Biology 113/114 FAQs (frequently asked questions)
	© Stephen T. Abedon
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	last updated on Wednesday, February 10, 1999

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What is the difference between valence, valence electrons, and a valence shell?

Valence electrons are indeed the electrons found in the outer shell of an atom. This outer shell is refered to as the valence shell. The valence of an atom, however, is it's bonding capacity. For example: Carbon has 4 valence electrons, 4 unpaired electrons, and a valence of 4. Hydrogen has 1 valence electron, 1 unpaired electron, and a valence of 1. Oxygen has 6 valence electrons, 2 unpaired electrons, and a valence of 2. Nitrogen has 5 valence electrons, 3 unpaired electrons, and a valence of 3. Phosphorus also has 5 valence electrons and 3 unpaired electrons. However, in the phosphate ion it is actually exhibiting a valence of 5 since it forms a total of five bonds with four molecules of oxygen. The important take home message is simply that hydrogen tends to form 1 bond, oxygen 2, nitrogen 3, carbon 4, and phosphorus, in the phosphate ion, 5.

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What is the definition of a nonpolar covalent bond?

Covalent (as opposed to ionic) bonds between atoms of similar electronegativity. The most important nonpolar covalent bonds we have talked about are C-C bonds and C-H bonds. These, by the way, are also the bonds associated with reduced (as opposed to oxidized) carbon. Any covalent bond (i.e., a bond in which electrons are shared between two or more atoms) between two atoms of similar electronegativity are considered non-polar. With ionic bonds, electrons are not shared between the two contributing atoms. Polar-covalent bonds lie somewhere between these two extremes.

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I have a question about the polarity in covalent bonds. It is how do you know that the bond is polar or nonpolar? Does it have to do with the elements location on the Periodic Table or is it something else? I am able to understand that the C-C bond is nonpolar because they are the same element, but the C-H covalent bond being nonpolar has really confused me. Can you explain why it is a nonpolar bond?

You are correct that it is easy to understand that carbon has the same electronegativity as itself (as does H to itself, O to itself, N to itself, ect.).

To judge degrees of polarity you have to know what the electronegativity of the two atoms are. These values are typically not found on periodic tables though a generalization may be made: The greater the number of valence electrons, the higher the electronegativity. In addition, the lower the atomic weight (i.e., going up columns) the higher the electronegativity. Hydrogen turns out to be somewhat exceptional, possessing a much higher electrogativity than the other column 1 elements. This probably has to do with hydrogen possessing only a single electron, and requiring only a single additional electron to fill its outer electron shell (recall that hydrogen requires only 2 electrons to fill its sole electron shell).

It turns out that the C-H covalent bond is indeed slightly polar. However, because of the unusually high electronegativity of hydrogen, C and H have sufficiently similar electronegativity that the polarity of the C-H bond falls on the nonpolar end of the continuum. In fact, there is sufficiently low polarity in this bond that Van der Waal's interactions between molecules containing numerous C-H bonds are greater than the hydrogen bonding capability of the H in the C-H bond. This contributes to hydrophobic exclusion, which we'll consider in more detail when we consider water on Wednesday.

I picked up a random inorganic chemistry text (that is, an intro chemistry text) and was able to find a table of electronegativity values which are given on something called a Pauling Scale. The higher the number, the greater the electronegativity. Here's a sample of values:

• H = 2.2
• C = 2.6
• N = 3.1
• O = 3.5
• F = 4.0
• Cl = 3.2
• P = 2.2
• Na = 0.9
• K = 0.8

An immediate observation would be that the electronegativity difference between C and H (=0.4) is not exactly trivial. However, the difference between O and C or N and C ranges from a little more than the C to H difference (N-C; =0.5) to more than twice the difference (O-C; =0.9). Furthermore, the difference between O and H or N and H are even greater (=1.7 and =0.9, respectively). Consequently, the C-O, C=0, O-H, and N-H bonds are considerably more polar than the C-H bond. We call the former polar covalent bonds, and we lump the latter (i.e., C-H) among the at best weakly polar bonds, which for our purposes act more non-polar-like than polar-like.

Note that even highly polar but still covalent bonds (e.g., C-O) only fall about half way on the continuum between truly non-polar covalent bonds (e.g., C-C) and the extremely polar ionic bonds (e.g., Na-Cl).

The take home message regardless is that we will be lumping together C-H and C-C bonds as more or less non-polar and C-N, C-O, C=O, N-H, and especially O-H as polar covalent bonds which are capable of participating in hydrogen bonding. Why this is important will become more obvious as we consider water and then the various biological molecules.

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Are ionic bonds polar or are they nonpolar?

If you think about it, regular ordinary bonds range in their polarity from complete sharing of electrons (i.e., non-polar covalent bond) to the complete donation of an electron by one atom to a second atom (i.e., an ionic bond). If it is only partial donation (due to sufficient differences in electronegativity) then we might call that bond a polar covalent bond. Therefore, increasing polarity is observed with increasing donation of electrons, and ionic bonds represent an extreme example of electron donation. Another way of thinking about this is that with a polar covalent bond, one of the atoms takes on a partial negative charge and the other atom a partial positive charge. From the existence of these partial charges we infer polarity in the bond (i.e., the electron is held more closely by one atom than it is by the other) and we would describe this bond as polar covalent. In an ionic bond the respective atoms take on not just a partial charge but a _full_ charge. Hence they are very polar, so polar that we don't even refer to them as covalently bonded (since covalent bonding implies a sharing of electrons).

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Is cohesion responsible for surface tension?

Yes, but also involved is the fact that water molecules don't bond very well with air molecules. For more on water, see biol1015.htm.

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Could you explain what hydrophobic exclusion is?

Very similar to surface tension. Here water molecules prefer to interact with themselves over interacting with a hydrophobic substance. This, however, reduces the number of hydrogen bonds water molecules participate in. Losing hydrogen bonds is energetically unfavorable. The number of hydrogen bonds lost is directly proportional to the area of contact between the water molecules and the hydrophobic substance. The smaller the area of contact, the fewer hydrogen bonds lost. Two things have a smaller combined surface area if they are smooshed together than if they are separated. Consequently, hydrophobic substances, suspended in water, tend to pool together, away from water. For example, if you place two drops of oil on the surface of a water solution, the oil drops will tend to coalesce into a single drop. For more on hydrophobic exclusion (see especially the figure) see biol1015.htm#hydrophobic_exclusion.

Why care? Lipid bilayer membranes spontaneous form as a consequence of hydrophobic exclusion. Globular proteins spontaneous fold so that their hydrophobic parts are inside, away from water (i.e., hydrophobic exclusion). Hydrophobic exclusion is also one of things that makes lipids better long-term (and compact) storage molecules than carbohydrates. In fact, to life, the two most important roles played by water are (i) water dissolves hydrophilic substances and (ii) water excludes hydrophobic substances, i.e., hydrophobic exclusion.

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How can I derive the electronegativity values from my understanding of the periodic table of elements?

Going from left to right in the periodic table atoms increasingly fill their outer shell while also gaining an increased nuclear charge. The increase in the volume of their outer shell is not as great as their increase in charge because they are filling equivalent outer shells rather than forming new ones. This means that electrons similarly distant from the nucleus are exposed to a nucleus with a greater positive charge.

In fact, far from gaining in size, atoms actually decrease significantly in size going from left to right on the periodic table. These electrons consequently are not only held more tightly, the nucleus possesses an increased propensity to attract additional electrons. The Column 1 elements display the least electronegativity because they have nuclei with the least positive charge in their row. This means that they tend to readily lose their single electron (which also serves to complete their now outer shell). In contrast, Fluorine displays the most electronegativity, readily filling its outer shell at the expense of other atoms.

The exception to these rules is Hydrogen, which is a column 1 element but which possesses comparatively significant electronegativity. This has to do with hydrogen only possessing a single electron and a single proton. That is, while the charge of the nucleus is small, electrons are held relatively close to the nucleus. Furthermore, hydrogen, like Carbon, Nitrogen, Oxygen, etc. but unlike other column 1 elements, can complete it's outer shell by gaining only a single electron.

Finally, as you go down in columns in the periodic table, elements become less electronegative. This is due to the increasing size of the outer shell.

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What reactions or bonds take place because of dehydration synthesis?

The most important thing to understand about dehydration synthesis is why it is named what it is (i.e., dehydration synthesis or condensation reaction). That is, these are reactions in which a water molecule is removed from two reactants. As a consequence the removal of the water, what is left of the two reactants (their residues) are bonded together, hence the use of the term synthesis: Dehydration synthesis = removal of water to achieve synthesis.

Since water is removed, there have to be the ingredients of water present on the two reactants to remove. These are H-O-H. More specifically, there will exist a hydroxyl group and a hydrogen typically bonded to an electronegative atom (i.e., O or N). That is, -OH and H-. Remove -OH and H- and you have all the ingredients for water. Left behind are a pair of elections which are responsible for creating the bond between what is left of the two reactants.

For example: C-OH + HO-C can react to give you C-O-C + H-O-H.

Note that only one of the carbons need be bound to an -OH (though at least one must). The other carbon could be bound to an -NH:

C-OH + HN-C can react to give you C-N-C + H-O-H.

In addition, the carbons are not limited in what else may be bonded to them nor the types of bonds (though the octet rule must always be adhered to, i.e., carbon can only have four bonds around it). Consequently, you can have dehydration synthesis between, for example, carboxyl groups and amino or hydroxyl groups:

O=C-OH + HO-C gives you O=C-O-C + H-O-H; This is how fatty acids (the carboxyl group) bind to glycerol (which supplies the hydroxyl group).

O=C-OH + HN-C gives you O=C-N-C + H-O-H; This is a peptide bond linking two amino acid residues.

In general, dehydration synthesis is how polymerization occurs in biological systems. Also, don't let the use of carbon throw you above. Dehydration synthesis can occur between two non-carbon containing molecules (or ions). An example of such a reaction is the binding of two phosphates together, e.g., as in the reaction ADP + Pi --> ATP + HOH.

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Low temperature stability, could you explain?

I'll assume the question is with regard to tryglyceride or membrane stability, or do you mean chemical stability?

The latter results from most reactions requiring a significant input of energy before they can proceed (all reactions that don't are so unstable they've probably already occurred). Without that input of energy, the reactions dont' start, so they don't occur. If a reactant is not converted to products, we might say that the reactant is stable under the existing conditions. In non-catalyzed reactions, the only way to speed up the reaction is to supply heat. The heat supplies the activation energy. Speeding up the reaction means that it happens faster. Slowing down the reaction means that it happens more slowly. If heat is used to speed up a raction, then removing heat slows it down. If you remove enough heat, you will slow the reaction down to essentially nil. Heat is proportional to temperature. Thus, it is possible to lower temperatures sufficiently far that reactions don't occur. We would therefore describe the reactants as stable at that temperature. All living forms of life exist at a temperature that is low enough that its biomolecules exist in a relatively stable state. Thus, we can owe the existance of organisms to the requirement of activation energy to effect the degradation of biomolecules. So long as temperatures are sufficiently low, these biomolecules don't degrade, i.e., they exibit stably at these relatively low temperatures.

The temperature stability of lipids can be described in similar terms except that it is not covalent bonds that are being broken. Instead, it is weaker bonds that occur between hydrophoblic molecules. The number of these bonds is proportional to how closely the two hydrophobic molecules can pack together. The more closely together they can pack, the more bonds. The more bonds, the more temperature stability (i.e., the more heat required to separate the molecules from each other). Double bonds in fatty acids put kinks in these fatty acids. Kinks inhibit close packing between the two fatty acids. Consequently, kinks lower higher-temperature stability. Why have them then? Because they simultaneously increase lower-temperature fluidity.

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Exergonic, exothermic, and spontaneity?

To those of you who are having troubling dealing with the terms exergonic and endergonic because you learned these concepts in chemistry class using the terms exothermic and endothermic, here's an attempt at a clarification. I follow this with a restatement of activation energy and why it is that all reactions can have an activation energy, regardless of whether they are endergonic or exergonic.

First, the various terms are not quite synonymous (i.e., neither exergonic and exothermic nor endergonic and endothermic). However, if you find it easier to think of them as synonymous, then go for it. The goal is to get across the concept of how some reactions require a net input of energy in order to go forward (endergonic and endothermic) while others net give off energy (exergonic and exothermic). Note that the -thermic terms tend to be limited to describing heat energy while the -gonic terms are broader, referring to free energy. That is, two possible things can drive a reaction spontaneously forward: A relesease of energy as reactants go to products or an increase in entropy as reactants go to products. The -thermic terms more or less only deal with the former while the -gonic terms consider both.

Second, keep in mind that even exergonic reactions will require some input of energy. That is, the exergonic terms does not mean no input of energy. Instead it means that the reactions net generate energy. In other words, when you sum together input energy and output energy, exergonic reactions will have produced more energy than they have consumed. The input of energy is called activation energy. See figure 6.9 of your text where the curve first rises (indicating a requirement for an input of energy, i.e., activation energy) then drops as this exergonic reaction goes to completion. If the drop results in the (free) energy associated with the products is less (i.e., the curve is lower) than that associated with reactants, then it is an exergonic reaction. If the drop results in the (free) energy associated with the products being more than that associated with the reactants, then it is an endergonic reaction, and clearly some net amount of energy must have been pumped into the system for what you ended with to have more energy associated with it than what you ended with.

Finally, keep in mind that the term "spontaneous" does not mean, in a chemical sense, that a reaction will happen fast. For a chemical reaction to happen at all, it must either be spontaneous or energy must be supplied to drive the reaction forward. The rate at which a reaction goes forward, however, depends on the amount of activation energy necessary to initiate the reaction. If a lot of activation energy is required, then the reaction will tend not to go forward (all else held constant). If little activation energy is required, then the reaction will tend to go forward very readily.

These are difficult concepts. In some ways understanding them too well may be counter-productive to your understanding of biology at this level. Just keep in mind that some reactions require a net input of (free) energy to forward, other reactions net give off some amount of (free) energy, but all reactions require some input of (free) energy (activation energy) before they can go forward.

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What exactly is compartmentalization?

The idea is that two otherwise incompatible chemical reactions can go on within the same cell so long as they don't (can't) come into contact with each other. How to keep them apart? By placing a membrane between the two reactions. Thus, within eukaryotic cells there exist numerous membrane-enclosed compartments such as lysosomes (and the rest of the endomembrane system), mitochondria, etc. This allows eucaryotes to perform more sophisticated intracellular chemistry than can procaryotes.

Golgi apparatus- a little more info dealing with the transport vesicles?

The golgi isn't directly connected to either the ER or any of its various targets (e.g., the plasma membrane). Movement of membrane-enclosed "compartments" (i.e., vesicles) to and from the golgi allows the movement of membrane as well as endomembrane lumenal contents (e.g., proteins) to and from the golgi. These vesicles form by pinching off from existing endomembrane system components and deliver by fusing with endomembrane components. They allow a communication between endomembrane components without disrupting compartmentalization (drastically). Vesicles differ according to their contents and targets. One job of the golgi is to properly match targets with contents.

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What is a vacuole, other than a component of the endomembrane system that are connected to the golgi?

Vacuoles aren't _physically_ connected to the golgi. A vacuole is just a big vescicle. That is, a part of the endomembrane system that is not physically continuous with the ER, the golgi, the plasma membrane, etc. There are a number of different, specialized endomembrane components that are called vacuoles including food vacuoles (where stuff engulfed during endocytosis ends up), contractile vacuoles (which pump water out of the highly hypertonic cytoplasm of protozoa), and, of course, the central vacuole in plant cells which is a storage area that serves, in part, to take up space within the plant cell. Cytoplasmic components are expensive (mitochondria, chloroplasts, ribosomes, proteins, etc.). Central vacuoles allow plant cells to have a relatively large volume while simultaneously have a relatively small cytoplasmic volume. Other functions are listed in your book.

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I am a bit confused on the osmolarity thing. Can you explain?

Osmosis is the movement of water across a membrane. It turns out that water can readilly cross lipid bilayers (despite water's being a polar molecule and lipid bilayers being relatively inmpermeable to polar molecules) so this is very relevant to biological systems. Given that water can cross membranes and that movement across membranes typically occurs going from a state of dissequilibrium (i.e., unequal concentrations on either side of the membrane) to equilibrium (i.e., equal concentrations on either side of the membrane), then one would expect a net movement of water across membranes when concentrations on either side of the membrane are unequal. Specifically, one would expect a net movement of water from the side that has more water on it to the side that has less water on it.

Up to now, this concept is exactly analogous to the movement by diffusion of anything across a membrane. Those dye molecules we looked at represent the net movement of a solute from a region of high concentration, across a mebrane, to to a region of low concentration. In other words, movement with (i.e., down) the concentration gradient (a.k.a., toward equilibrium). Water does the same thing, i.e., moves down its concentration gradient. The big difference, though, is that water is the solvent rather than the solute. Consequently, it is not quite as straightforward to calculates water's concentration in a solution as it is to calculate a solute's concentration.

To do this calculation, lets start with the idea that pure water contains some maximal concentration of water molecules, call this 100%. If pure water is maximum, then unpure water must have a lower than maximal concentration of water molecules, i.e., <100%. What kinds of things can lower the concentration of water in a solution? Just about anything that can go into solution. In other words, holding volume constant, the more of something other than water you have, the less water you have. If you have pure water on one side of a membrane and not pure water on the other side, then the not pure side will have a lower concentration of water. Water will move down its concentration gradient from the pure side to the not pure side, i.e., down its concentration gradient. We call this movement osmosis.

Osmosis can occur with or without _pure_ water on one side of the membrane, so long as the water concentration on either side of the membrane is different. (otherwise you will have equilibrium and no net movement will occur). That is, with a 10%-solute solution on one side of a membrane and a 20%-solute solution on the other side, there will be a net movement of water from the 10% side to the 20% side. This movement will continue, barring the application of any external forces, until the solute concentration on either side of the membrane is the same. Note that this equalization cannot occur if pure water is on one side of the membrane (i.e., there is no solute in pure water to equilibrate).

It turns out that solute concentration units are best expressed in terms of solute particle number when calculating osmotic movement. This is because it is the number of solute particles that determine the direction of water's movement (indeed, the relative number of solute particles) rather than the molecular weight, mass, etc. associated with the solute particle (i.e., it is a "colligative" property of solute particles). Given this understanding we can derive just how it is that osmosis works.

For a water molecule to cross a semipermiable membrane, the water molecule must first collide with the membrane. As you might expect, this happens quite often in a water solution. Depending on how many holes the membrane has in it, the colliding molecule will either bounce off the membrane, or pass through it. Thus, the rate of passage of a water molecule through a semipermiable membrane is proportional to the number of water molecule collisions and the number of holes in the membrane (as well as their size). From here on out we'll assume that the number and size of holes in the membrane are held constant.

If there are more molecules on one side of the membrane than on the other, it is obvious that there will be more collisions on the more-water-molecules side than there will be on the less-water-molecules side. All else held constant, therefore, there should be a net movement of water from the more-water-molecules side to the less-water-molecules side. That is, down water's concentration gradient (i.e., toward equilibrium). Now, lets assume that the number of collisions of anything with the membrane is the same on both sides of the membrane.

If you have pure water on one side of the membrane, then all collisions on that side of the membrane will be made by water molecules. However, if there is a solute present, some of those collisions will involve a solute molecule. In fact, the fraction of collisions made by solute molecules is proportional to the number of solute molecules present, the more present the more collisions. If a solute molecule collides, a water molecule cannot simultaneously collide at the same point, at the same time. Hence, there will be fewer collisions by water molecules on that side, hence there will be less movement of water from that side to across the membrane. Consequently, water will tend to move across a semipermeable membrane from a region of low solute concentration to a region of high solute concentration, and this we call movement osmosis.

See biol1053.htm for more on osmosis.

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Could you explain cotransport?

Active transport involves the expenditure of energy to pump something across a membrane and up its concentration gradient. That energy may be derived from ATP but that is not the only possible source. Another source is membrane potentials. That is, by pumping ions, a cell can set it up so that (typically) the interior of the cell has a net negative charge while the exterior has a net positive charge. This arrangement essentially represents a battery, i.e., stores potential energy. Allowing ions to cross the membrane by heading toward the side containing the net opposite charge allows the system to return to equilibrium. Movement toward equilibrium is exergonic, i.e., energy is liberated. This energy can be used to do work, such as the transport of other substances up their concentration gradient. The coupling of these two reactions is termed cotransport. Another way of looking at this is that the ions waiting to cross the membrane are equivalent to water found at the top of a waterfall. As they cross the membrane they are equivalent to water going over a waterfall. When they reach the other side they are equivalent to water found at the bottom of the waterfall. During movement over the waterfall, potential energy is converted to kinetic energy (by gravity in the waterfall; with membrane potentials this occurs via the attraction between opposite charges) which may be harnessed to do work.

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A girl is getting ready to go out. As she is getting ready to put her contacts in, she realizes that she is out of contact solution. Her mother has a bottle of distilled water that she uses for ironing sitting cloths. The girl picks up the bottle and uses the distilled water on her contacts. Her eyes get red and irritated and her contacts pop out. Why does this happen? I do not understand if it is hypertonic or hypotonic.

It's hypotonic. Her eyes are getting red because water is flowing into her cells and damaging and/or lysing those cells. Ideally contact lens solution is isotonic, i.e., a salt solution (NaCl) with the same osmolarity as is found in her extracellular tissues as well as inside of her cells.

The contrasting situation is placing too concentrated a salt solution in your eyes (sea water, for example). In this case the eye's cells are damaged by too much water flowing out of them, into the seawater. In this case the solution (the seawater) is hypertonic. There is too much salt.

The underlying mechanism of osmosis is the flow of water from a region of high water concentration to a region of low water concentration. However, the prefixes hyper and hypo refer to the relative salt (solute) concentrations. The hypertonic solution has too much salt (more than the reference solution) while the hypotonic solution has too little salt (less than the reference solution).

Finally, I keep track of hyper and hypo by thinking of "hypo"dermic needles. These are employed to deliver stuff to "beneath" the surface of the skin. The term "hypo"tonic, in turn, refers to a solution which has a salt concentration which is "beneath" that of the reference solution, e.g., the inside of a cell.

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What do you mean by "Energy in bonds"?

When electrons are locked into chemical bonds, there is a certain amount of energy associated with those electrons. This is the (chemically available) energy that exists within, for example, the food you eat. Recall that the farther an electron is from the atomic nucleus, the more energy it contains. This distance from an atomic nucleus can be locked into an electron when that electron is locked into a chemical bond. Indeed, one can think of the energy required to drive forward the endergonic dehydration synthesis reaction as energy that becomes trapped in chemical bonds and associated with electrons that are now farther from atomic nuclei than they otherwise might be (in fact, were). Finally, note that all else held constant, an electron that is shared between two atoms possessing relatively equal electronegativity will be trapped at a further distance from the two atomic nuclei than an atom locked between two atoms having dissimilar electronegativities. For example, an electron found between H and O will be much closer to an atomic nuclei (i.e., that of O) than an electron found between C and C, or even O and O.

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In Ch. 11 there are a lot of c-words, could you explain the difference between, centrosomes, centromere, sister chromatids, chromosomes, and chromatin?

A centrosome is the center of the microtubular array of the cytoskeleton. A centrosome consists of two, perpendicularly array centriols.

A centromere is a region on the DNA/chromosome at which sister chromatids are joined and to which kinetichores are bound.

A sister chromatid is one of two (a pair) of DNA double helices that result from the replication a single DNA double helix (as least as described in a eukaryotic cell). Sister chromatid pairs are joined at their centromeres.

Chromosome has two meanings, one more ambiguous, one less so. The less ambiguous meaning is one or two DNA double helices, complexed with proteins, that is visible during mitosis or meiosis. So long as the centromeres of a sister chromatid pair remain attached, the visible pair is described as a chromosome. When anaphase of mitosis (or anaphase II of meiosis) begins, the sister chromatids are separated. Each of the now autonymous sister chromatids is now referred to as a chromosome. More ambiguous, the term chromosome is often used to describe chromatin fibers, i.e., DNA double helices other than those visible through a light microscope during mitosos or meiosis. The problem is that the visible things were discovered before the chromatin was (since, of course, the former are visible though a light microscope) so chromosome has a technical meaning that is more precise than the tendency to use the term to decribe all nuclear DNA as chromosomal, independent of its degree of condensation.

Chromatin is less condenced and less organized than are chromosomes, senso stricto. For a more visual description of the difference between chromatin and chromosomes, as well as what just what the condensation of chromatin into a chromosome is all about, see Figure 18.1 of your text, page 353.

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Are mitotic spindles, kinetochore microtubules, and spindle fibers all connected, in other words do they all do the same task?

The mitotic spindle includes more than just the kinetichore microtubules (i.e., the non-kinetichore microtubules are also included among the mitotic spindle, which makes sense since the non-kinetichore microtubules also have a role in mitosis and meiosis). Spindle fibers are microtubules that are gathered together in sufficently large bundles that they are visible through the light microscope. Again, it is important to take a historical view. The spindle fibers and mitotic spindle were discovered before kinetichore microtubules because the spindle fibers are visible through a light microscope. It was only later that it was found that the microtubles of the mitotic spindle consist of at least two types, those connected to chromosomes (kinetichore microtubules) and those that are not. For that matter, it was only later that it was understood that the fibers of the mitotic spindle are microtubules.

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Photophosphorylation, explain please.

Photophosphorylation is similar to oxidative phosphorylation in that both involve a chemiosmotic mechanism of ADP phosphorylation. The difference is that while hydrogen ion pumping is driven in oxidative phosphorylation by electrons donated by NADH or FADH2, in photophosphorylation the electrons that drive pumping are donated by chlorophyl. Similarly, the energy of oxidative phosphorylation is ultimately derived from chemical bonds while the energy of photophosphorylation is ultimately derived from photons. Alternatively, you might consider photophosphoryaltion as the chemiosmotic phosphorylation that makes ATP during photosynthesis. See in particular Figure 10.15 of your text, page 195.

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I expect that majors' biology would be easier than either majors' physics or chemistry. Why is this not the case?

It is, unfortunately, just not the case that biology is an easier science to learn than either chemistry or physics, though it might have that reputation to some. Ponder for a moment which you think is a more difficult task: Obtaining a doctorate in physics or chemistry, or obtaining a medical degree? Regardless of what the answer to that question might be, it certainly is not obvious. For example, by reputation the medical degree is tough (though in reality it is not necessarily tougher). If medicine is tough, and medicine is merely applied biology, then does it make sense that majors' biology would be terribly easy? Furthermore, ponder where these expectations may have been forged. Was it from friends and relatives who had experience with these sciences and therefore could supply a reasoned comparison from experience? Or was it from rumor or your high school experience? Regardless, biology is neither harder nor easier than either chemistry or physics. It is, instead, different and not terribly easy.

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I put off studying and organizing my notes until the last minute. This works for me in all of my other classes. Why doesn't it work for me in a majors' biology course?

Putting off studying for a majors' biology exam until the last moment is a recipe for disaster. Certainly it is not a means for doing well on exams. Furthermore, note that studying for an exam really hasn't even begun until you have actually organized your notes for studying. In addition, the efficiency with which you are able to study your notes likely is directly proportional to how well you have organized them. If you are putting off the organization of the notes or the studying of notes to the last moment, you are not optimizing your ability to learn the material.

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Why doesn't my success in chemistry translate directly into success in majors' biology?

Because chemistry is not biology. Chemistry requires strong problem solving skills, and often these problems require an application of mathematics (well, algebra). Biology too requires strong problem solving skills. However, the material is far more complex than that presented in introductory chemistry. As a consequence, much of introductory biology involves the learning of complex systems rather than their application in problems. That is, biology requires a lot of memorization, unlike chemistry, and not a lot of problem solving, also unlike chemistry. Given that, doesn't it make perfect sense that one's ability to do chemistry would not necessarily predict one's ability to do biology, especially introductory biology?

Note that those of you who are going on in chemistry as well as many who stay in biology will eventually (sooner rather than later) be faced with taking organic chemistry. Organic chemistry has a rightly deserved reputation of being rather difficult. In particular this difficulty lies in its being an amalgam of the problem solving skills required to thrive in inorganic chemistry and the memorization required to thrive in introductory biology. In other words, you are expected to both memorize and apply vast amounts of information. Sound a bit like medical school doesn't it? And, of course, that is why medical schools are so interested in how well individuals do when they take organic chemistry.

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What exactly do you mean when you say that I've "got to learn how to study biology" if I want to do well on majors' biology exams?

Unless you are very good at picking up and applying large amounts information without first organizing and memorizing, then you are going to have to apply (or learn) organizing and memorizing skills in order to do well on majors' biology exams. Only the brightest among you (or the already most organized) are going to be able to just wing majors' biology as one might wing other classes. Instead, you are going to have to learn how to organize your notes, daily if at all possible, then learn all of the material found in your well organized notes well prior to the night before an exam.

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Biology in high school was easy. Why isn't majors' biology similarly easy?

High school biology is often (though certainly not always) a joke. It is very difficult to teach anything terribly meaningful in biology if, for example, chemistry, physics, evolutionary biology, and mathematics are either ignored or glossed over. Furthermore, as you will note, the amount of material which one acquires during an introductory majors' course is vast and certainly much greater than that presented in a typical undergraduate biology course. Therefore, one's high school experience of biology is very often misleading. However, I have had students who apparently have had excellent high school biology teachers who have provided them with an excellent set of tools allowing them to thrive in a college-level majors' course. A hearty thanks to all of you teachers who make high school biology a worthwhile and enduring experience.

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I'll bet majors' biology in Columbus is a lot easier than this. Why do you make biology so hard?

Could be that it is easier in Columbus. Of course, I hear that students complain about the difficulty of majors' biology in Columbus, too. Certainly I likely make some sections hard where others might make them more relaxed, but I also make other sections less hard, where others are more strict. This, of course, is one reason why a biologist must take more than one course from more than one instructor as they progress through their academic biology career. However, the problem is not that I make biology hard. The problem, instead, is that biology is hard, and the less biology you learn, the less hard is biology (and the more you have learned, the easier the rest becomes). I have defined a certain amount of information as being essential for a biology major to be exposed to. I hold biology students responsible for this material in their introductory course. If you care to argue that specifics are irrelevant to your biological career, then point out to me which ones you specifically don't think you should have to know and I will consider your arguments.

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But I'm not a biology major. I just need this course to graduate. Why can't you make majors' biology more expedient to my needs?

Presumably your department considered your exposure to majors' biology to be sufficiently important that they made it a requirement that you attend and pass this course. I teach majors' biology with the assumption that my students will all be going on as biology majors and therefore need to be exposed to all of the material which I present. Ideally, I would have more time (three quarters, say) and be able to expose students to even more of this material. Presumably, of course, your departments have this very much in mind when they made biology 113 or 114 a requirement for various non-biology majors.

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I'm pre-med. I've just got to do well in this class. Why are you ruining my GPA?

Think of majors' biology as Medical School Lite, same great taste, only fewer calories and less filling. If majors' biology is hard, medical school is going to be impossible. Wise up. Medical schools look for good grades by individuals because this is a convenient marker for an ability (willingness, drive) to perform well in difficult academic settings. Medical school, of course, is one such difficult setting. Therefore, individuals who do well in a majors' biology course should have a greater potential to do well in medical school than those who do poorly in majors' biology. Wake up! If you want to go to medical school, then the time is now to figure out how to do well in a majors' biology-like course. You are going to have to figure out how to do this eventually, so only you have youself to blame if you wait until after majors' biology to figure it out. By all means stop by and lets chat about how you might accomplish this.

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On an essay question, what exactly do you mean by "be as thorough and as detailed as you can be"?

One way in which I grade essay questions is as follows: (i) You get one relative point for each statement you make which is both correct and applicable to the question asked. (ii) You get one-half of a relative point taken off for each statement you make which is both incorrect and applicable to the question asked. (iii) Finally, I count up the net points earned, and then divide those points by the net number of points earned by the student's essay which earned the most points. In other words, when I ask for everything, I expect everything, and no BS. Look at the number of points you earned on an essay. If they were significantly less than the amount available, you need to rethink what it takes to write a successful essay for this course.

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