BIO 493 final exam questions

According to the journal by Borooah et al., in 2013 Using human induced pluripotent stem cells to treat retinal disease, what are the proposed clinical applications for the use of hiPSC derived retinal cells, and what are some limitations?

-The proposed clinical applications is using a disease modeling and a drug screening. For modeling, they are looking at the potential to differentiate phenotype-relevant cell types that would enable the investigation of disease mechanisms in the use of the ceullar physiology. The HiPSC derived retinal cells are able to function in vivo environments. For the drug screening, it could be used to make new therapies. They would need to look at proliferation, morphology, differentiation and viability of the cells. -Some limitations would be looking at genetic and epigentic differences from the cultures, to see the numbers of variations and mutations that can arise from reprogramming, there needs to be an efficient and scalable derivation of enriched, phenotype-relevant cell types, and a way to develop protocols that mirror in vivo cellular complexity.

list two types of "Restricted Mobility" that membrane proteins provide and describe their purpose.

-if they are found only on the edges of the plasma membrane, such as, peripheral proteins. They allow for exchange of molecules and ions to leave the cell -There can be integral proteins that are found attached across the cell membrane. They allow for diffusion of active transport to occur. they are open to the extracellular matrix and the cytosol

The fluid mosaic model states: Choose ALL that apply

-lipids are constantly in motion -proteins are constantly in motion -membrane components can rotate -membrane components can move laterally

Consider the following cells. If the STRIPPED cell secretes Ligand A and the DOTTED cell secretes Ligand B, which of the following statements about the modes of signaling are TRUE? Choose ALL that apply

-the stripped cell can do autocrine signaling -the stripped cell can respond to paracrine signaling -the stripped cell can do autocrine signaling -the spotted cell can respond to paracrine signaling

Fully folded proteins typically have polar side chains on their surfaces, where electrostatic attractions and hydrogen bonds can form between the polar group on the amino acid and the polar molecules in the solvent. In contrast, some proteins have a polar side chain in their hydrophobic interior. Which of the following would NOT occur to help accommodate an internal, polar side chain?

A hydrogen bond forms between a polar side chain and an aromatic side chain.

An asymmetrical division is best described as:

A parent cell dividing into two cells; one identical to the parent, one more differentiated

Which of the following would be an ideal location for the stem cell population? Choose ALL that apply.

Apical or luminal side of tissue Within an intestinal crypt (yes to bottom three) Near the basal lamina Within the bone marrow

Which of the following statements about apoptosis is TRUE?

Apoptosis can be promoted by the release of cytochrome c into the cytosol from mitochondria. FEEDBACK: Release of cytochrome c into the cytosol can promote apoptosis. Bcl2 tends to inhibit rather than promote apoptosis. The prodomain of procaspases does not contain the catalytic activity needed for procaspase activation and is usually discarded from the active caspase. When activated, Bax and Bak promote apoptosis by stimulating the release of cytochrome c from mitochondria into the cytosol, not by binding to procaspases in the apoptosome.

Autophagy is similar to Apoptosis in that:

Both can protect the organism

According to the journal article by Jan and Chaudhry in 2019 Understanding Apoptosis and Apoptotic Pathways Targeted Cancer Theraputics , what is the connection between death ligands and future treatments of cancer?

By triggering death liagands, this allows for the DISC method to be activated, which occurs during the extrinsic pathway. In relation to cancer cells, this complex/method allows for there to be an execution phase of apoptosis. It states in the article, "Apoptosis is the vital and crucial mechanism which maintains the balance between survival and death in cells to prevent cancer and other related diseases." Perhaps a way could be investigated for the cancer cells to not have the ability to develop an increase in their immunity to certain mechanisms of apoptosis. And then apoptosis can occur to create a programmed cell death by knowing that these cancer cells should not be there.

Which region on this microarray heatmap demonstrates the expression clustering of Stem Cell Genes?

C

(Q034) Figure 16-34 shows that intracellular signaling pathways can be highly interconnected. from the information in Figure 16-34, which of the following statements is false?

CaM-kinase is only activated when the GPCR is active and not when the RTK is active

Compare and contrast the internal vs external activation processes of apoptosis.

Contrast: -Internal: uses Bax and Bak that create pores in the mitocchondria. Bax and Bak are positive regulators and begins with the formation of a mature Apoptosome and pro-caspase 9 as the initiator. Once the mature apoptosome is formed, it cannot be reversibe. It has to do apoptosis. -External is it initaied by a Death Receptor and is initiated by pro-caspase 8. It is happening outside of the cell and relates to how the Fas Death Receptor is activated by an external signal. It will also use DISC to create the cascade. Compare: They both are able to be coupled together by an internal and external stimuli. They both have to be initated by a certain pro-caspase. And they both will allow for apoptosis to occur.

Which protein is NOT involved in autophagy?

Cytochrome C

match the three types of misfolded protein responses with their appropriate descriptions:

ERAD: degrades most misfolded sections UPR: corrects misfolded proteins RESET: degrades misfolded GPI-anchor

(Q006) Intermediate filaments are made from elongated fibrous proteins that are assembled into a ropelike structure. The figure below shows the structure of an intermediate filament subunit.You are interested in how intermediate filaments are formed, and you create an intermediate filament subunit whose α-helical region is twice as long as that of a normal intermediate filament by duplicating the normal α-helical region while keeping a globular head at the N-terminus and a globular tail at the C-terminus; you call this subunit IFαd. If you were to assemble intermediate filaments using IF2αd as the subunit, which of the following predictions below describes the most likely outcome?

Filaments assembled using IFαd will form dimers that are twice as long as dimers assembled from normal intermediate filaments.

the fluid mosaic model was established following the Human-Mouse Hybrid Experiment. Which of the following statements are true about the experiment? Choose all that apply

Human-specific and Mouse-specific membrane proteins were fluorescently labeled

which of the following amino acids wold you expect to find near the center of a folded globular protein? Ser Leu Lys Gln His Phe Val Ile Met

Leu, Phe, Val, Ile, Met

Stem cells display a distribution of hierarchy depending on their potency. Rank the following potencies in order from MOST potent (A) to LEAST potent (D).

Multipotent - C Unipotent - D Totipotent - A Pluripotent - B

should a genetically engineered protein, in which the original order of all amino acids is reversed, have the same structure as the original wild-type protein?

No

(Q008) You are studying nuclear lamins and use recombinant DNA technology to alter the coding sequence of a nuclear lamin gene. The alteration you make creates a situation such that the gene now codes for a nuclear lamin protein that can no longer be phosphorylated when the nuclear envelope is broken down during mitosis. What do you predict would happen if the cell only had the altered nuclear lamin gene (and not the unaltered version)?

Nuclear lamins will no longer disassemble properly during mitosis.

Which of the following statements about organoids is FALSE?

Organoids can only be made for organs that are made up of a single type of differentiated cell. FEEDBACK: The cells in an organoid can differentiate into multiple organ-specific cell types.

A 2012 study by Rifler et al. demonstrated that patients who drank 250 mL of Red wine for 14 days following a heart attack were able to improve their lipid health characteristics. Which statement is NOT accurate regarding the report?

Patients in the water control group experienced lipid parameters -red wine caused a decrease in MC540 staining indicating an increase in lipid organization -patients in the red wine experimental group saw a decrease in cholesterol levels -patients in both groups received equivalent amounts of exercise during the study

After graduating from Wingate you get a job at Organovo, Inc. You're assigned to a team working on tissue engineering for building a new heart for individuals on the heart transplant list. As the team is trying to generate cardiomyocytes for the heart, they continue to get fibroblasts in their cultures as well. Using knowledge from this course, describe a few ideas to the team that they should keep in mind while trying to get a pure cardiomyocyte culture.

Perhaps a reason why they are getting cardiomyocytes and fibroblasts is because of stem cells, like the diagram above shows from pluripotent stem cells. Pluripotent stem cells are the second most powerful stem cells and can become many differentiated cells. As both cardiomyocytes and fibroblasts can come from a same lineage of cells, the team needs to consider this. There could be a way to block the stem cell in differentiating into a fibtoblast and to only create a pure cardiomyocyte.

Which pro-caspase is considered the initiator caspase for the Extrinsic Apoptotic Pathway?

Pro-caspase 8

which molecule(s) require "phosphorylation" for activation? choose all that apply

RTK's and MEK

which of the following statements about a protein in the lumen of the ER is false?

Some of the proteins in the lumen of the ER can end up in the plasma membrane.

(Q031) You are studying a set of mouse genes whose expression increases when cells are exposed to the hormone cortisol, and you believe that the same cortisol-responsive transcriptional activator regulates all of these genes. Which of the following statements below should be true if your hypothesis is correct?

The cortisol-responsive genes share a DNA sequence in their regulatory regions that binds the cortisol-responsive transcriptional activator.

(Q032) Cells have oligosaccharides displayed on their cell surface that are important for cell-cell recognition. Your friend discovered a transmembrane glycoprotein, GP1, on a pathogenic yeast cell that is recognized by human immune cells. He decides to purify large amounts of GP1 by expressing it in bacteria. To his purified protein he then adds a branched 14-sugar oligosaccharide to the asparagine of the only Asn-X-Ser sequence found on GP1 (Figure Q15-48). Unfortunately, immune cells do not seem to recognize this synthesized glycoprotein. Which of the following statements is a likely explanation for this problem?

The oligosaccharide needs to be further modified before it is mature.

To study how proteins fold, scientists must be able to purify the protein of interest, use solvents to denature the folded protein, and observe the process of refolding at successive time points. What is the effect of the solvents used in the denaturation process? (a) The solvents break all covalent interactions. (b) The solvents break all noncovalent interactions. (c) The solvents break some of the noncovalent interactions, resulting in a misfolded protein. (d) The solvents create a new protein conformation.

The solvents break all noncovalent interactions.

Which of the following statement is TRUE regarding caspases? Choose ALL that apply.

They cause cytochrome C release They amplify the signal by activing multiple downstream executioners (yes) They are active once they are phosphorylated They are active once their prodomains are cleaved (yes)

(Q033) The ethylene response in plants involves a dimeric transmembrane receptor. When the receptor is not bound to ethylene, the receptor binds to and activates a protein kinase, which activates an intracellular signaling pathway that leads to the degradation of a transcriptional regulator important for transcribing the ethylene-responsive genes (see Figure Q16-60). You discover a phosphatase that is important for ethylene signaling, and you name it PtpE. Plants lacking PtpE never turn on ethylene-responsive genes, even in the presence of ethylene. You find that PtpE dephosphorylates serine 121 on the transcriptional regulator. Furthermore, plants lacking PtpE degrade the transcriptional regulator in the presence of ethylene.Which of the following statements is inconsistent with your data?

When the transcriptional regulator is phosphorylated, it activates transcription of the ethylene-responsive genes.

motor proteins use the energy in ATP to transport organelles, rearrange elements of the cytoskeleton during cell migration, and move chromosomes during cell division. which of the following mechanisms is sufficient to ensure the unidirectional movement of a motor protein along its substrate.

a conformational change is coupled to ATP hydrolysis

(Q015) You are interested in how cyclic-AMP-dependent protein kinase A (PKA)functions to affect learning and memory, and you decide to study its function inthe brain. It is known that, in the cells you are studying, PKA works via a signaltransduction pathway like the one depicted in Figure Q16-35. Furthermore, it isalso known that activated PKA phosphorylates the transcriptional regulator calledNerd that then activates transcription of the gene Brainy. Which situationdescribed below will lead to an increase in Brainy transcription?

a mutation in the gene that encodes cAMP phosphodiesterase that makesthe enzyme inactive

(Q022) the growth factor RGF stimulates proliferation of cultured rat cells. the receptor that binds RGF is a receptor tyrosine kinase called RGFR. which of the following types of alteration would be most likely to prevent receptor dimerization

a mutation that prevents RGFR from binding to RGF

(Q029) which of the following statements is false

actin filaments are usually excluded from the cell cortex

Molecules to be packaged into vesicles for transport are selected by

adaptins

(Q025) You are interested in further understanding the signal transduction pathway that controls theproduction of Pig1, a protein important for regulating cell size. Activation of the TRKreceptor leads to activation of the GTP-binding protein, Ras, which then activates aprotein kinase that phosphorylates the SZE transcription factor. SZE only interacts withthe nuclear transport receptor when it is phosphorylated. SZE is a gene activator for thePig1 gene. This pathway is diagrammed in Figure Q16-50Normal cells grown under standard conditions (without ligand) are 14 μm in diameterwhile normal cells exposed to TRK ligand are 10.5 μm in diameter. Given this situation,which of the following conditions do you predict will more likely lead to smaller cells?

addition of TRK ligand and a drug that inhibits the activity of thephosphatase that acts on SZE

(Q036) figure 16-36 shows how normal signaling works with a Ras protein acting downstream of an RTK. You examine a cell line with a constitutively active Ras protein that is always signaling. which of the following conditions will turn off signaling in this cell line

addition of a drug that blocks protein Y from interacting with its target

(Q013) the hydrolysis of GTP to GDP carried out by tubulin molecules

allows the behavior of microtubules called dynamic instability

match each mode of signaling with its proper description:

autocrine- a cell signaling to itself paracrine - signaling between two neighboring cells synaptic - signaling between two neighboring cells, one is neuron endocrine - signaling between two distant cells

beta sheets can participate in the formation of amyloid fibers, which are insoluble protein aggregates. what drives the formation of amyloid fibers?

beta-sheet stabilization of abnormally folded proteins

Which of the following may help the efficiency of signal transduction by localizing targets to a particular region of the cell? Choose ALL that apply

binding domains scaffolding proteins lipid rafts (I had selected the bottom two, but got partial credit).

(Q015) you discover a protein, Mta and find that it binds to the plus ends of microtubules in cells. the hypothesis that best explains this localization is that Mta

binds to GTP-bound tubulin on microtubules

(Q020) You are interested in the regulation of gene Q. Proteins G, H, and J are proteins that are important for regulating gene Q, and bind to its promoter region in a sequence-specific fashion. Proteins G and H both bind to site "A" but cannot bind to site "A" at the same time. Protein J binds to site "B" on the promoter. The promoter region is diagrammed in Figure Q8-29. which proteins are likely to act as gene activators?

both H and J

(Q012) You are interested in examining the Psf gene. It is known that Psf is normally produced when cells are exposed to high levels of both calcium (Ca2+) and magnesium (Mg2+). MetA, MetB, and MetC are important for binding to the promoter of the Psf gene and are involved in regulating its transcription. MetA binds to the "A" site in the promoter region, MetB to the "B" site, and MetC to the "C" site. You create binding-site mutations in the A, B, and C sites and observe what happens to transcription of the Psf gene. which of the following proteins are likely to act as gene activators

both MetA and MetC

Programmed cell death occurs...

by means of an intracellular suicide program. FEEDBACK: Programmed cell death results from an intracellular suicide program that eliminates unneeded, unwanted, or damaged cells. It occurs frequently and happens even in healthy cells throughout the lifetime of an individual.

Which of the following can be used to reprogram differentiated cells back into an embryonic-like state? Choose ALL that apply.

c-Myc LIN-28 HSPG Oct 3/4 KLF4 SOX2 NFkB Nanog AP-1

Induced pluripotent stem (iPS) cells

can be created by the expression of a set of key genes in most somatic cell types, including cells derived from adult tissues. FEEDBACK: iPS cells do not require donor egg cells and are made from adult (and not embryonic) cells. Embryonic stem cells can differentiate into all tissue and cell types. Human clones have not been created using iPS cells.

An adult hemopoietic stem cell found in the bone marrow

can undergo self-renewing divisions for the lifetime of a healthy animal. FEEDBACK: Stem cells undergo self-renewing divisions. Adult stem cells are specialized, and thus an adult hemopoietic stem cell does not produce epidermal cells and also stably expresses the transcriptional regulators that ensure that its progeny will become blood cells. An adult hemopoietic stem cell has the ability to produce all the many types of cell in the blood.

Apoptosis differs from necrosis in that necrosis...

causes cells to swell and burst, whereas apoptotic cells shrink and condense.

What are the Pillars of Tissue Engineering? Choose ALL that apply.

cell cycle cytoskeleton signals (yes to bottom 3) cells scaffolds

glycolipids and glycoproteins are used for all of the following except

cellular gene expression

Which of the following proteins are considered zymogens? Choose ALL that apply.

collagen (yes) caspases (yes) MMPs fibronectin

lipid rafts are specialized regions of the membrane that

contain elevated levels of cholesterol

What is considered the greatest challenge for successfully implementing tissue engineering?

creating functional blood vessels

(Q026) consider the mechanism by which actin and tubulin polymerize. which of the items below does not describe something similar about the polymerization mechanisms of actin and microtubules?

depolymerization initiates at the plus end of filaments

(Q031) which of the following statements is false?

dissolved gases such as nitric oxide (NO) can act as signal molecules, but because they cannot interact with proteins thy must act by affecting membrane lipids

(Q042) miRNAs, tRNAs and rRNAS all

do not code for proteins

Which is the correct order of the beginning portion of the RTK signal cascade?

either : -receptor dimerization > Grb2 >SOS > RasGDP > Ras GTP -receptor dimerization > Grb2 > PLC > IP3 > DAG > PKC -receptor dimerization > SOS > RAF > MEK > ERK > RasGTP > RasGDP

researcher are working to discover the function of a newly discovered protein, called Protein X. They decide to fuse the protein to GFP so they can visualize its location and behaviors in the cell. The results of a FRAP assay are shown. How can these results be interpreted?

either: -proteinX might be e-cadherin -proteinX might be an RTK -protein X might also be a GPCR

access the membrane shown here and indicate which lipid could require the activity of flippase, floppase, or scramblase to place the phosolipid in the correct orientation for a healthy cell. (AKA: which phospholipid is on he WRONG side?)

either: -phosphatidylinositol (PI) -phosphatidlyserine (PS) -phosphatidylethanolamine (PE) -sphinogomyelin (S)

immune cells are able to migrate through endothelial cells of the blood vessels thanks to

glycoproteins

Which cell adhesion structure is known to hold on to ECM with integrin proteins?

hemidesmosomes

Lysozyme is an enzyme that specifically recognizes bacterial polysaccharides, which renders it an effective antibacterial agent. Into what classification of enzymes does lysozyme fall?

hydrolase

(Q002) which of the following statements about membrane-enclosed organelles is True?

in a typical cell, the area of the endoplasmic reticulum membrane far exceeds the area of the plasma membrane

which of the following statements about membrane-enclosed organelles is TRUE?

in a typical cell, the area of the endoplasmic reticulum membrane far exceeds the area of the plasma membrane feedback: the area of the endoplasmic reticulum membrane is 20-30 times that of the plasma membrane in a typical cell. Like the nucleus, chloroplasts and mitochondria are also surrounded by a double membrane. The cytosol is about half the volume of a typical eukaryotic cell, with membrane-enclosed organelles making up the other half of the volume. Chloroplasts and mitochondria also carry their own genome, whereas the nucleus carries the genome of the organism.

which condition would make the membrane MORE FLUID?

increased fatty acid tail length

(Q030) all members of the nuclear receptor family

interact with signal molecules that diffuse through the plasma membrane

(Q009) what is the role of the nuclear localization sequences in a nuclear protein?

it is bound by cytoplasmic proteins that direct the nuclear protein to the nuclear pore

Cell type A secrets a growth factor signal ligand. Nearby in the environment are Cell types X, Y, and Z. Will the growth factor affect cell types A, X, Y, and Z? or only some? explain why

it will affect the nearby cell types such as X, Y, and Z because it would do paracrine signaling. If the cell types have the proper receptor to attract and bind to the growth factor signal ligand, then they will bind. If the cell types do not have the proper receptors than it will not be able to bind.

(Q045) which of the following statements about miRNAs is FALSE?

miRNAs are produced from rRNAS

(Q011) which of the following statements about the function of the centrosome is false?

microtubules emanating from the centrosome have alternating polarity such that some have their plus ends attached to the centrosome while others have their minus end attached to the centrosome

indicate whether the following property will make a lipid bilayer more fluid or more rigid: genetic mutation prevents body from making saturated fats

more fluid

indicate whether the following property will make a lipid bilayer more fluid or more rigid: child rescued from a frozen pond with cells at hypothermic temperature

more rigid

indicate whether the following property will make a lipid bilayer more fluid or more rigid: increased activity of enzyme that degrades fatty acid tails

more rigid

indicate whether the following property will make a lipid bilayer more fluid or more rigid: patient is found to have elevated levels of cholesterol at 37 degrees C

more rigid

(Q029) when the cytosolic tail of the ______ receptor is cleaved, it migrates to the nucleus and affects gene regulation

notch

(Q010) which of the following statements about nuclear transports is true?

nuclear pores contain proteins with disorder segments that fill the channel and allow small water-soluble molecules to pass through in a non-selective fashion

which of the following is a benefit of RESET?

occurs within minutes

What mode of signaling occurs when a liver cell secretes a ligand and neighboring liver cell receives the signal on its receptors?

paracrine

which mode of signaling occurs when a liver cell secretes a ligand and neighboring liver cell receives the signal on its receptors

paracrine

which type of signaling does NOT utilize a soluble/free floating signaling ligand?

paracrine autocrine direct contact -gap junctions (NO) synpatic (NO) direct contact -cell:cell recognition endocrine

Once a research group or biotech company believes they have established the right type of tissue, what is their next step?

perform functional assays to confirm the cell expresses the proper markers/secretes the right enzymes

caffeine keeps you alert because the GPCR signaling pathway keeps firing away! caffeine is a :

phosphodiesterase inhibitor

When a terminally differentiated cell in an adult body dies, it can typically be replaced in the body by a stock of

proliferating precursor cells. FEEDBACK: Proliferating precursor cells already within the tissue are typically used to replace terminally differentiated cells. Induced pluripotent cells are produced in the laboratory and are not typically used to replace adult terminally differentiated cells within the body.

which of the following statements about the endoplasmic reticulum (ER) is false?

proteins to be delivered to the ER lumen are synthesized on the smooth ER Feedback: proteins to be delivered to the ER lumen are synthesized on rough ER; these areas appear "rough" because ribosomes are attached to the cytosolic surface of these ER regions

integration of multiple, perhaps even contradicting, extracellular signaling ligands occur at which level(s) of protein signaling? Choose ALL that apply

response - YES (idk about the others) transduction reception

what compound in red wine has been shown to have a cardioprotective effect?

resveratrol

(Q006) which of the following statements about differentiated cells is True?

some of the proteins found in differentiated cells are found in all cells of a multicellular organism

lipid rafts establish rigid regions of the membranes that cluster proteins involved in a particular signaling pathway together so they can function efficiently. Which of the following components help create this rigidity? Choose all that apply

spingomyelin and cholesterol

figure 15-22 shows the organization of a protein that normally resides in the plasma membrane. The boxes labeled 1 and 2 represent membrane-spanning sequences and the arrow represents a site of action of signal peptidase. given this digram, which of following statements must be TRUE?

the C-terminus of this protein is cytoplasmic

(Q004) all intermediate filaments are of similar diameter because

the central rod domains are similar in size and amino acid sequence

(Q001) A neuron and a white blood cell have very different functions. For example, a neuron can receive and respond to electrical signals while a white blood cell defends the body against infection. This is because

the neuron expresses some mRNAs that the white blood cell does not.

Which of the following is considered a diffusion barrier?

tight junction

which cell adhesion structure would be located at the apical side (top side) of the cell to perform its job?

tight junctions

The artificial introduction of three key __________ into an adult cell can convert the adult cell into a cell with the properties of ES cells.

transcription factors

proteins that are fully translated in the cytosol do not end up in

transport vesicles feedback: proteins destined for transport vesicles will be translated on ribosomes associated with the endoplasmic reticulum

estrogen and other lipid hormone signal by

using a receptor located in the cytoplasm

(Q032) which of the following statements about how fruit flies can develop an eye in the middle of a leg is true?

when the Ey gene is introduced into cells that would normally give rise to a leg, the transcription regulators used to control its expression in the leg are different from those that are normally used to control Ey expression in the eye