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I forgot to mark this in blackbaud and it won't let me re-submit, but the three new standards I hope to address are

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Reception – ok so first let me describe – how does a cell receive the GPCR signaling molecule?

Let’s first dissect what the term GPCR even means. It means you have a G protein, specifically a Heterotrimeric G-protein, that is made up of alpha, beta, and gamma subunits. Note- hetero-TRI-metric. Basically, these 3 subunits make up one large G protein, and that G protein is coupled with receptors. This occurs within the plasma membrane which is in the cell membrane. Here, you have ligands that come over to the GPCR  receptor. And once they find their complementary receptor, it will fit in like a puzzle. THIS MEANS: once another ligand finds your GPCR, then the ligand attaches to its desired GPCR receptor. There are many different types of cells to carry out the GPCR's functions. Some examples include hormones, neurotransmitters, proteins, peptides, or even lipids.

Transduction – ok so next I’ll explain how the signal is passed along.

Basically, the alpha subunit of the G protein now bonds with either GDP or GTP, depending on whether the protein is active or inactive. GDP – meaning di, two proteins– is inactive – while GTP – tri, meaning three proteins and – is active. The GDP, which is the inactive part, will couple with the alpha subunit that binds to the GPCR to start signaling.

Now – what are some processes that occur to further the signal.

The G protein, now bound with the GPCR, regulates your adenylyl-cyclase – an enzyme that converts ATP (Adenosine triphosphate) energy into cAMP responses (cyclic AMP). These cAMP responses are the signal’s secondary messenger, which amplifies the signal. That’s why this part of the process is called signal amplification. So these messages that cAMP responses further then connect to other parts within the plasma membrane. These sections get closer and closer to the desired receptor. In our model, we used the example of Orexin Receptors – which are GPCRs that receive orexin, which is a neuropeptide that regulates things like sleep, wakefulness, and hunger. So in this hypothetical let’s say that the message one’s body signals is hunger. On a chemical, molecular level —The cAMP responses would then activate neurons and release ions to further their scope in order to get closer and closer to the point where the signal needs to go for the response to happen. that is the hypothalamus, which is one of the main parts of the brain that controls hormones. the final step in this transduction process is one in which a depolarization spike occurs. basically the electronegativity - specifically the accumulated difference in polarity on the other side of the cell - causes a big spike, meaning no more Na+ can scoot around the cell. the activation gate, which basically has been allowing all of these processes to occur, closes. at this point, there are already a bunch of neurons that have received the hunger signal, but one of them close to the hypothalamus sends the signal directly to it.

Finally, what does the cellular response look like? the neuron with the orexin receptor continues to relay the hunger memo along to the hypothalamus. now that the hypothalamus has received the message, your body tells you you are hungry!

but when you begin to eat a lot, your body becomes full. the only way you are able to know this is if you stop this process and shut off the signal from the orexin receptor. to do this, the active GTP will take over the inactive GDP. the subunits come together and the active part, the GTP, has now shut the hunger signal that the orexin receptor relays to the hypothalamus down.

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This is an annotation for standard 9: Gene Expression. Please look to both the writing below and my protein project (emailed – on 11/1, video format) to assess this standard.

So – what are transcription and translation? Simply put, transcription describes when DNA is copied into RNA, while translation is making that copy into information by turning amino acids into proteins. First, let's do a deeper dive into transcription. Two strands of DNA are held together by hydrogen bonds. Transcription describes the process of when the DNA is twisted, and the RNA comes to match the strands of the DNA. The first thing that happens in transcription is the DNA strands must be split apart. The protein that performs transcription is RNA polymerase because it is making RNA. RNA polymerase is an enzyme (something that starts a chemical reaction) that opens up this DNA with two strands with the goal that one strand of the uncovered nucleotides can be basically utilized as baseline (the base pair) for the synthesis of RNA. RNA Polymerase works because of chemical reactions. This "base pair" begins to exist once a ribonucleoside triphosphate (the nucleotide that is exposed) matches with the DNA. Notably, the template strand is the original, base, hard copy. The "A"s, "T"s, "G"s, and "C"s determine if they match. Also, “T”s are only in DNA, while “U”s are only in RNA. "A" pairs with "U" and "T" while "G" pairs with "C". Finally, in reality, As can try to fit with Gs but don’t fit chemically and so they fit with their pair. Next in the process, a chemical reaction takes place wherein electron-rich oxygen will attack an electron-poor molecule to create a new bond. After, the base pair shifts over 1 letter (as illustrated in the Concord Lab) to position the hydroxyl group closer to where the new nucleotide, so these chemical reactions can continue as new "A"s, "T"s, "G"s, or "C"s, match, and the process continues. Next, what is translation? Translation makes these new copies of RNA into actual information by turning amino acids into proteins. The ribosome is the machine that performs the translation. The ribosome will read the sequence of an mRNA to first get the message that it can then translate into amino acids. mRNA stands for messenger RNA – it is a codon, meaning triplets on mRNA that specify an amino acid and give instructions to the ribosome; I.e. adenine or guanine. Chemically speaking, the ribosome will translate each codon once tRNA – the transferer – will transfer amino acids to the ribosome. tRNA is an anticodon, which is complementary to codons. A complimentary sequence then occurs once the codons and anti-codons fit together. (and these nucleic acid sequences match base pairs; the As match with Ts, etc.) But how do the ribosome and tRNA “know” what amino acid corresponds with that DNA sequence? Its chemical structure which determines if they fit. Finally, polypeptides, which are the protein chains that exist after translation, are simply the physical manifestations of the information just transcribed and translated. They are the proteins that exist from amino acids through the process of translation. When there a tRNA visualizes a "stop codon" – which has matches of UAG, UGA, or UAA, and this stop codon will terminate the process of translation. Attached, find a visual representation of the process I just described.

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Attached, you'll find my data, goals for this conclusion and notes concerning the lab.

CONCLUSION:

(CLAIM AND INTRODUCTION): First, a hypothesis: as the agar cube decreases in size, its diffusion rate will increase and vice versa; thus, there is a correlation between surface area and diffusion rate. Next, let's clarify what the agar cube actually represents in this experiment:  the outer layer of the cell membrane (the cytoplasm). Throughout this experiment, I aimed to determine how the agar cube's size impacted its diffusion rate. But what do these terms actually mean? Writ large, this experiment concerns how molecules are even able to pass through the cell membrane. For these molecules and more to pass through, the outer layer cell membrane has to diffuse – spread out or widen. Thus, diffusion can be defined as the spread of the outer layer of the cell membrane becoming wider. This description is measured by the percent of diffusion in our data table. For added analysis, my hypothesis for why cells are limited in size is because their membrane can only diffuse to a certain extent – meaning much larger molecules such as Glucose are unable to pass through the cell membrane as the membrane is unable to diffuse to the extent necessary that would permit this occurrence.

(EVIDENCE): To begin, I will analyze the data my group came up with before analyzing that of the class through the lens of qualitative and quantitative reasoning. Qualitatively, my group and I noticed the color of the agar cube as more vinegar was added to its surface. We questioned: what does this signify? The agar cube's color change signified how much diffusion has occurred. From a molecular, chemical standpoint, when the agar cube was placed into vinegar, the agar cube's color changed as the hydrogen ions transferred from the vinegar to the cube. So, when an agar cube had a relatively small surface area was dipped in vinegar, more of its area changed colors as more of the area diffused. Quantitatively, both my group's data and that of the whole class back this hypothesis up. For my group's data, the percent of diffusion for the agar cube with the smallest surface area is nearly 38% greater than that of the agar cube with the largest surface area. Additionally, for the data for the whole class – taking Viraja and Chancey's data as an example – the comparative increase in the percent of diffusion between the largest and smallest agar cube is 21%. Finally, the time that it takes for a larger agar cube to diffuse appears to be longer as well; look toward Viraja and Chancey's data once again for a class comparative, wherein the 3x3 cube took 420 seconds, while the 1x1 cube took only 360 seconds.

(REASONING): The explanation for why the agar cube's diffusion rate increases when its surface area is smaller it has a smaller surface area to volume ratio. Note, as pictured above, volume is measured in mm cubed while surface area is measured in millimeters squared – the key difference: cubed vs. squared. The volume appears to become larger at a more rapid rate than surface area because its measurement multiplied by itself three times means the volume will increase more than surface area, as the surface area is only multiplied by itself twice. Connecting back to the core theme of the experiment concerning how molecules pass through the membrane, we can now conclude that increased amounts of volume and decreased amounts of surface area means that diffusion appears to be less effective and take more time. For molecules to pass through the membrane, the membrane has to diffuse and spread out. Thus, since bigger cubes diffuse slower than smaller ones and at a less efficacious rate, another conclusion we can make chemically is that some larger molecules are unable to pass through the membrane.