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We first started learning about phospholipid bilayers with envelope viruses. Viruses like Covid-19 and HIV have a lipid membrane made of 2 sheets of phospholipid molecules. These phospholipids have a hydrophilic/polar head and hydrophobic (nonpolar) tails. The hydrophilic head allows for water to pass through freely. The head has a phosphate group and glycerol making it polar due to the uneven charges. The tails are made of fatty acids that are uncharged making them non-polar.

I attached a phospholipid structure we used in class to look at these phospholipids to check for polarity. Additionally, since there are 2 sheets of the phospholipid molecules, the heads face water on the extracellular region and water in the intracellular region as they are hydrophilic. The hydrophobic tail section is isolated in the “inside” of the membrane or essentially not touching water. If this wasn’t the case and the hydrophobic fatty acids faced the water, it would just be washed away instead of mixing. In our bubble lab experiment, we learnt that membranes can flex without breaking in a controlled environment. They can repair small tears like in the case of bubbles in the lipid bilayer. So, we saw that small, non-polar molecules can get through the lipid bilayer without causing damage or major breakage. Additionally, pores, proteins with hydrophobic ends and hydrophilic centers can drift through the bilayer. This also connects with how pores show up as organelles in some cells since they can bring outer nutrients.

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To begin, my infographic addresses the question of: how did vaccine researchers figure out how to pre-emptively provide immunity to SARS-COV 2 through vaccines? It goes through the process from treatment -> how the mRNA vaccine instructions cause cells to make harmless spike protein -> how the body’s immune system creates antibodies to respond to that protein -> success/future effects.

Addressing Standard 3: Life, my infographic shows the process/flow of information of the Covid-19 vaccine. With SARS-COV 2, it hijacks a lung cell through a spike protein. The RNA sent from spike protein reproduces more viral spike proteins in the replication complex of the lung cell since the virus is a respiratory virus. These spike proteins spread to other lung cells where the immune system detects it and attempt to fight against it but might struggle depending on the immune system. SARS-COV 2 RNA never crosses the nucleus nor does it create viral DNA. It strictly creates it’s viral spike proteins through the replication complex. This is unlike the HIV hijack process where HIV attaches to CD4 proteins and pivots into the host immune cell. Viral DNA is then created through reverse transcription which is a process which takes RNA to create a copy of DNA. This viral DNA then crosses the nucleus and merges with host DNA to create new viral RNA. Then, this viral RNA creates more GP120 proteins to hijack more cells. With the mRNA vaccine to handle SARS-COV 2, it uses mRNA to send a specific message to the lung cell to replicate harmless spike proteins. These spike proteins are detected by the immune system as they are spread to other parts of the body. The immune system then creates antibodies to combat the intruding spike proteins. This process ensures the body has antibodies to fight against the actual virus if it comes into contact with its cells. If the virus does come into future contact with the body’s cells, the process is similar. The viral spike protein attaches to the lung cell membrane. The RNA of the virus tries to make contact with the replication complex but is blocked by the antibodies formed by the body’s response to the vaccine’s created spike protein. Since the virus cannot reproduce with the replication complex, it eventually dies out.

In addition, according to the Modern Cell Theory, SARS-COV 2 is not living as it violates the concept that all living cells arise from pre-existing cells by division. SARS-COV 2 requires the assistance of the lung cell to be able to replicate and spread. It is unable to reproduce with itself or other SARS-COV 2 cells.

Citations:
Centers for Disease Control and Prevention. (n.d.). Understanding mrna COVID-19 vaccines. Centers for Disease Control and Prevention. Retrieved September 27, 2021, from https://www.cdc.gov/coronavirus/2019-ncov/vaccines/different-vaccines/mrna.html.

Centers for Disease Control and Prevention. (n.d.). Myths and facts about covid-19 vaccines. Centers for Disease Control and Prevention. Retrieved September 27, 2021, from https://www.cdc.gov/coronavirus/2019-ncov/vaccines/facts.html.

“What Are Mrna Vaccines and How Do They Work?: Medlineplus Genetics.” MedlinePlus. U.S. National Library of Medicine, November 16, 2021. https://medlineplus.gov/genetics/understanding/therapy/mrnavaccines/.

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My infographic shows how polarity interacts with the membrane of the human cell. SARS-SOV 2 is classified as an envelope virus similar to HIV, herpes, and Influenza. It has an outer wrapping called the lipid membrane. This type of membrane is non-polar, i.e the electrons shared between two atoms in a molecule within the membrane are pulled towards each atom equally. There are no partial charges formed where electrons favor one atom more. In addition, since the membrane is non-polar it bonds to the non-polar cell lipid membrane of a human cell. If the lipid membrane of the virus was polar, it would not have bonded to the lipid membrane of the human cell since the partial charges wouldn’t distribute evenly. It would have bonded weakly to the H2O molecules surrounding the human cell membrane through an intermolecular force since water is polar.

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Plasma membranes are important in compartmentalization by protecting the cell from pathogens, transporting proteins/nutrients, and discarding toxic particles from the cell that might prevent the cell from functioning properly. They create safe compartments for specific jobs for organelles to make sure they work efficiently.

The cytoplasm is like the base of the cell where RNA ends up. It also aids in the process of diffusion – the way that particles can move around in a cell. The nucleus houses the genetic information like DNA/chromosomes. The process of transcription of matching base pairs occurs in the nucleus. And then the process of translation is done in the ribosomes, an organelle that makes proteins. The endoplasmic reticulum serves as an assembly line for proteins that eventually get post processed and ready to transport by the Golgi Body. Then, vesicles transport the proteins to other organelles. Another major organelle is the mitochondria which regulates energy needs of the cell. With cell signaling, the mitochondria plays a major role in giving proteins activated by conformational changes in a receptor on a fibroblast ATP to function. There are also lysosomes that help isolate infectious particles that works with the plasma membrane to discard those particles from a cell.

I attached a factory analogy we used throughout the year to this post.

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My cell cycle model in Blackbaud covers mitosis, and meiosis is different in the way that it creates 2 divisions with 4 sex cells in the case of reproduction. However, mitosis and meiosis are similar in the way that they rely on S phase DNA replication. I covered the central dogma aspect of replication and how that works in my cell cycle model as quoted below.

“In synthesis, as previously stated, the DNA copies and replicates. In class, we learned that Histones package DNA and DNA wraps around nucleosomes and supercoil – continually twist and form a double helix shape. With replication, the DNA uncoils and shows us 2 strands of DNA that are exactly the same. DNA polymerase, an enzyme, then is able to form base pairs with these individual strands thus replicating the DNA. At the end of synthesis, the cell has 2 full chromatids.”

Mitosis is used to make somatic cells with diploid daughter cells, i.e cells with 2 sets of chromosomes. Each daughter cell has a homologous pair of each chromosome type

However, meiosis makes gametes or sex cells. Its divisions creates haploid daughter cells that have 1 set of chromosomes. Gametes that come from the division in meiosis are different than mitosis in the way that each daughter cell only has 1 chromatid of each chromosome type.

Additionally, mitosis and meiosis both have similar phases of division. I extensively covered these stages in my cell cycle writeup on Blackbaud and considered cyclin production as factors that transition phases. Both start with the same number of organelles from the G1 phase. Both account for 92 total chromosomes and mark the start of a somatic cell.

We also learned that alleles or variations of genes can arise from the synthesis phase to prepare for meiosis. Offspring might produce different proteins from these alleles and errors in the synthesis phase which passes down through generations that follow.

I also attached the cell cycle write-up and model to this padlet if that is easier for you. Some of this information comes from my biology journal as well.

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I showed my understanding of this skill by showing the mechanisms and detailed process of chemical signals with a opioid molecule (signal molecule) and how it undergoes reception by binding to a G protein coupled receptor and causing it to have a shape change. I show how the transduction phase begins where the initial signal that causes a shape change which eventually causes a response which is where potassium molecules are blocked in a phosphorylated ion channel due to an overflow of sodium ions. The low concentration of potassium molecules in the ion channel causes the molecules to move in a euphoric state where they bounce off each other and move faster. I showed a more detailed process of all the parts of Reception, Transduction, and Response through my Cell Signaling model and write up which can be found on Blackbaud in the Cell Signaling Modelling assignment on Blackbaud.

I attached my write-up to this post and the model below if that is easier for you.

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Enzymes can increase the rate of biochemical reactions by rearranging the position of molecules that is more energetically favorable for a chemical reaction to happen. Molecules are constantly in motion, so enzymes help position them closer to each other to trigger certain reactions to happen. Some enzymes help reposition molecules to allow for bonds to form while other enzymes help reposition molecules to cause bonds to break. In our opioid cell signaling model, we used adenylyl cyclase which is an enzyme to break down an alpha molecule and GTP. The enzyme breaks down the alpha molecule and GTP weak bonds to create cAMP. Although we didn’t show the full enzyme process in our Cell Signaling Modelling assignment on Blackbaud, we referenced it in our model through AC/adenylyl cyclase.

I attached my cell cycle write-up to this post and the model below if that is easier for you.

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While I didn’t turn in a project necessarily for this standard, I understand the evolutionary process through my Bio Hour research. I researched about different animals evolving through physical alterations to adapt to climate change. According to paleontologist Jingmai O’Connor, possible surviving animals from an extinction level event caused by carbon emissions are rats, rodents, pigeons, and cockroaches. If they survive the ecological changes caused through carbon emissions destroying several climates, they will need to fill the jobs of other animals that go extinct. For example, they might need to fill spaces in the food chain due to certain predators or preys going extinct to keep the chain balanced to support life. Generally, mammal life is the main group that is being harmed by climate change which is why rodents are expected to do well in the future. Because humans have brought rats to different parts of the world, we have increased the genetic diversity of rats in different parts of the world. Because their genetic makeup is so diverse with different types of rats, they’re able to adapt much better to their new environments. They are able to change their physical features to match their environment which is similar to the arctic lizard example we saw in class where the lizard appeared white/blue to match its icy environment. It is very difficult to predict what these physical changes will be in the future, but they will most likely offer ways for animals to achieve homeostasis in their altered environments. Another big example of evolutionary process we learned about Umbilicaria, a genus of lichens that are found in rough climates. It’s made up of an algal partner and a fungus partner which use a symbiotic relationship to survive. The algal partner needs to fungus partner to find minerals and the fungal partner need the algal partner to produce sugar to be able to function. Both partners need each other to survive in their extreme climates so they merge together to be able to adapt to those conditions. In more tame climates, they do not require each other as they could function without each other. I concluded through this that in light of an environment with a lack of resources to sustain organisms, they evolve over long periods of time to adapt to changes and function more efficiently.

The research for Bio Hour can be found in my Bio Journal in entry 5 November 2021 – Golgi Body/Bio Hr. The analysis for Umbilicaria comes from the Braiding Sweetgrass Reading Discussion post in Blackbaud.

Here is the article I used:
https://www.vox.com/down-to-earth/22734772/future-animals-evolution-unexplainable

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This story is part of a group of stories called

The biodiversity crisis, explained

While it can sometimes seem like humanity is hell-bent on environmental destruction, it's unlikely our actions will end all life on Earth. Some creatures are sure to endure in this age of mass extinction and climate crisis. Over time, they will adapt to a harsher world we've helped create, evolving to meet the moment as best they can.

Some of these transformations have gotten underway in our lifetimes. Climate change, some research suggests, is already " shape shifting " animals - shrinking certain migratory birds and speeding up the life cycles of amphibians, for example. No one knows exactly what changes to plants and animals will transpire in the years to come. Still, evolutionary biologists say it's worth trying to imagine what creatures will evolve in the future.

"I do think it's a really useful and important exercise," Liz Alter, professor of evolutionary biology at California State University Monterey Bay, says on the latest episode of Unexplainable, Vox's podcast about unanswered questions in science. In thinking about the animals of the future, Alter says, we must consider how we're changing the environment now. "It's a very sobering thing to think about the long future," she says.

I spoke to several evolutionary biologists and paleontologists who, along with Alter, helped me imagine what animals might exist one day - say, millions of years into the future - and how our actions could spur their arrival. At the very least, it's reassuring to know that life almost certainly will find a way, with or without us.

But it may never be the same.

Animals that might make it

What animals are likely to exist tens of thousands, or even millions of years from now?

That's the big question I posed to everyone I spoke with, and their responses fell along three main lines of thinking.

Some started off by thinking about which animals alive today are most likely to endure human-caused climate change and mass extinction. (Scientists have identified five major extinction events in natural history, and many say we are living through or on the cusp of a sixth one now, caused largely by human activity.) Others began by imagining the potential environments of the future, and what adaptations might lead creatures to survive in them. A third group thought about the deep history of life on Earth, and what types of animals that used to roam the planet might return, in new forms, long after we are gone.

First off, the survivors: "These are rats, rodents, and also things like cockroaches and pigeons," said Jingmai O'Connor, a paleontologist at the Field Museum in Chicago. These animals "are doing just fine despite the worst that we're doing to this planet."

If these species survive the ecological changes that are occurring now, they might also evolve to fill ecological space left behind by extinct animals. For instance, if tigers go extinct in the next million years, perhaps flightless, carnivorous pigeons and rats will grow to the size of ostriches and snack on the animals that tigers once ate. It's impossible to predict which specific adaptations might emerge in which animals, but it's clear that as some species die off, they leave a gap in the food chain that can be filled by other species.

In the far, far future, rodents are especially well poised to thrive if mammal species continue to go extinct. By introducing rats everywhere we've settled, humans have increased the genetic diversity of rats, which makes them more adaptable to their surroundings. More genetic diversity means "potential solutions to different [environmental] challenges they might face," says Alexis Mychajliw, a paleoecologist at Middlebury College. Already, scientists have noted rats evolving adaptations to thrive in specific cities, like New York. They might even be able to further adapt to living amid heavy metal pollution and radioactivity, or to be able to eat toxic waste, Mychajliw says.

And if life on land grows too harsh, rats may be able to slowly adapt to water. Perhaps their evolutionary descendants will lose their fur or sprout flippers, developing streamlined bodies suited for a fully aquatic existence. Other marine mammals, like seals and whales, have followed this path in their transition from land-dwelling creatures to aquatic ones.

Again, these specific evolutionary paths are pure speculation. But experts say they're within the realm of possibility.

The environments of the future that will shape evolution

The second way to think about animals of the future is by imagining the environments of the future. Environments can drive evolution by exerting selection pressure, favoring some traits over others. For example, some birds have evolved long, pointy beaks to draw nectar out of flowers.

If anything, there will likely be plastic in the environment well into the future. Of all the elements that humans have introduced into the environment, plastic waste is already ubiquitous, and remnants of it might linger for millennia if humans go on producing it as we have. Plastic is "a big source of carbon, which all living things depend on," said Sahas Barve, an evolutionary ecologist at the Smithsonian National Museum of Natural History. Plastic, he added, could become food, and "any animal that can exploit that will be successful."

In a way, this development would kind of go full circle: Many plastics are made from petroleum, which is called a fossil fuel precisely because it derives from ancient, transmogrified plant and animal remains. So new life forms could learn to eat the leftovers of really, really old ones.

Termites could be one such critter. These insects already have a gut microbiome - a collection of microorganisms that help with digestion - that breaks down cellulose. Like plastic, cellulose is made of a complex carbon polymer, so it's not a stretch to imagine termites adapting to break down another polymer like plastic.

"I could easily imagine them evolving a microbiome that helps them then digest plastic," Barve says. Some fungi and bacteria, including some found in the stomachs of cows, are already able to break down plastic.

The distant future is also likely to be more watery, as sea-level rise decreases the portion of the planet covered by dry land. In envisioning a world of rising seas and altered coastlines, some scientists think about how certain animals might take to living in more marine environments.

Sharlene Santana, a professor of biology at the University of Washington, considers how a bat species might evolve to live off of, and around, the oceans. She imagines a bat with a six-foot wingspan taking shape, capable of gliding like an albatross instead of flapping its wings, perhaps covering hundreds of miles in search of food or islands to roost. It might use finely-tuned echolocation to sense ripples in the water in order to detect fish. (In fact, some bats already do this.)

"This bat is doing something that bats cannot do today, which is to sail and soar on ocean air currents for very long distances," Santana says. "I call it the sailing bat."

Looking to the past to predict the future

Many of the scientists who spoke to Vox imagined a future environment where humans are no longer around. In doing so, they often drew from animals that existed on Earth before our time - perhaps these types of creatures could make a return down the line.

If humans were to go extinct, our carbon emissions could still remain in the air for a long time, Alter, the Cal State professor of evolutionary biology, said. That could lead to boom times for plants, some of which can thrive in a CO2-dense atmosphere.

The increased density and diversity of plants, in turn, might eventually increase the concentration of oxygen in the atmosphere. Researchers have hypothesized that the growth of insects depends in part on the concentration of oxygen in the atmosphere, which could lead to insects developing larger bodies, Alter says. So a future, oxygen-rich world is one that might be able to foster rabbit-sized praying mantises, or "ants as large as hummingbirds and dragonflies as large as hawks," Alter said.

It sounds extreme and these visions of the future are merely educated guesses. Then again, something like it has happened before: About 300 million years ago, in the Carboniferous era, the atmosphere was more than 30 percent oxygen, compared with 21 percent today. The fossil record reveals that insects around that time were far larger.

Mairin Balisi, a paleoecologist at the La Brea Tar Pits in Los Angeles, thinks about what type of apex predators might rise to the top of the food chain if humanity does blink out. To that end, she considers what predators existed before humans.

"When we think about large predators in North America alone, we think of the gray wolves, the mountain lion, or the grizzly bear," Balisi says. But large predators on the continent were much more common up until around 12,000 years ago, during the Pleistocene epoch or most recent Ice Age, with many species of saber-toothed cats and bone-crushing canines roaming the land.

In a future world devoid of human beings, Balisi speculates, such large predators might be able to evolve once again. She is most confident about the saber-toothed cats, whose long, sharp teeth and bulky limbs "evolved independently multiple times in the last 40 million years." If some lineage of felines persists eons into the future, history could very well repeat itself.

What future do we want?

Modern humans have only been around a few hundred thousand years, but what we do today is likely to have ripple effects for how the natural world looks tomorrow.

The evolution of life depends on the "genetic and development toolkit" as we know it today, says Santana, the biologist at the University of Washington. Because there's natural variation between animals, some are better at competing for resources and surviving, with the least helpful traits tending to fizzle out, while others crop up with new adaptations. As species continue to go extinct, whether due to habitat loss, agriculture, poaching, or human-caused climate change, many potential sources of diverse life are extinguished from the future, too.

Scientists can still imagine a world where animals that are endangered today carry on and start new branches on the evolutionary tree. The future doesn't have to belong to just the rats, pigeons, and insects. As long as manatees, polar bears, and monarch butterflies are around, for example, there remains the possibility of their descendants entering the picture sometime in the future.

All of which is worth thinking about if we are to take full responsibility for our role in shaping what the planet will look and feel like long after we're gone. When we imagine what creatures could come next, we can ask ourselves: What future do we want for the planet? How hard are we willing to work so that future generations of humans are still around to live alongside it?

Giant bugs evolving in the future would be "really, really cool," Alter said. Especially so, she added, "if humans are actually around to see them."

In the meantime, while it's heartening to imagine how different species might bounce back in millions of years, "you don't want to stop investing in the life that's around us today," said Mychajliw, the Middlebury paleoecologist. "There's a lot we can do right now to ensure that we protect species, protect their genetic diversity, and protect their ability to respond to change."

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The animals that may exist in a million years, imagined by biologists

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The biodiversity crisis, explained While it can sometimes seem like humanity is hell-bent on environmental destruction, it's unlikely our actions will end all life on Earth. Some creatures are sure to endure in this age of mass extinction and climate crisis.

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Metabolism simply is the way our body converts nutrients that come from food and water into energy. Within cellular respiration, the process of oxidative phosphorylation within the inner membrane of the mitochondria shows how the electron transport chain in the mitochondria creates ATP. NADH gets its bond broken in Complex 1 which essentially donates 2 electrons to Complex 1. These donated electrons cause a pump in Complex 1 to push 4 Hydrogen protons into empty space and the outer membrane of the mitochondria. Then, FADH gets its bond broken by Complex 2 which donates the electrons from FADH to Complex 2. A mobile electron carrier, Q, carries these electrons through the chain to Complex 3. These donated electrons cause a pump in Complex 3 to push out 4 hydrogen protons as well. Then Complex 3 transfers the electrons to Complex 4 through the C electron carrier. Complex 4 uses these electrons to power the pump to push out 2 Hydrogen protons into open space or the outer membrane. Then the electrons are transferred out of the electron transport chain towards the outer membrane where they bind to Oxygen produced by breathing which creates H20. Finally, the electron gradient transfers the protons that were pushed from the pumps in each complex into the ATP Synthase, an enzyme that creates ATP from ADP and phosphate.

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Learning about the carbon cycle models this big picture energy flow with the laws of thermodynamics and the way organisms fuel growth. To begin, plants take in sunlight to be able to then fix carbon molecules from the air to itself in the process of photosynthesis to create glucose. A consumer might eat that plant and metabolize the glucose produced earlier. Then, they will release CO2 back into the atmosphere through respiration to harness energy. Plants and animals go through this process of respiration. When these organisms die, they decompose, releasing more CO2 into the atmosphere. Combustion is another factor in releasing CO2 into the atmosphere. Combustion is essentially burning something. In many cases, we burn fossil fuels, masses made up of carbon, which transforms potential energy from the fuels into thermal energy when we release carbon atoms back into the atmosphere through factories. Greenhouse gases are produced with continued carbon emissions from factories causing more heat and gas to be trapped in the atmosphere resulting in less heat escaping into space. With all of these factors like respiration, decomposition, and combustion releasing carbon into the atmosphere, there are also ways in which carbon moves from the air/atmosphere back towards the ground for organisms to use. When plants photosynthesize to create glucose as discussed previously, they take carbon from the air. Oceans can also interact with carbon. In class we discussed how the ocean is considered a carbon sink and we noticed that when carbonic acid is formed in oceans, they can damage clam shells.

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Gene expression controls when certain genes should be read in a cell. With transcription and translation, it is used within the nucleus to communicate when the nucleotides of mRNA match up with A to Us for example. Changes in gene expression over time causes evolution of body parts. I've shown the transcription and translation process of gene expression in my protein project with the human growth hormone.

Displayed below is when I transcribed DNA of a HGH gene to mRNA and translated mRNA to an Amino Acid Sequence.

DNA:

cgaaccactc agggtcctgt ggacagctca cctagctgca atggctacag gctcccggac

gtccctgctc ctggcttttg gcctgctctg cctgccctgg cttcaagagg gcagtgcctt

cccaaccatt cccttatcca ggccttttga caacgctatg ctccgcgccc atcgtctgca

ccagctggcc tttgacacct accaggagtt tgaagaagcc tatatcccaa aggaacagaa

gtattcattc ctgcagaacc cccagacctc cctctgtttc tcagagtcta ttccgacacc

mRNA:
gcuuggugag   ucccaggaca   ccugucgagu   ggaucgacgu   uaccgauguc   cgagggccug

cagggacgag    gaccgaaaac   cggacgagac   ggacgggacc    gaaguucucc   cgucacggaa

ggguugguaa   gggaauaggu  ccggaaaacu   guugcgauac   gaggcgcggg   uagcagacgu

ggucgaccgg    aaacugugga   ugguccucaa  acuucuucgg   auauaggguu  uccuugucuu

cauaaguaag   gacgucuugg   gggucuggag   ggagacaaag   agucucagau  aaggcugugg

Amino Acid Sequence:

Start codon is AUG

Met-Ser-Glu-Gly-Leu-Gln-Gly-Arg-Gly-Pro-Lys-Thr-Gly-Arg-Asp-Gly-Arg-Asp-Arg-Ser-Ser-Pro-Val-Thr-Glu-Gly-Leu-Val-Arg-Glu-x