C&M Exam III
Receptor tyrosine kinases
activate the Ras protein through adaptor proteins that bind to phosphotyrosines
Gαq
activates PLC-β, which hydrolyses an inositol phospholipid.
Gαs
activates adenylyl cyclase, which makes cAMP from ATP
Histones can be modified by a reaction that results in the addition of an acetyl group to the side chain of the amino acid lysine. Lysine acetylation in histones:
activates transcription by allowing access of the the transcriptional machinery to less condensed template DNA.
Glucose uptake from a lower to a higher concentration must be due to
active transport
A fluorescent dye, which is a small charged molecule, is injected into the cytoplasm of a cell. After some time is allowed for the dye to distribute, where would you expect to see the dye? (a) the cytosol (b) the nucleus (c) the intermembrane space of mitochondria (d) the lumen the ER and Golgi apparatus (e) all except (d)
all except (d)
Aminoacyl-tRNA synthetases have binding sites for: a) an amino acid. b) a tRNA. c) ATP. d) All of the above.
all of the above
Ca2+ is used as a transient intracellular second messenger -when inositol 1,4,5-trisphosphate (IP3) binds to its receptors on the endoplasmic reticulum -to activate protein kinase C (PKC) -at nerve terminals to cause release of synaptic vesicles -in response to Gαq-coupled serpentine receptors -all of the above
all of the above
The function of the 5′ cap and poly(A) tail includes: a) increased mRNA stability (protection from degradation). b) increased translational efficiency. c) transport to cytoplasm. d) All of the above.
all of the above
The water-splitting enzyme in photosynthesis (a) is present in photosystem II. (b) is driven by the removal of an electron from chlorophyll, creating a positively charged chlorophyll that has a greater affinity for electrons that O2. (c) has generated all of the O2 in the earth's atmosphere. (d) must keep reaction intermediates tightly bound so that superoxide radicals don't escape. (e) All of the above.
all of the above
Transcription regulation is characterized by: a) DNA-protein interactions. b) Protein-protein interactions. c) Response to environmental stimuli. d) All of the above.
all of the above
What is the similarity between pre-mRNA splicing and translation? (a) Involve large RNA-protein complexes.(b) Required for flow of genetic information.(c) Key reaction catalyzed by RNA. (d) All of the above.
all of the above
What type of energy is directly used to make ATP in mitochondria and chloroplasts?
A proton electrochemical gradient established by the electron transport chain.
You have reconstituted ATP synthase in a liposome with the orientation opposite to the one above, as shown in at right. What minimum combination of salts, buffers, and other soluble components would you place inside and/or outside of the vesicle to cause ATP synthase to lower the pH inside? Identify the component(s) and where it (they) is (are) to be placed.
ATP (1) outside (1) (protons come from ionization of water)
Apoptosis differs from necrosis in that necrosis
causes cells to swell and burst while apoptotic cells shrink and condense.
G-protein coupled receptors
change conformation in response to ligand (hormone) binding AND cause exchange of GTP for GDP in the α subunit of a trimeric GTP-binding protein
Proteins must be unfolded to get into
chloroplasts, ER, mitochondria, but not the nucleus
What causes trisomy 21, giving rise to Down's syndrome?
chromosome nondisjunction during meiosis
Operons:
contain a cluster of genes transcribed as a single mRNA.
tRNA:
contains many modified bases (such as pseudouridine, ribothymidine, and inosine).
What molecular switching mechanism(s) are commonly used in signal transduction?
covalent modification with phosphate derived from ATP; and GTP exchange and GTP hydrolysis
What is released by mitochondria to activate the intrinsic mechanism of apoptosis?
cytochrome c
In what part of the cell does glycolysis occur?
cytoplasm
Where in the cell does glycolysis occur?
cytoplasm (cytosol)
You use recombinant DNA technology to express a protein whose N-terminus has 24 amino acids in a row that have non-polar side chains. The rest of the protein has three regions containing 16-18 non-polar amino acids in a row interspersed with a mixture of polar and charged amino acids. Where will this protein be LEAST likely to be found when expressed in eukaryotic cells?
cytosol
In chloroplasts, carbon fixation in the Calvin cycle reduces carbon dioxide to glyceraldehyde 3- phosphate. The ∆G is positive for these reactions. Where does the energy directly come from to fix carbon in the Calvin cycle?
ATP and NADPH
You have reconstituted ATP synthase in a liposome with the orientation shown in at right in a buffer of neutral pH. What minimum combination of soluble components would you place inside and/or outside of the vesicle to cause ATP synthase to lower the pH inside?
ATP on the outside of the liposome.
Different vesicle coat proteins regulate membrane traffic in different intracellular locations. What general role, or what step(s) in membrane traffic, involves vesicle coat proteins?
transport vesicle budding
Which of the following is NOT a type of pre-mRNA processing: a) 5 ́ capping. b) 3 ́ cleavage and polyadenylation. c) RNA splicing. d) transposition.
transposition.
The process where actin filament monomers are added to one end and simultaneously removed from the other end is called
treadmilling.
Na+/K+ ATPase
uses ATP to drive sodium and potassium ions against their electrochemical gradients on the plasma membrane
What proteins ensure that transport vesicles don't randomly fuse with any organelle?
v- and t-SNARES (2)bonus (2): Rab proteins ensure targeting; SNAREs specify fusion
Transport of proteins from the endoplasmic reticulum to the Golgi apparatus involves what kind of mechanism?
vesicle budding and fusion
Transport of proteins from the endoplasmic reticulum to the Golgi apparatus involves what?
vesicle budding and fusion
Which of the following is required for the secretion of neurotransmitters at the synapse in response to an action potential?
voltage-gated Ca2+ channels
In the same graph as the questions above, what is happening in phase (3) of the action potential?
voltage-gated K+ channels remain open
In the same graph as the question above, what is happening in phase (2) of the action potential?
voltage-gated Na+ channels are inactivated and voltage-gated K+ channels open
The graph at right is an electrical recording from a neuron that has triggered an action potential, showing membrane potential (y-axis) vs. time (x-axis). The bottom is command voltage set by the experimenter. What is happening in phase (1) of the action potential?
voltage-gated Na+ channels open
Why did it take two billion years from the time when the first photosynthetic cells arose for oxygen to build up in the atmosphere?
Fe2+ ions dissolved in the ocean soaked up the oxygen: precipitated until Fe2+ was used up. Soluble iron soaked up the oxygen in the ocean until it all precipitated as iron oxide.
Why does fermentation enable glycolysis to continue? (a) Fermentation provides oxygen for the citric acid cycle. (b) Fermentation produces ethanol, which allows high-energy electrons to be channeled. (c) Fermentation releases CO2, which is used to make sugars in mitochondria. (d) Fermentation regenerates NAD+ so that it can be converted to NADH in glycolysis. (e) Fermentation has nothing to do with glycolysis, it has no relevance.
Fermentation regenerates NAD+ so that it can be converted to NADH in glycolysis.
why are replication origins AT-rich?
Fewer hydrogen bonds in an A=T base pair than a G≣C base pair make the two strands easier to separate to access the template
Bcl-2 and Bax antagonize each other in which specific mechanism?
Release of cytochrome c from mitochondria
Phosphorylation of the retinoblastoma protein (Rb)
Releases a transcription factor (E2F) to initiate the cell division cycle
How is it possible to create both viable fetus and a stem cell line from one zygote after in vitro fertilization?
Remove one blastomere at the 8-cell stage and create a stem cell line from that. The blastocyst then develops normally from the remaining 7 cells.
What is semidiscontinuous replication?
Replication is continuous on one strand (leading) and discontinuous on other strand (lagging)
Contiguous |kənˈtigyo͞ oəs| (adjective) is defined as sharing a common border; touching, as in: the 48 contiguous states. In eukaryotic cells, the nuclear membrane is contiguous with what?
The endoplasmic reticulum.
Reaction coupling is best described as
Using the energy of a reaction to drive formation of intermediates whose energy can be harvested in subsequent reactions.
Organelles with a low pH that contain proteases and lipases are
lysosomes
Briefly describe in three sequential phases of activity what is happening to sodium AND potassium channels in C. (8 points)
(1) Na+ channels open, membrane potential becomes more positive (2 points) (2) Na+ channels become inactivated (2 points); K+ voltage-gated channels open (2 points); membrane potential becomes more negative (3) K+ channels remain open for a short time (2 points); membrane potential becomes more negative than resting potential = after-hyper-polarization
Which organelle sorts proteins to different target destinations in vesicular membrane traffic? (a) endoplasmic reticulum (b) lysosomes (c) endosomes (d) trans Golgi network (e) (a), (c) and (d)
(a), (c) and (d)
Predict the membrane potential of the liposome above, with the different salt concentrations inside and outside as shown, in the presence of tetrodotoxin. The Nernst equation (simplified) is Veq = 58mV•log10Co/Ci at room temperature.
-58 mV (only K+ channels matter in the presence of tetrodotoxin)
Which of the following proteins must translocate across the endoplasmic reticulum membrane before delivery to their target organelle?
-ER membrane proteins -Plasma membrane proteins -Soluble secreted proteins
List three ways that eukaryotic transcription differs from bacterial (prokaryotic) transcription.
-Eukaryotic cells have three RNA polymerases.-Eukaryotic RNA polymerases need general transcription factors. -In eukaryotic cells, gene regulatory proteins can influence transcriptional initiation thousands of nucleotides away from the promoter.-Eukaryotic transcription is affected by chromatin structure and nucleosomes. -Eukaryotes separate transcription and translation in cellular compartments (nucleus and cytoplasm). -Eukaryotes process their RNA.
Name three purposes of programmed cell death (apoptosis) during development and/or in adult multicellular organisms.
-In response to excessive DNA damage (2). -Elimination during development because they are not needed (2). -Receptor-activated apoptosis is by killer cells in the immune system (2).
Telomerase catalyzes the synthesis of telomeres and is comprised of two subunits. What is each subunit made of and what is its function?
-Protein--> DNA polymerase/reverse transcriptase (catalyzes DNA synthesis). -RNA--> Template (for telomere synthesis).
Describe two methods that can be used to create pluripotent stem cells from an adult mammal. Include the different initial steps and the common final steps to create stem cells that can be grown in culture.
-iPS: made from adult somatic cell express 3 or 4 genes (transcription factors) (2) -------SCNT: transfer nucleus from adult cell into enucleated oocyte (2) -Both: allow cell to form a blastocyst, then take inner cell mass cells to grow in culture to make pluripotent stem cells (2)
The ∆G for the oxidation of glucose in cells
-is exactly the same as the ∆G from oxidation of glucose by combustion. -is the opposite sign of the ∆G for the synthesis of glucose after anabolic oxidative
How are induced pluripotent stem (iPS) cells made?
-made from adult somatic cell (2) -express 3 or 4 genes (transcription factors) (2)
A particular type of Drosophila mutant becomes paralysed, due to defects in synaptic transmission, when the temperature is raised. The mutation affects the protein dynamin, causing it to be inactive when the temperature is raised. Why would defects in dynamin block synaptic transmission? What would you expect to see in electron micrographs of the synapses of mutant flies exposed to elevated temperature?
-mutant dynamin can't pinch off vesicle (3) -endocytic vesicles remain attached to plasma membrane (3)
Acetylcholine can activate two distinct types of receptors, called nicotinic and muscarinic, that have very different effects on heart and skeletal muscle cells. What are these two types of acetylcholine receptors with different functional mechanisms?
-nicotinic - ion channel receptor -muscarinic - G-protein coupled receptor (GPCR) 2 points each
A 16 carbon fatty acid yields 31 NADH + 15 FADH2 + 8 GTP from fatty acid oxidation and the citric acid cycle. One glucose molecule yields 2 NADH + 2 ATP from glycolysis, and 8 NADH + 2 FADH2 + 2 GTP in mitochondria from the citric acid cycle. Each NADH produces about 2.5 ATP molecules, and each FADH2 produces 1.5 ATP molecules. How many glucose molecules would it take to produce more net energy than one 16 carbon fatty acid? Justify your argument by showing how many molecules of ATP the fatty acid and glucose make.
2 points: glucose makes 30 ATP (+2 GTP) (one point if they forget glycolysis and say 28); 2 points: palmitic acid makes 100 ATP (+8 GTP); 2 points: therefore it takes 4 glucose molecules to exceed the energy yield of one 16 carbon fatty acid
Match the parts of DNA to the labels (2 points for each correct match). Choose the most appropriate letter (A to E) and write it next to the number. Numbers have only one letter and all letters are used once and only once.
27. _B_ AT base pair. 28. _A_ GC base pair. 29. _E_ Deoxyribose. 30. _F_ Phosphodiester bond. 31. _C_ Purine base. 32. _D_ Pyrimidine base.
atch the functional elements of chromosomes
33. _B_ Site where DNA synthesis begins. 34. _C_ Ends required for linear DNA stability. 35. _A_ Confers correct mitotic segregation. A. Centromere. B. Replication origin. C. Telomere.
From the beginning of M (mitosis) phase to the next G1 phase in the cell division cycle, the number of chromosome copies in each cell goes from ___ to ___.
4n to 2n
From the beginning of meiosis, after S phase, to the production of gametes, the number of chromosome copies in each cell goes from ___ to ___.
4n to n
Name the three covalent modifications that are made to eukaryotic pre-RNA to convert them to mature mRNA
5′ capping RNA splicing 3′ cleavage and polyadenylation
If the potassium channels are open in the above vesicle, what will be the concentration of K+ inside the vesicle?
99.999 mM
Which dynamic process drives cytokinesis, the final separation of two cells after mitosis?
A contractile ring of actin and myosin
or each of the following sentences, fill in the blanks with the best word or phrase selected from the list below. Not all words or phrases will be used; each word or phrase should be used only once. (10 points)
A molecule moves down its concentration gradient by ____ passive ________ transport, but requires ____active____ transport to move up its concentration gradient. Carrier proteinsand ion channels function in membrane transport by providing a ____hydrophillic_______ pathway through the membrane for specific polar solutes or inorganic ions. ____carrier proteins________ are highly selective in the solutes they transport, binding the solute at a specific site and changing its conformation in order to transport the solute across the membrane. On the other hand, __ion channels_____ discriminate among solutes mainly on the basis of size and electrical charge.
Which of the following would decrease the transcription of only one gene in a bacterial cell?
A mutation that changes the promoter of the gene.
How is programmed cell death, or apoptosis, activated?
A protein causes mitochondria to leak proteins.
Glyceraldehyde 3-phosphate is a useful molecule. It is the product generated from the carbon fixation cycle that is the precursor to sugars, fats, and amino acids. It is also used in steps 6 and 7 in glycolysis. What energy carrier molecules are produced from the oxidation of the aldehyde in glyceraldehyde 3-phosphate to the carboxylic acid of 3-phosphoglycerate?
ATP; NADH
Which molecular mechanism is the best example of signal integration?
Activation of cyclin D/CDK kinase (G1 cyclin/CDK).
What causes Ca2+ to be released from the endoplasmic reticulum?
Activation of phospholipase C (PLC)
how is glucose transported from the lumen of the intestine after a long fast?
Active transport since glucose is flowing against its concentration gradient .
The difference between adult stem cells and embryonic stem cells is
Adult stem cells are multipotent whereas embryonic stem cells are pluripotent.
Excess cell proliferation can result from: Inactivation of tumor suppressor genes that put the brakes on the cell cycle Increased activity from oncogenes such as Ras Increased transcription of G1 cyclin D All of the above
All of the above
Programmed cell death in nerve cells Is a normal part of the development of the nervous system Is activated by caspases Is inhibited by growth factors secreted by the neuron's connecting partner All of the above
All of the above
What is the role of microtubules in mitosis? Motor proteins attached to aster microtubules attach to chromosomal centromeres Interpolar microtubules attach to the cell cortex and pull mitotic spindle poles apart Kinetochore microtubules are depolymerized at the kinetochore, shortening them, which helps pull daughter chromosomes apart Aster microtubules pinch cells away from each other during cytokinesis All of the above
All of the above
Which organelles have a lower pH (higher H+ concentration) than cytosol? (a) endoplasmic reticulum (b) the Golgi apparatus (c) endosomes (d) lysosomes (e) All of the above
All of the above
Mitochondria use which kind of energy transformations to convert pyruvate into ATP? (a) potential energy (electrochemical gradient) to enthalpy (chemical potential energy) (b) potential energy (enthalpy) to potential energy (enthalpy) in energy carrier molecules (c) enthalpy (chemical potential energy) to redox potential (energy stored in electrons) (d) redox potential (energy stored in electrons) to potential energy (electrochemical gradient) (e) All of the above.
All of the above.
The nuclear lamina is composed of lamins.is made up of a meshwork of intermediate filaments. is depolymerized during mitosis. is depolymerized by phosphorylation by cyclin B/Cdk1. All of the above.
All of the above.
What could happen to stem cells if they are transplanted and not fully differentiated into the cells required for tissue and organ generation? (a) Stem cells may form tumors. (b) Stem cells may migrate to different tissues and differentiate into different tissues outside the target for therapy. (c) Stem cells may not differentiate into a fully functional tissue or organ. (d) Stem cells may not survive in the target tissue or organ. (e) All of the above.
All of the above.
What is the similarity between pre-mRNA splicing and translation? a) Involve large RNA-protein complexes. b) Required for flow of genetic information. c) Key reaction catalyzed by RNA. d) All of the above.
All of the above.
Which organelles have a lower pH (higher H+ concentration) than cytosol? (a) lysosomes (b) endoplasmic reticulum (c) the Golgi apparatus (d) endosomes (e) All of the above.
All of the above.
Why is the maxim "one gene-one protein" not true for most eukaryotic genes?
Alternative splicing: most genes can be spliced in more than one way resulting in mRNAs containing different sequences and thus encoding different proteins
Why is the adage "one gene-one protein" not always true for eukaryotic genes?
Alternative splicing: the transcripts from some genes can be spliced in more than one way to give mRNAs containing different sequences, thus encoding different proteins. Therefore, a single eukaryotic gene may encode more than one protein.
The major theme of DNA binding is:
An alpha helix in the major groove.
The major theme of DNA-binding is:
An alpha helix in the major groove.
Which of the following is NOT involved in normal embryonic development?
Asymmetric distribution of chromosomes during mitosis
The protein, Bcl-2, was discovered to be mutated in a B-cell lymphoma: a chromosome translocation caused constant elevated transcription of Bcl-2. Why did this mutation cause lymphoma?
B cells failed to undergo programmed cell death normally.
Regarding the above diagram, why are two photosystems needed?
Because the energy of the electron donor from photosystem II is not sufficient to reduce NADP+ to NADPH. A second photosystem (K) is needed to excite electrons to a high enough energy state to do this.
What are the major similarities between replication and transcription?
Both DNA and RNA chains are produced using a DNA strand as a template. Both DNA and RNA strands grow in the 5 ́ 3 ́ direction.(Both DNA and RNA are synthesized in three stages: initiation, elongation, termination).
Why do mitochondria and chloroplasts have DNA inside a double membrane?
Both are derived by taking up a bacterium to form an endosymbiosis relationship.
What would be the result if one cell were simultaneously stimulated by two hormones, if one hormone activates a Gαs-coupled receptor and the other activates a Gαq-coupled receptor?
Both protein kinase A (PKA) and protein kinase C (PKC) would be activated.
What would be the result if one cell were simultaneously stimulated by two hormones, if one hormone activates a Gαs-coupled receptor and the other activates a Gαq-coupled receptor?
Both protein kinase A (PKA) and protein kinase C (PKC) would be activated.
If, during meiosis, cohesins were not degraded, what could result?
Both sister chromatids could end up in one daughter cell.
p53, the Guardian of the Genome, becomes activated to transcribe two key proteins to produce two different cellular response. What are these proteins that p53 transcribes, and what do they cause cells to do?
CKI p21 to halt the cell cycle (2). Bax to activate cell death (2)
Which of the following is NOT true about caspases?
Caspases are activated at key points during the cell division cycle.
Cyclin amounts rise slowly during the cell cycle, yet Cdk kinase activity rises sharply. Why?
Cdk activity is governed by phosphorylation (2) and cell division kinase inhibitors (CKIs) (1)
You want a bacterium to synthesize a eukaryotic protein; name two changes you need to make to the eukaryotic gene so that it can be expressed in the bacterium?
Change promoter Remove introns
Briefly define RNA editing.
Changing RNA sequence (after transcription).
Altered nuclear transfer, a new method to to create stem cells, attempts to solve which problem?
Chimeras are formed that are unable to implant and develop into a whole organism
Why do most bacterial chromosomes not need telomerase?
Circular chromosomes have no ends.
Which of the following statements about the cell cycle is TRUE? (a) Destruction of Cdk by the proteosome is the mechanism by which it's activity is turned off. (b) Cdk activity and Cdk protein amounts vary during the cell cycle. (c) There is a much sharper rise in Cdk protein synthesis due to cyclin activation. (d) Cyclin amounts rise slowly during the cell cycle, yet Cdk kinase activity rises sharply. (e) Activation of a cell surface receptor is required for Cdk transcription, which causes the cell to enter the next phase of the cell cycle.
Cyclin amounts rise slowly during the cell cycle, yet Cdk kinase activity rises sharply.
The lagging strand is synthesized discontinuously at the replication fork because:
DNA polymerase can polymerize nucleotides only in the 5′3′ direction.
Cells of the inner cell mass of the blastocyst differ from somatic, differentiated adult cells in several ways. In which ways are they primarily NOT different (except in special cases)?
DNA sequence
How does genetic information flow during gene expression?
DNA to RNA to protein.
What are the four principles of transcriptional regulation? (A phrase of about three words is sufficient for each.)
DNA-protein interactions Protein-protein interactions RNA-RNA interactions Response to environment
What are the three principles of transcriptional regulation?
DNA-protein interactions. Protein-protein interactions. Response to environment.
Which of the following DNA mutations is potentially the most damaging to the encoded protein?
Deletion of a nucleotide.
If you wanted to inhibit vascularization of a tumor, you could try to inhibit the signal for blood vessel formation: a polypeptide growth factor called VEGF. The VEGF receptor is a receptor tyrosine kinase. How might you try to inhibit this receptor or its signal transduction?
Design a molecule to uncouple it from Ras activation by interfering with adaptors that bind to the receptor's cytoplasmic tail. AND Design a molecule that inhibits the receptor's dimerization.
What mechanism in the cell division cycle ensures that each stage (e.g., S, M) cannot be reversed or started again once it is passed in a single cycle?
Destruction of cyclin by the proteasome is irreversible.
What mechanism(s) in the cell division cycle ensures that each checkpoint cannot be reversed once it is passed?
Destruction of cyclins by the proteosome is irreversible.
What is the significant feature of the oscillating amounts of cyclins during the cell cycle?
Destruction of cyclins is irreversible and ensures that the cell cycle goes in one direction.
Which of the following statements are TRUE? All hydrophobic signaling molecules bind to cell-surface receptors that contain at least one membrane- spanning domain. All extracellular signaling molecules are transported across the plasma membrane into the cytosol by their receptor. Cell-surface receptors capable of binding only one ligand can mediate only one kind of cellular response. Different cells having the same receptors can respond in different ways to the same ligand molecules. Foreign substances that occupy receptor sites normally bound by signal molecules always induce the same response that is produced by the natural ligand.
Different cells having the same receptors can respond in different ways to the same ligand molecules.
Dolly, the first cloned sheep, suffered various maladies and premature death. The process by which Dolly was cloned is called somatic cell nuclear transfer (SCNT). Identify the main reason that explains why Dolly was less healthy than normal.
Dolly was made from transfer of an adult nucleus =nuclear transfer (SCNT) (2)telomeres are shortened with every somatic cell division; telomerase was not re-expressed, so she had short telomeres (2)
If the bacterium Escherichia coli requires about 20 minutes to replicate its genome, how can the genome of the fruit fly Drosophila be replicated in only three minutes?
Drosophila DNA contains more origins of replication than E. coli DNA.
If a protein has a string of 18 hydrophobic amino acids on its N-terminus, and a string of 5 positively-charged amino acids on its C-terminus, to which organelle will it be first targeted? What are this protein's possible final destinations?
ER - (2 points; because N-terminus shows first, will be grabbed by the SRP) ER, Golgi, plasma membrane, early or late endosomes, lysosomes, secretory vesicles 1 point for any of these
A protein with 442 amino acids has a hydrophobic sequence of 20 amino acids on its N-terminus and five positively charged amino acids (four lysine residues and on arginine) at residues 374-377. (2 points) What is the specific function of each of these two regions identified in this protein? (2 points) Where in the cell will this protein likely be localized right after translation? (2 points) Why will this protein go to the location you indicate above and not go to the Other Place?
ER signal sequence: 18-30 hydrophobic amino acids on N-terminous Endoplasmic reticulum. Because the signal is recognized when they polypeptide nascent chain is emerging from the ribosome and the protein will begin translocation immediately.
DNA replication is considered semiconservative because:
Each daughter DNA molecule consists of one strand from the parent DNA molecule and one new strand.
What motivates electrons to flow from one reaction center to another in the mitochondrial electron transport chain?
Electrons flow between carrier molecules from lower to higher redox potential.
There are several inhibitors of RNA polymerase.a) (2 points) Rifampicin is an antibiotic used to treat tuberculosis; it binds to the β subunit of RNA polymerase and results in short RNAs of only two or three nucleotides. Which stage of transcription does rifampicin target? b) (2 points) α-amanitin is a deadly toxin found in the fungus death cap (Amanita phalloides); it inhibits RNA polymerase II and, to a lesser extent, RNA polymerase III. Which RNAs in a cell are not affected by α-amanitin poisoning?
Elongation. Pre-rRNA.
What would be the effect of a mutation in dynamin that impairs its ability to hydrolyze GTP?
Endocytosis from the plasma membrane would be impaired.
Why do fruit flies with the dynamin mutation, Shibire, exhibit paralysis when shocked?
Endocytosis is required for the recycling of synaptic membrane proteins during synaptic
When low density lipoprotein (LDL) and its receptor are taken into cells, what is the first destination, and what are two possible final destinations for LDL and its receptor?
Endosomes (2). From there they can go to late endosomes (2), or recycle back to the plasma membrane (s).
What is the main reason that a typical eukaryotic gene is able to respond to a far greater variety of regulatory signals than a typical bacterial (prokaryotic) gene or operon?
Eukaryotic gene transcription can be influenced by proteins that bind far from the promoter.
From the list above, write four compounds that are produced directly from the citric acid cycle.
FADH2, GTP, CO2, NADH
What causes a trimeric G-protein to return to its resting state?
GTP hydrolysis by the α subunit, which then binds to the βγ subunit.
What causes a trimeric G-protein to return to its resting, inactive state?
GTP hydrolysis by the α subunit, which then binds to the βγ subunit.
The endogenous cannabinoid, anandamide, is a lipophilic (hydrophobic) signaling molecule that activates the receptor, CB1, on interneurons that govern the synchronous action potential firing that creates rhythms in the brain. CB1 is one of the most widely expressed receptors in the brain. THC, which is derived from cannabis, activates CB1 and causes decreased production of cAMP and activation of potassium channels. What type of receptor is CB1, and what signaling mechanisms explain all of these results?
Gi-coupled GPCR; alpha-i inhibits adenyl cyclase; beta/gamma opens K+ channels
The lac operon is fully transcribed when:
Lactose is present and glucose is absent.
What is the structure of the excised intron from pre-mRNA splicing?
Lariat or branched.
What is the structure of the excised intron from nuclear pre-mRNA splicing?
Lariat.
What is wobble?
Less stringent base pairing between a tRNA and an mRNA.
(6 points) During the action potential in neurons, which voltage-gated ion channels open first? Which voltage-gated ion channels open second? Which voltage-gated ion channels open at the synapse to cause the release of synaptic vesicles containing neurotransmitters?
Na+ K+ Ca2+
Why does fermentation enable glycolysis to continue?
Regenerates NAD+
The genetic code.a) (2 points) This RNA includes the start codon that is the binding site for the initiator tRNA, which carries a Met (M): 5′-GUUUCCCGUAUACAUGCAUGCCGGGGGC-3′ Which amino acid will be carried by the aminoacyl-tRNA that is the first to bind to the A-site of the ribosome translating this RNA? b) (2 points) A mutation in a tRNA for the amino acid Val(V) results in the change of the anticodon sequence from5′-AAC-3′ to 5′-AAA-3′. This mutated tRNA will most likelycause the substitution of Val (V) for which amino acid during protein synthesis?
His (H) [histidine] Phe (F) [phenylalanine]
How do endocrine hormones signal to the correct cell surface receptors in tissues?
Hormones bind to receptors with a dissociation constant (Kd) less than 10-8 M.
What is the difference between translational initiation in eukaryotes and bacteria?
How the mRNA is recognized by the ribosome (5′ cap or Shine-Dalgarno sequence).
What is the advantage of alternative splicing to the cell?
Increases the coding capacity of the genome. Generates diversity.
In a normal cell, the protein Ras:
Is an essential component of many growth factor signaling pathways
What is the role of cyclin B/Cdk1 in the metaphase-to-anaphase transition?
It activates the anaphase promoting complex, which destroys a protein that inhibits the protein that cleaves cohesins, which hold sister chromatids together
Gαi opens K+ channels at the plasma membrane is released from the Gαβγ trimer after activation of a receptor tyrosine kinase activates PLC-β, which hydrolyses an inositol phospholipid. inhibits the release of Ca2+ from the endoplasmic reticulum none of the above
NONE OF THE ABOVE
If Na+ channels are opened in a cell that is at rest, what will happen to the membrane potential? (a) The membrane potential is not affected by Na+. (b) The membrane potential is will reach equilibrium at 0 mV. (c) It becomes more positive. (d) It becomes more negative. (e) It is permanently reset.
It becomes more positive.
All of the following are TRUE of p53 EXCEPT: It is a regulatory transcription factor. It inhibits progression through the cell cycle. It is a tumor suppressor gene. It can trigger apoptosis. It interferes with DNA replication by binding to DNA polymerase.
It interferes with DNA replication by binding to DNA polymerase.
Which of the following statements about the anaphase-promoting complex (APC) is FALSE? It promotes degradation of proteins that regulate M phase. It inhibits M-Cdk activity. It is active throughout the cell cycle.M-Cdk stimulates its activity. It can attach multiple ubiquitin molecules to a single substrate.
It is active throughout the cell cycle.
It took more than 700 attempts to make Dolly, the first cloned sheep. Somatic cell nuclear transfer (SCNT) was an inefficient way to clone animals in this experiment because
It is difficult to reverse chromatin remodeling and telomere shortening that occurs in cells during growth and development.
What prevents glucose from crossing a membrane bilayer?
It's big and contains polar hydroxyl groups that prefer to hydrogen bond with water.
TFIIH contains a:
Kinase to phosphorylate the C-terminal domain (CTD) of RNA polymerase II.
During mitosis ________ attach to the chromatids at the ______ .
Kinetechore microtubules, centromere
Most eukaryotic gene regulatory proteins are able to affect transcription when their binding sites are far from the promoter by:
Looping out the intervening DNA between their binding site and the promoter.
The destruction of M-cyclin in the graph above occurs by a mechanism that is both different from, and similar to, destruction of cyclins D, E, and A at other points in the cell cycle. What are the similarities and differences of these mechanisms of cyclin destruction?
M-CDK activates the proteasome by turning on an activating subunit (2), then the proteasome recognizes and degrades D-box-containing proteins, including M-cyclin (2). The other cyclins are degraded in response to phosphorylation. All are degraded in the proteasome (2).
As shown in the graph at right, M-cyclin amounts rise slowly during the cell cycle, yet M-Cdk kinase activity rises sharply. Why?
M-CDK activity is controlled by phosphorylation (2) on activating and $ inhibitory sites, and CKI proteins (2).
The rRNA genes of E. coli are present in seven copies to facilitate the production of many copies of rRNA during periods of rapid growth. Ribosomal proteins and rRNA need to be assembled in a 1:1 molar ratio, so why are single-copy genes adequate for ribosomal protein expression?
Many proteins can be synthesized (translated) from one mRNA
Which of the following statements is FALSE? (a) Mitochondria and chloroplasts both have their own genomes. (b) Mitochondria and chloroplasts both have porins on their outer membrane. (c) Mitochondria and chloroplasts both use a proton electrochemical gradient to make ATP. (d) Mitochondria and chloroplasts both cause the cytoplasm to be slightly acidic. (e) Mitochondria and chloroplasts both transform the energy from redox reactions into an electrochemical gradient.
Mitochondria and chloroplasts both cause the cytoplasm to be slightly acidic.
The citric acid cycle uses which three of the following compounds as input?
NAD+ FAD Acetyl CoA
Chemiosmotic coupling refers to
NADH and FADH2 donate high energy electrons to the electron transport chain that pumps protons across a membrane to create an electrochemical gradient
What are the two molecules that carry high energy electrons as the first input to the mitochondrial electron transport chain?
NADH, FADH2
What is the is the final electron acceptor in the photosynthetic electron transport chain?
NADPH (NADP+ ok)
Why are two photosystems needed for photosynthesis?
NADPH is a poor electron acceptor, so two steps are needed to elevate electrons to high enough energy to act as an electron donor to NADPH. One is not enough to elevate electron energy sufficiently to donate electrons to NADPH, the final electron acceptor. One is insufficient to produce a high energy electron donor for the acceptor, NADP+.
What is the nuclear localization signal? What is the signal sequence that targets proteins into the lumen of the endoplasmic reticulum?
NLS - a string of 5 positively-charged amino acids ( may be anywhere in the protein ) ER signal sequence - a string of 18 or more mostly hydrophobic amino acids
Why does the action potential go in only one direction in neuronal axons?
Na+ channels become inactivated, refractory, no longer respond to change in potential Na+ channels become inactivated, canʼt respond to ∆V Na+ (and K+) channels become inactivated, refractory, no longer respond to change in membrane potential shortly after opening.
The potent pufferfish neurotoxin called tetrodotoxin binds tightly to Na+ channels and blocks their activity completely. What would be the effect of tetrodotoxin on the action potential in neurons?
Na+ channels would not open (2), there would be no action potential (2)
Group II self-splicing introns are mobile DNAs; when many types of mobile DNA transpose into a gene, they disrupt the function of that gene. Why is there usually no effect if a group II self-splicing intron transposes into a gene?
No effect on protein (gene product) because the intron is spliced out
The retinoblastoma (Rb) gene is one example of a tumor suppressor in humans. Typically, when both copies of such genes are lost, cancers develop. Do you suppose that cancer could be eradicated if tumor-suppressor proteins such as Rb could be expressed at abnormally high concentrations in all human cells?
No, over-expression of Rb in all cells would stop all cell division, and the patient would die.
Regarding microtubules and microfilaments (actin filaments): (a) Both use ATP hydrolysis to govern dynamic instability (b) Both use the same molecular motors to move organelles on them (c) Are different because microtubules have polarity, while microfilaments do not (d) Both are attached to centrosomes (e) None of the above
None of the above
Scientists in a future martian colony think they can reduce the cost of food production by putting chloroplasts into animal cells. They use techniques of cell-cell fusion similar to those used now by fertility clinics to replace defective mitochondria the mother's eggs: they remove the plant cell wall and the plant cell nucleus and fuse the plant cell with a mouse egg. These scientists on Mars are not very well trained in basic cell biology and are surprised to find that the chloroplasts are not functional, and not maintained; chloroplasts are lost a few cell divisions after fertilization. Why won't chloroplasts be functional and maintained in animal cells? What would they need to do to make chloroplasts work in animal cells?
Nuclear genes from plants encoding chloroplast proteins would be required. Chloroplasts have their own genome but many chloroplast proteins, like mitochondrial proteins, are encoded by nuclear genes and imported into chloroplasts. This would require significant genetic engineering!
Why do you think that eukaryotic cells with mitochondria evolved after oxygen built up in the atmosphere?
O2 is required by the mitochondria electron transport chain as the final electron acceptor. So that oxygen (O2) could be the final acceptor of electrons in the electron transport chain.
Why are two photosystems needed for photosynthesis? (4 points)
One is not enough to elevate electron energy to donate electrons to NADPH, the final electron acceptor
Which of the following is cis-acting for lac operon regulation?
Operator.
After isolating the rough endoplasmic reticulum from the rest of the cytoplasm, you purify the RNAs attached to it. Which of the following proteins do you expect the mRNA from the rough endoplasmic reticulum to encode? (Circle ALL that apply.)
Plasma membrane proteins ER membrane proteins Soluble secreted proteins
Why is a primer required in DNA replication?
Provides a free 3 ́ hydroxyl (or an existing helix is needed for proofreading) (or DNA polymerase can add its first nucleotide only to an existing chain).
Protein kinase A is characterized by which of the following control mechanisms?
R2C2 + 4(cAMP) R2cAMP4 + 2C (active)
The signal recognition (SRP), which recognizes the N-terminal signal sequence of proteins destined for the secretory pathway, is composed mainly of
RNA
The distinct characteristics of different cell types in a multicellular organism are produced mainly by the differential regulation of the transcription of genes transcribed by:
RNA polymerase II.
Transcription is catalyzed by:
RNA polymerase.
Which molecular process is directly affected by the mutation in the lamin A gene that causes Hutchinson-Gilford progeria syndrome?
RNA splicing.
Which molecular process is directly affected by the mutation in the lamin A gene that causes Hutchinson-Gilford progeria syndrome?
RNA splicing.
What prevents transport vesicles from wantonly and promiscuously fusing with any organelle?
Rab GTP binding proteins and SNARE proteins.
Which protein could become activated by mutation and influence the cell cycle restriction point to cause the cell to divide?
Ras
What does the tumor suppressor Rb do to prevent transcription of cyclin D, and how is it regulated to enable cells to cross the Restriction Point of the cell division cycle?
Rb binds (inhibits) a transcription factor (E2F) that transcribes cyclin D (2). Phosphorylated Rb releases the transcription factor so that it may act to transcribe cyclin D (and cyclin E) (3).
People who inherit one copy of the Rb (retinoblastoma) gene that is normal and one copy that is mutated—that is, people who are heterozygous for Rb—have a greatly increased risk of cancer. Given this information, and what you know about Rb, which of the following statements is correct?
Rb is a tumor suppressor, which means that one good copy is insufficient to prevent tumor formation.
In the chloroplast electron transport chain, what directly provides the energy to pump protons across a membrane?
Reactions transferring electrons from good electron donors to good electron acceptors.
In the mitochondrial electron transport chain, what directly provides the energy to pump protons across a membrane?
Reactions transferring electrons from good electron donors to good electron acceptors.
Steroid hormones diffuse across membranes and interact with receptors in the cytoplasm. What happens to the receptor next to activate the response?
Receptor changes conformation, binds DNA, acts as a transcription factor. Bind DNA to activate transcription.
How do macromolecules carry (or encode) information?
Sequence of monomers.
How many amino acids long would the peptide (short protein) be in the absence of the antibiotic?
Seven.
Both Ca2+ and cAMP are found in very low concentrations in the cytosol of resting cells. Why?
So that a large increase in their concentration may be rapidly achieved upon activation of signal transduction mechanisms.
What is the similarity between group II self-splicing introns and nuclear pre-mRNA splicing?
Splicing is catalyzed by RNA.
What is unusual about TBP (TATA box-binding protein) binding to DNA?
TBP binds in the minor groove.
Which statement is FALSE about G-proteins coupled to 7-transmembrane-domain receptors:
The Gαβγ trimer inhibits signalling effectors; free Gα and free Gβγ have no activity.
For each of the following sentences, fill in the blanks with the best word or phrase selected from the list below. Not all words or phrases will be used; each word or phrase should be used only once.
The action potential is a wave of __depolarization___ that rapidly spreads along the neuronal plasma membrane. This wave is triggered by a local change in the membrane potential to a value that is ____less_____ negative than the resting membrane potential. The action potential is propagated by the opening of ______voltage_______-gated channels. During an action potential, the membrane potential changes from ___negative________ to ____positive_____. The action potential travels from the neuron's___cell body______ along the _____axon_______ to the nerve terminals. Neurons chiefly receive signals at their highly branched ___dendrites________.
Which of the following statements is FALSE? (a) The mitochondrial electron transport chain starts with high energy electron carriers that are good electron donors and the final step transfers electrons to a good electron acceptor. (b) The chloroplast electron transport chain starts with high energy electron carriers that are good electron donors and the final step transfers electrons to a good electron acceptor. (c) Mitochondria and chloroplasts both have porins on their outer membrane. (d) Mitochondria and chloroplasts both use a proton electrochemical gradient to make ATP. (e) Mitochondria and chloroplasts both have their own genomes and transcription and translation machinery.
The chloroplast electron transport chain starts with high energy electron carriers that are good electron donors and the final step transfers electrons to a good electron acceptor.
If the outer membrane of mitochondria were perforated, as happens during programmed cell death (apoptosis), allowing proteins to leak out of the inter-membrane space, cytochrome c would enter the cytosol. What would be the most immediate effect on metabolism?
The consumption of oxygen would fall.
Rotenone is still used as an insecticide, but is not available for general use. It is toxic to wildlife and to humans as well as to insects. Rotenone is an inhibitor of the electron transport chain in mitochondria. What molecular consequences would result from adding rotenone to animal or insect cells?
The consumption of oxygen would fall. The ratio of ATP to ADP in the cytoplasm would fall.
Which statement about intermediate filaments is TRUE? Their polymerization and depolymerization is governed by GTP hydrolysis by monomer subunits. Motor proteins that travel along intermediate filaments use ATP hydrolysis to achieve locomotion. The ends of intermediate filaments are indistinguishable: they have no polarity. The ends of intermediate filaments are distinguishable by the rate of subunit attachment and whether they are bound to ATP or ADP Capping proteins help stabilize intermediate filaments.
The ends of intermediate filaments are indistinguishable: they have no polarity.
Which of the following statements is NOT generally true about molecular switches that use GTP hydrolysis?
The energy of the phosphate bond in GTP is used by kinases to phosphorylate proteins.
Why is directionality of the polymer important for DNA?
The information (nucleotide sequence) would be different in the opposite direction.
Embryonic stem cells are derived from
The inner cell mass of the blastocyst
Nonviral retrotransposons encode enzymes that catalyze movement. Why do the genes encoding these enzymes lack introns?
The introns would be spliced out when the nonviral retrotransposon moved through its RNA intermediate.
If cells were exposed to an agent that causes both inner and outer mitochondrial membranes to become freely permeable to protons, which of the following effects would you expect to observe?
The ratio of ATP to ADP in the cytoplasm would fall.
If cells were exposed to an agent that causes both mitochondrial membranes to become freely permeable to protons, which of the following effects would you expect to observe?
The ratio of ATP to ADP in the cytoplasm would fall.
If mitochondria were exposed to an agent that causes their membranes to become freely permeable to protons, which of the following effects would you expect to observe?
The ratio of ATP to ADP in the cytoplasm would fall.
The final stage of the oxidation of food molecules, a gradient of protons is formed across the inner mitochondrial membrane, which is normally impermeable to protons. If cells were exposed to an agent that causes the membrane to become freely permeable to protons, which of the following effects would you expect to observe?
The ratio of ATP to ADP in the cytoplasm would fall.
Which statement about the steroid hormone receptor family is FALSE? The receptors contain DNA binding domains. The receptors release calcium from intracellular stores. The receptors interact with ligands that diffuse across membranes. The receptors act as transcription factors. None of the above
The receptors release calcium from intracellular stores.
Which of the following occurs after an mRNA is exported from the nucleus?
The ribosome binds to the mRNA.
In photosystems I and II, antenna chlorophyll molecules
absorb light energy, which excites electrons into a high energy state.
"Hybrid" aminoacyl-tRNAs can be formed by chemically converting the amino acid cysteine, attached to a tRNA, into the amino acid alanine; these "hybrid" aminoacyl-tRNAs were incubated in a test-tube translation system instead of normal cysteine-tRNAs and the resulting protein was found to have an alanine at every position that was supposed to be a cysteine. Briefly discuss what this experiment tells you about the role of aminoacyl-tRNA synthetases during the normal translation of the genetic code.
The ribosome does not check the amino acid that is attached to a tRNA: the matching of a codon with an amino acid required for the correct reading of the genetic code is performed by the aminoacyl-tRNA synthetases. (question 7-4)
Which of the following statements is TRUE? (a) The ∆G° for oxidation of glucose is more negative in cells than it is for combustion. (b) The ∆G° for oxidation of glucose is the same in cells as it is for combustion. (c) The ∆G° for oxidation of glucose is more positive in cells than it is for combustion. (d) All of the above, depending on the type of cell. (e) All of the above, depending on the concentration of ATP in cells.
The ∆G° for oxidation of glucose is the same in cells as it is for combustion.
Why are histones positively charged?
To interact with the sugar-phosphate backbone.
What is the function of the Ran GTP-binding protein?
To regulate directionality of cargo receptor binding and transport in and out of the nucleus.
What would happen to the brains of mice if a key caspase (caspase 3 or 9) involved in neuronal programmed cell death was knocked out?
Too many nerve cells (their brains actually spill out of their skull!).
An antibiotic is added to a test tube with all the components needed for translation using mRNA molecules with the sequence 5′-AUGAAAAAAAAAAAAAAAAAAUAA-3′. The only product made is a methionine-lysine dipeptide (a two amino acid-long "protein") that remains attached to the ribosome. a) (2 points) Which step of protein synthesis does the antibiotic inhibit?
Translocation of the ribosome relative to the mRNA.
An antibiotic is added to a test tube with all the components needed for translation using mRNA molecules with the sequence 5′-AUGAAAAAAAAAAAAUAA-3′ (AUG is the codon for methionine and AAA is the codon for lysine); the only product made is a methionine-lysine dipeptide (a two amino acid-long "protein") that remains attached to the ribosome: which step of translation does the antibiotic inhibit?
Translocation of the ribosome relative to the mRNA.
What allows proteins to span the lipid bilayer?
Transmembrane α-helix and β-sheets have non-polar amino acid side chains facing out.
Formation of a lipid bilayer might seem to be energetically unfavorable. However, this arrangement is actually favored because it allows a higher level of entropy than any other alternative. What makes bilayer formation energetically favorable?
Water molecules form cage-like structures around hydrophobic molecules.
Circle the statement that is FALSE:a) Genes are unstable in the absence of DNA repair.b) Wild type organisms have a mutation in their genome.c) None of the aberrant bases formed by deamination occur naturally in DNA. d) Cancer results from uncorrected mutations in somatic cells.
Wild type organisms have a mutation in their genome.
How does one tRNA recognize more than one codon?
Wobble: the first position in the anticodon (tRNA) can have less stringent base-pairing with the third position in the codon (mRNA); therefore, one tRNA can bind to more than one codon
Three phospholipids X, Y, and Z are distributed in the plasma membrane as indicated in the figure below. For which of these phospholipids does a flippase probably exist?
X and Z folder
Why is the study of cell division in yeast relevant to understanding human cancer?
Yeast cell cycle proteins and mechanisms are similar to those in all eukaryotic cells.
You isolate a mutant in lacI, the gene coding for the lac repressor (LacI), in which allolactose cannot bind to the mutant lac repressor. For each of the following situations (plus or minus glucose and plus or minus lactose), write "ON" to indicate if the lac operon is transcribed and "OFF" if the lac operon is not transcribed in the wild type and the lacI mutant.
You have discovered an operon in a bacterium that is transcribed only when the sugar sucrose is present and glucose is absent. There are two transcription factor-binding sites in the upstream regulatory region, A and B. You have isolated three mutants that have changes in the regulatory region at site A or B. The following table summarizes the transcriptional regulation of the operon in the wild- type cells and the three mutants:
Mammalian cells make the decision to divide or die based on
a combination of extracellular signals and intracellular checkpoint control systems
In addition to ATP, what is the final product of the mitochondrial electron transport chain?
a good electron acceptor
What is the final product of the mitochondrial electron transport chain?
a good electron acceptor
In addition to ATP, what is the final product of the chloroplast electron transport chain?
a good electron donor
What is the final product of the chloroplast electron transport chain?
a good electron donor
A gene is alternatively spliced to produce two mRNAs. Translation begins in exon 1. For both mRNAs, the encoded protein sequence is the same in the regions of the mRNA that correspond to exons 1 and 10. Exons 2 and 3 are alternative exons used in the different mRNAs. Exons 2 and 3 must contain:
a number of nucleotides that leaves the same remainder when divided by 3.
Which protein could become activated and positively influence the cell cycle restriction point to cause the cell to divide?
a receptor tyrosine kinase
Which type of receptor typically activates the MAP kinase cascade: MAPKKK, MAPKK, and MAPK?
a receptor tyrosine kinase
A transcription factor is only able to bind DNA after being phosphorylated on two different sites. Phosphorylation of one site is activated by by PKA, which is activated by a G-protein coupled receptor; the other site is phosphorylated by MAP kinase, which is activated by a receptor tyrosine kinase. This transcription factor would best be described as
a signal integrating device
What is the signal sequence for protein import into the lumen of the endoplasmic reticulum?
a string of hydrophobic amino acids on the N-terminus
Repressor and activator proteins both have which of the following structural features:
a) DNA binding domain.
What would be required to cause both protein kinase A (PKA) and protein kinase C (PKC) to be activated at the same time in cells? (a) Stimulation of two receptors: one activates a Gs-coupled receptor and another activates a Gq-coupled receptor. (b) Stimulation of two receptors: one activates a Gs-coupled receptor and another activates a receptor tyrosine kinase. (c) Stimulation of a Gq-coupled receptor and the addition of caffeine. (d) Stimulation of a receptor tyrosine kinase and the addition of caffeine. (e) All of the above.
all of the above
What would happen if a chromosome translocation caused elevated transcription of Bax? (a) cytochrome c would be released from mitochondria (b) initiator caspases would be activated, followed by effector caspases (c) nucleases would be activated that cleave DNA between nucleosomes (d) nuclear lamins would be degraded, and chromatin would condense (e) all of the above
all of the above
Which of the following is trans-acting for lac operon regulation? (a) Repressor (LacI). (b) Catabolite activator protein (CAP or CRP). (c) RNA polymerase. (d) All of the above.
all of the above
Which of the following is trans-acting for lac operon regulation? a) Repressor (LacI). b) Catabolite activator protein (CAP or CRP). c) RNA polymerase. d) All of the above.
all of the above
Which of the following may result in signal bifurcation? PLC-β hydrolysis of an inositol phospholipid Exchange of GTP for GDP from the α subunit of the Gαβγ trimer Release of Ca2+ from the endoplasmic reticulum Phosphorylation of two different transcription factors by protein kinase A all of the above
all of the above
An electrochemical gradient is formed when
an ion moves across a membrane while its counter ion of opposite charge does not
For the following processes, energy is transformed or conserved from one type of energy into another. For each of these process, name the type of energy harvested (input) and the type of energy into which the initial energy is conserved or transformed (output).
answer in folder
In the table below, match the type of energy that drives, is transformed by, or is directly involved in each process. Write the correct letter(s) in the space provided next to the process. Each letter may be used many times and each process may involve more than one type of energy.
answer in folder
In which membrane of chloroplast and mitochondria does proton translocation and ATP synthesis (ATP synthase) occur? In which compartment does the citric acid cycle and calvin cycle occur?
answer in folder
For the following graphs of an electrical recording from a neuron, showing membrane potential (y- axis) vs. time (x-axis): Briefly describe what is happening to sodium and potassium channels in A and B. (2 points)
answer in folder -Na+ (and K+) channels do not reach the threshold potential, do not open -Na+ (and K+) voltage-gated channels donʼt reach threshold potential
Molecular oxygen (O2) is required in eukaryotic cells
as a final electron acceptor in the mitochondria electron transport chain.
The proton ATPase (proton pump) that acidifies endosomes is a membrane protein that is translated on ribosomes
attached to the endoplasmic reticulum.
Both bacterial and eukaryotic ribosomes find the location of the start codon by:
binding an initiator tRNA.
TrpR is a repressor that regulates transcription of the trp operon, which encodes the enzymes that biosynthesize the amino acid tryptophan in Escherichia coli; TrpR is an allosteric protein whose DNA- binding activity is altered when tryptophan is bound; when tryptophan is present, TrpR:
binds the operator and represses trp operon expression.
TrpR is a repressor that regulates transcription of the trp operon, which encodes the enzymes that biosynthesize the amino acid tryptophan in Escherichia coli; TrpR is an allosteric protein whose DNA-binding activity is altered when tryptophan is bound; when tryptophan is present, TrpR:
binds the operator and represses trp operon expression.
Inositol triphosphate is a "second messenger" in signal transduction that
binds to a receptor in the endoplasmic reticulum and causes release of Ca2+
What molecular switching mechanisms are NOT commonly used in signal transduction? (a) ATP exchange and ATP hydrolysis (b) GTP exchange and GTP hydrolysis (c) covalent modification with phosphate derived from ATP (d) covalent modification with phosphate derived from GTP (e) both (a) and (d)
both (a) and (d)
If a tumor is known to be composed predominantly of cells in which p53 was entirely inactive, to which treatment would these tumor cells likely be resistant?
both radiation and chemotherapy (both a and b)
Programmed cell death occurs
by means of an intracellular suicide program
Steroid hormones
diffuse across membranes and interact with an intracellular receptor
Cells in the G0 state:
do not divide
Consider the different types of energy used or transformed in eukaryotic cells: (a) — radiant energy (kinetic energy of photons) (b) — energy stored in chemical bonds (enthalpy or chemical potential) (c) — energy stored in electrons (redox potential) (d) — potential energy stored in a concentration gradient (e) — potential energy created by a concentration gradient and separation of charge (electrochemical gradient) What type of energy makes the action potential possible? Which type of energy allows the active transport of glucose? What type of energy allows the passive transport of glucose?
e — electrochemical gradient e — electrochemical gradient d — concentration gradient
A planar lipid bilayer allows mitochondria and chloroplasts to produce energy carrier molecules and neurons to produce an action potential. What type of energy transformation makes these remarkable phenomena possible?
electrochemical gradient
A protein with 400 amino acids has a hydrophobic sequence of 18 amino acids on its N-terminus and five positively charged amino acids (four lysine residues and on arginine) at residues 324-327. Where in the cell will it likely be localized right after translation?
endoplasmic reticulum
influenza virus contains a protein that is capable of fusion with membranes, but only under certain conditions. Influenza virus fusion with membranes and thus entry into the cell (infection) only occurs after the virus is endocytosed. It has also been observed that incubation of cells with ammonia, which can neutralise acidic solutions (NH3 + H+ → NH4+), prevents viral fusion and infection. Based on these data, explain the mechanism by which influenza virus enters cells.
endosomes are acidified, which activates the fusion protein (4) bonus (2): NH4+ accumulates in endosomes and other acidic compartments because it's charged
The advantage to the cell of the gradual oxidation of glucose during cellular respiration compared with its combustion to CO2 and H2O in a single step is that
energy can be extracted in usable amounts
The concentration of mitotic cyclin (M cyclin)
falls toward the end of M phase due to ubiquitination.
Label the above diagram of the components of photosynthesis with the following terms (14 points; not all will be needed):
folder
Match the following list of energy forces with the biological processes that the forces drive. Some energy forces may be used more than once, or not at all. (14 points)
folder
Match the organelles with their functions from the list below by writing the correct letter in the organelle box.
folder
Crossing-over - homologous recombination - between duplicated maternal and paternal chromosomes in each bivalent during meiosis results in the exchange of genetic information between chromosomes. This process contributes to
genetic diversity in siblings
Pyruvate is a product of _______________________. cytosol mitochondria (matrix) It is made in the ____________________ (part of cell), then transported into________________, where pyruvate then undergoes oxidation in the _____________, which produces energy carrier molecules.
glycolysis cytosol mitochondria (matrix) citric acid (TCA, Krebs) cycle (pyruvate carboxylase OK)
Which of the following mutations would NOT be involved in cancer?
increased expression of a cell division kinase inhibitor (CKI)
Which of the following mutations would NOT be likely to be involved in cancer?
increased expression of a cell division kinase inhibitor (CKI)
Gαq activates phospholipase C. What happens next?
inositol phospholipid is cleaved to form inositol 1,4,5-trisphosphate (IP3) and diacylglycerol
A fluorescent dye, which is a small charged molecule, is injected into the cytoplasm of a eukaryotic cell. After some time is allowed for the dye to distribute, where would you expect to see the dye?
inside the nucleus
In cells, membranes are barriers for
ions and macromolecules
In cells, membranes are barriers for (a) potential difference (∆V) (b) ions and macromolecules (c) carbon dioxide and oxygen (d) small non-polar molecules (e) all of the above
ions and macromolecules
The MAP kinase pathway
is activated by the GTP-binding protein Ras
A kinase will act as an integrating device in signaling if it
is activated or inhibited by more than one protein.
Release of cytochrome c from mitochondria
is caused indirectly by p53 in response to DNA damage
The C-terminal domain (CTD) of RNA polymerase II:
is phosphorylated by the TFIIH kinase during initiation.
The ∆G for the hydrolysis of ATP in cells
is smaller than ∆G° because the concentration of ATP is higher than the concentration of ADP.
The fact that human cyclin/Cdk proteins functionally complement inactivating mutations in their counterparts in yeast, that is, that human cell cycle proteins work in yeast, is significant because
it shows that the eukaryotic cell cycle is evolutionarily ancient and highly conserved
A single-stranded DNA with the sequence 5ʹ′-TTTTTTTTTTTTTTTTTTTTTTTTT-3ʹ′ is attached to small beads. Total nucleic acids are extracted from a culture of eukaryotic cells and mixed in a test tube with these beads. Specifically, which molecule in the cell will bind to the beads?
mRNA
What cytoskeletal elements form the mitotic spindle?
microtubules
The polymerization and de-polymerization of microtubules and microfilaments is governed by the hydrolysis of which nucleotides?
microtubules: GTP; microfilaments: ATP
Direct protein targeting to which organelle(s) requires proteins to be unfolded and translocated?
mitochondria AND endoplasmic reticulum
Why is cytosol more acidic (pH 7.2) than the extracellular space (pH 7.4)?
mitochondria leak protons (3) through porins on outer membrane (1); protons are translocated from matrix across inner mitochondrial membrane (alt. 2)
Which intracellular organelle(s) have a higher pH (lower H+ concentration) than cytosol?
mitochondrial matrix
Bone marrow stem cells, which form all the white and red blood cells in the bloodstream, are:
multipotent stem cells.
p53, the Guardian of the Genome, is mutated in about half of all human cancers. What is the result of having a mutated p53 that cannot bind DNA?
mutated p53 cannot stop the cell cycle in response to DNA damage
What do the signal sequence that targets proteins to the endoplasmic reticulum and the nuclear localization signal have in common? (a) both have hydrophobic amino acids (b) both are typically localized anywhere in the protein (c) both have a string of positively-charged amino acids (d) both require proteins to be unfolded to be translocated (e) none of the above
none of the above
Which of the following stages in the breakdown of the piece of toast you had for breakfast - we hope you had breakfast - generates the most ATP?
oxidative phosphorylation
What is the final electron acceptor in the mitochondrial electron transport chain?
oxygen (O2)
Protein Kinase A (PKA), Protein Kinase C (PKC), and Protein Kinase B (AKT)
phosphorylate effector proteins on serine and threonine residues
Which of the following is NOT a mechanism to turn OFF cyclin/Cdk activity? destruction of cyclin phosphorylation by inhibitory kinase phosphorylation by activating kinase removal of activating phosphate transcription and translation of a cell division kinase inhibitor (CKI)
phosphorylation by activating kinase
Which is the water-splitting step in photosynthesis?
photosystem II
What are two key structural features of lipid molecules that make energetically favorable the formation of planar bilayers?
polar head group (2); two fatty acid tails, this makes a cylindrical shape (2)
The sigma subunit of bacterial RNA polymerase recognizes:
promoters on DNA.
Different vesicle coat proteins regulate membrane traffic in different intracellular locations. What general role, or what step(s) in membrane traffic, involves vesicle coat proteins?
transport vesicle budding
You have reconstituted ATP synthase in a liposome with the orientation as shown in at right. Liposomes can be prepared in a solution containing a buffer and soluble compounds, then transferred to a different solution to achieve a different concentration of solutes inside and outside. What minimum combination of salts, pH, and other soluble components would you place inside and outside of the vesicle to cause the enzyme to make ATP? Where would ATP accumulate? Identify the component(s) and where it (they) is (are) to be placed (inside or outside).
proton gradient: high [H+] outside (2) ADP inside (2)ATP will be made inside (2)
In general, kinases __________, and phosphatases __________
put phosphates on proteins / take phosphates off proteins
What is the end product of glycolysis that can be made into, or made from, amino acids?
pyruvate
The formation of peptide bonds between amino acids is catalyzed by:
rRNA.
The formation of peptide bonds linking amino acids is catalyzed by:
rRNA.
Using the energy of a reaction to drive formation of intermediates whose energy can be harvested in subsequent reactions is called
reaction coupling
In steps 6 and 7 of glycolysis, the oxidation of an aldehyde to a carboxylic acid employs ____________ to produce ___________ and __________.
reaction coupling, NADH, ATP
Transport of large (>100kD) proteins from the cytoplasm to the nucleus involves what kind of mechanism?
recognition of five adjacent positively charged amino acids in the protein
Transport of large (>100kD) proteins from the cytoplasm to the nucleus involves what kind of mechanism?
recognition of five adjacent positively charged amino acids in the protein
What energy transformation best describes what occurs directly in the mitochondrial electron transport chain?
redox potential (energy stored in electrons) to potential energy (electrochemical gradient)
The energy barrier that must be overcome for an ion to cross a membrane bilayer is primarily
release of an ion's water cage
The energy barrier that must be overcome for an ion to cross a membrane bilayer is primarily (a) friction to slide through the fatty acid tails (b) hydrophobic interactions (c) hydrogen bonding (d) release of an ion's water cage (e) van der Walls forces
release of an ion's water cage
In mammalian cells, which is NOT a possible fate of pyruvate?
serving as an electron donor in the mitochondrial electron transport chain
In programmed cell death, initiator caspases activating effector caspases is an example of
signal amplification
What information must a protein possess to cause it to be localized into intracellular compartments different from the cytosol?
signal sequence
What must a protein have to get into the ER or mitochondria, and what must it do (or what must be done to it) to get across the membrane?
signal sequence; must be unfolded to be translocated
Paracrine signalling is
signalling among cells near to each other
The Nernst equation (simplified) is:Veq = 58mV•log10Co/Ci.The membrane potential for a vesicle, with the concentrations of salts inside and outside the vesicle as shown at right, will be
somewhere between -58 and +58 mV, depending on the relative conductance of the Na+ and K+ channels
Which of the following is NOT a cell surface receptor?
steroid hormone receptor
The genetic material of an alien organism is structurally indistinguishable from DNA in cells on Earth. However, the alien DNA is synthesized from nucleoside triphosphates (NTPs) that contain 5′ hydroxyl groups and 3′ triphosphate groups. How must the alien's DNA polymerase be different from our DNA polymerase?
strand growth would need to occur in the 3′-to-5′ direction (opposite) to use the energy of hydrolysis of the 3′-triphosphate group for polymerization. (6-11)
Levels of cyclin-dependent kinase (Cdk) activity change during the cell cycle as a result of
the Cdks binding different cyclins to become active.
What would be the consequences of a mutation in the α subunit of a trimeric G protein that deactivates its ability to hydrolyze GTP?
the G protein would be continuously activated
What would be the consequences of a mutation in the α subunit of a trimeric G protein that inactivates its ability to hydrolyze GTP?
the G protein would be continuously activated
Considering the evolution of organelles in eukaryotic cells, the inside of the nucleus is topologically equivalent to
the cytosol
Oxidative phosphorylation refers to
the electron transport chain and ATP synthase.
The Nernst equation allows the cell biologist to calculate
the membrane potential for a charged ion at defined concentrations on either side of a membrane
Recall that ATP is made by ATP synthase using the proton electrochemical gradient across the inner membrane of mitochondria. Transporters then allow ATP to cross the inner membrane into the intermembrane space, and porins in the outer mitochondrial membrane then allow ATP to diffuse into the cytosol. From there, which of the following intracellular organelles could ATP flow into by simple diffusion, without any transporters?
the nucleus
Transporters ferry GTP across the mitochondrial inner membrane into the intermembrane space. From there, which of the following intracellular organelles could GTP flow into by simple diffusion, without any active transporters?
the nucleus
When a trimeric G protein is activated by a cell-surface receptor
the α subunit exchanges its bound GDP for GTP.
What would be the consequences of a mutation in the α subunit of a trimeric G protein that inactivates its ability to hydrolyze GTP?
the α subunit of the G protein not bind to βγ subunits
What is a uniformly common characteristic of all proteins that cross the lipid bilayer?
they have a region where non-polar amino acid side chains face the fatty acid tails
In which membrane of chloroplasts does proton translocation and ATP synthesis (ATP synthase) occur? Why is this arrangement more efficient for ATP synthase than the arrangement for proton translocation and ATP synthesis in mitochondria?
thylakoid membrane (or granum membrane) (2)protons are concentrated inside thylakoid space (2) mitochondria outer membranes leaks protons into cytosol the electrochemical gradient is therefore stronger in chloroplasts (2)
In chloroplasts, protons are pumped across the _________ and accumulate in the __________.
thylakoid membrane; thylakoid space
Cells from the first 2 or 3 divisions of the zygote are
totipotent, but not stem cells
Why is gene expression regulated (mostly) at the level of transcription in bacteria?
transcription is temporally and spatially coupled to translation in bacteria
The distinct characteristics of different cell types in a multicellular organism result mainly from the differential regulation of:
transcription of genes transcribed by RNA polymerase II.
