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Monthly Archives: March 2012

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 ūüôā

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 ūüôā

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:

  • 1¬†1‚ĀĄ3¬†cups¬†flour
  • ¬ľ¬†teaspoon¬†baking soda
  • 2¬†teaspoons¬†baking powder
  • ¬ĺ¬†cup¬†unsweetened cocoa powder
  • 1¬†dash¬†salt
  • 3¬†tablespoons¬†softened¬†butter
  • 1 ¬Ĺ¬†cups¬†sugar
  • 2¬†eggs, beaten
  • 1¬†teaspoon¬†vanilla
  • ¬ĺ¬†cup¬†milk
  1. Heat oven to 350¬įF.
  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 ūüôā
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!