Important words and concepts from Chapter 2, Campbell & Reece, 2002 (1/14/2005):

by Stephen T. Abedon (abedon.1@osu.edu) for Biology 113 at the Ohio State University

 

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(1) Chapter title: The Chemical Context of Life

(a)                    Found at this site (i.e., at www.phage.org) are additional pages of possibly related interest including: [fundamentals of chemistry] [history of earth] [origin of the universe]

(b)                    [chemical context of life (Google Search)] [index]

(2) Chemistry for biology

(a)                    In this chapter we will consider the chemical context of life

(b)                    To those students interested in going on in biology it makes sense to get as good a background in chemistry as you can; this lecture will be based as much on why a given concept is important to your understanding of biology as on teaching the concept (obviously this is not a chemistry class/I am not a chemistry instructor so there is only so much that can be taught)

(c)                    Note how chemistry (and physics) pervades biology, representing a dominant subject over chapters 3, 4, 5, 6, 9, 10, 11 and 26, plus this chapter of your text

(d)                   This lecture will consider

(i)                     The stuff you are made of (elements)

(ii)                   Energy

(iii)                 Chemical bonding

(iv)                 That, in biology, form consistently follows function

(v)                   Chemical equilibrium

(vi)                 (for those of you with some interest, I will additionally include links to material considering the history of chemistry -- and no, not the history of chemists that you learn about in chemistry class -- but, briefly, the history of the chemicals and, especially, the elements themselves)

(e)                    Note: though we won't be covering chapter 2 in its entirety in this lecture, there nevertheless are a number of concepts covered in the text chapter that are worth either learning or reminding yourself of, because these concepts are considered in subsequent chapters; it's a short chapter (12 pages with lots of pictures), so do yourself a favor and read the whole thing

(f)                     Note: a number of you have not completed a college chemistry sequence so will not have taken enough college chemistry to fully grasp all of the chemistry that we will be covering in this course (i.e., that is covered by your text) -- translation: don't assume that you know enough chemistry to blow off the earlier chapters of this text (and to those who have taken their majors' chemistry sequence as well as some or all of organic chemistry: Enjoy!)

(g)                    [chemistry for biology (Google Search)] [index]

 

CHEMICALS

 

(3) Essential elements (see also essential elements)

(a)                    The essential elements are what organisms are made of

(b)                    The most prevalent elements in your body (96%) are Carbon, Oxygen, Hydrogen, Nitrogen (essentially the elements that make up water plus the organic compounds that together make up the bulk of organisms)

(c)                    An additional 7 elements make of the bulk of the remaining 4% (Ca, P, K, S, Na, Cl, Mg--no need to memorize); the rest of the elements found in your body are considered trace elements

(d)                   Additional elements, called trace elements, are found in smaller amounts but are nevertheless essential to continued and healthful existence (understand concept, don't memorize list found in text); these are many of the minerals found in your daily multivitamin and mineral supplements

(e)                    See Table, Naturally occurring elements in the human body

(f)                     ["essential elements" and chemistry (Google Search)] [index]

 

CHEMICAL BONDS

 

(4) Energy (waterfall analogy) (see also energy)

(a)                    Energy = capacity to do work

(b)                    Potential energy = stored energy

(c)                    Waterfall analogy:

(i)                     Water at the top of a waterfall has potential energy which is realized (as kinetic energy) when the water flows over the falls

(ii)                   It is possible to capture some of that energy, transducing (changing) it into a different form (e.g., mechanical energy if you place a turbine or water wheel in the path of the flowing water, or electrical energy if you attach a generator to the turbine)

(d)                   The transduction of energy from one form to another, and the use of that energy to move or to create complex structures (particularly babies) is what life is all about

(e)                    Bioenergetics is the study of the movement of energy within living organisms

(f)                     [energy and "capacity to do work", waterfall and energy (Google Search)] [index]

(5) Electrons store energy (see also electrons store energy)

(a)                    Within organisms, stored energy is associated with the electrons found within biomolecules

(b)                    More energy associated with an electron = greater distance that electron is found from the nucleus the electron is associated with

(c)                    Note that this concept is analogous to the waterfall analogy:

(i)                     Water that is further from the center of the Earth possesses more potential energy than water that is closer to the center of the Earth; electrons that are further from the center of the nucleus they are associated with possess more energy than electrons that are closer to the center of the nucleus they are associated with

(ii)                   During the movement of water toward the center of the Earth the water possesses/releases energy that may be captured; during the movement of electrons toward the nucleus of an atom, energy is also released (and this energy may also be captured)

(iii)                 Movement of water away from the center of the Earth requires an input of energy; movement of electrons away from the center of a nucleus also requires an input of energy

(d)                   See Figure, Energy levels of an atom's electrons

(e)                    Less simplistically, electrons actually exist within specific energy levels or electron shells which exist as probabilistic clouds surrounding nuclei and it is the quantum changes in the shape of these clouds that correspond to changes in the energy associated with an electron (bigger cloud = more energy, smaller cloud = less energy associated with that electron; thus, the collapse of a larger cloud to a smaller cloud is associated with a release of energy, etc.)

(f)                     Quantum mechanics is (at least in part) the study of the discrete storage of energy by electrons

(g)                    An important part of understanding life is understanding how energy is stored and moved from molecule to molecule (in fact, bioenergetics along with cell biology, genetics, evolution, and ecology arguably are the five most important general concepts you will learn in introductory biology)

(h)                    ["energy storage" and "chemical bonds" (Google Search)] [index]

(6) Chemical bonds (see also chemical bonds)

(a)                    When a chemical reaction occurs, what is happening is the making or breaking (or both) of chemical bonds

(b)                    Chemical bonds consist of electrons that are shared, more-or-less, between the nuclei of the bonded atoms

(c)                    Chemical bonds come in a variety of types that may be characterized in terms of the shapes of the probabilistic clouds and the related concept of the degree to which the electrons are shared evenly between the atoms (or otherwise "hogged" by one atom relative to another)

(d)                   The degree of sharing impacts on the energy associated with a chemical bond (and living things store most of their energy within chemical bonds); greater "hogging" by one atom relative to another results in a decrease in the electron's distance from an atomic nuclei (relatively so, at least) and therefore a decrease in the amount of energy stored by the electron; the degree of sharing also impacts on the strength of the chemical bond

(e)                    Chemical bonds vary in strength ranging from very strong to very weak

(i)                     Covalent bonds (strong)

(ii)                   Polar covalent bonds (strong)

(iii)                 Ionic bonds (weaker, at least within the aqueous environments found in organisms, where ions are surrounded by hydration shells)

(iv)                 Hydrogen bonds (weak)

(f)                     FAQ: 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.

(g)                    [chemical bonds (Google Search)] [index]

(7) Representing chemical bonds

(a)                    We will be looking at a number of structural formulas of molecules in which chemical bonds are shown (we will be showing a lot of these especially as we introduce carbohydrates, lipids, proteins, and nucleic acids)

(b)                   (as an example I will draw glucose on board/show as overhead [glucose model])

(c)                    We will have a tendency in this course to not explicitly show C-H bonds

(d)                   We will less-frequently employ molecular formulas, i.e., representations in which atoms are listed; e.g., C6H12O6 , a.k.a., C6(H2O)6 (a.k.a., a hexose, e.g., glucose)

(e)                    Single and double covalent bonds will represent as in the following examples: C-C, C-H, and C=O (not all H's shown)

(8) Valence electrons (see also valence electrons)

(a)                    Valence electrons are electrons found in the outer shells of elements

(b)                    Knowledge of valence electrons is fundamentally helpful for understanding chemistry in general, and the chemistry of organic molecules in particular (and understanding how organic molecules work is fundamental to understanding how life works (as we will see in chapter 4)

(c)                    See Figure, Electron configurations of the first 18 elements

(d)                   Note the valence of the following atoms: Hydrogen = 1, Oxygen = 2, Nitrogen = 3, Carbon = 4, Phosphorus = 5 (note, though, that phosphorous is weird, not always following the octet rule)

(e)                    See Figure, Covalent bonding in four molecules

(f)                     FAQ: 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 referred 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.

(g)                    [valence electrons (Google Search)] [index]

(9) Covalent bonds (see also covalent bond)

(a)                    Covalent bonds are the strongest of bonds

(b)                    Covalent bonds involve a sharing of electrons between atoms

(c)                    Example: C-C (carbon-to-carbon) bonds that form the basis of most biomolecules [carbon and the molecular diversity of life, the structure and function of macromolecules (MicroDude)] [index]

(d)                   Covalent bond in which electrons are somewhat evenly shared (e.g., C-C, C-H, O=O) are important for understanding hydrophobicity as well as the structure of most organic molecules

(e)                    See Figure, Covalent bonding in four molecules

(f)                     [covalent bonds (Google Search)] [index]

(10) Electronegativity (see also electronegativity)

(a)                    The concept of electronegativity is important for understanding properties of water, polarity, hydrogen bonding, etc.

(b)                    Electrons show a greater attraction for atoms (or ions) that display greater electronegativity

(c)                    If two atoms are chemically bonded together, then the atom with the greater electronegativity will pull the electron associated with that bond closer to it (i.e., it will "hog" the electron)

(d)                   Note that such bonds, consequently, will have less energy associated with them than an otherwise equivalent bond in which the electrons are shared evenly between the two atoms

(e)                    FAQ: 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. 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 also possesses comparatively significant electronegativity. This exceptional behavior results from hydrogen only possessing only a single electron and only a single proton. That is, though hydrogen's nuclear charge is small, nevertheless its electrons are held relatively close to its nucleus. Furthermore, hydrogen, like Carbon, Nitrogen, Oxygen, etc. but unlike other column 1 elements, can complete its 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 electron shell.

(f)                     [electronegativity (Google Search)] [index]

(11) Polar covalent bond (see also polar covalent bond)

(a)                    Within an aqueous environment, polar covalent bonds are intermediate in strength between ionic and covalent bonds

(b)                    Polar covalent bonds result when electrons are not shared equally between atoms

(c)                    Example: the O-H (oxygen-to-hydrogen) bonds in water

(d)                   Example: the N-H (nitrogen-to-hydrogen) bonds found in nucleic acids and proteins

(e)                    Polar covalent bonds are important for understanding hydrogen bonding (as well as the structure of most organic molecules)

(f)                     See Figure, Polar covalent bonds in a water molecule

(g)                    FAQ: 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.

(h)                    FAQ: 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, etc.). To judge degrees of polarity you have to know what the electronegativity of the two bonded 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 in the periodic table) the higher the electronegativity. Hydrogen turns out to be somewhat exceptional, possessing a much higher electronegativity 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. 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 with C-N, C-O, C=O, N-H, and especially O-H considered 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.

(i)                      [polar covalent bonds (Google Search)] [index]

(12) Ionic bonds (see also ionic bond)

(a)                    Ionic bonds involve less (often much less) sharing of electrons between atoms

(b)                    Ionic bonds result from one atom essentially giving an electron to another atom

(c)                    Ionic bonds are typically not as strong as covalent bonds (at least as found in an aqueous solution)

(d)                   Example: Na-Cl (sodium-to-chlorine) bonds in table salt

(e)                    Ionic bonds represent an extreme of polarity and are represented in biological systems as the salt bridges within proteins, etc. (many biomolecules are salts at physiological pHs and therefore capable of forming ionic bonds)

(f)                     See Figure, Electron transfer and ionic bonding

(g)                    FAQ: 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 takes on 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, such bonds are very polar. So polar, in fact, that we don't even refer to them as covalently bonded (since covalent bonding implies a sharing of electrons).

(h)                    [ionic bonds (Google Search)] [are ionic bonds polar or are they nonpolar? (MicroDude)] [index]

(13) Weak bonds (noncovalent interactions, noncovalent forces, noncovalent bonds) (see also weak bonds)

(a)                    Relatively weak chemical bonds are a necessary requirement for chemical-based dynamic system (such as living things) just as precisely machined and well lubricated parts are important for mechanical-based dynamic systems (e.g., a bicycle)

(b)                    This is because living things are constantly making and breaking chemical bonds

(c)                    Often the energy required to make or break these bonds may be supplied solely by the ambient heat of the environment (e.g., your body temperature)

(d)                   If chemical bonds were universally too strong, then this making and breaking of bonds would require too much energy for life to exist (i.e., we would all be rocks)

(e)                    The hydrogen bond is the signature example of a weak chemical bond that plays numerous and important roles in biological systems (and which we will consider in much more depth during our water lecture -- pardon the pun)

(f)                     ("Covalent bonding alone cannot begin to describe the complexity of molecular structure in biology. Much weaker interactions are responsible for most the elegant cellular architecture... These are the noncovalent interactions, also called noncovalent forces or noncovalent bonds, between ions, molecules, and parts of molecules. Consider macromolecules... The linear sequence of the atoms in a strand of DNA is maintained by the covalent bonds between them. But DNA also has a highly specific three-dimensional structure, which is stabilized by noncovalent interactions between different parts of the molecule. Similarly, every kind of protein is made up of covalently linked amino acids but is also folded into a specific molecular conformation by noncovalent forces. Proteins interact with other protein molecules or with DNA to form still more complex structures. All of this complexity is accounted for by a myriad of noncovalent interactions within and between macromolecules. Moving up a step in the organization of life, we note that the cytoplasm of a cell is itself a highly organized structure, also held together for the most part by noncovalent forces. What makes noncovalent interactions so important in biology and biochemistry? The key is [that] [b]iologically important noncovalent bonds are 10 to 100 times weaker [than the covalent bonds between carbon and hydrogen]. It is their very weakness that makes noncovalent bonds so essential, for it allows them to be continually broken and re-formed in the dynamic molecular interplay that is life. This interplay depends on rapid exchanges of molecular partners, which could not occur if intermolecular forces were so strong as to lock the molecules in conformation and in place." p. 25, Christopher K. Mathews and K. E. Van Holde, 1996, Biochemistry, Second Edition, Benjamin/Cummings Publishing Company)

(g)                    [weak chemical bonds, noncovalent interactions, noncovalent forces, noncovalent bonds (Google Search)] [index]

(14) Hydrogen bonds (see also hydrogen bond)

(a)                    Hydrogen bonds are both covalent-bond-like and ionic-bond-like but nevertheless are very weak

(b)                    Hydrogen bonds are a consequence of one atom in one molecule (or different part of the same molecule) having too much charge (due to participation in a polar covalent bond) and a second atom having too little charge (ditto)

(c)                    These polar covalent bonds give atoms partial charges and partially charged atoms attract other oppositely partially charged atoms

(d)                   Example: O-H...O-H where the dotted line represents a hydrogen bond between a hydrogen (italicized) and an oxygen atom (also italicized)

(i)                     the former (H) has a partial positive charge -- a partial loss of electron to the polar covalently bonded, not-italicized oxygen to the left

(ii)                   the latter (O) has a partial negative charge -- a partial gain of an electron from the polar covalently bonded, not italicized hydrogen to the right)

(e)                    [hydrogen bonds (Google Search)] [hydrogen bonding, hydrogen bond (MicroDude)] [index]

(f)                     See Figure, A hydrogen bond

(g)                    See Figure, Hydrogen bonds between water molecules

 

CHEMICAL STRUCTURE

 

(15) Form follows function

(a)                    Molecule shape is very important for the functioning of organisms, just as the shape of parts is very important for the proper functioning of a bicycle

(b)                    The shape and chemistry of a biomolecule together define its form which in turn helps define its function; change the shape or chemistry of a molecule, even subtly, and typically you will make that molecule nonfunctional

(c)                    See Figure, A molecular mimic

(d)                   A wonderful example of the role of form in function in living things is the cell membrane which we will begin discussing in chapter 5

(e)                    See Figure, The structure of a phospholipid

(f)                     See Figure, Two structures formed by self-assembly of phospholipids in aqueous environments

 

METABOLISM

 

(16) Metabolism (see also metabolism)

(a)                    The sum of all of the chemical reactions that go on in an organism represent that organism's metabolism

(b)                    This concept is dealt with in much greater depth in Chapter 6

(c)                    [metabolism (Google Search)] [index]

(17) Reactant (see also reactant)

(a)                    In all chemical reactions, those chemicals that represent the starting material are called reactants

(b)                    [reactant and chemistry (Google Search)] [index]

(18) Product (see also product)

(a)                    Similarly, those chemicals that result from the chemical reaction are called products

(b)                    [product and chemistry (Google Search)] [index]

(19) Reversible reactions (see also reversible reaction)

(a)                    Many chemical reactions of biological importance are reversible such that the products of one reaction serve as the reactants of the same chemical reaction operating in reverse (reversible reactions)

(b)                    For example, in your text there is an equation found on page 34:

(i)                     3H2 +N2 <==> 2NH3 (pardon my non-standard arrow usage)

(ii)                   In this equation the rate of the forward reaction (read left to right) is proportional to rate of collision between molecular hydrogen and molecular nitrogen

(iii)                 The rate of this collision is dependent on the concentrations of the two reactants

(iv)                 The rate of reverse reaction (read right to left) is an intrinsic property of ammonia (i.e., NH3)

(c)                    Another, very important example of a reversible reaction is the dissociation of water: H2O <==> OH- + H+

(d)                   [reversible reaction (Google Search)] [index]

(20) Chemical equilibria (see also chemical equilibrium)

(a)                    Dynamic equilibrium occurs when the rate of the forward reaction is exactly equal to the rate of the reverse reaction in a reversible reaction

(b)                    (dynamic equilibria is a subcategory of chemical equilibria; the only chemical equilibria we will be concerned with are dynamic equilibria; in a dynamic equilibrium the reactions continue to proceed but there is no net gain or net loss in either products or reactants; in a static equilibrium no reaction proceeds)

(c)                    For example, again see the last equation on page 34 (3H2 +N2 <==> 2NH3); in this chemical reaction the point of the dynamic chemical equilibrium between molecular hydrogen, molecular nitrogen, and ammonia occurs when the reactant concentration is sufficiently low than the rate of collision leading to ammonia formation exactly equals the intrinsic rate of ammonium reversion to its parent gasses (i.e., H2 and N2)

(d)                   Equilibrium represents maximum disorder (maximum entropy) (and minimal energy) and all processes move toward increased entropy (and minimal energy), unless energy is employed to counter this process locally; thus, a scientist says grace: "Thank-you to all those who increased in entropy -- in particular the sun -- so that we may have this food."

(e)                    ["chemical equilibria" or "chemical equilibrium" (Google Search)] [index]

 

COSMOLOGY, ETC.

 

(21) Chemical history (not responsible for on exam)

(a)                    The energy and matter that make up your bodies were formed during the cosmological expansion of the universe known as the big bang

(b)                    According to the inflationary-universe hypothesis, all of the energy in the universe (and then some) was created during a brief interval very early in the cosmic big-bang expansion

(c)                    All of the elements that make up your body condensed as the young universe cooled, first as hydrogen (and a little helium and lithium), then into stars

(d)                   To a cosmologist metals are elements larger (in atomic number) than hydrogen and metals are formed within large stars via a process known as fusion

(e)                    Explosion of these large stars (type I supernovae) results in the fusion of many elements including transuranic (heavier than uranium) elements

(f)                     Subsequent fission (splitting of atoms) resulted in the formation of all known elements not formed within stars, as well as the radioactive decay (and loss) of all not-naturally-occurring elements (including those heavier than uranium)

(g)                    These various elements exist within diffuse clouds of hydrogen as interstellar dust

(h)                    Further star formation via the condensation of these clouds of dust leads to accretion of dust particles into planetesimals which, in turn, collide (accrete) into larger bodies (planets)

(i)                      Most scientists assume that any planet that possesses liquid water, organic molecules, and a reasonable supply of energy either has, or has the potential to evolve life

(j)                      Important to the evolution of life is the existence of a reducing atmosphere, that is, very little molecular oxygen (i.e., O2), since molecular oxygen decomposes organic molecules and therefore is toxic to all life forms except those that have evolved mechanisms by which they are protected from the toxic effects of oxygen

(k)                    [cosmology (Google Search), "star formation" and introduction, supernova and "chemical evolution", planetary science, "reducing atmosphere" and earth (Google Search)] [index]

(l)                      For more on chemical history and cosmology see: [index]

(i)                     [Au + Au collisions at BNL's relativistic heavy ion collider ("an attempt to simulate the hot, dense quark gluon plasma that existed just after the big bang" 1999, Science 286:1251) ]

(ii)                   [history of earth (MicroDude)]

(iii)                 [the evolution of man (MicroDude)]

(iv)                 [origin of the universe (MicroDude)]

 

VOCABULARY

 

(22) Vocabulary [index]

(a)                    Chemical bonds

(b)                    Chemical equilibria

(c)                    Chemical history

(d)                   Covalent bonds

(e)                    Electronegativity

(f)                     Electrons store energy

(g)                    Energy

(h)                    Essential elements

(i)                      Form follows function

(j)                      Hydrogen bonds

(k)                    Ionic bonds

(l)                      Metabolism

(m)                  Polar covalent bond

(n)                    Product

(o)                    Reactant

(p)                    Reversible reactions

(q)                    Valence electrons

(r)                     Weak bonds

(23) Practice questions [index]

(a)                    Which of the following covalent bonds is most polar? (consider only the bond between the atoms shown)

(i)                     C-C

(ii)                   C-H

(iii)                 C=C

(iv)                 C-N

(v)                   O=O

(vi)                 H-H

(b)                    In terms of relative volume, describe the probabilistic cloud associated with an electron which has absorbed a quanta of energy (i.e., unit of energy, e.g., a photon) as compared to that associated with the same electron prior to its absorbing that quanta of energy.

(c)                    What kind of bonds make up the salt bridges that are found in the interior of proteins?

(d)                   Describe how energy is stored in a chemical bond such that more obtainable energy may be found in one bond (e.g., nonpolar covalent) versus another (e.g., polar covalent).

(e)                    What does dynamic chemical equilibrium mean?

(f)                     How many valence electrons does the element Carbon have? What is the valence of Carbon?

(g)                    Describe a dynamic equilibrium in terms of two reactants, A and B, and one product, C. Assume that the reaction moves forward as fast as A and B collide and moves backward as a function of the instability of C (i.e., A + B C, where the symbol is meant to indicate that this is a reversible reaction). Be certain, in your answer, to capture the essence of what a dynamic equilibrium is, and note that this essence consists of two components, one that distinguishes a dynamic equilibrium from a static one and the other that distinguishes the state of equilibrium from a state of disequilibrium.

(h)                    Circle all of the polar covalent bonds.

(i)                     H-H

(ii)                   C-H

(iii)                 O-H

(iv)                 N-H

(v)                   C-C

(i)                      Describe electrons and energy using the waterfall analogy. That is, water at the top of the falls is equivalent to an electron that ____________________.

(j)                      Chemical elements found in very small quantities in your body but which are essential to your continued and healthful existence (often acting as enzyme cofactors) are called __________ elements. ("essential" not answer)

(k)                    Given that this is an overly simplified depiction of an excited atom, nevertheless, which electron possesses the most potential energy?

(l)                      In very general terms, the making or breaking of a chemical bond is called a(n) _________.

(m)                  Match the element with the number of covalent bonds it tends to form when incorporated into organic molecules: Number of bonds = (a) 1, (b) 2, (c) 3, (d) 4, (e) 5, or (f) 6.

(i)                     Carbon

(ii)                   Hydrogen

(iii)                 Nitrogen (uncharged)

(iv)                 Oxygen

(n)                    In this representation of a very weak but nevertheless biologically significant chemical interaction (as indicated by the dots), label the partial charges associated with each atom (not all atoms or chemical bonds in the various molecules are necessarily shown): O-HO-H

(o)                    True or False, the trace elements make up approximately 4% of the typical human body.

(p)                    Describe potential energy in terms of either the waterfall analogy or in terms of electrons with probabilistic clouds.

(q)                    Order in terms of their number of valence electrons: Carbon, Hydrogen, Nitrogen, Oxygen, Phosphorus.

(r)                     Compare the amount of potential energy associated with a chemical bond, between a highly electronegative element and a much less electronegative element, to the bond between two atoms of (the same) highly electronegative element.

(s)                     When two atoms possess an excess of charge, in opposite directions, then those opposite charges attract. If those charges are full charges then we call this attraction an ionic bond (or salt bridge in the context of proteins within an aqueous environment). If those charges are only partial, however, then the strength of their attraction is greatly diminished, though still chemically and biologically relevant. The best studied of interactions between atoms possessing opposite partial charges, within water solutions, we have studied extensively. They are called __________ bonds.

(t)                     The unequal but strong (i.e., not weak) sharing of elections within a molecule (such as a monosaccharide) defines a __________ __________ bond.

(u)                    What is valence of the following atoms?

(i)                     Carbon: _____

(ii)                   Hydrogen: 1

(iii)                 Nitrogen: 3

(iv)                 Oxygen: _____

(v)                   Phosphorus: 5

(v)                    Compare an electron that has absorbed a quantum (unit) of energy to an otherwise identical electron that has not (note, mention a property of the more-energetic electron other than that it is more energetic).

(w)                  A chemical bond in which electrons are shared by atoms, but with one atom (the more electronegative) pulling the electrons closer to it, we describe as a __________ __________ bond. (note, looking for two-word answer)

(x)                    Which involves an attraction of full charges?

(i)                     Covalent bonds

(ii)                   Double bonds

(iii)                 Hydrogen bonds

(iv)                 Ionic bonds

(v)                   Polar covalent bonds

(y)                    In the waterfall analogy of energy storage and release, we can speak of potential energy, kinetic energy, and, ultimately, waste heat. Draw a waterfall indicating (unambiguously) where water possesses maximal potential energy but minimal kinetic energy.

(z)                    The dissociation of water (i.e., into OH- and H+) is a very important example of a __________ reaction in which the reaction involving the association and the reaction involving the dissociation of the two ions are typically found in balance (i.e., at chemical equilibrium). (Hint: we also described the reaction 3H2 +N2 <==> 2NH3 using similar terms.)

(24) Practice question answers [index]

(a)                    C-N. All the rest except C-H are technically not polar and C-H bonds are considered effectively not polar

(b)                    The probabilistic cloud associated with an electron which has absorbed a quantum of energy is bigger than that associated with the same electron prior to its absorbing that quanta of energy. More energy means farther away from the nucleus. Think of in terms of the waterfall analogy: The taller the falls, the more potential energy the water has as it begins to go over the falls. The more energy an electron has, the farther it is able to wander from the nucleus, and therefore the larger its probabilistic cloud. Absorption of a quantum of energy by an electron increases its potential energy. Understanding this will be very important for your understanding of bioenergetics.

(c)                    Ionic bounds

(d)                   Obtainable (usable) chemical energy is stored in bonds by orbiting electrons. The farther an electron is from its associated nucleus, the more energy it possesses. The closer an electron is to its associated nucleus, the less energy it possesses. Allowing an electron to fall to a lower, less energetic orbital thus results in a release of energy. In nonpolar covalent bonds, electrons are shared more or less equally between atoms, and therefore, within a covalent bond, maximally distant from each atom. In polar covalent bonds, one atom is pulling the electron closer to itself, implying that the electrons are no longer maximally distant (i.e., they are closer to one atom than to the other) and therefore are less energetic (as well as imparting a partial negative charge on the pulling atom and a partial positive charge on the atom at the other end of the bond).

(e)                    in a dynamic chemical equilibrium reactants are converted to products as fast as products are converted to reactants, thus resulting in no net increase in the concentration of either products or reactants, despite the continual occurrence of chemical reaction

(f)                     4 and 4

(g)                    At the dynamic equilibrium A and B are colliding to form C exactly as fast as C is disassociating to form A and B. In other words, the reaction is effectively going forward as fast as it is going backward because the concentration of A and B are such that their collisions occur exactly as fast as the concentration and instability of C results in the reformation of A and B. The two key concepts that must be mentioned are that the reactions are dynamically moving both forward and backward (i.e., this is not a static equilibrium) and that they are regenerating each other (A, B, and C) such that the concentrations of all three players are essentially constant (i.e., this is an equilibrium).

(h)                    (iii) and (iv) are the polar covalent bonds

(i)                      Is not in its ground state. Has adsorbed a quanta of energy. Possesses a larger probabilistic cloud than it otherwise might. Is farther from its associated nucleus than it would be were it not more energetic than it had been in its normal, resting state.

(j)                      Trace

(k)                    Electron D

(l)                      Chemical reactions

(m)                  (i) (d) 4, (ii) (a) 1, (iii) (c) 5, (iv) (b) 2

(n)                    all oxygens are partially negative while all hydrogens are partially positive in their charge

(o)                    False, it is these elements, Ca, P, K, S, Na, Cl, Mg, that make up about 4% of your body

(p)                    Water at the top of a waterfall has potential energy that is a consequence of its ability to fall some distance, relatively unimpeded, towards the center of the Earth; the same is true for electrons that have absorbed energy and are now found at a greater distance from their associated nucleus; they can reemit a quantum of energy and in the process fall towards their nucleus; this potential to reemit the quanta of energy means that the electrons, in their larger probabilistic cloud, possess a potential energy

(q)                    Hydrogen (1), Oxygen (2), Nitrogen (3), Carbon (4), Phosphorus (5)

(r)                     There is less energy associated with the chemical bond between the two different atoms than there is between the same atoms

(s)                     Hydrogen

(t)                     Polar covalent

(u)                    (i) 4, (iv) 2

(v)                    The more-energetic electron should be farther from the nucleus

(w)                  Polar covalent

(x)                    (iv) Ionic bonds

(y)                    The water with maximal potential energy but minimal kinetic energy can be found at the top of the falls, before the water enters the falls, i.e., while it is still sitting on bedrock

(z)                    Reversible

 

Chapter 2, Bio 113 questions:

 

(#) Chemical equilibrium represents maximum disorder. What does it mean for a chemical reaction to be in equilibrium? For example A + B D C + D?

 

A: It means that the rate that A reacts with B to form C and D is the same as the rate that C reacts with D to form A and B.

 

(#) What does the word metabolism mean?

 

A: Metabolism is the sum of all of the chemical reactions within a body/organism; Metabolism = anabolism + catabolism.

 

(#) Give an example of a hydrogen bond by showing all atoms involved to achieve a hydrogen bond (though you don't necessarily need to show all atoms associated with the molecules involved).

 

A: E.g., O-HO-H

 

(#) Why is it preferable that the bonds within the chemicals making up our body are relatively weak bonds rather than very, very strong bonds?

 

A: Since weak bonds are relatively easy to break (as well as form) it allows our metabolism to be much more dynamic than would be the case were these bonds much more difficult to break and form. There likely are other answers that are similarly good.

 

(#) What does it mean that nitrogen is more electronegative then hydrogen?

 

A: It means that nitrogen will tend to pull electrons away from hydrogen when the two atoms are bonded together; it means that when nitrogen and hydrogen are bonded together, nitrogen will take on a partial negative charge whereas hydrogen will take on a partial positive charge; etc.

 

(#) Give the number of valence electrons associated with the following: Hydrogen, Carbon, Phosphorus.

 

A: 1, 4, 5, respectively, which happens to be the same as the valence of each of these atoms.

 

(#) Water at the top of a waterfall has __________ which is realized (as kinetic energy) when the water flows over the falls.

 

A: potential energy

 

(#) Four elements together make up about 96% of the elements in our bodies. These four most-prevalent elements are __________, __________, __________, and __________. (Hint, all four are light elements found in a gaseous form in the Earth's atmosphere.)

 

A: Hydrogen, Carbon, Nitrogen, and Oxygen.