4.A.6 Portfolio

Describe how ecosystems provide organisms with their energetic and matter requirements.

It starts off with the producers. This group is composed of plants and other organisms that are “photosynthetic,” meaning that they make their food and molecules necessary for life from the energy of the sun. This process is also known as photosynthesis. Then, the energy from the producers is transferred to organisms that eat the producers or primary consumers (herbivores), which break down the producer’s molecules. Then energy is transferred to secondary and tertiary consumers. When these animals die, the ecosystem’s decomposers will eat the dead animals for sustenance, transferring the dead animal's energy to both the ecosystem, in the form of heat energy, and the decomposer.

Explain how changes in climate can influence primary productivity in an ecosystem.

Climate change has forever been linked to changes in the ecosystem. Many animal species go extinct as they are unable to adapt to the changes presented in their environment. However, primary productivity is affected because the first ones to be affected by climate change are the producers. Due to this and the way energy is transferred within the ecosystem, humans will eventually these effects. 

If a certain species of plant died in the ocean because the water was too cold or hot, then all the fish eating that plant would eventually die off. Then the fish eating that fish would die off and so on. Eventually humans would notice this change in climate as the fish that they ate also died off to due a lack of prey caused by climate change.

Compare food chains and food webs.

Food chains differ from food webs in that food chains main focus is on how each organism in an ecosystem obtains its food. Food chains follow only one path and  contain arrows pointing from one organism to another to point out which organisms are eaten by which. Food webs aim more to demonstrating the flow of energy and nutrients in an ecosystem. They show more of how several animals and plants are connected.

Source: http://aisdvs.aldine.k12.tx.us/mod/book/view.php?id=169242&chapterid=32229

Describe the major interactions among organisms in a food web.

Each trophic level will contain less energy than the last as only a typical 5% to 10% of energy is passed down each organism. Therefore there are usually no more than four or five levels within a food chain. At first trophic level are the primary producers, plants and organisms that use the sun's energy to produce food. Then there are primary consumers, or herbivores. Then,  secondary consumers are carnivores that eat herbivores. On the top are tertiary consumers, carnivores that eat other carnivores.


Explain how modeling of the trophic structure of an ecosystem can be used to make predictions about the effects of changes in biotic and abiotic factors on that ecosystem.  

With the modeling of the trophic structure of an ecosystem, we are able to see how organisms and abiotic factors interact with each other and how the flow of energy and nutrients occurs. Having access to this, therefore, also allows us to predict how changes of biotic or abiotic factors will affect all others. In order to affect organisms, something in the ecosystem, whether abiotic or biotic, will increase or decrease the transfer of energy from each trophic level more or less than the typical 10% that is passed. Modeling the trophic structure would allow us to make predictions on which organisms would stop receiving energy due to changes in biotic or abiotic factors or receive an increase in energy instead.


Describe the strengths and limitations of this approach

This approach is helpful in the fact that it does help ecologist predict what might happen in ecosystems did undergo any major changes. However, this approach only allows ecologists to view one ecosystem at a time. This is limiting especially since there are a variety of ecosystems.

Provide examples to demonstrate how human activities have impacted ecosystems on local, regional, and global scales.  Describe the causes, and effects of these impacts, and discuss possible avenues of mitigating these impacts.

Deforestation is human activity that has had a serious impact on the ecosystem. Before we began to cut down habitats, forest used to account for 30% of the Earth’s land area. TOday, areas the size of Panama are being lost. This has caused several consequences. Millions of species have lost their homes, the soil of the forests becomes dry since trees no longer provide shade, and global warming has increased since trees that absorb the harmful greenhouse gases are being cut down. The most evident and quickest way to stop the effects of deforestation is to simply stop cutting down trees. However, given the power and motivation of large companies, a reasonable solution may be to end the practice of clear cutting. Instead, a balance of trees cut and new ones planted should be established.

Source: http://environment.nationalgeographic.com/environment/global-warming/deforestation-overview/

Provide examples of species that have been driven to extinction by human activities.

- Pyrenean Ibex: Went extinct in 2000 due to too much hunting

Source: WikiMedia

-Tasmanian Tiger: Lived in Australia; were often shot and trapped as people believed they killed livestock

Source: WikiMedia

- Javan Tiger: Became extinct around the mid-1970’s due to loss of their forest habitat and excess hunting  

Source: WikiMedia

Source: http://www.huffingtonpost.com/2013/10/22/11-extinct-animals_n_4078988.html

Predict the effect of a change in one of the components on the interactions within the community and matter and energy flow.

If one of the components were to change, this may allow the ecosystem for a greater variety of ways to react to the change in environment. A change in the molecule may possibly give cells the ability to have many different functions, since even the smallest change has an effect. Therefore with this genetic alteration, species may move up or down in the food chain due to their remarkable ability to adapt to the changes in the environment.

4.A.1

Compare the synthesis and decomposition of biological macromolecules.

Synthesis of macromolecules is the creation of macromolecules or when two or more simple molecules combine to form polymers. Synthesis is demonstrated in the process of dehydration synthesis. Polymers are formed when dehydration synthesis adds or creates a water molecule when combining a short polymer and a unlinked monomer. Decomposition of macromolecules is the process of taking these molecules apart or breaking them down. This occurs during hydrolysis, when a water molecule is added to a polymer to break it down.


Where does the energy needed to drive the synthesis of biological macromolecules come from?

Macromolecules are essentially composed up of polymers, large molecules with many monomers. These polymers are formed during dehydration synthesis. During the synthesis of biological macromolecules, a water molecule will created when two simpler molecule combine.

How does the structure of  polysaccharides, proteins, & nucleic acids influence the function of those molecules?

Polysaccharide, polymers primarily found in sugar, are responsible for structure and storage. The structure of these molecules is determined by the sugar monomers it is made up of and the positioning of the glycosidic linkages. Proteins serve for transport, storage, cellular communication, and structural support. Proteins are composed up of amino acids, whose sequence is determined by DNA. Changes in DNA will dictate changes in protein and affect its function. Nucleic acids, being composed of nucleotides, are divided into two categories. DNA will give directions for amino acid sequence and its own replication. On the other hand, RNA is in charge of protein synthesis. Nucleotides themselves are made up of a nitrogenous base, pentose sugar, and one or more phosphate groups.


How does the structure of DNA contribute to its roles in protein synthesis and heritability?


DNA is will affect the primary structure of proteins. Since DNA has information for its own replication, it directs the creation of mRNA and instructs it to carry the information for replication and to perform protein synthesis. During this process, amino acids are put in order so that they exactly replicate the amino acids that make up DNA.


Why is DNA a good molecule for information storage?

Due to its double helix shape, the DNA molecule is useful for storage. This double helix is created by DNA’s composition of two polynucleotides spiraling around an invisible axis. DNA also allow for flexibility and the creation of a large variety of proteins since it has an incrdibly large amount of sequences possible for nucleic bases.



How do the differences in the structure of DNA and RNA contribute to the difference in the functions of those molecules?


Even though there are differences, DNA and RNA are similar in that they are both composed of polynucleotides. These polynucleotides are each constructed from nucleotides. These nucleotides each contain a nitrogenous base, a five carbon sugar, and one or more phosphate groups. However, DNA is composed of a deoxyribose sugar and nitrogenous base Purine, which contains the Adenine and Guanine, giving DNA its spiral. RNA is composed of ribose sugar and pyrimidines, which contain Thymine, Cytosine, and Uracil. RNA is also only single stranded.


Explain how the sequence of amino acids in a protein determines each level of that protein’s structure.

The primary structure is directly affected by DNA. DNA is what contains the long sequence of amino acids that make up proteins and were inherited from our parents. The secondary structure deals with the protein coiling and folding due to  the formation of hydrogen bonds along the repeating chain of amino acids, also known as a polypeptide backbone. Tertiary structure deals with the interactions between these coils and folds due to the hydrogen and ionic bonds, and hydrophobic interactions. The formation of macromolecules by bonding several polypeptide bonds takes place during the last level, the quaternary structure.

Explain how the conditions of the environment that a protein is in effect the structure and function of that protein.

The bonds formed between the R groups of proteins are crucial in the tertiary structure of proteins and therefore to the function of the protein. Since these R groups are joined with hydrogen, ionic, and covalent bonds, and also hydrophobic interactions, anything that can destroy these bonds or interrupt the interaction may lead to protein malfunction. These bonds and interactions may be affected by a variety of things, ranging from changes in Ph, temperature, and salt concentrations. Eventually, it may even lead to the denaturation of proteins, making them biologically inactive.


Explain how the structure of lipids determines the polarity of the molecule.

Lipids are hydrophobic or nonpolar, meaning that they do not mix in with water. This is due to the nonpolar covalent bonds formed between hydrocarbons. Since lipids are not polar, meaning that they are not charged since the molecules they are composed up of share equal electronegativities, they will not mix with the hydrogen bonds that water molecules have.


If the chemistry of water occurs in aqueous solution, why are lipids useful in biological systems?

Lipids being hydrophobic is beneficial since they can then store energy for long periods of time, insulate temperatures and protect interior organs. Lipids are also what make the cell membranes work and protect the inside of the cell wall. Lipids are what give phospholipids their usefulness in creating cell membranes. The tail section of the phospholipid is non-polar and sticks to other non-polar ends keeping bad stuff out of our cells.


Why is starch easily digested by animals, while cellulose isn’t?

Starch is composed of alpha linkages, meaning that the OH is in the down position. Animals can therefore digest starch because they have the enzymes necessary to hydrolyze alpha linkages and therefore digest starch. Cellulose, on the other hand, is consturcted with beta-linkages. These are when the OH is in the “up” position and can from a straight line or wall. Animals do not have the enzymes necessary to hydrolyze beta-linkages and therefore cannot digest cellulose.


Explain how directionality influences structure and function of the following polymer:
 1.  Nucleic acids

Nucleic acids are what contain the information from the DNA to build what is our body. They provide directions for protein synthesis and replication. They are composed of nucleotides, with each nucleotide containing one pentose sugar, a phosphate group, and 1 out of the four nitrogen bases. It is these nitrogen bases where the information is found as their sequence determines a nucleic acids directions.
 2.  Proteins
Proteins are composed up of polypeptides that are built from only 20 different amino acids. These amino acids determine the function of the protein with the R-side chain. Each polypeptide will have a different amino acid sequence telling the protein what to do. These amino acid chains will has a carboxyl end and an amino end. Proteins will then coil, fold, or bend into a precise shape.
 3.  Carbohydrates

There are monosaccharides the most simplest of sugars. Then there are disaccharides and polysaccharides. While mono and disaccharide are quick sources of energy for our body, Polysaccharides play a major role in structure. If a polysaccharide is has alpha linkages then the molecule will be helical. Starch, which can be digested is composed like this. Carbohydrates will beta linkages will be straight. Cellulose, what makes plant membranes, is constructed like this and cannot be digested by animals  

Describe the basic structure and functions of key biological polymers (DNA, RNA, lipids, carbohydrates, proteins).

      DNA is composed of up of nucleic acids. These nucleic acids in turn are composed up of polymers that are made up of nucleotides. Nucleotides each contain deoxyribose, a phosphate group, and 1 out of the four nitrogenous bases. The deoxyribose will combine with the phosphate group using hydrogen bonds in order to create the DNA backbone. DNA contains our genetic, inherited material and the instructions to create everything that our body is.

      RNA is similar to DNA, with the exceptions that it has ribose sugar, is single stranded, and contains Uracil. RNA is what contains the instructions for the assembly of proteins on ribosomes. RNA also serves to deliver and link amino acids of the proteins.

      LIpids also serve as a variety of functions. They are used for the long-term store of energy, insulation of heat, and internal organ protection. They are composed of a glycerol molecule and three fatty acid molecules. The fatty acids molecules are long chains of carbon and hydrogen and end with a carboxyl group.  Unsaturated fats are liquid and saturated fats are solids. Phospholipids are what compose the cell membrane. The hydrophobic qualities of lipid is what makes phospholipids work for cell membranes to keep the bad stuff out.

Carbohydrates are the primary source of energy in our bodies. They are simply sugars. The most simple ones are known as monosaccharides and disaccharides. Common monosaccharides are glucose and fructose. Common disaccharides are sucrose. These are like tiny sources of energy that our body can easily use. Polysaccharides take on a more complex role in aiding to build several structures. The beta pleated cellulose is a polysaccharide that makes up plant cell membranes and gives them their crunch. Starch is what composes bread and allows our body to store this energy we get from the bread.

Proteins are like the building blocks for structures within our body. There are four levels of organization, with the first one, primary structure, being directed by our inherited DNA. Proteins are composed of amino acids, which are made up of one amino group, a carboxyl group, a hydrogen atom, and a R-side chain, which determines the structure and function of the protein. Proteins serve to do a variety of things within our bodies, ranging from regulating chemical processes, being antibodies, and being hormones. This is dependent on the amino acids that make up proteins.

Justify how structure imparts function for key biological molecules (DNA, RNA, lipids, carbohydrates, proteins, ATP) and cell organelles (nucleus, Golgi, ER, mitochondria, plasma membrane chloroplasts, vacuoles) and describe how they interact in key biological processes.

DNA and RNA are able to contain all the information necessary for the construction of an organism due to their complexity. DNA and RNA have an enormous amount of possible sequences for amino acids that they can produced many different types of proteins. Lipids are critical to the cell membrane as they hydrophobic quality is present in phospholipids and allows the cell membrane to be able to keep nutrients in and bad stuff out. Carbohydrates are the body’s primary molecule for energy and ATP. The body is able to break down carbs into glucose that is then used for cellular, tissue, and organ functions. Polypeptides are what make up proteins and are made up of 20 amino acids. The proteins created with polypeptides serve as structural support, storage, transport, and aid to the immune system.

2.A.3

1. Why is matter necessary for biological systems?

Matter is what everything is made up, including biological systems. Matter can neither be created nor destroyed, only transformed. Yet biological systems need matter in order to grow and reproduce. Trees, for example, aid in the transformation of matter as they take in carbon dioxide and produce oxygen. This oxygen is then used by humans and animals during cellular respiration to grow.

Explain the uses of carbon, hydrogen, oxygen, nitrogen, phosphorous and sulfur in biological systems.

These four elements alone make up 96% of all living things. Nitrogen and hydrogen are found in the air necessary for living organisms, including animals and humans. Air is actually composed of 78% nitrogen and 22% oxygen. Phosphorous and sulfur are found in electrolytes, which are necessary for homeostasis, digestion, neurological function, and several other functions of the body.

Oxygen, which composes roughly 20% of the air we breath is important to humans in order to be able to perform cellular respiration, during which carbs are broken down into ATP by our body.  Cellular respiration also creates water, carbon dioxide, and heat.

Carbon is important as it is used to build carbohydrates, lipids, proteins, and nucleic acids. What allows carbon to be the building block is its characteristic of having four valence electrons. This allows it to form a total of four other bonds, something that is important to the construction of the carbs, lipids, proteins, and nucleic acids.   

Diagram the exchange of matter between organisms and the environment.

Source: www.bigelow.org

What function does nitrogen serve in proteins?  In nucleic acids?

Nitrogen is found in amino groups necessary for the formation of peptide bonds, which will then form polypeptide bonds. Nitrogen then aids in the formation of hydrogen bonds in the secondary and tertiary structures of proteins, where polypeptide bonds are found.

With nucleic acids, nitrogen is what makes up the nitrogenous bases that are part of nucleotides, which then make up polymers that then make up nucleic acids.These nitrogenous bases are paired up Adenine to Thymine and Guanine to Cytosine to create DNA. The two long chains of  the DNA helix are paired together by the nitrogenous bases via hydrogen bonds.


What function does phosphorus serve in nucleic acids?  In phospholipids?

Phosphorus is what makes up the phosphate group found in nucleic acids. This phosphate group is important as it connects nucleotides, thus creating a sugar backbone. Phosphate in phospholipids make up the heads. These heads are hydrophilic and mix with water to make up the outside layer the plasma membrane and keep the structure of the cell.

Why do biological systems need water?

Water is necessary in hydration synthesis and hydrolysis in order to create and break down polymers for the body's use and the formation of proteins. Water also helps with the regulation of body temperature. Humans sweat to keep cool since water's high specific heat allows it to absorb more heat before changing temperature. Then, when sweat evaporates, it takes this heat with it. Water is also important due to it being the universal solvent. Within humans, it aids to dissolve urea and uric acids. Water also serves are transport within the body, moving hormones and cells.


How does the structure of a water molecule relate to its function(s)?

Water’s hydrogen bonds are what give water the ability to perform the majority of its functions since unique properties of water like adhesion and cohesion are due to these hydrogen bonds. Water contains one oxygen molecule and two hydrogen molecules, These molecules have unequal electronegativities, resulting in a partially negative charged oxygen molecule and a partial positive charge of the hydrogen molecules. Hydrogen bonds are formed when the negative oxygen molecule in one water molecule is attracted to the positive charged hydrogen atom in a different water molecule.



How does the polarity of water lead to the emergence of unique properties in liquid water?

Due to the unequal electronegativty between hydrogen and oxygen molecules, water is charged and said to be polar. This polarity then results in the formation of hydrogen bonds, whose strength comes in number. This polarity is what allows, for example, ice to float on water. Hydrogen bonds spread out when they freeze and make water less dense in the frozen states than in the liquid state. Polarity also gives water its adhesion and cohesion. Adhesion is what allows water to stick to the sides of trees and such to move up the trunk to the leaves. Cohesion is what allows water to stick to itself. For this reason, insects that are light enough are able to walk on water.



Explain why surface area-to-volume ratios are important in affecting a biological system’s ability to obtain necessary resources or eliminate waste products.

The surface area-to-volume decreases as a cell gets bigger. If a cell were to lose surface area, its need for nutrients would actually increase. This increase in nutrient demand would then lead to a demand for more cell surface area in order for an increased amount of nutrients exchanged to occur. This is what maintains the surface area-to-volume ratios.The cell membrane must be large enough to allow the necessary resources to pass through the membrane and wastes to exit. But also, the cell cannot be small enough that it does not allow for space of the necessary organelles for cellular functions.

Identify several (more than 4) chemical elements and molecules that function as key building blocks (e.g., C, N, H2O, sugars, lipids, proteins) or are eliminated as wastes.

1. Hydrogen
2. Oxygen
3. Hydroxyl
4. Glucose and Fructose
5. Nitrogen

Explain the physical considerations that determine the upper and lower limits to cell size.

Cells cannot expand to much because then they will be unable to sustain their large size. Diffusion of oxygen will be inefficient and the cell will need too many nutrients. It will no longer be able to feed itself. However, if a cell is too small, then there will not be enough space for the organelles necessary for cells to carry out their functions.

Explain why smaller cells have a more favorable surface area-to-volume ratio for exchange of materials with the environment.

Smaller cells have the more favorable ratio because they have the greater amount of volume for the least amount of surface area. Their smaller size allows cells to be more efficient in diffusion, since oxygen and carbon dioxide do not have to diffuse so much. We can also gets nutrients in more easily and waste products out.


Using any model, calculate simple surface area-to-volume ratios for cubic and round cells and explaining how this impacts procurement of nutrients and elimination of wastes.


Calculations being at minute 4:40 and end at minute 8:45. In order to calculate the cell value for round cells, follow the same procedure, except use formulas for the volume and surface area of a sphere instead. 

Explain how cell size and shape affect the overall rate of nutrient intake and the rate of waste elimination. [SP 6.2]

A perfectly, small round sphere is a shape that will be able to obtain the most volume for the least amount of surface area. The fact that cells are both very small and round aids the rates of nutrient intake and waste elimination. These processes are actually speed up. The more surface area, the more nutrients the cell can take in. Molecules will move into and out of the cell at a faster pace as well since they have less distance to cover if the surface area is high and the volumn is small. This increases the rate of diffusion and nutrients like oxygen can enter the cell more quickly and waste like carbon dioxide can leave quicker.



Represent graphically or model quantitatively the exchange of molecules between an organism and its environment, and the subsequent use of these molecules to build new molecules that facilitate dynamic homeostasis, growth and reproduction. [SP 1.1, 1.4]

Source: hyperphysics.phy-astr.gsu.edu

The molecules exchanged here are CO2 and oxygen. These are exchanged by trees into the environment. Animals then use these molecules in the production of ATP, their source of energy.