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My reassessment of these two standards is below, but for sake of including my original work on this padlet, here is my initial PDF from first semester.

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S.5 Reassessment) Initially, I falsely described a membrane made of cells as the phospholipid bilayer. Though I addressed the polarity aspect of this standard, I will continue to address the importance of channels in the membrane. Broadly, I will address what can and cannot move across the membrane and why. I'll contextualize this question by using the example of compounds that are touted with beauty products. To begin, primarily simple molecules can move across the membrane. Common examples include O2, CO2, and H20. These molecules accomplish this through diffusion. There is passive diffusion, in which molecules move from a low to high concentration, and there is active diffusion, in which molecules move from a high to low concentration. These molecules can move across the membrane because they are nonpolar (no positive/negative poles). Chemically, this makes sense because smaller, simpler, nonpolar compounds can easily travel through the nonpolar part of the phospholipid bilayer because of their size/shape. On the contrary, larger, polar molecules could not (at least without the assistance of transport proteins). These transport proteins facilitate the process of diffusion for larger and polar molecules because they can create openings/gaps, moving against the concentration gradient. In the context of my portfolio piece, this would mean that a compound touted in beauty products would be unlikely to be able to move across the membrane by itself. One could assume that these compounds are comparatively larger and polar. The more likely thing to occur in a beauty product is that it has a carrier to allow molecules to cross the membrane. On the contrary, cleaner compounds such as hyaluronic acid (which is known to heal tissue) might more easily pass through the cell membrane. Though it is polar, a transport protein could help move it across the membrane. It is mainly located in the extra-cellular matrix Hylauronic acid has receptors, which regulate cell adhesion and adversely healing of the cell. Another effect is migration - new cells need to migrate to where they are supposed to be. (A lot of this ties back to cell signaling, but that just notes the intersection of these standards). Given that "the synthesis of HA [hylauronic acid] increases during tissue injury and wound healing," (https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3583886/#:~:text=Biological%20function%20of%20HA&text=The%20synthesis%20of%20HA%20increases,49%2C50%20and%20epithelial%20cells), it is fair to assume that the receptors of hyaluronic acid aid it in passing through the membrane even as a polar compound.

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Abstract

Skin aging is a multifactorial process consisting of two distinct and independent mechanisms: intrinsic and extrinsic aging. Youthful skin retains its turgor, resilience and pliability, among others, due to its high content of water. Daily external injury, in addition to the normal process of aging, causes loss of moisture. The key molecule involved in skin moisture is hyaluronic acid (HA) that has unique capacity in retaining water. There are multiple sites for the control of HA synthesis, deposition, cell and protein association and degradation, reflecting the complexity of HA metabolism. The enzymes that synthesize or catabolize HA and HA receptors responsible for many of the functions of HA are all multigene families with distinct patterns of tissue expression. Understanding the metabolism of HA in the different layers of the skin and the interactions of HA with other skin components will facilitate the ability to modulate skin moisture in a rational manner.

Keywords: hyaluronic acid, hyaluronic acid synthases, hyaluronidases, CD44, RHAMM, skin aging

Skin aging

Human skin aging is a complex biological process, not yet fully understood. It is the result of two biologically independent processes. The first is intrinsic or innate aging, an unpreventable process, which affects the skin in the same pattern as it affects all internal organs. The second is extrinsic aging, which is the result of exposure to external factors, mainly ultraviolet (UV) irradiation, that is also referred to as photoaging.1 Intrinsic skin aging is influenced by hormonal changes that occur with age,2 such as the gradual decreased production of sex hormones from the mid-twenties and the diminution of estrogens and progesterone associated with menopause. It is well established that the deficiency in estrogens and androgens results in collagen degradation, dryness, loss of elasticity, epidermal atrophy and wrinkling of the skin.3

Even though intrinsic and extrinsic skin aging are distinctive processes, they share similarities in molecular mechanisms. For example, reactive oxygen species (ROS), arising from oxidative cell metabolism, play a major role in both processes.4 ROS in extrinsic or intrinsic skin aging induce the transcription factor c-Jun via mitogen-activated protein kinases (MAPK), leading to overexpression of matrix metalloproteinase (MMP)-1, MMP-3 and MMP-9 and prevention of the expression of procollagen-1.5 Therefore, elevated levels of degraded collagen and reduced collagen synthesis are pathologies occurring in intrinsically aged as well as photoaged skin.

Skin aging is also associated with loss of skin moisture. The key molecule involved in skin moisture is hyaluronan or hyaluronic acid (HA), a glycosaminoglycan (GAG) with a unique capacity to bind and retain water molecules.6 HA belongs to the extracellular matrix (ECM) molecules. During the past decades the constituents of the skin have been well characterized. In the beginning, most of the studies focused on the cells that comprise the skin layers, such as the epidermis, the dermis and the underlying subcutis. Recently, it is appreciated that ECM molecules that lie between cells, in addition to providing a constructive framework, they exert major effects on cellular function. These ECM molecules, although they appear amorphous by light microscopy, they form a highly organized structure, comprising mainly of GAG, proteoglycans, growth factors and structural proteins such as collagens. Yet, the predominant component of the skin ECM is HA.

Recent reviews have described the involvement of HA with respect to its role in angiogenesis,7 reactive oxygen species,8 chondrocytes,9 cancer,10,11 lung injury,12,13 immune regulation14,15 and skin.16 This review presents in brief recent knowledge in HA biology and function and focuses on its involvement in skin aging.

Hyaluronic acid

Chemistry and physicochemical properties

HA is a non-sulphated GAG and is composed of repeating polymeric disaccharides of D-glucuronic acid and N-acetyl-D-glucosamine linked by a glucuronidic β (1→3) bond.17,18 In aqueous solutions HA forms specific stable tertiary structures.19 Despite the simplicity in its composition, without variations in its sugar composition or without branching points, HA has a variety of physicochemical properties. HA polymers occur in a vast number of configurations and shapes, depending on their size, salt concentration, pH, and associated cations.20 Unlike other GAG, HA is not covalently attached to a protein core, but it may form aggregates with proteoglycans.21 HA encompasses a large volume of water giving solutions high viscosity, even at low concentrations.13

Tissue and cell distribution of HA

HA is widely distributed, from prokaryotic,22,23 to eukaryotic cells.24 In humans, HA is most abundant in the skin,25⁻29 accounting for 50% of the total body HA,30 the vitreous of the eye,31 the umbilical cord,17 and synovial fluid,32,33 but it is also present in all tissues and fluids of the body, such as skeletal tissues,27 heart valves,34 the lung,35⁻39 the aorta,40 the prostate,41 tunica albuginea, corpora cavernosa and corpus spongiosum of the penis.42 HA is produced primarily by mesenchymal cells but also by other cell types.34⁻38,43

Biological function of HA

Over the past 2 decades there was considerable evidence presented that unraveled the functional role of HA in molecular mechanisms and indicated the potential role of HA for the development of novel therapeutic strategies for many diseases.

Functions of HA include the following: hydration, lubrication of joints, a space filling capacity, and the framework through which cells migrate.34 The synthesis of HA increases during tissue injury and wound healing25,44,45 and HA regulates several aspects of tissue repair, including activation of inflammatory cells to enhance immune response46⁻48 and the response to injury of fibroblasts49,50 and epithelial cells.51⁻55 HA also provides the framework for blood vessel formation7,45 and fibroblast migration,56,57 that may be involved in tumor progression.58 The correlation of HA levels on the cell surface of cancer cells with the aggressiveness of tumors has also been reported.59

The size of HA appears to be of critical importance for its various functions described above. HA of high molecular size, usually in excess of 1,000 kDa, is present in intact tissues and is antiangiogenic and immunosuppressive, whereas smaller polymers of HA are distress signals and potent inducers of inflammation and angiogenesis.38,46,60⁻63

Biosynthesis of HA

HA is synthesized by specific enzymes called HA synthases (HAS). These are membrane bound enzymes that synthesize HA on the inner surface of the plasma membrane64 and then HA is extruded through pore-like structures into the extracellular space.24,65 There are three mammalian enzymes HAS -1, -2 and -3, which exhibit distinct enzymatic properties and synthesize HA chains of various length.66⁻68

Degradation of HA

HA has a dynamic turnover rate. HA has a half-life of 3 to 5 min in the blood, less than a day in the skin and 1 to 3 weeks in the cartilage.69⁻71 HA is degraded into fragments of varying size by hyaluronidases (HYAL) by hydrolyzing the hexosaminidic β (1-4) linkages between N-acetyl-D-glucosamine and D-glucuronic acid residues in HA. In humans, six HYAL have been identified so far: HYAL-1, -2, -3, -4, PH-20 and HYALP1.72 The family of HYAL enzymes received little attention until recently73,74 because they are found at extremely low concentrations and they are difficult to purify, characterize and measure their activity, which is high but unstable.16 New procedures have now enabled the isolation and characterization of HYAL.75,76 HYAL-1 is the major HYAL in serum.77 Mutations in the HYAL-1 gene are associated with HYAL deficiency and mucopolysaccharidosis type IX.78 HYAL-2 has very low activity in comparison to plasma HYAL-1 and it hydrolyzes specifically HA of high molecular weight, yielding HA fragments of approximately 20 kDa, which are further degraded to small oligosaccharides by PH-20.79 HYAL-3 is mainly expressed in bone marrow and testis,74 but also in other organs, such as the human lung.37,38 The role of HYAL-3 in the catabolism of HA is not clear and it is suggested that it may contribute to HA degradation by enhancing the activity of HYAL-1.80

HA can also be degraded non-enzymatically by a free-radical mechanism81 in the presence of reducing agents such as ascorbic acid, thiols, ferrous, or cuprous ions, a process that requires the presence of molecular oxygen. Thus, agents that could delay the free-radical-catalyzed degradation of HA may be useful in maintaining the integrity of dermal HA and its moisturizing properties.16

Hyaluronic acid receptors

There is a variety of proteins that bind HA, called hyaladherins, which are widely distributed in the ECM, the cell surface, the cytoplasm and the nucleus.15 Those that attach HA to the cell surface constitute HA receptors. The most prominent among these receptors is the transmembrane glycoprotein "cluster of differentiation 44" (CD44) that occurs in many isoforms, which are the products of a single gene with variable exon expression.82⁻84 CD44 is found on virtually all cells, except red blood cells, and regulates cell adhesion, migration, lymphocyte activation and homing, and cancer metastasis.

The receptor for HA-mediated motility (RHAMM) is another major receptor for HA, and it is expressed in various isoforms.85⁻87 RHAMM is a functional receptor in many cell types, including endothelial cells88 and in smooth muscle cells from human pulmonary arteries37 and airways.38 The interactions of HA with RHAMM control cell growth and migration by a complex network of signal transduction events and interactions with the cytoskeleton.89 Transforming growth factor (TGF)-β1, which is a potent stimulator of cell motility, elicits the synthesis and expression of RHAMM and HA, and thus initiates locomotion.90

Hyaluronic acid in skin

The use of biotinylated HA-binding peptide91 revealed that not only cells of mesenchymal origin were capable of synthesizing HA and permitted the histolocalization of HA in the dermal compartment of skin and the epidermis.26,92⁻94 This technique enabled the visualization of HA in the epidermis, mainly in the ECM of the upper spinous and granular layers, whereas in the basal layer HA is predominantly intracellular.26

The function of the skin as a barrier is partly attributed to the lamellar bodies, thought to be modified lysosomes containing hydrolytic enzymes. They fuse with the plasma membranes of mature keratinocytes and they have the ability to acidify via proton pumps and partially convert their polar lipids into neutral lipids. Diffusion of aqueous material through the epidermis is blocked by these lipids synthesized by keratinocytes in the stratum granulosum. This boundary effect corresponds to the level of HA staining. The HA-rich area inferior to this layer may obtain water from the moisture-rich dermis, and the water contained therein cannot penetrate beyond the lipid-rich stratum granulosum. The hydration of the skin critically depends on the HA-bound water in the dermis and in the vital area of the epidermis, while maintenance of hydration essentially depends on the stratum granulosum. Extensive loss of the stratum granulosum in patients with burns may cause serious clinical problems due to dehydration.16

As mentioned above, skin HA accounts for most of 50% of total body HA.30 The HA content of the dermis is significantly higher than that of the epidermis, while papillary dermis has much greater levels of HA than reticular dermis.92 The HA of the dermis is in continuity with the lymphatic and vascular systems. HA in the dermis regulates water balance, osmotic pressure and ion flow and functions as a sieve, excluding certain molecules, enhancing the extracellular domain of cell surfaces and stabilizes skin structures by electrostatic interactions.16 Elevated levels of HA are synthesized during scar-free fetal tissue repair and the prolonged presence of HA assures such scar-free tissue repair.95⁻97 Dermal fibroblasts provide the synthetic machinery for dermal HA and should be the target for pharmacologic attempts to enhance skin hydration. Unfortunately, exogenous HA is cleared from the dermis and is rapidly degraded.70

Hyaluronic acid synthases in the skin

In the skin, gene expression of HAS-1 and HAS-2 in the dermis and epidermis is differentially upregulated by TGF-β1, indicating that HAS isoforms are independently regulated and that the function of HA is different in the dermis and the epidermis.16,98 The mRNA expression of HAS-2 and HAS-3 can be stimulated by keratinocyte growth factor, which activates keratinocyte migration and stimulates wound healing, leading to the accumulation of intermediate-sized HA in the culture medium and within keratinocytes. The migratory response of keratinocytes in wound healing is stimulated by increased synthesis of HA.99 HAS-2 mRNA is also induced by IL-1β and TNFα in fibroblasts100 and by epidermal growth factor in rat epidermal keratinocytes.101

Dysregulated expression of HA synthases has been reported during tissue injury.102⁻104 HAS-2 and HAS-3 mRNA are significantly increased after skin injury in mice, leading to increased epidermal HA.104 In juvenile hyaline fibromatosis, which is a rare autosomal recessive disease characterized by deposition of hyaline material and multiple skin lesions, there is a significant decreased expression of HAS-1 and HAS-3, accounting for the reduced synthesis of HA in skin lesions.105 In dermal fibroblasts, where the HAS-2 is the predominant isoform, glucocorticoids inhibit HAS mRNA almost completely, suggesting a molecular basis of the decreased HA in atrophic skin as a result of local treatment with glucocorticoids.16

Hyaluronidases in the skin

In the skin, it has not been established which of the various HYAL controls the turnover of HA in the dermis and the epidermis. The elucidation of the biology of HYAL in the skin may offer novel pharmacological targets to confront age related turnover of HA in skin.

HA receptors in the skin

In the dermis and epidermis HA is co-localized with CD44. However, the exact CD44 variants in the different skin compartments have not yet been elucidated. CD44-HA interactions have been reported to mediate the binding of Langerhans cells to HA in the matrix surrounding keratinocytes by their CD44-rich surfaces, as they migrate through the epidermis.106,107 RHAMM is also expressed in the human skin.28,29 The TGF-β1 induced stimulation of fibroblast locomotion is mediated via RHAMM,90 while overexpression of RHAMM can lead to the transformation of fibroblasts.108

Hyaluronic acid and skin aging

The most dramatic histochemical change observed in senescent skin is the marked disappearance of epidermal HA, while HA is still present in the dermis.92 The reasons for this change in HA homeostasis with aging is unknown. As mentioned above, the synthesis of epidermal HA is influenced by the underlying dermis and is under separate controls from the synthesis of dermal HA.16,98 Progressive reduction of the size of the HA polymers in skin as a result of aging has also been reported.109 Thus, the epidermis loses the principle molecule responsible for binding and retaining water molecules, resulting in loss of skin moisture. In the dermis, the major age-related change is the increasing avidity of HA with tissue structures with the concomitant loss of HA extractability. This parallels the progressive cross-linking of collagen and the steady loss of collagen extractability with age.16 All of the above age related phenomena contribute to the apparent dehydration, atrophy and loss of elasticity that characterizes aged skin.

Premature aging of skin is the result of repeated and extended exposure to UV radiation.110,111 Approximately 80% of facial skin aging is attributed to UV-exposure.112 UV radiation damage causes initially a mild form of wound healing and is associated at first with an increase of dermal HA. As little as 5 min of UV exposure in nude mice caused enhanced deposition of HA, indicating that UV radiation induced skin damage is an extremely rapid event.16 The initial redness of the skin following exposure to UV radiation may be due to a mild edematous reaction induced by the enhanced HA deposition and histamine release. Repeated and extensive exposures to UV ultimately simulate a typical wound healing response with deposition of scarlike type I collagen, rather than the usual types I and III collagen mixture that gives skin resilience and pliability.16

In the skin, photoaging results in abnormal GAG content and distribution compared with that found in scars, or in the wound healing response, with diminished HA and increased levels of chondroitin sulfate proteoglycans.111 In dermal fibroblasts this reduction in HA synthesis was attributed to collagen fragments, which activate α vβ ₃-integrins and in turn inhibit Rho kinase signaling and nuclear translocation of phosphoERK, resulting in reduced HAS-2 expression.113 We have recently unraveled some of the biochemical changes that may distinguish photoaging and natural aging. Using photoexposed and photoprotected human skin tissue specimens, obtained from the same patient, we have shown a significant increase in the expression of HA of lower molecular mass in photoexposed skin, as compared with photoprotected skin. This increase of degraded HA was associated with a significant decrease in the expression of HAS-1 and an increased expression of HYAL-1, -2 and -3. Furthermore, the expression of HA receptors CD44 and RHAMM was significantly downregulated in photoexposed, as compared with photoprotected skin. These findings indicate that photoexposed skin, and therefore extrinsic skin aging, is characterized by distinct homeostasis of HA.29 We have also assessed photoprotected skin tissue specimens from adults and juvenile patients and observed that intrinsic skin aging was associated with a significant reduction in the content of HA and downregulation of HAS-1, HAS -2, CD44 and RHAMM.28 Similar results for photoprotected skin have also been reported for both genders for HA, HAS-2 and CD44.114

Conclusion

The available data suggest that HA homeostasis exhibits a distinct profile in intrinsic skin aging, which is totally different of that in extrinsic skin aging. Additional insight needs to be gained in understanding the metabolism of HA in skin layers and the interactions of HA with other skin components. Such information will facilitate the ability to modulate skin moisture in a rational manner and may contribute to the refinement of current drugs and the development of novel treatments for skin aging.

Glossary

Abbreviations:

UV

ultraviolet

ROS

reactive oxygen species

MMP

matrix metalloproteinase

HA

hyaluronic acid

GAG

glycosaminoglycan

ECM

extracellular matrix

HAS

hyaluronic acid synthases

HYAL

hyaluronidases

CD44

cluster of differentiation 44

RHAMM

receptor for HA-mediated motility

TGF

transforming growth factor

Disclosure of Potential Conflicts of Interest

No potential conflicts of interest were disclosed.

References

3. Brincat MP. Hormone replacement therapy and the skin. Maturitas 2000; 35:107-117. 9 Makrantonaki E, Zouboulis CC. Androgens and aging of the skin. Curr Opin Endocrinol Diabetes Obes. 2009;16:240-5. [ Google Scholar]

9. Knudson CB, Knudson W. Hyaluronan and CD44: modulators of chondrocyte metabolism. Clin Orthop Relat Res. 2004;(Suppl):S152-62. doi: 10.1097/01.blo.0000143804.26638.82. [[ PubMed] [ CrossRef] Google Scholar]

20. Laurent TC. Structure of hyaluronic acid. In: Balazs, EA, ed. Chemistry and Molecular Biology of the Intercellular Matrix, Academic Press: New York, 1970:p. 703. [ Google Scholar]

31. Meyer K, Palmer JW. The Polysaccharide of the vitreous humor. J Biol Chem. 1934;107:629-34. [ Google Scholar]

63. Papakonstantinou E, Klagas I, Karakiulakis G, Hostettler K, S'ng CT, Kotoula V, et al. Steroids and β2 Agonists Regulate Hyaluronan Metabolism in Asthma Airway Smooth Muscle Cells. Am J Respir Cell Mol Biol. 2012 doi: 10.1165/rcmb.2012-0101OC. In press. [[ PubMed] [ CrossRef] Google Scholar]

82. Laurent TC. The chemistry, biology, and medical applications of hyaluronan and its derivatives. London: Portland Press; 1998:621. [ Google Scholar]

Articles from Dermato-endocrinology are provided here courtesy of Taylor & Francis

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Hyaluronic acid: A key molecule in skin aging

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Skin aging is a multifactorial process consisting of two distinct and independent mechanisms: intrinsic and extrinsic aging. Youthful skin retains its turgor, resilience and pliability, among others, due to its high content of water. Daily external injury, in addition to the normal process of aging, causes loss of moisture.

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S.1 Reassessment) Initially, I did not cover all four macromolecules including the chemistry of the molecules and some of the details of how they are used in biological contexts. Though I accomplished this for phospholipids in my discussion of polarity and why they would form bilayers in water, I failed to explain how Proteins, Nucleic Acids, and Carbohydrates are also used. So, I'll do that here! To begin, in the context of the social construct of beauty – specifically with plastic surgery – proteins are vital in ensuring that tissue is healed. This would look like scarred tissue after plastic surgery (a rhinoplasty for example) that eventually heals because of proteins. Chemically, this occurs because proteins transport substances/nutrients through diffusion. Passive diffusion occurs when the transport of these molecules is from a low to high concentration (think of a food color droplet going into water), while active diffusion is vice versa (high to low). Next, nucleic acids store genetic information (DNA and RNA). On a broader scale, these are the building blocks of the body – they tell the body when/how to create the aforementioned proteins. This in turn allows for the proteins to accomplish their necessary functions and provides nutrients to allow tissue to heal in the first place. Chemically, DNA is made up of nucleotides which create strands – this is where the concept of As, Ts, Gs, and Cs play in, as they match with one another to create these strands, which inform bodily functions. Finally, carbohydrates give the body glucose. Glucose is eventually converted into energy through the process of cellular respiration in which glucose and O2 form ATP (Adenosine triphosphate, stored in the mitochondria). This is a vital function for the body not just for the healing process, but before that and throughout a given human's life. For instance, Carbohydrates are a necessary macromolecule before a patient goes under anesthesia or even simply at a doctor's visit, because the body practically always requires energy.

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In this standard, I aim to address the theory of evolution, and cite evidence that it is an ongoing process affecting our daily lives. I will contextualize this process on a deeper chemical level by discussing concepts of energy flow during metabolism. Additionally, I will explain how an enzyme increases the rate of a biochemical reaction in terms of thermodynamics, kinetics, and molecular interactions – and what this means for the energy flow process + evolution. The piece I am citing for these two standards is the "Energy and Metabolism" slideshow – specifically the first video on exercise (and rats) in slide two. I know this is a lot, but these three standards feel specifically interconnected to me. Using each as a mechanism to contextualize another has allowed me to better understand these concepts writ large.

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First, the theory of evolution describes how characteristics – whether external or internal – change in a given organism over a long period of time. Evolution is driven by mutation, a random process. Note that some traits are passed down to the next generation, but the initial process is random. Mutation is the changing of letters in genetic “code” – the building material, and it happens when mistakes are made in the genetic material. So, all of this genetic mutation occurs within genetic material such as DNA/RNA (but is most prominent in RNA). In the genetic code, nucleotides are represented in triplets on a chemical level. For example, ACU/ACA/AAU. Notably, there is a relationship between these triplets and PROTEINS – as proteins are also part of a sequence, meaning they have an “alphabet” too. This process eventually looks like changes in rats' genetic components, such as a stronger sense of smell, which I witnessed in the Energy and Metabolism slideshow. The process of energy flow during metabolism occurs by the movement of electrons. This broadly looks like enzymes continuously operating to spread "information." Enzymes primarily act as chemical catalysts for change – and they primarily do this by decreasing the energy of a given reaction. They tighten around a substrate (a reactant) on a chemical level, and this process minimizes the energy needed to activate a reaction. Though enzymes are catalysts for chemical change, they actually do not affect thermodynamics. While enzymes may speed up a chemical reaction, they don't change equilibrium concentrations. Enzyme kinetics, however, which is the reaction rate of a given enzyme, certainly changes based on the strength of the enzyme's role in metabolism. In this process of energy flow, one should expect an enzyme to increase the rate of kinetics, given that they are speeding up chemical reactions. Going back to the energy flow process, a flux of electrons is then sent down (as enzymes continue to operate) across the membrane after an organism consumes food. Large proteins pass these electrons down, resulting in an electrical current. This current drives expansion – these proteins pump protons to charge them, resulting in practical storage of protons.  This is a generator of energy for storage in a cell (all of this is called ATP synthase). You can think of this like a turbine; it just keeps going - and primarily occurs in the mitochondria, which is the "powerhouse" of the cell. All of this continues to occur (practically all the time) in organisms because enzymes speed up chemical reactions, forcing an increase in molecular reactions and continuing this cycle that drives energy. This process then relates to evolution because energy flow informs the evolutionary process, given that (a) the mitochondria is likely to have played at least some role in shaping the evolution of eukaryotic cells because, over time, its process of energy transfer may have changed components of the genome and (b) changes to the genome can only occur when an organism has energy and can live and reproduce for long periods of time. In daily life, evolution manifests itself by protecting organisms from what their ancestors may have faced, like deadly diseases – or even circumstances as simple as adapting to proximity to the equator.

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In this standard, I aim to describe in general terms how the information in a gene is stored, replicated, and transmitted to daughter cells.

Meiosis simply describes a cycle where one cell alone will isolate itself and divide twice to create four sex cells with fewer genes. The glial cell needs to make copies of its genetic materials in order to start the process of cellular division and reproduce its daughter cells. This means it chemically must create more DNA cells to be copied (before they are actually divided). Glial cells – which are eukaryotic because they have a nucleus – wrap their DNA to create chromosomes into bundles. These form tight chromosomes, which have two chromatids. (THIS IS HOW THE GENE IS STORED) The chromatids enter the new daughter cells that form after they’re divided. This means the glial cells, for example, have these chromatids. Chemically, chromatids separate because of enzymes, which speed up the process of chemical reactions. A chemical called cohesin, which previously kept the sister chromatids connected, now is being used to separate the chromatids. (THIS IS HOW THE GENE IS REPLICATED). After this happens, gametes are produced. Gametes are basically just sex cells. They have unique alleles, which chemically are simply changes to a gene strand. These gametes come together when they fertilize – X and Y chromosomes fertilize to creating a male sex, while XX makes a female sex offspring. (THIS IS HOW THE GENE IS REPLICATED). Diploid cells have 2 full sets of chromosomes, while haploids have 1. These cells are altered during meiosis – just look toward how the glial cells will condense and separate. That’s how cells separate during meiosis and inherit new genes!

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In this standard, I aim to contrast the features that distinguish viruses, bacterial cells, and eukaryotic cells from each other. The portfolio piece that coincides with this standard is the cell cycle project.

First, what is a virus? A virus is simply a tiny, infectious go-getter that aims to take over a host cell. A virus is non-cellular.

Second, what is bacteria? Bacteria are just germs. You can't see them, but they're everywhere. They can act positively or negatively and can work alongside enzymes (which is what kick-starts chemical reactions).

Third, what is the difference between prokaryotes and eukaryotes? In contrast with viruses and bacteria, prokaryotes and eukaryotes are cellular. They have cells. However, the difference between the two is that prokaryotes are cells that lack a nucleus, while eukaryotes have a nucleus.

Applying the knowledge I obtained from the portfolio project, Gliomas – which are the most common form of brain tumors – are not cells. It is possible (and probable) that bacteria grows on brain tumors. Still, gliomas are not viruses as they are created when the glia cells grow far-too-quickly. Glia cells are made of eukaryotic cells, not prokaryotic cells. At the same time, there are many other viruses that can infect the brain – tumors simply aren't one of them.

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In this standard, I aim to describe and justify the process of scientific research, and communicate about scientific topics in a level-appropriate way. I will use the Cell Cycle project to illustrate this standard. In my study of glias, gliomas, and brain cancer for the Cell Cycle project, I utilized scientific research and made notes for the project. Attached, you will find the highlighted and annotated PDF of published research from The Hidalgo Lab that demonstrates my knowledge and ability to conduct scientific research.

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

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.

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Above, I stated: "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 becomes wider. This description is measured by the percent of diffusion in our data table."

However, diffusion does not refer to the phospholipids of the bilayer membrane, as I assumed above. Rather, diffusion refers to molecules moving through the membrane and then into the cell. This means that my above description would not follow what diffusion truly looks like. So, an amended version would explain that diffusion could be defined as the process for how molecules move through the membrane and into the cell depending on the concentration of molecules that exist at a given point.

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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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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.