Skip to main content
Biology LibreTexts

12.1: Biochemical Reactions and Energy Changes

  • Page ID
  • \( \newcommand{\vecs}[1]{\overset { \scriptstyle \rightharpoonup} {\mathbf{#1}} } \) \( \newcommand{\vecd}[1]{\overset{-\!-\!\rightharpoonup}{\vphantom{a}\smash {#1}}} \)\(\newcommand{\id}{\mathrm{id}}\) \( \newcommand{\Span}{\mathrm{span}}\) \( \newcommand{\kernel}{\mathrm{null}\,}\) \( \newcommand{\range}{\mathrm{range}\,}\) \( \newcommand{\RealPart}{\mathrm{Re}}\) \( \newcommand{\ImaginaryPart}{\mathrm{Im}}\) \( \newcommand{\Argument}{\mathrm{Arg}}\) \( \newcommand{\norm}[1]{\| #1 \|}\) \( \newcommand{\inner}[2]{\langle #1, #2 \rangle}\) \( \newcommand{\Span}{\mathrm{span}}\) \(\newcommand{\id}{\mathrm{id}}\) \( \newcommand{\Span}{\mathrm{span}}\) \( \newcommand{\kernel}{\mathrm{null}\,}\) \( \newcommand{\range}{\mathrm{range}\,}\) \( \newcommand{\RealPart}{\mathrm{Re}}\) \( \newcommand{\ImaginaryPart}{\mathrm{Im}}\) \( \newcommand{\Argument}{\mathrm{Arg}}\) \( \newcommand{\norm}[1]{\| #1 \|}\) \( \newcommand{\inner}[2]{\langle #1, #2 \rangle}\) \( \newcommand{\Span}{\mathrm{span}}\)\(\newcommand{\AA}{\unicode[.8,0]{x212B}}\)

    Search Fundamentals of Biochemistry


    We have already discussed How Enzymes Work and Enzymatic Reaction Mechanisms in great detail in Chapter 6. Here we will focus on a lighter, less granular review of some key reaction mechanisms and the changes in Gibb's free energy associated with them, both in an uncatalyzed and enzyme-catalyzed reaction. Consider it a simple review of very basic organic reactions and thermodynamics in preparation for the comprehensive focus on reaction mechanisms in Unit 2: Bioenergetics and Metabolism.

    Breaking C-X bonds

    Many of the organic reactions involved in metabolism involve making and breaking bonds to carbon. There are three ways to break a bond to a C-X bond, producing either a carbocation, carbanion, or free radical intermediate, all of which are unstable and reactive, as illustrated in Figure \(\PageIndex{1}\). Both the carbocation and free radical are electron deficient, and the carbanion, although not electron deficient, has a negative on C, an atom that has a relatively low electronegativity.


    Figure \(\PageIndex{1}\): Ways to break a C-X bond

    These unstable intermediates are higher in energy than the reactants, and hence the transition state, which is even higher in energy than the intermediates, must have a structure that resembles the intermediates more than the reactants, as shown in Figure \(\PageIndex{2}\). For the charged carbanion and carbocation intermediates, there is a developing charge in the transition state.


    Figure \(\PageIndex{2}\): Gibb's free energy of reactants, transition state, and intermediate in breaking a bond.

    The thermodynamics of the reactions is determined by the change in free energy between the intermediates and the reactants, while the kinetics of the reaction is determined by the difference in free energy between the transition states and the reactants, as shown in Figure \(\PageIndex{3}\). A catalyst lowers the energy of the transition state without affecting the energies of the reactants or intermediates (assuming that these are free and not bound to the catalyst.


    Figure \(\PageIndex{3}\): Activation energy and ΔG for a simple uncatalyzed and catalyzed reaction

    The free energy diagram shown in Figure 3 is very simplistic. We need a diagram that better fits an enzyme-catalyzed reaction, using the simple reaction equation below.

    E + S ↔ ES → EP ↔ E + P

    A free energy diagram taking into account the binding of E and S followed by the conversion of bound S to bound and then the free product is shown in Figure \(\PageIndex{4}\).


    Figure \(\PageIndex{4}\): Simple free energy curve for the conversion for the enzyme-catalyzed conversion of substrate to product.

    Even this diagram is overly simplified since it suggest that the bound substrate in the ES complex is converted to the bound product in one step with no intermediates.

    The free energy diagram should include intermediates along the reaction pathway. An example of this is shown in Figure \(\PageIndex{5}\) for the reversible conversion of a 3-carbon sugar, dihydroxyacetone phosphate (DHAP) to another 3-carbon sugar, glyceraldehyde-3-phosphate, in a reaction catalyzed by the enzyme triose phosphate isomerase (we will study enzyme in the next chapter).



    Figure \(\PageIndex{5}\): Complete free energy profile for all the elementary steps of the triosephosphate isomerase catalyzed reaction. Aqvist J, Fothergill M. Computer simulation of the triosephosphate isomerase catalyzed reaction. J Biol Chem. 1996 Apr 26;271(17):10010-6. doi: 10.1074/jbc.271.17.10010. PMID: 8626554. Creative Commons Attribution (CC BY 4.0)

    Note that the enzyme lowers the activation energy of each of the steps in the overall reaction. Enzymes can also catalyze reactions by altering the reaction pathway although in this case, all the intermediates in the conversion are the same in both the uncatalyzed and catalyzed pathways.

    A comparison of the thermodynamic reactivity of molecules of similar structures can be made by determining the relative stability of the reactants and products from structural considerations. Consider two reactants, R1 and R2, which produce products P1 and P2, respectively. Any structural features that preferentially stabilize R2 compared to R1, or P2 compared to P1, but don't stabilize R2 and P2 to the same extent, will lead to a greater driving force for R2 → P2 compared to R1. This is shown graphically in Figure \(\PageIndex{6}\):


    Figure \(\PageIndex{6}\): Free energy reaction digrams for two similar molecules

    Mechanisms that lead to the stabilization of a reactant, intermediate, or product include resonance and inductive effects (electron release or withdrawal).

    An example of how the comparative acidity of two similar molecules can be determined through a comparison of their structures is shown below for acetic acid and ethanol is shown in Figure \(\PageIndex{7}\).


    Figure \(\PageIndex{7}\): Comparative acidity of two similar molecules

    The stronger acid, acetic acid, has the more stable (and hence less basic) charged product (the conjugate base)

    An example of how an intermediate can be stabilized through resonance is shown in Figure \(\PageIndex{8}\) for the keto-enol tautomerization reaction, which is favored in the direction of the keto form, a weaker acid than the enol.


    Figure \(\PageIndex{8}\): Comparative stability of keto and enol intermediates

    An example of how the inductive effect (electron release and withdrawal) stabilizes/destabilizes carbocations and cations is shown in Figure \(\PageIndex{8}\).


    Figure \(\PageIndex{8}\): Factors contributing to stabilization of carbocations and carbanions

    Also, remember that electron-withdrawing by the F's in the negatively charged conjugate base of trifluoracetic acid helps explains its lower pKa compared to acetic acid.

    Lastly consider how the stabilization of a tertiary carbocation below helps explain the preferential formation of the tertiary alcohol over the secondary alcohol, as shown in Figure \(\PageIndex{9}\).


    Figure \(\PageIndex{9}\): Preferential formation of tertiary alcohol

    Oxidation of Organic Molecules

    Organic molecules are usually oxidized in two-electron steps. Two methods can be used to determine if a C atom in an organic molecule has been oxidized.

    • If the number of bonds from C to oxygen increase, or the number of bonds to H decrease, the C is oxidized, More generally, if the number of bonds from C to a more electronegative atom increases, or the number of binds from C to a less electronegative atom decrease, the carbon is oxidized
    • A more powerful method involves determining the oxidation number of the carbon atoms in the reactant and product. If the oxidation number becomes more positive, the C is oxidized.

    The general rules for determining the oxidation numbers of the atoms in a molecule are:

    1. O is generally 2-
    2. H is usually 1+
    3. in molecules consisting of one type of atom, (like O2) - i.e. a polyatomic element, the atoms have an oxidation number of 0.
    4. the sum of the oxidation numbers of the atoms in a molecule equals the net charge on the molecule or ion.

    In general, the oxidation number can be calculated as follows:

    1. assign all nonbonded electrons of an atom to that atom
    2. assign all bonded electrons to the more electronegative atom of the two atoms bonded
    3. assign one electron of a bond to each atom if the two atoms are identical.
    4. sum up the assigned electrons from 1-3. Subtract this number from the total number of electrons usually present in the outer shell of the atom (the group number). The result is the oxidation number.

    An illustration of the sequential two-step oxidation of ethane to acetic acid and assigned oxidation numbers are shown in Figure \(\PageIndex{10}\).


    Figure \(\PageIndex{10}\): Change in oxidation number on the stepwise conversion of ethane to acetic acid

    Reactions of Carbonyls: Aldehydes and Ketones

    When water reacts with an aldehyde in a nucleophilic addition reaction, a 1,1 diol, or a geminal diol results. This reaction can be catalyzed by a base, which acts as the nucleophile (it's a stronger nucleophile than water) and adds to the carbonyl C. OH- is regenerated when the alkoxide produced abstracts a proton from water, regenerating OH-.

    When an alcohol adds to an aldehyde or ketone, a hemiacetal or hemiketal, respectively, is formed. In the presence of an acid catalyst, the acid protonates the carbonyl oxygen, making the carbonyl more electrophilic. After the alcohol adds and forms the hemiacetal or hemiketal, the acid can protonate the OH group, leading to its expulsion as water in an acid-catalyzed elimination. The carbocation or resonant-form oxonium ion can react with another ROH to form an acetal or ketal. These steps are summarized in Figure \(\PageIndex{11}\).


    Figure \(\PageIndex{11}\): Nucleophilic addition to an aldehyde

    If the nucleophile is an amine, an addition can occur, followed by an elimination to form an imine or Schiff base, as shown in Figure \(\PageIndex{12}\).


    Figure \(\PageIndex{12}\): Schiff base formation

    An acetal or ketal are geminal ethers (as water addition to aldehydes or ketones produced geminal diols). As with other ethers, these geminal ethers are stable to base and are hence often used as protecting groups to keep aldehydes and ketones from undesired reactions in basic solution. Acetal formation is favored by excess anhydrous alcohol in acetic conditions, while acetal breakdown is accelerated by high concentrations of water and the presence of an acid catalyst.

    Why are ethers and hence acetals/ketals resistant to bases? They are resistant to nucleophilic attack, such as by base, since the expelled group (alkoxide) is unstable. (Epoxides, in contrast, will react with OH- nucleophiles since the epoxide ring is strained and of high energy.). Ethers can react with acids, however, which protonate the ether O to form an oxonium ion. Nucleophilic attack (such as by Br-) on an adjacent C can occur (SN2), with electrons flowing to the protonated oxonium ion (a great electron sink) as it departs.

    Reactions of Carboxylic Acid Derivatives

    Carboxylic acids undergo nucleophilic substitution reactions, assisted by the fact that compared to aldehydes and ketones, they have good leaving groups. With the substitution reaction, the stability of the double bond in the carbonyl is retained. Two things control the reactivity of these derivatives: the stability of the reactants and the stability of the products. The relative reactivity of carboxylic acid derivatives is shown in Figure \(\PageIndex{13}\).


    Figure \(\PageIndex{13}\): Relative reactivity of carboxylic acid derivatives

    A reactant is less reactive if stabilized by resonance. Hence the relative reactivity is as follows: amide < ester < anhydride < acid chloride

    The nonbonded electron pair on N of the amide, a less electronegative atom than O, can delocalize and form a resonant structure with a double bond with the carbonyl C more readily than the O in the ester. An electron pair on the bridging O in the anhydride, since its ability to form a double bond in a resonance structure, is split between the two carbonyls C is less effective in stabilizing either side than in the. (This is called competing resonances.) The reactant less stabilized by resonance is the acid chloride since a nonbonded pair of electrons on the larger chlorine molecule can't delocalize as readily given the C-Cl bond distance.

    Notice this order of decreased stability based on resonance stabilization is also the order of increased electrophilicity of the carbonyl C (which is most electrophilic in the absence of electron delocalization from the adjacent N, O, or Cl.

    The stability of the products also is important. If the deprotonated leaving group is considered as one of the products (which differentiates the different reactions), then the order of decreased stability of products is Cl- > RCOO- > RO- > RHN-.  This is shown in Figure \(\PageIndex{14}\). (Note: the pKa of ROH = 16 and R2NH = 40)


    Figure \(\PageIndex{14}\): Relative stability of carboxylic acid derivative leaving groups

    What determines the stability of products compared to reactants is the strength of bonds made and broken during the reaction.

    In nucleophilic addition to aldehydes and ketones, the strength of the bond to the nucleophile must be greater than the strength of the pi bond broken in the carbonyl. A C-Cl bond strength is 81 kcal/mol (340 kJ/mol) compared to a pi C-O bond strength of 93 kcal/mol (389 kJ/mol). Hence a Cl- is not likely to add to a carbonyl C. Consider the hydration of formaldehyde (carbonyl with 2 H's), acetaldehyde (with 1 H and 1 methyl group, and acetone (with 2 methyl groups). The ΔGo for hydration of these is -19, -1, and +15 kcal/mol (63 kJ/mol), respectively, showing that increased electron release toward the carbonyl C, which makes it less electrophilic and more stable, decreases the reactivity of the carbonyl.

    In nucleophilic substitution, the leaving group (anion) must be more stable than the nucleophile.

    Kinetics of Reactivity of Carbonyls

    The relative kinetic reactivity of various carbonyls toward nucleophiles follows the order of electrophilicity of the C. (i.e the extent of the positive charge on the carbonyl C.) The slow step in a nucleophilic attack is breaking the pi-carbonyl bond. If the reactant is stabilized by resonance in ways that reduce the electrophilicity of the carbonyl C, the reaction is slowed.

    Nucleophilicity is a measure of the "affinity" of an atom or ion on an electrophilic C for the nucleophilic lone pair. This is similar to basicity which is a measure of the "affinity" of an atom or ion for a proton. Halides are not good nucleophiles for reactions with acid derivatives since the halide (like Cl-) is a better leaving group than the actual leaving group.

    Making C-C Bonds

    Metabolism can be divided into catabolic (breaking down) and anabolic (synthetic) reactions. To obtain energy, sugars, and fatty acids are converted to carbon dioxide. Hence C-C bonds must be broken. In contrast, C-C bonds must be synthesized in photosynthesis. In all reactions, electrons from bond broken flow to atoms where bonds will be made. Flow is from a source (a pair of electrons possibly with a negative charge) to a sink (a slightly or fully positive atom). Figure \(\PageIndex{15}\) shows a couple of ways to make a C-C bond using either the reaction of two carbon-centered radicals (free radical mechanisms are uncommon biologically) or a carbocation with a carbanion.


    Figure \(\PageIndex{15}\): Making C-C bonds

    A carbocation is unstable unless incorporated into a molecule in which it is stable, so instead of using them, the carbonyl C is used as the electrophilic carbon. (Instability of carbocations is reflected in their propensity to rearrangement.) Taking into account the resonance form of the C=O carbonyl bond with a positive on C and a negative on O, the net charge on the carbonyl is about +0.5. A carbanion, often stabilized as an enolate resonant form, is used as the negatively charged carbon. These features are illustrated in Figure \(\PageIndex{16}\).


    Figure \(\PageIndex{16}\): Carbonyl carbons as electrophiles and carbanions as nucleophiles

    One method of making a C-C bond is an aldol condensation, in which a carbanion formed by the deprotonation of a C-H alpha to a carbonyl (which is stabilized by the enolate resonance form) acts as a nucleophile which adds to a carbonyl C in an aldehyde or ketone. The reaction is illustrated in Figure \(\PageIndex{17}\).


    Figure \(\PageIndex{17}\): Aldol condensation

    In another C-C bond synthesis reaction, a Claisen Condensation, a carbanion formed by the deprotonation of a C-H alpha to a carbonyl (which is stabilized by the enolate resonance form) acts as a nucleophile that substitutes at a carbonyl C in a carboxylic ester or thioester. This is illustrated in Figure \(\PageIndex{18}\).


    Figure \(\PageIndex{18}\): Claisen condensation

    Breaking C-C Bonds

    In addition to a retroaldol condensation, a common method to break a C-C is through a decarboxylation reaction at a beta-keto acid. Notice in Figure \(\PageIndex{19}\) that the analogous reaction at an alpha-keto acid is unlikely since the electrons from the C-C bond that is cleaved have no "sink" to which to flow.


    Figure \(\PageIndex{19}\) C-C bond cleavage by decarboxylation of beta-keto acids.

    Alpha-keto acids can be decarboxylate using thiamine cofactors as discussed in Chapter 6.

    This page titled 12.1: Biochemical Reactions and Energy Changes is shared under a not declared license and was authored, remixed, and/or curated by Henry Jakubowski and Patricia Flatt.