MCB 305 EX 3 quiz, clicker, and preceptor review

Which molecular genetic technique would you use to RNAi?

"knock-down" a gene product

Which of the following statements represents a way that gene expression could produce two different cell types?

-alternative splicing of introns could result in the production of different, but similar, proteins from the same gene in 2 cell types -changes in DNA methylation and/or histone modification could result in the "silencing" of some genes in one cell type, but not another -an mRNA may be expressed from the same gene in 2 different cell types, but in one cell type, the mRNA has a very short half-life, whereas in the other cell type, the mRNA may persist for much longer -in one cell type, a regulatory protein may bind to the 5'UTR of a mature mRNA, reducing its ability to be translated, whereas in another cell type, there is no regulatory protein, so the mRNA is translated more frequently, resulting in higher protein levels -in one cell type, a set of 3 activator proteins is expressed, resulting in high level of transcription from a particular gene, whereas in another cell type, only 2 of the activator proteins are expressed, resulting in lower levels of transcription of that gene -in a particular cell type, an enzyme is present that "tags" a specific protein for degradation, whereas in another cell type, the enzyme is missing and the protein has a longer half-life

Why do researchers convert mRNA to cDNA?

-because cDNA is more stable -the process allows a fluorescent label to be incorporated

DNA methylation can turn genes off by

-blocking access of transcription factors -recruiting factors that deacetylate histones to close chromatin

In situ hybridization is an important technique in developmental biology that is used to determine where a particular gene is localized. This method:

-depends upon complementarity between a DNA or RNA probe and its mRNA target in the cell -uses either an enzymatic or fluorescent tag to label the probe

Stem cells can be derived from:

-early embryos -bone marrow -epidermis of skin

You are trying to find out about genes that control leg formation in Drosophila. You have just done a genetic screen and isolated a mutant that has no legs. What is the next step you need to take to ultimately find out what protein this gene encodes?

-genetically map the mutation to a chromosomal location -use whole genome sequencing to identify the mutation

Which of the following is/are trans-acting factors in gene regulation? (more than one answer can be correct)

-micro-RNAs -repressor proteins -co-activators

If a mutation causes the substitution of a single base, then what are the potential changes in the resulting amino acid sequence?

-no change to the sequence of amino acids -a single amino acid change -a truncated sequence

Which of the following structures or elements involved in gene regulation is a cis-regulatory factor?

-promoter -enhancer

Many experimental results described in Chapter 1 rely on being able to mark cells in the embryo and follow what they become. This technique is called fate mapping. Which of the following do you think would be a requirement for whatever substance you were using to make a fate map?

-the substance used to mark the cells in the embryo should be a "vital" marker; i.e. it doesn't kill the cells -the cell marker would not pass from cell to cell, but should stay only in the "marked" cell and its descendants -the substance has a long enough half-life to still be detectable after multiple rounds of division

Which of the following statements are true about the 5' and 3' UTRs found on an mRNA

-they can affect the stability of the mRNA -they can affect the rate of translation

GFP (green fluorescent protein) is a commonly used reporter gene in developmental biology (remember promoter-GFP constructs from MCB 304?)

-unlike in situ hybridization, they can be used to follow protein expression in live embryos -they can be made in different colors, so different proteins can be followed at the same time -the protein domains are very small and consequently don't usually interfere with normal protein function

In an embryo with wild-type parents, how many copies of a parentally imprinted gene are functional?

1

The DNA sequence that encodes the 3'UTR (untranslated region) would be found in which region of the above sequence of DNA?

3'UTR

What evidence supports the model that gill arches in fish are homologous to the middle ear bones in mammals?

A fate map of the pharyngeal arches in fish embryos and mammalian embryos

Correcting an error in a person's genome to cure a disease would use ______

CRISPR/Cas9

What is the best technique used to silence gene expression and observe the resulting phenotype?

CRISPR/Cas9

Which of the following techniques can be used to identify proteins that bind to a specific sequence of DNA?

ChIP-seq

Box 8D in your textbook describes that fibroblast cells can be transformed to induced pluripotent (iPS) stem cells by the introduction of 4 genes- Oct3/4, Sox3, Klf4, and c-Myc. If the Oct-4 and SOX2 genes cease to be expressed, which event would most likely take place?

ES cells would begin to differentiate

On your last trip to Rocky Point, you discover a new species of mud snail. You travel to Rocky Point to study the new species. You perform embryology experiments to study how cells differentiate in the new species. You wish to show that the early embryo undergoes mosaic development and that cleavage of the zygote produces two daughter cells that cannot regulate their cell fate. Which of the following experiments, and results, would demonstrate lack of equivalence of the two cells in the zygote?

Experiment: isolate the two cells and grow them to the larval stage Result: the two cells will each develop into only partial larvae

In work from the Melton lab, researchers tested the function of human stem cell derived beta cells by transplanting cells into immunocompromised mice. Recall that increased blood glucose normally stimulates secretion of insulin into the bloodstream. True or false: If the stem-cell-derived beta cells were functioning properly, researchers would test the ability of the transplanted cells to produce mouse insulin.

False

True or false: Human embryos form a syncytium for the first 20 days of development

False

True or false: In a forward genetic screen, we mutate specific genes related to the function we are trying to study

False

True or false: In situ hybridization is a move it experiment

False

True or false: Insulin is synthesized within the alpha cells of the islets of Langerhans in the pancreas

False

True or false: an active gene requires access to the chromatin through histone methylation

False

True or false: Trans acting factor bind to the 3' UTR to activate a gene. The 3'UTR is in the mRNA, so transcription cannot be activated by binding to it

False; although it is possible that a transcriptional enhancer could be found in the DNA sequence that encodes the 3'UTR

True or false: A morphogen has the highest concentration at the sink?

False; highest concentration at the source

True or false: Placing a cell in a neutral environment and analyzing its fate is a way to determine cell determination

False; it is tested in a non-neutral environment

True or false: If a test proves something sufficient, you can assume it is also necessary

False; many examples show gene activity can be sufficient but not necessary

True or false: The nucleotides that encode the 5' UTR are found upstream of a given gene's promoter in the gene sequence

False; the 5'UTR is encoded in an exon, downstream of the transcription start site

True or false: Only coding DNA is present in exons

False; they also encode 5' and 3' UTR of the mRNA sequence

True or false: Pluripotent cells can express all three primary germ layers and give rise to the placenta and the embryo

False; they are not totipotent

True or false: Move it experiments are experiments that generate correlative evidence

False; they prove whether an action is sufficient

True or false: The pulse-chase experiment with the insulin reporter provided definitive evidence for pancreatic stem cells

False; they provided no evidence for pancreatic stem cells

What type of evidence does the following experiment represent? Localization of Vg1 mRNA at the vegetal pole of the Xenopus egg

Find it

What type of evidence does the following experiment represent? Observing that the embryo always starts to gastrulate 180 degrees from the point of sperm entry

Find it

What type of evidence does the following experiment represent? The number of storks seen in West Germany from 1965-1980 is the same as the number of babies born

Find it

You are interested in the role of a particular protein in determining the germ-line cells of the embryo. You isolate the germ-line cells in embryos at different stages and use a Western blot to determine protein levels for the protein you are interested in. Is this a find it, move it, or lose it experiment?

Find it

Which is a fluorophore protein?

GFP

Which method could be used in an experiment designed to provide evidence for sufficiency?

Gal4/UAS

As drawn in the figure, which side of the cytosine pyrimidine ring forms hydrogen bonds in base pairing, and which side can be methylated?

H-bonds on the left, methylation on the right

What does it mean (molecularly) when we say that a cell is "determined" to take on a particular fate?

It can no longer respond to certain signals

What type of evidence does the following experiment represent? Finding that a sea urchin embryo depleted of sulfated proteoglycans (CSPGs) fails to undergo gastrulation

Lose it

What type of evidence does the following experiment represent? Loss of bithorax genes gives an extra set of wings on the fly

Lose it

What type of evidence does the following experiment represent? Dolly was cloned

Move it

What type of evidence does the following experiment represent? Expressing the gene pax 6 which is know to function in eye development in the antenna, resulting in extra eyes

Move it

Which of the following conditions is the best candidate for treatment by stem cell therapy?

Parkinson's disease

If the "battle of the sexes" theory is true, what kind of animals will not have imprinted genes?

Platypus (egg-laying mammal)

match the regulatory control mechanism to the mechanism: Mutations in an intron create a novel transcript with a new function

RNA processing control

match the regulatory control mechanism to the mechanism: During cleavage of the sea urchin, mRNA for gene x is more abundant in the nucleus than the cytoplasm

RNA transport control

True or false: A non-neutral environment test will tell you if the cell is determined

True

True or false: Addition of a polyA tail to a maternal mRNA can prevent degradation

True

True or false: Adult stem cells retain inherent pluripotency when harvested from specific organs

True

True or false: Beta cells in adults are derived only from existing beta cells

True

True or false: Modification of histones post translationally (eg. methylation) can regulate gene activity

True

True or false: Muscle cells are created from the mesoderm

True

True or false: Sperm and egg cells are not derived from the 3 tissue layers found in embryos

True

True or false: The "gold standard" scientists use to see if cells they have created are induced pluripotent stem cells is the formation of a teratoma in an immunosuprresed rat

True

True or false: The ectoderm gives rise to both epidermal and neural tissue

True

True or false: The mesoderm gives rise to the heart tissue

True

True or false: The technique in situ hybridization utilizes antisense mRNA

True

True or false: The technique of RNAi uses antisense RNA

True

True or false: Therapeutic cloning involves intentional destruction of a human blastocyst (the clone)

True

True or false: Transcription factors are considered trans-acting regulators of transcription

True

True or false: You can have something that is sufficient but not necessary

True

True or false: iPSC cells can be combined with gene therapy with patient specific cells to treat disease

True

True or false: iSCPs initially were made using viruses to express Yamanaka factors

True

True or false: the ectoderm gives rise to the brain

True

A stem cell can be defined as:

a cell that, when it divides, produces one cell that remains undifferentiated (i.e. a new stem cell) and another cell that differentiates

The advantage of using the Cre/loxP system for targeted mutagenesis is:

a gene can be deleted in a particular tissue or at a desired time in development

Which of the following cells has the greatest plasticity (ability to be converted to different cell types)?

a totipotent cell from the very early embryo

Genes imprinted in the maternal germ line normally ______ growth.

activate

Acetylation of histones in the vicinity of a gene causes the gene to be

activated because the histones bind less tightly to the DNA than the unacetylated histones

Stem cells can be obtained from a variety of structures. Which of the following options is NOT correct about sources for stem cells: -early embryos -bone marrow -epidermis of skin -any adult organ

any adult organ

In a developing organism, different cells exhibit different characteristics largely because they are making different sets of proteins. Sometimes when two daughter cells that originate from a single cell end up with different fates. Which of the following is/are NOT a general mechanism(s) that result in these two daughter cells being different?

asymmetric localization of DNA

In therapeutic cloning, you get the stem cells from the

blastocyst

All of the following result form the ectodermal germ layer EXCEPT: a) nervous system b) pigment cells c) bone d) skin

bone

If an organism exhibits mosaic (autonomous) development, and one cell of a four-celled embryo is removed without damaging it, what would you expect to develop from the cell you removed and the cells left behind?

cell removed: 1/4 of a normal embryo cells left behind: 3/4 of a normal embryo

Application of cytochalasin (inhibitor of actin polymerization) in a single-celled embryo will inhibit...

cytokinesis

An embryo is allowed to develop for around five days before it is inserted into a uterus. Why?

doctors are trying to simulate natural conditions of human development

In general, gain of function mutations are ________

dominant

The epidermis and the skin and the nervous system come from which germ layer?

ectoderm

The skin arises from which germ layer?

ectoderm

Which of these types of stem cells can potentially develop into the greatest number of different types of body cells?

embryonic stem cells

ES cells are

embryonic stem cells derived from the inner cell mass of a mammalian embryo

From what germ layer does the pancreas develop?

endoderm

From what germ layer does the pancreas form during embryogenesis?

endoderm

What germ layer does the thyroid come from?

endoderm

The general arrangement of the germ layers in an embryo after gastrulation, is, from the inside out:

endoderm, mesoderm, ectoderm

Which of the following describes the developmental pathway of a beta-cell?

endodermal precursor--> pancreatic precursor--> endocrine progenitor--> B-cell progenitor--> B-cell

If stem cells were replacing beta cells over time, what would the beta cell islets look like 12 months AFTER the chase

eventually would expect the islets to be unlabeled

Why do Tbx5 mutations affect both limbs and heart, but no other tissues?

every cell has the mutation, but expression of the Tbx5 protein is only necessary in the limbs and heart

To conduct a find it experiment, you can do one of the following:

fate mapping

The best evidence for pluripotency is:

formation of a teratoma with all 3 germ layers

Which of the following are examples of nonmendelian inheritance

genomic imprinting

Weisman predicted that embryos are a mosaic of localized cell fate determinants. If this is true, what do you predict the outcome if one of the two cells at the 2-cell stage is ablated?

half of the embryo will be missing

Where can we find induced pluripotent cells in an embryo?

iPS cells do not come from embryos

Embryonic stem cells are found:

in a developing blastocyst

Where and how is imprinting established in females?

in the oocyte by the activity of DNA methyltransferases

Which of the following would likely NOT effect the first 4 cleavage cycles of an early embryo?

inhibit cyclin D protein

In the experiment described in figure 3.15 in your book, how did Dr. Melton and colleagues deliver the 3 transcription factors to the mouse pancreas?

injecting with viral vectors

From which group of cells in the human embryo are embryonic stem cells derived?

inner cell mass

In Angelmann's syndrome the wild type allele

is silenced in the male germ line

Which molecular genetic technique would you use to EMS mutagenesis?

isolate mutations in genes involved in early development

A molecule is a morphogen if:

it forms a concentration gradient, and activates specific cellular responses at different concentrations

The mouse Igfr gene encodes a receptor protein that binds to IGF-2 and degrades it (preventing downstream effects of the growth factor). What would you predict about imprinting of the Igfr gene?

it is imprinted in males

You know from the fate map that a specific cell in the 24-cell embryo of the three-horned dinosaur contributes to the third horn. If you culture this cell in isolation, it grows into a third horn. If you transplant the cell to a new location in the embryo, it develops into gut. What can you say about this particular cell in the 24-cell embryo (using the language of an embryologist)?

it is specified to become a third horn

Which of the following could the experimenter use reverse genetics to answer?

loss of function mutations in the insulin related growth factor 2 are associated with longer life span in mice. Do mutations in this gene cause a similar phenotype in C. elegans?

A transcription unit that is 7,800 nucleotides long may use 1,200 nucleotides to make an mRNA that encodes a protein consisting of approximately 300 amino acids. This is best explained by the fact that

many noncoding stretches of nucleotides are present in mRNA

The kidneys develop from the:

mesoderm

The skeleton, muscle, kidney, heart and blood come from which germ layer?

mesoderm

Which germ layer does your cardiovascular system arise from?

mesoderm

434 sheep oocytes were used in the now famous experiment that resulted in the birth of Dolly. What did the researchers think was the primary cause of the failure of the other clones? (choose one)

methylation differences between the chromatin of the zygote and the donor cells derived from the udder cells

A signaling molecule that provides concentration-dependent positional information is called a ________.

morphogen

One characteristic of embryos that undergo autonomous development is:

morphogenic determinants that regulate cell fate are unequally distributed in the egg cytoplasm from the earliest stages

What general principle of developmental biology does the following experiment illustrate? -an unfertilized Xenopus egg is irradiated to destroy its nucleus -the nucleus from an adult Xenopus skin cell is injected into the egg -a normal tadpole develops from the egg

most of the somatic cells in an organism contain a complete set of genes as the original zygote (genetic equivalence)

You believe that a particular transcription factor is responsible for turning on genes that cause cells in a particular area of an embryo to develop into mouthparts. To test this, you use recombinant DNA technologies to put the coding sequence for the transcription factor under the control of a promoter that allows expression in the tail of the embryo. Is this a find it, move it, or lose it experiment?

move it

Using the pulse-chase method, will all cells in the pancreas be labeled?

no; only beta cells will be labeled

Sperm and eggs (the germ cells) are derived from which germ layer?

none; comes from separately derived germline cells

In this potential result from the pulse chase experiment, the cells that express the blue color are:

only descended from insulin-producing cells

If an embryo develops autonomously, which of the following will be the result of destroying one of the cells at the two-cell stage?

only half of the embryo will develop

Adult pancreas beta cells are formed by ______.

other pancreatic beta cells

Which of the following have NOT been used to make insulin secreting beta cells in the lab?

pancreatic stem cells

What types of cells can ES cells not differentiate into?

placenta cells

match the regulatory control mechanism to the mechanism: Covalent addition of a phosphate group

post-translational control

In general, loss of function mutations are _______

recessive

What advantage is there to cloning someone's stem cells rather than culturing already established stem cells?

rejection issues with transplants could be avoided

What type of cloning? I create a clone of my beautiful dog Cleo and name it Patra

reproductive cloning

Which of the following type of cell is an exception to "all cells have the same DNA"?

sex cells

What do we call a group of cells that differentiates according to its normal fate even after it has been isolated from the embryo and cultured in a neutral environment?

specified

The process of in vitro fertilization is best described as:

sperm fertilizing an ovum in a glass dish

What is the likely cause of a missense mutation?

substation of one base with a different base

We know that if you separate the four blastomeres of a 4 cell embryo, each cell can develop into a blastocyst and implant, suggesting each cell is equivalent. Fig. 2.13 in your book shows the results of labeling each of the 4 cells of a "Rainbow" mouse embryo a different color. What did these experiments show?

the contributions of each of the 4 cells to the embryo (ICM) or extraembryonic tissue (trophectoderm) is not random, suggesting the cells in a 4 cell embryo are not equivalent

Mutations that result in Holt-Oram syndrome (the heart and hand syndrome from the case study) were found in

the protein coding region of Tbx5 gene and a heart enhancer for the Tbx5 gene

Which of the following is NOT true of the somatic cell nuclear transfer (SCNT)?

the resulting embryo is genetically identical to the egg donor

The position in an embryo where a morphogen is at its highest level is called _______, and the point at which it is at its lowest level is called _______.

the source; the sink

A transgenic animal has:

the transgene present in every cell

What type of cloning? I make embryonic stem cells from a patient with a genetic disease to use these stem cells to test potential drug treatments

therapeutic cloning

Which molecular genetic technique would you use to create, transform, and express a transgene

to "ectopically" express a transcript

Which molecular genetic technique would you use to create, transform, and express a transgene?

to "ectopically" express a transcript

A goal of therapeutic cloning in stem cell research is:

to develop new medical treatments

Cloning stem cells from people with a genetic disorder would allow researchers:

to find and work with the DNA that causes the disease

Why are encapsulation devices needed for stem cell treatment?

to prevent destruction of stem cells by the patient's immune cells

Cells can be considered totipotent, pluripotent, multipotent, or unipotent. How do totipotent and pluripotent cells differ?

totipotent cells can give rise to a completely new animal; pluripotent cells can give rise to all the types of cells in the body

A cocktail of four genes can reprogram mature cell types into induced, pluripotent stem cells. These genes all encode

transcription factors

match the regulatory control mechanism to the mechanism: Pax 6 mRNA is expressed in the eye, but not the gut

transcriptional control

match the regulatory control mechanism to the mechanism: proteins bound to the 3'UTR of the mRNA

translational control

In 1903, Hans Spemann used a hair from his baby daughter to split a salamander embryo in half. What was the outcome of this experiment?

two normal/whole embryos

The data just presented on human twinning tells us that human embryos

undergo conditional development

The study of birth defects has taught us enormous amounts about human development. Chapter 1 gives a brief introduction to the effects of thalidomide, a mild sedative given to women to control morning sickness in the early 1960's. If a woman took a thalidomide pill 44 days after her last menstruation, what congenital defects might she have seen in her child?

very short arms and legs

Which molecular genetic technique would you use to in situ hybridization?

visualize expression of mRNA within an embryo

Igf2 encodes an insulin-like growth factor that stimulates growth of the placenta, which allows embryos to grow larger. Mouse embryos homozygous for a deletion of the Igf2 gene (Igf2delta/Igf2delta) have very small placentas ad the fetuses do not survive. When a heterozygous Igf2delta/+ male is amped to a normal female (Igf2+) mouse, the resulting Igf2delta/+ embryos also die as above. From these data alone, you might conclude that Igf2delta is

weird

What specific information does the mRNA extracted from a particular cell give?

what genes are being transcribed in that cell

Suppose you have a powerful microscope that allows you to follow all the cell divisions in a transparent embryo throughout normal embryogenesis, and to keep track if the progeny cells that arise from each cell in the early embryo and see what parts of the animal they become. From these observations alone, you CANNOT determine:

whether signaling from that cell affects the fates of other cells

Imprinted genes are the

wild-type condition

Which of the following statements is/are false? A genome-wide RNAi screen for a particular phenotype in C. elegant, e.g. egg-laying defective animals,

would identify loss-of-function as well as gain-of-function phenotypes of candidate genes

Diabetes happens because of which of these

your body can't use blood sugar the way it should