Biology Responses Answers Key

The addition of a phosphate group to a protein could cause the protein to have a conformational shape change. Due to this shape change, the protein can go from an active to an inactive form. During the process of a phosphorylation cascade, the intermediates that are activated will phosphorylate additional components in the pathway which will also activate additional components. For example, the activated receptor protein will activate one protein kinase A, this protein kinase A will activate 10 intermediate proteins, then those 10 intermediate proteins will activate 10 each of their target intermediate. As you see this signal is being amplified. The dependent variable is the variable that is measured due to the independent variable. The researchers changed the type of mutation (WT, pho81mt, pho4mt) in the yeast strains, which is the independent variable. The researchers measured the activity of the APase enzyme and the amount of mRNA for PHO1 that encodes the APase enzyme, which are the dependent variables. The researchers used the wild-type (WT) strain as a negative control. This allows the researchers to establish a baseline of the levels of APase and amount of PHO1 mRNA in each environment (without the treatment) to compare with the treatment groups to determine the effect of Pho81 and Pho4 on the activation of the target genes. ADDED: The wild-type has all of the genes for the PHO genes. By using the wild-type, you are able to ensure the gene with the mutation is the one being tested. By using a specific mutant, the researchers are able to isolate each protein on the overall pathway to see the specific function of each. Pho81 inhibits Pho80/Pho85 so the Pho4 is not phosphorylated, so if this process was inhibited by a mutant Pho81 in low-phosphate environment. Pho4 interacts with the DNA as a transcription factor, so if the Pho4 was non-functional. The yeast strain with the highest relative amount of PHO1 mRNA was the wild-type in Low-Pi environment. This strain has 10 +/- 2.0 (so 8.0 – 12.0) which does not overlap any of the other values and is the highest. % 𝑐ℎ𝑎𝑛𝑔𝑒 = 𝑓𝑖𝑛𝑎𝑙 − 𝑖𝑛𝑖𝑡𝑖𝑎𝑙 0.5 − 17.3 −16.8 𝑥100 = 𝑥100 = 𝑥100 = −97.1% 𝑖𝑛𝑖𝑡𝑖𝑎𝑙 17.3 17.3 There is a decrease of 97.1% between the low Pi and high Pi in the wild-type strain. If the Pho85 protein is nonfunctional, then it would not be able to complex with Pho80 to activate the Pho4. Traditionally, the phosphorylation of Pho4 leads to no transcription of the PHO1 gene (low levels of mRNA). Due to the mutation, the Pho4 is not phosphorylated so as seen in the lowphosphate environment the Pho4 will activate the transcription of PHO1 gene so expression will increase. There will be more mRNA synthesized (leading to more APase activity). Pho85 is unable to phosphorylate Pho4 leading to inducing expression of the target genes PHO1. The inner mitochondrial membrane is the site for oxidative phosphorylation. NADH and FADH2 are oxidized providing high energy electrons to the electron transport chain (in the cristae/inner mitochondrial membrane) generating a proton gradient that is used by ATP synthase to provide the energy for phosphorylation of ADP to ATP. The membrane provides the site for electron transport chain, barrier to generate a proton gradient, and site for phosphorylation of ADP. Special Notes: • The graph paper was on the question book is not released with the questions, so I used my own graph and was told the y axis was labeled with 0.0, 1.0, 2.0, and 3.0. (Clearly I didn’t have enough room on the y axis so my scale isn’t as narrow as it should be to graph the error bars) • I am graphing on a computer using drawing features, please excuse if things are not super accurate (and that there should have been more lines on my graph) • I used two different colors so you could see the error bars – the readers cannot see different colors All of the species comparison data is statistically significant between normal and elevated levels of CO2. All of the species show a difference in the number of the mitochondria between normal and elevated levels of CO2. The elevated CO2 shows an increase in number of mitochondria in plants. There is a direct relationship. Elevated CO2 has a higher average number of mitochondria per unit area of a cell than normal CO2 levels. Mitochondria have their own genetic material due to endosymbiotic theory. Due to this, the offspring from this cross will only inherit their mitochondria from the egg producing parent as the egg has all of the organelles for the zygote. The egg producing plant is a plant with green leaves (ovules are eggs) so ALL of the offspring will have green leaves WITHOUT the white stripe. The environment has an effect on gene expression. Organisms will respond to their environment through phenotypic plasticity which refers to how organisms have different phenotypes with the same genotype responding to changes in their environment. In addition, the mitochondria replicates by binary fission so this CO2 level could be a signal for a signaling pathway involved with increases the replication of the organelle. . An increase in biodiversity leads to an increase in resilience of an ecosystem in a changing environment. The increased biodiversity allows for multiple interactions between organisms in the community. For example, if there are 4 different primary producers consumed by multiple organisms, then the loss of one of those primary producers will not lead to high effects in the higher trophic levels as there is still enough food for the organisms versus if there was only one primary producer for an organism and the loss of that food source leads to a loss in the subsequent levels of the trophic levels. Sand lances typically develop and mature into adult fish at this level of CO2 and this temperature. This would be considered the negative control. This would allow the scientists’ to compare the effect of an increase of temperature or increase of CO2 levels on the maturation of the fish. OTHER TEACHERS: There is a debate currently occurring with other teachers that it might be a positive control since this is the baseline data. I think as long as you said control, you would get credit. I think the negative or positive is extra information that is not required. The null hypothesis states the treatment has no effect on the experiment. This experiment has two different treatments that are being observed. The increase of temperature has not effect on the survival rate of sand lance embryos. The increase of CO2 levels has no effect on the survival rate of sand lance embryos. Due to this, the survival rate will be the same with an increase in temperature. Due to this, the survival rate will be the same with an increase in the CO2 levels. The Ammodytes is a keystone organism and the removal of a keystone species will lead to the collapse of an ecosystem. The Ammodytes is a prey fish that supports organisms are higher trophic levels. As the population size decreases, the predator of this fish would see a decrease, and the predator on that organism would also see a decrease. Thus, there could be a decrease in the stability as trophic levels might die out due to loss of a food source. . . Chlorophyll is a pigment found in the thylakoid membrane in the photosystems. These pigments absorb light energy and funnel the energy to the reaction center complex (chlorophyll a). The process of the Calvin cycle requires an unequal number of ATP and NADPH. There needs to be 9 ATPs and 6 NADPHs for the synthesis of 1 G3P (glyceraldehyde-3-phosphate). Due to the ratio of NADPH increasing, there must be a buildup due to the need for the additional ATP in the Calvin cycle. This signals for additional usage of the cyclic electron flow to increase the usage of the electron transport chain to create the proton gradient used for phosphorylation of ADP to synthesize ATP. **oops… that wasn’t based on the figure 1 – let me try again** If there is a higher ratio of NADPH to NADP+, there will be less NADP+ to oxidize ferredoxin. These electrons need to go somewhere (or the electron transport chain will back-up). As seen in the figure, the electrons are used as energy for ATP synthesis. The biological explanation is that the electrons will go through the electron transport chain between PS II and PS I generating the proton gradient that will be used to phosphorylate the ADP to synthesize ATP. As the electrons cycle between PS I and the electron transport chain producing only ATP, this is demonstrating the usage of cyclic pathway as the ratio of NADPH to NADP+ increases. Without the usage of photosystem I, there is no NADP+ to NADPH nor cyclic electron flow to synthesize ATP. Without the NADPH and ATP, the chloroplast is unable to undergo the Calvin cycle to fix the carbon dioxide, then reduce to synthesize G3P (and rearrange back to RuBP for another cycle). Without the G3P, there is no glucose synthesized (2 G3Ps make a glucose). The rate of biomass accumulation will decrease. The Calvin cycle requires the NADPH and ATP synthesized from the electron flow pathways that move through photosystem I. The scientist would look at the number of nucleotide differences between the different organisms. Those with fewer nucleotide differences would be closer related than those with greater nucleotide differences representing a more recent common ancestor. For example, based on figure B the Bovidae and Moschidae are more closely related than the Bovidae and Giraffidae so there are less nucleotide differences between the Bovidae and Moschidae and more nucleotide differences between the Bovidae and Giraffidae. HAHA … really CollegeBoard – I just used this example in A *rolls eyes* Figure 1B is based on molecular data vs Figure 1A is based on morphological data. Based on morphological data (1A), the Bovidae is more closely related to Giraffidae which could be due to convergent evolution (due to similar environmental conditions, similar characteristics were selected as more favorable without common ancestry). Based on molecular data (1B), the Bovidae is more closely related to the Moschidae based on homology in DNA sequences. DNA is more accurate data for evolutionary relationships. (the questions do not include the template, some students told me it was figure 1A) Based on molecular data, they are not as closely related to each other as to other organisms. If they have a characteristic that is found in ONLY those two organisms, then it would have to have emerged independently on their branches similar to characteristic number 1’s emergence. This characteristic emerged independently in each of these organisms. The lowest median Cq -value would be RPS5. The box and whisker shows the data. The rectangle is showing Q2 and Q3 (ends of the rectangle) with the median as the line in the middle. The “whiskers” show Q1 and Q4. You can see the median of the data for RPS5 would be less than the other 3 samples. UPDATE: Apparently the whiskers are showing the minimum and maximum. The rectangle is Q1 & Q3 with the median as Q2. Please excuse my error. The gene TBP-AF has the highest Cq value in all variables. Recall, the prompt states the Cq is inversely proportional to the amount of mRNA. The lowest level of gene expression means the LEAST mRNA so the MOST Cq. I support this hypothesis. The TBP-AF has the shortest variance in the data for the sex. This shows that it would be unaffected by sex. In addition, it does not overlap with the other genes showing it is significantly different. Thoughts from Mr. Hornbeck The TBP-AF boxplots for developmental stage and sex has the least variability, their medians are roughly equivalent (which can’t be said about the other 3 genes), and they have no overlap with the other three boxplots. All three of these would be a reason why it would be the best control variable. (THANKS MR. H) GADPH is a gene for a glycolytic protein (*not needed to know*). Based on the processes within the cell type, the different genes will be used more or less frequently due to differentiation of cells. For example a cell that is responsible for motility probability has a large number of cilia and would use more GADPH for the increased amount of cellular respiration to provide the ATP needed for the movement. If a cell was responsible for secreting proteins (like pancreas in humans) there would be an increased amount of transcription and translation in those cells to provide the proteins needed to be secreted.