Biology 441, Spring 2014


REVIEW QUESTIONS FOR THIRD EXAM. Please be able to identify all the photographs and all the diagrams on the web pages.

You should also be able to explain what principles are illustrated by each photograph and diagram. You might be asked to label the parts of a photograph, or tell what part of what kind of animal it illustrates, or (like certain questions on the second exam about locations of cross sections) or you might be asked to sketch the plane in the body where a cross section was located.

These questions are taken directly from the web pages.

*Questions with a * in front of them are difficult, and you shouldn't worry if you can't think of the answer. Not many such questions will be on the exams.

90% of the third exam will come from these lists, photographs and diagrams.

Suppose that a mutation caused sperm carrying the "super-sperm" mutant gene to be able to overcome blocks to polyspermy: Would there be Darwinian selection in favor of that mutation?

Why or why not?

Suppose such a mutation also caused sperm nuclei to become able to destroy or inactivate other sperm that already had fertilized an oocyte? Would Darwinian selection favor this gene? Would the frequency of that mutation increase over time?

Suppose that a mutation increased the speed of sperm, or otherwise increased their competitive success rate in fertilizing oocytes?

Suppose that a certain "super-sperm" mutation had these two very different effects:

1) In the sperm (haploid, of course), the mutation greatly increases the frequency of success in fertilizing oocytes? (for example, if 90% of offspring of a heterozygous father resulted from fertilization by one of the 50% of his sperm that carried this mutation.)

2) Suppose that it is harmful or even lethal for animals to be homozygous for this "super-sperm" mutation, so that homozygotes leave fewer offspring.

Would the frequency of super-sperm mutant heterozygotes increase in the population? Or decrease?

What percentage increase in sperm success would balance what % decrease in survival or breeding success by individuals homozygous for the super-sperm mutation? Or is there a predictable percentage trade-off?

*) What if this mutation is sex-linked (= located on the X chromosome)?

*) What if this mutation is located on the Y chromosome?

Which probably evolved first, second, third and fourth:

    The use of action potentials to control directional swimming in protozoa?

    Or the use of action potentials to block polyspermy of oocytes?

    Or the use of action potentials to control contraction of muscle cells?

    Or the use of action potentials to propagate nerve impulses along nerve fibers?

In advanced courses it often is very important to understand the methods used to make a discovery, the logical reasoning that methods are based on, and their strengths and weaknesses. Future exam questions in this course may ask you to invent a bioassay capable of discovering what chemical produces a certain embryological effect. Your answer should include what might go wrong, and either prevent discovering any chemical with the expected function, or might result in the wrong chemical being discovered.

Questions that might be on the exams

I) What are three embryonic organs whose medio-lateral, anterior-posterior and dorso-vental axes become irreversibly decided during early development? hint: Limb buds, inner ears, retinas.

II) Are all three axes decided simultaneously, or one at a time, or sometimes one at a time, but other times simultaneously?

III) Does the answer to the preceding question differ between organs?

IV) Which axis is the last to become irreversibly fixed, which second, and which third?

V) What are two mesodermal organs that start development as two separate organs (right and left), but then their tissues fuse?

VI) Driesch discovered that very early echinoderm embryos will do what if the first two or the first four cells are separated?

VII) What happens if you put two one-cell stage embryos together when they are at their one cell stage?

VIII) Compare these phenomena discovered by Driesch to what happens in normal development of the mesodermal organs in question V.

IX) Why branch into three when a limb bud is grafted backwards?

X) How could you produce a 6 legged salamander (or chicken)? (Perhaps as extras in a John Carter of Mars movie?)

XI) Draw a sketch of the Apical Ectodermal Ridge in a bird embryo. Contrast the AER structure in embryos of birds, mammals, frogs, salamanders, and fish.

XII) From what you already know about the order in which axes become irreversibly fixed, are EphA gradients determined before EphB gradients, or the reverse. ( hint: which controls the dorso-ventral axis of retinal differences of adhesion?)

XIII) Based on what you know about pressures across flexible surfaces, and their expected equilibrium between Pressures, Tensions and Curvatures:

dP= Curvature x Tension + curvature x tension

Please estimate changes of tensions in different parts of a limb buds as it develops from a small hemisphere, into a complex limb bud.

XIV) Can you deduce what might be special about the tension in the surface membrane at the AER, relative to other parts of the skin? (There is more than one possibility.)

Can you invent experiments capable of proving and/or disproving which possibility is true?

XV) After I draw and describe what Nardi and Stocum discovered happens when salamander limb buds are cut off at different proximo-distal levels, and then grafted to different proximo-distal levels of another limb bud (that is still attached to the body), try to explain what patterns of contractile forces cause the base of the graft to be pulled longitudinally along the host limb bud.

Why do you think equilibrium become balanced only when the base of the graft has been pulled to the homologous part of the host limb?

    i.e. wrist next to wrist;
    elbow next to elbow;
    shoulder next to shoulder

XVI) When a salamander limb regenerates, the muscles near the cut surface "dedifferentiate" (become undistinguishable from cells that had been skeletal cells), and then grow and divide until the cell mass is nearly as big as the amount of tissue removed. Then muscle cells re-differentiate (only) into muscle cells, and skeletal cells redifferentiate (mostly) into skeletal cells.

What do you conclude about the mechanism of pattern formation?

Is it by rearrangement of cells according to cell type?

Or is it by re-differentiation of cells according to position?

XVII) Compare these alternatives to what H. V. Wilson hypothesized about the reformation of functional anatomy by dissociated sponge cells. hint: Wilson preferred to believe that sponges re-formed by differentiation of the equivalent of stem cells, or at least by switching from one cell type to another; He hated the idea that being differentiation causes cells to move actively to their correct relative locations, although rearrangement is really what happens, and what Wilson is credited with discovering.

XVIII) How are Nardi and Stocum's observations related to the question of rearrangement versus redifferentiation? hint: Rearrangement of cells and matrix requires mechanical forces; migration of limb explants along the leg proves the occurrence of physical forces acting at the right time in the right places.

XIX) Can you figure out any logical reason why the same category of protein (Fibroblast Growth Factor) induces third limbs and also causes the Medio-Lateral axis of limb buds? (I am not sure myself why this should be true.) hint: Substituting for the AER in maintaining limb proximo-distal development is kind of like inducing an additional limb to form.

XX) Would you expect that the paracrine protein "Sonic Hedgehog" controls which part of the retina becomes connected to which part of the brain? hint: Why not; it seems to do everything else; but please think of some analogous effects shh is known to have.

XXI) What about the paracrine protein Wnt? What axis does it control in developing limb buds? hint: dorso-ventral What properties of the neural retina does this axis correspond to? hint: Geometry of innervation of the brain by axons from retinal ganglion cells.

XXII) Invent a method for using fibroblast growth factor to change the result of the Nardi and Stocum experiment. hint: RA stimulates cells to change their proximo-distal behavior.

XXIII) If you sliced a salamander limb bud like a long boloney, and cultured each of the slices onto a thin sheet of rubber (to detect amounts and directions of contractility), what differences would you expect, based on the result of the Nardi and Stocum experiment? hint: Hand cells should contract more strongly than elbow cells, and much stronger than shoulder cells, according to the Broadland-Harris counter-theory

XXIV) Can you figure out whether and how the results of the Nardi and Stocum experiment can be explained by Steinberg's Differential Adhesion Hypothesis? hint: Neither can I

Would the embryonic limb need to become more adhesive near the outer end? Or more adhesive near the basal end? hint: the former, but please make sure that you understand the evidence and reasoning their interpretation is based on.

XXV) Could the same Nardi and Stocum effect be produced by gradients of strength of contractile strength of a developing limb bud? hint: If forces don't create shapes, what does?


What is chromatin?

What is the function of chromatin?

How do cells regulate chromatin compaction? What is an examples of epigenetic modification o DNA itself? What are three examples of modifications of the histones?

Which changes are associated with activation of gene expression? Which are associated with repression of gene expression?

How is chromatin structure help regulate hox gene expression?

What would go wrong in embryos (or adults) if gene transcription isn't properly controlled?



Questions added 1 pm Sunday

Why is it as bad for an oocyte to be fertilized by two sperm as not to have been fertilized at all?

List similarities between nerve impulses and the mechanisms that block polyspermy. Don't forget secretion of synaptic vesicles.

Explain why natural selection does not increase the frequency of mutations that increase the ability of sperm to overcome the blocks to polyspermy and penetrate oocytes that have already been fertilized.

What if such a mutation ALSO conferred an ability of sperm nuclei to cause destruction of other sperm nuclei that had already fertilized an oocyte? Would that mutation tend to increase in frequency in the population.

Incidentally, mutant genes that increase the success rate of fertilization by sperm are favored, even if they also cause harm to the zygote.

(Even if such a mutation kills zygotes that are homozygous for such a gene that improves the sperms' success rate, as is true of the tailess mutation.)

If you put unfertilized oocytes in a salt solution with a high concentration of dissolved potassium chloride, what would the effect be?

If they were mammal oocytes? If they were sea urchin oocytes?

The components of the fertilization membrane are located where in an unfertilized oocyte.

What substance is located in the equivalent locations of vertebrate oocytes?

Is the "zona reaction" in mammals the same thing as the slow block to polyspermy? Hint: yes.

What are some examples of galvanotaxis?

Do any differentiated cell types in the body besides oocytes, nerves and muscles, have the equivalent of resting potentials? Hint: remember those black pigment cells that form the stripes in zebra fish.

Name twelve other differentiated cell types that also have much higher concentrations of potassium ions in their cytoplasm than in the surrounding media. [Hint: can you name any cell types that don't?]

** What effect does an imposed electric current have on the potassium ion concentration in the cytoplasm of a cell?

What caused that ring of fluorescence to spread outward across that oocyte surface in the video shown in class? (see the lecture video for February 24th)

Please sketch a cross-section, and a longitudinal section. of an individual mammal hair.

Please sketch the pattern of formation of feather papillae in the skin of a developing bird embryo.

Papillae induce the differentiation of what?

Compare and contrast (list similarities and differences between) the embryonic development of hair, feathers, teeth and somites.

List as many birth defects as you can that result from failure of normal fusions between sheets of tissue that were originally separate.

* Please invent some additional birth defects (that you have never heard of) that could also be produced by failures of fusion between tissues during embryonic development.

List at least five organs, tissues, or differentiated cell types that develop from neural tube ectoderm.

List at least five organs, tissues, or differentiated cell types that develop from neural crest ectoderm.

List at least five organs, tissues, or differentiated cell types that develop from somatic ectoderm [Hint: don't forget placodes]

Sketch the geometric arrangement of the retino-tectal projection.

Be prepared to label the diagrams of the retino-tectal projection that are on the web pages (if their labels were removed).

Questions added 2:45 pm Sunday

What is the causal relation between the formation of the retinotectal projection and the concentration gradient of Eph "ligands" on the retinal ganglion cells and the concentration gradient of Ephrin "receptors" on the surface of the midbrain?

Steve Roth invented and used a bioassay to measure adhesiveness of radioactively labeled retinal cells to different parts of chick embryo brains. This bioassay is sketched at the bottom of one of the more complicated diagrams on the website; the one with the nerve cell stretched across the top.

Explain how or why his method was probably detecting the eph and ephrin gradients, instead of something more like gradients of cadherins (which is what he expected to find). *How could he have changed the bioassay to make it able to measure inhibitors of axon locomotion, or inhibitors of cell-cell adhesion?.

Explain why chemotaxis seems to exert a pulling force ("attraction") but really doesn't.

Look at the appropriate videos of cells undergoing haptotaxis (moving up adhesion gradients, and accumulating on little gray squares of greater adhesiveness), and explain why you conclude from the cells' movements whether adhesion forces are pulling the cells, or whether active cell contractility is pulling the cells, but adhesion differences are changing the effectiveness of contraction at different locations.

Argue pro or con, or just discuss, whether the eph & ephrin explanation of formation of retinotectal projections is an example of haptotaxis. Consider whether this depends on some additional facts, that we don't yet know; and what additional facts you would need to know in order to decide such questions. When in doubt, demonstrate your knowledge.

Does Steinberg's theory of cell sorting and engulfment depend on moving cells actually being pulled by forces of cell-cell adhesion, instead of pulling themselves by active contractions? [Hint: For sure, except this hasn't occurred to Gilbert] Argue pro or con, and/or discuss what additional observations are needed to settle disputes and move forward toward debating new questions.

* Imagine that optic nerve growth cones somehow got deviated by an experimenter, and tried to enter the tectum from the wrong side (where the ephrin is most concentrated), what should happen?

* Suppose that eph and ephrin were simple cell-cell adhesion proteins, and had the same concentration gradients that are actually observed, then which ganglion cell axons would accumulate where?

* How does the answer to this question depend on each of the following: *Whether the ganglion cell axons compete with each other, in the sense of a more strongly-adhering axon being able to force a less strongly adhering axon to shift over out of its way?

*Whether the strength of each ganglion cell axon's adhesion depends on its concentration of eph multiplied by the concentration of ephrin at whatever part of the tectum it is currently attached to.

*Whether (instead) the strength of each ganglion cell axon's adhesion depends on its concentration of eph added to the concentration of ephrin at a given part of the tectum.

*Whether (instead) the strength of each ganglion cell axon's adhesion depends on its concentration of eph subtracted from the concentration of ephrin at a given part of the tectum.

What are cotyledons? Draw the shape and locations of the two cotyledons of a peanut.

Is a plant seed equivalent to a newly laid egg; or is it more like a neurula stage that has gone into hibernation?

List major similarities and differences between development of higher plants and vertebrate animals.

*How is development of colonial sea squirts and corals somewhat more like plants, at least superficially?

What are meristems? What are several kinds of meristems, located in different parts of plants?

What is a cambium? What function does a cambium serve?

Describe the bioassay by which it was discovered which chemical is the (previously-hypothetical) auxin.

How does auxin participate in each of the following: Positive phototaxis? Negative geotaxis? Localization of root formation at the bottom of plants? Branching of plants after pruning?

Which of these effects was used in the actual bioassays by which indole acetic acid was discovered to be auxin?

Invent and describe a bioassay for discovering auxin by measuring each of the other three functions of auxin.

*Why were the bioassays for identifying auxin so much more successful that the bioassays used to try to identify noggin, chordin, sonic hedgehog, fibroblast growth factor, or other substance that control animal structure formation?

Argue pro or con: Plant hormones like auxin would be called morphogens (and not hormones) if the occurred in animals, and the key difference is whether a substance produces a localized, long-term effect, as compared with an organism-wide short-term effect.

Explain why a chemical morphogen will also be a teratogen. No exception.

*Design a bioassay for morphogens that works by comparing amounts of teratogenic effects (= birth defects).

*Are such bioassays currently going on, unintentionally?

If indole acetic acid were in diesel exhaust, how and when would auxin have been discovered?

(Actually, ethylene was discovered to be a normal plant hormone in a similar way)

What is the name of at least one other plant hormone, besides auxin?

Questions added 4:25 pm Sunday

What embryonic structure induces formation of the lens placode?

Who discovered this (not a German)?

Induction of the neural tube by the notochord was discovered by which two scientists, about what year?

By means of what experiment?

*What are some reasons why it took >50 years to discover the chemical basis of this induction?

What scientist was the first to prove that at least one case of induction is part of normal development in nematodes?

Argue pro and/or con (demonstrating knowledge) whether species with regulative development are more apt to control cell differentiation with induction, in contrast to species whose development is more mosaic

To put it another way, explain how induction can produce regulation.

By what experimental were chicken embryos induced to form teeth?

The results of this experiment indicate that the evolutionary loss of teeth resulted from natural selection of mutations in genes that normally would have coded for what proteins? (i.e. proteins that served what function; and please don't just say "genes for forming teeth". Genes for proteins that do what, in the formation of teeth). Hint: Induction of what by what?

Discuss some different meanings of the phrase "stem cells": Hint: Involved in constant replacement of blood cells, skin and intestinal cells; and as a future medical method.

Sketch a mammal or bird limb bud, at 3 or 4 stages of embryonic development.

How can you cause vertebrates to form 3 legs along each side, instead of two?

How can you cause legs to branch into three hands, wings or feet? How can you cause them to branch into four distal ends?

Who discovered both these phenomena?

Sketch the apical ectodermal ridge.

What happens to limb development if you surgically remove the apical ectodermal ridge at different stages of development?

What happens if you graft a second apical ectodermal ridge to a developing limb bud?

What is unusual about the apical ectodermal ridges in salamander limb buds?

What else is unique about salamander legs?

Argue pro or con: If the muscles of a regenerated leg consist entirely of cells that were muscles in the stump, and if all the skeletal cells in the stump become skeletal cells in the regenerated leg, that means that regeneration results from rearrangement of differentiated cells, instead of what most people assume (spatial control of undifferentiated stem cells).

Argue pro or con: Will stem cells be able to regenerate complicated anatomical structures (instead of just particular cell types, that either have a very simple geometry, like skin and intestine, or have no geometry, like blood.

Concentration gradients can be produced by diffusion (for example auxin, sonic hedgehog and retinnoic acid). But how can embryos form gradients of substances like eph and ephrin surface proteins, or messenger RNAs of transcription factors?

Hint: the answer will be demonstrated by a computer simulation in class this Monday morning.


90% of the third hour exam will be derived from the questions listed above.

At most, only one of the starred * questions will be asked.


back to syllabus