Cell Bio Cumulative Final

Arjun Clicker question The cell knows what phase of the cell cycle it is in based on: A. The rate of enzymatic activity of cyclins B. The concentration of cyclins C. The amount of DNA in the cell

B. The concentration of cyclins

Arjun Clicker question, page 40 (see figure) The transcriptional regulator is downstream of the protein kinase. A. False B. True

B. True

Arjun Clicker question Which of the following does not impact tissue size? A. Cell growth B. Cell division and death C. Cell signaling D. Extracellular matrix deposition

C. Cell signaling

Arjun Clicker question If a mutation led to the intermediate fibers not forming, we would expect ... A. The cells to be more difficult to displace from the tissue B. No effect on the structural integrity of tissue C. The cells to be more easily displaced from the tissue

C. The cells to be more easily displaced from the tissue

Midterm Questions How are prokaryotes and eukaryotes similar? A. They both contain membrane-bound organelles B. They both have nuclei. C. They both have cell membranes enclosing their cytoplasm. D. They both have chloroplasts.

C. They both have cell membranes enclosing their cytoplasm.

Arjun Clicker question Which of the following might impact how a cell responds to a signal? A. The signals the cell will be experience in the future B. The signals the cell has been exposed to the past C. The other signals the cell is receiving D. Both B and C

D. Both B and C

Weekly Assignment #10 Match the necrosis and apoptosis with their pathway properties (either necrosis or apoptosis). 1. accidental 2. plasma membrane loses integrity 3. immune response 4. plasma membrane belbing 5. no immune response 6. programmed

1. necrosis 2. necrosis 3. necrosis 4. apoptosis 5. apoptosis 6. apoptosis

Midterm Questions Number the following cells based on the proposed evolution (descending order, from most recent to earliest). Your answer should be a 5-digit string composed of numbers 1-5 e.g., 12345. 1. aerobic prokaryote 2. anaerobic prokaryote 3. photosynthetic eukaryote 4. aerobic eukaryote 5. photosynthetic prokaryote A. 3-4-1-5-2 B. 2-5-1-4-3 C. 5-4-3-2-1 D. 3-2-1-5-4

A. 3-4-1-5-2

Weekly Assignment #12 In an organ with many different cell types, what is the fundamental difference between them which leads to different behaviors? A. A different set of genes expressed. B. A different organization of the cytoskeleton. C. Differences in how the cells signal to their neighbours. D. A different set of genes in the genome of the cell.

A. A different set of genes expressed.

Arjun Clicker question, slide 35 (see figure) How does Proteins A and B affect apoptosis? A. A inhibits apoptosis, B inhibits apoptosis B. A inhibits apoptosis, B enhances apoptosis C. A enhances apoptosis, B inhibits apoptosis D. A enhances apoptosis, B enhances apoptosis

A. A inhibits apoptosis, B inhibits apoptosis

Arjun Clicker question, page 47 (see figure) If a chemical treatment decreased the activity of GAP (GTPase-activating proteins), thereby decreasing the conversion of GTP to GDP, we would expect: A. An increase in the GPCR based signaling occurring the cell. B. A decrease in the GPCR based signaling occurring the cell. C. No change in the GPCR based signaling occurring the cell.

A. An increase in the GPCR based signaling occurring the cell.

Arjun Clicker question All cells have cytoskeletons. A. True B. False

A. True

Weekly Assignment #7 Which of the following channels would not be expected to generate a change in voltage by movement of its substrate across the membrane where it is found? A. an aquaporin B. a proton channel C. a calcium channel D. a sodium channel

A. an aquaporin

Weekly Assignment #12 If we treated a developing tissue with a chemical that mimicked a chemokine which of the following developmental processes would we most likely disrupt? A. cell movement B. cell specialization C. cell proliferation D. cell interaction

A. cell movement

Weekly Assignment #2 What is the smallest distance two points can be separated and still resolved using light microscopy? A. 20 nm B. 0.2 μm C. 2 μm E. 200 μm

B. 0.2 μm

Weekly Assignment #8 When looking at a population of cells under a microscope you see one that is different from the others. It has a large expanded lamellipodium. You isolate it and sequence its genome to figure out if there is a mutation that is causing this behavior. Which of the following mutations is not likely to be the cause? 1. A mutation that increases the expression of profilin. 2. A mutation that decreases the expression of thymosin. 3. A mutation that knocks out the Arp2 gene. 4. A mutation that increases the expression of the Arp2 protein. A. 4 B. 3 C. 1 D. 2

B. 3, Without Arp2 the actin filaments would not form the fan shaped network necessary for lamellipodium creation.

Arjun Clicker question, page 34 (see figure) A mutation to the Bad protein changes it activity from inhibiting to enhancing Bcl2.How does Bad affect apoptosis in this mutant cell? A. Bad enhances apoptosis B. Bad inhibits apoptosis.

B. Bad inhibits apoptosis.

Arjun Clicker question, page 12 (see figure) If the dynein motors (red proteins) in this system were replaced with kinesin motors instead, we would expect: A. No bending to occur. B. Bending to occur in the opposite direction. C. Bending to occur in the same direction.

B. Bending to occur in the opposite direction.

Midterm Questions What is the name for the reactions in which biological polymers form and why is this a good name for these reactions? A. Condensation reactions, since water is consumed. B. Condensation reactions, since water is produced. C. Hydrolysis reactions, since water is produced. D. Hydrolysis reactions, since water is consumed.

B. Condensation reactions, since water is produced.

Arjun Clicker question Signaling that involves transcription and translation is more rapid than signaling that only involves post translational modifications. A. True B. False

B. False

Arjun Clicker question Stochastic expression of genes is due to coordinated signaling between cells. A. True B. False

B. False

Weekly Assignment #10 In a cell an intiator caspase is activated through colocalization with another caspase by interaction with an adapter protein. This cell is then treated with a chemical that inhibits the interaction of the intiator caspases with the adapter protein, making it no longer able to hold the initiator caspases together. We would expect this to result in the initiator caspase becoming deactivated. True or False? A. True B. False

B. False, The initiator caspase is activated via irreversible proteolytic cleavage. As a result once activated, it cannot be deactivated.

Weekly Assignment #10 If a chemical was able to activate flipase (XRP8) in the absence of caspase activity we would expect healthy cells to treated with this chemical to be less likely to be phagocytosed by immune cells. True or False? A. True B. False

B. False, We would expect healthy cells to treated with this chemical to be more likely to be phagocytosed by immune cells as XRP8 activity would lead to the formation of blebs and surface display lipids that act as signals to immune cells to phagocytose these cells.

Arjun Clicker question A mutation arises in a cell that reduces the capacity of Apaf1 to bind cytochrome C. We would expect this to: A. Increases apoptosis thanks to an increase in the available cytochrome C. B. Inhibit apoptosis due to reduced formation of apoptosome complexes C. Inhibit apoptosis due to reduced capacity of the apoptosome to recruit caspases.

B. Inhibit apoptosis due to reduced formation of apoptosome complexes

Arjun Clicker question If a mutation leads compromises P53's capacity to bind DNA, would we expect cells that have this mutation to have a higher or lower frequency of DNA damage? A. Higher B. Lower

A. Higher

Weekly Assignment #12 Induced pluripotent stem cells are generated by reprogramming differentiated cells using: A. The Yamanaka Factors. B. Morphogens. C. Mitogens. D. Differentiation signals.

A. The Yamanaka Factors.

Weekly Assignment #4 Which of the following is NOT true regarding the members of a protein family in general? A. They can functionally replace each other. B. They share an ancestry, i.e., they are homologs. C. They have similar three-dimensional conformations. D. Over evolutionary time scales, the family has expanded mainly through gene duplication events.

A. They can functionally replace each other.

Arjun Clicker question Select the analogy that most closely resembles the assembly of monomers into intermediate fibers. A. Threads being twined into a string B. Blocks being stacked into a column C. Links being locked together into a chain

A. Threads being twined into a string

Midterm Questions Choose the answer that best fits the following statement: Cholesterol is an essential component of biological membranes. Although it is much smaller than the typical phospholipids in the membrane, it is a/an __________ molecule, having both hydrophilic and hydrophobic regions. A. amphipathic B. hydrophobic C. polar D. oxygen-containing

A. amphipathic

Weekly Assignment #7 Proteins that are fully translated in the cytosol and lack a sorting signal will end up in the ----------- A. cytosol. B. nuclear membrane. C. interior of the nucleus. D. mitochondria.

A. cytosol.

Weekly Assignment #3 Both DNA and RNA are synthesized by covalently linking a nucleoside triphosphate to the previous nucleotide, constantly adding to a growing chain. In the case of DNA, the new strand becomes part of a stable helix. The two strands are complementary in sequence and antiparallel in directionality. What is the principal force that holds these two strands together? A. hydrogen bonds B. covalent bonds C. van der Waals interactions D. ionic interactions

A. hydrogen bonds

Midterm Questions, Question 29 (see diagram) The diagrams below represent the plasma membranes of various cells. Which part of the diagram (A, B, C or D) correctly depicts the major ion pumps and the resulting membrane potentials? (Larger fonts indicate higher concentrations; + and - signs indicate charge distributions for the membrane potential). D. B. A. C.

B.

Weekly Assignment #4 You have purified a multi-subunit extracellular protein that has several interchain disulfide bonds. Which of the following chemicals would you add to your purified protein mixture if you wanted to eliminate the disulfide bonds? A. NaCl, a salt B. DTT, a reducing agent C. H2O2, an oxidizing reagent D. Tris, a buffering agent E. SDS, an ionic detergent and denaturing agent

B. DTT, a reducing agent

Arjun Clicker question, page 17 (see figure) In a cell where myosin transports a cargo along the actin network formed by Arp2/3 shown on the right, where would we expect cargo to accumulate over time? A. Near the plasma membrane. B. Near the nucleus.

B. Near the nucleus.

Arjun Clicker question, slside 39 (see figure) The inhibitor protein is upstream of gene expression. A. False B. True

B. True

Arjun Clicker question Microtubules are _______ of _______ that form _______. A. Intertwined chains, monomers, flexible chains. B. Stacked columns, monomers, flexible tubes C. Stacked columns, dimers, stiff tubes.

C. Stacked columns, dimers, stiff tubes.

Midterm Questions The variations in the physical characteristics between different proteins are influenced by the overall amino acid compositions, but even more important is the unique amino acid -------- A. number. B. bond. C. sequence. D. orientation.

C. sequence.

Spontaneous generation

belief that living organisms develop from nonliving matter, because of some observations such as: appearance of maggots on decaying meat, pieces of cheese and bread wrapped in rags and left in dark corner through to produce mice. In 1859 Louis Pasteur put an end to this hypothesis by demonstrating that boiled broth never re-exposed to air remained sterile.

Whoever has the _________ is __________

electron, reduced

Weekly Assignment #12 Stem cells can be used to treat diseases by: A. using stem cell derived organs or tissue to replace diseased versions in a patients body. B. de-differentiating diseased cells into stem cells to cure the disease. C. using stem cell derived factors to cure diseased tissues in the body.

using stem cell derived organs or tissue to replace diseased versions in a patients body.

Energy can be stored/transferred in what 2 forms?

1. High energy chemical group ATP, Acetyl-CoA and UDP-glucose (function as a source of both energy and chemical group in biosynthetic reactions) 2. High energy electrons NADH, NADPH and FADH2 (oxidation-reduction coupled reaction)

Weekly Assignment #3 Your lab director requests that you prepare a new growth medium and add it to the mammalian cell cultures. One of the ingredients you know you need to add is a mix of the essential amino acids. On the shelf of dry chemicals, you find the amino acids you need, and you mix them into your medium, along with all the other necessary nutrients. Two days later, you came to check on your cells and find that the cells have not grown. You are sure you made the medium correctly, but on checking you see that somebody wrote a note on the dry mixture of amino acids you used: "Note: this mixture contains only ᴅ-amino acids." What is the meaning of the note? How does it explain the lack of cell growth in your culture? Are there any organisms that could grow using this mixture?

1. The meaning of the note is that the amino acids are not the right type for mammals, since they only use L amino acids. 2. This explains the lack of cell growth in the culture because mammals cannot use the right handed (D) amino acids, only the left handed amino acids (L). 3. No organisms could grow using this mixture because no organism uses solely just D amino acids, they need L amino acids to create proteins

Weekly Assignment #5 List any three features typically present in a plasmid used as a vector for cloning, expression and purification of a recombinant protein which can be used at a later stage as an antigen for production of antibody. Explain the significance of each feature you list. Be specific. If drawing a diagram will help you, please do so.

1. The origin of replication is important because it gives the ability to replicate. If the plasmid needs to replicate, it allows for the RNA polymerase to bind to the origin on the ribosome and start the replication process. 2. Multiple cloning sites (NCS) are significant because they are sites where restriction enzymes can be used to cut and open up the plasmid. The gene of interest can then be inserted into the plasmid at the area cut. The restriction site should be unique. 3. selective markers are important because after cloning is complete, the plasmid is inserted into a bacteria. The selective marker is then used to offer antibiotic resistance, which allows the bacteria to also become antibiotic resistant. This then eliminates all other types of bacteria.

1. Phosphate groups in NADPH do what? 2. NADPH serves as ______ to ________. 3.NADH serves as _____ that lead to _____formation of ATP during oxidation of food materials (respiration).

1. cause a slight conformational change that make them recognized by different enzymes, they deliver electrons to different targets 2. electron carrier in anabolic reactions, supply high-energy electrons needed to synthesize energy-rich biological polymers (e.g., in photosynthesis). 3. electron carrier in catabolic reactions.

Weekly Assignment #3, Question 11 (see figure) This figure represents reactions that happen in a cell. Molecule C changes to molecule D and molecule X changes to Y. Which of these reactions is favorable? Which of these molecules has the highest free energy? To what extent this reaction will continue in a test tube and in a cell? Why?

1. molecule c changing to molecule d 2. Molecule c 3. In a test tube this will continue to equilibrium because there are not other inputs and outputs. In a cell this will not continue to equilibrium because there are other factors such as exchanging materials with the environment, and replenishing nutrients.

1. What is Free energy (G)? 2. What is negative free energy (deltaG)? When do spontaneous reactions happen? 3. What is standard free energy (delta G 0)? 4. Will reactions inside the cell proceed until complete equilibrium? Why?

1. the energy stored in organic molecules. 2. Means the reactions have a higher energy than the product, loses energy to the system, energetically favorable or downhill. Spontaneous reactions happen only If delta G is negative. 3.What is standard free energy (delta G 0)? 4. No, because cells avoid equilibrium through a variety of methods: Exchanging materials with the environment Replenish the nutrients Eliminate waste products Connecting reactions ---> a product can be used as a substrate for anther reaction

what is the percentage of DNA sequence in exons (protein-coding sequences)?

1.5%

Arjun Clicker question, page 23 (see figure) If a population of cells is treated with a chemical that prevents the cyclin and CDK that regulate the cell cycle checkpoint between the G1 and S phase from interacting, how would we expect the cytometry readout to change compared to the wildtype shown on the right? A. B. c.

A.

Weekly Assignment #9, Question 6 (see figure) If a chemical treatment modified P53 such that it was always phosphorylated and active, how would you expect the histogram representing flow cytometry performed with a propidium iodide stain to look? B. A. C.

A. The constant P53 activity will produce P21 which will inactivate the G1/S-CDK checkpoint. This will result in cells accumulating in the G1 phase without being able to progress, which looks like a large accumulation in the first peak and less in the middle and second peak which correspond to S and G2/M.

Weekly Assignment #9 Condensins: 1. are degraded when cells enter M phase. 2. assemble into complexes on the DNA when phosphorylated by M-Cdk. 3. are involved in holding sister chromatids together. 4. bind to DNA before DNA replication begins. A. 2 B. 1 C. 4 D. 3

A. 2

Weekly Assignment #9 Which of the following statements about the anaphase-promoting complex (APC) is FALSE? 1. It promotes the degradation of proteins that regulate M phase. 2. It inhibits M-Cdk activity. 3. It is continuously active throughout the cell cycle. A. 3 B. 1 C. 2

A. 3, The APC becomes activated in mid- to late M phase thanks to the absence of free kinetochores which frees the activating subunit cdc20

Weekly Assignment #9 In which phase of the cell cycle do cells check to determine whether the DNA is fully and correctly replicated? 1. at the transition between G1 and S 2. when cells enter G0 3. during M 4. at the end of G2 A. 4 B. 3 C. 1 D. 2

A. 4, Cells will check whether the DNA is fully and correctly replicated at the end of G. It does not make sense to monitor DNA replication before S phase because DNA replication has not yet occurred. When cells enter G0, they do not replicate their DNA. During M phase, chromosomes are condensed for chromosome segregation, so it would be difficult for the cell to examine the replicated DNA for errors at that point.

Weekly Assignment #4 The phosphofructokinase (PFK) enzyme is one of the key players in the glycolytic pathway in which glucose eventually breaks down into pyruvate, some ATP is generated, and some NAD+ is reduced. PFK catalyzes the committed step in the pathway and is under extensive regulation. Which of the following compounds would you expect to activate PFK? A. ADP B. NADH C. Pyruvate D. ATP E. All are possible answers

A. ADP

Midterm Questions Which of the following statements about the unfolded protein response (UPR) is FALSE? A. Activation of the UPR is associated with increasing proteins synthesis. B. Activation of the UPR occurs when receptors in the cytoplasm sense misfolded proteins. C. Activation of the UPR results in the production of more ER membrane. D. Activation of the UPR results in the production of more chaperone proteins.

A. Activation of the UPR is associated with increasing proteins synthesis.

Arjun Clicker question Actin filaments differ from Microtubules in that they: A. Are more flexible B. Are made up of sub-units that are also enzymes C. Form dynamic networks

A. Are more flexible

Midterm Questions, Question 35 (see diagram) You would like to amplify the following piece of DNA by PCR. Which of the following pairs of primers (regions used to design the primers are highlighted) would direct the amplification of this DNA? All sequences are written from 5′ to 3′. B. CACCTAAATTGTAAGCGTT & CTTCCTTTCTCGCCACGT C. AACGCTTACAATTTAGGTG & GAAGGAAAGAGCGGTGCA A. CACCTAAATTGTAAGCGTT & ACGTGGCGAGAAAGGAAG

A. CACCTAAATTGTAAGCGTT & ACGTGGCGAGAAAGGAAG

Arjun Clicker question A chemical treatment increases the concentration of profilin and Arp2/3 proteins in cell A. A different chemical treatment increases the concentration of thymosin and decreases the concentration of Arp2/3 in cell B. Which cell would we expect to have a large and broad protrusion from the chemical treatment? A. Cell A B. Cell B C. They would both be the same because of compensatory effects.

A. Cell A

Arjun Clicker question If stem cells undergo continuous asymmetric cell division, the population of un-differentiated stems cells: A. Stays constant B. Increases over time C. Decreases over time

A. Stays constant

Midterm Questions Which of the following enzymes seals two fragments of DNA? A. T4 DNA Ligase B. Kinase C. DNA polymerase D. Phosphatase

A. T4 DNA Ligase

Midterm Questions Based on the two reactions below, indicate whether the following statements TRUE (T) or FALSE (F). Your answer would be a four-letter string composed of letters T and F only, e.g., TTTF. 1. ATP + Y à Y-P + ADP ΔG = −100 kcal/mole 2. Y-P + A à B ΔG = 50 kcal/mole 1. Reaction I is favorable because of the large negative ΔG associated with the hydrolysis of ATP. 2. Reaction II is an example of an unfavorable reaction. 3. Reactions I and II are coupled reactions, and when they take place together, reaction II will proceed in the forward direction. 4. Reaction II can be used to drive reaction I in the reverse direction. A. TTTF B. TTTT C. FTTF D. TTFT

A. TTTF

Weekly Assignment #2 Select the option that BEST finishes the following statement: Evolution is a process ______ A. That can be understood based on the principles of mutation and selection. B. That results from repeated cycles of adaptation over billions of years. C. By which all present-day cells arose from 4-5 different ancestral cells D. That requires hundreds of thousands of years

A. That can be understood based on the principles of mutation and selection.

Weekly Assignment #12 If a mutation in cell within a developing tissue caused it to begin to express a version of the Notch receptor that lacked its cytoplasmic tail domain, how would this impact the mutated cell and its neighbors? A. The mutated cell would become specialized, its neighbors would remain unspecialized. B. The mutated cell and its neighbors would both become specialized. C. The mutated cell and its neighbors would both remain unspecialized. D. The mutated cell would remain un-specialized, its neighbors would become specialized.

A. The mutated cell would become specialized, its neighbors would remain unspecialized.

Arjun Clicker question The change in concentration of cyclins of the course of the cell cycle is drivenby regulation of: A. Their transcription, translation, and proteasomal degradation B. Their transcription, translation, and localization in the cell C. The number of copies of DNA in thecell

A. Their transcription, translation, and proteasomal degradation

Weekly Assignment #7 Assume that there are 30 sodium ions outside the cell, and 20 potassium ions inside the cell. What will happen after one cycle of the sodium-potassium pump? A. There will be 33 sodium ions outside the cell and 22 potassium ions inside the cell B. There will be 28 sodium ions outside the cell and 17 potassium ions inside the cell C. There will be 32 sodium ions outside the cell and 23 potassium ions inside the cell D. There will be 27 sodium ions outside the cell and 18 potassium ions inside the cell

A. There will be 33 sodium ions outside the cell and 22 potassium ions inside the cell

Weekly Assignment #2 Mitochondria and chloroplasts are thought to have evolved from free-living aerobic bacteria that were engulfed by an ancestral anaerobic cell and established a mutually beneficial (symbiotic) relationship with it. Which of the following statements is NOT true about these organelles? A. They are found in all eukaryotes. B. They have their own transfer RNAs. C. They have their own ribosomes. D. They have their own circular genomic DNA. E. They are similar in size to small bacteria.

A. They are found in all eukaryotes.

Midterm Questions The study of enzymes also includes an examination of how the activity is regulated. Molecules that can act as competitive inhibitors for a specific reaction are often similar in shape and size to the enzyme's substrate. Which variable or variables used to describe enzyme activity will remain the same in the presence and absence of a competitive inhibitor? A. Vmax B. All variables change C. Vmax and Km D. Km

A. Vmax

Midterm Questions, Question 49 (see figure) The following Figure shows the orientation of the Krt1 protein on the membrane of a Golgi-derived vesicle that will return to the endoplasmic reticulum (ER). Given this diagram, which of the following statements is TRUE? A. When this vesicle fuses with the ER, the N-terminus of Krt1 will be in the ER lumen. B. When this vesicle fuses with the ER, the entire Krt1 protein will be secreted into the cytoplasm. C. When this vesicle fuses with the plasma membrane, the C-terminus of Krt1 will be inserted into ER membrane. D. When this vesicle fuses with the ER, the N-terminus of Krt1 will be cytoplasmic.

A. When this vesicle fuses with the ER, the N-terminus of Krt1 will be in the ER lumen.

Weekly Assignment #11 Match the class of cell-surface receptor with the statement that best matches them. A. G-protein-coupled receptors B. Ion-channel-coupled receptors C. Enzyme-coupled receptors

A. all receptors of this class are polypeptides with seven transmembrane domains B. alter the membrane potential directly by changing the permeability of the plasma membrane C.Ligand triggered dimerization causes enzyme activation in the cell

Weekly Assignment #2 Match the following types of microscopy (left) with the corresponding description provided (right). There is one best match for each. A. transmission electron B. fluorescence C. phase-contrast D. scanning electron E. bright-field

A. has the ability to resolve cellular components as small as 2 nm. B. requires the use of two sets of filters. The first filter narrows the wavelength range that reaches the specimen and the second blocks out all wavelengths that pass back up to the eyepiece except for those emitted by the dye in the sample. C. uses a light microscope with an optical component to take advantage of the different refractive indices of light passing through different regions of the cell. D. requires coating a sample with a thin layer of a heavy metal to produce three-dimensional images of the sample surface. E. employs a light microscope and requires that samples be fixed and stained in order to reveal cellular details.

Weekly Assignment #10, Question 7 (see diagram) Based on the regulatory pathway diagram below determine if Proteins A, B, C, and D activate or inhibit apoptosis. Protein A Protein B Protein C Protein D

A. inhibits apoptosis B. inhibits apoptosis C. inhibits apoptosis D. activates apoptosis

Midterm Questions Seed oils are often dehydrogenated and added back into processed foods. The new fatty acids have an increased number of carbon-carbon double bonds. The dehydrogenation reaction could also be described as a/an __________ reaction. A. oxidation. B. protonation. C. reduction. D. isomerization.

A. oxidation.

Arjun Clicker question The interphase starts with cells that are ______ and have _______, in a phase called ________.The DNA of the cell then duplicates in _________.By the end of the third phase of interphase, ________, the cells are _______and have _________. A. small, 1 copy of their DNA, G1, S, G2, large, 2 copies of their DNA. B. large, 1 copy of their DNA, S, G1, G2, small, 2 copies of their DNA. C. small, 2 copy of their DNA, G1, G2, S, large, 1 copies of their DNA.

A. small, 1 copy of their DNA, G1, S, G2, large, 2 copies of their DNA.

Midterm Questions Noncovalent interactions between macromolecules in the cell can be weak or highly specific. Which of the factors below is the most significant in determining whether the interaction will be transient or stable? A. surface complementarity between molecules which determines the free energy of the interaction. B. the size of each molecule C. the rate of synthesis D. the concentration of each molecule

A. surface complementarity between molecules which determines the free energy of the interaction.

Weekly Assignment #9, Question 7 (see diagram) A temperature dependent mutation in M-cyclin leads to its inability to interact with the activating subunit of the Anaphase-promoting complex (cdc20) at 37C. If cells these cells are grown at room temperature and treated with propidium iodide they have a flow cytometry profile shown below. If these cells are grown at 37C and the experiment is repeated, what would we expect the profile to look like? A. B. C.

B. If the M-cyclin cannot interact with the APC, it will not be degraded, so the cell will not be able to pass the M/Spindle checkpoint. As a result we would expect cells to stall in the M phase and majority of cells to appear in the G2/M peak in the flow cytometry profile.

Weekly Assignment #11, Question 6 (see figure) A hypothetical signaling pathway is shown in the graphic below. Signal perception is transduced into the production of a chemical output, shown in pink, which degrades over time. The concentration of the output over time for cells exposed to the signal during the period highlighted in orange is shown in the graph below as the green line. Predict how the change in the signaling pathway shown depicted the graphic below will affect the output production over time by selecting the correct graph. A. B. C. D.

B. Positive feedback results in signal amplification and persistence.

Weekly Assignment #8 Which of the following statements about the function of the centrosome is FALSE? 1. Microtubules emanating from the centrosome have alternating polarity such that some have their plus end attached to the centrosome while others have their minus end attached to the centrosome. 2. Centrosomes contain hundreds of copies of the γ-tubulin ring complex important for microtubule nucleation. 3. Centrosomes typically contain a pair of centrioles, which is made up of a cylindrical array of short microtubules. 4. Centrosomes are the major microtubule-organizing center in animal cells. A. 2 B. 1 C. 4 D. 3

B. 1, Microtubules emanating from the centrosome are all arranged with their minus ends at the centrosomes and the plus ends extending into the cytoplasm.

Weekly Assignment #8 A mutation to the actin monomer leads to a faster rate of ATP hydrolysis. This causes a defect in actin cytoskeleton, resulting from a change in in the normal length of actin fibers, which leads to disease. Which of the following interventions might return the actin filaments to the correct size. 1. A chemical treatment that increases the concentration of Arp2/3 in the cell. 2. A chemical treatment that increses the concentration of thymosin in the cell. 3. A chemical treatment that increses the concentration of profilin in the cell. A. 2 B. 3 C. 1

B. 3, An increased rate of ATP hydrolysis would lead to shorter actin filaments in the cell. This might could be counteracted by profilin which increases the rate of monomer addition, increasing the length of the fibers.

Midterm Questions Because there are four different monomer building blocks that can be used to assemble DNA polymers, the number of possible sequence combinations that can be created for an DNA molecule made of 600 nucleotides is ---------------- A. 600^4 B. 4^600 C. 4 × 600. D. 600/4.

B. 4^600

Weekly Assignment #4, Question 6 (see figure) For each of the following cartoon representations from left to right, indicate whether the protein structure is composed of only α helices (1), only parallel β sheets (2), only antiparallel β sheets (3), α helices plus parallel β sheets (4), or α helices plus antiparallel β sheets (5) as repetitive secondary structure elements. Your answer would be a four-digit number composed of digits 1 to 5 only, e.g. 5513. A. 4315 B. 5134 C. 2315 D. 1234

B. 5134

Arjun Clicker question, slide 38 (see figure) How does Proteins A and B affect apoptosis? A. A inhibits apoptosis, B inhibits apoptosis B. A inhibits apoptosis, B enhances apoptosis C. A enhances apoptosis, B inhibits apoptosis D. A enhances apoptosis, B enhances apoptosis

B. A inhibits apoptosis, B enhances apoptosis

Midterm Questions The hydrolysis of ATP to ADP +Pi can be described as ----------- A. Its free energy change (delta G) is negative. B. All are true. C. Favorable reaction D. Spontaneous reaction E. Downhill reaction

B. All are true.

Weekly Assignment #3 Oxidation is a favorable process in an aerobic environment, which is the reason cells are able to derive energy from the oxidation of macromolecules. Once carbon has been oxidized to __________, its most stable form, it can only cycle back into the organic portion of the carbon cycle through __________. A. CH3; combustion. B. CO2; photosynthesis. C. CO2; respiration. D. CO; reduction.

B. CO2; photosynthesis.

Arjun Clicker question Cells that have differentiated into different cell types likely have: A. Different signaling pathways B. Different genes expressed C. Similar responses to extracellular signals

B. Different genes expressed

Arjun Clicker question Intermediate fibers form dynamic networks. A. True B. False

B. False

Arjun Clicker question Kinesin and Dynein are the only proteins that regulate the structure and function of the microtubule network A. True B. False

B. False

Arjun Clicker question, page 48 (see figure) Using the pathway diagram on the right predict the impact of introducing an enzyme that breaks down cyclic AMP on the capacity of a cell to respond to an adrenaline signal. A. It would increase the response to adrenaline. B. It would decrease the response to adrenaline. C. It would have no impact on the response to adrenaline.

B. It would decrease the response to adrenaline.

Arjun Clicker question When observing a population of cells that have a mutation which prevents initiator caspases from interacting with their cognate adapter proteins, what would we expect to see in response to treatment with an apoptotic signal? A. More apoptosis in mutant cells versus wildtype cells. B. Less apoptosis in mutant cells compared to wildtype cells. C. The same amount of apoptosis in mutant cells and wildtype cells.

B. Less apoptosis in mutant cells compared to wildtype cells.

Arjun Clicker question In the _______ phase of mitosis the chromosomes are in the middle of the cell, whereas in the _________ phase they are pulled apart. Mitosis ends with a process called _________ when the cell divides into two new cells. A. Prophase, Metaphase, Chromatin condensation B. Metaphase, Anaphase, Cytokinesis C. Telophase, Metaphase, Cytokinesis

B. Metaphase, Anaphase, Cytokinesis

Midterm Questions During the production of monoclonal antibodies in tissue culture, which of the following cells can be selected (able to grow even for few cycles) on HAT medium? A. Un-fused myeloma cells that have HGRPT mutated gene B. Only b and c C.. Hybrid Myeloma cells fused with antibody-producing B-cells. D. B-cells

B. Only b and c

Weekly Assignment #5 --------- is large protein complex in the cytosol and nucleus with proteolytic activity and responsible for degrading the misfolded proteins after their ubiquitination. A. Ribosome B. Proteasome C. Exosome E. Chromatin remodeling complex

B. Proteasome

Arjun Clicker question, page 31 (see figure) The results of two western blots for proteins A and B extracted from cells exposed to either an apoptotic signal or to no signal are show below. Based on this: A. Neither protein is likely to be a caspase B. Protein A is more likely to be a caspase than protein B. C. Protein B is more likely to be a caspases than protein A.

B. Protein A is more likely to be a caspase than protein B.

Midterm Questions Which of the following light spectra most active in driving the electron transport chain in photosynthesis? A. Blue and green B. Red and Blue C. Only green D. Only blue E. Only red

B. Red and Blue

Arjun Clicker question Microtubule networks are organized around microtubule organizing centers (MTOCs) such that: A. The MTOC stabilizes the plus end of the micro tubule while the minus end can grow towards or shrink away from the cell periphery B. The MTOC stabilizes the minus end of the microtubule while the plus end can grow towards or shrink away from the cell periphery C. The cell periphery stabilizes the plus end of the microtubule while the minus end can grow towards or shrink away from the MTOC

B. The MTOC stabilizes the minus end of the microtubule while the plus end can grow towards or shrink away from the cell periphery

Midterm Questions Why does the sodium-potassium pump require ATP to function properly? A. The concentration of sodium and potassium ions is greater outside the cell. B. The concentration of sodium ions is greater outside the cell and the concentration of potassium ions is greater inside the cell. C. The concentration of sodium and potassium ions is greater inside the cell. D. The concentration of sodium ions is greater inside the cell and the concentration of potassium ions is greater outside the cell.

B. The concentration of sodium ions is greater outside the cell and the concentration of potassium ions is greater inside the cell.

Midterm Questions Protein folding can be studied using a solution of purified protein and a denaturant (urea), a solvent that interferes with noncovalent interactions. Which of the following is observed after the denaturant is removed from the protein solution? A. The polypeptide forms solid aggregates and precipitates out of solution. B. The polypeptide returns to its original conformation. C. The polypeptide adopts a new, stable conformation. D. The polypeptide remains denatured.

B. The polypeptide returns to its original conformation.

Arjun Clicker question Which of these cellular properties does the cytoskeleton NOT contribute to?A. The structure of the cell B. The production of energy within the cell C. The movement of molecules around the cell

B. The production of energy within the cell

Weekly Assignment #5 What would the expected effect be on a PCR reaction if the primers used were slightly shorter and more variable than the intended oligonucleotide sequences? A. The PCR reaction would end after one cycle B. The reaction would yield a mixture of non-specific products C. The reaction would generate a single short PCR product D. The PCR reaction would not commence

B. The reaction would yield a mixture of non-specific products

Weekly Assignment #5, Question 6 (see figure) A cellular enzyme catalyzes the catabolic reaction shown below. Its coenzyme is shown in the box. Which of the following is correct regarding this reaction? A. The substrate is oxidized in this reaction and the coenzyme is converted from state 2 to state 1. B. The substrate is oxidized in this reaction and the coenzyme is converted from state 1 to state 2. C. The substrate is reduced in this reaction and the coenzyme is converted from state 1 to state 2. D. The substrate is reduced in this reaction and the coenzyme is converted from state 2 to state 1.

B. The substrate is oxidized in this reaction and the coenzyme is converted from state 1 to state 2.

Weekly Assignment #11 The following happens when a G-protein-coupled receptor activates a G protein. A. It activates the α subunit and inactivates the βγ complex. B. The α subunit exchanges its bound GDP for GTP. C. The β subunit exchanges its bound GDP for GTP. D. The GDP bound to the α subunit is phosphorylated to form bound GTP.

B. The α subunit exchanges its bound GDP for GTP. When a G protein is active, the α subunit will exchange its bound GDP for GTP. Both the α subunit and the βγ complex can activate downstream targets.

Weekly Assignment #10, Question 5 (see diagram) We believe that a protein in a cell might be a caspase. To determine whether this is the case develop a labeled antibody for this protein and do a western blot on protein extracts from cells that were treated with either no apoptosis signal or an apoptosis signal. Based on the blot results shown below: A. This protein is not likely a caspase B. This protein is a caspase that is 90 kDa in its uncleaved state, and the cleaved small and large sub-units are approximately 15 kDa and 75 kDa respectively. C. This protein is a caspase that is 90 kDa in its uncleaved state, and the cleaved small and large sub-units are approximately 8 kDa and 82kDa respectively.

B. This protein is a caspase that is 90 kDa in its uncleaved state, and the cleaved small and large sub-units are approximately 15 kDa and 75 kDa respectively.

Weekly Assignment #5, Question 9 (see figure) You have a piece of circular DNA that can be cut by the restriction nucleases EcoRI, HindIII, and NotI, as indicated in this Figure. A. One piece of DNA will be obtained when this DNA is cut by NotI. B. Two DNA fragments of unequal size will be created when this DNA is cut by both HindIII and EcoRI. C. Two DNA fragments that cannot be cut by HindIII will be obtained when this DNA is cut by EcoRI and NotI. D. A piece of DNA that cannot be cut by EcoRI will be obtained by cutting this DNA with both NotI and HindIII.

B. Two DNA fragments of unequal size will be created when this DNA is cut by both HindIII and EcoRI.

Arjun Clicker question The burst of M-cyclin activity ends once M/spindle checkpoint is passed thanks to: A. Ubiquitination triggered degradation of the CDK in response to the build-up of S cyclin B. Ubiquitination triggered degradation of the M-cyclin that is conditional on the absence of unattached kinetochores C. Dissociation of the CDK from the M-cyclin that is conditional on the absence of unattached kinetochores D. Activity of a phosphatase that adds inhibitory phosphates to the M-cyclin

B. Ubiquitination triggered degradation of the M-cyclin that is conditional on the absence of unattached kinetochores

Arjun Clicker question GPCRs initiate signaling by: A. Transporting the signaling molecule into the cell B. Undergoing a conformational change. C. Activating a G protein through phosphorylation.

B. Undergoing a conformational change.

Arjun Clicker question Asymmetric cell division drives differentiation of daughter cells through: A. Differential signaling between the daughter cells B. Unequal division of differentiation factors between daughter cells C. Changes in protein expression in daughter cells.

B. Unequal division of differentiation factors between daughter cells

Arjun Clicker question Necrosis is __________ cell death, which is caused by __________, and it__________ the immune system. Apoptosis is ___________ cell death, which is caused by __________, and it__________ the immune system. A. accidental, loss of plasma membrane integrity, does not activate ,programmed, caspases, activates B. accidental, loss of plasma membrane integrity, activates, programmed, caspases, does not activate. C. programmed, loss of plasma membrane integrity, does not activate, accidental, caspases, activates

B. accidental, loss of plasma membrane integrity, activates, programmed, caspases, does not activate.

Weekly Assignment #3 Choose the answer that best fits the following statement: Cholesterol is an essential component of biological membranes. Although it is much smaller than the typical phospholipids and glycolipids in the membrane, it is a/an __________ molecule, having both hydrophilic and hydrophobic regions. A. hydrophobic B. amphipathic C. polar D. oxygen-containing

B. amphipathic

Arjun Clicker question Positive feedback ______ or ________ output, whereas negative feedback _______ output or ___________. A. amplifies, generates oscillations, dampens, prolongs B. amplifies, prolongs, dampens, generates oscillations C. dampens, prolongs, amplifies, generates oscillations

B. amplifies, prolongs, dampens, generates oscillations

Weekly Assignment #12 Which is not an example of a major process occurring during development? A. cell proliferation B. cell secretion C. cell movement E. cell specialization

B. cell secretion

Midterm Questions Which of the following occur WITHOUT coupling transport of the solute to the movement of a second solute? A. export of H+ from animal cells for pH regulation B. export of Ca2+ from the cytosol C. the export of Na+ from cells to maintain resting membrane potential. D. import of glucose into gut epithelial cells

B. export of Ca2+ from the cytosol

Midterm Questions If you feed a photosynthetic organism CO2 in which the oxygen (O) atoms are radioactively labeled (C18O2), in which bio-products will you find the radioactive O atoms? A. Radiolabeled CO2 cannot be utilized by a photosynthetic cell B. in the carbohydrates produced by the plant C. equally distributed over the oxygen and the carbohydrates produced D. in the oxygen produced by the plant

B. in the carbohydrates produced by the plant

Weekly Assignment #7 Why do cells not have membrane transport proteins for O2? A. Because they need to keep the oxygen concentration low inside the reducing environment of the cell. B. Because oxygen can dissolve in water and leak in via water channels. C. Because oxygen can dissolve in the lipid bilayer and diffuse in and out rapidly without the need for a transporter. D. Because oxygen is transported in and out of the cell in special oxygen-carrying proteins such as hemoglobin. E. Because oxygen transport across a membrane is energetically unfavorable.

C. Because oxygen can dissolve in the lipid bilayer and diffuse in and out rapidly without the need for a transporter.

Weekly Assignment #5 Two ligands, A and B, bind to two different conformations of the enzyme X. The ligand A is the enzyme's substrate, whereas ligand B binds to a remote allosteric site. Which of the following is a consequence of this arrangement. A. Binding of A to X does not affect the affinity of X for binding to B. B. Binding of B to X does not affect the rate of reaction catalyzed by X C. Binding of B to X decreases the affinity of X for A. D. Binding of A to X increases the affinity of X for B.

C. Binding of B to X decreases the affinity of X for A.

Weekly Assignment #2 Which of the following organelles has both an outer and an inner membrane? A. Chloroplast B. nucleus C. Both chloroplast and mitochondria D. mitochondrion E. endoplasmic reticulum

C. Both chloroplast and mitochondria

Weekly Assignment #11 Arrange the following kinds of extra cellular signaling based on the distance between the sender and receiver cells, the smallest distance on the left and the largest on the right. A. Contact dependent, Paracrine, Neuronal, Endocrine B. Contact dependent, Neuronal, Endocrine, Paracrine C. Contact dependent, Neuronal, Paracrine, Endocrine D. Neuronal, Contact dependent, Endocrine, Paracrine

C. Contact dependent, Neuronal, Paracrine, Endocrine

Arjun Clicker question Which of the following is not one of the components of the cytoskeleton? A. Actin filaments B. Microtubules C. Cytochromes D. Intermediate fibers

C. Cytochromes

Arjun Clicker question, page 54 (see figure) If a mutation made a cell stop expressing Delta we would expect its neighbors to: A. Remain in an unspecialized state B. Have less active Delta protein C. Differentiate into a specialized state

C. Differentiate into a specialized state

Weekly Assignment #4 Which of the following is FALSE about molecular chaperones? A. They help streamline the protein-folding process by making it a more efficient and reliable process inside the cell. B. They can isolate proteins from other components of the cells until folding is complete. C. They can interact with unfolded polypeptides in a way that changes the final fold of the protein. D. They assist polypeptide folding by helping the folding process follow the most energetically favorable pathway.

C. They can interact with unfolded polypeptides in a way that changes the final fold of the protein.

Weekly Assignment #12 Stems cells are defined by their capacity to: A. generate morphogen gradients. B. divide rapidly. C. differentiate into other cell types. D. move through the body.

C. differentiate into other cell types.

Midterm Questions The fluidity of plasma membranes ------------------ A. increases as the length of the fatty acid chains increases B. increases as the percent of saturated fatty acids increases. C. increases as the percent of unsaturated fatty acids increases. D. decreases as the percent of cholesterol increases.

C. increases as the percent of unsaturated fatty acids increases.

Arjun Clicker question The _________ poses a major barrier to hydrophilic signals entering the cell so they must be either _______, as in ion channel receptors, or________, as in GPCRs or enzyme coupled receptors. A. cytoskeleton, be transported across it, be cleaved B. plasma membrane, be packaged into vesicles, be transduced into different forms C. plasma membrane , be transported across it , be transduced into different forms

C. plasma membrane , be transported across it , be transduced into different forms

Midterm Questions, Question 9 (see figure) The graph in the Figure illustrates the relationship between reaction rates and substrate concentration for an enzyme-catalyzed reaction. What does the Km value indicate with respect to enzyme-substrate interactions? A. the maximum rate of catalysis B. the equilibrium rate of catalysis C. the enzyme-substrate binding affinity E. the number of enzyme active sites

C. the enzyme-substrate binding affinity

Weekly Assignment #4 The observation that proteins often renature into their original conformations after they have been unfolded by denaturing agents implies that ......................... A. All are possible answers B. the final folded structure of a protein is usually NOT the one with the lowest free energy. C. the information needed to specify the three-dimensional shape of a protein is encoded in its amino acid sequence. E. each protein folds into several different conformations inside the cell. E. the cell does not need molecular chaperones for survival.

C. the information needed to specify the three-dimensional shape of a protein is encoded in its amino acid sequence.

Midterm Questions Cell biologists employ targeted fluorescent dyes or modified fluorescent proteins in both standard fluorescence microscopy and confocal microscopy to observe specific details in the cell. Even though fluorescence permits better visualization, the resolving power is essentially the same as that of a standard light microscope because the resolving power of a fluorescent microscope is still limited by the __________ of visible light. A. absorption B. filtering C. wavelength D. intensity

C. wavelength

Midterm Questions Indicate whether each of the following descriptions better applies to the light-dependent (L) or light-independent or dark (D) reactions in plant chloroplasts. Your answer would be a five-letter string composed of letters L and D only, e.g., DDDLD. ( ) involves the activity of Rubisco enzyme. ( ) generates the reducing power needed in CO2 fixation. ( ) produces the 3-carbon sugar, glyceraldehyde 3-phosphate. ( ) involves the generation of proton gradient across thylakoid membrane. ( ) involves splitting of water. A. L-D-D-L-D B. D-L-L-D-L C. L-D-D-D-L D. D-L-D-L-L

D. D-L-D-L-L

Weekly Assignment #5 Which of the following statements is TRUE? A. Disulfide bonds are formed by the cross-linking of methionine residues. B. Disulfide bonds are more common for intracellular proteins, compared to extracellular proteins. C. Disulfide bonds are formed mainly in proteins that are retained within the cytosol. D. Disulfide bonds stabilize the protein tertiary structure but do not change a protein's final conformation.

D. Disulfide bonds stabilize the protein tertiary structure but do not change a protein's final conformation.

Midterm Questions Which of the following statements about PCR is FALSE? A. PCR uses a DNA polymerase from a thermophilic bacterium. B. For PCR, every round of replication is preceded by the denaturation of the double-stranded DNA molecules. C. The PCR will generate a pool of double-stranded DNA molecules, which will have DNA from primers at the 5′ ends. D. In PCR, ddNTPs are added for polymerization of the newly synthesized stands.

D. In PCR, ddNTPs are added for polymerization of the newly synthesized stands.

Midterm Questions A researcher analyzes the effects of a particular disease that affects the eye. He observes that the genes responsible for this disease are located on the mitochondrial genome. What can the researcher conclude about this disease? A. on a double-stranded DNA B. It is paternally inherited, and the disease-causing genes are located on a double-stranded RNA. C. It is paternally inherited, and the disease-causing genes are located. D. It is maternally inherited, and the disease-causing genes are located on a double-stranded DNA. E. It is maternally inherited, and the disease-causing genes are located on a double-stranded RNA.

D. It is maternally inherited, and the disease-causing genes are located on a double-stranded DNA.

Iclicker class 9 You wish to produce protein "A" by introducing its coding gene into bacteria. The genetically engineered bacteria make large amounts of protein A, but inside inclusions bodies in the form of insoluble aggregate with no enzymatic activity. Which of the following procedures might help you to obtain soluble, enzymatically active protein? Select all options that are worth trying. A. Make the bacteria synthesize protein "A" in smaller amounts B. Dissolve the protein aggregate in Urea, then dilute the solution and gradually removed the Urea by dialysis. C. Treat the insoluble aggregate with a protease D. Make the bacteria co-expresser molecular chaperone and protein A. E. Heat the protein aggregate to denature it, then cool the mixture. F. Choices a, b, and d are worth trying.

D. Make the bacteria co-expresser molecular chaperone and protein A.

Weekly Assignment #11, Question 8 (see figure) A hypothetical signaling pathway is shown in the graphic below. Signal perception is transduced into the production of a chemical output, shown in pink, which degrades over time. The concentration of the output over time for cells exposed to the signal during the period highlighted in orange is shown in the graph below as the green line. Predict how the change in the signaling pathway shown depicted the graphic below will affect the output production over time by selecting the correct graph. A. B. C. D.

D. Negative feedback with long delays, such as those produced by transcription and translation, can create oscillations or other dynamic responses over time.

Midterm Questions After isolating the rough endoplasmic reticulum from the rest of the cytoplasm, you purify the RNAs attached to it. Which of the following proteins do you expect the RNA from the rough endoplasmic reticulum NOT to encode? A. plasma membrane proteins B. ER membrane proteins. C. soluble secreted proteins D. Proteins involved in DNA replication

D. Proteins involved in DNA replication

Weekly Assignment #7 Which of the following statements about the endoplasmic reticulum (ER) is FALSE? A. Steroid hormones are synthesized on the smooth ER. B. The ER is the major site for new membrane synthesis in the cell. C. The ER membrane is contiguous with the outer nuclear membrane. D. Proteins to be delivered to the ER lumen are synthesized on the smooth ER.

D. Proteins to be delivered to the ER lumen are synthesized on the smooth ER.

Iclicker class 5 Macromolecules in the cell can often interact transiently as a result of noncovalent interactions. These weak interactions also produce stable, highly specific interactions between molecules. Which of the factors below is the most significant in determining whether the interaction will be transient or stable? A. the size of each molecule B. The concentration of each molecule C. The rate of synthesis D. Surface complentarity between molecules

D. Surface complementarity between molecules

Midterm Questions NADH and NADPH are activated electron carrier molecules that function in completely different metabolic reactions. Which of the following statements are True (T) or False (F)? Your answer would be a four-letter string composed of letters T and F only, e.g., TTTT. 1. Both are electron carriers in oxidation-reduction reactions. 2. NADPH is the electron donor in biosynthetic reactions while NAD+ is the 3. electron acceptor in catabolic reactions. 3. The reduced form of NADPH is present in the cell at higher ratio than the oxidized form. 4. The reduced form of NADH is present in the cell at higher ratio than the oxidized form. A. TTFT B. TFTT C. FTFT D. TTTF

D. TTTF

Midterm Questions One of the most important membrane proteins is the sodium-potassium pump. What would happen to a cell if this pump suddenly stopped working? A. The cytoplasm would become hypertonic, and the cell would shrivel. B. The cell sap would become hypotonic, and the cell would lyse. C. Nothing, the cell would be fine. D. The cell sap would become hypertonic, and the cell would lyse.

D. The cell sap would become hypertonic, and the cell would lyse.

Weekly Assignment #4 Evolutionary tracing has identified clusters of the most invariant amino acids in the SH2 domain family of proteins. Which of the following is true regarding these sites? A. The invariant amino acids generally have negatively charged side chains. B. These sites have evolved fast because they have critical functions. C. The amino acids at these sites are generally hydrophobic. D. These sites correspond to the binding site for interacting proteins containing phosphorylated tyrosine. E. Mutation in these sites generally keeps the protein functional.

D. These sites correspond to the binding site for interacting proteins containing phosphorylated tyrosine.

Midterm Questions Molecular chaperones can work by creating an "isolation chamber." What is the purpose of this chamber? A. This chamber serves to transport unfolded proteins out of the cell. B. The chamber acts as a garbage disposal, degrading improperly folded proteins so that they do not interact with properly folded proteins. C. This chamber is used to increase the local protein concentration, which will help speed up the folding process. D. This chamber serves to protect unfolded proteins from interacting with other proteins in the cytosol, until protein folding is completed.

D. This chamber serves to protect unfolded proteins from interacting with other proteins in the cytosol, until protein folding is completed.

Weekly Assignment #3 Given what you know about the differences between prokaryotic cells and eukaryotic cells, rate the following biological processes as suitable (S) or unsuitable (U) for study using E. coli, a prokaryotic organism, as the model organism. Your answer should compose of 5 letters string composed of S and U only. 1. formation of the endoplasmic reticulum 2. DNA replication 3. how the actin cytoskeleton contributes to cell shape 4. how cells decode their genetic instructions to make proteins 5. how mitochondria get distributed to cells during cell division A. USUSS B. SSUSU C. SUSSU D. USUSU

D. USUSU

Midterm Questions Protein structures have several different levels of organization. The primary structure of a protein is its amino acid sequence. The secondary and tertiary structures are more complicated. Consider the definitions below and select the one that best fits the term "protein domain." A. a complex of more than one polypeptide chain B. a small cluster of α helices and β sheets C. the tertiary structure of a substrate-binding pocket D. a protein segment that folds independently

D. a protein segment that folds independently

Weekly Assignment #2 Biologists cannot possibly study all living species. Instead, they try to understand cell behavior by studying a select subset of species. Which of the following characteristics are useful in an organism chosen for use as a model in laboratory studies? A. amenability to genetic manipulation B. ability to grow under controlled conditions C. rapid rate of reproduction D. all are desirable characteristics

D. all are desirable characteristics

Weekly Assignment #3 When there is an excess of nutrients available in the human body, insulin is released to stimulate the synthesis of glycogen from glucose. This is a specific example of __________ process, a general process in which larger molecules are made from smaller molecules. A. catabolic B. oxidation C. hydrolysis D. anabolic

D. anabolic

Midterm Questions The advantage to the cell of the gradual oxidation of glucose during cellular respiration compared with its combustion to CO2 and H2O in a single step is that --------------- A. more CO2 is produced for a given amount of glucose oxidized. B. more free energy is released for a given amount of glucose oxidized. C. no energy is lost as heat. D. energy can be extracted in usable amounts.

D. energy can be extracted in usable amounts.

Weekly Assignment #7 Some cells express aquaporin proteins—they are channel proteins that facilitate the flow of water molecules through the plasma membrane. What regulates the rate and direction of water diffusion across the membrane? A. aquaporin conformation B. resting membrane potential C. availability of ATP D. solute concentrations on either side of the membrane

D. solute concentrations on either side of the membrane

Weekly Assignment #7 Transporters, in contrast to channels, work by ------------------- A. filtering solutes by size. B. a gating mechanism. C. filtering solutes by charge. D. specific recognition of transport substrates.

D. specific recognition of transport substrates.

Weekly Assignment #2 To trace family relationships between distantly related organisms such as humans, algae, bacteria, and archaea, one should compare their genomes in regions ---------------- A. that evolve rapidly. B. that have a higher mutation rate. C. that code for proteins. D. where mutations are hardly tolerated. E. where most mutations are selectively neutral.

D. where mutations are hardly tolerated.

Weekly Assignment #5, Question 11 (see figure) Which of the regulatory interactions 1 to 5 depicted in the following diagram is NOT an example of a negative feedback regulation? A. 3 B. 1 C. 4 D. 2 E. 5

E. 5

Weekly Assignment #2 Based on the variation of genome size and gene number in the organisms presented in the following graph, which organism has the highest number of genes per unit length of their genome? (Note the logarithmic scale.) SEE WK 2 ASSIGNMENT QUESTION A. H. sapiens B. M. musculus C. A. thaliana D. C. elegans E. E. coli

E. E. coli

Weekly Assignment #7 Imagine a small synthetic vesicle made from pure phospholipids enclosing an interior lumen containing 1 mM glucose and 1 mM sodium chloride. If the vesicle is placed in pure water, which of the following happens faster? A. Glucose diffuses out. B. Sodium chloride diffuses out. C. Cl- diffuses out. D. Na+ diffuses out. E. H2O diffuses in.

E. H2O diffuses in.

Midterm Questions Nicotiana benthamiana (tobacco) is a flowering plant. Botanists have chosen it to serve as a model plant for genetic engineering over hundreds of thousands of other flowering plant species because: A. can withstand extremely cold climates. B. has short generation time, takes 3-4 months from seed to seed. C. produces thousands of seeds per plant. D. its genome can be manipulated easily. E. all except "a".

E. all except "a".

List the reasons that sugar is important for cells

Glucose has a central role as an energy source for cells, glucose is the preferred respiratory fuel, even some cells such as nerve cells use glucose as the sole respiratory fuel Stored food material (glycogen in animal cells and starch in plant cells), Structural role, cellulose of cell was in plant cells and chitin in fungal cell wall and insect exoskeleton Carbon in lipids are higher reduced than carbon in sugars

Weekly Assignment #2 You have generated strains of Drosophila melanogaster that are expected to show interesting developmental phenotypes such as misplaced organs in the adult fly. However, some of these phenotypes are not readily seen with light microscopy. You therefore fix each mutant fly, dry it, coat it with a thin layer of gold, and place the entire fly into an electron microscope for viewing. What type of microscope are you using?

SEM (Scanning Electron Microscope)

Eukaryotic cells may have originated as a predator and evolved over billions of years in number of steps. What are the steps?

Size is enlarged, nuclear envelope evolved, engulfed an aerobic bacterium, engulfed a photosynthetic bacterium

Weekly Assignment #8 In under 100 words explain why the cytoskeleton is needed to actively transport molecules through cells.

The cytoskeleton is needed to actively transport molecules because the microtubules do active transport with "walking" motors. Using the cytoskeleton, Kinesin walks towards the plus end of the microtubule while Dynein walks towards the minus end of the microtubule. Myosin uses ATP hydrolysis to "walk" along Actin (actin fibers are part of the cytoskeleton).

Weekly Assignment #12 If two related species have diverged over evolutionary time resulting in slightly different body structure, what is the most likely to have changed within their genomes that explain these differences? A. Changes in transcription factor binding sites upstream of Hox genes. B. Deletion of one or more hox genes C. Acquisition of novel hox genes though genome duplication. D. Changes to the coding sequences of hox genes

A. Changes in transcription factor binding sites upstream of Hox genes.

Arjun Clicker question Differentiated cells can be reprogrammed to turn back into stem cells by: A. Expressing a specific set of transcription factors in the cells B. Providing the appropriate morphogen chemicals to the cells C. Exposing them to signals from stem cells.

A. Expressing a specific set of transcription factors in the cells

Arjun Clicker question As cells differentiate over the course of the development, their degree of specialization ____________. A. Increases B. Decreases C. Stays constant

A. Increases

Weekly Assignment #11 If we introduced a GAP (GTP-ase activating protein) enzyme whose activity was activated by cyclic AMP, how would this change the properties of the GPCR-based adrenaline signaling pathway? Hint: Draw out a regulatory pathway diagram based on what we disucssed in class. A. It would introduce negative feedback that would dampen the response to adrenaline. B. It would introduce positive feedback that would amplify the response to adrenaline. C. It would have no impact on the response to adrenaline

A. It would introduce negative feedback that would dampen the response to adrenaline. Perception of adrenaline would result in cyclic AMP production. This would activate the GAP which would inhibit GPCR signaling. As a result this is a negative feedback.

Weekly Assignment #11, Question 4 (see figure) Given the generic signaling pathway in the figure, match the letter with its corresponding descriptor below. A. B. C. D.

A. Ligand B. Receptor proteins C. Intercellular signaling proteins C. Effector proteins

Weekly Assignment #5 You have purified DNA from your recently deceased goldfish. Which of the following restriction nucleases would you use if you wanted to end up with DNA fragments with an average size of 70 kilobase pairs (kb) after complete digestion of the DNA? The recognition sequence for each enzyme is indicated in the right-hand column. A. NotI GCGGCCGC B. Sau3AI GATC C. BamHI GGATCC D. XzaI GAAGGATCCTTC

A. NotI GCGGCCGC

Weekly Assignment #3 Consider an analogy between reaction-coupling and money. In a simple economy, barter provides a means of direct exchange of goods. For example, the owner of a cow may have excess milk and need eggs, whereas a chicken owner has excess eggs and needs milk. Provided that these two people are in close proximity and can communicate, they may exchange or barter eggs for milk. But in a more complex economy, money serves as a mediator for the exchanges of goods or services. For instance, the cow owner with excess milk may not need other goods until three months from now or may want goods from someone who does not need milk. In this case, the "energy" from providing milk to the economy can be temporarily "stored" as money, which is a form of "energy" used for many transactions in the economy. Using barter and money as analogies, describe two mechanisms that can serve to drive an unfavorable chemical reaction in the cell.

Energy can be stored and transferred in the form of goods. High energy chemical groups such as ATP, Acetyl-CoA and UDP-glucose, and high energy electrons such as NADH, NADPH and FADH2 temporarily store "money"/"energy" in order to drive unfavorable chemical reactions in the cell.

Explain how photosynthesis and respiration are two complementary processes

Energy stored in the chemical bonds in the organic molecules is extracted in living cells by a process of gradual or stepwise oxidation/controlled burning (respiration). Cell obtains energy by oxidation of organic molecules. Electron from water is charged by sun, given to CO2, reduced to sugar ----> photosynthesis. Sugar (electron is highly charged), sugar burned, electron released, energy stored in useful form, oxygen reduced into water again ------> cellular respiration

Arjun Clicker question If we added an extra layer to a caspase cascade, we would expect: A. Faster activation of the executioner caspases at the bottom of the cascade. B. Faster activation of initiator caspases. C. No change in caspase activation speed.

A. Faster activation of the executioner caspases at the bottom of the cascade.

Arjun Clicker question If a chemical treatment made the beta-tubulin in a cell hydrolyze its GTP to GDP more slowly we would expect the microtubules to: A. Grow from the plus end. B. Shrink from the plus end.

A. Grow from the plus end.

Midterm Questions The followings steps (not in order) are among steps used to clone insulin-encoding gene in E. coli to purify insulin. ligation of insulin gene with the vector Introduction of the recombinant vector onto competent E. coli known as transformation Amplification of insulin gene by PCR Digesting both vector and PCR-amplified gene by the same restriction endonuclease Selection of the recombinant E. coli cells that harbor the plasmid Affinity purification of the recombinant insulin Which of the following is the logic sequence of events to follow for cloning and purification of insulin? D. VI - II - I - III - IV - V A. III - IV - I - II - V - VI B. III - I - II - IV - V - VI C. I - II - VI - III - IV - V

A. III - IV - I - II - V - VI

Arjun Clicker question If cell had two mutations, one that slowed down Kinesin movement and the other that sped up Dynein movement, we would expect to see cargos shuttled along the microtubule network to be: A. More concentrated around the minus ends of the microtubules at the MTOC when compared to unmutated cells. B. More concentrated at the plus ends of microtubules at the cellperiphery when compared to unmutated cells. C. Similarly distributed to unmutated cells thanks to compensatoryeffects of the mutations.

A. More concentrated around the minus ends of the microtubules at the MTOC when compared to unmutated cells.

Midterm Questions Your friend works in a biotechnology company and has discovered a drug that blocks the ability of Ran to exchange GDP for GTP. What is the most likely effect of this drug on nuclear transport? A. Nuclear transport receptors would be unable to release their cargo in the nucleus. B. Nuclear transport receptors would be unable to bind cargo. C. Nuclear transport receptors would interact irreversibly with the nuclear pore fibrils. D. Nuclear transport receptors would be unable to enter the nucleus.

A. Nuclear transport receptors would be unable to release their cargo in the nucleus.

Midterm Questions Which of the following statements about restriction nucleases is FALSE? A. Restriction nucleases recognize specific sequences on single-stranded DNA. B. A reproducible set of DNA fragments will be produced every time a restriction nuclease digests the same piece of DNA. C. Some restriction nucleases cut in a staggered fashion, leaving short, single-stranded regions of DNA at the ends of the cut molecule. D. Restriction endonucleases like CRISPR-Cas9, both protect bacteria from foreign DNA.

A. Restriction nucleases recognize specific sequences on single-stranded DNA.

Weekly Assignment #7 A geneticist has devised a strategy to study protein translocation into the ER in yeast cells. She is interested in two different signal sequences that operate via slightly different translocation mechanisms. Using genetic engineering, she has fused the first signal sequence to a protein whose cytosolic expression is absolutely necessary for cell survival in the selective medium but is inactive when in the ER. In the same cell, she has also fused the second signal sequence to a toxic protein whose cytosolic expression leads to cell lysis but is harmless when in the ER. Whereas wild-type cells undergo lysis upon the expression of these fusion proteins, she has been able to identify viable mutants, each of which has a loss-of-function mutation in a gene encoding a protein involved in membrane translocation. The products of these genes are probably ---------------- A. involved in the general transport of proteins into the ER, regardless of the type of signal sequence. B. involved in the transport of proteins with the first signal sequence but not the second one. C. involved in the transport of proteins with a novel signal sequence (i.e., neither the first signal sequence nor the second one). D. involved in the transport of proteins with the second signal sequence but not the first one.

B. involved in the transport of proteins with the first signal sequence but not the second one.

Weekly Assignment #10 The reason necrosis triggers an immune response is: A. it causes the formation of blebs which activate immune cells B. it is associated with a rupture of the plasma membrane that releases cytoplasmic constituents which activate immune cells. C. it leads to the expression of surface ligands that activate immune cells.

B. it is associated with a rupture of the plasma membrane that releases cytoplasmic constituents which activate immune cells.

Arjun Clicker question If cells were treated with a chemical inhibitor of flipase (XRP8) activity, we would expect cells undergoing apoptosis to: A. lose plasma membrane integrity. B. not form blebs. C. not have fragmented genomes

B. not form blebs.

Weekly Assignment #11, Question 7 (see figure) A hypothetical signaling pathway is shown in the graphic below. Signal perception is transduced into the production of a chemical output, shown in pink, which degrades over time. The concentration of the output over time for cells exposed to the signal during the period highlighted in orange is shown in the graph below as the green line. Predict how the change in the signaling pathway shown depicted the graphic below will affect the output production over time by selecting the correct graph. A. B. C. D.

C. Negative feedback would result in signal dampening.

Weekly Assignment #8, Question 8 (see figure) Consider the hypothetical cellular structure depicted below. Here one microtubule is fixed to the plasma membrane at its positive end, and the other is attached to the microtubule organizing center. The microtubule attached to the MTOC has kinesin motors tethered to it. Assumue that the MTOC is fixed in the center of the cell. What would you expect the outcome of the movement by the kinesin motor to be? 1. The cell membrane is pushed away from the MTOC. 2. The cell membrane is pulled closer to the MTOC. 3. Both microtubules bend to the right. A. 1 B. 3 C. 2

C. 2, As the tethered kinesin moves to the positive end of the microtubule not attached to the MTOC it will pull it towards the MTOC and thus pull the membrane down towards the MTOC as well.

Midterm Questions In 2001 the first human genome sequence and annotation were completed. Scientists were surprised from the results because --------------- A. Genes were found to represent about 2% only of the whole genome. B. Number of protein-coding genes was much less than what they expected. C. All are reasons for their surprise. D. The size of the genome did not reflect the size of the organism as compared to other mammals. E. About 50% of the genome was repeated sequences.

C. All are reasons for their surprise.

Weekly Assignment #8 Intermediate filaments are made from alpha helical monomers that are assembled into a rope like structures. A mutation occurs to the genome which leads to a change in this monomer such that it forms three more bonds in the coiled coil dimer. How would this mutation affect the eventual tissue formed from such cells? 1. It would result in an increase in the stiffness of the network and change the shape of the cells and the resulting tissue. 2. It would result in an increase in the strength of the network and lead to a tissue in which the cells were more tightly linked together. 3. It would reduce the capacity of the monomers to be able to form fibers and result in a weaker network leading to a tissue where the cells were more loosely attached to one another. A. 3 B. 1 C. 2

C. 2, Increasing the number of non-covalent bonds between monomers would increase the strength of the resulting intermediate fibers and enhace their capacity to confer structural strength to the cells in a tissue.

Weekly Assignment #5 You collect the following kinetic data for your favorite enzyme: [S] 1 2 3 4 5 6 10 20 30 [V] 1 10 20 34 36 37 38 39 41 What is the approximate Km? A. 20 B. 40 C. 3 D. 10

C. 3

Weekly Assignment #8, Question 6 (see figure) Figure A shows how the movement of dynein causes the flagellum to bend. If instead of the normal situation, the polarity of the adjacent doublet of microtubules were to be reversed (see Figure B), what do you predict would happen? 1. No bending would occur. 2. Bending would occur exactly as diagrammed in Figure 17-24A. 3. Bending would occur, except that the right microtubule doublet would move down relative to the left one. 4. The two microtubule doublets would slide away from each other. A. 2 B. 1 C. 3 D. 4

C. 3, Because the polarity of the microtubule bundle is reversed, the dynein motors should walk in the opposite direction from the normal situation diagrammed in Figure 17-40A. Microtubule sliding would occur if the linking proteins were absent, which is not true here.

Weekly Assignment #8 Which of the following statements regarding dynamic instability is FALSE? 1. Each microtubule filament grows and shrinks independently of its neighbors. 2. The GTP cap helps protect a growing microtubule from depolymerization. 3. GTP hydrolysis by the tubulin dimer promotes microtubule shrinking. 4. The newly freed tubulin dimers from a shrinking microtubule can be immediately captured by growing microtubules and added to their plus end. A. 3 B. 2 C. 4 D. 1

C. 4, A newly dissociated tubulin dimer will be bound to GDP; this GDP will need to be exchanged for GTP before it can be added to a newly growing microtubule.

Weekly Assignment #9 What would be the most obvious outcome of repeated cell cycles consisting of S phase and M phase only? 1. The cells would not be able to replicate their DNA. 2. The mitotic spindle could not assemble. 3. The cells would get larger and larger. 4. The cells produced would get smaller and smaller. A. 1 B. 2 C. 4 D. 3

C. 4, The cells produced would get smaller and smaller, as they would not have sufficient time to double their mass before dividing.

Arjun Clicker question, page 20 (see figure) Which cell cycle phase corresponds to each of populations measured by cytometry? A = S, B = G1, C = G2,M B. A = G2, M, B = S, C = G1 C. A= G1, B = S, C = G2, M

C. A= G1, B = S, C = G2, M

Weekly Assignment #2 Gene duplication can give rise to homologous genes that are part of gene families. For example, there are six actin genes in the genome of most mammalian species. In humans, the ACTB gene, which encodes a cytoskeletal actin, is expressed ubiquitously, while ACTC1 is expressed mainly in cardiac cells. Although bacteria lack the eukaryotic cytoskeletal organization, the bacterial MreB gene bears recognizable sequence similarity to mammalian actin genes and codes for a protein that is similar to actin in structure and function. Which of the following statements is true about these genes? A. ACTB is paralogous to both ACTC1 and MreB. B. MreB is orthologous to ACTB but not to ACTC1. C. ACTB is paralogous to ACTC1 but not to MreB. D. ACTB is orthologous to ACTC1 but not to MreB. E. ACTB is homologous to ACTC1 but not to MreB.

C. ACTB is paralogous to ACTC1 but not to MreB.

Midterm Questions, Question 44 (see figure) The following schematic graph shows the result of two quantitative RT-PCR experiments. Total mRNA from two tissue samples (1 and 2) was isolated and subjected to RT-PCR using primers designed to amplify the tissue-specific genes (1 and 2). Added to the reaction was a fluorescent dye that fluoresces only when bound to double-stranded DNA. According to the graph, which tissue has a higher level of this mRNA? By how much? A. About 1000-fold higher in tissue 2 B. About 2-fold higher in tissue 1 C. About 1000-fold higher in tissue 1 D. About 2-fold higher in tissue 2

C. About 1000-fold higher in tissue 1

Arjun Clicker question The burst of M-cyclin activity is generated at the start of M phase by: A. Rapid transcription and translation of the M cyclin B. Association of the M-cyclin with its cognate CDK C. Activity of a phosphatase that removes inhibitory phosphates D. Degradation of an inhibiting kinase

C. Activity of a phosphatase that removes inhibitory phosphates

Weekly Assignment #5 The use of Insulin hormone to purify its receptor is an example of -------------- A. Gel filtration chromatography B. Ligan-mediated chromatography C. Affinity chromatography D. Ion exchange chromatography

C. Affinity chromatography

Weekly Assignment #7 Which of the following statements about transport into mitochondria and chloroplasts is FALSE? A. Signal peptidase will remove the signal sequence once the protein has been imported into these organelles. B. The signal sequence on proteins destined for these organelles is recognized by a receptor protein in the outer membrane of these organelles. C. After a protein moves through the protein translocator in the outer membrane of these organelles, the protein diffuses in the lumen until it encounters a protein translocator in the inner membrane. D. Proteins that are transported into these organelles are unfolded as they are being transported.

C. After a protein moves through the protein translocator in the outer membrane of these organelles, the protein diffuses in the lumen until it encounters a protein translocator in the inner membrane.

Weekly Assignment #4 From the amino acid chart shown in the lecture and presented in the slides, which of the following stretches of amino acid residues would you expect to find in the interior of protein molecules? A. Gly-Lys-Ser-Pro-Thr B. Ala-Asp-Asp-Tyr-Arg C. Ala-Val-Leu-Ile-Trp D. Phe-Glu-Gln-Glu-Asn

C. Ala-Val-Leu-Ile-Trp

Midterm Questions Which of the following enzymes is used in RT-PCR when using RNA as a template for PCR? A> CRISPR-Cas9 B. RNA polymerase C. Reverse transcriptase D. Restriction endonuclease

C. Reverse transcriptase

Weekly Assignment #11 Which of the following statements is TRUE? A. To function, all extracellular signal molecules must be transported by their receptor across the plasma membrane into the cytosol. B. A cell-surface receptor capable of binding only one type of signal molecule can mediate only one kind of cell response. C. Extracellular signal molecules that are hydrophilic must bind to a cell-surface receptor so as to signal a target cell to change its behavior. D. Any foreign substance that binds to a receptor for a normal signal molecule will always induce the same response that is produced by that signal molecule on the same cell type.

C. Extracellular signal molecules that are hydrophilic must bind to a cell-surface receptor so as to signal a target cell to change its behavior. A hydrophilic molecule cannot diffuse across the membrane and it can therefore only affect a cell if it binds to a cell-surface receptor. Most signal molecules remain bound to the extracellular domain of the receptor, whereas the intracellular domain mediates signal transduction; although many signal molecules are endocytosed with their receptor, they remain inside membrane-bounded compartments and are therefore not transported into the cytosol. A cell-surface receptor capable of binding only one type of signal molecule can stimulate more than one kind of cell response, depending on the types of intracellular signaling pathway it activates. Foreign substances that bind to a receptor for a normal signal molecule can sometimes induce the same response as the natural signal molecule, but in other cases they can block the binding of the natural signal molecule without activating the receptor.

Midterm Questions Indicate whether each of the following transport processes occurs via the mechanisms described as gated transport (G), membrane translocator (T), or vesicular transport (V). Your answer would be a four-letter string composed of letters G, T, and V only, e.g., VTTTG. ( ) Import into nucleus ( ) Export to cell exterior ( ) Import into thylakoid lumen of chloroplast ( ) Return from Golgi to ER A. V-T-G-T B. V-T-T-G C. G-V-T-V D. G-T-V-G

C. G-V-T-V

Iclicker Class 10 Based on what you have learned about antibodies, which of the following do you think is not a use of monoclonal antibodies? A. pregnancy test B. Blood and tissue type C. Identification of chromosome normality D. Organ transplant rejection E. Immunotherapy

C. Identification of chromosome normality

Arjun Clicker question If a mutation reduced the ATPase activity of actin monomers (the rate at which they convert ATP to ADP) we would expect: A. Monomers to be added to the plus end slower leading to shorter actin fibers compared to unmutated cells. B. Monomers to be added to the minus end slower leading to shorter actin fibers compared to unmutated cells. C. Monomers to fall off the minus end slower leading to longer actin fibers compared to unmutated cells.

C. Monomers to fall off the minus end slower leading to longer actin fibers compared to unmutated cells.

Weekly Assignment #5 Which of the following cell is made deficient of hypoxanthine guanyl phosphoribosyl transferase (HGPRT) enzyme for production of monoclonal antibody? A. No need to have HGPRT mutant cells while producing monoclonal Ab B. Hybrid cells C. Myeloma cells D. B cells

C. Myeloma cells

Arjun Clicker question If a mutation caused a Hox gene to not be expressed in a particular segment of a developing embryo we would expect: A. A change in the morphogen gradient across the embryo B. A duplication of the segment of the body whose development the hox gene regulates C. No development of the segment of the body that the hox gene regulates

C. No development of the segment of the body that the hox gene regulates

Iclicker Class 17 You discovered a drug that blocks the ability of nuclear transport receptors (importins) to recognize nuclear localization signals. What is the most likely effect of this drug on nuclear transport? A. nuclear transport receptors would be unable to enter the nucleus B. nuclear transport receptors would be unable to release their cargo in the nucleus C. No nuclear proteins will be imported to the nucleus D. Nuclear transport receptors would interact irreversibly with the nuclear pore fibrils.

C. No nuclear proteins will be imported to the nucleus

Midterm Questions Which of the following is not true regarding mitochondria and chloroplasts? A. Chloroplasts are only found in photosynthetic cells, whereas mitochondria are found in animal and plant cells. B. Both mitochondria and chloroplasts have two membranes C. Only mitochondria are thought to have genome and arisen via endosymbiosis D. Chloroplasts contain pigment molecules that absorb sunlight and perform photosynthesis, while mitochondria do not absorb sunlight

C. Only mitochondria are thought to have genome and arisen via endosymbiosis

Midterm Questions Which of the following statements is true for proton motive force (PMF)? A. PMF across mitochondrial inner membrane composed solely of delta V. B. PMF across thylakoid membrane composed solely of delta V. C. PMF across thylakoid membrane composed solely of delta pH. D. PMF across mitochondrial inner membrane composed solely of delta pH

C. PMF across thylakoid membrane composed solely of delta pH.

Weekly Assignment #5 Which of the following methods would be the most suitable to assess the relative purity of a protein in a sample you have prepared? A. gel-filtration chromatography B. Western blot analysis C. Polyacrylamide gel electrophoresis D. ion-exchange chromatography

C. Polyacrylamide gel electrophoresis

Arjun Clicker question, page 41 (see figure) A. Negative, Negative, Positive, Positive B. Positive, Negative, Positive, Negative C. Positive, Negative, Negative, Positive D. Positive, Negative, Negative,Negative

C. Positive, Negative, Negative, Positive

Weekly Assignment #5 Which of the following statements about restriction nucleases is FALSE? A. A reproducible set of DNA fragments will be produced every time a restriction nuclease digests a known piece of DNA. B. Some bacteria use restriction nucleases as protection from foreign DNA. C. Restriction nucleases recognize specific sequences on single-stranded DNA. D. Some restriction nucleases cut in a staggered fashion, leaving short, single-stranded regions of DNA at the ends of the cut molecule.

C. Restriction nucleases recognize specific sequences on single-stranded DNA.

Weekly Assignment #3 Generate an analogy to describe the cell as the simplest unit of life to somebody who has not studied biology. Be sure to incorporate the observable features of living organisms, which distinguishes them from inanimate objects.

Cells are the simplest units of life and can be described as small individual factories. For instance, the plasma membrane helps to ship and recieve items in and out of the cell, and act as security. The nucleus is the president of the company, and tells the workers what and when to build things based off of the blueprints the president has. As a feature of living organisms this means that the cell is highly complex and very organized. The endoplasmic reticulum assemble components. The observable features of living organisms like cells also include maintaining homeostasis, acquiring and utilizing energy from the environment, carrying out chemical reactions, responding to stimuli, adapting to the environment. Additionally, to be categorized a sa living organism you need to have genetic material and the means to use it, reproduce, and grown and develop from simple beginnings. These observable features distinguish cells from inanimate objects, and make them the simplest unit of life.

Weekly Assignment #5, Question 1 (see figure) In the following diagram, which kind of inhibition is represented? A. Non-competitive inhibition B. Uncompetitive inhibition C. Mixed inhibition D. Competitive inhibition

D. Competitive inhibition

Weekly Assignment #9 Which of the following events does NOT usually occur during interphase? 1. Cells grow in size. 2. The nuclear envelope breaks down. 3. DNA is replicated. 4. The centrosomes are duplicated. A. 1 B. 3 C. 4 D. 2

D. 2

Weekly Assignment #8 Which of the following statements about the cytoskeleton is FALSE? 1. The cytoskeleton is made up of three types of protein filaments. 2. The cytoskeleton controls the location of organelles in eukaryotic cells. 3. Covalent bonds between protein monomers hold together cytoskeletal filaments. 4. The cytoskeleton of a cell can change in response to the environment. A. 2 B. 4 C. 1 D. 3

D. 3, The protein monomers of the cytoskeleton are held together by noncovalent interactions between the protein monomers. All the other statements are true.

Weekly Assignment #8 The hydrolysis of GTP to GDP carried out by tubulin molecules: 1. provides the energy needed for tubulin to polymerize. 2. occurs because the pool of free GDP has run out. 3. tips the balance in favor of microtubule assembly. 4. allows the behavior of microtubules called dynamic instability. A. 1 B. 2 C. 3 D. 4

D. 4, The hydrolysis of GTP to GDP occurs after a GTP-bound tubulin molecule is incorporated into a microtubule, and it makes the microtubule more susceptible to disassembly. It is the resulting switch in microtubule stability that gives rise to the phenomenon known as dynamic instability.

Weekly Assignment #3 Because there are four different monomer building blocks that can be used to assemble RNA polymers, the number of possible sequence combinations that can be created for an RNA molecule made of 100 nucleotides is ---------------- A. 4100. B. 4 × 100. C. 100/4. D. 4^100

D. 4^100

Midterm Questions, Question 50 (see diagram) In the following simplified diagram of the Calvin cycle, which step (1 to 5) is catalyzed by the abundant enzyme Rubisco? A. 4 B. 3 C. 2 D. 5 E. 1

D. 5

Weekly Assignment #2 Prokaryotic cells do not possess__________ A. membrane bilayers. B. ribosomes. C. replication machinery. D. a nucleus.

D. A nucleus

Midterm Questions Activated energy carriers are small molecules that can diffuse rapidly and be used to drive biosynthetic reactions in the cell. Their energy is stored in a readily transferable form such as high-energy electrons or high-energy chemical groups. Which of the molecules below donates a chemical group rather than electrons? A. NADPH B. NADH C. FADH2 D. ATP

D. ATP

Weekly Assignment #4 The process of generating monoclonal antibodies is labor intensive and expensive. An alternative is to use polyclonal antibodies. A subpopulation of purified polyclonal antibodies that recognize a particular antigen can be isolated by chromatography. Which type of chromatography is used for this purpose? A. ion-exchange B. all can be used C. gel-filtration D. Affinity purification

D. Affinity purification

Arjun Clicker question How does the proteolytic activity of caspases activate apoptotic processes? A. Cleavage of proteins inhibiting enzymes that disassemble cellular components. B. Cleavage of plasma membrane lipids. C. Removal inactivating domains from proteins that drive apoptotic processes via cleavage. D. Both A and C

D. Both A and C

Arjun Clicker question What are the benefits of Caspase being a Zymogen? A. Does not rely on functional transcription and translation. B. Decreases the immune response due to cell death. C. Enables a rapid response. D. Both A and C.

D. Both A and C.

Arjun Clicker question Which of the following are outcomes attributable to a scaffold in a signaling pathway? A. They promote signal propagation down the pathway. B. They inactivate other signaling pathways C. They prevent cross activation of signaling pathways D. Both A and C.

D. Both A and C.

Arjun Clicker question The extrinsic pathway is similar to the intrinsic pathway in that it: A. is initiated by an extracellular signal. B. is driven by the formation of an oligomerizing complex that co-localizes initiator caspases C. uses similar or the same executioner caspases. D. Both B and C. E. Both A and B.

D. Both B and C.

Midterm Questions Which of the following kind of plants will do photosynthesis better in hot/dry environment? Why? A. C3 plants because they have mechanism to overcome photorespiration. B. C4 plants because they do not have mechanism to overcome photorespiration. C. CAM plants because they do not have mechanism to overcome photorespiration. D. C4 plants because they have mechanism to overcome photorespiration

D. C4 plants because they have mechanism to overcome photorespiration

Midterm Questions Once carbon has been oxidized to __________, its most stable form, it can only cycle back into the organic portion of the carbon cycle through __________. A. CO2; respiration. B. CH3; combustion. C. CO; reduction. D. CO2; photosynthesis.

D. CO2; photosynthesis.

Iclicker Class 10 Some of the enzymes that oxidize sugars to yield usable cellular energy (for example ATP) are regulated by phosphorylation. For these enzymes, would you expect the inactive form to be the phosphorylated form or the dephosphorylated form?

Phosphorylated

Where does heat energy come from?

Photosynthetic cells take advantage of the first tlaw of thermodynamics and convert light energy of the sun into chemical energy stored in organic molecules Some of the chemical energy is converted into thermal motion (heat energy), (respiration) in all forms of life

Weekly Assignment #10 In under 100 words describe the two reasons for cells in our bodies to be programmed to die.

Programming cells to die serves multiple purposes. The first is to remove "bad" cells due to irreparable damage, cancer, and pathogen infections. The second is to remove cells that are mislocated, misconnected, or excessive. This is a normal part of both development and multicellular life.

Weekly Assignment #3 Two college roommates do not agree on the best way to handle the clutter piled up in your dorm room. Roommate 1 explains that chaos is inevitable, so why fight it? Roommate 2 counters that maintaining an organized environment makes life easier in many ways, and that chaos is not inevitable. What law of thermodynamics drives the thinking of Roommate 1? What thermodynamic argument can be used to support Roommate 2?

Roommate one's thinking is by the second law of thermodynamics, which is that things in the universe move spontaneously towards the arrangement that have the greatest probability (or the highest disorder). Roommate 2 can counter that by arguing that living organisms are highly ordered and cells defy the second law of thermodynamics, so chaos is not inevitable.