Cell bio unit 3 study guides

Your friend has cut a 3000-nucleotide-pair circular plasmid with either or both restriction enzymes A and B, and has separated the digestion products by electrophoresis. The results are shown in the schematic drawing below, with the approximate size of the fragments indicated above each band. Based on these results, what is the closest distance (in nucleotide pairs) between an A restriction site and a B restriction site on this plasmid?

1000

RNA-seq and ribosome profiling experiments have been carried out on the same cells. The following simplified graphs show the results for the same genomic region containing a gene with three exons. Which graph (1 or 2) do you think corresponds to the RNA-seq results?

2 (square one)

in the following schematic drawing of an abundant plasma membrane phosphoglyceride, which part is positively charged? (lots of shapes) A. A B. B C. C D. D E. E

A

in the reaction below, which enzymes joins the two DNA fragments? An endonuclease. A DNA polymerase. A DNA ligase. A restriction enzyme. A DNA helicase

A DNA ligase.

Given the absorption and emission spectra of three fluorescent dyes in the simplified diagrams below, which pair of dyes is better suited for a fluorescence resonance energy transfer (FRET) study? (boobie hump pics) A. AB B. AC C. BC

A. AB

Which of the following molecules would be found in detergent resistant membranes or liquid ordered domains in the cellular membranes? A. Cholesterols B. GPI-anchored proteins C. Cerebrosides D. Myrystolylated Src kinases E. All of the above

A. Cholesterols

Considering the following hydropathy plot for a multipass transmembrane protein in the plasma membrane, are the protein termini expected to be located inside (I) or outside (O) of the cell? Which of the regions indicated as 2 and 3 in the plot is expected to have more positively charged residues? The position of positively charged residues near the first transmembrane helix is indicated by an asterisk on the plot. A. I; 2 B. I; 3 C. O; 2 D. O; 3

A. I; 2

Sanshool is a natural compound found in Sichuan pepper, which is commonly used in making spicy Asian food, and creates a numbing sensation in the mouth. It is known to inhibit a subset of potassium leak channels involved in maintaining the resting membrane potential in sensory neurons. How do you think sanshool affects these sensory neurons? A. It elevates the resting potential (to less negative values) and makes it easier to excite the neuron. B. It elevates the resting potential and makes it harder to excite the neuron. C. It lowers the resting potential and makes it easier to excite the neuron. D. It lowers the resting potential and makes it harder to excite the neuron. E. It causes hyperpolarization and decreases the spontaneous firing of the neuron.

A. It elevates the resting potential (to less negative values) and makes it easier to excite the neuron.

What is the effect of defective or missing N-acetylglucosamine phosphotransferase on lysosomal protein sorting? A. Lysosomal proteins are secreted from the cell. B. Lysosomal proteins are retained in the Golgi network. C. Lysosomal proteins are retained in the ER. D. Lysosomal proteins remain tightly bound to M6P receptors. E. Nonfunctional lysosomal proteins accumulate in the lysosome.

A. Lysosomal proteins are secreted from the cell.

BiP is a soluble protein normally found in the ER lumen. You added the following amino acids to the middle of the BiP protein sequence: LAILIFVVLLFWLVILLIAAIV. What is the topology of this new protein? A. N out and C in B. N in and C out C. N out and C out D. N in and C in E. None of above

A. N out and C in

According to the model for nuclear transport described in the classroom, what do you think would happen if you could artificially limit all Ran-GAP activity to the nucleus and all Ran-GEF activity to the cytosol? A. Proteins containing an NLS would be actively exported from the nucleus, while NES-containing proteins would be actively imported. B. Both import and export of nuclear proteins would be stalled, as they lose their directionality. C. Protein import into the nucleus would be reversed, but export would be unaffected. D. Protein import into the nucleus would be stalled, but export would be unaffected. E. Nothing would change; this is the normal Ran-GAP and Ran-GEF distribution.

A. Proteins containing an NLS would be actively exported from the nucleus, while NES-containing proteins would be actively imported.

The twenty three groups of yeast sec mutants isolated by Randy Schekman's group _____________________. A. are conditional. B. have gain-of-function mutations. C. fail to secrete proteins at the permissive temperature. D. all show enlarged ER. E. fail to internalize growth factor receptors

A. are conditional.

Transmission electron microscopy achieves a better resolution than light microscopy. A. True. B. False.

A. true

indicate which one of the indicated types of coat proteins (A, B, and C) in the schematic diagram below corresponds to COPI, COPII, and clathrin, respectively. Your answer would be a three-letter string composed of letters A to C only, e.g. CBA

ACB

In the simplified diagram below depicting exocytosis of synaptic vesicles, which components (A to D) correspond to each of the following? Your answer would be a four-letter string composed of letters A to D only, e.g. DBCA. (Chain diagram) ( ) Ca2+ ( ) Complexin ( ) Synaptotagmin ( ) SNARE complex

ACBD

In sequence alignments such as those generated by a BLAST search, the significance of the alignment can be presented as an E-value, which specifies how likely it is for a match this good to be found in a database of a given size by chance. You have scanned a large sequence database with a sequence query, hoping to find a significant match. Which one would you look at: (A) a match with an E- value of 100, or (B) one with an E-value of 0.001?

B

The figure below shows RNAseq reads aligned to the Plasmodium genome. Which one of the genes is transcribed in male and female gametocytes?

B and C

In Sanger sequencing, what blocks further elongation, if incorporated into the growing DNA strand? ???? A. Deoxyribonucleoside triphosphates B. Dideoxyribonucleoside triphosphates C. Ribonucleoside triphosphates

B. Dideoxyribonucleoside triphosphates

Which of the following is NOT correct regarding the restriction enzyme EcoRI? A. It is an endonuclease. B. It creates double-strand breaks in DNA. C. It recognizes the target sequences with the help of guide RNAs. d. It is greatly useful in manipulating DNA and studying gene expression and function.

B. It creates double-strand breaks in DNA.

Channels, transporters, and pumps regulate membrane permeability of a cell. Which of the following correctly describe about them? A. Channel transport solutes faster than transporters. B. The rate of glucose transport via a glucose-uniporter depends on membrane potential. C. Channels do not undergo a conformational change for their action. D. A transporter forms a continuous pore when it opens. E. None of above.

B. The rate of glucose transport via a glucose-uniporter depends on membrane potential.

Which of the following would be true in a sar1 (a small G protein) mutant? A. There would be a normal number of ER to Golgi vesicles. B. Translation of a secretory protein would be arrested. C. Translocation of a secretory protein into the ER lumen would fail to occur. D. COPI vesicles would fail to bud off the Golgi membrane. E. The ER cisternae would be dilated.

B. Translation of a secretory protein would be arrested.

Sort the following events to reflect the order in which they occur during vesicle docking onto a target membrane, starting with an inactive Rab in the cytosol. Your answer would be a four-letter string composed of letters A to D only, e.g. DACB. A. Rab is bound to its effector (tethering protein) on the target membrane B. Rab is bound to its Rab-GDI. C. Rab is bound to the membrane in its GTP-bound form. D. Rab dissociates from the membrane.

BCAD

Sort the following events to reflect the order in which they occur during the formation of vesicles from the ER destined for the Golgi apparatus. Your answer would be a four-letter string composed of letters A to D only, e.g. DACB. A. Sar1 GTP hydrolysis B. Sar1 GTP binding C. Sar1-Sec23 binding D. Sar1 membrane association

BDCA

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

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

A piece of DNA has been sequenced by Ion TorrentTM sequencing. The result corresponding to a six-nucleotide segment of this DNA is presented in the graph below, in which pH change is recorded after the addition of each of the four nucleotide triphosphates in cycles. What is the sequence of this segment? All sequences are written from 5′ to 3′. A. TACGTA B. CGTACG C. CCGTAA D. CGGTTA E. ATTGGC

C. CCGTAA

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.

Compared to the cytosol, which of the following is generally true about the lumen of the endoplasmic reticulum in our cells? A. It has a higher pH. B. It has a more reducing environment. C. It has a much higher calcium ion concentration. D. It has a higher density of ribosomes. E. All of the above.

C. It has a much higher calcium ion concentration

For each membrane protein in the following schematic drawings, indicate whether the cytoplasmic side of the membrane is more likely to be on the left (L) or on the right (R). Your answer would be a four-letter string composed of letters L and R only, e.g. RRRR. (black squiggle image) A. LLL B. RLL C. LRL D. LLR E. LRR

C. LRL

You suspect a mutation in the DNA binding domain of the tumour suppressor gene p53. You decide to determine whether this is true by mRNA isolation, reverse transcription, and PCR with primers specific for that specific region. You finally use ________ to determine the nucleotide sequence of p53. A. Pyrosequencing B. Illumina sequencing C. Sanger sequencing D. Ion Torrent sequencing

C. Sanger sequencing

Select all the lipids that help form a liquid ordered state. A. Phosphatidyl choline B. Phosphatidyl ethanolamine C. Sphingomyelin D. Phosphatidylinositol E. Cholesterol

C. Sphingomyelin & E. Cholesterol

Which of the following is correct for the plasma membrane and its proteins in the cell? A, All membrane proteins are evenly distributed in the plasma membrane of a sperm. B. he tight junction of intestinal epithelial cells allows the diffusion of small membrane proteins across the junction. C. The tight junction of intestinal epithelial cells separate the lateral membrane from the basal membrane of the plasma membrane. D Some membrane proteins are confined to the tail of a sperm because the tail is not part of the plasma membrane. E None of above.

C. The tight junction of intestinal epithelial cells separate the lateral membrane from the basal membrane of the plasma membrane.

You have carried out a genetic screen in a species of fish, and have identified a new gene in this organism. You have cloned and sequenced the gene, but do not know anything about the biochemical function of the gene product. Which of the following is the most sensible next step in order to get clues about the function? a. Purifying the protein product and determining its structure by x-ray diffraction b. Screening for small molecules that perturb gene function C. Using the BLAST algorithm to scan sequence databases for similar sequences D. Using MS/MS to sequence the gene product without the need for purification E. Mutating the gene and performing reverse genetics

C. Using the BLAST algorithm to scan sequence databases for similar sequences

(this pic looks like a PCR image) You know that a particular sequence at the C-terminus of the ERGIC53 protein enhances its exit from the endoplasmic reticulum (ER). You create two mutant versions of the protein, one without the suspected sequence (1) and one in which the sequence is replaced with an ER retention signal (2). You transfect a fibroblast cell line with a plasmid that encodes either wild-type ERGIC53 (0) or one of the engineered versions of it (1 or 2). After inducing the expression of the proteins, you lyse the cells and either treat the lysate with endoglycosidase H (Endo H) or leave the lysate untreated, as indicated below. You then separate the proteins by SDS-PAGE and perform a Western blot to detect the bands corresponding to ERGIC53. Your results are represented in the following drawing. Which lanes (A to C) do you expect to correspond to each of the proteins 0, 1, and 2, respectively? Your answer would be a three-letter string composed of letters A to C only, e.g. BCA.

CAB

The permeability of a protein-free lipid bilayer to various molecules depends on their properties. Sort the following in order of low to high permeability from left to right. Your answer would be a six-letter string composed of letters A to F, e.g. ACBDFE. A. O2 B. ATP C. RNA oligonucleotide D. Na+ E. Glucose F. Urea

CBDEFA

Indicate whether each of the following descriptions better applies to cDNA libraries (C) or genomic DNA libraries (G). Your answer would be a five-letter string composed of letters C and G only, e.g. CGCGC. ( ) Their production requires use of reverse transcriptase. ( ) They are enriched in protein-coding genes. ( ) Different sequences are represented in them based on their transcription level. ( ) They contain intronic sequences. ( ) They are cell-type specific.

CCCGC

Indicate whether the location of each of the following is topologically equivalent to the cytosol (C) or the extracellular space (E). Your answer would be a five-letter string composed of letters C and E only, e.g. CCECE. ( ) Ribosomes ( ) Chromatin ( ) Lysosomal hydrolases ( ) Calcium ions in the ER ) Peroxisomal catalase

CCEEE

Indicate whether the C-terminus (C) or the N-terminus (N) of each of the following proteins is expected to be located in the cytosol upon membrane integration of the protein. Your answer would be a three-letter string composed of letters C and N only, e.g. CCC. A. ( ) A single-pass transmembrane protein that has one N-terminal signal sequence and one internal stop-transfer signal B. ( ) A single-pass transmembrane protein that has one internal signal sequence that is preceded by a patch of positively charged residues C. ( ) An ER tail-anchored protein

CNN

Consider a transmembrane protein with the following topology that has an internal signal sequence (helix 1). If you fuse a canonical ER signal sequence at the N-terminus of this protein, how would you expect the topology to change? The ER lumen is at the bottom in all drawings. For simplicity, assume that the effect of charged residues flanking the transmembrane helices is negligible in this case. (U squiggle) ABCDE

D

portion of RNA-seq data obtained from two tissue samples is plotted in the following schematic diagram. Which region (A to E) corresponds to an alternative exon? (muscle liver charts) A, B, C, D, E

D

The following diagram depicts the topology of a multipass transmembrane protein in the endoplasmic reticulum (ER) membrane. Which set of helices act as stop-transfer signals in this protein? A. 1, 2, 3 B. 4, 5, 6 C. 1, 3, 5 D. 2, 4, 6 E. 1, 6

D. 2, 4, 6

The cytoplasmic C-terminal KKXX sequence of transmembrane proteins interacts with ... A. t-SNAREs B. v-SNAREs C. AP2 D. COPI coatomers E. COPII coatomers

D. COPI coatomers

You mixed the 600g supernatant with 65% sucrose solution so that the final concentration of sucrose becomes 55%. Then, you loaded the mixture at the bottom of the sucrose gradient you set up in Question 10. After centrifugation, you observed four bands in the centrifuge tube. What are the identities of these bands from top to bottom of the tube? A. Mitochondria, Plasma membrane, Lysosomes, and Golgi B. Plasma membrane, Golgi, Lysosomes, and Mitochondria C. Lysosomes, Mitochondria, Plasma membrane, Golgi D. Golgi, Lysosomes, Plasma membrane, and Mitochondria E. Mitochondria, Lysosomes, Golgi, and Plasma membrane

D. Golgi, Lysosomes, Plasma membrane, and Mitochondria

Which of the following is NOT correct regarding the molecule whose structural formula is shown below? 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 membranes of virtually all living cells.

Which of the following is correct for the critical micelle concentration (CMC)? A. All additional detergents added to the system above the CMC become monomeric. B. It is the concentration of detergents at which 50% of total detergents go to micelles. C. Different detergents tend to have a similar CMC. D. It is the concentration of detergents above which micelles form. E. None of above.

D. It is the concentration of detergents above which micelles form.

The AgeI restriction enzyme recognizes the sequence ACCGGT and cuts each strand between the first (A) and the second (C) nucleotide. This can be represented as A|CCGGT (i.e. ), with the vertical bar indicating the cleavage position. If a DNA fragment is cut with AgeI at both ends, CCGGT cutting a plasmid TGGCCA A with which of the following enzymes would then allow insertion of the fragment into the plasmid by simple ligation of sticky ends? A. FseI, with the recognition sequence GGCCGG|CC B. AatI, with the recognition sequence AGG|CCT C. BstZI, with the recognition sequence C|GGCCG D. MroI, with the recognition sequence T|CCGGA ??? E. None of the above

D. MroI, with the recognition sequence T|CCGGA or??? E. None of the above

Which of the following lipids do you expect to be a canonical scramblase substrate in the plasma membrane? A. Ganglioside GM1 B. Cholesterol C. Glycosylphosphatidylinositol D. Phosphatidylethanolamine E. Galactocerebroside

D. Phosphatidylethanolamine

You injected purified botulinum toxins into a neuronal cell. What will be an expected phenotype? A. Synaptic vesicles lack neurotransmitters. B. Synaptic vesicles are not formed. C. Release of neurotransmitter is enhanced dramatically. D. Synaptic vesicles fail to fuse with the plasma membrane. E. All of the above.

D. Synaptic vesicles fail to fuse with the plasma membrane.

Which of the following transporters mediates primary active transport when transporting the solutes in the directions indicated? The concentration of both solutes (shown as small circles and squares) is higher outside of the cell. ABCDE

E-Small circle and square are going OUT

In Sanger sequencing, does each labeled DNA molecule have a fluorescently labeled dideoxyribonucleotide at its 5′ end or its 3′ end? Do the labeled nucleotides lack the 2′ or 3′ hydroxyl group? a. 3′ end; 2′ hydroxyl group only b. 3′ end; 3′ hydroxyl group only c. 5′ end; 2′ hydroxyl group only d. 5′ end; 3′ hydroxyl group only E. 3′ end; both hydroxyl groups

E. 3′ end; both hydroxyl groups

An ion channel ... A. always mediates passive transport. B. is ion-selective. C. can be several orders of magnitude faster than a transporter. D. is usually gated. E. All of the above.

E. All of the above

Glycolipids such as gangliosides ... A. may contain oligosaccharide chains with negatively charged residues. B. are found to constitute about 10% of the total lipid mass in the plasma membrane of neurons. C. are found in the extracellular leaflet (facing away from the cytosol) in the cellular membranes. D. affect the electrical environment of the membrane. E. All of the above

E. All of the above

In SDS-PAGE of proteins, ... A. the proteins are unfolded while being separated. B. the proteins are separated by size, mostly independent of their native charge. C. large proteins move more slowly. D. a detergent is used. E. All of the above.

E. All of the above.

Indicate true (T) and false (F) statements below regarding receptor-mediated endocytosis of LDL particles. Your answer would be a four-letter string composed of letters T and F only, e.g. TTTF. A. ( ) LDL receptors are normally degraded in the lysosome along with their LDL ligands. B. ( ) LDL receptors that do not bind to extracellular LDL cannot be internalized in clathrin-coated vesicles. C. ( ) A mutation that impairs the attachment of an LDL receptor to a clathrin-coated pit would cause depletion of blood LDL levels. D. ( ) The cytosolic tail of the LDL receptor interacts with clathrin coats for internalization.

FFFT

Both Sanger and Ion Torrent sequencing employ fluorescently labelled nucleotides. True False

False

Indicate whether each of the following transport processes occurs via the mechanisms described as gated transport (G), transmembrane translocation (T), or vesicular transport (V). Your answer would be a five-letter string composed of letters G, T, and V only, e.g. VTTTG. ( ) Import into nucleus ( ) Export from nucleus ( ) Import into mitochondria ( ) Return from Golgi to ER ( ) Return from ER to cytosol

GGTVT

Indicate whether you would use a fluorescent organic molecule (O), in situ hybridization (H), or a coupled fluorescent protein (P) to visualize the cells and their molecules in each of the following cases. Your answer would be a five-letter string composed of letters O, H, and P only, e.g. OHOOO. ( ) You would like to see where in the early Drosophila embryo the mRNA encoding a certain transcription regulator is located. ( ) You would like to see the nuclei and count them in an early mouse embryo. ( ) You would like to visualize chromosome 3 in a human cell culture derived from a patient's tissue, based on specific sequences present on this chromosome. ( ) You would like to observe the oscillations in Ca2+ ions inside a fertilized frog egg. ( ) You would like to compare the localization of two transcription regulatory proteins in cultured human T cells.

HOHOP

ndicate whether each of the following descriptions better applies to Illumina® sequencing (I), Ion TorrentTM sequencing (T), or both sequencing technologies (B). Your answer would be a four-letter string composed of letters B, I, and T only, e.g. IBBB. ( ) It uses fluorescently labeled nucleotides. ( ) It uses PCR-generated copies of DNA. ( ) It is a second-generation sequencing technology and employs a cyclic wash-and-measure paradigm. ( ) It relies on the fidelity of DNA polymerase for its accuracy.

IBB

Indicate whether each of the following descriptions better applies to N-linked (N) or O-linked (O) glycosylation. Your answer would be a four-letter string composed of letters N and O only, e.g. OONO. ( ) It is abundant in proteoglycans. ( ) It involves the attachment of a preassembled block of oligosaccharide onto a protein. ( ) It is attached to a serine or threonine residue in the protein. ( ) It involves heavily sulfated sugars.

ONOO

Indicate whether each of the following descriptions matches an ABC transporter (A), a P-type pump (P), or a V-type pump (V). Your answer would be a five-letter string composed of letters A, P, and V only, e.g. PPVVV. ( ) The pumps in this family are phosphorylated at a key Asp residue in each transport cycle. ( ) This family is the largest among membrane transport proteins. ( ) The pumps in this family are responsible for the acidification of synaptic vesicles. ( ) The sodium-potassium pump is a member of this family. ( ) The multidrug resistance protein is a member of this family.

PAVPA

In the schematic drawing below, a protein is present on one side of a membrane in a high-enough quantity to induce curvature in this region of the membrane. In each of the following scenarios, indicate whether the protein would induce positive (P) or negative (N) curvature in the membrane. There reference of curvature is the side where the proteins is. Your answer would be a three-letter string composed of letters P and N only, e.g. PPP. ( ) The protein inserts a hydrophobic domain into the membrane leaflet that is facing it. ( ) The protein is a phospholipase that cleaves the head group in specific phospholipids. ( ) The protein binds cooperatively to multiple phospholipids with very large head groups.

PNP

You are viewing a sample of pond water under the microscope. The sample contains a variety of microorganisms, some moving faster than others. You spot a Paramecium that is being followed by a Didinium almost as large as itself; the Paramecium initially swims away and tries to escape, but Didinium, which moves in faster bursts, finally stops it and attaches firmly onto the side of the Paramecium and proceeds to eat it. What type of endocytosis will ensue? Write down the name of the process as your answer. Do not use abbreviations.

Phagocytosis

You have grown cultures of the yeast Saccharomyces cerevisiae in a complex medium alone or supplemented with either glucose or ethanol. In the presence of glucose, available energy is abundant and the cells can therefore grow by fermenting glucose. In the presence of ethanol, however, the cells switch to a mostly aerobic respiration to meet their energy demands. They also shut down many of their anabolic pathways and activate catabolic pathways to produce more energy to better survive under these conditions. After the growth phase, you extract total mRNA from the cells, convert them to cDNA, and label them with a fluorescent molecule. You then hybridize the cDNAs to a yeast DNA microarray. Part of the results obtained by cluster analysis after fluorescent measurements is summarized in the following simplified diagram. Here, red and green indicate increase and decrease, respectively, in expression of a gene compared to that in the nonsupplemented medium. Which row (1 or 2) do you think corresponds to the glucose-supplemented medium? RED: UP-regulated transcription GREEN: DOWN-regulated transcription

ROW 1

Which methodology was most likely used to discover a novel ORF (open reading frame) coding for a small, 20-amino acid protein; shown are the number of (RNAseq) reads aligned to the genome. RNA-seq RT-PCR DNA microarray analysis ChIP-seq Ribosome profiling

Ribosome profiling

Indicate true (T) and false (F) statements below regarding N-linked glycosylation of proteins. Your answer would be a four-letter string composed of letters T and F only, e.g. TTTF. ( ) N-linked glycosylation can be carried out co-translationally, possibly at multiple asparagine residues on the same protein molecule. ( ) N-linked glycosylation is a gradual process, with step-by-step addition and trimming events that commence with the addition of N-acetylglucosamine to an asparagine side chain. ( ) Many proteins synthesized in the rough ER are N-glycosylated, and some of them require this modification for their correct folding. ( ) Once a protein is properly folded in the ER, its attached oligosaccharides are quickly removed by an N-glycanase, although it may be glycosylated again later.

TFTF

Indicate true (T) and false (F) statements below regarding the nucleus and nuclear protein transport. Your answer would be a four-letter string composed of letters T and F only, e.g. TTTF. ( ) The inner and outer nuclear membranes are continuous with each other, yet maintain distinct protein compositions. ( ) The outer nuclear membrane is studded with ribosomes engaged in protein synthesis. ( ) The endoplasmic reticulum lumen is continuous with the nuclear interior. ( ) Ribosomal proteins pass through the nuclear pore complexes twice; they are imported into the nucleus after synthesis, and are exported from the nucleus after assembly with ribosomal RNA.

TTFT

indicate whether each of the following descriptions better applies to t-SNAREs (T) or v-SNAREs (V). Your answer would be a three-letter string composed of letters T and V only, e.g. TVV. ( ) They are usually located on the target membrane. ( ) They are composed of a single polypeptide chain. ( ) They are targets of tetanus and botulinum toxins. ( ) They are usually located on the vesicle membrane

TVTV

Indicate whether each of the following descriptions better applies to the cisternal maturation model (C) or the vesicle transport model (V) for the organization of the Golgi apparatus. Your answer would be a four-letter string composed of letters C and V only, e.g. CVCV ( ) Golgi cisternae are static organelles. ( ) Golgi cisternae exchange material exclusively by retrograde vesicular transport. ( ) A cis Golgi cisterna becomes a medial cisterna which becomes a trans cisterna. ( ) Any protein that passes through the Golgi apparatus should be incorporated into transport vesicles several times.

VCCV

You want to determine a genome-wide mutational profile of hundreds of skin cancer autopsies. An appropriate methodology is: a. Illumina sequencing b. Sanger sequencing c. Mass-spectrometry d. Ribosome profiling

a. Illumina sequencing

High salt would be used to extract the following from microsomes: A. SRP B. SRP receptor C. Sec61 D. LDL receptor E. BiP

a. SRP

Cas9 induced double-stranded DNA breaks can be repaired by homologous directed repair. This can be through providing an exogenous DNA molecule such as a plasmid. A. True B. False

a. true

you would like to clone a gene by PCR. The sequence of the two ends of the coding strand for the gene is provided below. Which following pair of primers would direct the amplification of this gene? All sequences are written from 5′ to 3′. ATGAAATCTACGTTTCAC......CCCCCAGTACCCCCCTTA a. ATGAAATCTACGTTTCAC ; CCCCCAGTACCCCCCTTA b. ATGAAATCTACGTTTCAC ; TAAGGGGGGTACTGGGGG c. TACTTTAGATGCAAAGTG; ATTCCCCCCATGACCCCC d. TACTTTAGATGCAAAGTG ; CCCCCAGTACCCCCCTTA e. GTGAAACGTAGATTTCAT; ATTCCCCCCATGACCCCC

b. ATGAAATCTACGTTTCAC ; TAAGGGGGGTACTGGGGG

Indicate which of the following descriptions applies to Sanger sequencing. a. It uses fluorescently labeled nucleotides. b. It can use PCR-generated copies of DNA. C. It is a second-generation sequencing technology and employs a cyclic wash-and-measure paradigm. D. It relies on the fidelity of DNA polymerase for its accuracy.

b. It can use PCR-generated copies of DNA.

Which of the following is correct regarding Green fluorescent protein? It is a small molecule used to detect calcium ions in vivo. a. It is a fluorescent dye. b. It emits green light. c. It can be used in animal cells but not plant cells. d. All of the above.

b. It emits green light.

Glucose is transported into intestinal epithelial cells against its concentration gradient using __________ which uses the ion gradient established by the _____________. a. K+ symporter; K+ channel b. Na+ symporter; Na+/K+ ATPase c. Na+ antiporter; Na+/K+ ATPase d. K+ symporter; Na+/K+ ATPase e. Na+ symporter; Glucose uniporter

b. Na+ symporter; Na+/K+ ATPase

Which of the following methods provides the most sensitive and accurate way of measuring and comparing mRNA levels of a single gene in two different tissues. The genes are expressed at relatively low levels in these tissues, and do not necessarily code for protein. a. RNA-seq b. RT-PCR c. DNA microarray analysis d. ChIP-seq e. Ribosome profiling

b. RT-PCR

Using RNAseq you have identified a change in gene expression in cultured cells following the application of an experimental drug. Gene ontologies provide "function with respect to three aspects: molecular function (molecular-level activities performed by gene products), cellular component (the locations relative to cellular structures in which a gene product performs a function), and biological process (the larger processes, or 'biological programs' accomplished by multiple molecular activities)." Many genes you have identified belong to the ontology "mitochondrial part; mitochondrial subcomponent, mitochondrion component; this defines a: a. molecular function b. cellular component c. biological process

b. cellular component

For a single Sanger sequencing reaction you require template DNA (a plasmid for example), DNA polymerase, dNTPs, ddNTPs as well as both forward and reverse primers. a. true b. false

b. false

Which of the following is correct regarding Cas9 BUT NOT restriction enzyme HindIII? a. It is an endonuclease. b. It creates double-strand breaks in DNA. c. It recognizes its target sequences with the help of guide RNAs. d. It is part of bacterial defense mechanisms against foreign DNA. e. It is greatly useful in manipulating DNA and studying gene expression and function.

c. It recognizes its target sequences with the help of guide RNAs.

Two segments (S1 and S2) in a viral protein are suspected to be responsible for the nuclear localization of the protein in infected human cells. You have engineered a plasmid to encode the green fluorescent protein (GFP) fused to either or both of these peptide segments, and have introduced the plasmid into the cells. After the expression of the fusion protein is induced, you visualize the cells using a fluorescence microscope equipped with filters appropriate for detection of GFP. Your results are presented in the following schematic drawings in which the GFP signal is represented in green. Which of the following is more consistent with these observations? The nucleus is defined as the round feature in all four squares. a. Both S1 and S2 are required for nuclear localization. b. S1 is required and sufficient for nuclear localization. c. S2 is required and sufficient for nuclear localization. d. S1 is required but not sufficient for nuclear localization. e. S2 is required but not sufficient for nuclear localization.

c. S2 is required and sufficient for nuclear localization.

Which of the following is NOT correct regarding both Cas9 and EcoRI? a. They are both endonucleases. b. They both create double-strand breaks in DNA. c. They both recognize their target sequences with the help of guide RNAs. d. They are both part of bacterial defense mechanisms against foreign DNA. e. They are both greatly useful in manipulating DNA and studying gene expression and function.

c. They both recognize their target sequences with the help of guide RNAs.

A piece of DNA has been sequenced by automated dideoxy sequencing, in which each dideoxyribonucleoside triphosphate was labeled with a fluorescent tag of a different color. The data corresponding to a small segment with the sequence 5′-TGCCACA-3′ is shown in the following diagram. Knowing that ddGTP has been labeled with green fluorescence, what color do you think was the fluorescent tag used to label ddTTP in the sequencing experiment? a. blue b. green c.red d.yellow

c. red

You have separated proteins from liver cells using SDS-PAGE. After transferring the proteins to a PVDF membrane you use an antibody to check whether protein A is expressed. This methodology is known as _________ blotting. a. southern b. northern c. western d. eastern e. southwestern

c. western

You performed a co-immunoprecipitation experiment to identify cellular proteins associated with protein X. To identify these associated proteins you now use: a. SDS-PAGE b. Microarray analysis c. Next-generation sequencing d. Mass-spectrometry e. Ribosome profiling

d. Mass-spectrometry

he p53 gene is an important tumor suppressor gene in our genome. It codes for a transcription regulatory protein that can assemble into tetramers. A number of mutations in p53 render the protein inactive. These mutant protein molecules form mixed tetramers with wild-type p53 proteins and, in this case, the tetramer is inactive. The mutations can therefore be categorized as ... a. null. b. gain-of-function. c. recessive lethal. d. dominant-negative. e. suppressor.

d. dominant-negative.

Indicate which of the following manipulations or procedures used in current recombinant DNA technology commonly rely on an enzyme. a. Cleavage of DNA at specific sites b. DNA ligation c. PCR Synthesis of DNA of any desired specific sequence d. DNA sequencing e. All of the above

e. All of the above

You have identified a new gene in the fruit fly Drosphila. You have cloned and sequenced the gene, but it is not related to any known gene products. Which of the following is the most sensible next step in order to get clues about the function? a. Purifying the protein product and determining its structure by x-ray diffraction b. Screening for small molecules that perturb gene function c. Using the BLAST algorithm to scan sequence databases for similar sequences d. Using MS/MS to sequence the gene product without the need for purification e. Mutating the gene and performing reverse genetics

e. Mutating the gene and performing reverse genetics

Consider a protein composed of only 21 amino acids encoded by a short ORF (open reading frame) that is located between two known genes in a mammalian genome. Due to its length, the ORF had not been annotated as a gene. Which of the following methods can demonstrate that it is indeed a gene that is actively translated to protein? a. RNA-seq b. RT-PCR c. DNA microarray analysis d. ChIP-seq e. Ribosome profiling

e. Ribosome profiling

Fluorescent proteins such as Green fluorescent proteins (GFP) can be fused to a protein of interest. This allows you to determine: a. the cellular localization of the protein. b. the temporal expression pattern of the protein, for example during embryonic development. c. protein interaction partners through immunoprecipitation. d. protein mobility using fluorescence recovery after photobleaching (FRAP). e. All of the above.

e. all of the above

The light used to excite a fluorescent molecule (such as fluorescent proteins or small organic molecules) carries ________ energy and has a __________ wavelength compared to the light that is then emitted from the molecule. greater; longer greater; shorter the same amount of; shorter less; longer less; shorter

greater; shorter

a method known as bioID the bacterial E. coli protein biotin ligase can be used to identify: protein-protein interactions DNA-protein interactions RNA-protein interactions DNA-RNA interactions

protein-protein interactions