BIO 3450 Final Questions

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10. Dendritic cells, macrophages and other cells of the innate immune system recognize potential pathogens by___ a. receptors that recognize common pathogen-associated molecular patterns such as bacterial flagellin and double-stranded RNA b. cell surface immunoglobulins that are specific for particular foreign antigens c. chemokine receptors that respond to secreted bacterial signaling molecules d. MHC molecules binding bacterial and viral peptides e. all of the above

10. In apoptosis, Caspases function as 'Executioners'. Which one does describe the function/feature of them? a. Caspases are a family of cysteine proteases. b. Major caspase in C. elegans is CED 9. c. Among mammalin caspases, caspase 9 functions as effector caspase. d. Red blood cells use caspase-mediated apoptotic pathway to maintain homeostatis.

10. Which is activated when PI-3 kinase (PI-3K) phosphorylates phosphatidylinositol 4-phosphate to phosphatidylinositol 3,4-diphosphate? a) activation of PKB and PDL1 b) ADAM 10 cleavage of Notch protein c) phosphorylation of Smad2/3 and assembly of the Smad2/3-Smad4 complex d) translocation of pro-SREBP from the ER to the Golgi by Sec24 binding to SCAP e) phosphorylation and dimerization of STAT proteins

11. Newly synthesized membrane phospholipids are first inserted in ______ a) the cytosolic leaflet of the endoplasmic reticulum b) the exoplasmic leaflet of the endoplasmic reticulum c) the cytosolic leaflet of the plasma membrane d) either leaflet of the endoplasmic reticulum e) either leaflet of the plasma membrane

11. Something is out of order in this sequence of events—what? Growth factor receptor with bound growth factor → GRB2 → SoS → Ras-GDP → ras-GTP → Active Raf → MAP kinase → MEK →phosphorylation of nuclear transcription factor(s) a) the order should be: MEK → MAP kinase b) the order should be: Ras-GDP → SoS c) the order should be: Raf → ras-GTP d) nothing is out of order

12. Which of these molecules would most rapidly cross cell membranes via simple diffusion? a) ethylene (H2C=CH2) b) ethanol c) acetate d) H+ e) H2O

13. One common laboratory test for cell death is to stain for membrane lipids that are normally present only on the cytoplasmic leaflet to appear on the exoplasmic leaflet (the cell surface). What such membrane lipid could be used to identify dying cells? a. phosphatidyl serine b. cholesterol c. sphingomyelin d. phosphatidyl choline

13. Which of the following is the term used to describe a thin, sheet-like meshwork of extracellular matrix components that can be found in epithelial tissue? a) basal lamina b) basement membrane c) gap junction d) cell wall

15. 5'-UAUAUGGCAAGACAU....3' What are the first 3 amino acids that will be translated from this mRNA? a. Met-Ala-Arg b. His-Met-Ala c. His-Ile-Tyr d. Lys-Asn-Gly

15. This figure shows a construct for replacement of gene X. Recall that cells that express tkHSV are sensitive to ganciclovir. Cells that have knocked out Gene X (replaced the wild type copy of gene X with the neor disrupted copy of gene X) will have what phenotype? a. resistant to neomycin, resistant to ganciclovir b. resistant to neomycin, sensitive to ganciclovir c. sensitive to neomycin, resistant to ganciclovir d. sensitive to neomycin, sensitive to ganciclovir

15. Which cells produce myelin sheaths? a) Schwann cells and oligodendrocytes b) astrocytes c) afferent neurons d) interneurons

16. Pyruvate is a common intermediate in the metabolism or synthesis of which types of molecules? a. glucose and some amino acids b. glucose and fatty acids c. fatty acids and some amino acids d. glucose and nitrogenous bases in DNA and RNA

16. Something is out of order in this sequence of events—what? Growth factor receptor with bound growth factor → GRB2 → SoS → Ras-GDP → ras-GTP → Active Raf → MAP kinase → MEK →phosphorylation of nuclear transcription factor(s) a. the order should be: MEK → MAP kinase b. the order should be: Ras-GDP → SoS c. the order should be: Raf → ras-GTP d. nothing is out of order

16. The Class I MHC protein cannot fold properly until it partners with another small protein called beta-2-microglobulin and binds an antigen molecule. What proteins bind to the nascent protein in the ER lumen to prevent it from misfolding and aggregating? a. chaperones like calnexin and calreticulin b. chaperonin complexes made of Hsp60 c. ubiquitin ligases d. BiP

17. The actin filaments at the leading edge of the migrating cell (shown in the region labeled #17 in this diagram) form a complex network of filaments called the _______________. a) Lamellipodium b) Stress fibers c) Flagellium d) Sarcollium e) Linoleum

17. The deltaG for H+ translocation across the mitochondrial inner membrane is about -4.8 kcal/mol, enough for the movement of 3 H+ to power the synthesis of 1 ATP by the F0/F1 ATPase. However, the 1 pH unit concentration difference across the membrane accounts for only -1.4 kcal/mol. What, then, accounts for the rest of the free energy change? a. The large electrical potential across the mitochondrial inner membrane b. ATP hydrolysis c. Symport with Cl- ions d. The high permeability of the membrane to H+ ions

17. What does the Cas9:gRNA complex do by itself? a. it cleaves DNA at sites where the guide RNA forms an RNA:DNA duplex b. it mediates non-homologus end-joining to repair double-strand DNA breaks where the ends match parts of its guide RNA c. it performs homologous recombination of the target DNA sequence with its guide RNA d. it uses the guide RNA as a template to edit the target DNA sequence e. it can do all of the above

18. In the absence of oxygen, what molecules can the cell metabolize to make ATP? a. glucose b. pyruvate c. alanine d. acetyl-coA e. all of the above

18. Which of these molecules would most rapidly cross cell membranes via simple diffusion? a) O2 b) glycerol c) pyruvate d) K+ e) H2O

19. In normal cellular respiration pyruvate ____ a) enters the mitochondria and is oxidized to CO2 and acetyl-CoA b) stays in the cytoplasm to be reduced by NADH to produce lactic acid and NAD+ c) stays in the cytoplasm and is oxidized to CO2 and acetyl-CoA d) enters the mitochondria to be reduced by NADH to produce lactic acid and NAD+

19. In the mouse embryo, pluripotent stem cells are found in the: a) inner cell mass. b) trophectoderm. c) zona pellucida. d) blastocoel.

19. Which of the following does NOT function as a second messenger? a. PKA b. cAMP c. DAG d. IP3

2. Which of the following amino acids does NOT have a sidechain hydroxyl group, therefore, cannot be the amino acid that is being phosphorylated by a protein kinase in the diagram on the right? a) leucine b) serine c) threonine d) tyrosine e) pick this if all of the above amino acids have a hydroxyl group on their sidechain

20. NADH and FADH2 are both reduced electron carriers produced by the citric acid cycle. The redox potential of NADH is -0.320 V. FADH2 redox potential is +0.03 V. Which compound has greater reducing power (potential energy)? a) NADH b) FADH2

20. What would happen if a chromosome lost one of its telomeres? a. the chromosome end would get shorter during each round of DNA replication b. the chromosome would not segregate properly during mitosis and meiosis c. the chromosome would not replicate during S phase d. all of the above

21. Upon opening of the Na+ and K+ channels, there is net movement of cations but: a) more Na+ move inside than K+ move outside, so the there will be a transient net negative charge on the outside face of the plasma membrane. b) more Na+ move inside than K+ move outside, so the there will be a transient net positive charge on the outside face of the plasma membrane.

22. ( A ) phosphorylate ( B ) and free NF-κB subunit, p65 and p50. Name them in order from A to B. a. I-κB kinases, I-κBα b. BMPR-I, Smad4 c. PI3 kinases, PKB d. TGF-β receptor, Smad3

22. A diagram of a voltage-gated ion channel in the resting state is shown on the right in case this helps you with this question. The channel opens when the event described in question 21 happens because_____. a) voltage-sensing -helices are attracted to the exterior of the plasma mambrane and the protein conformation change opens the gate. b) voltage-sensing -helices are attracted to the inside of the plasma mambrane and the protein conformation change opens the gate

22. Mammalian cells in culture have been transfected with the plasmid shown at right. The transfected cells will: a. Express the spCas9 protein for a few days, but lose the plasmid as they divide by mitosis b. Replicate and maintain this plasmid and continue expression of the spCas9 protein through many rounds of cell division c. Transcribe the spCas9 gene but not translate it because it lacks introns d. Integrate the spCas9 gene into one of its chromosomes

23. If the proton gradient across the inner mitochondrial membrane is depleted via H+ transporters that allow facilitated diffusion of H+ ions, what will happen to the rate of ATP synthesis? a. the rate of ATP synthesis will decline b. the rate of ATP synthesis will stay the same c. the rate of ATP synthesis will increase

23. The catalytic activity of spliceosomes is performed by: a. snRNAs b. snoRNAs c. a spliceosomal protein called RNA ligase d. miRNAs e. siRNAs

24. Actin assembly has three steps, nucleation, elongation, and steady state. Which step takes the most of the time to occur? a. Nucleation b. Elongation c. Steady state d. all of the above

24. What causes condensation of chromatin into transcriptionally inactive heterochromatin? a. methylation of lysines on histone tails b. acetylation of lysines on histone tails c. ubiquitination of lysines histone tails d. phosphorylation of serines on histone tails

25. Cytotoxic T cells conduct surveillance against intracellular pathogens by___ a. inspecting the antigens presented on Class I MHC molecules b. inspecting the antigens presented on Class II MHC molecules c. inspecting cell surfaces for proteins bound by immunoglobulins d. inspecting cell surfaces for non-self MHC molecules

26. Vesicles in retrograde transport from the Golgi to the ER have what kind of coat? a) COPI b) COPII c) clathrin/AP1 d) clathrin/AP2 e) AP3

26. When membrane depolarization reaches the synapse, what connects the depolarization to release of neurotransmitters? a) a Ca2+ channel is opened and Ca2+ signals the secretory pathway b) the voltage is dissipated as a spark that opens holes in the membrane for neurotransmitters to leak out. c) a Na+ co-transporter is activated and as Na+ floods into the cell via the last channels, the Na+ returns to the neuron in exchange for the neurotransmitter that is released (i.e., via a Na+/neurotransmitter antiport system).

28. Many of the sensors for small molecules activate ion channels as part of the signaling mechanism, but for some (such as olfactory receptors and taste receptors for sweet, bitter, and umami ligands), the initial signaling mediator (i.e., immediately after the receptor binds it's ligand) is _______. a) activation of a G-protein b) activation of a protease to cleave the cytoplasmic domain and release the signaling mediator c) internalization of the ligand, it's association with a cytosolic binding protein, then import into the nucleus d) addition of a fatty acyl-group to the receptor to convert it from an extracellular protein to a protein associated with the plasma membrane

29. Early in mitosis the nuclear membrane seems to disappear, which is due to ____________ of the nuclear lamins and retraction of the nuclear membrane lipids and most other components into _________. a) phosphorylation..................the endoplasmic reticulum b) phosphorylation..................lysosomes c) dephosphorylation..................the endoplasmic reticulum d) dephosphorylation..................lysosomes

29. If the polyA tail of an mRNA is deleted, what will be the consequence? a. The mRNA will not be translated as efficiently b. The mRNA will be protected from degradation c. The mRNA will be rapidly degraded by a 5'->3' exonuclease d. The mRNA will return to the nucleus

3. P53 gene is an important tumor suppressor gene that is mutated in 50% of all tumors. Which of the following statement about P53 is INCORRECT? a) DNA damage triggers P53 degradation. b) P53 activates C D K I P21. c) P53 is a transcription factor. d) Phosphorylation of P53 by A TM/A TR stabilizes P53.

3. You learn that a protein you are studying has a basic helix-loop-helix (bHLH) domain. You therefore suspect that: a) the protein binds to DNA b) the protein binds a zinc ion c) the protein functions as a monomer d) all of the above

30. Which of the following statement regarding collagen is FALSE? a) Collagen is elastic thus allowing connective tissue to be stretched extensively. b) Collagen fibers are formed by triple helix of collagen proteins. c) Collagen is the major component in tendon and cartilage. d) Collagen can be cleaved by metalloproteinases, such as collagenase

31. Plants also have a mechanism that allows molecules to pass through complex channels connecting the cytosols of adjacent cells. These channels are called ____. a) plasmodesmata b) exosomes c) phytoconnexins d) fillipodia

33. Which end of a microtubule is attached to the MTOC? a. the (-) end b. the (+) end c. both can bind

34. Epo and the Epo receptors regulate ( ). a. how many red cells are made by the body b. contraction of smooth muscle cells c. movement of fluids d. cell motility

34. Which of these transposable elements encode a transposase? a. DNA transposons b. LINEs c. SINEs d. endogenous retroviruses e. LTR retrotransposons

35. If Ras was genetically mutated so that it would not hydrolyze bond GTP (but its other structural features were normal), which of the following do you think would occur? a. Ras would always be in the "on" state and bind to Raf, etc. b. Ras would always be in the "off" state and not participate in cell regulation c. Ras function would not be affected by this mutation

35. Which of the attachments of sister chromatids to the mitotic spindle shone in the diagram to the right will generate the correct tension for chromosome segregation and completion of mitosis? a) amphitelic attachment b) merotelic attachment c) syntelic attachment d) monotelic attachment

35. Which presents mainly cellular antigens (such as dysfunctional proteins)? a) MHC class I b) MHC class II c) CD1

38. What part of a chromosome ensures proper segregation in cell division? a. centromeres b. telomeres c. origins of DNA replication d. the short arm e. the long arm

4. The diagram shows you the exocytosis of neurotransmitters. What triggers the exocytosis? a) action potential triggerd Ca2+ influx b) molecules secreted by astrocytes c) interactions between the dendrite and the axon at the synaptic cleft d) clathrin mediated membrane fusion

4. Which of the following DNA or chromatin modifications are associated with heterochromatin? a. cytosine methylation at CpG sites and deacetylated histones b. unmethylated cytosines at CpG sites and acetylated histones c. both cytosine methylation at CpG sites and acetylated histones d. unmethylated cytosines at CpG sites and deacetylated histones

40. Microtubule (+) ends is exposed with ( A), whereas (-) end is exposed with ( B ). Name them from A to B. a. β-tubulin, α-tubulin b. α-tubulin, β-tublin

42. Development of the neural tube occurs early in vertebrate development (for humans, the fourth week of pregnancy—i.e., 28th day after conception) and is sensitive to deficiencies in ____, which is why it is important to maintain adequate amounts of this nutrient, such as by supplementation at least one month before conception and continuing until at least two months after conception. a) folate b) vitamin B2 c) carnitine d) chromium e) chocolate

46. During signal transduction, which of the following is NOT a method of signal amplification? (a) each ligand can bind to two receptors at the same time. (b) each pair of ligand bound receptor can activate multiple downstream effectors (c) each activated enzyme can work on many substrates (d) None of the above

48. Which is one of the first things that happens when EGF is bound by the EGF receptor, and is a common feature for many receptor tyrosine kinases (RTKs)? (a) the EGF-EGFR receptor complex is dimerized. (b) the EGF-EGF receptor complex converts ATP into cAMP. (c) the EGF-EGF receptor complex is translocated to the nucleus. (d) the EGF-EGF receptor complex is endocytosed.

5. 5'-UAUAUGGCAAGACAU....3' What are the first 3 amino acids that will be translated from this mRNA? a. Met-Ala-Arg b. Tyr-Met-Ala c. Tyr-Ile-Tyr d. Cys-Arg-Thr e. Met-Ser-Cys

5. In many G-protein coupled signaling pathways, binding of the agonist to the receptor causes a conformation change in the receptor that is transmitted to the G-protein to cause GDP to be replaced by GTP, then dissociation of the Gα and Gβγ subunits to affect downstream effector(s). Which of the following statements about the subsequent events is NOT correct? a) The downstream effects are always induced by Gα and involve activation b) Some downstream effectors are inhibited by inhibitory subcategories of Gα c) Some downstream effectors are regulated by Gβγ d) Select this option of all of the above are correct

5. Which of the following nerve cells is responsible to form the blood-brain barrier? a) astrocytes b) microglia c) schwann cells d) ependymal cells

58. In MPF, the oscillation of the mitotic Cyclin is controlled by its degradation by _______. (a) APC (b) Cdh1 (c) CDK (d) Cdc14

6. Which RNA polymerase transcribes 18S and 28S ribosomal RNAs? a. pol I b. pol II c. pol III d. all of the above

6. Which eukaryotic RNA polymerase transcribes rRNAs? a. RNA pol I b. RNA pol II c. RNA pol III d. all of the above

6. Which of the following accurately describe the uptake of LDL cholesterol? a) the LDL binds to the LDL-receptor, which is internalized via clathrin-coated pits and vesicles. b) the LDL binds to the LDL-receptor, which is internalized via non-clathrin-coated pits and vesicles c) the LDL binds to the LDL-receptor, which is internalized via non-specific pinocytosis d) the LDL binds to the LDL-receptor, then the cholesterol is transferred to the outside of the plasma membrane and internalized via an ABC transporter e) the LDL binds to the extracellular matrix and is digested by secreted proteases to release the cholesterol

67. Which of the following correctly describes embryonic stem cells (ESCs)? (a) ES cells are derived from inner cell mass of mammalian blastula. (b) ES cells can give rise to all cell types in the embryo and are thus totipotent. (c) ES cells can be induced by applying several transcription factors to differentiated cells. (d) ES cells can grow into an animal in culture.

7. The LDL receptor and the transferrin receptor enter the cell by endocytosis, then: a. the vesicles undergo acidification. b. they fuse with the lysosome and everything (including the receptor) is degraded. c. the vesicles fuse with the nuclear membrane to release transcription factors. d. the vesicles dissolve, releasing their contents into the cytoplasm. e. all of the above are correct.

70. Which of the following correctly describes the interaction between stem cell and stem cell niche? (a) Stem cell niche helps with asymmetric cell division and provide signals to stem cell to suppress differentiation. (b) The mitotic spindle of stem cell always orients parallel to the stem cell niche. (c) Stem cell niche sometimes maintain their interaction with stem cell by forming tight junctions in between. (d) There is always signal from the stem cell niche to the stem cell, but never from stem cell back to stem cell niche.

8. Which membrane lipids are asymmetrically distributed between the exoplasmic and cytosolic leaflets of the plasma membrane? a) phosphatidylcholine on the exoplasmic face, phosphatidylserine on the cytosolic b) phosphatidyserine on the cytosolic face, phosphatidylcholine on the cytosolic c) phosphatidylcholine on the exoplasmic face, sphingomyelin on the cytosolic d) sphingomyelin on the exoplasmic face, phosphatidylcholine on the cytosolic

8. Which of the following is TRUE for the iPS (induced pluripotent stem cells)? a) They are induced by adding defined transcription factors. b) They are derived from inner cell mass. c) They are derived from adult stem cells. d) They are induced by nuclear transfer.

8. Which of the following is the function of the mitotic Cyclin B? a) activates CDK1 b) separate the sister chromatids c) phosphorylates cdh1 d) dephosphorylates MPF

8. Which sequence element(s) is or are present in promoters of genes that are transcribed at high levels? a. TATA box b. Initiator c. CpG islands d. both a) and b) e. both a) and c)

11. What do induced pluripotent stem cells and embryonic stem cells have in common? a) they are both derived from blastocyst stage embryos b) they both express SOX-2 and OCT-4 c) they are both totipotent d) all of the above e) none of the above

12. Fatty acid biosynthesis uses what common intermediate found in cellular metabolism? a. pyruvate b. acetyl-CoA c. citric acid d. succinyl-CoA

12. Which is activated by binding of the protein to the Delta protein of an adjacent cell? a) activation of PKB and PDL1 b) ADAM 10 cleavage of Notch protein c) phosphorylation of Smad2/3 and assembly of the Smad2/3-Smad4 complex d) translocation of pro-SREBP from the ER to the Golgi by Sec24 binding to SCAP e) phosphorylation and dimerization of STAT proteins

12. Which of the following primers will have the highest annealing/melting temperature when bound to their complementary DNA sequence? a. AAGATTCAGT b. AGGCGCTACG C. TCAATGAGAC d. TCGATCTGTG

13. Researchers use the ( ) technique to measure the membrane potential. a. Electron microscope b. Patch clamp c. Brainbow d. Optogenetic

13. What type of bonding is important for formation of secondary structure? a) hydrogen bonds between amino acid side chains b) hydrogen bonds between peptide backbone atoms c) ionic bonds between amino acid side chains d) covalent bonds between cysteine residues e) all of the above

13. Which DNA repair system fixes mis-incorporated bases after DNA replication? a. base excision repair b. mismatch repair c. nucleotide excision repair d. homologous recombination repair

13. Which type of cell in adult animals divides most rapidly? a) stem cells b) transient amplifying cells c) differentiating cells

14. A particular Class I MHC molecule is able to bind a number of different peptides with low affinity. Which of these side-chain interactions would explain low-affinity binding of peptides with different amino acid sequences? a. hydrogen bonds b. hydrophobic interactions c. ionic bonds d. van der Waals interactions e. covalent disulfide bonds

14. Most cells in the body, including red blood cells, use GLUT1 as the plasma membrane glucoses transporter. Neuronal cells, however, have GLUT3 as their plasma membrane glucose transporter. GLUT3 has a five-fold lower Km for glucose than GLUT1. Therefore, a) neuronal cells need higher glucose concentrations to take up glucose at the same rate as red blood cells b) neuronal cells can take up glucose at lower extracellular glucose concentrations than red blood cells c) when glucose concentrations are at their respective Km values, neuronal cells take up glucose 5x faster than red blood cells

14. The following are the steps of the sequential activation of gated ion channels at a neuromuscular junction: Voltage gated Ca2+ channel → nicotinic acetylcholine receptor → voltage gated Na+ channel → ( ) -release channel in sarcoplasmic reticulum a. K+ b. Ca2+ c. Na+ d. Cl-

14. What is the function of the thing labeled "mAKAP" in this diagram? a. mAKAP is an adenylylate cyclase that generates cAMP beside the catalytic subunit of PKA (labeled C) to enhance its activation b.mAKAP is an A-kinase-associated protein that associates a phosphodiesterase (PDE) in close proximity to PKA so it can participate in the shutting off of PKA in this system. c . mAKAP is a mitochondrial associated kinase for A-type protein kinases which is important in coordinating the production of ATP with the use of ATP (as a substrate to make cAMP) for signaling

14. Which of the following statement about integrin is FALSE? a) Integrins are heterodimers composed of alpha and beta subunits. b) Integrins mediated cell-cell adhesion by binding to integrins on adjacent cells. c) Integrin - extracellular ligand binding leads to its conformational change and activates intracellular signaling pathways. d) Intracellular adapter protein binding can modify integrin's ability to bind extracellular ligands.

15. After activation, some receptors bind ( ) on the cytoplasmic domain of the receptor to mediate it's endocytosis by binding of AP2 and clathrin. a. β-Catenin b. β-Arrestin c. β-Amyloids d. β-Endmorphins

15. The resting potential of a neuron of around ___ mV can be attributed to ___: a. -120, high Na+ concentrations in exterior and low K+ concentrations in cytosol b. -60, high Na+ concentrations in exterior and high K+ concentrations in cytosol c. +120, low Na+ concentrations in exterior and high K+ concentrations in cytosol d. +60, low Na+ concentrations in exterior and high K+ concentrations in cytosol

15. What happens when channels selective for Na+ ions are opened in the membrane separating the two chambers in this figure? a) Na+ ions move from the cytosol side to the extracellular medium side b) Na+ ions move from the extracellular medium side to the cytosolic side c) There is no net movement of Na+ ions because the membrane potential is zero

16. Chimeric mice are created by: a. mating two different strains of mice b. injecting embryonic stem cells from one strain into the blastocyst stage embryos of a different strain c. using a marker to color patches of fur on newborn mice d. surgically grafting organs and body parts from one mouse to another

16. Proteins that are bound to B-form DNA will be on the same side of the DNA molecule if they bind to nucleotides that are: a. 5 bases distant b. 10 bases distant c. 15 bases distant

17. Action potentials: a) vary in intensity b) vary in frequency and timing c) result in a decrease in resting potential d) all of the above

17. Myelination increases the velocity of impulse conduction. Which cell(s) is responsible for generating myelin sheath in the PNS (peripheral nerve system)? a. Olygodendrocyte b. Schwann cell c. Neuron d. Stellate cell

17. Which of the following proteins is required for the elongation of the leading strand at a DNA replication fork? a. primase b. DNA polymerase c. a ssDNA binding protein d. a DNA ligase e. all are required for leading strand elongation at a DNA replication fork

18. Which of these proteins assembles to form the apoptosome? a) Bcl-2 b) Apaf-1 c) Caspase-9 d) Caspase-3 and Caspase-7 e) Cytochrome c oxidase

2. Mannose 6-phosphate is a tag that is used to target proteins to the _________. a. mitochondria b. lysosomes c. peroxisomes d. nuclear membrane

2. What is the effect of TBP (TATA binding protein) binding on DNA structure? a. The DNA unwinds where TBP binds b. The DNA bends 90 degrees where TBP binds c. The cytosine bases nearby are methylated d. The histones nearby are deacetylated

2. Which is the main mechanism how differentiated cell types are formed from stem and precursor cells? a) Symmetric cell division b) Asymmetric cell division c) Self renewal d) Apoptosis/necrosis

20. Development of the vertebrate starts with zygote. The zygote undergoes massive cell division (morula/blastula stages) followed by ____ stage. In this stage, three germ layers of body are established. a) organogenesis b) gastrulation c) segmentation d) none of the above

20. Ribosomes translating secreted proteins are targeted to the ER via _____ a. A C-terminal GPI anchor on the secreted protein b. An N-terminal hydrophobic signal peptide on the secreted protein c. A cluster of basic residues on the secreted protein d. A C-terminal prenylation on the secreted protein

20. What transporter is primarily responsible for generating and maintaining a mammalian cell's plasma membrane potential? a. the K+ ion channel b. the Na+/K+ ATPase c. the F1/F0 ATPase d. the Ca2+ ATPase e. an ABC transporter

20. Which signaling pathway uses the protein cleavage mechanism to relay the signal? a. TGF-β signaling b. Notch-Delta signaling c. Wnt signaling d. Bmp signaling

21. A newly sequenced bacterial genome has > 60% G+C content. In comparison, the E. coli genome has about 45% G+C content. What is a reasonable hypothesis based on this information? a. The newly sequenced bacterium is adapted to live at colder temperatures than E. coli. b. The newly sequenced bacterium is adapted to live at higher temperatures than E. coli c. No hypothesis should be made about adaptation to temperature based on G+C content of an organism's DNA.

21. In the presence of high levels of Ca2+, muscle myofibrils will ________. a) relax b) contract

21. Maturation Promotion Factor (MPF) is: a) a single protein important in the cell cycle b) composed of cyclin and cyclin dependent kinase (CDK) c) a phosphatase d) none of the above

21. The mitochondrial electron transport chain uses the free energy released by redox reactions to: a) synthesize ATP from ADP and inorganic phosphate b) pump H+ ions across the inner mitochondrial membrane to generate and maintain a pH gradient and membrane potential c) consume oxygen and make water molecules d) produce NADH from NAD+ and H+

22. If the inner mitochondrial membrane becomes selectively leaky to H+ ions (due to facilitated diffusion), what will happen to the pH gradient and the membrane potential? a) the pH gradient and membrane potential will increase b) the pH gradient and membrane potential will decrease c) the pH gradient will increase, membrane potential will decrease d) the pH gradient will decrease, membrane potential will increase

24. An action potential can travel from the cell body to the axon terminal at speeds of up to ____. a) 100 kilometers/sec b) 100 meters/sec c) 100 cm/sec d) 100 mm/sec e) 100 m/sec

24. Which enzyme converts hydrogen peroxide to water? a) cytochrome c oxidase b) catalase c) superoxide dismutase d) NADH oxidase

24. Which enzyme converts oxygen free radicals and turns them into hydrogen peroxide? a. catalase b. superoxide dismutase c. cytochrome c oxidase d. NADH dehydrogenase e. ribulose-1,5-bis-phosphate carboxylase/oxygenase

25. Actin assembly is nucleated by two classes of proteins, ( A ) for unbranched filaments and (B ) for branched filaments. Name them in order from A to B. a. Arp2/3 complex, Formin b. Formin, Arp 2/3 complex c. CAD, STIM1 d. STIM1, CAD

25. Free tubulin exists as a dimer of -tubulin and -tubulin in which the of -subunit contains a trapped and non-hydrolyzable GTP and the -subunit has an exchangable and hydrolyzable _____. a) ATP b) GTP

25. Somatic ____ occurs in immunoglobulin and T cell receptor, whereas somatic ____ occurs only in immunoglobulin. a) hypermuation..............recombination b) recombination..............hypermutation

25. What is the human homologue of the worm (C. elegans) CED3 gene involved in apoptosis? a) Caspase 3 b) Caspase 9 c) Apaf-1 d) Bcl-2

26. The enzyme AID (activation-induced cytosine deaminase) deaminates cytosines to form uracil. What DNA repair process acts before DNA replication to repair damaged or mismatched DNA bases? a. mismatch repair b. base excision repair c. nucleotide excision repair d. homologous recombination

27. Clonal selection theory of B-cells states that there is a large number of B cells each with its own antigen specific receptor. During infection: a) There is no specific expansion of any of these B cells b) There is expansion of B cells that are able to bind the antigen such that these B cells can produce copious amount of antibodies against the antigen c) B cells are involved in direct killing of pathogen-infected cells. d) B cells are not involved in the adaptive immune response.

27. Phospholipid synthesis (addition of fatty acids to glycerol-phosphate) occurs in what part of the eukaryotic cell? a. cytosol b. endoplasmic reticulum c. nucleus d. Golgi e. plasma membrane

27. The limit of resolution of ordinary light microscopy is___ a. about equal to 10X the wavelength of light b. about equal to 1/2 the wavelength of light c. inversely proportional to the wavelength of light d. both a) and c) e. both b) and c)

27. The structure shown on the right is a ____________ bound to a microtubule. a) kinesin b) dynein c) fishing reel d) none of the above

27. What technique separates proteins by their molecular weight? a) mass spectrometry b) SDS-polyacrylamide gel electrophoresis c) centrifugation d) chromatography

28. All assays for following the trafficking of proteins through the secretory pathway in live cells require a way to label a cohort of secretory proteins and a way to identify the compartments where the labeled proteins are subsequently located. One of the most informative was to prepare cells with a GFP-tagged protein (VSVG-GFP) that is biosynthesized in the rough ER but does not progress through other intracellular compartments until the cells are shifted to a new temperature. When this assay was employed, the time that it took for most of the most intense fluorescence to appear in the Golgi apparatus was: a) 40-50 seconds b) 40-50 minutes c) 4 to 5 hours d) never (it did not move to the Golgi apparatus)

28. Compared to the culture medium for primary, non-transformed cell lines, the culture medium for transformed (cancerous) cell lines should have___ a. lower glucose concentration b. higher glucose concentration c. more growth factors and hormones that stimulate cell growth and proliferation d. a more acidic pH

28. Which of the following will occur when drugs interrupting actin assembly is applied? a) Cdc42 will no longer accumulate at the budding site in budding yeast. b) Cells can no longer bind firmly to extracellular matrix. c) Focal adhesions can no longer be dissembled. d) Cadherins cannot bind to each other to make adherens junctions.

29. Dynein binds with ( ) to induce transport. Without binding ( ), its function cannot be properly performed. a. APC complex b. Dynactin complex c. PRC1 d. mTORC1

3. _______ is the main mechanism how differentiated cell types are formed from stem and precursor cells. a. Symmetric cell division b. Asymmetric cell division c. Self renewal d. Apoptosis/necrosis

30. Activation of dyneins associated with the microtubules of cilia and flagella so they move as much as they can (i.e., until they are blocked by constraining nexin linkers) causes cilia and flagella to _____. a) undergo endocytosis and degradation b) bend c) double in length and width d) break off and release exosomes

30. Compared to genes expressed at low levels, highly expressed genes will have promoter regions that are a. hypomethylated at CpG sites and packaged in nucleosomes with deacetylated histones b. hypomethylated at CpG sites and packaged in nucleosomes with acetylated histones c. hypermethylated at CpG sites and packaged in nucleosomes with deacetylated histones d. hypermethylated at CpG sites and packaged in nucleosomes with acetylated histones

30. Which one of the following cytoskeletal structure is NOT made with actin? a. Cell cortex b. Ram's horns c. Stress fibers d. Filopodia

31. TGF-b signaling uses ( A ), whereas Bmp signaling uses ( B) to relay signal. Name them from A to B. a. Smad 1/5/8, Smad 2/3 b. Smad 2/3, Smad 1/5/8 c. Smad 1/5/8, Smad 1/5/8 d. Smad 2/3, Smad 2/3

31. The immune system uses both the blood circulatory system and the interstitial fluid/lymphatic system. Which has the higher total fluid volume? a) the blood circulatlry system b) interstitial fluid/lymphatic system c) they both are about the same

33. If you discover that a secreted protein also has an alternative splice form that has a KDEL sequence, the alternative splice form of the protein is likely to be _______. a) secreted via a different pathway b) retained in the ER c) converted from a protease to a phosphatase d) all of the above e) none of the above1.

34. Cyclin D-CDK4/6 phosphorylates Rb, which causes Rb to _______ E2F so it (i.e., E2F) can serve as a transcription factor to up-regulate expression of cyclins E or A a) bind tightly to b) release c) polyubiquitinate d) none of the above

34. Which is expressed primarily by professional APCs: phagocytic dendritic cells and macrophages, and B cells? a) MHC class I b) MHC class II c) CD1

35. Fibronectin is a very important protein of the extracellular matrix and has many functions, such as to regulate cell shape, organization of the cytoskeleton, cell migration, and cellular differentiation. Which of the following statements most accurately describes how it's structure achieves these functions? a) fibronection has one region (an RGD domain) that is responsible for all these functions b) fibronectin has multiple binding sites for ECM and cell surface integrins. c) figronection has no bindings sites per se, it only functions as a soft buffer to help reduce mechanical damage to cells that it surrounds

36. In a cancer cell exhibiting the Warburg effect, how is most pyruvate metabolized? a. It is respired in the mitochondria via pyruvate oxidation and the citric acid cycle b. It is fermented to lactic acid in the cytoplasm c. It is used to make glucose d. It is secreted from the cell

36. In telophase, lamins are ________ to reorganize the membrane around the nuclear components to form the intact nuclear membrane. a) phosphorylated b) dephosphorylated c) ubiquitinated d) deubiquitinated

37. If you have determined that a T-cell is CD8+, you would classify it as: a) a helper T-cell b) a cytotoxic (Killer) T-cell

37. The power stroke of a myosin motor occurs when ( ). a. ATP is bound b. phosphate is released c. ADP is released d. ATP is hydrolyzed

39. In this diagram for activation of a T-cell by interaction of it's TCR with an APC MHC plus co-stimulatory receptor interaction (CD28 on the T-cell and APC CD80/CD86, the next step is shown to be increased CTLA4 expression and recruitment to the cell surface. How does increased surface expression of CTLA4 affect the activated T-cell? a) it enhances the response b) it terminates the response c) it converts the T-cell into a B-cell d) it converts the T-cell into a plasma cell for production of IgM

39. Which of the following myosin is abundantly expressed in the cleavage furrow (contractile ring) during cytokinesis? a. Myosin I b. Myosin II c. Myosin IV d. Myosin V

4. Adenylyl cyclase is activated by an _______ category G protein and inhibited by ______ category G protein. a) Gs for both blanks b) Gs for the first blank and Gi for the second blank. c) Gi for the first blank and Gs for the second blank. d) Gi for both blanks

4. For chromosome segregation to occur in anaphase, the securins must be poly- ubiquinated by and degraded by a) Anaphase Promoting Complex / Cyclosome (APC/C), cell lysis b) Anaphase Promoting Complex / Cyclosome (APC/C), proteasome c) SCF, caspases d) SCF, separase

4. Lysosomes are protected from self-digestion by: a) not containing any enzymes that can digest lipids b) having an inner layer of complex carbohydrates that protects the inner surface of the lysosomal membrane from digestion c) being made of stainless steel

40. Which of the following is found in meiosis but not in mitosis? a) Cell division occurs in mitosis but not in meiosis. b) During prophase of meiosis, homologous chromosomes undergo recombination; recombination usually does not occur in prophase of mitosis c) Meiosis does not utilize cohesins for any function whereas in mitosis, cohensins are responsible for holding chromosomes together

43. Which of the following is NOT a domain that transcription factors use to bind to DNA? (a) Zinc finger (b) SH3 (c) Leucine zipper (d) Basic helix loop helix

45. Many morphogenes (e.g. TGFbeta, Wnt) are secreted by cells and generate a local gradient which cells will response to depending the concentration of the ligand they expose to. Which type of extracellular signaling does it belongs to? (a) endocrine signaling (b) paracrine signaling (c) autocrine signaling

5. Only DNA replication initiation factors can assemble pre-replication complex on the DNA replication origin. a) phosphorylated b) unphosphorylated c) methylated d) ubiquitinated

5. The name for the double-membrane vesicles/vacuoles that are formed from the ER to turn over old or damaged organelles and other processes that allow cells to remove unnecessary components and generate needed ones (such as essential amino acids) are called are: a) phagosomes b) autophagosomes c) automatic recovery and reinvestment vesicles d) peroxisomes

5. What initiates coat protein assembly to form a vesicle bud? a. v-SNARE binding to t-SNARE b. GDP bound to Sar1 or ARF is exchanged for GTP c. GTP bound to Sar1 or ARF is hydrolyzed to GDP d. Adaptor proteins bind to membrane at site of vesicle bud formation

5. Which of the following makes unidirectional conduction of action potential possible? a. interneurons b. refractory period c. oligodendrocytes d. hyperpolarization period

54. Microtubule undergo assembly when there is _________ at its plus end, when GTP-beta-tubulin is lacking, the microtubule switches to ___________. (a) GDP-beta-tubulin, rescue (b) GTP-beta-tubulin, catastrophe (c) GDP-alpha-tubulin, catastrophe (d) GTP-alpha-tubulin, rescue

55. Which of the following is not a mitochondria organization center (MTOC)? (a) centrosome (b) kinetochore (c) basal body (d) spindle pole

56. In anaphase, the spindle pole is separated by coordinated work of the microtubules. Which of the following does NOT correctly match the microtubule and the movement in spindle pole separation? (a) Kinetochore MT shrinks to pull the chromosome closer to the pole. (b) Polar MT extended to push the two spindle poles farther away from each other. (c) Polar MTs slide relative to each other to push the two spindle poles farther away from each other. (d) The astral MT is pulled closer to the cell cortex.

57. Maturation promoting factor (MPF) is a protein complex consists of ______. (a) Cyclin A and CDK1 (b) Cyclin B and CDK1 (c) Cyclin D and CDK4 (d) Cyclin E and CDK2

59. During mitosis, the nuclear envelope is disassembled by _______ and the sister chromatids are separated when _______ is active. (a) lamin digestive enzyme, Securin (b) MPF, APC (c) APC, Separase (d) MPF, ADAM13

6. If you discover that a secreted protein also has an alternative splice form that has a KDEL sequence, the alternative splice form of the protein is likely to be _______. a) secreted via a different pathway b) retained in the ER c) converted from a protease to a phosphatase d) all of the above e) none of the above1.

9. Cell membranes from animals whose body temperature is 37 degrees would have higher proportions of which lipids, compared to cell membranes from animals whose body temperatures operate around 20 degrees? a) cholesterol and cis-unsaturated fatty acids b) cholesterol and saturated fatty acids c) cholesterol and trans-unsaturated fatty acids d) both trans-unsaturated and saturated fatty acids e) both cis-unsaturated and trans-unsaturated fatty acids

9. What is the major (most frequent) pathway for degradation of mRNAs in the cytoplasm? a. decapping and 5-exonuclease digestion b. deadenylation-dependent pathways initiated by polyA shortening c. endonucleolytic pathway initiated by endonucleolytic cleavage of the mRNA

9. Which of the following describes the function of APC (anaphase promoting complex)? a) It leads to the degradation of CDK1 at the end of mitosis. b) It leads to the separation of sister chromatids by degrading Securin. c) It adds ubiquitin tail to proteins and leads to their degradation in Lysosome. d) It digested nuclear envelop at M-phase.

a8) Hydrolysis of PI(4,5)P2 (phosphatidylinositol 4,5-bisphosphate) by phospholipase C releases ____ that acts as a second messenger to elevate ____. a) phosphatidic acid ............... protein kinase B b) inositol 1,4,5-triphosphate (IP3) .............. cytosolic Ca2+ c) phosphatidylinositol 4-phosphate PI(4)P ........... cTMP d) phosphatidylinositol ......... N2O

b2. For the signaling switch shown on the right, the reaction shown from the top to the bottom (i.e., the conversion of the phosphorylated target protein to the target protein with a free -OH) is catalyzed by _____. a) a protein kinase b) a phosphoprotein phosphatase c) a pyrophosphorylase

1. Which region(s) of a protein-coding gene are transcribed in the nucleus, but are not present in the mRNA that is exported to the cytoplasm? a. the promoter b. the exons c. the introns d. the 5' and 3' untranslated regions e. all of the above except exons are transcribed but are not present in the mRNA

10. The hematopoietic stem cells in the bone marrow are able to differentiate into various types of white and red blood cells. These hematopoietic stem cells are____: a) totipotent b) pluripotent c) multipotent d) unipotent

11. In the absence of trophic factors, ( ) molecules forms the ionic channels to influx ions into mitochondria for cytochrome C release. a. Bcl-2 b. Bcl-2 and Bcl-XL c. Bax d. Apaf1

11. Which of the following statements about MHC molecules is TRUE? a. MHC I molecules are present only on professional antigen-presenting cells b. MHC II molecules present antigen to cytotoxic T lymphocytes (CTLs) c. MHC I molecules present peptides from proteins made by the cell's ribosomes d. MHC molecules can bind and present carbohydrate antigens

12. Cadherin cellular adhesion molecules promote: a) collagen binding. mito b) multiadhesive matrix protein binding. c) cell-specific homophilic interactions. d) all of the above

12. Which of the following components is NOT a part of the intrinsic apoptotic pathway in vertebrates? a) Cytochrome C b) Aparf-1 c) Death receptor d) Pro-Caspase 9

12. Which of the following is NOT the part of three germ layers to establish body plan in vertebrate? a. endoderm b. mesoderm c. trophoectoderm d. ectoderm

13. A protein that transports protons into the vacuole, creating a pH gradient across the vacuolar membrane, is most likely a ______ a) proton channel b) a P-class pump c) a V-class pump d) an ABC transporter e) an F-class ATPase

14. What is NOT needed for transient expression of a foreign gene in cultured mammalian cells? a. a plasmid or other vector for cloning the gene b. a promoter to drive transcription of the gene c. a drug resistance gene to select cells that have taken up the vector

15. The Na+/K+ ATPase transports 3 Na+ ions out of the cell and 2 K+ ions into the cell with every cycle of ATP hydrolysis and phosphorylation/dephosphorylation. Which statement is FALSE? a. The enzyme is a P-type ATPase b. The activity of the enzyme helps generate or maintain a membrane potential c. The enzyme is a symporter d. The enzyme transports Na+ ions against the Na+ concentration gradient e. The enzyme transports K+ ions against the K+ concentration gradient

15. The SR proteins in the cross-exon recognition complex bind what sequences in the pre-mRNA? a. GU and AG b. The branch point A c. exonic splice enhancers (ESEs) d. all of the above

15. What component of the TGF-b/Smad signaling scheme shown on the right is responsible for the trafficking of the final complex into the nucleus? a) the complex binds the transcription factor in the cytosol and is carried into the nucleus with the transcription factor. b) the complex is only used during the cell cycle where there is no nuclear membrane; therefore, an import mechanism isn't needed. c) the binding of the NLS sequence on Smad2/3 by Imp-β is responsible for its transport into the nucleus d) pick this option is the premise of the question is incorrect (i.e., this complex does not function in the nucleus so transport isn't needed).

16. At what point will the system reach equilibrium, once channels selective for Na+ ions are opened in the membrane separating the two chambers? a) the system is already at equilibrium and opening Na+ channels will have no net effect b) Na+ ions will move down their concentration gradient until the Na+ ion concentrations are equal on both sides c) Na+ ions will move down their concentration gradient until the membrane potential created by the movement of Na+ ions counterbalances the Na+ concentration gradient

16. Cells of the mammalian embryo remain totipotent through a) the 2-cell stage b) the 4-cell stage c) the 8-cell stage d) the 16-cell stage and compaction e) all the way through to the blastocyst stage at 32 cells

16. Which of the following represents a correct structure-function relationship for neurons? a) cell body - sends signal to another cell b) axon - contains the nucleus of the cell c) dendrite - forms synapses with other neurons d) axon termini - receive incoming signals

17. This diagram from Lodish et al. shows the intrinsic apoptotic pathway in mammals. What would be the phenotype of an individual who had no functional XIAP gene? a) all the cells would die even without apoptotic stimuli b) all the cells would be resistant to apoptotic stimuli c) cells would be more likely to die by apoptosis in response to weak apoptotic stimuli d) cells would show no change in apoptotic behavior.

17. What enzyme cleaves double-stranded RNA to generate both miRNAs and siRNAs? a. 5'-3' exonuclease b. 3'-5' exonuclease c. Dicer d. Argonaute

18. After the Class I protein associates with beta-2-microglobulin and is loaded with antigen, it is ready to depart the ER via coated vesicles. What initiates coated vesicle bud formation? a. Coat proteins binding to phosphatidyl ethanolamine on the outer leaflet b. v-SNARE insertion into the ER membrane triggered by ATP hydrolysis c. insertion of Sar1 or ARF into the membrane triggered by GTP binding d. Sar1 or ARF hydrolyzing GTP to GDP e. Coat proteins spontaneously self-assemble

19. In extrinsic apoptotic pathway, which caspase binds to adaptor protein(s), and activate caspase 3? a) caspase 9 b) caspase 7 c) caspase 8 d) caspase 10

19. Which category of myosin shown below moves along actin in large "steps" of approximately 36 nm for the motor overall? a) Class I b) Class II c) Class V

19. Which of the factors listed below are NOT required for culturing mammalian cells? a. glucose b. vitamins and essential amino acids c. light energy d. growth factors like insulin e. all of the above are required

19. Which of the following cells do NOT fall under the broad category of "glial" cells? a) Astrocytes b) Schwann cells c) Neurons d) Oligodendrocites e) Pick this if all of the above are glial cells

19. cdc42 also activated dynein in the leading edge of the migrating cell (the region labeled #17 & #19 in the diagram). The involvement of dynein tells you that _____________ are also involved in this process because dynein is ______________. a) intermediate filament lamins.........a kinase that phosphorylates lamins b) intermediate filament desmins........a phosphatase that dephosphorylates desmins c) microtubules.............................a motor protein for (+) to (-) end migration along microtubules d) β-catenin.................................a scaffold protein that regulates turnover of β-catenin

2. What is necessary for Apaf-1 activation prior to apoptosis of human cells? a. Bcl-2 up-regulation b. tBID down-regulation c. Release of cytochrome C from mitochondria d. None of the above

20. Which of the following is NOT an example of using iPSC in personalized medicine? a) growth of neurons in cell culture containing mutations associated with Alzheimer's for drug screening. b) make patient-specific cartilage cells from iPSCs to replace those lost in injury. c) transplant bone marrows from a donor to leukemia patient. d)correct mutations in patient's iPSCs and differentiate them into pancreatic beta cells to replace those in type I diabetes.

21. Cytokine receptors do not have intrinsic kinase activity so ( ) tightly binds to the cytokine receptors to phosphorylate them. a. PDK1 b. PKA c. JAK d. PKC

21. One of the polymerization conditions for actin filaments is referred to as treadmilling. This is the condition where ___________. a) no polymerization is occurring from either end b) there is growth from the (-) end only (and the (+) end usually shortens) c) there is growth from the (+) end only (and the (-) end usually shortens) d) there is growth from both ends

22. In a respiring cell, where do electrons go from the end of the electron transport chain? a. to the ATP synthase b. to ADP to make ATP c. to oxygen to make water d. to carbon dioxide to make carbohydrate e. to water to make oxygen

23. B cells internalize antigens bound to their cell surface receptor via receptor-mediated endocytosis. What coat protein is involved in forming these endocytotic vesicles? a. COP I b. COP II c. Clathrin d. AP1 e. the coat protein for receptor-mediated endocytosis is unknown at this time

23. Closing of the channel occurs when ______. a) the channel-inactivating segment is proteolyticall cleaved b) the channel-inactivating segment phosphorylates the voltage-sensing -helix c) the channel-inactivating segment folds into and blocks the ion-conducting pore d) the channel-inactivating seqment triggers endocytosis of the channel

23. How do mitochondrial proteins that are encoded by nuclear genes get to the mitochondria? a. Their mRNAs are imported into the mitochondrial matrix by the Tom and Tim translocation complexes, then translated in the mitochondria. b. Their mRNAs are translated by ribosomes docked to the ER membrane, sorted in the Golgi, and then transported by vesicles to the mitochondria. c. Their mRNAs are translated by cytoplasmic ribosomes, and the proteins have targeting sequences that allow import into the mitochondria by the Tom and Tim translocation complexes.

23. Which of the following are considered innate immune cells: a) B and T cells b) Liver cells c) Dendritic cells, NK cells, macrophage cells d) None of the above

23. Which of the myosins shown on the right functions in the transport of vesicles (organelle transport)? a) Class I b) Class II c) Class V

25. Which of the following enzymes will have the highest activity under all substrate concentrations? a) an enzyme with high Km and high Vmax b) an enzyme with high Km and low Vmax c) an enzyme with low Km and high Vmax d) an enzyme with low km and low Vmax

26. How do nascent proteins (proteins in the act of being synthesized by the ribosome) fold into their proper shapes? a) by being ubiquitinated b) by being phosphorylated c) by binding to molecular chaperones d) by being inserted into the lumen of the ER e) most proteins fold spontaneously into their proper shapes with no assistance

26. There are three common classes of myosins. Which one does NOT belong to them? a. Myosin I b. Myosin II c. Myosin IV d. Myosin V

26. Which of the following proteins facilitate microtubule disassembly? a) Kinesin-13 b) Stathmin c) both Kinesin-13 and Stathmin facilitate disassembly d) neither Kinesin-13 nor Stathmin facilitate disassembly

27. Mitosis promoting factor (MPF) promotes early mitotic events and induces depolymerization of nuclear envelope (NE). Which of the following protein does MPF phosphorylate to start NE disassembly? a. Keratin b. Vimentin c. Lamin d. GFAP

27. Plasma membrane receptor proteins are sometimes degraded instead of being recycled after releasing their ligands. What membrane compartment do they end up in if they are going to be degraded? a) early endosomes b) clathrin-coated pits c) multivesicular endosomes d) trans-Golgi e) retrograde vesicles

28. When a mitochondrion is moved from a location near the plasma membrane of a cell to a position nearer the center of the cell (the nucleus)—i.e., in the direction "+ -" along the microtubule, the motor protein that effects this transport is most likely to be a ________; whereas, when a mitochondrion is moved from the center of the cell to the periphery (i.e., near the plasma membrane)—i.e., in the direction "- +" along the microtubule, the motor protein that effects that transport is most likely to be a ________. a) kinesin .......... kinesin b) kinesin .......... dynein c) dynein .......... kinesin d) dynein .......... dynein

28. Which of the following is NOT involved in some aspect of chromosome capture and congression in prometaphase or spindle formation and anaphase (the steps shown on the right)? a) microtubules b) kinesin 13 c) β-Kinactin d) tethered dynactin-dynein complexes

29. The diagram on the right shows a synapse with AMPA glutamate receptors in the basal state. When this hippocampal synapse has undergone long-term potentiation (LTP), it will have a higher postsynaptic response to glutamate due to: a) large shifts (i.e., by several orders of magnitude) in the affinity of each receptor for glutamate b) a decrease in the specificity of the AMPA receptor so it can be stimulated by any neurotransmitter released in the synapse at the same time that glutamate is secreted c) an increase in the exocytosis of AMPA receptors and an increase in their diffusion into postsynaptic density d) the elimination of glutamate re-uptake by the presynaptic nerve terminal so it is continuously present whenever secreted

3. What do you think would happen to newly-synthesized lysosomal enzymes in cells that lacked mannose-6-phosphate receptors? a. They would still be transported to lysosomes b. They would be degraded in the endoplasmic reticulum c. They would be secreted out of the cell at the plasma membrane d. The cells would sense this and no longer synthesize lysosomal enzymes

3. Which of these mutations is least likely to disrupt a protein's tertiary structure and its function? a) E (glutamic acid) to Q (glutamine) b) C (cysteine) to P (proline) c) W (tryptophan) to F (phenylalanine) d) V (valine) to G (glycine)

30. Innate immunity is mediated by ALL OF THE FOLLOWING EXCEPT: a) the complement system b) neutrophils c) B lymphocytes d) macrophages e) pick this if all of the above are classified as mediating innate immunity

30. Which of the following statements about miRNAs is true? a. miRNAs regulate transcription of their target genes b. miRNAs each regulate expression of a single target gene c. miRNAs often inhibit translation of their target mRNAs d. miRNAs must have perfect complementarity to their target mRNAs

32. Cryo-electron microscopy is particularly useful for biological samples because_ a. it requires no vaccuum b. it uses high energy electrons for better resolution c. biological samples are frozen in their native state d. all of the above e. both a) and c) but not b)

32. The enzyme activation-induced deaminase (AID, also abbreviated AICDA) catalyzes this reaction: a) deamination of glutamines and asparagines on proteins to glutamates and aspartates, respectively b) deamination of the N-terminal amino acid of a protein to interfere with its intracellular trafficking c) deamination of cytosine, which turns it into uracil d) deamination of surface proteins of bacteria so they cannot evade the immune system

32. To activate Wnt signaling, ( ) need to be dephosphorylated and translocated into the nucleus. a. GSK3 b. Axin c. β-Catenin d. Dishevelled

33. A protein without a transmembrane domain can still be anchored to lipid bilayer membranes via: a. C-terminal myristoylation or palmitoylation b. N-terminal prenylation c. C-terminal GPI-anchor d. all of the above

33. Which usually presents lipid antigens? a) MHC class I b) MHC class II c) CD1

34. In the biosynthesis of fibrillar collagens by fibroblasts, after the folded and bundled procollagens have been prepared in the rough ER and Golgi, they are secreted and _______ so the trimers can assemble into covalently cross-linked fibrils. a) phosphate groups are removed from serine residues at the N- and C-terminal ends b) phosphate groups are added to serine residues at the N- and C-terminal ends c) N- and C-terminal propeptides are removed d) cysteine-rich peptides are added to the N- and C-terminal ends

35. Which of these molecules cross cell membranes via facilitated diffusion through a specific channel complex? a. carbon dioxide b. oxygen c. water d. nitrous oxide e. steroid hormones

36. Which cell type uses perforin and granzyme as it's major mechanism of cell killing? a) neutrophils b) monocytes c) cytotoxic T-cells d) gram-negative bacteria

37. Lamins are in what category of cytoskeletal proteins? a) microfilaments b) microtubules c) intermediate filaments

37. The human genome contains approximately how many protein-coding genes? a. 1 million b. 100,000 c. 20,000 d. 10,000 e. 6,000

38. Early signaling from both B cell receptors and T cell receptors uses a family of protein kinases called ___ family kinases. a) FAK b) B/T kinases c) Src d) PKZ

38. Which of the following is associated with the regulation of microtubule diassmebly? a. kinesin 1 b. kinesin 5 c. kinesin 13

39. A nucleosome consists of___ a. 100 bp of DNA plus 2 each of histones H1, H2a, H2b, and H3 b. 200 bp of DNA plus 4 each of histones H2a and H2b c. 200 bp of DNA plus 2 each of histones H2a, H2b, H3 and H4 d. 50 bp of DNA plus 2 each of histones H1, H2, H3 and H4

39. In response to DNA damage, two protein kinases, ______, are recruited to the site of the damage, where they activate signaling pathways that lead to cell cycle arrest, DNA repair and under some circumstances, apoptosis. a) PKA and PKC b) PDK1 and PDK2 c) ATM and ATR d) MEKK and MAPK

4. How do nuclear proteins like DNA polymerase become localized to the nucleus? a. They are synthesized inside the nucleus by ribosomes located in the nucleus. b. They are synthesized by ribosomes docked to the nuclear envelope and translocated into the nucleus during translation. c. They are synthesized by cytoplasmic ribosomes and then translocated into the nucleus by proteins that recognize their nuclear localization signal. d. They are synthesized by ribosomes that bind to the nuclear pore complex and co-translationally insert the proteins into the nucleus.

40. Clusters of basic amino acids may function for import of the protein into__ a. mitochondria b. peroxisomes c. nucleus d. endosomes e. vacuoles

41. Chromatin IP experiment was performed and the results show that both transcription factors MyoD and Sox10 can bind to the same enhancer of Twist gene. We know that MyoD is expressed in somites while Sox10 is expressed in neural crest. Which of the following statement is CORRECT based on the experiment? (a) There must be something wrong with the experiment, since MyoD and Sox10 can not be expressed in the same cell. (b) In somite, Twist and MyoD proteins binds to each other. (c) In neural crest, Twist gene is transcribed when Sox10 binds to its enhancer. (d) MyoD and Sox10 cooperate and together binds to Twist enhancer to promote its transcription.

42. During transcription, RNA polymerase binds to _______ of a gene and transcription activators are recruited to RNA polymerase and basic transcription factors by binding to _________ sequences to promote gene transcription. (a) promoter, silencer (b) mediator, enhancer (c) promoter, enhancer (d) intron, exon

44. Which of the following chromatin modification may be found at an actively transcribed gene? (a) H3K9me3 (b) H3K27me3 (c) H3K9ac

5. The fibronectin diagram above also shows a site labeled "heparan sulfate binding." Which of the following best describes what heparan sulfate is? a) an inorganic ion comprised of the transition metal Hp as the sulfate salt b) a zinc-finger protein with sulfated Gln and Asn residues c) a linear polysaccharide chain with N- and O-linked sulfate groups d) a protein of the nuclear membrane that imports fibronection into the nuclear matrix e) a sulfo-lipid comprised of a diglyceride with O-acyl and O-sulfate groups on some hydroxyls

50. The diagram on the right illustrates Delta-Notch pathway. Which of the following statement is CORRECT? (a) Delta and Notch binding detach Notch from Notch receptor. (b) Notch receptor is cleaved and degraded. (c) cytoplasmic portion of Notch receptor acts as transcription factor. (d) Delta-Notch signaling is autocrine signaling.

51. Which of the following does NOT contribute to actin treadmilling? (a) actin filament is polarized that all of actin monomers are oriented to the same direction. (b) actin filaments assemble faster on the "+" end then the "-" end. (c) the speed of actin polymerization is fixed on both ends. (d) At certain G-actin concentration, the net rate of polymerization at the "+" end and the net rate of depolymerization at the "-" end are the same.

52. Which of the following structure and cytoskeleton pairs INCORRECTLY matches the cytoskeleton components with the structure they form? (a) contractile ring - actin filaments (b) flagella - microtubule (c) nucleus envelop - actin filaments (d) spindle - microtubule

53. Myosin binds to actin filament with its _________, and its "walking" on actin filament is powered by ________. (a) head domain, mitochondria (b) neck domain, hydrophobic interaction (c) head domain, ATP (d) neck domain, non-covalent interaction

6. If you have not eaten recently and you have much circulating glucagon (or you have been frightened and have high epinephrine), cAMP in liver will be high and the events shown on the right will occur to activate glycogen phosphorylase, which hydrolyzes glycogen as shown. Liver also contains glycogen synthase (GS, not shown in the diagram) that can synthesize glycogen. How does the liver control this pathway so that it is not simultaneously breaking down and making glycogen? a) glycogen synthase is not active until GS is phosphorylated by a different protein kinase b) glycogen synthase is a mitochondrial enzyme so it is separated from PKA regulation by a membrane barrier c) glycogen synthase is phosphorylated by PKA and in the phosphorylated state is inactive

6. Retinoblastoma gene is a and it inhibits the transcriptional activity of a) Transcription factor, MDM2 b) Pro-survival gene, P53 c) Tumor suppressor, E2F d) Transcription factor, APC

6. Which of the following will have an anti-apoptotic effect and promote cell survival? a) Caspase 9 overexpression b) Release of cytochrome C from mitochondria c) Bcl-2 overexpression d) Bax overexpression

61. Rb is a ______ and it needs to be _________ to allow cell cycle progress through restriction point. (a) tumor suppressor, unphosphorlated (b) proto-oncogen, unphosphorylated (c) tumor suppressor, phosphorylated (d) proto-oncogen, phosphorylated

62. Which of the following statement about p53 is INCORRECT? (a) p53 is a transcription factor. (b) p53 is normally unstable and have a very short lifetime. (c) p53 is stabilized during G1-S transition. (d) p53 can turn on genes to induce apoptosis.

68. Which of the following is NOT a factor used to generate Induced pluripotent stem cells (iPS cells)? (a) Sox2 (b) Oct4 (c) MyoD (d) c-Myc

69. Which of the following is NOT required for asymmetric cell division? (a) Polarized distribution of cellular material. (b) Directed movement of polarity determinants. (c) Directional migration of the cell. (d) Correct orientation of the mitotic spindle.

7. In addition to the GU-AG rule, what sequence elements help determine which potential splice junctions are actually used for nuclear pre-mRNA splicing? a) an adenine nucleotide 20-50 bases near the 3' splice site b) a purine-rich stretch near the 5' splice site c) exonic splicing enhancer sequences d) all of the above

7. In this diagram, ligand-bound receptor functions as ( A ), Gα functions as ( B ), and effector functions as ( C ). Name them in order from A to C. a. GAP, GEF, GTPase b. GTPase, GEF, GAP c. GEF, GTPase, GAP d. GEF, GAP, GTPase

71. The executioner of apoptosis, _______ is activated by __________. (a) Bcl2, mitochondria (b) Apaf-1, cytochrome C (c) Caspases, apoptosome (d) Death signal, trophic factor

77. Which of the following is NOT one of the reasons making cancer difficult to treat? (a) Cancer consists of heterogeneous cells and carry different mutations. (b) Cancer cells tend to have mutations in genome stability and thus are generating new mutations as it divides. (c) Cancer cells are resistant to cell death and thus can not be killed. (d) Cancer cells can spread to new sites through metastasis thus are hard to eliminate.

78. Which of the following is NOT one of the causes for cancer? (a) Tobacco smoke (b) UV radiation (c) rapid cell division (d) genetic translocation/recombination

79. ErbB is a proto-oncogene because ________. (a) loss of ErbB will leads to cancer. (b) ErbB promotes embryogenesis. (c) gain-of-function mutations of ErbBs may lead to cancer. (d) ErbB is receptor tyrosine kinase.

8. Botulinum toxin (Botox) is one of the most potent neurotoxins known. It binds to neuronal synaptic membranes via gangliosides (glycosphingolipids with sialic acid attached) and to a neuronal membrane protein and is endocytosed via receptor-mediated endocytosis. What kind of vesicles are involved? a. COPI vesicles b. COPII vesicles c. Clathrin-coated vesicles d. endocytotic vesicles have no coat proteins

8. The basal lamina is _____. a) the phosphorylated state of lamins when cells are not dividing b) an alternative splice form of laminins c) a thin meshwork of extracellular matrix molecules d) the protein component of the myelin sheath e) a basil rich dish from Lamina's Kitchen

9. Cells ensure that DNA is replicated only once per cell cycle. By which mechanism, it is possible? a. Only methylated DNA replication initiation factors can be assembled on origin recognition complex. b. Only unmethylated DNA replication initiation factors can be assembled on origin recognition complex. c. Only unphosphorylated DNA replication initiation factors can be assembled on origin recognition complex. d. Only phosphorylated DNA replication initiation factors can be assembled on origin recognition complex.

9. During this exam right now, which neurotransmitter is most likely being released? a) Dopamine b) Histamine c) Epinephrine d) Serotonin

9. Which of the following types of DNA sequences is MOST prevalent (makes up the highest percentage) in the human genome? a. sequences that code for amino acids in proteins (the exons) b. sequences that code for introns in protein-coding genes c. sequences that code for transposable elements, or that degenerated from transposable elements (LINEs, SINES, DNA transposons and retrotransposons) d. segmental duplications

16. Cell migration is usually stimulated by factors that bind to receptors on the leading edge of the cell (which would be at the right of this diagram), which in turn send signals that induce changes in actin filaments. Two of the intracellular signaling mediators are named cdc42 and Rac in this diagram. Which of the following statements best fits how cdc42 and Rac are involved in signaling? a) cdc42 and Rac are protein kinases that phosphorylate tyrosine residues on actin that change its tendency to polymerize. b) cdc42 and Rac are ion channels for Ca2+ that open when activated so the influx of Ca2+ causes these changes in actin structure. c) cdc42 and Rac are transcription factors that are translocated to the nucleus when activated and induce expression of mRNAs for the proteins that are needed for cell migration. d) cdc42 and Rac are G proteins that undergo conformation changes upon activation by the exchange of GDP for GTP, then interact with other proteins that change the polymerization state of actin filaments

16. Which of the following does NOT belong to the neurotransmitter? a. Acetylcholine b. Glutamate c. Dopamine d. Metronidazole

17. What post-translational modifications occur in the ER lumen? a. addition of N-linked oligosaccharides b. rearrangement of disulfide bonds by protein disulfide isomerase c. cleavage of the signal peptide d. all of the above e. a) and c) but not b)

18. In this light-activated rhodopsin pathway, A, B, and C play essential roles. Name them in order from A to C: a. cGMP, GMP, PDE b. GMP, cGMP, PDE c. PDE, GMP, cGMP d. PDE, cGMP, GMP

18. Neurotransmitters are stored in: a) the cell body. b) the dendrite. c) the axon hillock. d) synaptic vesicles.

18. Pyruvate is generated during catabolism of ____ a) glucose b) some amino acids like alanine c) fatty acids d) a) and b) e) a) and c)

18. Some of the actin filaments in the region shown in #16 are branched. Which of the following are involved in formation of these branches (these, by the way, were described in this figure as being activated by Rac)? a) γ-actinin b) gelsolin c) katanin d) Arp 2/3 e) Wyett Arp

18. When DNA damage occurs, the cell cycle will be arrested through DNA-damage checkpoints at: a) G1 phase. b) S phase. c) G2 phase. d) All of the above.

20. A resting neuron carrying no signal has ATP powered pumps that move ions across the plasma membrane. The outward movement of ____ ions creates a net negative charge inside the cell called the resting potential of about _____. a) Na+ .......... -70 V b) Na+ .......... -70 mV c) K+ .......... -70 V d) K+ ........... -70 mV e) Ca2+ .......... -170 mV

21. which of these is a component of the adaptive immune system that must be activated first to activate other cells of the adaptive immune system? a. dendritic cells b. macrophages c. B cells d. CD4+ T cells e. CD8+ T cells

22. Cells use ______ to inhibit polymerization of actin filaments on the (+) end. a) profilin b) metformin c) formin d) thymosin β4 e) all of the above

22. During the lecture we learned about the survival of motor neurons which innervate muscle. Based upon it: a) Motor neurons depend on muscle innervation for survival b) Adding a limb bud to one side of the chick embryo will increase survival of motor neurons on that side of the embryo c) Removing a limb bud on one side of the chick embryo will increase apoptosis of motor neurons on that side of the embryo d) All of the above

23. Which one of the following does NOT belong to the GTPase family proteins that function in cell migration? a. Cdc42 b. Rho c. Rac d. Ras

24. What causes coat proteins to dissociate after a coated vesicle has been fully formed? a. fusion of the vesicle with the target membrane b. v-SNARE coiling with t-SNARE c. GTP binding to Sar1 or ARF d. GTP bound to Sar1 or ARF being hydrolyzed to GDP

24. Which of the following statements about innate immune response with complement system is FALSE? a) Innate immune response is activated within minutes or hours upon infection. b) All three pathways of complement system merge into C3. c) It forms membrane attack complex. d) It is activated by type I interferons.

25. An important factor in achieving this speed is the myelination of the neurons and the jumping of action potentials from _____. a) plasma membrane to endosomes b) plasma membrane to exosomes c) neurons to astroglial cells d) node to node (of Ranvier) e) voltage-gated Na+-channels to myelin basic protein

26. An mRNA that loses most of its poly(A) tail would__ a. undergo rapid degradation by 3'-5' exonuclease b. be cleaved by an endonuclease and the fragments degraded c. be translated less efficiently d. both a) and c) e. both b) and c)

26. During which stage of the cell cycle is the chromosome content of a mammalian liver cell 1n? A) G1 B) S C) G2 D) none of the above

26. In the absence of trophic factors, ______molecules form the ionic channels to influx ions into mitochondria for cytochrome C release. a) Bad and Bim b) Bcl2 c) Bcl2 and Bcl2-XL d) Bax and Bak

27. The TATA box____ a. serves as a promoter sequence for genes transcribed by RNA polymerase III. b. is located approximately 100 base pairs upstream of the start site for mRNAs. c. is present in all eukaryotic genes. d. acts to position RNA polymerase II for transcription initiation.

27. Which of the following events does NOT involve tight junction? a) blood-brain barrier b) skin epithelium defensive against environmental pathogen c) prevention of protein exchange between apical and basolateral membrane d) muscle fibers bind firmly to each other

28. Which of the following is not a structural motif found in a DNA-binding domain? a. Leucine zipper b. zinc-finger c. helix-loop-helix d. SH3 domain

28. While Dynein facilitates ( A ) transport, Kinesin promotes ( B ) transport. Name them from A to B. a. (-) end to (+) end; (-) end to (+) end b. (+) end to (-) end; (+) end to (-) end c. (-) end to (+) end; (+) end to (-) end d. (+) end to (-) end; (-) end to (+) end

29. Biological roles of proteoglycans and hyaluronan include all of the following, except: a) maintenance of porosity for the diffusion of small molecules between cells and tissues. b) presentation of growth factors to cells. c) resistance to compression. d) storage sites for extracellular energy reserves.

29. Epigenetics marks refer to modifications to DNA and proteins that in turn regulate gene expression. Which statement is true regarding these specific types of modifications? a. They have the ability to both silence and activate genes. b. They can involve the methylation of cytosine bases. c. They can be the acetylation of histones. d. All of the above

3. The enzyme that is removing the phosphate (on the right half of the diagram) is called a _______. a) ABC protein b) ATPase c) de-kinase d) phosphatase e) zymase

3. Which of the following is NOT the part of voltage-gated Na+ channel component? a) voltage sensing alpha helix b) ion-selective pore c) channel-inactivating segment d) clathrin

31. What binds first to the 5' cap of mRNAs to initiate translation? a. methionyl tRNA b. 40S ribosomal subunit c. 60S ribosomal subunit d. eIF4 e. polyA binding protein

32. Growth promoting signaling pathways, such as the MAPK pathway and -catenin, induce expression of cyclin ___, which is one of the G1 cyclins. a) A b) B c) C d) D

32. Which of the following steps in vesicular transport of proteins requires the hydrolysis of ATP? a) assembly of the sar1 complex b) disassembly of the sar1 complex c) assembly of the SNARE complex d) disassembly of the SNARE complex e) none of the above

36. The NF-kB pathway mediates the response of immune cells to ( ). a. Bacterial and fungi b. Virus infection c. TNFα d. all of the above

38. Cell cycle checkpoints are found at: a) S phase entry b) S phase and late replication c) M phase entry d) all of the above

4. A cytoplasmic enzyme in the cell is found to have a Km of 10 micromolar for its substrate. The concentration of the enzyme's substrate is around 1 micromolar. How can the cell double the rate of the reaction performed by the enzyme? a. the cell should use an allosteric regulator to decrease the enzyme's Km by 50% b. the cell should use an allosteric regulator to increase the enzyme's Km by 2X c. the cell should make twice as much enzyme d. the cell should make twice as much substrate for the enzyme

4. Which of the following is NOT the part of voltage-gated Na+ channel component? a. voltage sensing alpha helix b. ion-selective pore c. channel-inactivating segment d. antiporter

40. After antigen-presenting cells interact with T cells in lymph nodes to activate T helper cells, what help does the activated T helper cells provide? a) they provide antigen-specific assistance for B cells to fully differentiate into plasma cells to produce IgM. b) they activates B-cell antibody hypermutation and class-switch recombination after interaction with B-cells through additional ligand-receptor interactions (e.g., CD40L and CD40). c) they produce cytokines that stimulate antibody production d) all of the above

47. Which of the following statement concerning G protein is INCORRECT? (a) G protein is activated when it switches from GDP-bound to GTP-bound. (b) G protein is activated by GEF and inactivated by GAP. (c) The time G protein remain GTP bound determines how many downstream effectors it can activate. (d) G protein can only activate enzymes to regulate metabolism.

49. Which of the following statement on JAK-STAT pathway is INCORRECT? (a) dimerization of cytokine receptors bring JAK kinases together and activation. (b) activated JAK phosphorylates of STAT. (c) STAT can act as transcriptional factor. (d) JAK-STAT signal can be reversibly terminated by ubiquitination of cytokine receptor and JAK kinase.

5. Which of the following statements about enhancers is true? a. each enhancer has a single binding site for just one transcriptional activating protein b. enhancers must be located within 100 bases upstream of the transcription start site c. enhancers are where RNA polymerases initiate transcription d. proteins bound at enhancers interact with general transcription factors and mediator to regulate transcription by RNA pol II

60. DNA replication only occurs once per cell cycle. Which of the following is NOT a mechanism that ensures this event during S phase. (a) Only unphosphorylated replicative helicases can load on DNA. (b) Only unphosphorylated initiation factors can assemble pre-replication complex on origin. (c) Once detached from DNA, activated replicative helicases will be degraded. (d) DNA is synthesized in a 5' to 3' sequence.

66. Which of the following correctly matches matrix proteins with their function? (a) laminin - elasticity in connective tissue (b) fibronectin - strength in basement membrane (c) collagen - sequester molecules from cell surface (d) proteoglycan - cushioning

7. Hallmarks of programed cell death (apoptosis) include: a) Breakdown of nuclear envelope b) Nuclear fragmentation c) Blebbing of apoptotic bodies d) All of the above

7. Rb is the first discovered tumor suppressor gene. Much research has been focus on characterizing its function. Which of the following statements about Rb is NOT true? a. Rb binds to transcription factor E2F, inhibiting its activity. b. Rb is a substrate of G1 cyclin-CDKs. c. Rb mutations cause retinoblastoma. d. Rb is a major sensor for DNA damage.

7. What mechanism would most likely sort membrane proteins with cytoplasmic sorting signals into the right vesicles? a. a GPI anchor at the C-terminus b. N-glycosylation patterns c. terminal mannose-6-phosphate oligosaccharide modification d. interaction with vesicle coat or adaptor proteins e. interaction with vesicle cargo proteins

8. CRISPR-Cas9 is being widely used for genome editing. When Cas9 cuts DNA to create a double-strand break, what is the predominant cellular response? a. base excision repair b. mismatch repair c. nucleotide excision repair d. non-homologous end joining e. homologous recombination

80. Which of the following is NOT suggested by the cancer "multi-hit" model. (a) It takes more than one mutation for cancer to occur. (b) People with genetically inherited mutation on cancer-related genes have higher chance of getting cancer. (c) People tend to get cancer at older age. (d) Man are at higher risk of getting cancer than women.

9. Which of the following membrane proteins on endothelial cells or leukocytes is/are involved in endothelium-leukocyte interaction (binding loosely or tightly)? a) P-selection b) L2-integrin c) ICAM d) all of the above e) none of the above

b8) Hydrolysis of PI(4,5)P2 (phosphatidylinositol 4,5-bisphosphate) by phospholipase C releases ____ that acts as second messengers to activate ____. a) phosphatidic acid and phosphate ............... protein kinase B and Akt b) phosphatidylinositol 4-phosphate, PI(4)P, and pyrophosphate ........... thymidylate cyclase and glycogen pyrophosphorylase c) phosphatidylinositol (PI) and inositol phosphate (IP) ......... N2O synthase and vascular smooth muscle contraction d) diacylglycerol (DAG) and inositol 1,4,5-triphosphate (IP3) .......... Ca2+ release from the ER and activation of protein kinase C

10. Which of these proteins may be most easily dissociated from membranes without breaking any covalent bonds? a) integral membrane proteins b) acylated proteins c) prenylated proteins d) GPI-anchored proteins e) peripheral membrane proteins

12. The Par genes, including aPKC, are involved in establishing cell polarity in: a) budding yeast b) nematode embryos c) mammalian epithelial cells d) all of the above e) both b) and c) but not a)

15. A stem cell niche____ a) provides an external polarizing signal to induce asymmetry b) regulates stem cell division to prevent stem cell overproliferation c) provides differentiation signals to one of the daughter cells of an asymmetric stem cell division d) maintains stem cell self-renewal and viability e) all of the above

19. A membrane-localized protein that transports lipids or lipophilic drugs out of the cell using the energy from ATP hydrolysis is most likely a: a. an ion channel b. a P-class pump c. a V-class pump d. an F-class pump e. an ABC superfamily transporter

19. According to the Warburg hypothesis, the reason most cancer cells make most of their ATP via glycolysis and fermentation is that: a. cancer cells live only in anaerobic environments in the body b. cancer cells have defective mitochondria c. oxygen kills cancer cells d. cancer cells are sensitive to reactive oxygen species (superoxides, peroxides) generated by aerobic metabolism e. cancer cells can grow faster by using food molecules to build cell mass instead of burning them through respiration

19. Which immunoglobulin isotype is made first by B cells and can be pentameric in the secreted form, with a valence of 10? a. IgA b. IgD c. IgE d. IgG e. IgM

2. Which of the following small RNA molecules is present in spliceosomes? a. tRNA b. snoRNA c. miRNA d. siRNA e. snRNA

2. Which of these post-translational modifications occur in the ER? a. N-glycosylation b. Cleavage of leader signal peptides c. rearrangement of disulfide bonds d. protein folding & assembly assisted by chaperones e. all of the above

20. The Rag1/Rag2 recombinase is responsible for____ a. V(D)J rearrangement of immunoglobulin genes in B cells b. V(D)J rearrangement of T-cell receptor genes c. alternative splicing of mRNAs to produce both secreted and membrane forms of immunoglobulins d. all of the above e. a) and b) but not c)

21. The Warburg effect, also called aerobic glycolysis, is found in many cancer cells. If most of the pyruvate generated from glycolysis is not respired in the mitochondria, what other compounds would be produced from pyruvate? a. acetyl-coA b. the amino acid alanine c. lactic acid d. all of the above e. both alanine and lactic acid

22. A B cell that is activated because its cell surface immunoglobulin has been cross-linked by antigen will: a. proliferate and turn into long-lived memory cells b. undergo somatic hypermutation of the immunoglobulin locus c. undergo class switching to produce IgG, IgA, or IgE d. proliferate and differentiate into plasma cells e. all of the above

22. What happens to proteins that are prevented from being glycosylated, either by addition of tunicamycin or genetic mutation of the glycosylation site? a. the protein does not fold properly b. the protein becomes less stable c. the protein is retained in the ER and does not make it to the Golgi d. the protein binds BiP or other chaperones in the ER e. all of the above

23. What type of cells, or under what conditions, will cells get most of their energy from glycolysis and fermentation to lactic acid? a) cells that are starving for glucose b) many types of rapidly growing cancer cells c) cells that are starving for oxygen d) both a and b) e) both b) and c)

24. Signaling by the T-cell receptor (TCR) requires a complex of signaling proteins associated with the TCR. This complex is located in membrane rafts. What lipids are highly enriched in lipid rafts? a. sphingolipids b. cholesterol c. phosphatidyl serine d. all of the above e. a) and b) but not c)

24. Which of the following statements about αβ-tubulin dimers and their assembly into microtubules is NOT correct? a) they assemble into microtubules in a polarized manner b) GTP is bound to α-tubulin and is non-exchangeable c) GTP is bound to β-tubulin, but once assembled into microtubules is hydrolyzed to GDP d) the nucleotide bound by β-tubulin is exchangeable e) pick this option if none of the statements above are incorrect

25. Many secreted proteins have an N-terminal signal peptide. Which of the following statements are true concerning this signal peptide? a. the signal peptide is bound by SRP when the signal peptide emerges from the ribosome b. the signal peptide is cleaved in the lumen of the ER by a signal peptidase c. the signal peptide is inserted into the ER membrane lipid bilayer d. all of the above e. a) and b) but not c)

25. Suppose the carboxy terminal domain (CTD) of RNA Pol II became drastically shortened as a result of a mutation. What processes would be affected? a. 5' capping would be hindered b. splicing of introns would be slowed c. cleavage and polyadenylation would be reduced d. Transcription of pre-mRNA would be slowed e. All of the above

25. What do vesicle coat proteins (and adapter proteins) do? a. enforce membrane curvature b. promote fusion of the vesicle to the right target membrane c. sort receptor proteins via their cytoplasmic motifs d. both a) and b) e. both a) and c)

27. Which of the following is NOT a small molecule neurotransmitter? a) acetylcholine b) -aminobutyric acid (GABA) c) dopamine d) histamine e) pick this if all of the above are neurotransmitters

3. This figure shows one model for the role of IRE1 in activation of Hac1 and the unfolded protein response. Which of the following would prevent or reduce the unfolded protein response? a. A mutation in IRE1 that prevents it from binding BiP b. A mutation in IRE1 that prevents dimerization c. overexpression of BiP d. A mutation in IRE1 that reduces the endonuclease activity e. either b) or c)

33. Proteoglycans are glycoproteins w/covalently attached glycosaminoglycans (GAG) that are comprised of which of the following anionic disaccharides? a) lactose b) sucrose c) chondroitin sulfate d) heparan sulfate e) c and d

36. Platelet activating factor (PAF) and secreted activators (including chemokines) activate leukocyte ______ to enable them to tightly bind to endothelial ICAMs and participate in the extravasation of the leukocyte. (hint: The answer to this question is also one of the types of proteins shown in the figure above.) a) lamins b) desmosomes c) E-cadherin d) connexin e) integrins

4. Hydrogen bonds between side chain atoms of polypeptide chains stabilize what level(s) of protein structure? a) secondary b) tertiary c) quaternary d) both secondary and tertiary e) both tertiary and quaternary

6. Eukaryotic mRNA molecules that lose their cap ____ a. will be degraded more quickly b. will not be translated very efficiently c. will not exit the nucleus d. all of the above e. both a) and b)

9. PKB is activated by ____. a) IP3 b) cGMP c) DAG d) cAMP e) none of the above

Which is activated when a cytokine binds to its receptor and activates JAK? a) activation of PKB and PDL1 b) ADAM 10 cleavage of Notch protein c) phosphorylation of Smad2/3 and assembly of the Smad2/3-Smad4 complex d) translocation of pro-SREBP from the ER to the Golgi by Sec24 binding to SCAP e) phosphorylation and dimerization of STAT proteins

15. Alzheimer's disease is associated with inappropriate cleavage of amyloid precursor protein (APP) by β-secretase and γ-secretase to produce ____ that spontaneously form oligomers that aggregate into the large amyloid plaques found in the brains of patients with Alzheimer's disease. a) an active protein kinase that phosphorylates cell membrane proteins b) substantial amounts of a 42-amino-acid Aβ42 peptide c) large amounts of an unnatural amino acid with a D-stereochemistry

18. Since the cellular concentration of actin is usually much higher than the critical concentration, the major mechanisms used to regulate microfilament growth and shortening are ___. a) synthesis of more actin in the location where needed by nearby polysomes and actin mRNA b) proteins such as profilin, formin, thymosin-4, etc. that interact in some manner with actins or microfilaments to alter their rate of formation/dissociation. c) proteolysis of the ends of the microfilaments so that the faster proteolysis shortens the microfilament but when proteolysis is inhibited, the microfilament undergoes net growth.

22. This diagram illustrates the role of Rac in regulating Lamellipodia formation during cell migration. Note that one of the components of the signaling pathway is Arp2/3. When you see that Arp2/3 is participating in an actin assembly mechanism, you know that the process involves ______. a) formation of a filament that will be associated with muscle myelin b) assembly of actins to from a branched filament c) recruitment of tubulins to co-polymerize with actins to form a mixed filament of alternating actins and tubulins.

23. Is Arp2/3 only involved in cell migration, or does it participate in other cellular processes? a) Arp2/3 is only involved in cell migration b) Arp2/3 also participates in actin assembly during endocytosis and phagocytosis and possibly other cell processes.

26. The transfer of oligosaccharide from dolichol-phosphate to asparagine residues of proteins occurs in: a. the cytoplasm b. the lumen of the ER c. the ER membrane d. the peroxisome e. the Golgi

5. What type of bonding is important for formation of protein secondary structures such as alpha helices and beta sheets? a) van der Waals interactions b) hydrogen bonds between peptide backbone atoms c) ionic bonds between amino acid side chains d) covalent bonds between cysteine residues

c2. For the signaling switch shown on the right, the reaction shown from the bottom to the top (i.e., the conversion of the inactive G protein to active G protein) is accelerated by _____. a) PKG, G-protein kinase b) GAP, GTPase activating protein c) GEF, GTP exchange factor d) all of the above

5. Regulation of gene expression by PKA signaling in the nucleus is usually mediated via _______. a) Ca2+/calmodulin b) MAPK c) NFB d) the cAMP-response element (CRE)

4. You wish to create a yeast plasmid that is replicated once each cell cycle and segregates to both daughter cells during mitosis. What DNA sequence elements must be present on the plasmid? a. an origin of DNA replication b. a centromeric sequence c. a telomeric sequence d. all of the above e. both a) and b) but not c)

D or E

10. What is (are) the role(s) of general pol II transcription factors (TFIIA,B,D,E,F, and H)? a. They bind to transcription factors such as TBP b. They recruit RNA polymerase II c. They bind to mediator d. They phosphorylate the carboxy terminal domain of RNA pol II e. All of the above

26. Which of the following statements is(are) true? a. cellular membranes all have the same composition b. the exoplasmic leaflet has a different lipid composition than the cytosolic leaflet c. different organelles within the same cell have different membrane lipid composition d. all of the above e. both b) and c) but not a)

3. Which transposons encode a reverse transcriptase? a. LINEs b. LTR-retrotransposons c. DNA transposons d. SINES e. both a) and b)

11. The image at right shows the structure of a calcium-dependent protein kinase. The kinase is activated when calcium ions bind to the EF-hands within the CaM-like portion of the protein. Which description uses the correct terminology? a. The CaM-like motif contains 4 EF-hand calcium binding domains b. The CaM-like domain contains 4 EF-hand calcium binding motifs c. CDPK contains both a kinase motif and a CaM-like domain d. CDPK contains both a kinase domain and a CaM-like motif

12. Which proteins assemble to form barrel-shaped chambers where unfolded or mis-folded proteins go and are attempted to be refolded? a. chaperones b. chaperonins c. ubiquitin d. all of the above

13. Which of the following domains bind(s) to phosphotyrosine on an activated growth factor receptor? a) Akt b) SH2 (Src homology 2 domain) c) PH (pleckstrin homology domain) d) choose this if all of the above bind phosphotyrosine

14. What sequence in the pre-mRNA signals polyadenylation? a. GU and AG b. AAUAAA c. CG d. UAUA e. TATAA

10. PKC is activated by _____. a) cGMP b) DAG c) cAMP d) none of the above

1. Which domains of cellular life are classified as prokaryotes? a) bacteria only b) bacteria and archaea c) bacteria and eukarya e) archaea and eukarya d) archaea only

1. Which of the following describes the function of APC (anaphase promoting complex)? a. It leads to the degradation of CDK1 at the end of mitosis. b. It leads to the separation of sister chromatids by degrading Securin. c. It adds ubiquitin tail to proteins and leads to their degradation in Lysosome. d. It digested nuclear envelop at M-phase.

1. Which of the following makes unidirectional conduction of action potential possible? a) depolarization period b) refractory period c) polarization period d) hyperpolarization period

1. The primary subcellular location where proteins are sorted for secretion, transport to the plasma membrane, etc. is the _____. a) cis Golgi network b) trans-Golgi network c) early endosome d) autophagosome

1. What does the signal recognition particle (SRP) do? a. SRP mediates fusion of coated vesicles with their target membranes b. SRP binds to leader signal peptides on nascent proteins and docks them to the translocon in the ER membrane c. SRP forms a channel in the ER membrane and directs co-translational translocation of ER proteins into the lumen. d. SRP recognizes misfolded proteins in the ER and triggers the unfolded protein response.

6. In S. pombe, loss of function mutation in the wee1 gene leads to a "wee" phenotype because wild-type Wee1 protein: a. is essential for taking up nutrients in the media. b. phosphorylates MPF to inactivate it. c. is a chaperon protein required for proper protein folding. d. dephosphorylates MPF to activate it.

6. Vesicles in anterograde transport from the ER to the Golgi have what kind of coat? a. COPI b. COPII c. clathrin/AP1 d. clathrin/AP2 e. AP3

6. Which proteins form gap juctions? a) Occludins b) Connexins c) Claudins d) Gapsins e) Junxins

63. Which of the following pairs INCORRECTLY matches the cell junction and molecules? (a) adherens junction, Cadherin (b) gap junctions, Occludin (c) tight junctions, Claudin (d) focal adhesion, Integrin

64. Both cell-cell and cell-matrix adhesions are strengthened by ________. (a) parallel alignment (b) linkage to cytoskeleton (c) hydrophobic interactions

65. Which of the following statement correctly describes the activation of integrins? (a) Integrin dimers have a "bent" confirmation when activated. (b) Integrins can be activated by binding to matrix proteins with their extracellular domain. (c) When activated from inside-out, integrins no longer binds to matrix proteins. (d) Once activated, integrins can activate cellular signal pathways such as RTKs and Wnt pathways.

7. Which of the following can pass through gap junctions? a) fibronectin b) glucose c) ribosomes d) viruses e) none of the above

7. Which of the following proteins is required for the elongation of the leading strand at a DNA replication fork? a. primase b. DNA polymerase c. a ssDNA binding protein d. a DNA ligase e. all are required for leading strand elongation at a DNA replication fork

72. Which of the following condition will NOT leads to apoptosis? (a) DNA damage. (b) Overexpression of Bcl-2 (c) Cytochrome C release from mitochondria. (d) Activation of Caspase 3.

73. Which of the following correctly matches cell type and function? (a) neuron - nutrition (b) Schwann cell - myelination (c) Astrocyte - immunity (d) Oligodendrocyte - blood brain barrier

74. Which of the following statement correctly describes the firing of action potential along axon? (a) Axon membrane has a negative resting potential because Na+ and K+ pumps pump positively charged ions outside the axon. (b) Voltage-gated Na+ channel opens up in response to local depolarization and results in further depolarization of the membrane potential. (c) Non-gated K+ channel opens up to repolarize the membrane potential. (d) Voltage-gated K+ channel leads to rapid K+ influx and restore the membrane potential to resting potential.

75. Which of the following makes unidirectional conduction of action potential possible? (a) depolarization period (b) refractory period (c) polarization period (d) hyperpolarization period

76. Which of the following correctly describes the sequence of events during synapse? (a) action potential reaches axon hillock, fusion of synaptic vesicle, uptake of neurotransmitters by recipient cell, recycling of neurotransmitters back to synaptic vesicle. (b) action potential reaches axon terminus, fusion of synaptic vesicle, uptake of neurotransmitters by recipient cell, opening of ion channels in the recipient cell leading to changes of membrane potential. (c) action potential reaches axon terminus, recovery of synaptic vesicle, release of neurotransmitters, recycling of neurotransmitters back to synaptic vesicle. (d) action potential reaches axon terminus, release of neurotransmitters, recycling of neurotransmitters, fusion of synaptic vesicle.

8. After activation, some receptors bind _______ on the cytoplasmic domain of the receptor to mediate it's endocytosis by binding of AP2 and clathrin. a) β-Catenin b) β-Arrestin c) β-Amyloids d) β-Endmorphins

8. p53 gene/protein is the genome gate keeper. Which one does NOT describe function/feature of p53? a. In normal cells, p53 is at low concentration. b. When bound to p53, MDM2 protein leads to p53 activation. c. ATM/ATR phosphorylate p53 and stabilizes p53. d. p53 activates expression of genes involved in DNA repair/replication.

9. Botulinum toxin undergoes proteolytic processing after endocytosis, to release an active protease. In what cellular compartment is this proteolytic processing most likely to occur? a. in early endosomes, pH = 7 b. in late endosomes, pH = 5 c. in the cytoplasm after release from the endosomal compartment, pH = 7 d. in the proteasome

14. Which of the following is(are) characteristic of necrotic cell death but not apoptotic cell death? a) DNA fragmentation b) nuclear fragmentation c) appearance of phosphatidylserine on the outer leaflet of the plasma membrane d) holes appear in the plasma membrane e) all of the above except d)

10. The activated Botulinum toxin protease specifically cleaves SNARE proteins. What is the result? a. coated vesicles cannot form b. coated vesicles form but cannot uncoat c. uncoated vesicles cannot be transported to their target membranes d. uncoated vesicles cannot fuse with their target membranes

10. Which of the factor is NOT responsible for the restriction point control? a) p53 b) Rb c) P21 d) CDK1

10. Which of the following is NOT a component found in a synapse? a) neurotransmitter b) presynaptic cell c) action potential d) axon hillock

11. The functions of the extracellular matrix include: a) supporting differentiation. b) inducing morphogenesis. c) binding growth hormones. d) all of the above

16. The major component of microfilaments is _____. a) actin b) tubulin c) actinin d) filamentin

16. What would happen to an mRNA that loses its poly(A) tail? a. it would be rapidly degraded b. it would be translated more efficiently c. it would not be exported from the nucleus to the cytoplasm d. it would not undergo splicing to remove introns

17. The diagram from the text that gives the critical concentrations for actin polymerization at the (-) and (+) ends is shown below: One of the things that you learn from the rate constants that explain the critical concentrations for the two ends of the filament is: a) the rate constant for association of actin monomers at the (+) end is about 10-fold higher than at the (-) end b) the rate constant for association of actin monomers at the (-) end is about 10-fold higher than at the (+) end c) the rate constants for association of the actin monomers at the (+) and (-) ends are about the same

2. the aggregation of lipid molecules in water is driven primarily by: a. an increase in entropy of the water molecules surrounding the lipid molecules b. the formation of hydrogen bonds between the lipid molecules c. increased van der Waals interactions between the lipid molecules d. a decrease in the entropy of lipid molecules

20. Myosins convert ________ into mechanical work, with the myosin head undergoing binding and releasing from actin, and processes such as "cocking" and the "power stroke," through conformation changes as __________. a) ATP hydrolysis ............. ATP is bound, hydrolyzed, phosphate is released and ADP is released so another ATP can be bound b) ATP synthesis ............. ADP is bound, phosphate is bound and the mechanical motion causes loss of water to produce ATP

24. Which of the following G-proteins is/are also associated with regulation of actin during cell migration? a) Rho b) Roc c) Rol d) Roc & Rol are both involved in cell migration

27. The (-) end of a microtubule is generally anchored to ___ . a) the microtubule organizing center b) the endoplasmic reticulum c) the trans-Golgi d) the late endosomes formed by endocytosis of a growth factor

30. For all of the GTP-binding proteins discussed in the preceding question, the proteins are active when GTP/GDP (pick one) is bound. By active, one means that the proteins that control polymerization of coat proteins are promoting coat assembly (not disassembly, which is what they do when they are considered to be switched "off"). a) GTP b) GDP c) actually, it doesn't matter. The phosphorylation state of the guanine nucleotide doesn't affect the function of the proteins.

31. ______ are present only during the cell cycle stage that they trigger, whereas, _____ are present throughout multiple cell cycle stages. a) Cyclins ............... cyclin-dependent kinases (CDK) b) Cyclin-dependent kinases (CDK) .......... cyclins

4. Another depiction of fibronectin is shown here. What binds fibronectin at the site designated by a question mark (i.e., the RGD sequence) and communicates the binding to intracellular signaling pathways? a) an integrin b) E-cadherin c) -catenin d) -catenin

4. Which of the fatty acids below has the highest melting temperature, and pack most tightly in cell membranes? a. stearic acid 18:0 b. oleic acid 18:1 cis c. elaidic acid 18:1 trans d. linoleic acid 18:2 cis, cis

8. The imidazole side chain of histidine has a pKa of 6. At pH 7, what will be the ratio of positively charged (protonated) to uncharged (unprotonated) histidine residues? Recall pH = pKa + log([A-]/[HA]) a. 1:10 charged:uncharged b. 1:1 charged:uncharged c. 10:1 charged:uncharged d. 2:1 charged:uncharged

3. Fibronection type III and talin are thought to undergo the types of conformation changes shown on the right in response to: a) pH change b) ubiquitination c) dark energy d) mechanical force/stretching e) binding to Cu2+

31. Each v-SNARE in a vesicular membrane specifically binds to a complex of cognate ________ proteins. a) ARF b) Clathrin c) v-SNARE d) t-SNARE e) SNIP

9. Which type of promoter often generates bidirectional transcription by RNA pol II? a. TATA box b. Initiator c. CpG islands d. both a) and b) e. both a) and c)

13. Which of the following pre-mRNA processing steps occurs first? a. addition of the 7-methyl guanosine at the 5' end b. splicing to remove introns c. cleavage and polyadenylation of the 3' end d. these steps occur in random order

6. If you have not eaten recently and you have elevated circulating glucagon (or you have been frightened, such as by this exam, and have high epinephrine), cAMP in liver will be high and PKA will activate glycogen phosphorylase kinase, which in turn activates glycogen phosphorylase (GP) to hydrolyze glycogen stored in liver to glucose 1-phosphate. There is also an enzyme that synthesizes glycogen in the fed state (glycogen synthase), so why doesn't it reverse the process and cause the glucose to continuously cycle back and forth (glycogen glucose) and make this an inefficient waste of energy? a) glycogen phosphorylase is only present in liver and glycogen synthase is only in lung, so these metabolic processes do not occur in the same part of the body b) glycogen phosphorylase and glycogen synthase are both present in liver, but glycogen synthase is also phosphorylated by PKA and phosphorylated glycogen synthase is inactive. c) glycogen phosphorylase and glycogen synthase genes are found in liver, but transcription and translation of the gene for glycogen phosphorylase only occurs in the fasting state and transcription and translation of the gene for glycogen synthase only occurs in the fed state.

6. Which of these mutations is most likely to disrupt a protein's tertiary structure and its function? a) E (glutamic acid) to D (aspartic acid) b) C (cysteine) to G (glycine) c) W (tryptophan) to F (phenylalanine) d) S (serine) to T (threonine)

7. At equilibrium, the deltaG of a chemical reaction is: a. negative b. zero c. positive d. negative for exergonic reactions and positive for endergonic reactions

7. One of the functions on the protein -Arrestin it to bind to the cytosolic domain of some G-protein coupled receptors and induce their _______. a) secretion from the cell b) endocytosis c) covalent cross-linking with spectrins to permanently anchor them in the plasma membrane d) all of the above

1. Which of the following cell adhesion molecules (CAM) form Ca2+-dependent extracellular homophilic interactions with themselves (i.e., proteins in the same category of CAM) on adjacent cells (trans interactions) as well as cis- interactions that cluster them on the same cell? a) Selectins b) Integrins c) Cadherins d) All of the above e) None of the above

10. A cytoplasmic enzyme in the cell is found to have a Km of 1 micromolar for its substrate. The concentration of the enzyme's substrate is around 20 micromolar. How can the cell double the rate of the reaction performed by the enzyme? a. the cell should use an allosteric regulator to decrease the enzyme's Km by 50% b. the cell should use an allosteric regulator to increase the enzyme's Km by 2X c. the cell should make twice as much enzyme d. the cell should make twice as much substrate for the enzyme e. any of the above, except b)

11. Which is activated when TGF- binds to it's receptor and the ligand-bound RII component of the receptor recruits and phosphorylates the RI receptor, releasing inhibition of RI kinase activity? a) activation of PKB and PDL1 b) ADAM 10 cleavage of Notch protein c) phosphorylation of Smad2/3 and assembly of the Smad2/3-Smad4 complex d) translocation of pro-SREBP from the ER to the Golgi by Sec24 binding to SCAP e) phosphorylation and dimerization of STAT proteins

13. Damaged proteins and proteins that cannot refold properly are____ a. escorted to the proteasome by chaperones b. ubiquitinated and degraded by chaperonins c. ubiquitinated and degraded by the proteasome d. ubiquitinated and secreted from the cell

14. Which of the following is NOT possible, according to what we currently know about how information flow can occur in nature? a. a nucleotide change in DNA causes a change in the protein amino acid sequence b. a nucleotide change in an RNA sequence causes a change in the DNA sequence c. a change in the protein amino acid sequence causes a change in the mRNA sequence d. a change in the mRNA sequence causes a change in the protein amino acid sequence

23. Which cellular DNA repair system repairs thymidine dimers caused by UV-irradiation? a. mismatch repair b. base excision repair c. nucleotide excision repair d. non-homologous end-joining e. homology-directed recombination repair

24. HMG-CoA is the precursor for which class of membrane lipids? a. phosphoglycerides b. sphingolipids c. sterols d. all of the above e. both phosphoglycerides and sphingolipids

26. The process shown here, where a microtubule is undergoing assembly and disassembly via catastrophe and rescue is referred to as ________. a) decapping b) explosive decomposition c) dynamic instability d) an entropic adjustment

27. How do nuclear-encoded mitochondrial proteins become localized to the mitochondria? a. They are synthesized by cytoplasmic ribosomes docked to the mitochondrial outer membrane. b. Their mRNAs are transported into the mitochondria for translation by mitochondrial ribosomes. c. They are synthesized by cytoplasmic ribosomes and then transported into the mitochondria by Toms d. This is a trick question: all mitochondrial proteins are encoded by the mitochondrial genome.

29. The small GTP-binding protein _____ controls polymerization of coat proteins in the ER, the initial step in vesicle budding and trafficking to the Golgi. A second category of GTP-binding proteins, the ____ proteins, label specific vesicle types and enable their targeting to the appropriate membrane. Which pair or proteins below accurately fit in these blanks? a) Sar1......ARF b) Sar1......Sar2 c) Sar1......Rab d) Sar2......Sar1 e) Rab.......ARF

29. Which category of kinesin shown on the right would be responsible for the sliding of microtubules relative to each other, as shown in the diagram below at the position labeled B1: a) Kinesin-1 b) Kinesin-2 c) Kinesin-5 d) Kinesin-13

33. Cyclins are degrated through the action of _______. a) the ubiquitin-protein ligase SCF b) the anaphase-promoting complex, APC/C c) both of the above d) none of the above

5. Chromatin is isolated from a eukaryotic cell, and then digested to completion with micrococcal nuclease (cuts naked DNA). The DNA is then purified away from bound proteins and electrophoresed on an agarose gel. What size DNA fragments would you expect to see? a. No DNA - it will have been digested to single nucleotides b. A smear of very small fragments - oligonucleotides c. A blob of DNA fragments at around 140-150 nucleotides d. A ladder of DNA fragments of 200, 400, 600, etc. e. Long DNA molecules greater than 10 kbp (kilobasepairs)

11. Recruitment of which enzyme(s) to a region of chromatin would cause it to become more condensed? a. DNA methyl transferase (DNMT) b. histone deacetylase (HDAC) c. histone acetyl transferase (HAT) d. both a) and b) e. both a) and c)

12. What is the target of the maintenance DNA methylase, DNMT1? a. any cytosine in the DNA b. any cytosine in newly replicated DNA strands, where the partner DNA strand has methylated cytosines c. any cytosines that are 5' to a guanine d. cytosines that are 5' to a guanine, where the partner DNA strand has methylated cytosine e. guanines that are 3' to a cytosine, where the partner DNA strand has methylated guanine

14. Which of the following pathways involves proteolytic cleavage of one of the signaling components as part of the intracellular signaling mechanism (by proteolytic cleavage the question means that the signaling protein can either be cleaved itself or something that is inhibiting it can be destroyed by proteolysis)? a) the Hedgehog pathway b) the activation of SREBP (sterol-regulatory element binding protein) c) NF-B d) all of the above e) none of the above

18. CRISPR-Cas9 is being widely used for genome editing. When Cas9 cuts DNA to create a double-strand break, what is the predominant cellular response? a. base excision repair b. mismatch repair c. nucleotide excision repair d. non-homologous end joining e. homologous recombination

2. The cytoplasmic domains of CAMs bind adapter proteins that mediate interactions with: a) cytoskeletal fibers b) intracellular signaling proteins c) collagen IV d) a and b e) a and c

20. The resolution of optical fluorescence microscopy can be enhanced by using: a. an objective with a greater angle alpha b. a medium (such as oil) with a greater refractive index than air c. a fluorescent label that emits bluish light at 450 nm instead of a fluorescent label that emits red light at 700 nm d. all of the above e. none of the above

25. Proteins can be associated with the membrane by which post-translational modifications? a. acylation of their N-terminus such as myristoylation and palmitoylation b. prenylation of their C-terminus c. addition of a GPI anchor at their C-terminus d. all of the above

BIO 3450 Final Questions

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