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To Dye For (Part II)

A while back I wrote a post about dying yarn. I like to knit so I thought it would be pretty interesting. Well, I got a bit over my head when I realized that artificial and natural yarns are dyed with completely different processes! So the first post was the science behind artificial yarn dyeing and today’s is about natural yarn. I am excited for this one, which I expect to have a littlemore BIO in biochemistry.

Wondering if your yarn is natural or artificial? Try burning a little piece of it. If it melts, it is artificial :)

Natural yarn is made of either plant or animal fibers. Of plant fibers, cotton is the most common. Wool is the most common animal fiber. Let’s get started with dyes used for cotton.

Here’s a refresher of what cotton looks like when it is grown, its fibers, and the cellulose they are composed of.

Cellulose is a made up of chains of glucose molecules, so it is actually a sugar. Before you go and start gobbling up your yarn stash, remember that while our bodies use glucose, we do not have the proper enzymes to digest cellulose. I suppose you would get a good dose of fiber.

The “n” under the cellulose means that this pattern repeats “n” number of times. So imagine this pattern repeated several, several times until a long chain forms.

Zhou et al., 2008. Functional nano-composite oxides synthesized by environmental-friendly auto-combustion within a micro-bioreactor. Materials Research Bulletin. 43: 2248-59.

The “n” under the cellulose means that this pattern repeats “n” number of times. So imagine this pattern repeated 30 thousand times until a long chain forms.

Many of the dyes we learned about in Part I formed ionic bonds with the fiber molecules. In direct dyeing, a common method for dyeing cotton, this is not the case. The affinity of the dye for cotton actually comes from its shape. Direct dyes are planar (flat), allowing them to fit in among the fibers. This allows for Van-Der-Waals, hydrogen, and dipole bonds to form.  See the image below for an example of a direct dye molecule.

There are a couple spots where charges could occur- the sulfonate groups- but these are mainly to give the molecule solubility in water.

Vat dyes are another good method for coloring cotton fiber, but I do not have time to elaborate on them. We must move on to wool!

I know, I know, I already started this post with a goat picture. Just one more!

What is wool made of? What properties of wool can be exploited for dyeing purposes?

Simpson, W.S. & Crawshaw, G.H. (2002) Wool: Science and Technology. Woodhead Publishing.

Simpson, W.S. & Crawshaw, G.H. (2002) Wool: Science and Technology. Woodhead Publishing.

Keratin is a protein, and since a variety of amino acid side chains are charged, we could expect dyes that have a charge to work well. These are called acid dyes. Kool-aid is actually an acid dye, and many people  for dyeing wool. It is also nice to use because it is nontoxic. According to Wikipedia, wool can be used as a fertilizer, since it is made of protein. Maybe that is what I will do with my failed knitting projects….

But what about the cuticle of the hair?? Does it get in the way of the dye and does it need to be removed? According to the book “Wool: Science and Technology,” it is believed that the dye can squeeze in between the scales of the cuticle. However, the condition of the cuticle can have an effect on dye uptake. For example, lipids can be present on the cuticle and prevent the dye from doing its job (hydrophobic lipid, hydrophilic dye). In addition, damage to the cuticle-such as from the sun or chlorine- can affect the way that the wool responds to dye.

One blog I visited said that dreadlocks are basically felted hair. This makes sense. Of course, this blogger was felting her own hair to make a hat or something..

This website  and that website about the chemistry of dye is super awesome, and I recommend you go there if you would like to learn more from the experts.

Ok, just one more cute baby animal pic! How can baby hedgehogs be SO adorable?!

Everydaybiochemistry Recap

It has been FOREVER since I have had time to blog. First studying for exams, then taking the exams, and then a crazy hot experiment that lasts a whole month. So my personal life has been pretty minimal, and blogging time nonexistent.

My original intention for this blog was to help me study for my comprehensive exams. So did it help? Yes and no. It definitely helped me get comfortable with biochemistry lingo- how many times can I forget the difference between hydrophobic and hydrophilic?? Well, never again! As far as helping me with specific content I was tested on… not so much. There was so much on that exam that it would take a lifetime of blogging to cover it all. (And it would be so boring that no one would care to read it!)

Not that I don’t find biochemistry interesting. I do! But I don’t think anyone here wants to learn how to create a titration curve. Ya know, for all those buffers you make in your everyday life :p Once I started blogging, I found that I really enjoyed it, and I still have several topics I would like to cover. So I will continue to blog, but probably not at the same rate as I was pre-exams.

Note: The orange mango smoothies at a certain famous coffee shop that rhymes with Carbucks do not taste like orange OR mango. All I taste is banana :/ FYI.

To Dye For

I enjoy knitting- I have made scarves, hats, and am currently working on the ugliest sweater in the world. It is my first attempt at a sweater, and I knew it was going to be ugly, so I used some free Red Heart yarn that I didn’t know what to do with. I was wondering if there was any biochemistry behind knitting… and what do you know there is! I decided to research the biochemistry behind dying yarn.

The first thing I realized was that dying natural yarn-for example, wool- is WAAAY different than dying acrylic yarn such as Red Heart. In fact, a lot of knitters hate Red Heart with a passion because they say it is scratchy and squeaks when you knit. I was hoping to do half of the post on natural yarn and the other half on acyrlic, but quickly realized that it would turn into the longest post in the world. So this week we are looking just at the biochemistry behind dying acrylic yarn.

The first thing to know about acrylic fiber is that it is made a polymer, which is composed mostly of monomers of polyacetonitrile, or PAN.

Acrylic fiber also contains monomers of vinyl acetate or methyl acrylate.

Acrylic is composed of copolymers; that is, the monomers that create the chain are not all the same. For example, an acrylic copolymer may be composed of 5 monomers of PAN, followed by 1 monomer of methyl acrylate and one monomer of vinyl acetate. Or maybe 3 monomers of PAN, followed by 2 monomers of vinyl acetate. I couldn’t find out exactly what the pattern/arrangement is in Red Heart yarn–it is probably top secret haha. But we do know that most of it is PAN.

Acrylic yarn starts out as a liquid and ends up as a soft string. How does that work? I found a great website that explains how this transformation occurs. Basically, the liquid is squirted through a nozzle that looks like a shower head. Once dried, those strands are combined and twisted into strands of yarn.

Interestingly, the yarn made at Red Heart is dyed while it is still liquid, so the fiber is already colored as it is stretched out and wound. This is of course different from natural fibers, which are typically a white color which is dyed, then stretched out and wound. However, you CAN dye acrylic yarn after it has been made. Since acrylic fiber is very different from natural fiber, different dyes must be used.

Acrylic polymers typically have an overall negative charge. It was really difficult to find out exactly why this is, because most websites just repeated the same explanation using the same wording. When I tried to find some primary sources, I found out that my university does not have access to any of the articles I found interesting :( The little information I found explained that the acrylic polymers had anionic (negative) groups attached to them, mostly sulphonate and carboxylate. It seems that persulfate is used to initiate the polymerization of the acrylic in its liquid form. No idea where the carboxylate groups come from.

Whether or not we know where these groups come from, they are present, and they are making the polymers have a negative charge. This property is taken advantage of in order to dye acrylic. Basic, or cationic, dyes have a positive charge and work great to dye acrylic fibers. The positive dye and the negative polymer undergo an ionic interaction-kind of like a magnet.

Before you run out and start dying all your Red Heart yarn, I should tell you that these basic dyes are very toxic. And they PERMANENTLY stain ANYTHING they touch. AND they might be carcinogenic. So I don’t think I will be dying my Red Heart yarn anytime soon!

Here are some links to more information about the creation and dying of acrylic fibers:

And here is an adorable baby walrus that I found while writing this post:

This week’s post has turned out to be a bit more chemistry than biology, but come back next time for the scoop on dyeing natural fibers!

The Business of Running a Lab

This week’s post is a bit off-topic for everydaybiochemistry. Normally we talk about the biochemistry behind common activities, processes, foods, etc. We are still going to learn how something works, but not in a biochemical sense. This week we are learning how to run a lab. Ok, we are not learning EVERYTHING about running a lab, but we are learning about the business side. Many Ph.D. students go to grad school in hopes to one day run their own lab. They want to be the one calling the shots, not the underling. So you would think that grad school would teach you how to call the shots, right?


Grad school teaches you how to DO science. Hopefully how to plan experiments well. But how about managing people? Finances? Not so much. Some (not all, sadly) departments at my institution require graduate students to write a grant proposal for their comprehensive exams, and some have courses dedicated to grant writing. Which is great! But I think we could learn a whole lot more. One side comment: grad schools should provide a foundation for Ph.D. students to pursue a variety of science careers- not just academic tenure. But that’s a whole other post.

I believe that running a lab is a lot like owning a business, and that many of the skills needed to succeed in business can be applied to science. Mr. Braaains has been toying with the idea of running his own business, and recently shared with me a few reasons why he would like to own a business: He wants to be his own boss. He has some ideas of his own that he would like to try out. He thinks it would be fun.

Those reasons sound a bit familiar… They are practically the same reasons why I want to get my Ph.D. I want to run my own lab. I have some personal research ideas that I would like to explore. And I think it sounds like a lot of fun (nerd, I know). So I decided to search the interwebz to see how other scientists are applying business skills to their own science.

And I found some awesome resources! For example, Lab Manager Magazine and Morgan on Science. I also found the results of a survey which showed that 80-90 % of scientists receive little or no formal training on people or money management. About 50% of scientists surveyed said they received informal training on managing people, but only 30% received any informal money management training. So sad. I like what Dr. Morgan Giddings from Morgan on Science has to say about the topic:

People like me who have climbed up the science career ladder have had to learn these things, usually by trial-and-error, and sometimes by getting lucky and having a really good mentor.  But career success in science shouldn’t be a matter of luck. What is lacking is a systematized approach, e.g. a “blueprint” for success.

Why are things this way? I have found a few explanations that seem to make sense.

1. You are expected to learn lab management from your PI, not in class.

Currently, there are no classes in grad school on lab management. My best theory is that people assume you will learn how to manage a lab by watching your PI. Working in a lab is a lot like an apprenticeship. Or like following a rabbi. If you follow your boss around enough you will learn how to manage a lab. Note that I did not say you will learn how to manage a lab well. If any of you have worked in a lab, you know what I am talking about.

2. PI’s don’t get credit for teaching lab management skills.

If your PI is anything like mine, he is always running around putting out fires (not literal ones hopefully!) in the lab, writing grants, editing papers, teaching classes, writing grants, at faculty meetings, writing grants, advising students, oh, and did I say writing grants? Money is really tight now days, so researchers must make more time for writing grant proposals and publishing papers in order to keep the lab going. Lab management training is bound to fall to the wayside.

3. The teachers don’t have training.

Just because you publish a lot of papers does not mean you are a good manager. This reminds me of the pre-grad school advice I received: don’t pick a lab to work in just because the scientist is “famous” or well-published. Rather, try to find an PI who will be a good advisor to you. In fact, I have even heard people say that it doesn’t even matter what the PI is researching as long as he is a good advisor and advocate for grad students. I find it sad that this is true. Maybe I am wishing for too much, but I think students should be able to find a PI who is a good advisor AND studies a topic in which they are interested.

I would like to comment here that lab management skills are not the only thing required for research success. You still need creativity, perseverance, intelligence, etc. But I think that good lab management skills will enhance the success that you already have, and make life easier. And I am all about that.

So, what some business skills that can be applied to research? From my reading, the following four business skills are the most important for running a lab: budgeting, leadership, intellectual property management, and marketing. For each skill set, I have listed a few sites that I found very informative and plan on reading myself.


Budgeting skills are important for getting grants and maintaining them. When writing a grant proposal, you must be able to accurately estimate the amount of money that you will need. Too much, and the reviewers will get suspicious. Too little, and you run out of money before your project is done. The three main components of a budget include personnel, major equipment, and supplies. From my reading, personnel take up the most of your budget. Major equipment can often be shared with other labs in order to reduce expenses. One common tip I have seen for maintaining a lab budget is to set a monthly spending limit, and then monitor how often you spend above or below that limit.


There are different leadership styles, and I recommend that you find out what yours is. That way you can enhance your leadership abilities (or switch to a better leadership style!). One interesting comment I found in my reading is that there is a difference between a leader and a manager. Understanding if you are better at being a leader or a manager will allow you to improve in the area you are lacking.

Intellectual property management

There are increasingly greater connections between academia and business, which I think is great! Our university is making an effort to connect researchers with businesses and vice versa. One of the greatest things I learned about intellectual property management is that you can publish information that you have patented. You do not have to choose academic or industry for success. HOWEVER, you must register your intellectual property BEFORE you publish it. If you publish a paper describing your new scientific technique before letting your patent office know, it is now public information and you cannot patent it.

Marketing your research

The most important lesson I learned from my college speech class was this: Understand your viewers. This has changed not only my oral presentations, but how I write as well. It also applies to grant writing. I have not written any grants yet, but the most common advice I hear are related to the grant reviewer’s experience. The teacher of my grant writing class would always tell us to imagine that our grant reviewer is reading our proposal while riding a cramped airplane on his way to the review session. So plan accordingly when you write.

I think that the ability to market your science will only become more important as funding gets tighter and tighter. If you have to equally interesting proposals before you written by equally qualified investigators, you are going to pick the one that has more significance and impact. If your research is important but you cannot communicate that, your grant will be the one left behind.

Last, if scientists could better market their research, I think that the American public would find science to be more important. The lack of communication between scientists and the public is, in my opinion, the main reason why kids are not going for science careers. I also think that more government funding for science could happen in the future if scientists were better at marketing their research.

Also here is an interesting paper titled, “Research efficiency: Perverse Incentives” that discusses the correct way to use monetary incentives in science.

I know that this is a very cursory review of business and management skills, but I hope it is a starting point for anyone who wants to learn more how to successfully run a lab. I do not claim to know how to succeed in science since I am still a grad student, but I think that it is better to start early than get left behind. So email me in about 10 years when I have my own lab up and running, and we will see if my post is still relevant :)

See You Later

I have had a heavy load of homework the past few weeks, so I have not had a chance to post much. But I am back! I just presented a Nature article about vision at my department’s Journal Club, so I thought we would learn about the biochemistry of vision.

Let’s begin with the basics of vision:

The basic path that visual information follows is

  1. Eyes
  2. Optic chiasm
  3. Lateral geniculate nucleus (LGN) of the thalamus
  4. Visual cortex
  5. Various feedback routes

I am going to focus on the eyes- in particular, the cells that detect light and turn that information into electrical signals.

Those cells are found in the retina, shown here at the back of the eye.

Below is a drawing of the retina by my neuroscience hero, Santiago Ramon y Cajal.


Santiago Ramon y Cajal–not so beautiful, but awesome! I had this picture as my desktop background, but I think it scared my labmates :)

The cells that detect light are called photoreceptor cells, and they contain proteins called opsins. You have your rod and cone opsins; rods help you see in low light conditions, and cones help you see at normal light and distinguish color. Opsins are G-protein coupled receptors (GPCRs)–that is, they are receptors that cooperate with a certain protein, called a G-protein, to produce an effect when something activates the receptor.

The star of today’s post is retinal, a molecule that fits perfectly into a pocket in the opsin protein. Retinal changes structure when light hits it. This changes is called isomerization. Retinal is originally in the cis formation, and light causes it to isomerize to the trans formation. Its original form is called 11-cis retinal. Cis/trans isomerization is a way of describing the orientation of the functional groups in a molecule. As seen in the picture below, “rotation” occurs at a double bond, which is typical of cis/trans isomerization.

Cis means on the same side, while trans means on the opposite side. In cis retinal, the hydrogens are on the same side of the double bond. In the trans isomer, the hydrogen bonds are on either side of the double bond.

The reason why I put rotation in quotes earlier is that double bonds don’t rotate. When a photon of light hits cis-retinal, the double bond is broken, the rotation occurs, and then the double bond is reformed. Breaking and reforming double bonds requires energy, which the photon of light happily provides. This isomerization occurs in the span of a few PICOseconds. Sweet!

The change in retinal alters the shape of  the molecule, from a bent formation to a straight-ish formation. When retinal changes, the opsin protein surrounding retinal is forced to shift its conformation. It’s like when you are cuddling with someone, and after a while you get uncomfortable. So you switch positions. But now your cuddling partner is uncomfortable. So they switch positions, too. Then you cuddle some more :)

So opsin shifts and shifts until it finally gets comfortable. The last conformational shift in opsin just so happens to bind especially well to G-protein. We talked about G-protein earlier; it is a separate protein that hangs out at the cell membrane near opsin. To continue our analogy, you and your cuddling partner finally get comfortable in your new position. But all that moving around woke the baby.

I would assume that the G-protein is randomly bumping up against opsin, but only sticks when opsin is in the new conformation. There are many types of G-proteins in the human body; the one discussed here is called transducin.  Transducin normally is bound to GDP, or guanosine diphosphate. When transducin attaches to opsin, GDP is exchanged for a molecule of GTP, or guanosine triphosphate.


An interesting note here: one photon of light activates one opsin protein, but does not lead to to the recruitment of only one G-protein. Rather, each opsin protein recruits 10 G-proteins (not all at once, of course) in a process called signal amplification. Signal amplification is the specialty of GPCR’s. Without signal amplification, we would not be able to see as well, as the signals coming in to the brain would be very weak.

The replacement of GDP for GTP causes a subunit of transducin to break off and leave the retinal-opsin-transducin party that we have going on. This transducin subunit moves on to other proteins in the cell and continues sending the signal that light has hit the cell, much like runners in a relay race take turns carrying the baton from start to finish. In addition to passing on the signal, downstream players again amplify this signal 1000 times. From beginning to end,  we have the signal from one photon of light amplified 10 x 1000= 10,000 times!

Eventually, the signal travels to the other side of the cell, where neurons wait for the signal. These neurons can then carry the message from the eye at the front of the head, past the optic chiasm, past the lateral geniculate nucleus, and finally to the visual cortex at the back of the brain.

Below are some websites that were especially helpful in understanding how light is turned into a signal that is sent to the brain:

If you are looking for more fun science, check out Ze Frank’s hilarious True Facts series on YouTube. Here is a sample:


Crash Course

In lieu of a post, today I will be sending you to check out Hank Green’s awesome set of YouTube videos about biology. He does a GREAT job of explaining the properties of the basic building blocks of our body: protein, lipid, carbohydrates, and nucleic acids. He also explains the chemistry behind biology in a fun and easy to understand manner. Check it out! Here’s a sample:

The Science of Cupcakes

I have been in a bit of a baking mood lately, and after watching a couple episodes of DC Cupcakes, I decided to do another molecular gastronomy post. So today, we are going to learn about substitutions in baking. Since this is everydaybiochemistry, why are not just going to learn about the possible substitutions. We are going to learn WHY and HOW they work. For example, why can you substitute vinegar for eggs in a cupcake recipe?

So to start out, let’s look at a basic chocolate cupcake recipe:

  • 13 cups flour
  • ¼ teaspoon baking soda
  • 2 teaspoons baking powder
  • ¾ cup unsweetened cocoa powder
  • 1 dash salt
  • 3 tablespoons softened butter
  • 1 ½ cups sugar
  • 2 eggs, beaten
  • 1 teaspoon vanilla
  • ¾ cup milk
  1. Heat oven to 350°F.
  2. Put cupcake liner in muffin tin OR grease very well muffin tin.
  3. sift flour, baking powder, baking soda, cocoa and salt.
  4. The in another bowl beat together the butter and sugar and then add the eggs beating very well then mix in the vanilla.
  5. Add the flour mixture alternately with the milk to the sugar and be sure to beat well each time.
  6. Spoon batter into the muffin cups 2/3 full.
  7. Bake for 15 to 17 minutes oven, or until a toothpick inserted into the cake comes out clean.
  8. It really depends on how full you fill the muffin tin to decide on the yield. If you want really domed cupcakes fill them almost full.
Now let’s look at some substitutions:
Flour: We’re not going to screw with this one, as I can’t find any substitutions for flour on the internet. You can, however, make flourless chocolate cupcakes. It looks like you remove the flour, baking powder, baking soda, and milk. And add a ton more chocolate :)
Baking soda: Baking soda is commonly used as a leavening agent. Also known as sodium bicarbonate, it is alkaline and also used to balance out acidic ingredients, such as vinegar, citrus juice, sour cream, chocolate, etc.). In the case of our cupcakes, my bet is that it balances the cocoa powder, which is acidic. Since the recipe we are working with also includes baking powder, I think that the baking soda is being used less as a leavening agent and more as a balance to acidic ingredients. Since there is no vinegar in this recipe, no volcano.

While most sites say that baking soda can be replaced with baking powder, I do not think that would be the case for our cupcakes. Baking powder, though also a leavening agent, has a neutral pH and cannot balance the acidity of the cocoa powder. According to this site, it does alter the taste much if you do not balance the acidity of cocoa powder. In conclusion, you probably do not need to substitute baking soda with anything when baking chocolate cupcakes. Another option would be to use alkalized, or Dutch cocoa powder.

Baking powder: Baking powder is a commonly used leavening agent composed of baking soda, cream of tartar, and starch. The cream of tarter is acidic, which counteracts the basic baking soda. Starch acts as a drying agent. In a recipe such as our chocolate cupcakes which calls for both baking soda and baking powder, the baking powder is likely the main leavening agent. Substituting baking powder is pretty easy, as long as you have baking soda and cream of tartar. The basic recipe is 2 parts cream of tartar to 1 part baking soda. No starch is needed if you are immediately using your homemade baking powder. Other recipes  for baking powder use alternative acidic ingredients such as buttermilk or yogurt. TLC has a great post about baking powder and how it works. Baking powder does not react with vinegar to create carbon dioxide, as is the case for baking soda. Instead, the baking soda in baking powder reacts with the cream of tartar to produce carbon dioxide.

NaHCO3 + KHC4H4O6 —-> KNaC4H4O6 + H2O + CO2

NaHCO3 + KHC4H4O6 —-> KNaC4H4O6 + H2O + CO2

Most baking powder is double-acting. This means that some bubbles of CO2 are produced when the baking powder gets wet, and the rest of the bubbles are produced when the baking powder gets hot in the oven. One last note about baking powder: the reason why recipes tell you to sift or whisk in the baking powder (which I NEVER do) is to prevent big holes caused by carbon dioxide bubbles.

Unsweetened cocoa powder: If you don’t have unsweetened cocoa powder, you can use Dutch cocoa powder. Of course, then you would not need the baking soda either to balance the cocoa powder, since the Dutch cocoa powder is neutral! Another suggested substitution is unsweetened chocolate. When using unsweetened chocolate, the fat in the recipe should be reduced by one tablespoon. “Why is that?” you may ask. I am beginning to realize that baking is all about balance.

Unsweetened chocolate, or baking chocolate, is made of chocolate liquor plus some type of fat, which makes the chocolate solid. Therefore, you do not need as much fat in your other ingredients. For our cupcakes, we could reduce the butter.

If you don’t want to use any type of chocolate in your substitution, there are some other options. Some healthy chocolate substitutes include carob, chocolate sapote (AKA black persimmon), and acai berry.

Salt: According to The Cake Bible, the function of salt is to accentuate or heighten flavor. Without salt, the cupcakes would have a “flat” taste. When looking up the use of salt in baking, I found this interesting article about the obstacles bakers face in trying to make healthier, low-sodium sweets. Salt substitutes are often used to reduce the amount of salt while maintaining flavor in food. While normal salt is sodium chloride, salt substitutes are usually a mix of potassium chloride and sodium chloride. Be careful, however, when using salt substitutes. Certain diseases and drugs reduce the body’s ability to excrete potassium. If you have this condition, eating potassium chloride could lead to hyperkalemia = not good.

Butter: Oh, butter. You make the world go round. According to In the Sweet Kitchen, butter, a solid fat, acts as a leavener when creamed with sugar. The granular sugar traps air as it is creamed into the soft butter. When the batter is heated, these bubbles expand, causing the cupcake to rise. With this in mind, it is easy to see why oil as a butter substitute could be a problem, as it will not trap air like the more solid butter. Second, oil is 100% fat while butter only contains 80% fat. When oil is being used to replace butter, less should be used. So fat is the ingredient that we really care about. Other sources of fat include shortening and lard. Another explanation that I have found for using fat in baking cakes and cupcakes is to prevent gluten from forming a network. When gluten forms this network, the cupcake can get tough or chewy. How this process actually works, I am uncertain, as I could not find good primary sources on the topic. There are some other alternatives to butter that are healthier, such as applesauce or any other type of pureed fruit.

Sugar: As mentioned previously, sugar assists butter to leaven the cake batter. Because of this, fine grained sugars are not recommended for baking cupcakes. Another nice thing about sugar is that it is hygroscopic–that is, it absorbs water. Because of this property, sugar prevents baked goods from drying out. Possible substitutions include agave nectar, Splenda, honey, maple syrup, and brown rice syrup. Agave sugars are about 11/2 times sweeter than normal sugar, so that should be taken into account. Cupcakes baked with honey will probably be more dense, with a higher moisture content, and may brown faster. When replacing sugar with a liquid sweetener, you may need to reduce the other liquids in your batter. Many baking websites that I have visited do not recommend artificial sweeteners, as they do not contribute the same amount of tenderness, moisture, or browning as real sugars. This is a great post explaining what type of sugar substitutes work well, and which don’t, when baking cupcakes.
Eggs: Egg whites act as a drying and leavening agent, while the yolk is an emulsifier. Vinegar and baking soda may replace eggs in cupcake batter, as the reaction mimics the leavening that the eggs provide. So NOW we can have our volcano!
Silken tofu, banana, and flax seed are commonly found substitutions. I cannot find much more detail on why eggs are used in cupcakes, or how the egg white acts as a leavening agent.
Vanilla: It appears that vanilla is only here to add flavoring. So substitute it with any extract you want (within reason)!
Milk: The primary function of milk in our cupcakes is to act as a liquid to lubricate all the dry ingredients and bind them together, along with the egg. Because of this, soy milk and other non-dairy “milks” can certainly be used. I bet even water would work.
So there you have it! The how and why behind all the ingredients in chocolate cupcakes. I am slightly tempted to make a batch of normal cupcakes and a batch of cupcakes with every single ingredient replaced…I’ll let you know the results if I do!

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