Cell Biology Exam Practice Questions

Weak noncovalent attractions in the cell can be very strong in a nonaqueous environment. Some of these attractions are as strong as covalent interactions in a vacuum (their bond energy is approximately 340 kJ/mole), but become more than twenty-five times weaker (their bond energy becomes approximately 13 kJ/mole) in water. What type of attraction shows this phenomenon? a. Electrostatic attractions b. Hydrogen bonds c. van der Waals attractions d. Hydrophobic force e. All of the above

A. Electrostatic attractions

A cell expresses a transmembrane protein that is cleaved at the plasma membrane to release an extracellular fragment. The fragment binds to receptor proteins on nearby cells and activates signaling pathways resulting in altered gene expression patterns in the cells. What form of intercellular signaling does this represent? a. Contact-dependent signaling b. Paracrine signaling c. Synaptic signaling d. Endocrine signaling e. Autocrine signaling

B. Paracrine signaling Paracrine signaling acts on neighboring cells via local mediators

Imagine a small synthetic vesicle made from pure phospholipids enclosing an interior lumen containing 1 mM glucose and 1 mM sodium chloride. If the vesicle is placed in pure water, which of the following happens faster? a. Na+ diffuses out b. Cl- diffuses out c. H2O diffuses in d. Glucose diffuses out e. Sodium chloride diffuses out

C. H2O diffuses in If the solute concentration inside the vesicle is too high, the rapid influx of water can even burst the vesicles

The permeability of a protein-free lipid bilayer to various molecules depend on their properties. Sort the following in order of low to high permeability from left to right. (A) O2 (B) ATP (C) RNA oligonucleotide (D) NA+ (E) Glucose (F) Urea

CBDEFA

Which of the following is NOT correct regarding the molecule whose structural formula is shown below? (MT2 #3) a. It is an amphiphilic molecule b. It is a sterol c. It makes the membrane less permeable to small hydrophilic molecules d. It is found in membranes of virtually all living cells e. It affects the fluidity of the lipid bilayer

D. It is found in the membranes of virtually all living cells The structure shown is that of cholesterol, an amphiphilic sterol that affects the permeability and fluidity of the membranes in eukaryotic cells. Most prokaryotic membranes lack cholesterol

Consider a human liver hepatocyte. Among the following membranes, which one has the largest total area? a. Plasma membrane b. Nuclear inner membrane c. Mitochondrial outer membrane d. Rough ER membrane e. Smooth ER membrane

D. Rough ER membrane The plasma membrane accounts for only a small percentage of the total cell membrane area, while the endoplasmic reticulum (ER) membranes (including those of the smooth and rough ER) comprise about half the total membrane area. The liver plays the major role in producing proteins that are secreted into the blood, including major plasma proteins, factors in hemostasis and fibrinolysis, carrier proteins, hormones, prohormones, and apo-lipoprotein, all of which undergo co-translation at the rough ER. In cells such as hepatocytes, which are rich with mitochondria, the inner mitochondrial membrane also has a noticeable surface area, due to its extensive invaginations called cristae. See table 12-2 in the textbook

Which of the following structures is exclusively found in eukaryotic cells? a. Plasma membrane b. Cell wall c. Chromosome d. Ribosome e. Lysosome

E. Lysosome

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

E. They are found in all eukaryotes

Identify whether the following statements are True (T) or False (F) regarding cell junctions ( ) Integrins directly bind to components of the extracellular matrix ( ) Tight junctions facilitate the polarized transport of metabolites such as glucose from the apical side of the epithelium to the basal side ( ) Focal adhesions are highly stable structures that remain intact during cell migration ( ) Both cadherins and integrins exert force through their interactions with the actin cytoskeleton ( ) The basal lamina is an impermeable barrier that cells are unable to pass through

FTFFT

Neurotrophic factors are...? a. Secreted proteins that promote neuronal survival b. Important components of cell:cell adhesions c. Signals for detachment of epithelial cells from the extracellular matrix d. Used by the immune system to produce antibodies e. Attachments used in the extracellular matrix to crosslink collagen fibrils

a. Secreted proteins that promote neuronal survival This is the only option that is relevant

How does the affinity of M6P receptor proteins for the mannose 6-phosphate marker change between the TGN and early endosome? Which coat protein is mainly responsible for their transport from the TGN to the endosome? a. The affinity is higher in the TGN; clathrin b. The affinity is higher in the TGN; retromer c. The affinity is higher in endosomes; clathrin d. The affinity is higher in endosomes; retromer

a. The affinity is higher in the TGN; clathrin In the trans Golgi network (TGN), mannose 6-phosphate (M6P) receptor proteins bind to hydrolases that carry the M6P group and mediate their incorporation into clathrin-coated vesicles destined for endosomes. In the lower pH of the endosome lumen, the hydrolases are released and the receptor proteins are retrieved by incorporation in retromer-coated vesicles.

When is a kinetochore assembled onto the centromere? a. during prophase b. during anaphase c. during telophase d. during metaphase e. during interphase

a. during prophase

In CRISPR which of the following is required for Cas9 to induce double-strand breaks in specific locations within a DNA sequence? a. small guide RNA (sgRNA) b. piRNA (piwi-interacting RNA) c. histones d. ribosomes e. DNA polymerase

a. small guide RNA (sgRNA) Small guide RNAs are used to direct the Cas9 enzyme to specific sequences

The unusual stretch of repeated DNA sequences at the end of a eukaryotic chromosome is called a _____. a. telomere b. chromomere c. centromere d. telophase e. karyomere

a. telomere

Which of the following graphs better represents the change in the relative conductance of Na+ and K+ channels during an action potential in a neuronal membrane? (MT2 #13) a. Na+ peaks at 1 sec at 50 mS/cm2; K+ peaks at 1 sec at 25 mS/cm2 b. Na+ peaks at 1 sec at 50 mS/cm2; K+ peaks at 2 sec at 25 mS/cm2 c. Na+ peaks at 2 sec at 50 mS/cm2; K+ peaks at 1 sec at 35 mS/cm2 d. Na+ peaks at 1 sec at 50 mS/cm2; K+ peaks at 2 sec at 25 mS/cm2 e. Na+ peaks at 1 sec at 50 mS/cm2; K+ steadily increases

b. The voltage-gated Na+ channels open quickly during an action potential and are then rapidly inactivated. The voltage-gated K+ channels open and close more slowly and repolarize the membrane potential.

The nucleotide at which transcription is initiated is labeled as the _____ nucleotide and is represented by a transcriptional arrow. a. 0 b. +1 c. -1 d. A of the 'ATG' codon e. first (fixed) nucleosome

b. +1

At physiological pH, what is the approximate net charge of a hexapeptide with the following amino acid sequence? Asp-Val-Ile-Glu-Arg-Ser a. -2 b. -1 c. 0 d. +1 e. +2

b. -1

What is the typical thickness of a lipid bilayer such as the plasma membrane of our cells? a. 0.5 nm b. 5 nm c. 50 nm d. 100 nm e. 500 nm

b. 5 nm

What is the major way by which the monomeric G protein Ras is activated in receptor tyrosine kinase signaling? a. Activation of Ras-GAP b. Activation of Ras-GEF c. Inactivation of Ras-GAP d. Inactivation of Ras-GEF e. Inactivation of Ras-GDI

b. Activation of Ras-GEF

In addition to their respiratory function, mitochondria have other important roles in cellular metabolism. Which of the following processes is NOT carried out mainly by mitochondria? a. Biosynthesis of cardiolipin b. Biosynthesis of fatty acids c. Catabolism of amino acids d. Biosynthesis of heme e. Biosynthesis of iron-sulfur clusters

b. Biosynthesis of fatty acids Fatty acid biosynthesis is confined to the cytosol. where the citrate exported from mitochondria is used to produce acetyl CoA in the initial step

You wish to experimentally determine whether centromeric H3 (cenH3 or CENP-A) is differentially localized across the chromosomes in a human cell. You also have access to a cenH3-specific antibody? Which of these methods could be useful? a. Whole-mount antibody staining or immunofluorescence b. ChIP-seq or ChIP-chip c. Transmission electron microscopy d. Representational Difference Analysis e. All of the above

b. ChIP-seq or ChIP-chip

Accessory proteins that bind to inactive monomeric G proteins and stimulate dissociation of the bound GDP are called: a. GAPs b. GEFs c. GDIs d. RASps e. MAPs

b. GEFs

Cells were first seen by the end of the sixteenth century with compound microscopes. What characterizes a compound microscope? a. It has a moveable stage b. It has two lenses c. Its lens is double the size of the original microscopes d. The lens has two different colors e. They have two different light sources

b. It has two lenses

How is Ras activity turned off? a. It is turned off by phosphorylation b. It is turned off by hydrolysis of its bound GTP to GDP c. It is turned off by hydrolysis of its bound GDP to GTP d. It is turned off by an allosteric inhibitor e. It is turned off by hydrolysis of its bound GTP to GMP

b. It is turned off by hydrolysis of its bound GTP to GDP

What evidence suggests that a cell spends the majority of its time in interphase? a. Interphase is more useful b. Only a small percentage of cells in a tissue or cell culture are in mitosis at any given time c. A large percentage of cells in a tissue or cell culture are seen to be in mitosis at any given time d. A moderate percentage of cells in a tissue or cell culture are in mitosis at any given time e. Mitosis is too intricate a process to last very long

b. Only a small percentage of cells in a tissue or cell culture are in mitosis at any given time

What triggers the entry of a cell into mitosis? a. the addition of inhibitory phosphate groups to Cdk1 by the Cdc25 phosphatase b. the removal of inhibitory phosphate groups from Cdk1 by the Cdc25 phosphatase c. the addition of inhibitory phosphate groups to Cdk1 by the Wee1 kinase d. the removal of inhibitory phosphate groups from Cdk1 by the Wee1 kinase e. the removal of phosphate groups from the Wee1 kinase

b. the removal of inhibitory phosphate groups from Cdk1 by the Cdc25 phosphatase

The bond energies associated with noncovalent attractions in the cell are too weak to resist disruption by thermal motion. However, cellular macromolecules can interact specifically AND strongly with each other (or fold by themselves) merely via such interactions. How is this possible? a. The bond energies increase radically when two interacting molecules approach each other. c. Many weak bonds together in a complementary geometry can afford a strong binding d. The cell lowers its internal temperature to reduce thermal motion of molecules and enhance the weak attractions

c. Many weak bonds together in a complementary geometry can afford a strong binding

This question refers to eukaryotic cis-regulatory modules (CRMs). Which of the CRM types are typically paired and found to define the boundaries of a chromosomal domain? a. Enhancers b. Silencers c. Insulators d. Core promoters e. Locus control regions (LCRs)

c. Insulators

Which of the following pairs of amino acid residues would you expect to form ionic bonds? a. Glutamic acid and glutamine b. Arginine and lysine c. Lysine and glutamic acid d. Tryptophan and tyrosine e. Tyrosine and glutamine

c. Lysine and glutamic acid

Quantitative Real Time PCR measures which of the following? a. protein phosphorylation b. DNA methylation c. mRNA abundance d. protein abundance e. Protein translation

c. mRNA abundance This method detects mRNA from a tissue or cell extract and uses PCR to quantify the abundance of mRNA molecules

What is the most appropriate unit of measurement for macromolecular complexes including ribosomes and microfilaments? a. picometers b. angstroms c. nanometers d. micrometers e. centimeters

c. nanometers

Specificity in MAP kinase pathways is sometimes achieved by spatial localization of the pathway's component proteins. Spatial localization of these components is done by structural (i.e., non-enzymatic) proteins called _____________. a. sequestration proteins b. partitioning proteins c. scaffolding proteins d. framework proteins e. spatial organization proteins

c. scaffolding proteins

A mitochondrion has just been engulfed by a cup-shaped isolation membrane as it undergoes mitophagy. Before lysosomal fusion, how many membranes separate the cytosol from the matrix of the engulfed mitochondrion? a. None b. 2 c. 3 d. 4 e. 5

d. 4 Two membranes from the cup-shaped structure and two membranes from the original mitochondrion surround the mitochondrial matrix. After fusion of the outermost membrane with the lysosomal membrane, the three inner membranes would be digested away in the process of autophagy

What is a point centromere? a. One sub-component of a centrosome b. The location where condensin is attached c. A centromere composed of special repeat sequences and an extended chromatinized neighborhood features centromeric H3 (as in human chromosomes) d. A centromere with a single nucleosome modified with variant centromeric H3 and serving as the contact point with the kinetochore (as in yeast) e. None of the above

d. A centromere with a single nucleosome modified with variant centromeric H3 and serving as the contact point with the kinetochore (as in yeast)

In eukaryotic transcription, what feature of chromatin is the most essential for RNA pol II holoenzyme to gain access to a gene's core promoter? a. A properly localized TATA-box element in the DNA sequence b. A properly localized initiator element (Inr) in the DNA sequence c. A properly localized downstream promoter element (DPE) in the DNA sequence d. A characteristic nucleosomal landscape involving fixed (positioned) nucleosomes preceded by a nucleosome free region (NFR) e. All of the above

d. A characteristic nucleosomal landscape involving fixed (positioned) nucleosomes preceded by a nucleosome free region (NFR) (The answer is NOT all of the above because each core promoter element is dispensable)

Which of the following stretches of amino acid residues would you expect to find in the interior of protein molecules? a. Ala-Asp-Asp-Tyr-Arg b. Gly-Lys-Ser-Pro-Thr c. Phe-Glu-Gln-Glu-Asn d. Ala-Val-Leu-Ile-Trp e. Gly-Tyr-His-Arg-His

d. Ala-Val-Leu-Ile-Trp

A gene that had been turned off in a liver cell has just been induced to be highly expressed as the cell responds to a new metabolic load. What observations do you expect to accompany this change? a. More than 100 proteins would become associated with the gene for its transcription b. The nuclear position of the gene would change to place it in a "transcription factory" c. Chromatin modifications associated with the gene would change in favor of higher expression d. All of the above

d. All of the above

You are culturing epithelial cells in the lab. They form a monolayer in a petri dish and establish contacts with other cells. You treat this monolayer with a solution that contains a compound called EGTA - which chelates extracellular calcium and makes calcium unavailable. Which of the following describes what will happen? a. Cell adhesions will strengthen due to enhanced cadherin association b. Cells will maintain adhesions, but lift off the plate together as a monolayer c. The cells will condense together and form multiple layers based on their cadherin expression levels d. Cadherin connections will break apart and the cells will dissociate from one another e. Gap junctions will open and use ATP to pump calcium back into the cell

d. Cadherin connections will break apart and the cells will dissociate from one another Cadherins are calcium-dependent cell junction proteins. By removing calcium from the media, cadherin connections will be lost so the cells will become disconnected and dissociate from one another.

In the following schematic drawing of the inner and outer mitochondrial membranes, in what region (A to D) would you expect to find more ATP synthase dimers? (MT2 #23) a. A b. B c. C d. D

d. D The ATP synthase dimers tend to localize at the tip of the cristae where the membrane curvature is greatest

Which of the following proteins is NOT in the same superfamily as the other four? The other four share an overall architecture composed of seven closely-packed transmembrane helices. a. Bacteriorhodopsin b. Channelrhodopsin c. G-protein-coupled receptor d. Aquaporin e. Rhodopsin

d. aquaporin

The signal-recognition particle (SRP)... a. is a heterodimeric protein b. transiently inhibits transcription and polypeptide elongation by binding to and inhibiting the elongation factors c. accompanies the nascent polypeptide all the way into the ER lumen d. binds GTP e. is permanently attached to the cystolic face of the ER membrane, thus bringing the ribosomes into close proximity of the translocon

d. binds GTP

GTPases are featured in many functions, including nuclear import. In that context, what is used to maintain the Ran-GTP gradient across the nuclear envelope? a. energy released by ATP hydrolysis b. a proton gradient c. a H+ gradient d. energy released by GTP hydrolysis e. energy released by GDP hydrolysis

d. energy released by GTP hydrolysis

In bacterial transcription, what factor is critical for targeting the core enzyme to specific promoters? a. alpha subunit b. beta subunit c. gamma subunit d. sigma subunit e. the TBP subunit of TFIID

d. sigma subunit

Outside of a living cell, the virus exists as a particle called a(n) ______, which is little more than a macromolecular package. a. virulent b. virusette c. virulant d. virion e. infectoid

d. virion

What factor or factors discovered with electron microscopy distinguished prokaryotic from eukaryotic cells? 1. their size 2. their color 3. the types of their internal structures or organelles 4. their fragility a. 1 b. 2 c. 3 d. 4 e. 1 and 3

e. 1 and 3

Which of the following numbered statements pertain to Cell Theory? 1. All organisms are composed of one or more cells 2. The cell is the structural unit of life 3. Cells can arise only by division from a preexisting cell 4. Cells divide only by fission a. 1 b. 2 c. 3 d. 4 e. 1, 2, and 3

e. 1, 2, and 3

This question refers to eukaryotic cis-regulatory modules (CRMs). Which of these statements describes the function of the core promoter? a. It defines the position of the first template nucleotide b. It renders the locus competent for transcriptional initiation c. It harbors short 5-10 bp sequences called core promoter elements that interact with subunits of the general transcription factors of the pol II holoenzyme d. It harbors diffuse, helically-phased, dinucleotide sequences that promoter nucleosome positioning via intrinsic DNA bending e. All of the above

e. All of the above

Which of these represent cells assimilated via endosymbiotic events? a. Proteobacterial ancestor of the mitochondrion b. Cyanobacterial ancestor of the plastid (called the chloroplast in plants) c. Rhodophyte ancestor of some secondary (higher-order) eukaryotic hosts d. Chlorophyte ancestor of some secondary eukaryotic hosts e. All of the above

e. All of the above

Axonal connections in the nervous system are guided by which of the following? a. Chemoattraction b. Chemorepulsion c. Guidance by pioneer axons d. Contact inhibition e. All of the above

e. All of the above Axonal connections use many different strategies to find their targets. All of these options are correct

An ion channel... a. always mediates passive transport b. is ion-selective c. is typically several orders of magnitude faster than a transporter d. is usually gated e. All of the above

e. All of the above Ion channels are ion-selective and can fluctuate between open and closed states. They can only mediate passive transport of ions, and do it at remarkable rates, typically several orders of magnitude higher than the rate of transport through transporters.

What is the cellular function of plant vacuoles? a. They store nutrients and waste products b. They help increase cell size and maintain turgor pressure c. They are used for degradation of cytoplasmic components d. They help maintain cystolic pH e. All of the above

e. All of the above Vacuoles in plants are equivalent to lysosomes in animal cells, and are remarkably versatile in function

What characteristics distinguish prokaryotic and eukaryotic cells? a. Eukaryotes have membrane-bound organelles; prokaryotes do not b. Prokaryotes have relatively little DNA; eukaryotes generally have much more c. Eukaryotic chromosomes are linear; prokaryotic chromosomes are circular d. Prokaryotic DNA is "naked" relative to eukaryotic DNA, which is heavily chromatinized e. All of these are correct

e. All of these are correct

Which of the following characteristics is (are) a basic property of cells? a. Cells are highly complex and organized b. Cells possess a genetic program and the means to use it c. Cells are capable of producing more of themselves d. Cells acquire and utilize energy e. All of these are correct

e. All of these are correct

In actively respiring mitochondria, where in the following schematic drawing of the inner and outer mitochondrial membranes would you expect to find the lowest local pH? (MT2 #24) a. A b. B c. C d. D e. E

e. E The ATP synthase dimers create proton "sinks" or "traps" at the cristae tips, which helps them make efficient use of the protons that are pumped out of the matrix

Imagine a protein that has been engineered to contain a nuclear localization signal, a nuclear export signal, a C-terminal peroxisomal targeting sequence, and a canonical endoplasmic reticulum (ER) signal sequence. With all of these signals, where would you expect to find the protein after its synthesis? a. Cytosol b. Nucleus c. Shuttling between the cytosol and the nucleus d. Peroxisomes e. Endoplasmic reticulum

e. Endoplasmic reticulum The N-terminal ER signal sequence is recognized first and used to target the protein to the endoplasmic reticulum co-translationally

Connexins are the principal component of which adhesion complex? a. Tight junctions b. Adherens junctions c. Desmosome d. Hemidesmosome e. Gap junctions

e. Gap junctions Connexins assemble into trancellular pores that connect the cytosol of two cells. These are called Gap Junctions.

Which of the following is NOT a likely ER signal sequence recognized by the signal recognition particle? All sequences are written with their N-terminus on the left. a. Met-Lys-Leu-Ser-Leu-Val-Ala-Ala-Met-Leu-Leu-Leu-Leu-Ser-Ala-Ala-Arg-Ala b. Met-Glu-Met-Phe-Gln-Gly-Leu-Leu-Leu-Leu-Leu-Leu-Leu-Leu-Ser-Met-Gly-Gly-Thr-Trp-Ala c. Met-Lys-Ala-Lys-Leu-Leu-Val-Leu-Leu-Tyr-Ala-Phe-Val-Ala-Gly-Asn d. Met-Met-Ala-Ala-Gly-Pro-Arg-Thr-Ser-Leu-Leu-Leu-Ala-Phe-Leu-Leu-Cys-Leu-Pro-Trp-Thr-Gln-Val-Val e. Met-Leu-Ser-Leu-Arg-Gln-Ser-Ile-Arg-Phe-Phe-Lys-Pro-Ala-Thr-Arg-Thr-Leu-Ser-Ser-Arg-Tyr-Leu

e. Met-Leu-Ser-Leu-Arg-Gln-Ser-Ile-Arg-Phe-Phe-Lys-Pro-Ala-Thr-Arg-Thr-Leu-Ser-Ser-Arg-Tyr-Leu Note the presence of a positively charged residue (arginine or lysine) at regular intervals in sequence E, which places these residues on one side of an amphiphilic helix. This protein is destined for mitochondria. In the endoplasmic reticulum signal sequences, the longer uninterrupted hydrophobic cores are usually preceded immediately by positively charged residues

Which of the following is correct regarding the electrical properties of cellular membranes? a. Setting up (or changing) the membrane potential requires changing the bulk concentrations of the ions on the two sides of the membrane b. The resting potential in most animal cells is between 20 mV and 120 mV (positive inside) c. If the membrane is impermeable to an ion, the membrane potential approaches the equilibrium potential for that ion d. The resting potential decays immediately following the inhibition of the Na+-K+ pump by a drug e. None of the above

e. None of the above Changing the membrane potential can be achieved by the transport of a small number of ions across the membrane and does not require concentration changes. The resting membrane potential in most cells is close to the K+ equilibrium potential (and is negative inside) because the plasma membrane is most permeable to this ion

For each of the following classifications, indicate whether you would expect to find an actively transcribed gene in the first category (1) or the second (2). Your answer would be a six-digit number composed of digits 1 and 2 only, e.g. 222121 ( ) 1: Heterochromatin, or 2: euchromatin ( ) 1: Chromosome puffs, or 2: condensed chromosome bands ( ) 1: Nuclear periphery, or 2: the center of the nucleus ( ) 1: Within the chromosome territory, or 2: extended out of the territory ( ) 1: Apart from, or 2: close to actively transcribed genes within the nucleus ( ) 1: 11-nm "beads on a string" fibers, or 2: 30-nm fibers

212221

Indicate whether each of the following descriptions better applies to COPI-(1), COPII-(2), or clathrin-(3) coated vesicles. Your answer would be a four-digit number composed of digits 1 to 3 only, e.g. 1322. ( ) They mediate transport from the ER to the cis Golgi network ( ) Their coat protein forms a three-legged structure called a triskelion ( ) They are pinched off from their donor compartment by a dynamin collar ( ) They are involved in retrograde transport in the Golgi apparatus

2331 Typically, transport vesicles from ER to CGN are COPII-coated vesicles. Clathrin-coated vesicles are involved in traffic from the plasma membrane as well as between the endosomal and Golgi compartments, and require dynamin for pinching off efficiently. Clathrin triskelions assemble into a basket-like cage that envelopes these budding vesicles.

Immortalized cell lines are a common model system to study cell biology and possess important strengths and weaknesses over primary cells. In the space below, identify one advantage and one disadvantage of using a cell line over a primary cell model.

Advantages: Easier to grow and manipulate. Do not undergo senescence, many different options Disadvantages: Do not always model tissue very well, can be polyploidy or incur mutations

For mitochondria that are active in respiration, indicate whether the movemembt of each of the following molecules into (I) or out of (O) the matrix is thermodynamically favorable. Your answer would be a four-letter string composed of letters I and O ony, e.g. IOOI ( ) O2 ( ) H+ ( ) ADP ( ) CO2

IIIO: In mitochondria that are active in respiration, O2 and ADP are constantly consumed to produce H2O and ATP, respectively. This creates concentration gradients that favor the movement of these molecules into the organelle. The opposite is true for CO2, which is generated inside the matrix in decarboxylation reactions of the citric acid cycle. Protons are actively pumped out of the matrix by the proteins of the electron-transport chain, and power ATP production when they move into the matrix down their electrochemical gradient.

You have performed a chromosome conformation capture (3C) experiment to study chromatin looping at a mouse gene cluster that contains genes A, B, and C, as well as a regulatory region R. In this experiment, you performed in situ chemical cross-linking of chromatin, followed by cleavage of DNA in the nuclear extract with a restriction enzyme, intramolecular ligation, and cross-link removal. Finally, a polymerase chain reaction (PCR) was carried out using a forward primer that hybridizes to a different location in the locus. The amounts of the PCR products were quantified and normalized to represent the relative cross-linking efficicency in each analyzed sample. You have plotted the results in the graph below. The same experiment has been done on two tissue samples: fetal liver (represented by red lines) and fetal muscle (blue lines). Interaction of the A, B, and C genes with the regulatory R region is known to enhance expression of these genes. Indicate true (T) and fale (F) statements below based on the results. Your answer would be a four letter string composed only of letters T and F, e.g. TTTF ( ) The B gene would be predicted to have higher expression in the fetal liver compared to the fetal muscle tissue ( ) Interaction between the R region and the B gene involves the A gene looping out ( ) Interaction between the R region and the B gene involves the C looping out ( ) In fetal muscle, the B gene definitely does not engage in looping interactions with any other elements in the cluster

TTFF

Which of the following can be visualized by conventional light microscopy and doesn't require super resolution. Indicate with a Yes (Y) or No (N) ( ) The movement of mitochondria tagged with a fluorescent protein in an axon segment ( ) Comparing phospholipids on opposite sides of the plasma membrane ( ) Two adjacent ribosomes on a mRNA transcript that is being translated ( ) Filamentous actin labeled with rhodamine-phalloidin ( ) Two proteins that are localized to the opposite poles of a bacterial cell

YNNYY The average length of a bacterial cell is 1 micrometer

What happens when histone H1 is selectively extracted from compacted chromatin (30 nm fibers)? a. 30-nm fibers uncoil to form a thinner, more extended beaded filament b. 30-nm fibers coil to form a thicker, less extended cylindrical filament c. 30-nm fibers completely disassemble to their component nucleotides d. 30-nm fibers break into small fragments e. 30-nm fibers break up into large fragments

a. 30-nm fibers uncoil to form a thinner, more extended beaded filament

In the following schematic drawing of an abundant plasma membrane phosphoglyceride, which part is positively charged? (MT2 #1) a. A b. B c. C d. D e. E

a. A In the drawing, A can be one of many possible choices (including the positively charged choline or ethanolamine), B is the phosphate moiety, C is the glycerol, and D and E are fatty acids

The referred sequences referred to in the previous question have which of the following function? a. Ensuring that nearby genes are protected from shrinking DNA edges b. Providing a gene neighborhood to harbor the ribosomal RNA gene arrays c. Providing a place for DNA double-strand break repair machinery to aggregate d. Providing a place for attachment of the kinetochore e. None of the above (they are junk DNA sequences with no function)

a. Ensuring that nearby genes are protected from shrinking DNA edges (the previously referred sequences are telomeres)

The period in the cell cycle between the end of cell division and the beginning of DNA synthesis is called the _____ phase. a. G1 b. S c. G2 d. M e. G0

a. G1

Which of the following changes would you expect to increase the phase transition temperature of a synthetic bilayer composed of phosphatidylserine? a. Incorporation of phospholipids with longer fatty acid chains b. Introduction of double bonds in the fatty acids c. Addition of cholesterol d. Removal of serine from the head group e. None of the above

a. Incorporation of phospholipids with longer fatty acid chains With longer hydrocarbon chains, the phase transition temperature increases, i.e. the membrane can freeze more readily. In contrast, introduction of double bonds in the fatty acid chains creates kinks in the chains and makes it harder to pack them together. At physiological pH, removal of serine adds a negative charge to the head group, also tending to limit tight packing. The effect of cholesterol is more complicated, but at the high concentrations found in eukaryotic plasma membranes, cholesterol also prevents the hydrocarbon chains from crystallizing.

What is the reason for the withdrawal of cells from the cell cycle after exposure to stressful stimuli, like X-rays and damaging chemicals? a. It gives the cell time to repair damage resulting from such adverse conditions b. It allows the cell to initiate programmed cell death c. It allows cells to initiate sodium transport d. It allows the cell to secrete defensive chemicals e. It gives the cell time to switch its developmental pathways

a. It gives the cell time to repair damage resulting from such adverse conditions

DNA replication and synthesis of additional histones occur during what part of the cell cycle? a. G1 phase b. S phase c. G2 phase d. M phase e. G0 phase

b. S phase

Which of these is a family of proteins that is homologous to the products of the CED-3 gene in C. elegans and plays an important role in the apoptosis of animal cells? a. capsidases b. caspases c. capsasins d. capsulases e. apoptases

b. caspases

What is responsible for holding sister chromatids together after replication? It holds the two chromatids together through G2 and into mitosis. a. compressin b. cohesin c. condensin d. connexin e. contractin

b. cohesin

The separation of the cell and its cytoplasm into two daughter cells is known as _____. a. meiosis b. cytokinesis c. chromokinesis d. chromatosis e. mitosis

b. cytokinesis

The light used to excite a fluorescent molecule carries ___ energy and has a ___ wavelength compared to the light that is then emitted from the molecule. a. greater; longer b. greater; shorter c. the same amount of; shorter d. less; longer e. less; shorter

b. greater; shorter Greater energy is needed to activate a fluorescent molecule because some energy is lost to entropy when it is emitted. Shorter wavelengths are higher energy

What apparently drives the separation of centrosomes? a. motor proteins associated with microfilaments b. motor proteins associated with adjacent microtubules c. contraction of individual microfilaments d. sliding of adjacent microfilaments over one another e. contraction of adjacent microtubules

b. motor proteins associated with adjacent microtubules

Consider a transcription regulatory protein that has both a nuclear localization and a nuclear export signal and is normally found in both the nucleus and in the cytosol at comparable concentrations. This protein has a high-affinity binding partner in the nucleus. Upon activation of a certain signaling pathway, the binding protein ubiquitylated and degraded. As a result of this... a. the transcription regulatory protein accumulates in the nucleus b. the transcription regulatory protein accumulates in the cytosol c. the distribution of the transcription regulatory protein does not change, but the expression of its target genes may be altered d. the distribution of the transcription regulatory protein does not change, and the expression of its target genes is not necessarily changed as a result of the degradation event

b. the transcription regulatory protein accumulates in the cytosol A high-affinity binding partner in the nucleus inevitably shifts the steady-state distribution of the protein toward this compartment. Once the partner is eliminated, the now-dominating export route leads to accumulation of the protein in the cytosol. An effect on gene expression does not depend on localization alone

You isolate genomic DNA from a population of cancer cells derived from a malignant tumor. You perform a screen to identify genetic mutations that might be responsible for tumor formation. Which of the following mutations would represent a good candidate for this activity? a. Point mutations in p53 that stabilize the protein and enhance activity b. Mutations that destabilize Myc so that it is constantly degraded c. A truncation in EGFR that creates a constitutively active protein d. Gain of function mutations in Rb that enhance interactions with E2F e. Mutations in beta-catenin that promote its degradation by APC

c. A truncation in EGFR that creates a constitutively active protein This is the only choice that would generate a protein which is expected to promote cell proliferation and survival. The other options would be expected to prevent cancer. For example, p53 promotes DNA repair or apoptosis when it accumulates. Myc overexpression promotes cell proliferation. Rb interactions with E2F suppress the cell cycle. Beta catenin can also promote cell proliferation, but it is normally degraded by APC

Which of the following events normally activates a GTP-binding protein? a. GTP hydrolysis by the protein b. Activation of an upstream GTPase-activating protein c. Activation of an upstream guanine nucleotide exchange factor d. Phosphorylation of a bound GDP molecule by an upstream phosphorylase e. Pi release after GTP hydrolysis

c. Activation of an upstream guanine nucleotide exchange factor Activation of an upstream guanine nucleotide exchange factor (GEF) activates a GTPase by facilitating its conversion into a GTP-bound form through guanine nucleotide exchange

The lateral diffusion of a plasma membrane protein has been studied using the fluorescence recovery after photobleaching (FRAP) technique in a cell under normal conditions, and the following plot has been obtained (MT2 #7). Under a different condition (e.g., when a signaling pathway is turned on), the protein binds to a few other proteins and protein complexes in the plasma membrane. As a result, its lateral diffusion coefficient is reduced and a significant fraction of the molecules of this protein are immobilized in large aggregates. How would you expect the FRAP curve to change under these new conditions? The dotted line in each graph is the original curve shown for comparison. a. A - falls slightly below the original curve b. B - slightly above the original curve c. C - half as large the original curve d. D - flattens off just beneath the original curve e. E - follows the original curve and then dips

c. C The fraction of the molecules that are practically mobile is represented by the final fluorescence recovery. The diffusion rate can also be deduced from the curve and is related to the rate of recovery.

Which of these is a term for sphere-shaped prokaryotic cells? a. Amoebas (or Amoebae) b. Bacilli c. Cocci d. Spirilli e. All of the above

c. Cocci

What happens if any of the condensin proteins are removed from the frog egg extracts within which chromosome compaction can occur in vitro? a. Compaction continues unabated b. Compaction occurs more quickly than normal c. Compaction is prevented d. The DNA expands further and fills the entire cell e. Compaction occurs but occurs more slowly

c. Compaction is prevented

The motion of lipid molecules in a synthetic bilayer can be studied by various techniques. Which of the following has been observed in these systems? a. Phospholipids diffuse rapidly within and between the two leaflets of a bilayer b. An average lipid molecule can diffuse the length of about 2 micrometers in a fraction of a millisecond c. The flip-flops are very rare for phospholipids but cholesterol molecules flip-flop more often d. Within a bilayer, lipid molecules rarely rotate about their long axis, but diffuse laterally at very high rates e. All of the above

c. The flip-flops are very rare for phospholipids but cholesterol molecules flip-flop more often In contrast to high lateral diffusion and rotation rates, flip-flop rates are very low for phospholipids, although not so low for cholesterol. Due to the high lateral diffusion coefficients, an average lipid molecule can travel the length of a bacterial cell (approximately 2 micrometers) in about a second

Polytene chromosomes are useful for studying chromatin because they... a. are smaller than regular chromosomes and easier to manipulate b. lack heterochromatin c. have distinct visible banding patterns d. can make polyploid cells e. All of the above

c. have distinct visible banding patterns

During maturation of early endosomes to late endosomes... a. the vacuolar domain of the endosome is shed, whereas the tubular domain is retained b. the endosome migrates along actin filaments away from the cell interior c. the lumen of the endosome becomes more acidic d. intralumenal vesicles disappear e. all of the above

c. the lumen of the endosome becomes more acidic During maturation, the endosome sheds its tubular domains and retains its vacuolar domains, the lumen of which becomes more acidic. The endosome moves along microtubule tracks toward the cell interior, and acquires intralumenal vesicles for membrane protein degradation. It also receives new components from the trans Golgi network

What is the name of an extracellular messenger protein that is named for its ability to kill tumor cells and also serves as an apoptic stimulus? a. tumor angiogenesis factor b. tumor death factor c. tumor necrosis factor d. necromancer factor e. tumorigenic factor

c. tumor necrosis factor

This question refers to eukaryotic cis-regulatory modules (CRMs). Which of these statements about transcriptional enhancers is incorrect? a. Enhancers contain clusters of sequence-specific TF binding sites (cis-elements) b. Enhancers are typically 200 to 800 bp long c. Enhancers bind TFs and thereby recruit larger complexes that can remodel the chromatin environment d. Enhancers function to insulate a gene from the inappropriate activation by upstream enhancers e. Multiple enhancers acting independently can collectively shape the overall expression pattern of a single gene

d. Enhancers function to insulate a gene from the inappropriate activation by upstream enhancers

This family of ATPases is structurally related to the turbine-like pumps that acidify lysosomes and vesicles; however, they usually function in reverse, generating ATP from ADP and Pi using proton gradients across membranes. What are they called? a. P-type pumps b. ABC transporters c. V-type pumps d. F-type pumps e. Permeases

d. F-type pumps The F-type pumps usually function in reverse, and are responsible for the majority of ATP production in our cells

Five major types of chromatin were identified in studies performed on D. melanogaster cells, although much more remains to be learned about chromatin diversity and dynamics. Which of the following is correct regarding these findings in Drosophila? a. These results were obtained using the 3C technique, which determines the positions of loops in the chromatin b. According to these results, there are four types of heterochromatin and only one type of euchromatin c. The polycomb form of chromatin belongs to the euchromatin type d. In addition to these five major types of chromatin, there seem to be additional minor types as well e. The pattern of chromatin types in the chromosomes is constant across the different cell types in a multicellular organism

d. In addition to these five major types of chromatin, there seem to be additional minor types as well

In the following schematic diagram of a nuclear pore complex, on which side is the cytosol located? What is the approximate diameter of the pore, as indicated by the vertical bar? (MT2 #14) a. Right; 1-micrometer b. Right, 0.1-micrometer c. Left, 1-micrometer d. Left, 0.1-micrometer

d. Left, 0.1 micrometer The structure of the nuclear pore complex usually shows an eightfold symmetry and contains cytoplasmic fibrils and a nuclear "basket". Its diameter is approximately 100 nm and differs in different organisms

Based on cell activities readily visible in the light microscope, there are two major cell cycle phases, ________ and __________. a. M phase, cytokinesis b. interphase, cytokinesis c. M phase, C phase d. M phase, interphase e. C phase, interphase

d. M phase, interphase

Transgenic mice were generated that overexpress the proto-oncogene Myc. However, these mice do not develop cancer unless combined with another cancer-linked mutation. What does this observation tell us? a. Myc is not important in cancer progression. b. Mice are a poor model for cancer c. Genetics does not have influence on cancer d. Multiple mutations are often required for cancer progression e. Loss of Myc function is important for cancer

d. Multiple mutations are often required for cancer progression Many cancer-linked mutations do not promote cancer alone. However, they are still important.

The synthetic toxin 2,4-dinitrophenol can uncouple ATP synthesis from mitochondrial respiration by decreasing the permeability of the inner membrane to protons. What would be the effect of dinitrophenol treatment on the amount of ATP produced by mitochondria and on the rate of ATP transport across the inner membrane, respectively? a. Positive, positive b. Positive; negative c. Negative; positive d. Negative; negative

d. Negative; negative By diminishing the electrochemical gradient across the inner membrane, the toxin interferes with ATP synthesis and ATP/ADP exchange, both of which are driven by the gradient

In order to execute apoptosis, caspases must be activated by which of the following: a. Phosphorylation b. Ubiquitination c. Exocytosis d. Proteolysis e. Acetylation

d. Proteolysis Caspases are activated by proteolysis which rapidly stimulates the protease activity of this enzyme. This is a potent strategy for preventing spontaneous activation and also creating a signal that cannot be rapidly turned off.

You treat sensory neuron cultures with a molecule that blocks activity of the TrkA receptor. Which of the following do you expect to observe? a. Enhanced cell:cell adhesion b. Differentiation of the sensory neuron into a glial cell c. The neuron enters mitosis d. The appearance of cleaved caspases e. Degradation of p53

d. The appearance of cleaved caspases TrkA is the receptor for nerve growth factor. Loss of TrkAor nerve growth factor promotes apoptosis. Caspase cleavage is an important marker for apoptosis.

Which of the following is NOT a common second messenger in cell signaling? a. Ca2+ b. Cyclic adenosine monophosphate c. Diacylglycerol d. Tyrosine e. Inositol triphosphate

d. Tyrosine Second messengers are small chemical generated in large amounts in response to receptor activation signaling pathways and diffuse away from their source to spread the signal. Some are water-soluble [e.g. calcium ions and cyclic adenosine monosphate (cAMP)] and some are lipid-soluble [e.g. diacylglycerol (DAG) and inositol triphosphate (IP3)]

What kind of enzyme is the Ras protein? a. an ATPase b. a kinase c. a phosphodiesterase d. a GTPase e. a phosphatase

d. a GTPase

Adaptor proteins select cargo proteins that will be incorporated into clathrin-coated vesicles. An adaptor protein such as AP2... a. can induce membrane curvature even before clathrin molecules bind b. acts as a coincidence detector, assembling only when a number of requirements are met c. binds to phosphoinositides in the cytosolic leaflet of the membrane d. alternates between a locked cytosolic form and an unlocked membrane-bound form e. all of the above

e. all of the above When bound to the phosphoinositide PI(4,5)P2, the adaptor protein AP2 changes conformation (or "unlocks") and binds to cargo receptors in the membrane, inducing membrane curvature. Since several requirements must be met for stable AP2 binding to a membrane, the protein only assembles at the right place and at the right time

The free-energy change of ATP hydrolysis to ADP inside the cell is about -50 kJ/mole. The standard free-energy change for the same reaction is about -30 kJ/mole. This necessitates that [ATP] inside the cell be... a. higher than that under standard conditions b. greater than [ADP] c. greater than [ADP] x Pi d. greater than [ADP] x Pi x Keq e. greater than [ADP] x Pi/Keq

e. greater than [ADP] x Pi/Keq The equilibrium constant for the hydrolysis reaction (not considering water) is: Keq = [ADP]eq x [Pi]eq / [ATP]eq DeltaG will have a greater negative value than deltaGstandard if and only if concentrations deviate from Keq such that [ADP] x Pi / [ATP] < Keq

The separation of duplicated chromosomes into two daughter nuclei is known as ________. a. meiosis b. cytokinesis c. chromokinesis d. chromatosis e. mitosis

e. mitosis