Toothpickase…Or Shall We Say HENRYASE!

So recently in AP Biology, we did an enzyme lab. We used toothpicks to represent what the enzymes take apart. So, what were the enzyme? Well, that would be Henry and I! This was quite an adventure! So hold on for the ride!

So, we started out by deciding who was going to be breaking toothpicks and since Henry and I are OBVIOUSLY the most aggressive, we got to do it! ūüôā We also had to have counters to count the amount of toothpicks we have broken and a recorder to make the table. So, we had count out 60 toothpicks each and put them in a dish. Every 30 seconds, we would pause the breaking and Michael would write down the amount that we had broken so much. Then Henry and I were blindfolded and it started. It is actually really fun and in all honesty, a little harder than you would think! Sometimes you can’t tell if it had already been broken or not and drove me crazy! But, I still DESTROYED Henry!

So this first trial I just described is the Baseline trial. Then, we got to make things interesting. The next experiment we did involved an idea called Denaturation. This is when the protein’s shape is changed. When ever you do this, this changes how it acts and in our case makes it a lot harder to break be enzymes. To illustrate this Henry and I had to tape our forefingers and thumbs together. Yes things just got interesting! So you can see through the graphs below that the denaturation process definitely slowed me down. Not only are the toothpicks harder to break, but it is also hard to tell if they are already broken or whole.

And the last change we did; we added inhibitors. This symbolizes when there is something blocking the enzyme from doing it’s job. To stimulate this one, we added in plastic toothpicks, so they can’t be broken. This also slowed us down but not quite as bad as the denaturation. The graphs are all below!

These are mine because I totally destroyed Henry (Love ya Henry)! ūüôā


And here’s Henry’s!



Thanks for reading! Hope you enjoyed! Maybe you should go try it for yourself! ūüôā


Immune Responses

Okay! Well, hello again my fellow learners! To prepare for the AP Bio test we are basically reviewing things that we were a little weak on on our practice.  As you can tell, this one is about the Immune System/ Immune Responses.  While we had this discussion I took notes write in here, so this blog post is basically taking my notes and turning them into sentences! I really hope it makes sense.  If nothing else, I get credit for making a blog post and actually having it done a little early! Have fun!


So, first off, there are two types of immunity. ¬†The first is Innate Immunity (also known as Non-specific. ¬†With this type of immunity there is no activating, it is not specific to a certain microbe, it is just there. ¬†Part of this Innate Immunity is the epithelial tissue (for a good description on this see my Anat and Phys Blog Post) that lines everything that has an external entrance. ¬†The epithelial tissue secretes mucus that can get organisms stuck until they get into your stomach and are dissolved. ¬†However, occasionally, this immunity doesn’t catch something and then you are infected. ¬†The virus gets down to your epithelial protection and disguises itself as a protein and the cell unknowingly opens it doors to the virus. ¬†So, the virus takes over the cell and uses it to create more viruses (a virus army, OH NO!). ¬†However, there is a basic defense for this.

Part of this immunity is phagocytic cells (crazy, crazy words) and these are cells that attack anything that isn’t identified as a natural part of your body. ¬†These cells “swim” around and when they find something like this, they kill that cell and possibly surrounding cells. ¬†However, by this time, not only one cell is affected but lots. ¬†So, these cells (Killer T Cells) are going through and trying to kill all of these cells. ¬†This is why we can get sore throats and such. ¬†This pain can actually be a sign to your body to slow down because it isn’t doing so hot. ¬†Actually, our symptoms when we are sick are cause not by the virus, but by the immune system fighting it. ¬†So, it is good thing that this isn’t the way it continuously works, because I have feeling that wouldn’t end well.

Well that basically sums up your Innate Immunity (or at least what we reviewed) and I hope you got all that.  As I said earlier, there are TWO types of immunity.  The next is Specific/Adaptive Immunity.  This immunity targets specific cells and this is the part that I like.

So, when a cell becomes infected, it will take a piece of the virus and grind it up and make something called and antigen. ¬†An antigen is the thing that tells other cells that there is something wrong with that cell and that it needs help. ¬†And this is where all the different Immune Cells come in. ¬†So, I mentioned earlier, something called a T cell. ¬†Well there are three different types of T cells (isn’t this fun!). ¬†T cells are both helpers and suppressors. ¬†The helper T cells are the cells that recognize and grab the antigen. ¬†The killer T cells are part of the innate immunity system, killing infected cells.

No, here is gets a little crazy.  If there are three types of T cells, there has to be two types of helper T cells, and there are.  There is T subscript H 1, which will take the antigen to the macrophage, a cell that we will talk about a little bit later.  And there is T subscript H 2, which will take the antigen to the Lymphnode and more specifically to the B cells.

B cells can almost be thought of as memory cells.  This is because they are the key to how the body fights infection.  Each B cell (and there a TON of different types and only one or two that the same) has unique cell surface proteins that detect specific viruses.  This takes me back to why B cells are memory cells.  Each B cell is equipped to fight a virus.  So, lets say you get a vaccine for something.  You body will take that and make sure that you have B cell to fight off that infection.  Each B cell holds the key to virus it will fight.

So, the B cells are located in the Lymphnodes. ¬†When the antigen gets taken here, it gets released among the B cells. ¬†The cell that responds to the virus then gets cloned thousands of time, and releases the antibodies that can fight the virus. ¬†The antibodies aren’t actually what ends up destroying the virus either. ¬†They go into the body and flag the bad cells. ¬†This is when the macrophages come in and destroy these cells, there by getting rid of the virus.

Now, you want to learn something interesting about HIV? I know, who wants to learn about that? But this is worth your time I promise. ¬†HIV is a special virus that attacks Helper T cells (which have a CD4 marker.) ¬†The HIV comes in and takes over that CD4 marker. ¬†This means that the T cells no longer work. ¬†When people get infected with HIV, they don’t die from the virus, they die from immune deficiency.

Do you know why?

With out T cells, your body can’t tell that there is something infecting it and it can send for B cells to fight the infection. ¬†Therefore, a mere cold could kill some one with HIV.


Well, there you go! It was little messy but I hope you learned something from it.  Thanks for reading!