PHOTOSYNTHESIS

DATE: Monday, December 14, 2015

TIME: 2:00 PM

WEATHER CONDITIONS: At the time of observation, it was approximately 67˚F outside. There was a 50% chance of precipitation throughout the day, and it was cloudy and misty with some light sprinkles. There was 29.77 in. of atmospheric pressure. The average humidity was 93%. There was 11 mph wind throughout the day.

CHANGES: TBD. 

LEAF ANATOMY:

Source

STRUCTURES AND FUNCTIONS:

1. Cuticle: The cuticle of most plant leaves is thick and waxy, which enables it to resist losing too much water. 
2. Upper & lower epidermis: The upper epidermis of a leaf is a single layer containing transparent cells that allow most of the light that strikes them to pass through to the rest of the plant. This layer is also covered with the cuticle, which prevents water loss. The lower epidermis is where most of the stomata (the leaf's pores) are located. The cells inside this layer closely resemble those of the upper epidermis, however there are two guard cells. These cells control the opening and closing of the stomata. 
3. Guard cells (& stomata): These surround the stomata and are shaped like two cupped hands. If the guard cells fill with water, they swell and bend away from each other. This movement opens the stoma (the singular form of stomata, or the leaf's pores). If the guard cell has no water, it closes the stoma. Open stomata enables the flow of gas, which is beneficial because it allows for oxygen gas to be released during the process of photosynthesis.   
4. Spongy mesophyll: These are more loosely fit together and they lie between the palisade layer and the lower epidermis. Because there are air spaces in between each spongy cell, this allows for more air to enter the cell and for gas exchange. 
5. Palisade mesophyll: These are column-like cells that lie just under the epidermis of the plant leaf. Because of their irregular shape, they also have space in between that allows for the passage of gas. This particular structure comes in handy during the process of photosynthesis, because it allows for the passage of carbon dioxide gas into the stroma, which works to create glucose. 

PLANT CELL:

Source

CHLOROPLAST:

Source

PHOTOSYNTHESIS EQUATION:
                          (sunlight)
6H2O + 6CO2  ---------  6O2 + C6H12O6

PHOTOSYNTHESIS SUMMARY:
This is the process where autotrophic organisms use sunlight or another form of energy to produce glucose from water and carbon dioxide. The glucose is eventually made into ATP through cellular respiration. Oxygen is also formed but is released back into the environment. Photosynthesis takes place in two reactions, the light reaction and the dark reaction (Calvin Cycle). In the light reaction, the chlorophyl found inside the chloroplast of the plant cell works to absorb the sunlight. It converts this light into forms of chemical energy called ATP and NADH. Oxygen gas is released back into the atmosphere from the plant's stomata, or pores. ATP and NADH then travel over to be used in the Calvin Cycle, and they join with carbon dioxide to produce the glucose molecules.

CHART:

Reactants	Where in the chloroplast is the reactant used?	Is the reactant used during the Light reactions or Calvin cycle?
6 H2O	thylakoid stacks	Light reactions
6 CO2	stroma	Calvin cycle

Products	Where in the chloroplast is the product made?	Is the product made during the Light reactions or Calvin cycle?
6 O2	stomata	Light reactions
C6H12O6	stroma	Calvin cycle

RESOURCES:

• http://www.biologycorner.com/worksheets/leaf_coloring.html
• https://www.msu.edu/user/morleyti/sun/Biology/photochem.html
• http://www.rsc.org/Education/Teachers/Resources/cfb/Photosynthesis.htm
• http://biology.about.com/od/plantbiology/a/aa050605a.htm
• http://users.rcn.com/jkimball.ma.ultranet/BiologyPages/L/Leaf.html
• https://www.boundless.com/biology/definition/cuticle/

UPDATE

DATE: Tuesday, November 17, 2015

TIME: 10:20 AM

WEATHER: At the time of observation, it was 61˚F outside. There was no precipitation. There was 30.36 in. of atmospheric pressure. The average humidity was 40%. There were light winds and it was mostly sunny. 

CHANGES: The only change I notice is that there are almost no leaves left on the tree. There are also not many dead leaves around the trunk of the tree like there used to be. This means that there were less dying leaves on the branches to begin with, so there weren't as many that had to fall off. 

CELL TRANSPORT

DATE: Tuesday, November 10, 2015

TIME: 12:00 PM

WEATHER CONDITIONS: At the time of observation, it was approximately 70˚F outside. There was no precipitation during the time of observation, and it was sunny throughout the entire day. There was 29.98 in. of atmospheric pressure. The average humidity was 52%. There was 9 mph wind throughout the day.

CHANGES: The most noticeable change is that the tree pretty much has no leaves left, and the reaming few are orange/brown and dead. The fallen leaves have been left scattered around the trunk. Looking back at the entry from two weeks ago, it's amazing and very interesting to see such a dramatic shift in that short period of time. 

1. Molecules diffuse due to the movement of particles in liquids and gases. This is affected by temperature, as the particles move faster and diffuse at a quicker rate in a warmer environment, and slower in a cold environment. This idea is called thermal motion. 





BEFORE: this diagram shows a normal plant cell

ISOTONIC: this diagram shows that there is equal water concentration inside and outside of the cell. This solution will also reach dynamic equilibrium, meaning that water is moving in and out of the cell at equal rates. Therefore, this diagram resembles the normal plant cell picture almost exactly, because not much changes between the two. 


HYPOTONIC: this diagram shows that there is a higher water concentration outside of the cell, because as the arrows show, water is moving from outside the cell (the higher concentration) to inside of the cell (the lower concentration). This pattern of diffusion causes the vacuole to expand, the turgor pressure to increase, and therefore the cell wall to eventually burst.


HYPERTONIC: this diagram shows that there is a higher concentration of water inside the cell, because as the arrows show, water is moving from inside the cell (the higher concentration) to outside the cell (the lower concentration). This pattern of diffusion causes the vacuole and cytoplasm to shrink, which shrivels up the overall plant and eventually causes it to die. 

2. See diagrams above.
3. The water will move out of the plant cell. Because water naturally flows from a high to low concentration, water will leave the highly-concentrated cell and move into the surrounding area, since it has a lower concentration.
4. The water will diffuse up into the roots, and then throughout the rest of the plant. This is because water naturally diffuses from a high to low concentration, and 0 bars (the distilled water) is greater than -2, -6, -15, and -1000. Therefore, the more highly concentrated distilled water will move to the lower-concentrated areas, such as the leaves and the roots. 
5. If a farmer applied salt to their plant's roots on a regular basis, the plant would quickly shrivel up and die. This is because salt creates a hypertonic solution, and it decreases the turgor pressure. This means that inside the cell, the vacuole and cytoplasm are shrinking. And in terms of the overall tree, the farmer would notice its begin to shrivel up, die, and fall off the branches. This is also due to the fact that osmosis and the net diffusion of water causes the majority of the water supply to diffuse out of the cell, therefore drying out the plant cells in the tree to the point where they shrivel up. The water diffuses in a patter of high to low water potential. 

REFERENCES

• http://www.mun.ca/biology/Osmosis_Diffusion/tutor2.html
• https://en.wikipedia.org/wiki/Turgor_pressure (used only for pictures!!)
• http://freecoloringpages.co.uk/?r=unlabeled%20plant%20cell
• http://alevelnotes.com/Osmosis/143?tree=

CELL STRUCTURE

DATE: Monday, October 26, 2015

TIME: 2:00 PM

WEATHER CONDITIONS: At the time of observation, it was approximately 56˚F outside. There was no precipitation during the time of observation, although it was very cloudy and grey throughout the entire day. There was 30.39 in. of atmospheric pressure. The average humidity was 69%. There was 9 mph wind throughout the day.

CHANGES: It seems as if almost overnight the Turkey Oak changed! Almost all of its leaves are now either completely or partially yellow. There are also less dead leaves scattered around the trunk, although that might have to do with the heavier winds that occurred throughout the day of observation.

DIAGRAM: (source)

PLANT VS. ANIMAL CELLS:

• Similarities vs. Differences
• A plant cell is typically larger in size.
• A plant cell cannot change shape, because it is enclosed by a rigid cell wall. An animal cell can and often does change shape because its cell wall is composed of thin, flexible plasma membrane.
• However, the two cell walls are similar because both have plasma membrane.
• A nucleus lies on one side of the plant cell, and it lies in the middle of an animal cell.
• Plant cells contain chloroplasts which perform photosynthesis, and animal cells completely lack chloroplasts.   
• Both the plant and animal cell are Eukaryotes.
• The nuclei of both cell structures contain DNA, which is assembled from chromosomes. 
• Plant cells are capable of making their own food while animal cells cannot. 
• Both have mitochondria, ribosomes, Golgi Apparatus, and vacuole

EUKARYOTIC VS. PROKARYOTIC CELLS:

• Similarities vs. Differences
• Eukaryotes have true nuclei containing DNA whereas prokaryotes do not. 
• The prokaryotes have DNA within the cytoplasm.
• The genetic material in prokaryotes is not membrane-bound.
• Prokaryotes are generally much smaller than eukaryotes.
• Both prokaryotes and eukaryotes contain: DNA, ribosomes, cytoplasms, cell membrane, and flagella. 
• Because they both have DNA/genetic codes to carry out basic functions, both perform many of the same functions in similar fashion. 

REFERENCES:

• http://waynesword.palomar.edu/lmexer1a.htm
• http://www.majordifferences.com/2013/10/difference-plant-cell-vs-and-animal-cell.html#.Vi7Z02SrTR0
• http://www.biologyexams4u.com/2013/02/difference-between-plant-cell-and.html
• https://www.brainpop.com/health/bodysystems/cells/qanda_popup.weml?qanda_id=1081&category_safe_name=health
• http://www.diffen.com/difference/Eukaryotic_Cell_vs_Prokaryotic_Cell
• https://quizlet.com/7264170/prokaryotes-vs-eukaryotes-similaritiesdifferences-flash-cards/

BIOCHEMISTRY

DATE: Wednesday, October 21, 2015

TIME: 1:45 PM

WEATHER CONDITIONS: At the time of observation, it was approximately 74˚F outside. There was no precipitation during the time of observation. There was 30.25 in. of atmospheric pressure. The average humidity was 75%. There was very little wind throughout the day, and it was sunny all day.

CHANGES: There aren't many changes to report. The tree mostly has green leaves with a few dead, brown ones mixed in. There weren't any animals observed around the tree at the time of observation, except for several tiny bugs crawling up the trunk. There are a ton of dead leaves scattered around at the base of the trunk, and several acorns are sprinkled in.

AUTUMN FOLIAGE: Leaves change colors due to the four different pigments found inside them: chlorophylls, carotenoids, anthocyanins, and tannins. The amount of production of these pigments determines the leaf's overall color.

TRANSPIRATION:
Transpiration is the process by which water and moisture is carried throughout the plant, changing into vapor at some point and releasing back into the atmosphere. It's not really known for sure why plants, such as the Turkey Oak, perform transpiration, but it is thought to have something to do with temperature control. In order for any plant to grow and thrive, water must reach all parts of the plant, including far down into its roots. But also by spreading the water out among the plant, the plant maintains constant homeostasis.

CAPILLARY ACTION:
Cohesion describes a water molecule sticking together with another water molecule through hydrogen bonding, the type of bonding the exists between polar molecules. Capillary action is the process of water flowing from the roots of trees up to other parts of the tree, such up the trunk and to the leaves. This is a scientific phenomenon, because the water is flowing against gravitational forces. The cohesive forces occurring between the water molecules are what force the water to maintain the certain shape necessary for moving up the trunk of the tree. Adhesion is another property that is essential for this process to occur. This occurs between water and other polar molecules, and capillary action can only occur when adhesive forces are stronger than cohesive forces.

PROPERTIES OF WATER:
1. Ability to Moderate Temperature: Hydrogen bonding is very strong BETWEEN MOLECULES, and it takes a lot of energy to disrupt them. This allows the water molecule to resist temperature change, because not many molecules can break the bonds that exist between them. This property is important to Earth because it keeps Earth's bodies of water at a temperature that is suitable to all life forms that use them for their habitats.

2. Expansion upon Freezing: When water reaches a near-freezing temperature, the hydrogen bonds between the water molecules become stronger. The molecules are harder to break apart, and they form refined crystal-like structures that take up more space. Unlike when the water is at a warmer temperature, the water molecules are not moving around, so they remain clumped together, and the overall collection of water molecules expand. This property is crucial to life because ice sheets forming on the top of bodies of water contribute to the polar environments, and allow many organisms to live below the ice in the freezing water. It also prevents oceans from freezing completely solid.

3. Versatility as a Solvent: In aqueous solutions, ionic compounds and polar molecules can dissolve in water. Because many molecules are polar or charged, water readily dissolves with most molecules. Hydrogen bonding is what makes it possible for these bonds between water and the other molecule to exist. The positive hydrogen atom is able to bond with many other negative ions. This property is essential to life on earth because wherever water exists, it is bonding with other essential nutrients, chemicals, and minerals.

pH:
Acidic Solution: pH is less than 7; any substance that increases the H+ concentration of any solution to become a positive ion (a molecule with an overall positive charge).
Neutral Solution: pH is 7
Basic Solution: pH is greater than 7; any substance that reduces the H+ concentration of any solution to become a negatively charged ion.

ACID RAIN:
Acid rain is formed when compounds such as sulfur dioxide and nitrous oxide enter the atmosphere and create a chemical reaction. If these compounds rise high enough into the atmosphere, they mix with other elements such as oxygen and water to form acidic pollutants, or acid rain. The pollutants are carried far by the wind and then get mixed with the fog, sleet, and rain environments sometime experience. The acid rain, when it lands on the earth, will dissolve the essential nutrients and minerals that plants and animals need in order to grow and thrive. Acid rain also causes aluminum, which is a toxic element to the plants and animals, to release into the soil.

REFERENCES:

• http://harvardforest.fas.harvard.edu/leaves/pigment
• http://water.usgs.gov/edu/watercycletranspiration.html
• http://www3.epa.gov/acidrain/education/site_students/whatcauses.html
• http://chemwiki.ucdavis.edu/Physical_Chemistry/Physical_Properties_of_Matter/Bulk_Properties/Cohesive_And_Adhesive_Forces/Capillary_Action
• http://socratic.org/questions/how-do-water-hydrogen-bonds-moderate-temperature
• Water and pH lecture on class page
• https://en.wikibooks.org/wiki/Structural_Biochemistry/Unique_Properties/Expansion_upon_Freezing
• http://water.usgs.gov/edu/qa-solvent.html

EVOLUTION & TAXONOMY

DATE: Tuesday, October 13, 2015

TIME: 10:47 AM

WEATHER CONDITIONS: At the time of observation, it was 68˚F outside. There was no precipitation during the time of observation. There was 29.79 in. of atmospheric pressure. The average humidity was 73%. It was pretty breezy throughout the day of observation, and it was mostly sunny. 

CHANGES: Some of the leaves are beginning to turn brown, and there are many dead leaves scattered around the trunk. Some of the branches are completely bare. I observed several acorns around the base of the trunk, but I did not observe any squirrels or bugs on or around the tree.

EVIDENCE OF EVOLUTION: Green algae have the same photosynthetic pigments found in other plants. There is many structural, genetic, and chemical data that also justifies this hypothesis.

ADAPTATIONS: 

1. Vascular Tissue - This is the tissue in plants that carry water and nutrients throughout the plant. This is considered an adaptation because not all plants live adjacent to a body of water, so they had to develop other ways to spread water throughout their systems. 

2. Seeds - A seed is essentially a miniature plant with a protective cover that has a built-in food supply made up of proteins, carbohydrates, or fats. This is considered an adaptation because it has allowed plants to overcome dry environments and the lack of upright growth.

3. Flowers - A flower is the seed-bearing part of the plant. It is considered an adaptation because different flowers adapt to the specific climate and environment their tree lives in. For an example, flowers that are pollinated by the wind are much smaller and have a flatter surface, therefore making it easier to be swept up by the wind and transported long distances. 

4. Others - In terms of the Oak tree, 3 helpful adaptations include: deep taproots that help gather water, single trunks with high branching that allows them to stretch tall over all other trees, and holding on to its brown leaves well into the winter.

PLANT PHYLOGENY:

PLANT CLASSIFICATION:

1. Bryophytes (mosses) - Small, non-vascular land plants that grow clumped together on rocks, soil, or the trunks of trees. One example is Capillary Thread-moss (Bryum Capillare).

2. Seedless vascular plants (ferns) - Contain vascular tissue, but do not produce flowers or seeds. One example is Whisk Fern (Psilotum).

3. Gymnosperms (pine trees) - Plants that have seeds unprotected by an ovary or fruit. One example is a Cycad (Cycadophyta).

4. Angiosperms (flowering plants) - Plants that have flowers and produces seeds that are enclosed within a carpel, or the female reproductive organ in a flower. One example of this very broad group is a Magnolia Tree (Magnolia Grandiflora).

SPECIES: A species is a group of similar organisms living and reproducing with one another. The Turkey Oak is considered its own species, separate from the broader Oak umbrella, because of its many unique distinctions. It has a much more rapid growth, mossy-cupped acorns, and it keeps its leaves on its branches well into the winter season, unlike most other tree species. 

REFERENCES:

• http://www.ext.colostate.edu/mg/gardennotes/137.html
• https://wikispaces.psu.edu/display/110Master/Plants+I+-+Evolution+and+Diversity,+and+Non-Vascular+Plants
• http://www.botanical-online.com/floresadaptacionesangles.htm
• http://garden.lovetoknow.com/wiki/Oak
• http://bryophytes.plant.siu.edu/bryojustified.html
• https://www.boundless.com/biology/textbooks/boundless-biology-textbook/seedless-plants-25/seedless-vascular-plants-157/seedless-vascular-plants-613-11833/

BIG IDEAS & ECOLOGY

DATE: Tuesday, September 22, 2015

TIME: approximately 11:45 AM

LOCATION: If you are standing facing Stinson Hall, I am the massive Turkey Oak tree on the right side of the house.

WEATHER: At the time of observation, it was 66ºF outside. There was no precipitation before or during the time of observation. There were 30 in. of atmospheric pressure. There was an average of 85% humidity throughout the day. There was no wind. The weather was gray and overcast.

IDENTIFICATION: Turkey Oak (White Oak) Quercus Laevis Walt

BIG IDEAS:
1. The Turkey Oak is known for being drought-resistant, and has therefore become dominant in drier, infertile communities. The species most likely evolved due to the fact that it held the favorable trait in its environment: being able to go without much water for an extended period of time. Over time, other tree species would have died out because they needed a lot of water to survive, leaving only the Turkey Oaks to survive and reproduce.

2. Homeostasis is an essential process that all living things must go through to ensure that they maintain a stable internal environment. For trees, this means temperature and water regulation. In terms of water, the Turkey Oak absorbs water through its roots, and then releases that water through leaves in the form of vapor. This is a molecular process is called osmosis, and it is essential in ensuring that water is being distributed to all parts of the tree so that it can continue to grow and reproduce.

3. The Turkey Oak tree, along with all other trees and plants, receives important messages from its environments through receptors located in the plasma membranes of the cells. These messages can be about a change in season, or the shift from day to night. These are all important messages for a tree to understand, because some are more suited for longer amounts of sunlight and warmer weather, and would thus be better suited for a particular environment.

4. In terms of interactions within its community, the Turkey Oak provides many services to its community. In the winter, its leaves do not fall off, which makes it the perfect home for birds and small mammals year round. These animals also utilize its leaves for their nests, and are able to do so even in the winter as this is one of the only sources for leaves during that time. This tree also grows acorns, which are an essential part of many small mammal's diets, such as the squirrel.

ENVIRONMENT: 
Climate - Can be anywhere from the low negatives (F) during the winters to around 86ºF in the summer. There is about 30-60 inches of rainfall per year.
Plants - Trees such as oaks, maples, and beeches, shrubs, mosses, and perennial herbs.
Animals - Birds such as hawks, snowy owls, cardinals, and woodpeckers. Mammals such as deer, raccoons, opossums, porcupines, and foxes.
Important Factors - Temperate deciduous forests are unique because they are one of the only biomes that experiences all four seasons. This means that the plants and animals living in this community need to be able to adapt to a cold winter, but also a hot summer.

COMMUNITY MEMBERS: As you can see in the picture above, there is green moss and lichen covering the bottom third of the tree trunk. Although these are both non-parasitic, they often indicate the old age and deterioration of a tree. When I observed the tree, I did not see any birds nests within the branches or any birds flying around. However, I did find several red and black ants crawling up the trunk, as well as acorns scattered across the base of the trunk, which indicates that this particular tree is a favorite food source for squirrels.

SUCCESSION: Because my tree is located next to a building and walkway, the space surrounding it had to be cleared to make room for these structures. This means that the previously existing ecosystems in these areas were destroyed and cleared out in order to make room for the new structures. In the walkway adjacent to the tree, grass surrounding the pavement most likely grew first in terms of ecological succession. Next, smaller organisms such as ants, beetles, and spiders populated the area. Lastly, as trees and shrubs were planted along the walkway and acorns grew from them, small mammals like squirrels arrived.

NUTRIENT CYCLES:
Water - The Turkey Oak tree, as well as all other trees in general, play an important role in the water cycle. In a process called evapotransporation, the tree soaks up the precipitation in its roots, and then releases small amounts of water through its small pores along the branches and trunk back into the atmosphere. This water that is added back into the air then condensates in the atmosphere and helps produce more rain and precipitation.
Carbon - The Turkey Oak tree absorbs atmospheric carbon dioxide and uses it in the photosynthesis process to produce glucose cellulose that is then stored in the tree. The tree also uses the CO2 to put oxygen back into the atmosphere, which is necessary for all other living things.
Nitrogen - Nitrogen is essential to the Turkey Oak tree because the tree needs this nutrient in order to grow, reproduce, and survive. The tree soaks up this nutrient through the soil, and then other animals who use the tree's resources such as its oxygen or acorns benefit because the tree remains healthy.
Phosphorous - Similar to nitrogen, phosphorous is the second most vital nutrient to a plant's health. The Turkey Oak tree absorbs the phosphates through its root hairs, and in turn remains healthy and thriving. All living organisms are then able to enjoy the tree's resources, such as its oxygen, food, shelter, and shade.

REFERENCES:

• http://www.wunderground.com/personal-weather-station/dashboard?ID=KNCDAVID5&scrollTo=historyTable#history/s20150922/e20150922/mdaily
• http://www.fcps.edu/islandcreekes/ecology/white_oak.htm
• http://www.fs.fed.us/database/feis/plants/tree/quelae/all.html
• https://prezi.com/eenyrutqbuel/homeostasis-in-oak-trees-and-elephant/
• Campbell Biology Tenth Edition textbook
• http://earthobservatory.nasa.gov/Experiments/Biome/biotemperate.php
• http://www.nhptv.org/natureworks/nwep8c.htm
• https://www.rhs.org.uk/advice/profile?pid=411
• http://climate.ncsu.edu/edu/k12/.watercycle
• http://www.nrs.fs.fed.us/niacs/carbon/forests/
• http://lifeofplant.blogspot.com/2011/03/phosphorus-cycle.html