Biochemists Way of Baking Bread - Snuggle Up to Yeast

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About: I consider myself a maker. Skilled in combustion engines and cars, 3D printing, cooking, backing and liquid handling including cocktails, brewing and barrista stuff. I would like to live a life as an invent...

A few years ago, I wondered how bread is made so I taught myself how to bake bread using my skills in biology & chemistry and till then, I eat my own bread every day. There are awesome HowTo's on baking beautiful bread (I only saw them too late) but what I am aiming to explain here is to bake a bread by understanding the needs of yeast. The bread that we are baking consists of any ingredient you have in your household. Only tools needed are bowl, fork, oven. I will not state any amounts of ingredients nor will I write about additives you must add into your bread just about the consistency or color we are aiming for.

I approach baking in an engineering way of thinking and encounter any phenomenons occurring while baking with simple biochemical explanations. I would like you to understand the behavior of the yeast,so you can determine what to change to change your result. I make use of the autolyze technique which is described below.

I will put the main learnings after each step in a form of if that than that

*** Thanks for asking lots of questions via private message. Curiosity of people makes me very happy. Please post them as comments as more people can benefit from it and i dont have to answer them individually. Keep it up! ***

Step 1: Bases of Every Bread

Bread is a solid but flexible structure from cereal. The basic idea of making bread is to soluble grinded cereal in water so its doughy and keeps it structure. Then, little helpers introduce gas bubbles inside the dough after which we remove between 30% and 40% of the water via heat to harden the structure to get bread. The bridges between the individual cereal particles and the bubbles are added by little living cells (I will call them microorganisms or MOs in short) which surrounds us and are everywhere. Therefore (in theory) there is no need to add MOs (e.g. yeast which is the main MO I'm refering to) to your dough because you have wild yeasts traveling around your kitchen however clean it is (this is how brewing beer was “invented”).

As we need to have bridge builder and bubble maker in our dough and don’t want to wait a week, people add yeast from the supermarket. Yeast digests sugars in the flour into carbon dioxide (CO2) and sometimes ethanol (C2H5OH). They do it to survive and to grow. They grow through dividing itself (meaning 1 cell divides into 2, those divide into 4, those divide into 8,16,32,64, ... every approx. 90 min @28°C (82 F) (see picture)
Further information:
Precisely: Yeasts grows through budding.
Clarification on growth: it is not purely exponential but a mixture due to multiple MOs. See comment of Joerg Engles if you are interested in further detail.

. That means, that if we already have a few MOs, they will digest more and bubble more and make more bridges even faster than if we would have started from scratch with only one. This is essential. If you have a strong kingdom of highly active MOs, you can bake a bread in 2 hours. The kingdom might be a sourdough which I will refer to later.

Bread baking microorganisms procreate themselves by dividing. Number of cells doubles every step. The growth exponential.

Excurse: Understand what exponential growth is.
check out this gif that illustrates exponential growth of bacteria! Further reading and nice examples in the Wikipedia article here.

Now, there are basically two ways here. You either buy yeast in the supermarket or you cultivate your own micro organsim tribe which lives in your kitchen anyway. This is called sourdough. Just google it, lots of HowTos online. Cultivating yeast and lactic bacteria at home brings not only the benefit of baking whenever you feel like it but also the more "bready" taste due to lots of other MOs that feel happy in your sourdough (e.g. lactic acid bacteria).

more MOs (yeast) --> more bubbles

Step 2: How to Encourage the MOs

As mentioned above, growth is exponential. Before we are getting to make the bread, we therefor need to dope our MOs and give them best possible preconditions. The needs of yeast are just like the ones of your own. They want air and food. The aim here is to maximize the number of cells to make the 2nd proving possible & faster (we employ the exponential growth)

Food is provided through flour. You could add sugar here but MOs that can (only) eat sugar are not really the ones we want to have. The main content of flour is starchwhich consists of many many sugars coupled together. Thinking of a sugar crystal like the ones we use in coffee doesn’t work here, you must picture it in a smaller, atomic scale. Some MOs have special tools, so called enzymes, to cut this long string of sugars into “normal” sugars which are then the same sugars we would put into our coffee.

Sugar is a popular food for MOs. Some can cut starch down to gain sugar. Those are the ones we want to have because they can eat flour.

Experiment: Try holding a piece of bread in your mouth and taste how it gets sweeter and sweeter? That’s the enzymes in our mouth, breaking down the starch into sugars. They are called amylases and are used by MOs as well.

However, giving the MOs sugar makes it too easy for them. We don’t want to spoil them. Giving them flour (=starch) lets them do a work-out so they are well prepared for the later task in our dough. The main benefit here is, that MOs able to digest starch from flour will grow strong but MOs only capable of digesting sugar will not. Further sugar cutting enzymes are won out of the flour which will help later when we do the final proving which we would not have when feeding with sugar. By that, we grow a culture, trained on eating starch from flour.

Air is provided due to stirring a few times whenever you feel like it. Not stirring results in an anaerobic digestion which leads to ethanol, but yeast still grows but slower (so it’s all good).

In this stage, you want to have it as liquid as possible because the yeast and the flour need to find each other (need to diffuse through the liquid). Stirring is easier when more dough is more liquid plus if the yeast produces CO2 (the bubbles) it just bubbles out without influencing the height of your dough (it doesn’t spill due to overflowing, see picture #4).

You might want to add some heat (depending where you live as temperature optimum is around 28°C (82F)), so the yeast grows faster. Time invested here reduces time invest later and is curcial for succes. (more MOs produced in this step reduce time when proving our dough later because there are more work bees - this is crucial!). Invest at least 1 h growing your culture. It is possible to let it stand on the kitchen bench the whole day (yes, unchilled).

heat --> yeast eats more --> grows faster

viscosity low --> diffusion is easier for yeast and flour --> yeast eats more --> grows faster

optional reading:

Regarding MOs in our dough

Every living cell needs stuff to produce energy. In the case of yeast cells, it is sugar. In the case of lactic acid bacteria its sugar as well. Letting a dough grow at room temp without covering doesn’t lead to mold because the cultivated MOs in the dough (mainly yeast) takes all the food and doesn’t leave anything to invaders (mold). Controlling parameters like food (flour) influences the population and the inhabitants. After a while, a circular economy establishes. It is self-stabilizing. This is the basic concept of building up your own organism tribe.

Step 3: Optional - Future Sourdough

Just take a jar of your dough and reuse it the next time you bake (store in fridge, this slows the yeast down extremely and the leftover food is enough, so it doesn’t starve). By this, it is possible to gain some extra sourdough taste.

older dough --> broader taste spectrum

Step 4: What Kind of Bread Are We Making?

As we have set the base for our MOs to produce bubbles and bridges, we can add special flour like whole grain flour or spelt flour. This is where we set the consistency and the taste of the bread. It is however important to have enough standard wheat flour for our MOs to work.

different flour --> later structure & taste plus added volume of water

Step 5: Knead As Soon As Possible

Use whatever flour you want (or had in your kitchen drawer) and add it to the dough. As soon as it reaches viscosity of honey or you are too tired to stir, it’s time to use your hands to knead.

Step 6: Putting Personality in Your Bread

Put some flour on your working surface so your dough doesn’t stick to the surface.

Step 7: ... and Knead Until You Have an Almost Bread Looking Thing

MOs like, just like humans, closeness & cuddles to feel better and digest happily. Adding warmth through your hands makes the dough more homogenous and livelier.

MOs need love <3

Step 8: Further Refining of the Later Structure - Everything That Needs to Be Distributed Fine

We now add everything, that needs to be distributed equally like salt, fat and herbs. knead until everything is distributed well. As described in the science of baking class, adding fat influences later taste. See class for further info’s. As a rule of thumb, I feel like more oil leads to a more Italian bread style like ciabatta.

MOs can eat fat, salt and herbs. However, adding the salt (and herbs and fat) not from the beginning but rather here, has an impact on our dough due to some chemical complexes forming without the salt. Further reading here. It correlates to the earlier mentioned autolyse. Therefore, we let our MO population rise in step 2 because now it is not as easy to travel through the dough and salt is toxic to them.

Step 9: Adding the Chunky Toppings

Just do a calzone / bun first and then knead until you are happy with the result.

Step 10: 2nd Proving - How Is Your Bread Going to Look Like?

At this point, everything should be in your dough. It will have to reach its almost final size now before we fire up the oven and fix the structure at its temporary state (= back it). We must wait until the MOs have produced enough CO2 (enough gas holes in the bread) to gain a fluffy bread afterwards. For that, it is important that the dough surface is closed, meaning, CO2 cannot leave the dough through openings in the top layers (picture it as a balloon that is inflated by the farts of our MOs). If that is not the case, your dough won’t rise. (Not trapping the CO2 is what we wanted when we did the 1st proving with the almost liquid dough, remember?) If you have problems closing your surface, just use water and stroke softly above the dough surface. The aim in this step is not to raise the number of cells like in step 2 but to let the yeast produce CO2 and bridges for later. Yeast cells can barely move due to the high viscosity of the bread. Therefore, we need lots of them so the don’t have to move and just use the flour around them (this is why step 2 is important)

There are two main ways to go here:

I - your dough is viscous enough (not liquid anymore) to stand by its self without changing its from. You acquire that by adding more and more flour when kneading until reached. In this case, flour needs to be put in a bowl and the dough on top (it is possible with a layer of oil as well). It is important that the dough does not stick to the surrounding when rising. If that’s the case, you will rip of parts when trying to get out of the bowl, destroy the outer wall, let CO2 escape, loose the nice fluffy structure. That's a demotivating moment but no need to throw your dough away. Just take everything out, add some more food (flour), knead it in and let it prove again until reaching its desired volume.

ii - your dough is liquid and will not retain its form by itself. Just fat some baking from (the ones from baking cake) and add some flour on the fat (this makes the bread not stick to your form). There is no point in proving in a bowl in this scenario. Just let it prove inside the baking form and bake when size appears to be nice.

In any case, letting it prove on the heater or at 35°C (95 F) in the oven doesn’t hurt but fastens up the proving a lot. Yeast dies above ~45°C (113 F).

Step 11: Optional - Use Everything

Everything that is leftover can be but into your sourdough glass!

Step 12: Baking

After proving in a bowl, put your dough into the oven on a baking plate. If you want to let it rise a bit more, don’t let the oven preheat. Adding a bowl of water might increase your volume of the bread, depending on its water content. In the picture, there are two breads from earlier baking’s. The right one was relatively dry due to whole corn flour which is why it kept it form on its own. When temperature rise above 100°C (212 F), water evaporates and forms holes in the bread (we have two hole formation mechanisms, yeah!). If there is no water bowl, more water from the bread will evaporate until the air in the oven is saturated with water (which makes it drier but also more holes).

if you already have a pretty dry bread (keeps form by its own), put a bowl of water.

The left front bread was way wetter due to some oil and dates. This bread did not keep his form and needed support, so I just put a springform around it when I saw that it just flattened out in the oven. this bread would have not needed a bowl of water because I wanted to get some moist out of it.

if bread needs support in the oven to keep its structural integrity, don’t add a bowl of water

in this case, I didn’t add a bowl because one bread gave moist and the other needed a bit.

Baking conditions are around 230°C (446 F), something around 45 minutes (until you like the color) and (!) upper- & down heat. This is crucial as air circulation will dry the bread out. Circulating air means that the air in the oven exchanges with the air in the surrounding. This means, the moist from the bread does not only needs to wetten the air in the oven but the whole atmosphere of your kitchen! Obviously, this needs a lot of water which needs to come from the bread which makes the bread really dry.

When putting in the oven, the brown crust will form. The process leads to tension in the crust. Therefore, you need to cut in predetermined breaking points. If not, it will break up somewhere which is almost every time somewhere bummer like splitting the top half and the bottom half.

cutting in predetermined breaking points gives a better-looking bread and assures structural integrity

Step 13: Looking at Results and Determine Impact of Earlier Decisions

The pictures from step 1 - 10 refer to bread on the right picture. I added quite a bit of oil and large chunks of fruit and spelt. This bread needed support in the oven due to its low viscosity.

The pictures from step 11 refer to breads in the picture left. The darker bread is just a whole corn flour bread (40% of all flour whole corn). It kept its form without support, had no oil in it. The lighter bread contained again some spelt flour and oil. I kind of like this combination for fruity breads.

Baking bread after recipe doesn’t bring out the same bread every time in my case so I figured why using a recipe?

The single most important fact is to take good care of your MOs. You want to have lots of MOs (yeast) due to proving in liquid phase and waiting until reaching a nice volume in 2nd proving. The taste will always be nice if you only add things you like :)

Good luck

Step 14: Appendix - What’s Possible

Picture #1 shows a homemade sourdough pizza which was made with the dough I describe above.

Picture #2 shows a bread which had not been cut in properly (predetermined breaking points – step “baking”)

Picture #3 shows the same dough in two different shapes. I think the round one looks cooler but it is harder to eat and cut properly ;)

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    24 Discussions

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    prickly vegan

    3 months ago

    I'm so happy to see so many instructables coming out of different corners of the world (with METRIC!). This is a lovely and detailed look at dough making. Just one suggestion for clarity, the text states 'whole corn' flour. For non-German speakers, this might be confused with flour from maize/corn, instead of being understood as 'whole grain' flour.
    Thanks for posting this. Now I can't wait to start playing with yeast! Vielen Dank!

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    Joerg Engels

    4 months ago

    This instructables should be called "The Imaginary Way of Baking Bread" because step 1 and 2 are unscientific and have many logical fallacies.
    First of all how exactly do you want to achieve exponential growth if you starve the yeast?
    As a biochemist you should know you are then in the https://en.wikipedia.org/wiki/Bacterial_growth curve, with the stationary phase when they are eating the proteins. Because wild yeast unlike baker's yeast likes to eat the amino acids when it is "starving" to gain ammonia, sulfur and phosphorus.
    "after which we remove the water via heat to harden the structure to get bread."
    No. The baking process vaporises only between 30% and 40% of the water, otherwise the bread wasn't flexible.
    "They procreate through dividing itself"
    No. Bacteria divide. Yeast is budding. https://en.wikipedia.org/wiki/Budding
    "every two hours @28°C (82 F)"
    No. Baker's yeast every 90 minutes and brewing yeast every 75 minutes.
    "or you cultivate your own yeast tribe which lives in your kitchen anyway. This is called sourdough."
    No. Sourdough contains mainly lactic acid bacteria which make the dough sour. https://en.wikipedia.org/wiki/Sourdough
    "acetic acid bacteria which transfers ethanol into vinegar"
    No. We want lactic acid. https://en.wikipedia.org/wiki/Lactobacillus
    "The needs of yeast are just like the ones of your own. They want air and food."
    No. You want the yeast for anaerobe fermentation for alcohol to gain more gas. https://en.wikipedia.org/wiki/Yeast#Nutrition_and_growth
    "You could add sugar here but MOs that can (only) eat sugar are not really the ones we want to have."
    No. We absolutely want the ones who eat sugar and not the proteins. https://en.wikipedia.org/wiki/Saccharomyces_cerevisiae#Nutritional_requirements
    "However, giving the MOs sugar makes it too easy for them. We don’t want to spoil them. "
    No. We do want to spoil them since you said you want to make a bread within 2 hours and not 2 days.
    "Air is provided due to stirring a few times whenever you feel like it."
    No. Stirring distributes the nutritions. Air bubbles come into place when you slam the dough on the table like a baker. https://en.wikipedia.org/wiki/Kneading
    "Not stirring results in an anaerobic digestion which leads to ethanol, but yeast still grows but slower"
    No. We want the anaerobic "digestion". https://en.wikipedia.org/wiki/Ethanol_fermentation#Bread_baking
    "you want to have it as liquid as possible because the yeast and the flour need to find each other (need to diffuse through the liquid)."
    No. Are we making beer now?
    "You might want to add some heat, so the yeast grows faster."
    No. You just said yourself that yeast likes 28°C to propagate. With heat you increase the metabolization and reduce reproduction.
    "Invest at least 1 h growing your culture."
    No. You yourself said they need 2 hours to double in numbers.
    "In the case of acetic bacteria its ethanol."
    No. No. No. In the sourdough there are homofermentative and heterofermentative bacteria. Some People confuse heterofermentative bacteria with acetic bacteria. https://en.wikipedia.org/wiki/Lactic_acid_fermentation#Heterofermentative_process
    "without covering doesn’t lead to mold"
    No. The top will dry out and allow mold to start propagating before the "MO" have created enough acidity in the top. Covering helps also against fruit flies etc.
    "acetic bacteria produces vinegar"
    No. You want lactic acid in your dough and not formic acid. https://en.wikipedia.org/wiki/Formic_acid
    "MOs cannot eat fat, salt and herbs"
    No. "MO" absolutely love herbs because they provide them with trace minerals.
    "salt is toxic to them."
    No. Salt helps preventing big bubbles and promotes the coagulation of proteins.
    "Baking bread after recipe doesn’t bring out the same bread every time in my case so I figured why using a recipe?"

    What?

    You can find some ibles in my profile which will provide you with very reliable results. Since the only external resource you provided was about exponential growth, I hope my links help you and other readers to understand the processes behind baking bread, and if you have any questions, feel free to ask me.

    1 reply
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    marlin_makerJoerg Engels

    Reply 4 months ago

    Thanks a lot for your effort and time spend in working through my article and the indication of my mistake regarding acetic acid.

    Below my answers as bullets to your comments and a few questions you might be able to answer.
    ________________________________________________________________________
    “First of all how exactly do you want to achieve exponential growth if you starve the yeast?
    As a biochemist you should know you are then in the https://en.wikipedia.org/wiki/Bacterial_growth curve, with the stationary phase when they are eating the proteins. Because wild yeast unlike baker's yeast likes to eat the amino acids when it is "starving" to gain ammonia, sulfur and phosphorus.”

    --- As we are looking at multiple different microorganisms, one may not talk about the exponential phase, yes. However, going into detail here would move the focus away from baking bread. I will reference to this comment to clarify thinks for interested readers.

    "You want the yeast for anaerobe fermentation for alcohol to gain more gas. https://en.wikipedia.org/wiki/Yeast#Nutrition_and_growth

    --- Yeast are obligate anaerobes. Why would I want anaerobe fermentation in the case of
    yeast?

    “"Air is provided due to stirring a few times whenever you feel like it."

    No. Stirring distributes the nutrition. Air bubbles come into place when you
    slam the dough on the table like a baker. https://en.wikipedia.org/wiki/Kneading
    "Not stirring results in an anaerobic digestion which leads to ethanol, but yeast still grows but slower" No. We want the anaerobic "digestion".
    https://en.wikipedia.org/wiki/Ethanol_fermentation#Bread_baking
    "you want to have it as liquid as possible because the yeast and the flour need to find each other (need to diffuse through the liquid)." No. Are we making beer now?”

    --- In this stage we are still liquid (autolyse, https://www.bakerybits.co.uk/resources/autolyse-wh...)

    “"You could add sugar here but MOs that can (only) eat sugar are not really the ones we want to have."

    No. We absolutely want the ones who eat sugar and not the proteins. https://en.wikipedia.org/wiki/Saccharomyces_cerevisiae#Nutritional_requirements

    --- You may misunderstand me here. What I’m trying to encourage here are microorganisms, having extracellular amylases. Are all the amylases in the dough extracted from the flour?

    “"Invest at least 1 h growing your culture."

    No. You yourself said they need 2 hours to double in numbers.”

    --- Yes, but it’s not like the start growing when I start and stop growing when I stop.I might missunderstand your point here...

    “"without covering doesn’t lead to mold"

    No. The top will dry out and allow mold to start propagating before the "MO" have created enough acidity in the top. Covering helps also against fruit flies etc.”

    --- Obviously, you may not leave it for multiple days without touching it. It is less “vulnerable” to mold as if you would leave another liquid.

    “"MOs cannot eat fat, salt and herbs"
    No. "MO" absolutely love herbs because they provide them with trace minerals.
    "salt is toxic to them."
    No. Salt helps preventing big bubbles and promotes the coagulation of proteins.”

    --- You are right, they can. However, salt may be cell toxic and has an influence on the chemical complexes in the dough. Whether it is cell toxic here or not is something I’m not 100% sure about.

    “"Baking bread after recipe doesn’t bring out the same bread every time in my case so I figured why using a recipe?"

    What?”

    --- in my case

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    marlin_makerMarthaA11

    Answer 4 months ago

    Thanks for your question and the additional link to such nice resource!
    Autolyse is used in Step 2. I dont know how many glycosidases come from the flour but, I think, the sourdough bacteria produce more especially because the flour is unmalted. However, this step is essential for my way of baking as the total enzyme and gluten yield is high due to the high diffusion possibilities. Regarding formation of Gluten; I'm not sure what kind of effect that has as I never bake with a timer nor a scale which is why I couldn't compare differences.
    Does that answer your questions?

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    MarthaA11marlin_maker

    Reply 4 months ago

    Sorry, the step "Step 5: Knead As Soon As Possible" which comes after adding the rest of your flour to make a dough did not sound like the autolyse method I was referring too. Still, kudos for a great article.

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    WestWindsDemon

    4 months ago

    Taking this on from a microbiologist point of view is amazing! Thanks to you I now feel confident enough to make my own bread from scratch. Thank you!!

    2 replies
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    WestWindsDemonmarlin_maker

    Reply 4 months ago

    Most likely store bought yeast, but I will treat them nicely! I'll work my way up to sourdough.

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    seamster

    4 months ago

    This is an excellent article, well done!

    I think you might draw a decent number of readers if you update your cover image to one of photos of some finished bread. The first image in step 13 would be an excellent cover image, I'd think. Just a tip! : )

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    marlin_makerseamster

    Reply 4 months ago

    Thanks a lot. I just did :)
    I'm happy for any advise as this is my very first instructable.

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    audreyobscuramarlin_maker

    Reply 4 months ago

    Hey there, I noticed you had an explicit word in your 10th and 12th steps - I would encourage you to find alternatives to these like 'bummer' or 'failed' - and while I'm all-for being colloquial in-person, we try and keep our audience of youngsters in mind :D I loved some of your tips, thanks for sharing this to Instructables, can't wait to see what you share next!

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    jvector

    4 months ago

    Very informative and I really enjoyed reading this.Thank you! And don't let the comments about grammar get you down :-)

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    jcherniak

    4 months ago on Step 13

    This is the most delightful scientific description of bread baking I have ever read! I had to teach myself to bake gluten free bread for my children and as a science teacher the best way to do this was to learn the chemistry of the different flours. Thank you for a good read.

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    marlin_makerjcherniak

    Reply 4 months ago

    Thanks for the compliment. Comming from a science teacher has a special weight for me as my former teachers inspired me to get engineer. Good look in forming future scientists!

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    JohnW42

    4 months ago

    Many thanks for this highly informative article. And so to the kitchen! - John

    1 reply