Test 1 - Biology 230 - Sherry Krayesky-Self
Which of the following motifs would be predicted to form a coiled-coil dimer? "X" represents any of the 20 amino acids, and n = repeating unit.
(Leu-X-X-Leu-X-X-X)n
In the first reaction of glycolysis (the pathway that begins the oxidative breakdown of sugars), the enzyme hexokinase uses ATP to catalyze the phosphorylation of glucose to glucose 6-phosphate and ADP. The ΔG° of this reaction is a favorable -16.7 kJ/mole. Another sometimes active enzyme, called glucose 6-phosphatase, effectively "reverses" this reaction, hydrolyzing glucose 6-phosphate back to glucose and releasing a phosphate. The ΔG° of this reaction is -13.8 kJ/mole. Based on these values, what is the ΔG° for the hydrolysis of ATP: ATP + H2O → ADP + Pi?
-30.5 kJ/mole
In a chemical reaction, substrate molecule A is broken down to form one molecule of product B and one molecule of product C. The equilibrium constant, K, for this reaction is 0.5. If we start with a mixture containing only substrate A at a concentration of 1 M, what will be the concentration of A when the reaction reaches equilibrium?
0.500 M
You are in charge of buying new microscopes for your company, and you have been comparing different types of microscopes. One important property for microscopy is the resolution, which measures the ability to distinguish two small objects that are close together. Rank the following list of microscopes from lowest to highest resolution.
1. Infrared microscope (780nm-1mm) 2. Confocal fluorescence microscope (488nm) 3. Ultraviolet microscope (100-400nm) 4. X-ray microscope (0.01-10nm) 5. Transmission electron microscope
Watch the animation about lysozyme reactions, and then answer the questions. Place the following steps of polysaccharide chain cleavage by lysozyme into the correct order.
1. Lysozyme and substrate form an enzyme-substrate complex, forcing one sugar molecule into a strained conformation 2. Glutamic acid donates a proton to one sugar as aspartic acid attacks the C1 carbon of a second sugar 3. A covalent bond forms between the aspartic acid and the sugar, and the sugar-sugar bond is hydrolysed 4.Glutamic acid polarizes a water molecule, drawing a proton away from the water 5.The water oxygen attacks the C1 carbon, breaking the sugar aspartate bond 6. Lysozyme and product dissociate
Approximately how much does a mole of carbon atoms (each having an atomic weight of 12) weigh?
12 g
For the reaction ATP + H2O → ADP + Pi, the ΔG° = −30.5 kJ/mol. What would be the associated equilibrium constant for this reaction?
135,000
Consider a protein that is a polypeptide 20 amino acids long, what are the potential number of different possible sequences that could be produced?
20^20
The amount of free energy released from the oxidation of glucose to carbon dioxide is −2867 kJ/mole. The amount of free energy released from the oxidation of stearic acid to carbon dioxide is −11,342 kJ/mol. In theory, how many more ATP molecules could be produced by the oxidation of one mole of stearic acid than from the oxidation of one mole of glucose?
277 ATPs
You want to test pentapeptides (short peptides with only five amino acids) for their ability to bind to and inhibit a particular receptor. To do this, you set out to synthesize all possible pentapeptides and test each individually. Assuming you'll use just the 20 common amino acids, how many different pentapeptides will you have to test for receptor binding?
3,200,000
For the reaction A → B, what would the equilibrium constant be if ΔG° = −15 kJ/mol?
335
Carbon, which has four electrons in its outer shell (with a capacity of eight electrons), can form a maximum of how many covalent bonds with other atoms?
4
When NADH or NADPH transfers electrons to a recipient molecule, the recipient becomes reduced and the activated carriers are oxidized (to NAD+ or NADP+, respectively). What else happens during this reaction?
A proton is taken up by the recipient molecule.
The two monolayers of the plasma membranes of eukaryotic cells are asymmetric with different membrane lipid compositions in the extracellular and cytoplasmic monolayers. Neurons contain high quantities of galactosylceramide (a glycolipid) in the extracellular monolayer. Phosphatidylethanolamine is a specific membrane phospholipid found mainly in the cytoplasmic monolayer. Figure 11-19 below shows a section of plasma membrane. Glycolipids are shown in blue and phosphatidylethanolamine is shown in yellow. How is phosphatidylethanolamine found mainly in the cytoplasmic monolayer?
A specific flippase moves phosphatidylethanolamine to the cytoplasmic monolayer.
In the electron micrograph, identify the bacterial cell features by dragging the labels to their targets.
A- Cell Wall B- Plasma Membrane C- Cytoplasm D- Outer Membrane
Identify the types of chemical bonds illustrated by dragging the labels to their targets.
A- covalent bond B- ionic bond
In the light microscope image below, identify the parts of the cell by dragging the three labels to the three targets.
A- nucleus B- plasma membrane C- cytoplasm
Which of the following would most likely interact by forming an ionic bond?
ATP and magnesium cations
Which statement represents the cell theory?
All cells are formed by the growth and division of existing cells.
The accumulation of mutations in DNA is the basis for evolution and organismal divergence. The amount of divergence can be measured by comparing the sequences of homologous genes. Which of the following statements is most likely to be true?
Although animals and fungi diverged over 1 billion years ago, it is possible to learn about the function of human genes by studying their homologs in yeast.
Watch the Analogy of Enzyme Catalysis animation and answer the following questions. All four possible reactions in the animation are energetically favorable; the energy of the four products is lower than the energy of the original starting molecule. Why does the starting molecule not completely and quickly convert to its possible products before the addition of heat or an enzyme?
An activation energy barrier exists that must be overcome for conversion to products.
Watch the Analogy of Enzyme Catalysis animation and answer the following questions. Compared to adding heat to the system, what is the advantage of using an enzyme to overcome an energy barrier?
An enzyme is specific for one desired pathway and end product.
Shown is a schematic diagram of a membrane phospholipid. Which segment will always carry a negative charge?
B
Consider the following enzymatic pathway: Although individual reactions in the cell may be energetically unfavorable and not spontaneous, they can be driven forward if they are linked to another highly favorable chemical reaction. Given the reaction A → B where the ΔG° = +15 kJ/mol, which of the following reactions would be considered a sequential reaction that is spontaneous? Choose more than one response.
B → D with a ΔG° = −17.5 kJ/mol and B → C with a ΔG° = −17.5 kJ/mol
Radioactive isotopes (radioisotopes) of elements are commonly used in biological experiments as tracers to follow and detect molecules of interest. For example, photosynthetic intermediates produced during carbon dioxide conversion to sugars were detected by exposing algae to carbon dioxide containing a radioactive form of carbon. This radioactive carbon could be rapidly detected in molecules produced by the algae during carbon fixation and sugar production. Why can radioisotopes substitute for non-radioactive isotopes of elements in experiments?
Because radioisotopes of an element differ only in the number of neutrons, they still behave the same way chemically.
Watch the animation about lysozyme reactions, and then answer the questions. What happens to glutamic acid 35 and aspartic acid 52 at the end of the reaction?
Both amino acids are restored to their original forms.
We have learned a great deal about human cell biology from human cell lines grown in tissue culture. Both primary cell lines (cells isolated from normal differentiated tissue that maintain the properties of the original tissue) and some cell lines derived from embryonic (i.e., nondifferentiated) cells can be induced in culture to show the properties of mature differentiated cells. Given this information, which of the following statements describes how we should think about cultured cells as a tool to study human biology?
Both embryonic and primary cell lines may provide useful but different information about the working of normal cells, but we should be careful about interpreting results.
You are studying amoebas and paramecia, two different single-celled protozoans. You have at your disposal a standard white light (known as "bright-field") microscope, a fluorescence microscope, a scanning electron microscope, and a transmission electron microscope. For each of the following studies, indicate which type of microscope would be most useful.
Bright-Field: Take movies of unmanipulated cells swimming or crawling in a drop of water. View cytoplasmic streaming (movement of organelles within the cytoplasm) in a paramecium. Fluorescence: Stain and visualize chromosomes and mitotic spindles in dividing amoebae. Use labeled antibodies to locate and make color images of lysosomes in both types of cell. Scanning Electron: View three-dimensional images of the outer surface of a paramecium, including cilia. Transmission Electron: Visualize ribosomes in the cytosol and mitochondria of amoebas.
Energy is released and harnessed in the cell from the gradual oxidation of molecules in metabolic pathways. The amount of energy released is based upon the extent to which the molecule can be oxidized. Given the 1-carbon molecules below, which would release the most energy from its complete oxidation?
C. methane
Sort the following techniques into those that can help determine protein tertiary structure and quaternary structure (where applicable) and those that cannot.
Can Determine 3-D: Nuclear magnetic resonance (NMR) spectroscopy; X-ray crystallography; Cryoelectron microscopy Cannot determine 3-D: Two-dimensional polyacrylamide-gel electrophoresis; Mass spectrometry
Condensation reactions and hydrolysis reactions are two important (and opposite) classes of chemical reactions performed by cells. Classify each of the reactions described below as either a condensation reaction, a hydrolysis reaction, or neither.
Condensation: glucose + glucose yields maltose + H2O Hydrolysis: ATP + H2O yields ADP + phosphate, Phosphatidylinositol-4,5-bisphosphate (PIP2) + H2O yields diacylglycerol (DAG) + inositol-1,4,5-trisphosphate (IP3) Neither: CH3OH + HCl yields CH3Cl + H2O, H2O2 + H2O2 yields 2 H2O + O2
You discover what you think is a new macromolecule in a bacterium isolated from a pond near where you live. The following questions ask you why you think it is a macromolecule and what properties you predict it has. What evidence may have led you to conclude that the molecule is a macromolecule?
During centrifugation, the proposed macromolecule sediments as a single, discrete band in the centrifuge tube.
Naïve B cells found in our immune system each contain a specific cell-surface receptor capable of binding to a specific foreign antigen such as a protein from a pathogen like a bacterium or virus. Binding to an antigen triggers a process whereby the naïve B cell can differentiate into a plasma cell that secretes large quantities of an antibody that specifically binds to an antigen from the pathogen. Because plasma cells are long-lived cells, the immune system is then primed to rapidly respond to that antigen in the future if the person is again exposed to the pathogen. During differentiation, the cell rapidly expands the amount of endoplasmic reticulum and Golgi membranes needed for secreting the antibodies. Which organelle(s) will become particularly active in synthesizing new membrane lipids?
Endoplasmic reticulum
Consider this evolutionary tree and then answer the questions. Scientists study model organisms within these groups to gain insight into these types of organisms and their genetic heritage. Is the following statement true, false, or impossible to determine? Photosynthetic bacteria contain chloroplasts.
False
Which statement concerning feedback inhibition is false?
Feedback inhibition is difficult to reverse.
Within the microscope image below, identify the type of microscopy used by dragging the correct label to the target in the image.
Fluorescence Microscope
Transcription factors generally consist of two distinct domains: 1) an activation domain (AD) and 2) a DNA-binding domain (DBD). Green fluorescent protein (GFP) is widely used in genetic engineering as a reporter—that is, a fluorescent tag that allows researchers to track the location of protein inside the cell. Given the proteins listed below, which could be precipitated with DNA?
GFP-AD-DBD engineered protein and GFP-DBD engineered protein
The cell regulates its metabolism through a vast interconnected web of anabolic and catabolic chemical pathways. Which of the following would be expected to release energy and generate activated carriers to drive energetically unfavorable reactions?
Glycolysis, where each glucose molecule is broken down into two molecules of pyruvate.
Phosphofructokinase catalyzes a key control point in the glycolytic pathway, which ultimately leads to ATP production. The activity of phosphofructokinase as a function of ATP concentration was studied in vitro. Purified enzyme was added to test tubes. Each tube contained the same amount of fructose 6-phosphate and a different ATP concentration. As ATP levels increased, enzyme activity initially rose, then plateaued, and finally decreased at higher ATP levels, as shown here. As seen in the graph of the data, high ATP levels inhibit enzyme activity. What is a reasonable explanation for the inhibition of enzyme activity at high ATP levels?
High levels of ATP allosterically inhibit the enzyme.
Which of the following statements is not true?
Hydrogenation reactions are oxidations, and dehydrogenation reactions are reductions.
An amphipathic molecule contains one region that is polar and/or charged and therefore hydrophilic, and another that is nonpolar and therefore hydrophobic (these molecules are also sometimes called amphiphilic). Sort the following list of molecules based on whether they are largely hydrophilic, hydrophobic, or amphipathic.
Hydrophilic: glucose (a monosaccharide), serine (amino acid with -OH as its side chain) Hydrophobic: benzene (a ring hydrocarbon with the formula C6H6), triacylglycerols (a.k.a. fats and oils) Amphipathic: phosphatidylcholine (a phospholipid)
The final three-dimensional shapes of proteins (and other macromolecules) are directed by the noncovalent interactions that are able to form as the molecules fold. Hydrogen bonds, electrostatic attractions (a.k.a. ionic bonds or salt bridges), and hydrophobic interactions all play important roles in protein folding. Based on the properties of these interactions, which of the following statement is true?
In aqueous solution, a folded protein would likely have hydrophobic amino acid side chains concentrated in the interior, and polar and charged side chains concentrated on the protein surface.
True or False? Within a developed multicellular organism, all cells possess the ability to divide and do so regularly.
It is false, because some cells lose the ability to replicate their DNA and divide.
You discover what you think is a new macromolecule in a bacterium isolated from a pond near where you live. The following questions ask you why you think it is a macromolecule and what properties you predict it has. Based on your knowledge of other biological macromolecules, what are reasonable assumptions about your macromolecule?
Its cellular synthesis is directed by enzymes and it contains carbon-carbon bonds.
Consider the reaction A + B → AB. How is the equilibrium constant expressed for this reaction with two substrates and a single product?
K = [AB] / [A][B]
The figure below is a graphical comparison of the relative sizes of the genomes of different organisms. The table provides the sizes and number of protein-coding genes in commonly studied model organisms. Use the data in the figure and table to answer the question below. Different organisms have widely varying genome sizes and different numbers of protein-coding genes. Based on the information in the figure and table above, which of the following statements is a conclusion that can reasonably be made?
Less than 5% of the human genome is likely to be composed of protein-coding sequences.
Which is not evidence for the endosymbiotic origins of mitochondria and chloroplasts?
Mitochondria and chloroplasts have similar DNA.
Throughout the 1920s, Otto Meyerhof, A. V. Hill, and colleagues investigated how cells use energy to power muscle contraction. They determined that during muscle contraction, glycogen is broken down into lactic acid, a product of fermentation. Originally Meyerhof thought that the conversion of glycogen into lactic acid directly powered muscle contraction. This idea was overturned by experiments performed by Einar Lundsgaard. What evidence did Lundsgaard provide to suggest that glycogen breakdown and lactic acid production did not directly power muscle contraction?
Muscle contraction could continue for some time after inhibition of fermentation.
What is the difference between NAD+ and NADH?
NADH carries an extra proton and two high-energy electrons.
The figure below shows a comparison of the relative abundances of the most common elements found in the human body and the Earth's crust. Based on this graph, please answer the question below. The proportions of elements in the human body and the Earth's crust are quite different. Which of the following statements is a conclusion that can be drawn from the data? Choose all that apply—there may be more than one correct answer.
Organisms that live on land (like humans) must expend energy to concentrate some elements that are found in relatively low amounts in the Earth's crust and the proportions of elements in humans reflect chemicals that readily dissolve in water, rather than the relative amounts found in the Earth's crust.
Both photosynthesis and cell respiration involve the use of enzyme catalysts, which direct the participating molecules through a series of chemical reactions. Both also rely on a transfer of electrons to power these chemical transformations. Reactions of this type are called oxidation-reduction reactions. Given the reactions below, sort them based on whether the central atom becomes reduced or oxidized.
Oxidation of carbon: Formic acid to carbon dioxide; Methane to methanol Reduction of carbon: Formaldehyde to methanol; Formic acid to formaldehyde
Use the periodic table of the elements to help you answer the question below. Which of the following elements would you expect to be chemically MOST similar to nitrogen?
Phosphorus (P), atomic number 15
Not all cellular membranes have the same relative quantity of cholesterol. Generally, the plasma membrane of animal cells contains higher amounts of cholesterol than organelle membranes such as the endoplasmic reticulum (ER) membrane. Thus, different cholesterol levels lead to different characteristics of diverse cellular membranes within the cell. Sort each of the following membrane characteristics into those more likely to apply to the ER membrane and those more likely to apply to the plasma membrane.
Plasma Membrane: Relatively thicker membrane; Relatively stiffer membrane; Relatively decreased permeability Endoplasmic Reticulum: More water molecules found in the hydrophobic core; Increased thermal movement
Although the influenza virus and the SARS-CoV-2 virus are two completely unrelated viruses, both have RNA genomes, and both infect humans by binding to cells of the respiratory tract. Based on the success of the SARS-CoV-2 vaccine, you have decided to try to develop an influenza vaccine that takes the same strategy. Which of the following describes the approach you should use to follow the SARS-CoV-2 vaccine approach?
Produce mRNAs for the hemagglutinin and neuraminidase proteins (two cell surface proteins that are important for binding to and infecting cells of the respiratory tract), and use these mRNAs to construct a vaccine.
Consider this evolutionary tree and then answer the questions. Scientists study model organisms within these groups to gain insight into these types of organisms and their genetic heritage. Which of these statements is consistent with the data presented in the evolutionary tree?
Saccharomyces cerevisiae do not contain chloroplasts.
Consider this image depicting aspartate transcarbamoylase regulation and then answer the question. Enzymes can have both active and regulatory sites. What is the purpose of these sites?
The binding of CTP at a regulatory site on the protein causes decreased production of carbamoyl aspartate.
The evolution of eukaryotes has involved many important adaptations, including acquisition of mitochondria and chloroplasts, and the development of multicellularity. Based on the relationships between different groups of eukaryotes shown in Figure 1-33 above, which of the following statements is MOST likely to be true?
The endosymbiotic event leading to mitochondria happened once, in a common ancestor of plants and animals.
Investigators wish to purify an enzyme—a serine protease—using affinity chromatography. They attach to the matrix of an affinity column an antibody molecule that binds specifically to a short sequence of amino acids located in the enzyme's active site. When they apply a mixture of proteins to the column, the protease adheres to the column and the other proteins pass through. To extract their purified enzyme from the column, the investigators add a large excess of the peptide that the antibody recognizes. What should they expect to occur after this treatment?
The enzyme will remain bound to the column and none of the fractions will contain the enzyme of interest; only flow-through will leave the column.
In 1925, scientists exploring how lipids are arranged within cell membranes performed a key experiment using red blood cells. Using benzene, they extracted the lipids from a purified sample of red blood cells. Because these cells have no nucleus and no internal membranes, any lipids they obtained were guaranteed to come from the plasma membrane alone. The extracted lipids were floated on the surface of a trough filled with water, where they formed a thin film. Using a movable barrier, the researchers then pushed the lipids together until the lipids formed a continuous sheet only one molecule thick. The researchers then made an observation that led them to conclude that the plasma membrane is a lipid bilayer. Which of the following would have allowed the scientists to come to this conclusion?
The extracted lipids covered twice the surface area of the intact red blood cells.
Consider the following image of a protein-ligand interaction and then answer the question. Which of the following best describes the stable protein-ligand interaction that is represented in the image? Be sure to use the image as a guide but apply your knowledge regarding how protein and ligand commonly interact with each other. A note of caution though: the red lines in the figure are merely representing interactions and are not meant to be quantified.
The formation of a set of many weak, noncovalent interactions maintains the interaction between protein and ligand.
Which statement is true?
The heat released by an animal cell comes from the chemical bond energy present in the food molecules it metabolizes.
The melting point of an ionic solid is the temperature at which the crystal separates into its constituent ions. For sodium chloride, the melting point in air is 801°C. However, when sodium chloride is added to water at 37°C (human body temperature), the sodium and chloride ions separate readily. How can we explain this apparent paradox?
The highly polar water molecules are able to interact with the charged sodium and chloride ions, shielding the charges from each other and allowing them to separate at a much lower temperature, whereas the nonpolar molecules of air do not readily interact with the ions.
As described in the figure below, the technique of ultracentrifugation can be used to demonstrate whether a substance is composed of large covalently linked molecules, or smaller molecules held together in a complex by noncovalent bonds. You are studying two substances that both have very high molecular weights: hyaluronan, a carbohydrate found in the extracellular matrix with a MW of ~8 x 106 daltons, and the bacterial ribosome, with a MW of ~2.5 x 106. Hyaluronan is a single, long-chain polymer, while the ribosome subunit is a complex of 55 different proteins plus three long RNA molecules. Which of the following describes the pattern you would expect to see from ultracentrifugation of these two substances?
The hyaluronan would show a single band at ~8 x 106 daltons, but the ribosome would show a smear with a wide range of molecular weights.
You are studying a recently discovered protozoan and have found what appears be a new organelle of unknown function. You hypothesize that it may have resulted from a new endosymbiotic event. Which of the following properties of the organelle would support this hypothesis? Choose all that apply—there may be more than one correct answer.
The new organelle contains DNA and the new organelle is surrounded by two independent membranes.
The hydrophobic "force" results from the fact that it is energetically unfavorable for hydrophobic molecules to disrupt the hydrogen bonding network of water. This drives hydrophobic amino acid side chains to interact with each other during protein folding, typically in the interior of the protein. What would you expect to happen if a protein folded in a hydrophobic environment such as the lipid bilayer of a cellular membrane?
The polar and charged amino acid side chains would repel the hydrophobic molecules of the environment, and would be forced into the interior of the protein, while the hydrophobic side chains would be exposed on the exterior.
You are part of an exobiology (the branch of science that deals with the possibility and potential nature of life on other planets) team studying potential life-forms on an asteroid. Your team is testing the hypothesis that alien life-forms would also be composed of cells, just like terrestrial (Earth-based) life-forms. You have identified several structures that you think might be cells of alien life-forms. Which of the following criteria would be MOST useful in determining whether or not these structures could be cells?
The presence of catalytic molecules arranged in an organized structure (Do they have molecules that function as enzymes? Are these arranged in the cell in an organized fashion?)
Scientists were studying yeast cells in which a mutation inactivated a gene required for cell division. Without this gene—and the protein it encoded—these mutant yeast cells were unable to divide normally. But the scientists discovered that introducing a related protein from human cells could "rescue" these mutant yeast cells, allowing the cells to resume normal division. Based on this finding, what is the most likely conclusion you could make?
The proteins that control cell division in yeast and humans are functionally equivalent and have been conserved, almost unchanged, for more than a billion years.
The two monolayers of the plasma membranes of eukaryotic cells are asymmetric with different membrane lipid compositions in the extracellular and cytoplasmic monolayers. Neurons contain high quantities of galactosylceramide (a glycolipid) in the extracellular monolayer. Phosphatidylethanolamine is a specific membrane phospholipid found mainly in the cytoplasmic monolayer. Figure 11-19 below shows a section of plasma membrane. Glycolipids are shown in blue and phosphatidylethanolamine is shown in yellow. How is galactosylceramide (a glycolipid) found in the extracellular monolayer?
The sugar groups are added to the membrane glycolipids by enzymes found inside the Golgi.
Consider the image that depicts the binding experiment of a series of molecular interactions and then answer the question. Which of the following is consistent with the data presented in the figure, which depicts three hypothetical interactions between macromolecule A and macromolecules B, C, and D?
The surfaces of A and D match well and therefore can form enough weak bonds to withstand thermal jolting; they therefore stay bound to each other during the experiment.
Watch the animations on α helices and β sheets, and then answer the questions. Predict what would happen to the secondary structure of a protein if an alcohol that disrupts hydrogen-bonding were added.
The β sheets would unfold, disrupting protein structure and the α helices would unfold, disrupting protein structure.
Investigators decide to analyze the purity of a preparation of antibody molecules using SDS polyacrylamide-gel electrophoresis (SDS-PAGE). On Lane 1 of the gel, they load a sample of the antibody. On Lane 2, they load an antibody sample that has been treated with a reducing agent called mercaptoethanol, which breaks disulfide linkages. Following electrophoresis, they see distinct bands representing polypeptides with molecular weights of 50 kD and 25 kD in Lane 2 and only one band weighing 150 kD in Lane 1. What can the investigators conclude about their antibody based on the results of this experiment?
Their antibody is composed of subunits (50 kD and 25 kD in molecular weight) that each must include at least one cysteine residue.
How do most motor proteins ensure their movements are unidirectional?
They couple a conformational change to the hydrolysis of an ATP molecule.
Ras is a GTP-binding protein involved in cell proliferation (division). In its active form, with GTP bound, Ras activates cell signaling pathways that promote cell division. Mutations in the gene that encodes Ras can lead to cancer. How might mutations in the gene encoding Ras lead to the uncontrolled proliferation characteristic of cancer cells?
They decrease the rate at which Ras hydrolyzes GTP.
The bacterial cell micrograph in Part I is most likely a _______ electron micrograph.
Transmission
The HER2 protein is a transmembrane receptor protein found on the plasma membrane of cells. The intracellular domain of the protein contains a kinase domain that phosphorylates target proteins, leading to cell proliferation. About 20% of human breast cancers have high levels of HER2 and are referred to as HER2-positive cancers. Women with HER2-positive breast cancer generally have a worse prognosis than those with other types of breast cancer. Newer drugs like lapatinib target and inhibit the HER2 kinase domain, decreasing HER2 activity levels and slowing the growth of the cancer. Interestingly, higher HER2 levels have been found on the plasma membranes of cells with rigid plasma membranes, and lower HER2 levels on the plasma membranes of cells with less rigid plasma membranes. Which of the following treatments could potentially be added to the lapatinib treatment to further reduce cancer cell growth?
Treat with a drug to lower the patient's cholesterol levels.
If you wanted to purify the insulin receptor from a mixture of proteins, what methods could you use? Choose TWO of the following selections.
Use affinity chromatography with beads coated with insulin and Use affinity chromatography with beads coated with anti-insulin receptor antibodies.
Determination of the three-dimensional structure of proteins yields a wealth of information about their structure and function. Such knowledge is critical for developing a basic understanding of how cells operate. Given the methods below, sort the information based on the given technique described.
X-ray crystallography: Gold standard for protein structure determination; Uses wavelength approximately equal to the diameter of a hydrogen atom NMR: Useful for proteins 50,000 daltons or less; Can be used to study changes in protein shape in solution CryoEM: Can be used for large integral membrane proteins; Uses liquid ethane to process sample
Why do cell biologists study yeast?
Yeast carries out all the basic tasks that a eukaryotic cell must perform and yeast is more closely related to animals than to plants.
The hydrolysis of phosphate bonds provides the chemical energy to drive reactions in the cell. The amount of free energy contained in these bonds is dependent upon the donor potential of the molecule, where good donors have a reduced affinity for the phosphate group relative to those that are poor donors. Creatine phosphate can be hydrolyzed to creatine and has a ΔG° = −43 kJ/mol. This allows the cell to generate ATP from ADP. Which of the following conditions would allow for ATP hydrolysis to generate creatine phosphate from creatine with an inorganic phosphate concentration of 10 mM?
[ADP]/[ATP] = 5.75 x 10^−9
You have developed a promising anti-cancer agent, but it has poor solubility in water. Which of the following changes should improve water solubility?
adding a hydroxyl group and adding a carboxyl group
Consider the following image of a protein-ligand interaction and then answer the question. Which of the following chemical group interactions may be represented by the red lines in the image?
an -OH of the ligand interacting with an -SH of the protein
At equilibrium, the free energy of a reaction is which of the following?
at its lowest point
Consider the figure that outlines the assembly of the ribosome and then answer the question. What type(s) of bonds link together the components of a ribosome, as shown in the figure?
both the types of bonds that involve the sharing of electrons between atoms and the types of bonds that involve electrostatic interactions between atoms
Animals exploit the phospholipid asymmetry of their plasma membrane to distinguish between live cells and dead ones. When animal cells undergo a form of programmed cell death called apoptosis, phosphatidylserine—a phospholipid that is normally confined to the cytosolic monolayer of the plasma membrane—rapidly translocates to the extracellular, outer monolayer. The presence of phosphatidylserine on the cell surface serves as a signal that helps direct the rapid removal of the dead cell. How might a cell actively engineer this phospholipid redistribution?
by activating a scramblase and inactivating a flippase in the plasma membrane
Phosphofructokinase catalyzes a key control point in the glycolytic pathway, which ultimately leads to ATP production. The activity of phosphofructokinase as a function of ATP concentration was studied in vitro. Purified enzyme was added to test tubes. Each tube contained the same amount of fructose 6-phosphate and a different ATP concentration. As ATP levels increased, enzyme activity initially rose, then plateaued, and finally decreased at higher ATP levels, as shown here. How could enzyme activity levels have been determined?
by measuring the accumulation of fructose 1,6-bisphosphate
Antibiotics tend to target features that are unique to bacterial cells and absent from eukaryotic cells such as our own. Which of the following would present a safe target for a new antibiotic?
cell wall
In 1970, Frye and Edidin published research describing the mobility of plasma membrane proteins. They fused mouse and human cells together, creating a hybrid cell, and then examined the localization of mouse and human proteins over time. Initially mouse and human proteins were each restricted to one-half of the heterokaryon, but over time the mouse and human proteins mixed, with each being present over the entire cell surface. What technique did Frye and Edidin likely use to examine the mouse and human proteins?
fluorescence microscopy
Consider this representation of an antibody and answer the questions. This antibody is composed of _______ polypeptide chains.
four
Your company has developed an organic molecule with commercial potential and you know how to produce it in the lab. You want to increase production and make as much of the molecule as possible, but the reaction has a positive ΔG°. What can you do to try to drive the reaction toward your desired product?
increase the concentration of reactants and continually remove products
In an electron transport chain, electrons are passed from one transmembrane electron carrier to another, driving proton movement across a membrane (see image below). The protons then flow through ATP synthase (not shown) to generate ATP. In a 2018 article (Budin, et al., Science vol. 362) researchers probed how membrane fluidity affects electron transport chain activity and ATP production in E. coli by manipulating membrane fluidity and measuring respiration. How could researchers have increased membrane fluidity?
increase the proportion of phospholipids with unsaturated fatty acids
Investigators are studying a protein that must be phosphorylated to be activated. Which method could be used to separate the phosphorylated form of the protein from the form that lacks an activating phosphate group?
ion-exchange chromatography
You are a biologist interested in studying how eukaryotic cells obtained their unique features during their evolution from a prokaryotic ancestor. Which cellular features, unique to eukaryotes, might you focus on?
mitochondria and the nucleus
To identify genes coding for essential proteins, researchers can create temperature-sensitive mutations. These mutations allow proper protein folding and cell proliferation at the permissive temperature of 22ºC, but they cause protein misfolding and reduced cell proliferation at a higher restrictive temperature, such as 37ºC. Which of the following mutations might increase protein flexibility and lead to a temperature-sensitive phenotype?
mutation of a bulky isoleucine that was buried in the protein interior to a glycine (side chain = H) and mutation of a lysine (that was involved in an ionic bond with a glutamic acid) to a glycine
The ultracentrifuge is an important piece of laboratory equipment frequently used by cell biologists. What are some applications for the ultracentrifuge?
separating different cellular organelles from each other
Which type of covalent bond allows for rotation about the bond axis?
single bond
Why must all living cells carefully regulate the fluidity of their membranes?
to permit membrane lipids and proteins to diffuse from their site of synthesis to other regions of the cell; to ensure that membrane molecules are distributed evenly between daughter cells when a cell divides; to allow membranes, under appropriate conditions, to fuse with one another and mix their molecules
Consider this representation of an antibody and answer the questions. If SDS-PAGE were used for a pure sample of this protein that was preincubated with mercaptoethanol, then there would be ________ bands expected.
two
On the basis of weight, which is most abundant in a living bacterial cell?
water
Watch the animations on α helices and β sheets, and then answer the questions. Sort the following secondary structure characteristics into the correct categories.
α helix only: Cylindrical structure, One full turn every 3.6 amino acids β sheet only: Consists of antiparallel or parallel strands, Side chains alternating above and below the structure Both α helix & β sheet: Can be formed by many sequences, Formed by hydrogen-bonding between backbone atoms
