Supplemental Lecture (97/02/06 update) by Stephen T. Abedon (

  1. Chapter title: Biochemistry
    1. A list of vocabulary words is found toward the end of this document
    2. "All organisms. . . must use nutrients to make chemical building blocks that are used for growth and for all the other functions essential to life. For most (organisms), synthesizing these building blocks requires them to breakdown nutrient substances and use the energy released to assemble additional resulting molecular fragments into new substances." (p. 23, Tortora et al., 1995).
    3. Bottom line: Life is best understood as dynamic aggregations of specific chemicals or, as more commonly described, biochemicals. Furthermore, because all extant terrestrial life apparently shares a common ancestor, a great deal of biochemistry is shared among all forms of life. Thus, we may discuss basic biochemical concepts, some of which are applicable to all forms of life currently existing on this planet, and many of which are shared by very large numbers of these organisms.
    4. Before we continue, it is also necessary to be aware of a significant caveat. That is, there exists a dismaying tendency among beginning biologists to universalize biochemistries, once learned, to all organisms. In fact, all organisms differ in the details of their biochemistries such that seemingly shared biochemistries diverge more and more with increasingly resolution. Furthermore, the biochemistries of many organisms, particularly unicellular organisms, can differ from those of the more familiar animals and plants to a very large degree.
    5. Having said all that, allow me to give the appearance of contradicting myself by stating that in this lecture we will discuss basic biochemical concepts which really are applicable to all organisms.
  2. Reactant
    1. Starting chemicals in a chemical reaction.
    2. For example, A or B in: A + B à AB
  3. Product
    1. The substance(s) that results from the occurrence of a chemical reaction.
    2. For example, AB in: A + B à AB
  4. Synthesis (biosynthetic) reaction
    1. A chemical reaction in which new bonds are formed.
    2. For example: A + B à AB where A and B have been joined by a new bond to form AB (i.e., A-B).
    3. The word synthesis, of course, means to produce something via a synthesis reaction and the prefix bio refers to this occurring within or by a living organism.
  5. Exchange reaction
    1. An individual reaction than involves both synthesis and decomposition. For Example: AB + CD à AD + BC.
    2. Implied in this definition is the idea that a collision between two molecules occurs which results in some degree of exchange of atoms and bonds, for example as occurs in hydrolysis.
  6. Condensation reaction [dehydration synthesis]
    1. An exchange reaction in which two substances are joined such that a water molecule is lost. For example: A-OH + H-B à AB + HOH
    2. See hydrolysis (which is the inverse of dehydration synthesis). See figure below.
  7. Anabolism
    1. The sum total of synthesis reactions exhibited by an organism.
    2. Note that the term anabolic, as in anabolic steroids, refers to this building up process that occurs through the formation of new bonds.
  8. Decomposition (degradation) reaction
    1. A chemical reaction in which bonds are broken. For example: AB à A + B.
  9. Hydrolysis
    1. The opposite of condensation reaction, hydrolysis is a reaction in which water is added to a molecule . . .
    2. . . . thus effecting its decomposition. For example: AB + HOH à A-OH + H-B.
    3. Exchange reaction:
      1. Hydrolysis is basically an exchange where one of the reactants is water and the other reactant is the compound being hydrolyzed.
      2. Note how the water molecule in the above reaction has now been split between the two products, an -OH going to one product and an -H going to the other.
      3. This adding of an -H and an -OH in the case of hydrolysis, or their removal in the case of dehydration synthesis, is invariant.
      4. See figure below.
  10. Illustration, dehydration synthesis (hydrolysis)
  11. Catabolism
    1. The sum total of decomposition reactions exhibited by an organism.
  12. Coupled reaction
    1. Two reactions that occur simultaneously with typically one reaction supplying the energy that drives the second, energy-requiring reaction forward.
    2. In biological systems the former, energy-supplying reaction is often the hydrolysis of ATP. Such ATP driven coupled reactions are very important in biological systems.
    3. Not identical to "exchange reaction":
      1. Note that the coupling of reactions is not synonymous with exchange reaction.
      2. In a coupled reaction two otherwise independent reactions simply are linked together.
      3. In exchange reaction two distinguishable, potentially independent reactions do not actually occur.
  13. Metabolism
    1. The sum of all anabolic and catabolic reactions occurring in an organism.
    2. "We use the term metabolic to refer to the sum of all chemical reactions within a living organism. . . In living cells, the chemical reactions that release energy are generally the ones involved in catabolism, the breakdown of complex organic compounds into simpler ones. These reactions are called catabolic, or degradative, reactions. However, the energy requiring reactions are mostly involved in anabolism, the building of complex organic molecules from simpler ones. These reactions are called anabolic, or biosynthetic, reactions. Anabolic processes often involve dehydration synthesis reactions (reactions that release water) and require energy to form new chemical bonds. Examples of anabolic processes are the formation of proteins from amino acids, nucleic acids from nucleotides, and polysaccharides from simple sugar. . . An example of catabolism occurs when cells break down sugars into carbon dioxide and water. Catabolic reactions furnish the energy needed to drive anabolic reactions. This coupling of energy-requiring and energy-releasing reactions is made possible through the molecule adenosine triphosphate (ATP). ATP stores energy derived from catabolic reactions and releases it later to drive anabolic reactions and perform other cellular work (i.e., ATP is the currency within cells). . . Thus, anabolic reactions are coupled to ATP breakdown, and catabolic reactions are coupled to ATP synthesis. . . It is important to understand that a cell's metabolic pathways are determined by its enzymes, which are in turn determined by the cell's genetic makeup." (p. 103, Tortora et al., 1995)
  14. Metabolize
    1. To process chemically.
  15. Reversible reaction
    1. A chemical reaction that is easily reversed.
    2. Many metabolic reactions are reversible.
    3. Driven by thermal motion:
      1. Reactions which are not strongly exergonic (energy liberating) or strongly endergonic (energy requiring) typically are spontaneous both forwards and backwards under typical physiological conditions.
      2. What that basically means is that so long as the reaction can be driven forward basically relying only on thermal motion for energy, and liberating or gaining little net energy in the process (i.e., beyond that supplied or which may be supplied by thermal motion), products remain sufficiently energetically similar to reactants that the reverse reaction may occur without significant input of energy into the system (i.e., beyond that which may be supplied by thermal motion).
    4. Presenting reversible equations:
      1. Reversible reactions are indicated by two arrows, each pointing in opposite directions. Note that due to font limitations, these arrows are not drawn correctly in the following example: A + B ß à AB or AB + CD ß à AD + BC
      2. Note that easily is a key word here. Thus, under the physiological conditions at which the following reaction occurs: A + B à C. Two reactions can occur if the above reaction is reversible and the reverse reaction is represented as follows: C à A + B with the combined reaction represented like this: A + B ß à C or this: C ß à A + B
  16. Multistep reaction [reaction pathway]
    1. Chemical reactions joined together serially. A + B + C à AB + C à ABC à A + BC (Arrows are shown as not reversible for legibility; any or all of these individual reactions could be reversible.)
    2. Metabolism essentially is a series over interlocking anabolic and catabolic multistep reactions.
    3. Note that in multistep reactions any blocks on individual steps serve also as blocks on all subsequent steps.
  17. Intermediate
    1. A substance that is formed and then consumed along the way in a multistep reaction.
  18. Special conditions required for reaction
    1. Many chemical reactions occur only under certain conditions. For example, the reaction below: A à (heat)à B + C is a decomposition that only occurs in the presence of heat. That is, heat is a special condition required for this reaction to proceed.
    2. Note that the way this special condition has been indicated: à (heat)à is not standard notation, only a more simple way to present a special condition when employing a computer that has font limitations. More correctly the special condition would be presented as follows: A + heat à B + C or some additional variation on this notation.
  19. Activation energy
    1. The energy required to start a chemical reaction. See figure below.
  20. Illustration, activation energy
  21. Reaction rate
    1. The speed with which a chemical reaction progresses.
    2. For very simple reactions this step is often the activation step since, once a reaction has started, it usually progresses rapidly.
    3. For multistep reactions the reaction rate is controlled by the slowest step.
  22. Catalyst
    1. A chemical that affects the reaction rate of a chemical reaction by lowering the activation energy of the reaction.
    2. This has the effect of speeding up the reaction.
    3. Equally important, the catalyst is not used up by the reaction, i.e., it participates reversibly.
    4. Biological catalysts are called enzymes.
  23. Biochemical pathway
    1. Enzyme catalyzed multistep reaction:
      1. A multistep reaction within a cell that is catalyzed by enzymes.
      2. Almost every reaction that occurs within an organism (which is to that organism's benefit) occurs along a biochemical pathway and is catalyzed by one or a series of enzymes.
    2. "Biochemical pathways are the organizational units of metabolism, the pathways that energy and materials follow in the cell." (p. 154, Raven & Johnson, 1995)
    3. A biochemical pathway may be anabolic, catabolic, or both.
    4. An anabolic biochemical pathway may be referred to as a biosynthetic pathway.
    5. An example of a catabolic biochemical pathway is transduction of the chemical energy found in foods into a usable form (digestion, glycolysis, cellular respiration).
  24. Example of a biochemical pathway
    1. As an example of a biochemical pathway, note the first four reactions of glycolysis as follows:
      1. glucose + ATP (hexokinase)à glucose-6-phosphate + ADP
      2. glucose-6-phosphate ß (phosphoglucose isomerase)à fructose 6-phosphate
      3. fructose 6-phosphate + ATP (phosphofructose kinase)à Fructose 1,6-diphosphate + ADP
      4. fructose 1,6-diphosphate -(aldolase)à dihydroxyacetone phosphate + glyceraldehyde 3-phosphate
    2. Reaction (i) is an exchange, irreversible reaction (note that ATP is hydrolyzed) that is catalyzed by the enzyme hexokinase.
    3. Reaction (ii) is a reversible reaction catalyzed by the enzyme phosphoglucose isomerase.
    4. Reaction (iii) is another exchange, irreversible reaction (again, note that ATP is hydrolyzed) that is catalyzed by the enzyme phosphofructose kinase.
    5. Reaction (iv) is another reversible reaction catalyzed by the enzyme aldolase. Note that there are two products. However, this is not hydrolysis because water was not employed in the splitting of the fructose 1, 6-diphosphate reactant.
    6. For more information on this pathway see glycolysis.
  25. Polymer
    1. Long organic compound synthesized from smaller organic compounds.
  26. Macromolecule
    1. Large polymeric biomolecules.
  27. Building block
    1. A variety of small organic compounds that make up macromolecules.
  28. Monomer
    1. A building block that has not yet been joined to other building blocks in a synthesis reaction.
    2. See figure below:
  29. Illustration, polymerization
  30. contents | lecture: biochemistry | top of page

  31. Phosphate group [pi]
    1. An inorganic ion consisting of one phosphate atom and four oxygen atoms.
    2. A phosphate group has a charge of up to -3 (i.e., PO43-).
    3.     OH             O-         
          |              |          
      O = P - OH ß
       O = P - O- + 3H+
          |              |          
          OH             O-        
    4. Phosphate groups' claim to fame stems, in part, from their high concentration of negative charges (and consequent hydrophilicity) under physiological conditions.
  32. Links
    1. Biochemistry, Medical Education (video and animated stuff)
  33. Vocabulary
    1. Activation energy
    2. Activation energy, illustration
    3. Anabolism
    4. Biochemical pathway
    5. Biosynthetic pathway
    6. Catabolism
    7. Catalyst
    8. Condensation reaction
    9. Decomposition reaction
    10. Dehydration synthesis
    11. Dehydration synthesis, illustration
    12. Denaturation
    13. Exchange reaction
    14. Hydrolysis
    15. Macromolecule
    16. Metabolism
    17. Metabolize
    18. Multistep reaction
    19. Organic compound
    20. Phosphate group
    21. Polymerization, illustration
    22. Product
    23. Reactant
    24. Reaction rate
    25. Reversible reaction
    26. Special conditions required for reaction
    27. Synthesis (biosynthetic) reaction
    28. Synthesis reaction
  34. Practice questions
    1. If the reaction "A + B à C + D" is a condensation reaction and D is water, then which substance probably has the larger molecular weight (circle best answer below)? [PEEK]
      1. A
      2. B
      3. C
      4. insufficient data
    2. If the reaction "A + B à C + D" is hydrolysis and D is water, then which substance probably has the larger molecular weight (circle best answer below)? [PEEK]
      1. A
      2. B
      3. C
      4. insufficient data
    3. True or False, Metabolism - Anabolism = (sum total of all synthesis reactions in an organism) (circle best answer). [PEEK]
    4. Many metabolic reactions are? (circle best answer) [PEEK]
      1. Anabolic
      2. Catabolic
      3. Reversible
      4. Catalyzed
      5. all of the above
      6. none of the above
    5. True or false, organismal biochemistries are universal (well, at least "terraversal"). (In other words, if an enzyme catalyzed reaction works one way in one organism, you can assume it will be present or work in the exact same way in every other organism; circle correct answer) [PEEK]
    6. What molecule can you be sure is a reactant in a hydrolysis reaction? [PEEK]
    7. True or False, a biochemical pathway may be anabolic, but a biosynthetic pathway is not. [PEEK]
    8. Very large biomolecules assembled by linking hundreds of smaller molecules into long chains are known (generally) as polymers or __________. [PEEK]
    9. Few metabolic reactions . . . (circle best answer) [PEEK]
      1. can occur in the absence of catalysts
      2. are either catabolic or anabolic
      3. occur in solutions of water
      4. are components of biochemical pathways
      5. all of the above
      6. none of the above
    10. Enzymes (circle correct answer) [PEEK]
      1. speed up reactions
      2. lower activation energy
      3. are proteins
      4. are numerous in biological systems
      5. all of the above
      6. none of the above
    11. Draw Pi. [PEEK]
    12. Enzymes don't affect the total change in energy associated with reactants or products as compared with the same reaction occurring in the absence of an enzyme (i.e., the difference in energy associated with reactants less that associated with the products remains constant). Nevertheless, in terms of the input and liberation of energy, in what manner do enzymes affect the progress of biological reactions? [PEEK]
    13. Catabolism is [PEEK]
      1. some fraction of the synthesis reactions occurring within an organism
      2. all of the reactions occurring within an organism
      3. the sum of the decomposition reactions occurring within an organism
      4. some fraction of the degradation reactions occurring within an organism
      5. all of the above
      6. none of the above
    14. __________ is a degradative exchange reaction which is routinely employed in biological systems. (less than five word answer) [PEEK]
    15. In the following reaction, if I were to tell you that C has a greater molecular weight than both A and B, and that the overall reaction is an example of a synthetic exchange reaction that commonly occurs in a biological system, then what molecular species, most likely, is represented by D? [PEEK] A + B à C + D
  35. Practice question answers
    1. iii, C; if D is water and this is a condensation reaction, then C consists of both A and B minus one water molecule. Chances are, then, that C is a larger molecule than either A or B. Furthermore, since water is a relatively small molecule, then chances are also reasonable that C is larger than D. Thus, C is the largest of the chemical species involved in this reaction.
    2. iv, insufficient data; This reaction makes no sense except as a hypothetical reaction in which water is first added and then removed. In such a case either A or B is a water molecule, as well as D. If water is the smallest molecule that participates in this reaction, then C as well as the non-water participant among A and B is the largest participant (indeed, if all of the participants are shown, then there must be two largest partipants having identical molecular weights). There is no way to tell whether it is A or B which is the non-water species, therefore there is no way to say with condidence which two species are not water. Thus, the answer to this question could be C and A, or C and B, but there is insufficient data given to distinguish these two possibilities. In short, an understanding that water should be on the left side of the equation in a hydrolysis reaction should lead one to quickly realize that the question posed is not solvable.
    3. False, Metabolism - Anabolism = Catabolism which is not the sum total of all synthesis reactions in an organism. That is the definition of Anabolism.
    4. v, all of the above
    5. False
    6. Water
    7. False; a biosynthetic pathway is an anabolic biochemical pathway.
    8. Macromolecules
    9. i, can occur in the absence of catalysts
    10. v, all of the above
    11. As below with any variation on degree of dissociation you like. Try to make sure you include in some manner the negative charges if you choose to show Pi as dissociated.
    12.     O-    
      O = P - O-

    13. lower activation energy
    14. iii, the sum of the decomposition reactions occurring within an organism
    15. hydrolysis.
    16. water.
  36. References
    1. Raven, P.H., Johnson, G.B. (1995). Biology (updated version). Third Edition. Wm. C. Brown publishers, Dubuque, Iowa. pp. 39-41.
    2. Tortora, G.J., Funke, B.R., Case, C.L. (1995). Microbiology. An Introduction. Fifth Edition. The Benjamin/Cummings Publishing, Co., Inc., Redwood City, CA, pp. 30-33.