Important words and concepts from Chapter 9, Campbell & Reece, 2002 (1/30/2005):

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

 

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(1) Chapter Title: Cellular Respiration: Harvesting Chemical Energy

(a)                    Found at this site are additional pages of possibly related interest including: [energetics of life] [glycolysis and fermentation] [glycolysis in detail] [cellular respiration]

(b)                    Cellular respiration links include: [index]

(i)                     [cellular respiration: harvesting chemical energy, cellular respiration (Google Search)]

(ii)                   [metabolism problem set (The Biology Project)]

(c)                    Cellular respiration is how the body (i.e., cells) oxidizes carbon compounds and generates ATP

 

"BURNING" ORGANIC MOLECULES

 

(2) Oxidation of organic compounds (see also organic)

(a)                    The complete oxidation of an organic compound looks like this:

(i)                     Organic compound + O2 --> CO2 + H2O + energy (plus other components if more than C, H, and O are present in the original compound)

(b)                    Note how the reaction consists basically of the combination (chemical reaction) of the organic compound with some amount of oxygen

(c)                    This is followed by the chemical conversion of all carbons to carbon dioxide (CO2) and all hydrogens from the organic compound to water (H2O)

(d)                   Though activation energy is, of course, required to get this reaction started, ultimately there is a net gain in energy from the reaction... it is an exergonic reaction

(e)                    In biological systems, the steps involved in the oxidation of organic compounds are not nearly this simple, but ultimately the result is the same though with one major difference: the energy liberated during the oxidation of organic compounds by organisms is employed to generate ATP

(f)                     See Figure, Methane combustion as an energy-yielding redox reaction

(g)                    [oxidation of organic compounds (Google Search)] [index]

(3) Oxidation of glucose (complete) (see also glucose oxidation)

(a)                    Glucose (whose molecular formula is C6H12O6) is the organic compound typically employed to illustrate the oxidation of organic compounds in biological systems

(b)                    C6H12O6 + 6O2 --> 6CO2 + 6H2O + energy

(c)                    In biological systems, energy = ATP + heat

(d)                   Note that each carbon of glucose is converted to a CO2

(e)                    Note that each hydrogen of glucose is converted to 1/2 H2O

(f)                     (for the sake of completeness, note that each oxygen atom of glucose liberated during cellular respiration ultimately is found in CO2 and which are liberated just prior to (1/3) and then during (2/3) the Krebs citric acid cycle)

(g)                    [oxidation of glucose (Google Search)] [index]

(4) Oxidation of carbon (see also organic)

(a)                    Recall that carbon may be oxidized in subsequent steps characterized (or exemplified) by the following succession:

(i)                     CH4 (a.k.a., methane)

(ii)                   CH3OH (a.k.a., methanol)

(iii)                 CH2O (a.k.a., formaldehyde)

(iv)                 CHOOH (a.k.a., formic acid)

(v)                   CO2 (a.k.a., carbon dioxide)

(b)                    Keep in mind in the above succession that all that is being considered is the oxidation of carbon (i.e., the oxidation of hydrogens in the above examples were ignored)

(c)                    Note that as carbon is increasingly oxidized, fewer and fewer hydrogens are bound to the carbon

(i)                     The above succession's hydrogen count goes: 4, 4, 2, 2, 0

(ii)                   However, the number of hydrogens bound directly to carbon decreases with each step: 4, 3, 2, 1, 0

(d)                   Note that as carbon is increasingly oxidized, more and more oxygens are bound to carbon

(i)                     The above succession's oxygen count goes: 0, 1, 1, 2, 2

(ii)                   However, the number of oxygen-to-carbon bonds increases with each step: 0, 1, 2, 3, 4

(e)                    [oxidation of carbon (Google Search)] [index]

 

OXIDATION-REDUCTION

 

(5) Oxidation (see also oxidation)

(a)                    Oxidation is the movement of electrons away from an atom (or, more precisely, away from an atom's nucleus)

(b)                    Thus, when oxygen oxidizes something, it pulls the electrons away from that something and towards itself (in the process, oxygen, serving as an oxidizing agent, is itself reduced)

(c)                    Note that oxidation refers to this movement of electrons even when oxygen atoms are not involved in the process

(d)                   [oxidation (Google Search)] [index]

(6) Reduction (see also reduction)

(a)                    The movement of electrons towards an atom (or, more precisely, towards an atom's nucleus)

(b)                    Because carbon is not terribly electronegative, the reduction of (donation of electrons to) carbon tends to result in the formation of energy-rich bonds (e.g., C-C and C-H bonds)

(c)                    Why "reduction"? Think of reduction as the reduction in electrical charge (increasing negativity) an atom or molecule (or ion) experiences as it gains electrons

(d)                   Note, however, that reduction does not always result in a decline in electrical charge since protons often are donated to a compound simultaneously with the donation of electrons

(7) Redox reactions (oxidation-reduction reactions) (see also redox)

(a)                    In order for electrons to move away from something, they invariably move towards something else

(b)                    Consequently, oxidation and reduction tend to be coupled

(c)                    We abbreviate this coupling using the phrase "redox reaction" meaning chemical reactions in which both oxidation and reduction occur

(d)                   See Figure, Methane combustion as an energy-yielding redox reaction

(e)                    [The rusting of metals, the process involved in photography, the way living systems produce and utilize energy, and the operation of a car battery, are but a few examples of a very common and important type of chemical reaction. These chemical changes are all classified as "electron-transfer" or oxidation-reduction reactions. The term, oxidation , was derived from the observation that almost all elements reacted with oxygen to form compounds called, oxides. A typical example is the corrosion or rusting of iron... Reduction, was the term originally used to describe the removal of oxygen from metal ores, which "reduced" the metal ore to pure metal... Based on the two examples above, oxidation can be defined very simply as, the "addition" of oxygen; and reduction, as the "removal" of oxygen. But there is a lot more to "oxidation-reduction"... (Internet Chemistry)]

(f)                     [Oxidation-reduction reactions always involve a change in the oxidation state of the atoms or ions involved. This change in oxidation state is due to the "loss" or "gain" of electrons. The loss of electrons from an atom produces a positive oxidation state, while the gain of electrons results in negative oxidation states. (Internet Chemistry)]

(g)                    Oxidation/reduction links: [index]

(i)                     [oxidation-reduction, redox (Google Search)]

(ii)                   [oxidation/reduction (Internet Chemistry)]

(iii)                 [oxidation/reduction (Online Biology Book)]

(iv)                 [oxidation and reduction in organic chemistry (The Australian National University)]

(8) Oxidizing agent (see also oxidizing agent)

(a)                    A substance capable of stealing electrons (i.e., oxidizing another substance) is called an oxidizing agent

(b)                    Oxygen atoms tend to be good oxidizing agents

(c)                    [oxidizing agent (Google Search)] [index]

(9) Reducing agent (see also reducing agent)

(a)                    A substance that allows its electrons to be stolen (i.e., thereby reducing another substance) is called a reducing agent (i.e., reducing agents tend to donate there electrons to other substances)

(b)                    Substances with carbon-to-carbon and carbon-to-hydrogen bonds tend to be good reducing agents (well, good at reducing molecular oxygen, at least)

(c)                    For example, these substances can react with O2 thereby reducing oxygen (i.e., donating electrons to oxygen--in the process the reducing agent is oxidized, e.g., the carbon or the hydrogens)

(d)                   The more C-C or C-H bonds a substance has, the more that substance may be successively oxidized, e.g., upon reaction with oxygen

(e)                    [reducing agent (Google Search)] [index]

(10) Energy in bonds (see also energy in bonds)

(a)                    Recall that the farther an electron exists from the atom's it is associated with, the more energy that electron possesses (a generalization, sure, but let's attempt to avoid complicating things more than we have to)

(b)                    Highly electronegative atoms hold electrons more tightly to themselves than do less electronegative atoms

(c)                    Consequently, the electrons held by more-electronegative atoms/nuclei store less energy than the electrons that are held by less-electronegative atoms

(d)                   By the second law of thermodynamics, the transfer of an electron from a less electronegative atom to a more electronegative atom therefore must result in some transfer of energy from that electron to the surrounding environment

(e)                    Thus, the transfer of an electron from a C-H or C-C bond to a C-O or H-O bond must release energy

(f)                     That energy may be harnessed to do work, e.g.,

(i)                     ADP + Pi + energy --> ATP +H2O

(g)                    FAQ: What do you mean by "Energy in bonds"? When electrons are locked into chemical bonds, then 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 is associated with electrons locked into chemical bonds. Recall that the farther an electron is from the atomic nucleus, the more energy the electron contains (indeed, must contain). 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 is associated with electrons that are now farther from atomic nuclei than they otherwise might have been (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.

(h)                    [energy in bonds (Google Search)] [ATP links (MicroDude)] [index]

 

OXIDATION-REDUCTION IN CELLS

 

(11) Hydrogen atoms (see also hydrogen)

(a)                    H (hydrogen) = e- + H+

(b)                    In biological systems, electrons typically move around in conjunction with protons, i.e., electrons move around (or are moved around) as free hydrogen atoms

(c)                    [hydrogen atoms reduction (Google Search)] [index]

(12) NAD+ reduction (NADH) (see also NAD+ and NADH)

(a)                    NAD+ + 2e- + 2H+ --> NADH + H+

(b)                    NAD+ (a.k.a., nicotinamide adenine dinucleotide) is a biologically important oxidizing agent

(c)                    That is, NAD+ is an electron acceptor

(d)                   NAD+ receives electrons in pairs (see above reaction)

(e)                    NAD+ receives one proton while it receives its electrons

(f)                     The reduced form of NAD+ is NADH + H+ (note that both NADH and H+ are products of this reduction reaction, and that both protons are accounted for)

(g)                    See Figure, NAD+ as an electron shuttle

(h)                    [NAD reduction, nicotinamide adenine dinucleotide, nicotinamide adenine dinucleotide reduction (Google Search)] [NAD+/NADH image (Anabolism/Photosynthesis -- Biology for Engineers)] [index]

(13) Dehydrogenase (see also dehydrogenase and dehydrogenation)

(a)                    Enzymes called dehydrogenases are involved in these pair-wise oxidations of organic molecules

(b)                    For example: H-C-OH + NAD+ + dehydrogenase --> C=O + NADH + H+ + dehydrogenase

(i)                     Note the loss of 2 H's from H-C-OH

(ii)                   Note that, as shown, neither the structure H-C-OH nor C=O are complete molecules, i.e., two H's are missing from each

(iii)                 Note that the complete reaction between two one-carbon compounds would be: CH3OH + NAD+ + dehydrogenase --> CH2O + NADH + H+ + dehydrogenase (that is, note the removal of two hydrogen atoms and their acceptance by NAD+)

(iv)                 Note that dehydrogenase is found on both sides of the equation; that is, it is rejuvenated in the course of the reaction and thus, like all enzymes, truly is a catalyst in this regard

(c)                    The additional electrons now associated with NADH may be harnessed in subsequent reactions of cellular respiration to generate ATP

(d)                   See Figure, An introduction to electron transport chains

(e)                    [dehydrogenase (Google Search)] [index]

 

CELLULAR RESPIRATION

 

(14) Cellular respiration, overview (see also cellular respiration)

(a)                    See Figure, An overview of cellular respiration

(b)                    Cellular respiration is a series of chemical and physical processes which together serve to remove potential energy-containing electrons from organic compounds, use the energy thus liberated to generate ATP, and then donate these now energy-spent electrons to oxygen

(c)                    The steps of cellular respiration include:

(i)                     Glycolysis

(ii)                   Pyruvate oxidation (acetyl-CoA production)

(iii)                 Krebs (citric acid) cycle

(iv)                 Electron transport

(v)                   Chemiosmosis

(d)                   ATP is generated by two types of processes:

(i)                     Substrate-level phosphorylation

(ii)                   Oxidative phosphorylation

(iii)                 By far, in humans, oxidative phosphorylation is the more important of these processes in terms of total ATPs directly generated

(e)                    [cellular respiration (Google Search)] [cellular respiration links (MicroDude)] [index]

(15) Oxidative phosphorylation (1) (see also oxidative phosphorylation)

(a)                    Oxidative phosphorylation is the phosphorylation of ADP using a mechanism powered by reduced electrons which, once their potential energy has been removed, are ultimately donated to atoms of oxygen

(b)                    See Figure, An introduction to electron transport chains

(c)                    [oxidative phosphorylation (Google Search)] [oxidative phosphorylation links (MicroDude)] [index]

(16) Substrate-level phosphorylation (see also substrate-level phosphorylation)

(a)                    Substrate-level phosphorylation is the donation of a phosphate directly to ADP from a phosphorylated organic intermediate

(b)                   See Figure, Substrate-level phosphorylation

(c)                    Note the difference between oxidative phosphorylation and substrate-level phosphorylation:

(i)                     In oxidative phosphorylation the energy associated with electrons follows this path:

      Substrate (e.g., glyceraldehyde phosphate--Figure, A closer look at glycolysis)

      NADH + H+

      Electron transport system

      Chemiosmosis

      ATP

(ii)                   In substrate-level phosphorylation the energy associated with electrons follows this path:

      Phosphorylated substrate (e.g., 1, 3-biphosophoglycerate--Figure, A closer look at glycolysis)

      ATP

(d)                   Substrate-level phosphorylation occurs four times per glucose during glycolysis and again twice per glucose during the Krebs cycle

(e)                    [substrate-level phosphorylation (Google Search)] [index]

 

CELLUILAR RESPIRATION: GLYCOLYSIS

 

(17) Glycolysis (see also glycolysis)

(a)                    The reactions of glycolysis are the first reactions of cellular respiration

(b)                    Glycolysis occurs in the cytosol of eukaryotic cells (i.e., glycolysis does not occur in the mitochondrial matrix)

(c)                    Glycolysis involve the conversion of glucose to ATP, NADH + H+, and pyruvic acid

(d)                   ATP is generated in glycolysis only by substrate-level phosphorylation

(e)                    In cellular respiration, the NADH + H+ and pyruvic acid (a.k.a., pyruvate) are subsequently oxidized to generate additional ATPs; this subsequent oxidation occurs in the mitochondria

(f)                     [glycolysis (Google Search)] [glycolysis links (MicroDude)] [index]

(18) Glycolysis, overview (see also glycolysis and glucose stoichiometry)

(a)                    The following steps (and level of detail) of glycolysis I expect you to know (note that I use "P" to imply phosphate group and that lots of detail is ignored):

(i)                     C6 (a.k.a., glucose) + ATP --> C6-P + ADP

(ii)                   C6-P + ATP --> P-C6-P + ADP

(iii)                 P-C6-P --> 2C3-P (this is the sugar-splitting step)

(iv)                 (note: the stoichiometry of all of the following are 2 for every one glucose)

(v)                   C3-P + NAD+ + Pi --> P-C3-P + NADH + H+

(vi)                 P-C3-P + ADP --> C3-P + ATP

(vii)               C3-P + ADP --> C3 (a.k.a., pyruvate) + ATP

(b)                    For the above to have any meaning to you (i.e., to avoid rote memorization and instead to try giving understanding the process a chance), See Figure, A closer look at glycolysis

(c)                    The net ATP produced is two per glucose, i.e., 2 ATP are hydrolyzed and 4 ATP are produced per glucose per round of glycolysis

(d)                   Notice that all of the ATPs generated directly by glycolysis are generated via substrate-level phosphorylation

(e)                    See Figure, The energy input and output of glycolysis

(f)                     Don't forget that the primary "purpose" of glycolysis is the generation of ATP, NADH + H+, and pyruvate from glucose (i.e., from carbohydrate / from food)

 

CELLUILAR RESPIRATION: INSIDE MITOCHONDRIA

 

(19) Mitochondrion (see also mitochondria)

(a)                    The first post-glycolysis step of cellular respiration is the movement of pyruvic acid (pyruvate) from the cytosol into the matrix of the mitochondria

(b)                   See Figure, An overview of cellular respiration

(c)                    See Figure, Conversion of pyruvate to acetyl CoA, the junction between glycolysis and the Krebs cycle

(d)                   mitochondria4

(e)                    [mitochondria or mitochondrion (Google Search)] [index]

(20) Acetyl CoA (pyruvate oxidation) (see also pyruvate oxidation)

(a)                    Once in the mitochondria, the pyruvate is converted to acetyl CoA

(b)                    CoA is short for Coenzyme A, a compound that holds a two-carbon acetyl group (-CO-CH3) in a reactive state

(c)                    This conversion of pyruvate to acetyl CoA generates one CO2 and reduces one NAD+ (i.e., makes one NADH + H+) per pyruvate (i.e., twice per glucose)

(d)                   See Figure, Conversion of pyruvate to acetyl CoA, the junction between glycolysis and the Krebs cycle

(e)                    This is the first step of cellular respiration that generates a CO2

(f)                     CO2's are waste products of cellular respiration and represent the elimination as waste of one C and in the above reaction two O's from pyruvate

(g)                    [acetyl CoA, pyruvate oxidation (Google Search)] [index]

(21) Glucose stoichiometry (see also glucose stoichiometry)

(a)                    Keep in mind that there are two pyruvates per glucose and therefore two acetyl CoA's generated per glucose as well as two CO2's generated at this step

(b)                    All subsequence steps also have their stoichiometry doubled when considered on a per-glucose basis

(c)                    [glycolysis stoichiometry (Google Search)] [index]

(22) Krebs cycle (see also Krebs cycle)

(a)                    In the next step of cellular respiration acetyl CoA donates the two-carbon acetyl group to oxaloacetic acid to enter the Krebs cycle

(b)                    The product of the above reaction is citric acid (acetyl CoA + oxaloacetate --> citric acid/citrate + CoA-SH)

(c)                    See Figure, A closer look at the Krebs cycle

(d)                   This first/last step of the Krebs cycle involves the conversion of a four-carbon bicarboxylic acid to a six-carbon tricarboxylic acid, citric acid:

 

C -- COOH

|

HO - C -- COOH

|

C -- COOH

 

(e)                    The Krebs cycle is a mechanism whereby the acetyl group is oxidized to

(i)                     two CO2's (one for each carbon of the acetyl group)

(ii)                   three NADH + H+

(iii)                 one FADH2

(iv)                 one ATP (via substrate-level phosphorylation)

(f)                     See Figure, A summary of the Krebs cycle

(g)                    [Krebs cycle (Google Search)] [Krebs citric acid cycle: one turn of the cycle (2-D version) (3-D version) (start with the former, though the latter is very cool -- try manipulating the molecules with your mouse) (Metabolic Pathways in Biochemistry)] [Krebs cycle (Caduceus MCAT Review)] [index]

(23) FAD reduction (FADH2) (see also FAD and FADH2)

(a)                    FAD (flavin adenine dinucleotide) works similarly to NAD+

(i)                     FAD + 2e- + 2H+ --> FADH2

(b)                    A major difference is that FAD binds to electrons that hold less energy than the electrons that NAD+ binds

(c)                    [FAD reduction not diet not diets (Google Search)] [index]

(24) Not-yet-complete oxidation of glucose

(a)                    Following the oxidation of glucose to CO2's, cellular respiration has generated a net total of 4 ATP

(b)                    This is not yet a complete oxidation of glucose, however, since, although all electrons associated with glucose have been removed, these electrons have not yet been donated to oxygen to form water (i.e., what I mean by not-yet-complete oxidation is that not all of the original glucose's energy has been dissipated as heat or used to phosphorylate ADP)

(c)                    Instead, the electrons removed from glucose during its oxidation are still tied up in 10 NADH + H+ and 2 FADH2

(i)                     Two NAD+ were reduced during glycolysis

(ii)                   Two NAD+ were reduced during the oxidation of pyruvate to acetyl CoA, each, and

(iii)                 An additional three NAD+ were reduced during the Krebs cycle per pyruvic acid

(d)                   In order for glycolysis, generation of acetyl CoA, or Krebs cycle to continue, there must be a regeneration of NAD+

(e)                    In addition, the electrons stored in NADH + H+ and FADH2 can still provide quite a bit of energy capable of being harnessed to phosphorylate ATP

 

CELLUILAR RESPIRATION: CHEMIOSMOSIS

 

(25) Electron transport chain (electron transport system, ETS) (see also electron transport chain)

(a)                    The electrons carried by NADH + H+ or FADH2 are utilized via their donation to an electron transport chain (ETS)

(b)                   See Figure, An introduction to electron transport chains

(c)                    The ETS is a series of proteins and other compounds found in the mitochondria inner membrane

(d)                   Large numbers of copies of these compounds are accommodated in the inner membrane of the mitochondria via surface area-increasing infoldings called cristae (i.e., more folds allow more membrane allowing more ETS)

(e)                    The ETS is a series of these compounds that remove energy from these electrons in a series of oxidation-reduction reactions

(f)                     See Figure, Free-energy change during electron transport

(g)                    Note how FADH2 donates lower-energy electrons to this chain (i.e., farther down on the chain) than does NADH + H+; this is because FADH2's electrons are less energetic than those associated with NADH

(h)                    [chain or system "electron transport" (Google Search)] [index]

(26) Pumping hydrogen ions (pumping protons) (see also generation of proton motive force and proton pump)

(a)                    Some of the compounds in the ETS accept electrons along with the hydrogen ions associated with these electrons

(b)                    Other compounds of the ETS, on the other hand, accept electrons without the associated hydrogen ion

(c)                    All hydrogen ions (as well as electrons) are acquired from the mitochondrial matrix

(d)                   During donation from a compound that accepts hydrogen ions to one which does not accept hydrogen ions, something has to be done with the excess hydrogen ions

(e)                    These are released into the intermembrane space of the mitochondria

(f)                     Since hydrogen ions are moved during this process from the mitochondrial matrix to the mitochondrial intermembrane space, the ETS serves as a oxidation-reduction driven hydrogen ion (proton) pump

(g)                    This pumping of protons generates a hydrogen-ion electrochemical gradient

(h)                   See Figure, Chemiosmosis couples the electron transport chain to ATP synthesis

(i)                      [pumping hydrogen or proton or protons "electron transport" (Google Search)] [index]

(27) Proton-motive force (see also proton-motive force)

(a)                    Proton-motive force is the name given to the hydrogen ion electrochemical gradient produced by the ETS

(b)                    [proton motive force (Google Search)] [index]

(28) Reduction of O2 (see also reduction of oxygen)

(a)                    At the end of the ETS, electrons are now very depleted of energy

(b)                    The only common substance that will still accept these energy-depleted electrons is molecular oxygen

(c)                    See Figure, Chemiosmosis couples the electron transport chain to ATP synthesis

(d)                   Remember, oxygen atoms are very electronegative so are willing to accept electrons even if they are not very energetic (another way of stating this is that electrons that are bound to very electronegative atoms, in polar bonds, are not very energetic)

(e)                    We breathe, in part, in order to supply oxygen to our mitochondria (the other part is to remove the CO2 given off by our mitochondria; we are slaves to our mitochondria; who owns whom?)

(f)                     ["reduction of oxygen" and "electron transport" (Google Search)] [index]

(29) Final electron acceptor (see also final electron acceptor)

(a)                    Molecular oxygen thus serves as the final electron acceptor in cellular respiration

(b)                    Without oxygen serving as the final electron acceptors, electron transport chains would not have any way of getting rid of their excess, unenergetic electrons, and all of cellular respiration would back up and shut down

(c)                    See Figure, Chemiosmosis couples the electron transport chain to ATP synthesis

(d)                   [final electron acceptor (Google Search)] [index]

(30) Metabolic water (see also metabolic water)

(a)                    Along with two electrons, at the end of the ETS each oxygen atom also is combined with two hydrogen ions

(b)                    The net result is water (i.e., 2e- + 2H+ + 1/2O2 --> H2O)

(c)                    This water is termed metabolic (as in, metabolic water)

(d)                   Thus, one of the products of the complete oxidation of glucose is water which, of course, is as we expect (e.g., C6H12O6 + 6O2 --> 6CO2 + 6H2O + energy)

(e)                    [metabolic water (Google Search)] [index]

(31) Chemiosmosis (ATP synthase) (see also chemiosmosis and ATP synthase)

(a)                    Note that we've done a lot of manipulations starting with NADH + H+ and FADH2, but we still haven't generated a whole lot of additional ATP

(b)                    The way the ETS is linked to ATP synthesis is through the generation of the proton-motive force

(c)                    This proton-motive force drives in reverse an ATP-dependent proton pump, called ATP synthase, that is located in the inner membrane of the mitochondria

(d)                   See Figure, ATP synthase, a molecular mill

(e)                    Thus, protons are allowed back into the mitochondrial matrix, through this pump (running in reverse, i.e., not expending energy to pump protons but instead capturing the energy of the protons rushing through in the opposite direction), and ATP is the byproduct

(f)                     [chemiosmosis, ATP synthase (Google Search)] [ATP synthase links, ATP links (MicroDude)] [index]

(32) Oxidative phosphorylation (2) (see also oxidative phosphorylation)

(a)                    This use of an electron transport chain, coupled with hydrogen ion pumping, coupled with reduction of molecular oxygen, coupled with ATP generation via the harnessing of the hydrogen-ion electrochemical gradient are together termed oxidative phosphorylation

(b)                    Note how oxidative phosphorylation contrasts mechanistically with substrate-level phosphorylation

(c)                    In short hand (and it's anything but short), oxidative phosphorylation = glucose --> NADH --> ETS --> proton-motive force --> chemiosmosis --> ATP

(d)                   Substrate-level phosphorylation, instead, simply involves: substrate-P + ADP --> substrate + ATP

(e)                    Oxidative phosphorylation links: [index]

(i)                     [oxidative phosphorylation (Google Search)]

(ii)                   [aerobic respiration (Online Biology Book)]

(iii)                 [oxidative phosphorylation (graphic) (Metabolic Pathways in Biochemistry)]

(iv)                 [phosphorylation (Caduceus MCAT Review)]

 

CELLUILAR RESPIRATION: ATP BOOKKEEPING

 

(33) ATP bookkeeping

(a)                    On average, note the approximate number of ATP generated by each of the following:

(i)                     Substrate-level phosphorylation = 1 ATP

(ii)                   NADH = 3 ATP

(iii)                 FADH2 = 2 ATP

(b)                    Note that it takes one ATP to move each of the glycolysis-generated NADH into the matrix of the mitochondria

(c)                    (it makes sense that only the NADH would be moved in, not NADH + H+, since leaving the H+ outside the mitochondria prevents it from mitigating the proton-motive force--also note that when O2 is reduced to water then further H+ are sequestered within the matrix of the mitochondria, thus further adding to the proton-motive force)

(d)                   Glucose generates 2 ATP, 2 NADH + H+, and 2 pyruvate (net) via glycolysis

(e)                    Pyruvate generates 1 CO2, 1 NADH + H+, and 1 acetyl CoA upon conversion to acetyl CoA

(f)                     Acetyl CoA generates 2 CO2, 3 NADH + H+, 1 FADH2, and 1 ATP per turn of the Krebs cycle

(g)                    In total (net), then, there are 4 ATP, 10 NADH + H+, and 2 FADH2 generated during the oxidation of glucose to 6 CO2 less 2 ATP to pump the NADH from glycolysis into the mitochondria:

(i)                     4 ATP - 2 ATP + 30 ATP + 4 ATP = 36

(h)                   See Figure, Review: how each molecule of glucose yields many ATP molecules during cellular respiration

(i)                      ["ATP bookkeeping", cellular respiration bookkeeping (Google Search)] [index]

 

ATP GENERATION WITHOUT OXYGEN

 

(34) Anaerobic generation of ATP (see also fermentation and anaerobic respiration)

(a)                    Without oxygen, cellular respiration backs up and won't function

(b)                    Many organisms can still generate ATP from glucose, without oxygen present, by relying entirely on glycolysis

(c)                    Note that glycolysis only generates a total of two ATP, maximum, net, per glucose

(d)                   Two ATP, however, are a lot better than none

(e)                    (the above statements are a simplification; in truth there are many organisms, all different types of bacteria, that can use substances other than oxygen as final electron acceptors to their electron transport chains, but we will not delve here into these latter processes)

(f)                     [anaerobic generation of ATP (Google Search)] [fermentation links (MicroDude)] [index]

(35) Regeneration of NAD+ (see also NAD+ regeneration)

(a)                    Just as cellular respiration backs up in the absence of oxygen, glycolysis backs up in the absence of NAD+ regeneration

(b)                    In fact, NAD+ regeneration is one of the functions of the ETS

(c)                    [regeneration of NAD (Google Search)] [index]

(36) Organic final electron acceptor

(a)                    In the absence of oxygen, NAD+ is regenerated via the reduction of a non-oxygen compound

(b)                    That non-oxygen compound typically is pyruvate

(c)                    Pyruvate thus serves as the final electron acceptor in the anaerobic generation of ATP that occurs via the glycolytic pathway

(d)                   [organic final electron acceptor (Google Search)] [index]

(37) Fermentation (see also fermentation)

(a)                    Fermentation is the name given to this glycolytic generation of ATP employing an organic final electron acceptor

(b)                    Fermentation also involves the generation of waste products which typically accumulate in the fermenter's environment

(c)                    Such waste products are reduced products derived from pyruvic acid

(d)                   These waste products include such things as ethanol and carbon dioxide, or lactic acid

(e)                    See Figure, Fermentation

(f)                     {The word fermentation has a number of related meanings, depending on context. For the most part these meanings describe similar processes that involve either energy production in the absence of air or the associated production of byproducts (a.k.a. wastes, but often quite valuable to you or me). Historically (if not actually) all of the following have at their root fermentation as defined in its strictest (i.e., most scientific) sense (see definition numbers 5 & 6, below) (p. 124, Tortora et al., 1995, for definitions 1-5).

      Any process that produces alcoholic beverages or acidic dairy products (general use).

      Any spoilage of food by microorganism (general use).

      Any large-scale microbial process occurring with or without air (common definition used in industry).

      Any energy-releasing metabolic process that takes place only under anaerobic conditions (becoming more scientific).

      All metabolic processes that release energy from a sugar or other organic compound, do not require molecular oxygen or an electron transport system, and use an organic compound as the final electron acceptor.

      "An energy-yielding metabolic pathway that involves no net change in oxidation state." (p. 449, Christopher K. Mathews & K. E. Van Holde, 1996, Biochemistry, Second Edition, Benjamin/Cummings Publishing Company)

      "A chemical change with effervescence." (ditto)}

(g)                    [fermentation links (including links to the fermentation of various alcohol-containing beverages and food-fermentation links) (MicroDude)] [index]

(38) Facultative anaerobes (see also facultative anaerobe)

(a)                    Organisms that are able to generate ATP via either cellular respiration (when O2 is around) or via fermentation (when O2 is not present) are called facultative anaerobes

(b)                    An example of facultative anaerobes are our own muscles (lactic acid fermentation), many yeasts (alcohol fermentation), and many bacteria (numerous additional kinds of fermentation)

(c)                    [facultative anaerobes or anaerobe or anaerobic (Google Search)] [index]

 

VOCABULARY

 

(39) Vocabulary [index]

(a)                    Acetyl CoA

(b)                    Anaerobic generation of ATP

(c)                    ATP bookkeeping

(d)                   ATP synthase

(e)                    Cellular respiration, overview

(f)                     Chemiosmosis

(g)                    Dehydrogenase

(h)                    Electron transport chain

(i)                      Electron transport system

(j)                      Energy in bonds

(k)                    ETS

(l)                      Facultative anaerobes

(m)                  FAD reduction

(n)                    FADH2

(o)                    Fermentation

(p)                    Final electron acceptor

(q)                    Glucose stoichiometry

(r)                     Glycolysis

(s)                     Glycolysis, overview

(t)                     Glycolysis, summary

(u)                    Hydrogen atoms

(v)                    Krebs cycle

(w)                  Metabolic water

(x)                    NAD+ reduction

(y)                    NADH

(z)                    Not-yet-complete oxidation of glucose

(aa)                 Organic final electron acceptor

(bb)                Oxidation

(cc)                 Oxidation of carbon

(dd)               Oxidation of glucose

(ee)                 Oxidation of organic compounds

(ff)                  Oxidation-reduction reactions

(gg)                Oxidative phosphorylation (1)

(hh)                Oxidative phosphorylation (2)

(ii)                    Oxidizing agent

(jj)                    Proton-motive force

(kk)                Pumping hydrogen ions

(ll)                    Pumping protons

(mm)            Pyruvate oxidation

(nn)                Redox reactions

(oo)                Reducing agent

(pp)                Reduction

(qq)                Reduction of O2

(rr)                   Regeneration of NAD+

(ss)                  Substrate-level phosphorylation

(40) Practice questions [index]

(a)                    What is the role of NAD+ in glycolysis? (note that I did not ask what the role of NAD+ is in cellular respiration, but instead have limited the question to what is its role in glycolysis)

(b)                    Given an organism that can use glycolysis but is unable to use cellular respiration pathways given a lack of oxygen (an example is our own muscles during anaerobic exercise), what is the most important (i.e., immediately useful) chemical product of glycolysis?

(c)                    What is the overall (balanced) equation of the complete oxidation of glucose? Remember to place "energy" in its proper place.

(d)                   What fraction of the CO2 you exhale is generated during the Krebs cycle (i.e., during the conversion of acetyl CoA to CO2)? Assume that the CO2 you exhale is derived only from the cellular respiration of glucose. [Bonus point if you can tell me why this assumption is flawed, beyond that things other than glucose can be catabolized by your body, i.e., what is it about the catabolism of things other than glucose that could result in a modification of your answer to this question?]

(e)                    What, specifically, connects electron transport to the protein-mediated phosphorylation of ADP in oxidative phosphorylation?

(f)                     What fraction of the ATPs generated by the cellular respiration of glucose are generated by substrate-level phosphorylation? [Hint #1: To answer this question you need to consider the gross total of ADP phosphorylated, NOT net total!!!! Hint #2: This means that you should not be subtracting from your calculations the ATPs employed to motivate the various steps of cellular respiration forward. Hint #3: Do not forget that I asked for the fraction of ATPs generated by substrate-level phosphorylation of all ATPs generated during cellular respiration, not simply the total generated by substrate-level phosphorylation.]

(g)                    In general, how do heterotrophs regenerate NAD+ during fermentation?

(h)                    True or false, substrate level phosphorylation occurs before the carbon oxidation step of glycolysis.

(i)                      Where does mitochondrion-generated metabolic water come from (i.e., what chemical reaction/process generates water; the answer is not, "The oxidation of glucose," or some such variation on this theme; I'm looking for a very specific chemical reaction that occurs, in eukaryotes, solely within the matrix of mitochondria)?

(j)                      The complete oxidation of glucose yields what compounds in what stoichiometry (i.e., number per glucose)? Assume this oxidation is occurring as you burn glucose in air (i.e., don't worry about the ATPs or NADHs, etc. that are specific to the catabolism of glucose within cells).

(k)                    Which molecule is more oxidized?

 

A.

B.

C.

D.

OH

|

O=C

|

H-C-H

|

H-C-H

|

C=O

|

OH

OH

|

H-C-H

|

H-C-H

|

H-C-H

|

C=O

|

OH

OH

|

O=C

|

C=O

|

H-C-H

|

C=O

|

OH

OH

|

O=C

|

H-C-OH

|

H-C-H

|

C=O

|

OH

(l)                      Show a specific chemical reaction that is plausibly catalyzed by a dehydrogenase. Try to keep it simple but do show all chemical players.

(m)                  What percentage of ATPs produced directly by glycolysis are products of oxidative phosphorylation?

(n)                    In glycolysis, keeping with the same level of detail, fill in what is missing in the following reaction:

 

C3-P + NAD+ + __________ --> __________ + NADH + H+

 

(o)                    What fraction of CO2's generated by cellular respiration are generated specifically by the Krebs cycle?

(p)                    How many ATP's are on average generated from the H+ pumped by the electron transport chain per NADH?

(q)                    The specific term used to describe how the electron transport system is linked to an ATP-dependent proton pump in chemiosmosis is ___________.

(r)                     Name two molecules that are reduced over the course of cellular respiration (i.e., glycolysis followed by oxidative phosphorylation).

(s)                     The final electron acceptor in fermentations is __________.

(t)                     How many ATP's are generated per glucose, net, in a typical lactic acid fermentation?

(u)                    Because they can generate ATPs when oxygen is not present, but can utilize oxidative phosphorylation when oxygen is present, organisms such as yeasts, many bacteria, and your own muscle cells may be described as __________.

(v)                    In cellular respiration, per starting glucose how many ATPs and GTPs, gross, are generated by substrate-level phosphorylation? Remember that gross means the total number generated with no consideration of number subsequently or previously lost to motivate the process along.

(w)                  In cellular respiration, where specifically in the cell does the oxidation of pyruvate occur?

(x)                    Acetyl CoA reacts with oxaloacetic acid at the start of the Krebs cycle to generate what organic compound?

(y)                    The oxidation of methanol via NAD+ gives rise to what? Draw the structural formula of this product. Methanol's molecular formula is CH4O.

(z)                    The electron transport chain in humans ends with the reduction of what molecule?

(aa)                 Name three oxidizing agents employed in cellular respiration.

(bb)                Why, in biological systems, does oxidation and reduction often (though not always) occurs with no net change in charge of the molecular species involved?

(cc)                 What kinds of enzyme catalyzes reactions such as: H-C-OH + NAD+ --> C=O + NADH + H+

(dd)               Fill in the blank: Cellular respiration involves: glycolysis, pyruvate oxidation and acetyl CoA production, the Krebs citric acid cycle, electron transport, and __________.

(ee)                 In substrate-level phosphorylation, what is the phosphate donor?

(ff)                  Name the three intervening steps, in order, that occur during the majority of oxidative phosphorylations on the path from substrate to ATP generation. Note that glycolysis, the Krebs cycle, etc. serve to generate the already mentioned substrates so they and their ilk are not answers. Note also that the first of these steps is a chemical reaction while the last two are more complicated than that (i.e., are complex chemical and physical processes... and no, while a proton-motive force is certainly a component of these processes, it is not one of the three answers). Please try to employ the common names for these last two processes rather than a complicated description.

(gg)                Complete this reaction of glycolysis: C3-P + NAD+ + __________ --> __________ + NADH + H+

(hh)                Complete this reaction: pyruvate + __________ + coenzyme A --> acetyl CoA + __________ + __________ + H+

(ii)                    How many CO2's are given off per turn of the Krebs cycle?

(jj)                    If we consider cellular respiration to progress sequentially, then how many substrate-level phosphorylations have occurred, per starting glucose, by the time glucose has been completely converted to CO2 and water?

(kk)                Where is the cellular respiration electron transport chain located?

(ll)                    What is done with the excess of hydrogen ions that electron transport system members fail to accept in the normal course of mitochondrial electron transport?

(mm)            What is the name given to the electrochemical gradient generated in the course of cellular respiration?

(nn)                Explain where the different substances come from in the chemical reaction that generates metabolic water.

(oo)                Considering both substrate-level phosphorylation and the oxidative phosphorylation that eventually occurs, how many ATPs does one turn of the Krebs cycle generate? (assume standard ATP estimations from chemiosmosis)

(pp)                How do facultative anaerobes regenerate their NAD+ when oxygen isn't present?

(qq)                In the complete oxidation of glucose, ultimately all carbons are found incorporated into what molecule?

(rr)                   Balance the equation: C6H12O6 + XO2 -> YCO2 + ZH2O + energy

(ss)                  Name/draw an inorganic compound in which oxygen has been oxidized relative to its state found within H2O.

(tt)                   The reduction of a compound in a biological system does not always result in an increase in a negative charge because __________ are typically acquired by electron acceptors such as FAD along with electrons.

(uu)                Which bond is most energetic? (that is, possesses the most biologically available chemical energy)

(i)                     C=O

(ii)                   C-H

(iii)                 C-N

(iv)                 C-O

(v)                   O-H

(vv)                Name a biologically important electron acceptor employed, for example, during the Krebs citric acid cycle.

(ww)            What is a dehydrogenase? Be specific including indicating what it does.

(xx)                In which are ATPs generated by substrate-level phosphorylation? (choose all that apply)

(i)                     Chemiosmosis

(ii)                   Electron transport

(iii)                 Glycolysis

(iv)                 Krebs citric acid cycle

(v)                   Pyruvate oxidation (acetyl CoA production)

(yy)                In which steps are CO2's generated? (choose all that apply)

(i)                     Chemiosmosis

(ii)                   Electron transport

(iii)                 Glycolysis

(iv)                 Krebs citric acid cycle

(v)                   Pyruvate oxidation (acetyl CoA production)

(zz)                 Arrange in order:

(i)                     Chemiosmosis

(ii)                   Electron transport

(iii)                 Glycolysis

(iv)                 Krebs citric acid cycle

(v)                   Pyruvate oxidation (acetyl CoA production)

(aaa)             Indicate during which step the most ATPs are actually, physically generated.

(i)                     Chemiosmosis

(ii)                   Electron transport

(iii)                 Glycolysis

(iv)                 Krebs citric acid cycle

(v)                   Pyruvate oxidation (acetyl CoA production)

(bbb)            What aspect of cellular respiration occurs in the Eukaryote cell cytoplasm rather than within the mitochondria?

(i)                     Chemiosmosis

(ii)                   Electron transport

(iii)                 Glycolysis

(iv)                 Krebs citric acid cycle

(v)                   Pyruvate oxidation (acetyl CoA production)

(ccc)             If the overall reaction is C6 + ATP -> C6-P + ADP; C6-P + ATP -> P-C6-P + ADP; P-C6-P + 2NAD+ + 2Pi + 4 ADP -> 2C3 + 4ATP + 2 NADH + 2H+, then complete the following specific reaction: C3-P + __________ + __________ -> P-C3-P + __________ + H+.

(ddd)          Where physically in a cell does one find the compound acetyl CoA? Be specific.

(eee)             Why do we go through two turns of the Krebs cycle per glucose that enters glycolysis?

(fff)               During the complete oxidation of glucose during cellular respiration (including glycolysis) a grand total of how many NADH are generated? (note that for those of you who are worried about NADH transportation costs, I'm assuming that "generated" is not necessarily synonymous with "presented to the electron transport system")

(i)                     2

(ii)                   4

(iii)                 6

(iv)                 8

(v)                   10

(ggg)            What do cristae and ETS have to do with one another?

(hhh)            The excess hydrogen ions during electron transport are deposited into the __________.

(i)                     Cytoplasm

(ii)                   Endoplasmic reticulum

(iii)                 Intermembrane space

(iv)                 Matrix

(v)                   Outer membrane

(iii)                  Which is most intimately (closely/directly) involved in the reduction of O2?

(i)                     Generation of CO2

(ii)                   Intermembrane space

(iii)                 Phosphofructokinase

(iv)                 Proton-motive force

(v)                   Substrate-level phosphorylation

(jjj)                  In the generation of metabolic water in the accompanying figure, what is the name of the physical location in the mitochondria in which the generating reaction occurs? (might want to modify figure) mitochondria4

(kkk)            In mitochondria, give the name of a specific protein that is involved in depleting the proton-motive force.

(lll)                  What do such small carbon-containing compounds as ethanol, carbon dioxide, and lactic acid have in common such that they may be associated in some manner with the compound pyruvate?

(mmm)      Chemically, why is O2 toxic?

(nnn)            Which occurs soonest, subsequently, in the same biochemical pathway as that shown in the figure? glucose-6

(i)                     ADP + Pi + energy --> ATP

(ii)                   Completion of dark reaction of photosynthesis

(iii)                 Doubly phosphated sugar

(iv)                 Oxidative phosphorylation

(v)                   Regeneration of NAD+

(ooo)            The energy liberated during the oxidation of organic compounds by organisms is employed to generate ___________.

(ppp)            In the complete oxidation of glucose, each carbon is converted into what compound?

(qqq)            The majority of release of CO2 during cellular respiration (given glucose as the fuel) occurs during what biochemical pathway?

(rrr)                Name two oxidizing agents, other than O2, commonly employed by cells.

(sss)               How many (total) electrons does one NAD+ ion receive?

(i)                     0

(ii)                   1

(iii)                 2

(iv)                 3

(v)                   4

(ttt)                Indicate which is the more reduced form:

(i)                     CH3OH or CH2O

(ii)                   FADH2 or FAD

(iii)                 Fe2+ or Fe3+

(iv)                 NAD+ or NADH + H+

(uuu)            What is the principal function of an enzyme designated as a dehydrogenase?

(vvv)            What is the generic name of an enzyme that can catalyzes the reaction, H-C-OH + NAD+ --> C=O + NADH + H+ (not all atoms associated with substrates or products are necessarily shown)?

(www)      Arrange the following in the proper order for the cellular respiration of glucose:

(i)                     Chemiosmosis

(ii)                   Electron transport

(iii)                 Glycolysis

(iv)                 Krebs cycle

(v)                   Pyruvate oxidation

(xxx)            During cellular respiration ATP is generated using two fundamentally different mechanisms, termed oxidative phosphorylation and __________.

(yyy)            Pyruvate serves as the final product of the biochemical pathway called __________.

(zzz)             How many NADH are produced per glucose by glycolysis?

(aaaa)          Pyruvate oxidation to acetyl CoA physically occurs where within a cell?

(bbbb)        How many carbon atoms does the acetyl portion of a single acetyl CoA contain?

(cccc)          What is the name of this substance?

 

C -- COOH

|

HO - C -- COOH

|

C -- COOH

 

(dddd)      Where, physically, is the electron transport chain located?

(eeee)          In electron-transport-mediated proton pumping, all of the hydrogen ions are acquired specifically from where?

(ffff)            The ETS serves as a oxidation-reduction driven __________ pump.

(gggg)        What is metabolic water? That is, what specific chemical reaction gives rise to it?

(hhhh)        This use of an electron transport chain, coupled with hydrogen ion pumping, coupled with reduction of molecular oxygen, coupled with ATP generation via the harnessing of the hydrogen-ion electrochemical gradient are together termed __________ phosphorylation.

(iiii)                In cellular respiration each acetyl CoA generated 2 CO2, _____ NADH, _____ FADH2, and _____ ATP (or equivalent) by substrate-level phosphorylation.

(jjjj)                The general term for the regeneration of NAD+ via the reduction of pyruvate is __________.

(kkkk)        Because they can generate ATP either via cellular respiration (oxidative phosphorylation) or by employing glycolysis linked with a fermentation pathway, such cells as those found in our own skeletal muscles, yeasts (that we employ to make bread and beer), and many bacteria (including Escherichia coli) may be described as __________ anaerobes.

(llll)                For cellular respiration from Glucose through its complete oxidation including the reduction of molecular oxygen, indicate (i) all of the types of molecules net produced (i.e., the cellular respiration end/final products). (ii) Indicate the numbers produced per glucose (assuming human cell metabolism). (iii) Give the names of at least four non-protein organic intermediates (e.g., Glucose-6-phosphate is an example of an organic non-protein intermediate as are various additional intermediates of the Krebs cycle, glycolysis, etc.--but don't use G6P as one of your answers). Note, neither nicotinamide adenine dinucleotide nor flavin adenine dinucleotide, in either their oxidized or reduced forms, are answers to this question. Part (iii) also should not be answered with the names of any nucleic acids.

(mmmm)                        What is the complete, balanced equation for the complete oxidation of glucose, e.g., as would occur during the burning of glucose in air.

(nnnn)        For the complete oxidation of an organic compound, e.g., C6H12O6 + 6O2 --> 6CO2 + 6H2O, indicate which atoms have been oxidized and which reduced.

(oooo)        Besides oxygen, name a biologically important oxidizing agent.

(pppp)        What is the complete equation for the reduction of nicotinamide adenine dinucleotide?

(qqqq)        The reduction of what is catalyzed by an enzyme described as a dehydrogenase?

(rrrr)              Which occurs first in the course of cellular respiration?

(i)                     Chemiosmosis

(ii)                   CO2 liberation

(iii)                 Electron transport on electron transport chain

(iv)                 Pyruvate oxidation

(v)                   Substrate-level phosphorylation

(ssss)            Fill in the blanks in these equations describing glycolysis:

(i)                     C6 + ATP --> C6-P + ADP

(ii)                   C6-P + ATP --> P-C6-P + ADP

(iii)                 P-C6-P --> __________

(iv)                 C3-P + NAD+ + Pi --> P-C3-P + NADH + H+

(v)                   P-C3-P + __________ --> C3-P + __________

(vi)                 C3-P + ADP --> C3 + ATP

(tttt)              In the following reactions describing glycolysis, what is the name (or structural formula) of the final three-carbon compound?

(i)                     C6 (a.k.a., glucose) + ATP --> C6-P + ADP

(ii)                   C6-P + ATP --> P-C6-P + ADP

(iii)                 P-C6-P --> 2C3-P (this is the sugar-splitting step)

(iv)                 (note: the stoichiometry of all of the following are 2 for every one glucose)

(v)                   C3-P + NAD+ + Pi --> P-C3-P + NADH + H+

(vi)                 P-C3-P + ADP --> C3-P + ATP

(vii)               C3-P + ADP --> C3 (a.k.a., __________) + ATP

(uuuu)        The conversion of pyruvate to acetyl CoA occurs specifically where in a eukaryotic cell?

(vvvv)        How many CO2's per glucose, in the course of cellular respiration, are generated upon the Acetyl CoA synthesis?

(wwww)                        Name this compound:

 

C -- COOH

|

HO - C -- COOH

|

C -- COOH

 

 

(xxxx)        During what step of cellular respiration is FAD converted to FADH2?

(yyyy)        In cellular respiration, post Krebs cycle, how many NADH and FADH2 molecules have been generated per glucose?

(zzzz)          Where, specifically, does one find the proteins and other compounds that make up the electron transport system employed by eukaryotes during cellular respiration?

(aaaaa)      The energy associated with electrons during electron transport down the electron transport chain in mitochondria is directly used to generate what?

(bbbbb)    What serves as the final electron acceptor during cellular respiration?

(ccccc)      Where does "metabolic water" come from?

(ddddd) What is the name of the protein that is employed to transduce the proton motive force into energy employed to phosphorylate ADP?

(eeeee)      If we assume 3 ATPs per NADH and 2 ATPs per FADH2, then how many ATPs (or ATP equivalents) are generated as a consequence of one turn of the Krebs cycle?

(fffff)         In the absence of oxygen, how is NAD+ regenerated?

(ggggg)    In terms of ATP generation, what is a facultative anaerobe?

(hhhhh)    (bonus) What are the two missing components?

(iiiii)              In the complete oxidation of a hydrocarbon, what are the fates of the atoms involved (i.e., what chemical species--molecules--are they ultimately found in)? Assume that only three different types of atoms are involved in such a chemical reaction.

(jjjjj)              What is the definition of "reducing agent"?

(kkkkk)    What does NAD+ strip from biomolecules?

(lllll)              What, specifically, do dehydrogenases catalyze?

(mmmmm)                  Order the following (i.e.,. in terms of the order in which they must occur over the course of cellular respiration):

(i)                     Chemiosmosis

(ii)                   Electron transport

(iii)                 Glycolysis

(iv)                 Krebs (citric acid) cycle

(v)                   Pyruvate oxidation (acetyl CoA production)

(nnnnn)    Which of the following occurs in the cytosol?

(i)                     Chemiosmosis

(ii)                   Electron transport

(iii)                 Glycolysis

(iv)                 Krebs (citric acid) cycle

(v)                   Pyruvate oxidation (acetyl CoA production)

(ooooo)    Complete this reaction: C3-P + __________ + __________ --> P-C3-P + __________ + H+

(ppppp)    What role does acetyl CoA play in cellular respiration?

(qqqqq)    Citric acid consists of a three-carbon backbone to which three carboxyl groups and one hydroxyl group is attached. Draw citric acid (also known as tricarboxylic acid).

(rrrrr)           In one turn of the Krebs cycle citric acid is converted into oxaloacetic acid. What are the other products (with correct stoichiometry) of the Krebs cycle. Name them all with stoichiometry equivalent to that produced by one turn of the Krebs cycle. Disregard in your calculation any subsequent steps such as electron transport.

(sssss)         The useful energy extracted from electrons in the electron transport system is employed to immediately do what? (i.e., what is the immediate consequence of electron transfer in terms of energy transfer)

(ttttt)           What serves as the final electron acceptor in cellular respiration?

(uuuuu)    What is "metabolic water"?

(vvvvv)    What is ATP synthase?

(wwwww)                  Please describe (in detail) the bookkeeping underlying the generation of 36 ATP in the course of a complete oxidation of glucose via cellular respiration. That is, how many are produced, how, and where per glucose.

(xxxxx)    In the anaerobic generation of ATP via the glycolytic pathway, what serves as the final electron acceptor?

(yyyyy)    What property of an organism would allow us to call it a facultative anaerobe?

(41) Practice question answers [index]

(a)                    It serves as an oxidizing agent; its role in cellular respiration is in addition as a carrier or reduced electrons.

(b)                    ATP.

(c)                    C6H12O6 + 6O2 --> 6CO2 + 6H2O + energy.

(d)                   2/3; things other than glucose are broken down via cellular respiration and these things enter catabolism at points other than at or prior to pyruvate. For example, for fatty acids all of the CO2 is generated during the Krebs cycle.

(e)                    proton-motive force; pumping of protons to create proton electrochemical gradient which is then harnessed via the ATP-dependent proton pump running in reverse to phosphorylate ADP

(f)                     A total of 6 ATP are generated by substrate-level phosphorylation (4 during glycolysis and 2 during the Krebs cycle). A total of 40 ATP are generated (gross) during the cellular respiration of glucose. Therefore, the fraction generated by substrate-level phosphorylation is 6/40 = 3/20. Note that this is not a trick question since there is no hard and fast reason to assume that NADH transport into the mitochondria (2 ATP per glucose) and the priming of glycolysis (2 ATP per glucose) are achieved via the utilization of ATPs generated by substrate-level phosphorylation versus oxidative phosphorylation. Therefore, it would be misleading to claim that, for example, the answer to this question might be 4/36 = 1/9, i.e., basing your answer on some sort of determination of net generation of ATP.

(g)                    By employing pyruvate as a final electron acceptor.

(h)                    False, all of the substrate-level phosphorylation steps occur after NAD+ oxidizes glyceraldehyde-3-phosphate.

(i)                      The reduction of molecular oxygen by the electron transport chain.

(j)                      6CO2 and 6H2O from each glucose (a.k.a., (CH2O)6)

(k)                    C (A has 6 C-O bonds; B has 4; C has 8; D has 7)

(l)                      e.g., CH3OH + NAD+ --> CH2O (i.e., H2C=O) + NADH + H+

(m)                  0%

(n)                    Pi and P-C3-P, respectively

(o)                    2/3

(p)                    3, i.e., three ATP's generated via oxidative phosphorylation per NADH

(q)                    proton-motive force

(r)                     the easy ones are NAD+ and FAD. Others included the various members of the ETS as well as oxygen

(s)                     pyruvate/an organic compound

(t)                     2 net, 4 gross

(u)                    facultative anaerobes

(v)                    6 (4 during glycolysis and 1 for each turn of the Krebs cycle)

(w)                  the matrix of the mitochondria

(x)                    citric acid

(y)                    H2C=O

(z)                    O2

(aa)                 O2, NAD+, FAD

(bb)                Because electrons tend to be transferred along with oppositely charged protons

(cc)                 Dehydrogenases

(dd)               Chemiosmosis

(ee)                 A substrate (i.e., not a proton-motive force)

(ff)                  NADH + H+ --> electron transport chain --> chemiosmosis

(gg)                Pi, P-C3-P

(hh)                NAD+, CO2, NADH

(ii)                    2

(jj)                    four in glycolysis and two in the Krebs cycle for a total of six

(kk)                within the inner membrane of mitochondria

(ll)                    they are deposited (pumped) into the intermembrane space

(mm)            proton-motive force

(nn)                H+ come from the mitochondrial matrix, electrons come from the electron transport chain, and O2 comes from the environment

(oo)                3 NADH, 1 FADH2, and one substrate-level phosphorylation per turn of the Krebs cycle, for a total of 3x3 + 1x2 + 1 ATP = 12

(pp)                via fermentation

(qq)                CO2

(rr)                   X=6, Y=6, Z=6

(ss)                  O2, for example

(tt)                   Protons; H+

(uu)                (ii) C-H

(vv)                NAD+

(ww)            A dehydrogenase is an enzyme whose job is the removal of electron pairs from substances, e.g., in the context of removal of electrons to NAD+

(xx)                (iii) Glycolysis; (iv) Krebs citric acid cycle

(yy)                (iv) Krebs citric acid cycle; (v) Pyruvate oxidation

(zz)                 (iii) Glycolysis, (v) Pyruvate oxidation, (iv) Krebs citric acid cycle, (ii) Electron transport, (i) Chemiosmosis

(aaa)             (i) Chemiosmosis

(bbb)            (iii) Glycolysis

(ccc)             NAD+, Pi, NADH

(ddd)          Matrix of mitochondria

(eee)             Glucose is split into two three carbon compounds during glycolysis, a derivative of each goes through one round of the Krebs cycle

(fff)               (v) 10

(ggg)            The inner membrane of mitochondria is greatly expanded to accommodate large quantities of electron transport system (ETS) components, creating folds in this membrane we call cristae

(hhh)            (iii) Intermembrane space

(iii)                  (iv) Proton-motive force

(jjj)                  Matrix of mitochondria

(kkk)            ATP synthase

(lll)                  Ethanol, carbon dioxide, and lactic acid are all fermentation products and are all derived in this process from pyruvate

(mmm)      O2 and its metabolic products are potent oxidizers, i.e., the steal electrons from other compounds including the organic compounds that organisms consist of such as DNA

(nnn)            (iii) Doubly phosphated sugar

(ooo)            ATP

(ppp)            CO2

(qqq)            Krebs citric acid cycle

(rrr)                NAD+ and FAD

(sss)               (iii) 2

(ttt)                CH3OH, FADH2, Fe2+, NADH + H+

(uuu)            Removal of hydrogens (i.e., oxidation)

(vvv)            Dehydrogenase

(www)      Glycolysis, Pyruvate oxidation, Krebs cycle, Electron Transport, Chemiosmosis; (iii), (v), (iv), (ii), (i)

(xxx)            Substrate-level

(yyy)            Glycolysis

(zzz)             2

(aaaa)          Within the mitochondria (within the matrix of the mitochondria)

(bbbb)        2

(cccc)          Citric acid

(dddd)      The inner membrane of the mitochondria

(eeee)          The matrix of the mitochondria

(ffff)            Proton

(gggg)        The reaction of the hydrogen ions, electrons from the ETS, and molecular oxygen (as the final electron acceptor) gives to metabolic water

(hhhh)        Oxidative

(iiii)                3, 1, 1

(jjjj)                Fermentation

(kkkk)        Facultative

(llll)                36 ATP, 6 CO2, 6 H2O plus pyruvate, acetyl CoA, citrate, and oxaloacetate, for example

(mmmm)                        C6H12O6 + 6O2 --> 6CO2 + 6H2O (plus energy)

(nnnn)        C and H are oxidized

(oooo)        NAD+ or FAD; in fermentation pyruvate or various pyruvate metabolic products; also various members of the electron transport chain serve as oxidizing agents

(pppp)        NAD+ + 2e- + 2H+ --> NADH + H+

(qqqq)        NAD+ or FAD

(rrrr)              (v) Substrate-level phosphorylation

(ssss)            2C3-P, ADP, ATP

(tttt)              Pyruvate

(uuuu)        Matrix of the mitochondria (latter sufficient)

(vvvv)        Two (one for each pyruvate)

(wwww)                        Citric acid; citrate, tricarboxylic acid

(xxxx)        The Krebs cycle

(yyyy)        10 NADH and 2 FADH2

(zzzz)          The inner membrane of the mitochondria

(aaaaa)      A proton-motive force

(bbbbb)    Molecular oxygen

(ccccc)      From the reduction of molecular oxygen as the final step of electron transport

(ddddd) ATP synthase

(eeeee)      3 * 3 + 2 + 1 = 12

(fffff)         Via fermentation

(ggggg)    A facultative anaerobe generations ATP via oxidative phosphorylation when oxygen is present (under aerobic conditions) but only via glycolysis followed by fermentation when oxygen is not present (under anaerobic conditions); however, ATP generation and growth are possible in either case

(hhhhh)    CO2 & Ethanol

(iiiii)              CO2 and H2O

(jjjjj)              A reducing agent is a substance that donates electrons to another substance

(kkkkk)    Electrons, hydrogen atoms, electrons plus protons, etc.; protons alone is an insufficient answer to this question (i.e., it misses the point of what NAD+ mediated oxidation, or oxidation period is all about

(lllll)              The removal of hydrogen atoms from molecules

(mmmmm)                  (iii) Glycolysis, (v) Pyruvate oxidation, (iv) Krebs cycle, (ii) electron transport, (i) chemiosmosis

(nnnnn)    (iii) Glycolysis

(ooooo)    Pi + NAD+... + NADH

(ppppp)    It is the intermediate between pyruvate oxidation (or glycolysis if you prefer) and the Krebs cycle

(qqqqq)    This is citric acid (without many of the Hs shown):

 

C -- COOH

|

HO - C -- COOH

|

C -- COOH

 

(rrrrr)           3 NADH + H+, 1 FADH2, 3 CO2, one ATP (or GTP)

(sssss)         Pump protons; create/maintain the proton motive force; create/maintain an electrochemical/chemiosmotic gradient

(ttttt)           Molecular oxygen

(uuuuu)    Metabolic water is the water created when oxygen is reduced in cellular respiration

(vvvvv)    ATP synthase is the enzyme (reverse-acting proton pump) responsible for transducing proton motive force into ADP phosphorylation

(wwwww)                  Two ATP via substrate-level phosphorylation from glycolysis plus two ATP (per glucose) from substrate-level phosphorylation from the Krebs cycle; Two NADH + H+ from glycolysis + six (per glucose) from the Krebs cycle; Two FADH2 per glucose from the Krebs cycle; Each NAD H+ results in an estimated 3 ATP for a total of 3 x 10 = 30; Each FADH2 gives rise to 2 x 2 = 4 ATP; plus 4 substrate-level phosphorylations gives you 38 ATP, though remember that in fact the total is actually 36 because of the cost of one ATP to bring NADH into the mitochondrial matrix

(xxxxx)    An organic molecule; pyruvate

(yyyyy)    It can grow both with and without oxygen, but can utilize oxygen in cellular respiration when present

 

 

s 1) Draw oxaloacetate.

 

A: untitled

 

Chapter 9, Bio 113 questions:

 

(#) What are the products of complete oxidation of a organic compound such as a hydrocarbon? Don't worry about stoichiometries.

 

A: CO2 and H2O

 

(#) What does it mean in chemical terms for a compound to be reduced?

 

A: It means that it has acquired electrons

 

(#) Indicate all that is removed from a compound by the actions associated with the coenzyme, NAD+.

 

A: 2e- + 2H+ or simply 2H

 

(bonus) Show me the product of the reaction catalyzed by glyceraldehydes-3-phosphate dehydrogenase. Hint, G3P looks like this:g3p_large

 

A: The H in the upper left is replaced with a phosphate group as indicated on the bottom right.

 

(bonus) What is wrong with this statement: "Substrate-level phosphorylation occurs twice times per glucose during glycolysis and again twice per glucose during the Krebs cycle"

 

A: The first "twice" actually should read "four times" per glucose.

 

(#) Acetyl CoA is a product of pyruvate _________.

(i)                       Anabolism

(ii)                     Glycolysis

(iii)                    Oxidation

(iv)                   Reduction

(v)                     Synthesis

 

A: (iii) Oxidation

 

(#) How many carbon atoms are found in citric acid, a.k.a., tricarboxylic acid?

(i)                       3

(ii)                     4

(iii)                    5

(iv)                   6

(v)                     7

 

A: (iv) 6

 

(#) During electron transport along the electron transport chain of mitochondria, protons are pumped. These protons are pumped from where to where?

 

A: from the matrix to the intermembrane space. I'll give you full credit for just one of these answers, at least so long as you correctly identify it as the donor vs. target.

 

(#) How do electron transport chains within mitochondria get rid of their excess, energy-depleted electrons?

 

A: by passing them on to molecular oxygen.

 

(#) How is the electron transport chain biochemically (or, if you prefer, biophysically) linked to the ATP synthase enzyme responsible for ATP synthesis?

 

A: via the proton-motive force, i.e., chemiosmosis

 

(#x2) Account for the estimated 36 ATP produced per glucose by cellular respiration in human cells. That is, indicate where each ATP came from, including any ATP losses pertinent to the bookkeeping giving rise to this total.

 

A: 2 ATP from glycolysis, 4 ATP from FADHs as generated by the Krebs cycle (per glucose), 2 ATP from substrate-level phosphorylation during the Krebs cycle, 30 ATP from NADH generated 2 from glycolysis, 2 from pyruvate oxidation, and 6 from the Krebs cycle, all minus 2 ATP involved in getting the NADH from glycolysis into the mitochondria

 

(#) Note, need question directly addressing the steps of glycolysis I've asked them to memorize.