/Why are enzymes so big?

Why are enzymes so big?

[Back to part 1]

PART II

What can we learn more from the asymmetrical energy distribution (see part 1), besides the interesting fact that particles moving at 25 °C do not have enough energy to drive biochemical reactions?  At the end of this page you will find another video, explaining the Maxwell-Boltzmann energy distribution in more detail.

Life makes a leap of joy in the spring

Shifting the temperature up and down (left and right in the video) is not a simple linear process. Increasing the temperature leads to a sudden – non linear – increase in hot particles, that have enough energy to participate in chemical reactions and vice versa. This observation aligns with the lively activity we see in nature when temperatures go up a bit in Spring, or when climate researchers warn us that even a small increase in temperature can have a substantial impact on our planet or when we experience a fever, marked by a small change in our bodies temperature.
So how do we relate this to bread?

Bread dough is said to be alive, since gluten and starch form an organ-like texture and this in combination with yeast, bacteria and water transform the dough into a lively body that is very sensitive to temperature and the function of enzymes. It requires some imagination, but making bread  Spring, climate change and even our own body are somehow connected. In the biochemical symphony of life all molecules are important, but some instruments play a key role.

Perhaps you once wondered what the substance is from which Shakespeare’s dreams were made of? There is a good chance its enzymes, large molecules that give meaningless vibrations and collisions  direction and transform them into a chemically meaningful story. Enzymes play a key role in life and it will not surprise you that they also play an important role in making bread. Enzymes are relatively large proteins, a kind of ingenious complex machines. They help break and form bonds and have extremely specific binding areas for target molecules. So where do these nano machines get their energy from and how can we relate it to our video (part 1)?

The underlying biochemical reactions change course when our dough is cooled or warmed and these changes are intimately related to how enzymes affect these reactions. To understand how this is related to the video and the Maxwell-Boltzmann energy distribution we should review the nature of chemical bonds, but that’s obviously not the purpose of this article. Nevertheless, lets try to see if can dig a bit more while we try to incorporate the Maxwell-Boltzmann distribution into our dough. As we dig further we should of course not forget our perspective.

fata morgana, but one with exceptionally good predictive values

Science is based on abstract models to help understand phenomena that are invisible to us. What an atom, small molecule or large enzyme is can only be explained through models. Science is to some extent a fata morgana, but one with exceptionally good predictive values.

Chemical bonds vary, both in type and strength, leading to a variety of interactions between atoms. Biochemical reactions include reactions between molecules in which all of these chemical forces play an important role. The point of this article is that the weak forces are actually very important. Enzymes use these weak energies and bonds to change shapes, to destabilize a strong bond of a target molecule and therefore reduce the so called  activation energy needed to break this bond and create a new one. This speeds up reactions (up to a million time faster or more). Without enzymes almost nothing would be happening at room temperature! Enzymes help streamline the transformation process by actually using much lower energies (temperatures, around 2.5 kj/mol, or 1 /40 ev, 25 °C, ) than those mentioned by Sadoway (part 1) to prepare target molecules for their energy demanding transformation, which does involve higher collision energies (+/-100 kj/mol).

The asymmetrical Maxwell-Boltzmann distribution has a particular energy balance, which seems to fit remarkably well with the biochemical enzymatic reaction path, that involves both low and high interaction energies. Note that too many hot particles (too warm temperatures) would actually overcook life’s delicate thermal balance. One should give it more thought, since it’s this balance (equilibrium) between many cold and few hot particles that actually allows enzymes to direct and speedup life at moderate temperatures! So how do enzymes harvest their energy?

Could the form of the Maxwell-Boltzmann distribution at room temperature be the underlying reason why enzymes are so much larger in relation to the reactants (substrates) they work on? Saldoway in the video: “How do you suck enough energy at room temperature to make all these biochemical reactions possible?” Perhaps enzymes are large because their size helps them to harvest and add up the abundant number of weak forces (energies) available in water at moderate temperatures? From an energy perspective we could define enzymes as follow. Enzymes are large molecules, their particular size and form allows them to harvest the widely available weak energies in an aqueous environment at moderate temperatures. They add up these energies, directing them into an active site to destabilize a specific target bond and reduce the final energy required to break that bond and form a new one. There is enough food for thoughts embedded into our logo.

More about enzymes:
For enzymes the bigger is better.

Enough 🙂
Lets zoom out again and return to reality.

The making of bread involves a journey through many different temperatures, dominated by different chemical reactions. As we start to bake our bread we move away from  comfort zone of biochemistry. The rising temperature eventually inactivates enzymes,  kills yeast and bacteria. The wet crumb of the bread will be confined to the boiling point of water  (100 °C), limiting the type of reactions that occur inside the bread. In contrast, the crust will dry out and will be marked by a new set of flavour reactions. As we pass the 100 °C, reactive sugars and proteins fragments obtain enough energy to engage in new type of reactions. Between the 110 °C and 165 °C we accumulate sufficient – or violent – thermal energy to caramelize sugars and above the 140 °C these sugars also start to react with protein fragments, the Maillard reaction. This reaction continues up to 180 °C. Above the 200 °C, the thermal energy is strong enough to break down some of these newly formed products, the so-called pyrolysis reactions. The crust of bread baked at 235 °C is therefore composed of these different type of thermal reactions, which you can now link to the temperatures mentioned in your baking books.

Baking bread is simple, yet it is not as simple as cooking soup or roasting meat, and neither is it a piece of cake. It is a process involving the exploration of shapes and the use of living cells to produce a range of flavors. And that’s perhaps why making bread may remind us of the intriguing chemistry of life. More than enough reasons to keep exploring the story of bread while baking the elements from our universe.

Jechiam Gural
Baking Lab Amsterdam