Spring2013_Lab6

=Digestion and Metabolism, Lab 6 - Tues 3/5/13=

This week we will do lab 6 (Digestion) on Tuesday, and then on Thursday we will do lab 7 (Hormones). So for each day, you will have one worksheet to turn in. Both worksheets will be due two weeks from now on the same day. The quizzes during this week will cover this new material for lab 6 on Tues and Lab 7 on Thursday. Please read over the Lab 6 material before Tuesday, and read over Lab 7 material before Thursday. This will also help you on the quizzes.

Quiz topics
Quiz 3 will be on Tue the 5th, and it will cover the Plant lab (this is old material, not many points), Animal Diversity (this is the last lab, the most points will cover this), and Digestion (future lab, not many points here).

Quiz 4 will be on Thurs. the 7th, and it will cover the Data Analysis and Digestion as the old material, and Hormones (Lab 7) as the current material.

=Worksheet hints:= In order to answer the worksheet questions, you will need to look information up in your lecture textbook, or other biology textbooks. The information I presented in class was not information that will help you answer the questions directly. Instead, my mini-lecture was information that (hopefully) gave you a general overview of the biology of digestion.

If the worksheet asks you to explain your results, and your results do not match what you think should be happening based on your scientific understanding of digestion, then you should give an explanation of why the two do not match.

=Lecture topics:=

Like water off a duck's back
Every organism needs to do two things: survive day to day, and reproduce a next generation. Both of these activities require energy. Energy is obtained, for example, from food or sunlight. Both food and sunlight contain energy, but the organism must first extract the energy from the food or sunlight. Sunlight is a form of invisible energy called radiation, and the radiation is called electromagnetic radiation. When you stand in sunlight, you get hot, or get a suntan/sunburn, due to this radiation. It's not like nuclear radiation from an atom bomb, but it's called thermal radiation like from a tanning booth. The thermal radiation results in heat on your skin. The sun is the source of the heat, and plants can convert the radiation of sunlight into energy that the organism can use.

An example of how energy can be extracted from something like an old fashioned water wheel. Back in the days before electricity was everywhere, folks needed to grind wheat and corn into flour. They had to do this in order to make pastries. And human civilization would have ground to a halt without baked goods. Okay, maybe not. Anyhow, to make flour or meal, pre-modern civilizations would grind the grain between rocks by hand to produce flour or meal. The next bit of technological advancement was to built a water wheel. This contraption would used a river as the source of grinding energy.

To build a water wheel mill, folks would built a huge stone apparatus that would grind the grain. Then they would connect this stone to a wheel that would spin on an huge axis. Everything had to be huge back then, but I don't know why. Next, they would put the grinding mill near a river. When they put the wheel in the river, water flowing downhill would turn the wheel, and this would then turn the stone, and then the stone would mill the grain into a flour meal. That is so totally better than doing it by hand.

But the real question is, where does the water begin its flow? Water flows downhill because of gravity, and the original source of water is from snow or rain on higher ground, such as a mountain. Thus, because the water has mass and will be pulled downhill because of gravity, it has the potential to move the wheel. The motion of the river water can then be converted into energy that can be used to perform work, like grinding flour to make a cinnamon roll. Mmmmm, I love cinnamon rolls....

Here's an example: (The "flume" is where the river water enters the wheel)



Batteries are great
Energy is a lot like a battery, for example a 9 volt battery. If you want to experience electrical energy, stick the 9 volt battery prongs on your tongue. But do it quickly! If the battery is charged, you'll feel a small electrical shock. If you feel nothing, then it's not charged very much.

Anyhow, the two prongs of the battery represent the positive or negative charges of electricity. The positive and negative charges, in real life, are atomic particles (such as protons (+) or electrons (-)) which have a positive or negative charge in and of themselves. If you get two positive charges and put them close to one another, they will repel each other and move away from each other. The same things happens with two negative charges. If you have a positive and a negative charge and put them close to each other, they will attract each other, and move towards each other. A similar principle acts on magnets. Magnets have a "north" or "south" pole, much like the poles of the earth, opposite magnetic poles will move towards each other. Similar magnetic poles will repulse each other. It's the force that you feel when you try to pull apart two magnets that are stuck, or when you try to force two "north" magnets together. The reason of the magnetic and electrical charge attraction and repulsion has to do with quantum physics or something. So I'll just skip over that topic for now.

Okay. Back to the battery. We said the two prongs contain negative or positive charges. This means that the charges are inside the battery, and the prongs allow you to access the positive or negative charges inside the battery. Now imagine you take a wire -- or some other electrically conductive material (like your wet tongue) -- and connect the two prongs to each other. Now the positive and negative charges will have a path to travel towards each other (because opposites will move towards each other). The negative charges will move through the wire (or your tongue -- yikes!) to the side of the positive charges. This movement of charges will either heat up the wire or give your tongue a gentle (or harsh) shock, depending on how charged the battery is. In fact, this flow of electrons is how the old fashioned Edison-style light-bulbs worked. In this case, the light bulb was hooked up to a positive and negative charge (like a battery or an electrical outlet) and the electricity would travel through a wire in the light bulb. This flow of electrons would heat of the wire until it glowed and gave off light (and heat). I don't know how the new-fangled mercury bulbs work.

Anyhow, the battery is really just a little box with electrical charges stored inside. But the positive and negative charges are separated from each other in the box. When you connect the two prongs, the charges can move towards each other. If you put something in the path of the electrical charge, like a motor, the electrical charges can cause the motor to move.

For example, a battery can make an electrical car move forward. If, on the other hand, the battery was all out of juice and didn't have any more charge, you'd be stuck in the middle of no where. But there is hope! You could, in principle, reverse the direction of the car and re-charge the battery. So, if you took the electrical car and moved it backwards (while the car was in "drive"), it would reverse the flow of negative charges back to the negative side and re-establish the separation of the negative and positive charges*. It's like taking the water and hauling it back up the mountain. But I guess nature already does this for us, just on its own schedule.


 * Some batteries cannot be recharged safely, but this is because of the chemical makeup of the battery. A French company has built a recharger for "non-rechargeable" batteries (see the photo on the right).

Cinnamon roll digestion
But what about digestion and food and energy? If you really think about it, the cinnamon roll that you ate yesterday (at least I ate a cinnamon roll yesterday) is really just a bunch of molecules. And molecules are made of atoms. Why don't these atoms just fly off and go do their own thing? The reason is the electromagnetic bond that hold the atoms together. And I'm sure you remember the electromagnetism from when we chatted about the sunlight. Yup, it's really the same thing. Also, these bonds are also like little batteries, like the 9 volt battery. If you break a bond, you are releasing pent-up energy, just like the water in the river flowing downhill. If you break these bonds in the atoms of the food, then your body can store this released energy into little batteries, if it had little biomolecular batteries. And it does! These batteries are molecules called ADP or ATP. The "D" stands for double and the "T" stands for triple. They refer to how many "P"hosphate atoms the molecule has. As you add energy to an ADP, it can store it in it's own chemical bond with another phosphate and now it becomes an ATP molecule. The reverse can happen also. If your body needs energy, it can take an ATP, break one of the phosphate bonds and release energy for your body to do things like move around, repair itself, or grow. The ATP in this case becomes an ADP. And then you just eat more food and turn more ADP into ATP and your ready to go.

But how do you get the energy in the first place to turn ADP into ATP? The food itself is made of molecules and atoms, and these atoms are also bonded together with electromagnetic bonds. As you put food into your system, your body has made molecules of its own, which can interact with the food particles. These molecules are called enzymes. If the enzyme can break the bond in the food particles, then you can get energy form your food. Enzymes can do this breaking-up, and it uses the idea of like charges repel and opposite charges attract. This repulsion or attractive forces between charges can be used to break the bonds in the food. The way it does this is, the enzymes are made of atoms, and the food is made of atoms. The atoms themselves can have charges in and of themselves. This means that the enzyme atoms and the food atoms can interact between each other. In the case of an enzyme, it works best with one particular type of food molecule (for example, carbohydrates or lipids or proteins), and it can break up the bonds in these food types the best.

The enzyme and the food are molecules, but these molecules are three-dimentional structures that are also slightly changing shape all the time. They don't move much, but they move enough to not be totally frozen in space. At the same time, food and enzymes are floating around in the liquid environment of your gut (from mouth to intestine to colon). Each enzyme is shaped in a particular way that actually physically fits with a particular food particle. This allows the enzyme to interact with the food particle. It also allows the individual atoms that make up the enzyme to interact with the individual food atoms. Remember: each atom can be charged either negative or positive or neutral. So, when the enzyme atoms interact with the food particles, the charges in the enzyme atoms can actually pull apart the atoms in the food molecule (or, alternatively, push together other atoms, for example when adding phosphate to an ADP). As these food atoms are pulled apart, the force of pulling can break the electomagnetic bond between the atoms in the food. In this way energy is released. The released energy can then be stored in the biomolecular battery of ADP (by turning ADP into ATP). Magic! The body has taken food and converted the energy in the food into energy that can be used by the body.

pHat environmental science
The last things to consider is the environment of the enzymes (we won't consider its effect on food molecules). An enzyme may not be very effective in some environments, due to how the environment may alter the enzyme itself. The environment is the liquid that covers the gut. This environment can actually alter the charge of the atoms in the enzyme. The environment contains isolated charges (free-floating (+) and (-) charges) that float around in the liquid and also interact with the enzymes. These free-floating charges can then change the charge of the atoms themselves. The charges do not break the bonds of food, because the food bonds are the very strong bonds between carbon atoms. The charges can, however, alter the charges of individual atoms of the enzyme. If the charges of the enzyme change, then this can alter how the enzyme interacts with the food. Remember, like charges repulse and opposite charges attract. These repulsive and attractive forces allow the enzyme to break the bonds of food when the enzyme interacts with the food. So, if the charges on the enzyme change, then the enzyme might not be able to break the bonds of food very well. This can alter the effectiveness of the enzymes, depending on the environment of the enzyme.

The amount of free-floating charges is measured by a things called pH. The pH is either a low number or a high number or it is number 7. If it's number 7, then there are as many positive charges floating around as there are negative charges. If the pH is low (say 2 or lower) then there are many many more positive charges than negative charges floating around. This is called acidic. If it's high, say 14 or higher, then it's the opposite and there are many more negative charges floating around. This is called basic or alkaline. Remember, the acid or base itself does not break the bonds in food in order to perform digestion. The pH can, though, alter how effective an enzyme is at breaking food bonds. Thus, the pH can indirectly affect digestion, but it does not in itself explain digestion.

Other environmental considerations are the temperature of the environment. Temperature is really just describing how molecules move. At high temperatures, things move a lot. At cold temperatures, things don't move a lot. When there is more movement, there is more chances for enzymes to interact with food molecules (substrates).

Overall, there are lots of things happening with digestion. By thinking about the elecromagnetic forces that are happening at the molecular and atomic level, we can begin to explain how animals get energy from food. We can also better understand how our digestive system is built, in order to compartamentalize each phase of the digestive process, since the environment is so important to making sure the enzymes are working most effectively.