3D Game Lab - Endergonic vs Exergonic Reactions

Endergonic: An example of an endergonic reaction is photosynthesis. This is an endergonic reaction because photosynthesis requires energy to be absorbed from the sun in order for autotrophs to be able to produce food molecules, such as glucose. The diagram below illustrates how light energy must be absorbed by the plant in order for photosynthesis to occur.

Source: sites.saschina.org

Exergonic: An example of an exergonic reaction is cellular respiration. This process is exergonic because it produces energy and releases it in the form of ATP. The diagram below illustrates how cellular respirations results in the production of ATP/energy.

Source: Pearson Prentice Hall 

3D Game Lab - Essential Knowledge 1.A.2 - Moth Simulation

21. 

22. Explain how the color of the moths increases or decreases their chances of survival.

Moths that are able to blend in with their surroundings are the ones who have the best chance of survival since it is harder for a predator to spot them. Dark moths will thrive in dark forests while light moths will do well in light forests.

23. Explain the concept of "natural selection" using your moths as an example.

Natural selection is how a species adapts to changes in its environment by having only the most beneficial traits be passed on. In the case of the pepper moths, when in a dark forest, the population of dark moths increased since dark moths were able to mate and produce offspring before being eaten, while light moths were quickly spotted and eaten by predators. After multiple generations, it is likely that the majority of moths will be black instead of white due to how the environment has impacted natural selection of the moths color.

24. What would happen if there were no predators in the forest? Would the colors of the moths change over time? Defend your answer?

If there were no predators in the forests it is likely that both black and white moths would be prominent throughout either forests. It is unlikely that the colors would change over time since both black and white moths will be able to reproduce with no predators hunting and killing off the most easily spotted moths.

3D Game Lab - Essential Knowledge 1.A.2

Using any of the examples cited above in the quest, explain and justify how an evolutionary change in a population is related to a change in the environment. What role do humans play in this change? What is the impact in the future of this change?

As the climate on Earth changed to one that was more suitable for humans, humans strayed from the nomad life and began to settle down. However, they faced challenges from predators such as wolves. Humans then began to employ the method of artificial selection to domestic wolves. Humans picked the tamest of all of the wolves and allowed those to reproduced. One the other hand, wolves remained under the care of humans because this meant being fed regularly and always having a food source. Over the years, as only the tamest wolves were allowed to produced offspring, the offspring inherited genes that were considered favorable by humans, such as looking cute, being loyal, and being tame. Over thousands of years, with this artificial selection wild wolves were bred into being what today we know as dogs.

Chapter 11 Portfolio

• Describe how signals are received by cells.

Cells are able to communicate with each other via chemical signals. Through a signal transduction pathway, cells are able to send signals step by step that will lead to a specific cell response. Both animal and plant cells contain cell junctions that connect the cytoplasm of cells that are next to each other. This then allows for what is knows as local signaling, or the cells ability to communicate via direct contact or cell-cell recognition. 

Cells may able communicate long-distance with the use of hormones. Hormones will stimulate a cell only if the cell has the receptor specific to that signal. This is further demonstrated in the first step of cell signaling, reception. The signaling molecule will have to bind to the specific receptor protein in order for the cell to recognize the specific message. This binding between a signal molecule and a receptor is very specific and is known as a ligand. It is also important to note that the majority of signal receptors are plasma membrane protein, meaning that signals are usually received on the membranes of cells.

• Use an example to explain how a receptor protein recognizes signal molecules, causing the receptor protein’s shape to change, which initiates transduction of the signal.
  

A type of signal receptor is a ligand-gated ion channel. This type of receptor acts as a type of gate and changes shape. For example, when a signal molecule acts as a ligand by binding the the receptor, the ligand-gated ion channel will then allows only certain ions, like NA+ or Ca+ to pass through the channel found in the receptor. However, in order to open the gate, the ligand-gated ion channel must change shape to open the pathway. Once the ions pass the channel, transduction occurs.

• Describe the process of signal transduction - include a model in your discussion.

Signal transduction is when a signal molecule binds to a receptor protein and changes the shape of that receptor proteins, thus initiating the steps necessary for the cell signal to take a form that will cause a cellular response. For example, epinephrine will bind to a receptor protein found in the plasma of a liver cell. Once this binding occurs, it will lead to the activation of glycogen phosphorylase, which causes the response. Though in this example, transduction occurs in  a single step, it is more common for transduction to occur in a series of steps that causes changes in varis different molecules. This series of steps in knowns as a transduction pathway, and the molecules in the pathway are referred to was relay molecules.

• Explain the concept of signaling cascades - include a model in your discussion.
  

It usually takes multiple steps for a cell signal to initiate a response. Even though the signaling molecule is the molecule that initiates the entire process of cell signalling, that molecule usually does not even enter the cell. What occurs instead is that it begins a cascade, or a series of events with each one leading to the next. As the signal is passed along the pathway, at each step the signal is transduced into a different form, usually due to a change in shape of the next protein. This change of shape is many times brought about by phosphorylation. The entire series of many steps and the pathway in which the signal travels after being delivered by the signaling molecule is a signaling cascade.

For example, in a phosphorylation cascade, the series of proteins in the signal pathway are phosphorylated in order. This occurs because each pervious protein added a phosphate group to the next one in line as a way to carry along the signal by activating the necessary proteins. As these steps occur and the signal is passed on, dephosphorylation will return each activated protein to its inactive state.

Source: 2011 Pearson Education, Inc. 

• Use an example to explain how second messengers are often essential to the function of a signaling cascade.

Second messengers are small, non-protein molecules or ions that are soluble in water. One of the most commonly used ones is cyclic AMP, also known as cAMP. In order to understand the role and importance of cyclic AMP it is important to note that is has been found that epihpihprine will lead to the breakdown of glucose without penetrating the plasma membrane of liver or muscle cells. This is because, even though the signal is initiated by epinephrine it is cyclic AMP that carries the signal to the interior of the cell and eventually brings about the breakdown of glucose. The role of epinephrine is to begin the reaction that will cause the synthesis of many molecules needed for the creation of cAMP. Yet, it is cAMP, a second messenger, that carries the signal started by epinephrine and leads to glucose breakdown.

• Explain the key features of a model that illustrates how changes in a signal pathway can alter cellular responses.

An important function of signaling pathways is to sometimes regulate protein synthesis. This means that signaling pathways have the potential to turn certain genes on or off. For example, for an activated steroid receptor, the last activated molecule in that signaling pathway may be a transcription factor, which activates transcription, where mRNA is translated into specific proteins.

However, some pathways activate cell division. If the pathways were to malfunction, either a mutation in one of the genes that is turned off or on  by the way in which mRNA is transcribed then the pathways could lead to uncontrolled cell division, also known as cancer and have fatal effects.

- Use any of the examples below to explain how it relates to cell communication over short distances.

Neurotransmitters
Plant immune response
Quorum sensing in bacteria
Morphogens in embryonic development

Neurotransmitters are cells that use short distance communication. It begins with an electrical signal traveling down along a nerve cell. This electric signal is signal to the nerve cell to release a neurotransmitter. This neurotransmitter will then diffuse in the synapse, the space between two nerve cells. Once it crosses the synapse the neurotransmitter will stimulate the new nerve cell.

Source: 2011 Pearson Education, Inc. 

- Use any of the examples below to explain how endocrine signals are produced by endocrine cells that release signaling molecules, which are specific and can travel long distances through the blood to reach all parts of the body.

Insulin
Human growth hormone
Thyroid hormones
Testosterone
Estrogen

Whenever hormones are used for cell signaling, it is known as endocrine signaling. This type of signaling is classified as long distance signaling because the signal  will travel long distances in the body instead of just traveling to the adjacent cell. It will be able to do this because the hormone carrying the signal will enter the bloodstream and travel via this method.

In the case of insulin, it is a protein composed of thousands of atoms. It will enter the bloodstream and travel all the way down to the liver, will it will stimulate it to regular the sugar levels in the blood.

Source: 2011 Pearson Education, Inc. 

- Use any of the below examples to explain how, in multicellular organisms, signal transduction pathways coordinate the activities within individual cells that support the function of the organism as a whole.

Epinephrine stimulation of glycogen breakdown in mammals
Temperature

determination of sex in some vertebrate organisms
DNA repair mechanisms

Epinephrine will first bind to the plasma membrane of a liver cell. Once tis occurs, it will trigger elevated levels of cyclic AMP within the cell. This is done because when epinephrine binds to the specific receptor protein, the receptor protein will then activate adenylyl cyclase. The adenylyl cyclase will then catalyze the synthesis of the molecules necessary to create cAMP. The cAMP molecules will then tell the rest of the cell to break down glucose. However, it is important to note that the signal transmitted by cAMP does not last long enough, due to the enzyme phosphodiesterase, which converts cAMP to AMP. Therefore, another round of epinephrine is necessary to once again increase elves of cAMP in the liver cell.

-List the types of signals involved in communication and where they come from.

There are several different types of signaling that a cell may use. The two broad types are long distance and short distance. Short distance signaling involves the use of cell junctions and cell-cell recognition. Long term signaling involves synaptic signaling and endocrine signaling.

Short Distance Signaling:

For cell junctions, the substances that carry the signal between cells have the ability to pass freely between adjacent cells by dissolving in the cytosol.

Source: 2011 Pearson Education, Inc. 

For cell-cell recognition, this is more of a direct contact method. Cells will recognize other molecules on the membranes of other cells This type of cell communication is important for embryonic development and immune responses.

Source: 2011 Pearson Education, Inc. 

Long Distance Signaling :

Synaptic signaling is used primarily by animal nervous system. Electrical signals traveling along the nerve cells will cause the secretion of neurotransmitters. Neurotransmitters then act as chemical signals and travel across synapses to each next nerve cell.

Endocrine signaling involves hormones acting as chemical signals. Specialized cells will secrete these hormones. The hormones will then travel via the bloodstream to the target cells in order to deliver their message.

-Describe why signal transduction pathways that are under strong selective pressure.

The pressure to be very selective and be specific is due to the large amount of things that could go wrong. Changes in the pathways can lead to terrible consequences. For example, if a signaling pathway were to go wrong, an incorrect gener may be turned off and on. This mutation in genes is known to cause serious illness, including cancer that can be fatal.

- Use an example to explain how signal transduction pathways influence how the cell responds to its environment in unicellular organisms.

Cell signaling is very important to the microbial world. Bacteria cells will secrete molecules detectable for other neighboring bacterial cells. The neighboring bacteria will monitor its environment for the amount of these specific signaling molecules in it, a technique that is known as quorum sensing. This will aid bacteria in the production of biofilm, an aggregation of bacteria on a surface, of which they will derive the majority of their food.

- Using an example to explain how signal transduction pathways coordinate the activities within individual cells that support the function of the organism as a whole in multicellular organisms.

It is important to note that for some kinds of signals, it is possible to trigger responses in one or two different organs. This is because each different organ cell is equipped with its individual collection of signal receptor proteins, relay proteins, and proteins needed to carry out the response. The coordination in the body as a whole that this allows for can be seen in the effects of epinephrine on the heart and the liver. Epinephrine is a hormone that can stimulate a response in both the heart and the liver. However, the response will be different in each organ. For the liver, epinephrine will stimulate the breakdown of glucose. For the heart, epinephrine stimulates contractions, which then lead to an increased heart rate. In this way, epinephrine affects the activity of individual cells, but of different organs, helping the organism function as a whole. Again, this is due to the heart and the liver each having its different set of signal transduction pathways that will respond differently to the epinephrine.

Chapter 9 & 10 Portfolio

• Compare the major features of chemoheterotrophic and photoautotrophic nutritional processes.

Chemoheterotrophic processes:  

These processes occur in organisms that cannot create their own food, and instead must ingest a combination of proteins, lipids, and carbohydrates to create their food. It is the equivalent of cellular respiration. Organisms that depend on chemoheterotrophic processes will obtain their energy by consuming other organisms.

Photoautotrophic processes:

If an organism is dependent upon photoautotrophic processes, it will obtain its energy from primarily the sunlight and the carbon dioxide in the air. These organisms are primarily plants and will perform processes such as photosynthesis to convert sunlight, CO2, and water into sugar necessary to carry out cellular functions.

• Explain the inputs, major processes, and outputs of glycolysis, fermentation, and aerobic cellular respiration.

Glycolysis:

During glycolysis,a glucose molecule will be broken down to create two pyruvate molecules, which will then go on to become acetyl CoA before entering the Citric Acid Cycle. The breakdown occurs in two phases. During the first phase, the Energy Investment phase, 2 molecules of ATP are consumed and turned into 2 ADP molecules and 2 Phosphate molecules.

In the second stage, the Energy Payoff phase, 4 ATP molecules are formed and NAD+ is reduced into 2 NADH and 2 H+, by the addition of 4 electrons and 4 H+. 2 Pyruvate and 2 H2O molecules are also formed.

Copyrigth @ 2008 Pearson Education Inc., publishing as Pearson Benjamin Cummings.

Fermentation:

Fermentation will occur in the case that there is no oxygen readily available. For this reason it is considered an anaerobic process. Fermentation will use substrate-level phosphorylation to generate ATP and regenerate NAD+, the electron acceptor in glycolysis.

The two types of fermentation that occur are alcohol and Lactic Acid fermentation. In alcohol fermentation, pyruvate is converted into ethanol and CO2 is released. NADH is also regenerated into NAD+. Alcohol fermentation usually deals with yeast and bacteria.

In Lactic Acid fermentation, pyruvate is reduced into NADH, instead of ethanol. Lactate is a by product. However, no CO2 is released. This process occurs mainly in animals and is the cause for muscle fatigue. Yet, only 2 ATP molecules will be produced instead of the usual 38 ATP created during cellular respiration.

Aerobic Cellular Respiration:

For this process to occur it is necessary that oxygen be present. There are three phases in cellular respiration. The first phase is glycolysis.  The input for this phase is 1 glucose molecule. The output of the process will be 2 molecules of pyruvate. These molecules will then be transported from the cytosol into the mitochondrial matrix by transport proteins to be oxidized into acetyl CoA. From there, the Citric Acid cycle will occur. Since each cycle requires only 1 molecule of CoA, the cycle will run twice. After the cycle has run twice, the net outputs will be:

• 4 CO2
• 6 NADH
• 2 FADH2
• 2 ATP

The energy created by the Citric Acid Cycle will be stored in the electron carriers, NADH and FADH2. This energy is then used in the third and final phase of cellular respiration, the Electron Transport Chain (ETC). Embedded in the inner membrane of the mitochondria, the ETC is where O2 will pull along the electrons from NADH and FADH2 in order to create energy. The main process occurs in the ATP Synthase, a protein used to channel the H+ molecules and create ATP. This process is known as chemiosmosis, and it is when the ATP synthase uses the proton-motive force to phosphorylate ADP into ATP.

Copyrigth @ 2008 Pearson Education Inc., publishing as Pearson Benjamin Cummings.

• Trace the movement of energy and matter through all cellular respiratory processes.

Glycolysis: Here, the energy begins being stored in the glucose molecule. Then it is broken down and the energy moves into the pyruvate molecule. This pyruvate molecule will then be converted into Acetyl CoA in order to be used in the Citric Acid cycle. The energy is removed from the CO2 and is used to convert NAD+ into NADH, with the addition of coenzyme A in order to convert pyruvate into CoA. This CoA is then passed into the Citric Acid cycle, where the energy will come out in the form of electron carriers, NADH and FADH2. This energy will then be used in the Electron Transport Chain. Once in the ETC, the electrons from NADH and FADH2 will flow through the chain, loosing energy. This loss of energy is what powers the hydrogen pumps. These electrons will be pulled by oxygen. Then H+ ions will flow against their concentration gradient through the ATP Synthase. This then uses the proton-motive force to convert or phosphorylate ADP into ATP.

• Match all cellular respiratory processes to their locations in a typical eukaryotic cell.

Glycolysis occurs within the cytosol of the cell. Once the glucose has been broken down into pyruvate, these pyruvate molecules will be transported to the Mitochondrial Matrix, where the Citric Acid Cycle will take place. After NADH and FADH2 have been formed, they go on to the inner membrane of the mitochondria, where the Electron Transport Chain processes will occur.

• Explain the inputs, major processes, and outputs of the light reactions and the Calvin Cycle.

The Calvin Cycle occurs in the stroma of plants. It is similar to the Citric Acid cycle in that it regenerates photosynthesis starting material. At the beginning of each Calvin Cycle, 1 molecules of CO2, one molecule of ATP, and one molecule of NADPH will be put in. The Calvin cycle is broken up in three phases. The first phase, Carbon Fixation. The second phase is Reduction, and the third phase is Regeneration. The main purpose of the Calvin cycle is to convert 3 CO2 molecule into one net molecule of the sugar G3P, glyceraldehyde 3-phosphate. Due to this, the Calvin cycle will run a total of three times before producing a G3P molecule. In addition, the NADPH will be reduced into NADP+ and ATP will be converted into ADP. The CO2 acceptor, RuBP, will also be regenerated.

Copyrigth @ 2008 Pearson Education Inc., publishing as Pearson Benjamin Cummings.

• Trace the movement of energy and matter through all photosynthetic processes.

At first, all of the energy enters the plant cells in the form of light. Then in the the light reactions, the energy will be turned into the form of ATP from ADP. At the same time, H2O is split into O2 and NADP is reduced into NADPH. After this, the energy stored in the ATP will go on to the Calvin Cycle. In this cycle, carbon dioxide will be converted into G3P sugar using the ATP and NADPH created in the light reactions.

• Match all photosynthetic processes to their locations in a typical eukaryotic, autotrophic cell.

There are several steps to the photosynthetic process. This first stage, the light reactions, will take place in the thylakoids. These thylakoids are found in the granum of the chloroplasts. The second stage of the photosynthetic process is the Calvin cycle. This stage occurs in the chloroplasts as well.

Copyright @ 2008 Pearson Education, Inc., publishing as Pearson Benjamin Cummings 

• Describe the process of chemiosmosis and compare its function in photosynthetic and respiratory pathways.

      Chemiosmosis occurs during the last stages of cellular respiration. When the electrons of the electron transport chain cause H+ to be moved from the mitochondrial matrix to the intermembrane space, the H+ molecule will then move against their gradient. Chemiosmosis will use this energy stored in the form of H+ gradient to create ATP. This is when ATP Synthase uses the proton-motive force to phosphorylate ADP into ATP.

      For photosynthetic pathways, chemiosmosis will occur when the ETC utilize the flow of the electrons to move protons across the thylakoids membrane. Chemiosmosis also involved in the phosphorylation of ADP into ATP in photosynthetic pathways as well.

• Explain the relationship between photosynthesis and cellular respiration at the molecular, organismal, and ecosystem levels of organization.

Both photosynthesis and cellular respiration serve to provide the cells with the necessary energy to function and live. Everything begins with sunlight. When sunlight enters the plant’s cells it will begin the process of photosynthesis. Through a series of steps, such as light reactions and the Calvin cycle, the plants cells will be able to produce glucose for its energy source. However, it will also produce oxygen and six molecules of water as by produces. This oxygen will then be used in cellular respiration during the electron transport chain. However, a byproduct of cellular respiration is CO2. This CO2 will then once again be used during photosynthesis in plant. In this way, photosynthesis and cellular respiration are dependent on one another to a certain extent. For this reason, ecosystems tend to have both plants and animals that will replenish each other's supply of CO2 and O2.

• Explain how energetic requirements contribute to the adaptations of organisms.  Provide examples to support your statements.

In order to survive changes to the environment, it is necessary for plant species and animal life to evolve. This evolution is driven by the changes in energy required by the organism. These new requirements  may lead to the organism to begin to synthesize new molecules in order to survive. For example, as the environment of the Earth changed, it is likely that plants learned to synthesis the new components of the air, along with sunlight, in order to stay alive. This may had lead to an increase in the amount of oxygen in the air and a decrease in the amount of carbon dioxide, allowing for animal life to occur on the Earth.

Source: http://science.psu.edu/news-and-events/2001-news/Hedges8-2001.htm

• Propose experimental designs by which the rate of photosynthesis and respiration can be measured and studied.

For an experiment that could measure the rate of photosynthesis, it is possible to use a dye reduction technique. In this experiment, the experimenter would measure how different frequencies of light would affect the rate of photosynthesis. Gathering a sample of plant pigments, and replacing NADP, plants natural electron acceptor, with DPIP, one could measure the rate at which photosynthesis occurs given certain conditions of the chloroplasts. As more light is absorbed and more DPIP is reduced, similarly to how NADP would be, DPIP will become colorless. This will increase the light transmission in a spectrophotometer, which will tell us the rate at which photosynthesis is occurring. To test the rate of cellular respiration, one would have to create an experiment that could possible measure the amount of oxygen that is consumed.

• Describing 2–3 different strategies that organisms employ to obtain free energy for cell processes (e.g., different metabolic rates, physiological changes, variations in reproductive and offspring-rearing strategies).

1. One interesting strategy is used by animals cells during the electron transport chain. The cell will use the electronegativity of an oxygen molecule in order to cause the electrons to move up the chain towards the oxygen molecule. As the electrons move, they will release free energy to power the ETC.
2. Plant cell will use the carbon dioxide that is released as a byproduct of cellular respiration in the process of photosynthesis in order to generate ATP. This carbon dioxide, alongside water and sunlight,  will be used to create the sugar that is necessary for the plant cell to live.

• Refine or revise a visual representation to more accurately depict the light-dependent and light-independent (i.e., Calvin cycle) reactions of photosynthesis and the dependency of the processes in the capture and storage of free energy.

Source: www.wisegeek.com

The picture above is very accurate in that the inputs of photosynthesis are CO2, water, and light and that the outputs are sugar and oxygen. However, it this picture were to be more accurate it would also have to depict how light energy is only used in the first phase of photosynthesis, the light reactions. It would also have to depict that from these light reactions, ATP and NADPH are produced. Then, the picture would have to show how the Calvin Cycle, the dark reactions which require no sunlight, will regenerate these two substances back into ADP and NADH as it produces the sugar the plant uses for energy, along with the byproduct oxygen. This whole process however, it driven by the capture of sunlight and the creation of free energy and ATP and is necessary for the plant to be able to live.

• Pose scientific questions about what mechanisms and structural features allow organisms to capture, store, and use free energy (e.g., autotrophs versus heterotrophs, photosynthesis, chemosynthesis, anaerobic versus aerobic respiration).

1. Is there a difference between how much energy is created by plant cells during the summer or in the winter? Or in other words, is photosynthesis greatly affected by the changes in temperature during the season?

Since the pigment of the plants is found in the chloroplasts of the plant cell and does play a role in light absorption, it may be plausible to believe that as the chlorophyll breaks down, there is a lower amount of light able to be absorbed during the winter. Due to this is may be likely that there is a lower rate of photosynthetic reactions during the winter.

2. Is it plausible to believe that oxygen could be replaced in the electron transport chain by another molecule?

The main feature of oxygen that is helpful to the ETC is that its high electronegativity is what draws the electrons down the chain as the oxygen molecule pulls the electrons to it. It may be plausible to believe then, that another molecule with high electronegativity may be able to cause the same reaction. However, problems may occur as the different electronegative may speed up the rate at which the electrons travel down the chain. The molecule may also cause problems in different parts of the cell and may be more difficult for the cell to acquire naturally from the environment.

3. Why is Mercury a toxin to our body?

Mercury is especially detrimental towards the body because it causes a decay in the membranes of several organs, such as the liver, brain, and kidneys. It does this due to its high density, as that causes Mercury to accumulate inside of the body. Yet, Mercury is also dangerous because it causes damages to not only these organs, but also the body’s DNA and chromosomes.

Source: kids.britannica.com

• Create a visual representation to describe the structure of cell membranes and how membrane structure leads to the establishment of electrochemical gradients and the formation of ATP.

The image below describes how the proteins that carry electrons that are embedded in the membrane serve to establish the electrochemical gradients, used especially in the Electron Transport Chain to create ATP.

This occurs in the inner membrane of the mitochondria. 

Sources:

https://www.boundless.com/microbiology/textbooks/boundless-microbiology-textbook/microbial-metabolism-5/types-of-metabolism-41/chemoautotrophs-and-chemoheterotrophs-285-6153/

https://www.boundless.com/microbiology/textbooks/boundless-microbiology-textbook/microbial-metabolism-5/types-of-metabolism-41/photoautotrophs-and-photoheterotrophs-284-7651/

https://thescienceinformant.wordpress.com/2011/08/25/why-is-mercury-so-poisonous/