2018 Free Response

[Figure 1: Phylogenetic tree (cladogram) representing the evolutionary relatedness among bear populations based on mitochondrial DNA sequence comparisons. The tree branches, from top to bottom: Black Bears, European Brown Bears, Polar Bears, Western North American Brown Bears, Asian Brown Bears. European Brown Bears and Polar Bears share a node; that node and (Western North American Brown Bears + Asian Brown Bears, which share their own node) share a deeper node; that node and Black Bears share the deepest node shown. Below the tree is a time axis labeled "Hundreds of Thousands of Years Ago" with tick marks at 50, 40, then a break (squiggle) then 4, 3, 2, 1, with the deepest node aligning near 40-50 and shallower nodes aligning at successively smaller values toward 1. Caption: "Figure 1. Phylogenetic tree representing the evolutionary relatedness among bear populations based on mitochondrial DNA sequence comparisons."]

Polar bears are highly adapted for life in cold climates around the North Pole. Brown bears, black bears, and pandas are found in warmer environments. Researchers collected complete mitochondrial DNA sequences from several populations of bears and constructed a phylogenetic tree to represent their evolutionary relatedness (Figure 1).

A researcher studying adaptation in bears sequenced the nuclear gene encoding a lysosomal trafficking protein (LYST) in polar bears, brown bears, black bears, and panda bears. There are seven inferred amino acid substitutions that are found only in polar bears. Mutations that cause similar substitutions in the human LYST protein are associated with Chediak-Higashi syndrome, an autosomal recessive condition in which pigment is absent from the hair and eyes. The researcher used the inferred amino acid sequences to build the distance matrix shown in Table 1.

TABLE 1. AMINO ACID DIFFERENCES IN THE LYST PROTEIN AMONG BEAR SPECIES

[Figure 1: Diagram of cellular response to infection by pathogenic bacteria. At the top is a double-line "Cell Membrane" with two small vertical channel/pore segments embedded in it, arrows converging up into the pore from below (labeled with circled "3"), and one arrow pointing up and out through the membrane at the far left (from the Active Interleukin). Below the membrane, left region: "Inactive Interleukin" (drawn as a triangle attached to an oval) is converted via a step labeled circled "2" into "Active Interleukin" (an oval with a triangle nearby, arrow pointing up out of the membrane, showing the active portion is released from the cell). Middle-right region: "N-terminal Gasdermin" (a small rectangle/bracket shape) sits just below the membrane pore; "Gasdermin" (a rectangle attached to a filled black square) is converted via a step labeled circled "3" into N-terminal Gasdermin, which is shown assembling into the membrane pore. Bottom-left region: "Inactive Caspase-1" (a filled circle attached to an oval) is converted via a step labeled circled "1", triggered by "Bacterial Infection" (arrow pointing up into step 1), into "Active Caspase-1" (an oval with a filled circle nearby); Active Caspase-1 then has arrows pointing to both step 2 (activating Interleukin) and step 3 (activating Gasdermin). Caption: "Figure 1. Cellular response to infection by pathogenic bacteria."]

Some pathogenic bacteria enter cells, replicate, and spread to other cells, causing illness in the host organism. Host cells respond to these infections in a number of ways, one of which involves activating particular enzymatic pathways (Figure 1). Cells normally produce a steady supply of inactive caspase-1 protein. In response to intracellular pathogens, the inactive caspase-1 is cleaved and forms an active caspase-1 (step 1). Active caspase-1 can cleave two other proteins. When caspase-1 cleaves an inactive interleukin (step 2), the active portion of the interleukin is released from the cell. An interleukin is a signaling molecule that can activate the immune response. When caspase-1 cleaves gasdermin (step 3), the N-terminal portions of several gasdermin proteins associate in the cell membrane to form large, nonspecific pores.

Researchers created the model in Figure 1 using data from cell fractionation studies. In the experiments, various parts of the cell were separated into fractions by mechanical and chemical methods. Specific proteins known to be located in different parts of the cell were used as markers to determine the location of other proteins. The table below shows the presence of known proteins in specific cellular fractions.

CELL FRACTIONS CONTAINING DIFFERENT CELLULAR PROTEINS

• = presence of protein

Seagrasses are aquatic plants that reproduce sexually. Male seagrass flowers produce sticky pollen that is carried by circulating water to female flowers, resulting in fertilization. A researcher claims that mobile aquatic invertebrates can also transfer pollen from male to female flowers in the absence of circulating water. To investigate this claim, the researcher set up aquariums to model the possible interactions between the invertebrates and seagrasses.

[Figure 1: Bar graph titled with y-axis "Percent Survival" ranging from 0 to 100 in increments of 20. Five bars correspond to Strains I-V of bedbugs treated with beta-cyfluthrin, with 95% confidence interval error bars: Strain I ≈ 71% (error bar roughly 60-79%); Strain II ≈ 39% (error bar roughly 29-49%); Strain III ≈ 23% (error bar roughly 16-35%); Strain IV ≈ 56% (error bar roughly 36-75%); Strain V ≈ 10% (error bar roughly 5-15%). Below the graph is a table:

• = Wildtype; – = Deletion

Caption: "Figure 1. Percent survival of five strains of bedbugs treated with beta-cyfluthrin. A (+) indicates the gene is present; a (–) indicates the gene is deleted. Error bars represent the 95% confidence interval."]

The common bedbug (Cimex lectularius) is a species of insect that is becoming increasingly resistant to insecticides. Bedbugs possess several genes suspected of contributing to the resistance, including P450, Abc8, and Cps. To investigate the role of these genes in insecticide resistance, researchers deleted one or more of these genes in different strains of bedbugs, as indicated in Figure 1, and treated the strains with the insecticide beta-cyfluthrin. Each strain was genetically identical except for the deleted gene(s) and was equally fit in the absence of beta-cyfluthrin. The percent survival of each strain following beta-cyfluthrin treatment is shown in Figure 1.

[Figure 1: Bar graph titled "Probability of Nest Success in an environment with predators" (y-axis "Probability of Nest Success" from 0.0 to 0.8 in increments of 0.2). Two bars separated by a vertical divider line: "Warblers Only" = 0.4; "Warblers and Cuckoos" = 0.6.]

Some birds, including great spotted cuckoos, lay their eggs in the nests of other birds, such as reed warblers. The warbler parents raise the unrelated chicks and provide them with food that would otherwise be given to their biological offspring. A researcher conducted an investigation to determine the type of relationship between warblers and cuckoos in an environment without predators. The researcher found that nests containing only warblers were more likely to be successful than nests containing warblers and cuckoos (data not shown). A successful nest is defined as a nest where at least one chick becomes an adult warbler.

In some geographic areas, several species of nest predators are present. Researchers have found that cuckoo chicks, while in the nest, produce a smelly substance that deters nest predators. The substance does not remain in the nest if cuckoo chicks are removed. Figure 1 shows the probability that nests containing only warblers or containing both warblers and cuckoos will be successful in an environment with predators. In a follow-up experiment, the researchers added cuckoos to a nest that contained only warblers (group 1) and removed cuckoos from a nest containing warblers and cuckoos (group 2).

Cystic fibrosis is a genetic condition that is associated with defects in the CFTR protein. The CFTR protein is a gated ion channel that requires ATP binding in order to allow chloride ions (Cl$^-$) to diffuse across the membrane.

[Diagram: a model of a generalized animal cell (rounded rectangle outline representing the cell with a rounded-rectangle "Plasma Membrane" boundary), containing labeled organelles: "Golgi Apparatus" (stack of curved membranes, left side), "Mitochondrion" (oval with folded internal cristae membrane, upper right, surrounded by small dots representing free ribosomes), "Lysosome" (small circle, right side, surrounded by small dots), "Endoplasmic Reticulum" (folded membrane studded with small dots representing ribosomes, lower left/center, connecting toward the nucleus), and "Nucleus" (large circle, bottom center). Small dots scattered throughout the cytoplasm represent free ribosomes.]

In the tongue sole fish (Cynoglossus semilaevis), sex is determined by a combination of genetics and environmental temperature. Genetically male fish have two Z chromosomes (ZZ), and genetically female fish have one Z chromosome and one W chromosome (ZW). When fish are raised at 22°C, ZZ fish develop into phenotypic males and ZW fish develop into phenotypic females. However, when fish are raised at 28°C, the Z chromosome is modified (denoted as Z*). ZW individuals develop as phenotypic males that are fertile and can pass on the Z chromosome to their offspring even when the offspring are raised at 22°C. A cross between a ZW female and a Z*Z male is shown in the Punnett square below.

Acetylcholine receptor (AChR) proteins are found at the synapse between neurons and skeletal muscle cells. Acetylcholine released from neurons binds to a specific site on the receptor proteins, which causes an ion channel in the receptors to open and allow sodium ions (Na$^+$) to enter muscle cells. The resulting depolarization of muscle cells initiates muscle contractions. Another molecule, nicotine, can also bind to certain types of AChR proteins and activate the receptors.

A researcher is investigating two different types of AChR proteins: type 1 and type 2. To determine which stimuli activate the receptors, the researcher exposes muscle cells expressing the different types of receptor proteins to stimuli and observes the results indicated in Table 1.

TABLE 1. RESPONSE OF AChR PROTEINS TO DIFFERENT STIMULI

• indicates activation; – indicates no activation