Overview

There are five essential steps between “a collection of molecules” and “a living creature.” Interestingly, they do not seem to all occur in the same location in nature. In this lab, we will explore those steps at four different stations.

Science Question

How do the “warm little ponds” and “deep sea vent” hypotheses address the five events that must occur for life to arise (i.e. “abiogenesis”)?

Chemistry

These five steps are as follows:

1. Amino acids must arrive intact on the planet
2. Amino acids must come together into long chains of molecules (“polymers”)
3. The cell must metabolize, or take energy from its environment and use it
4. The cell must have a boundary that allows useful molecules in and keeps bad molecules out
5. The cell must be able to make copies of itself

STATION 1: AMINO ACIDS AND PROTEINS

Materials

• Pipe cleaners (one color)

• Construction paper:
  • 100 Hydrogen (red squares with one hole)
  • 50 Carbon (blue squares with 4 holes)
  • 25 Nitrogen (green squares with 3 holes)
  • 50 Oxygen (yellow squares with 2 holes)
  • 25 Side “R” chain (orange squares with 1 hole)

This is the molecular structure of an amino acid. The circles represent atoms, and the lines between them represent a type of bond called a “covalent” bond.

Atoms will make a covalent bond with each other when they are missing electrons in their outermost electron orbital. In the bond, they will share one or two or even three electrons. In the first row of the periodic table, there are two elements, and room for two electrons in the first orbital. Hydrogen has one electron, which means that it wants a second one. That is why there is one hole in the paper hydrogen atoms.

Carbon (six electrons) is in the second row of the periodic table, which has eight elements, and eight possible electrons in the second orbital. Carbon’s first two electrons fill the first orbital. Its remaining four partially fill the second orbital. It has four available spots for bonds, which is why the paper carbon atoms have four holes.

The orange paper “R” side chains are different. They are molecules in themselves. The side chain is what makes amino acids different from one another. There is a single covalent bond that attaches this side chain to the rest of the amino acid.

When amino acids bond together to become chains of amino acids (proteins), this process is called polymerization. This bond is different from a covalent bond—it removes one hydrogen and one oxygen from the right ends of one amino acid, and one hydrogen from the end of a different amino acid. The two hydrogens and oxygen that are removed will form a water molecule. The remaining carbon end and nitrogen end will make a new covalent bond, effectively making a chain of two amino acids. This process is called a “peptide bond”.

Instructions:

1. In your groups, use ten pipe cleaner bits, four hydrogens, two oxygens, two carbons, one nitrogen, and one side chain to construct one amino acid per group member.
2. Chain your amino acids together using peptide bonds. Each bond will free two hydrogens and one oxygen. Make those into water molecules.

Questions:

1. What is a covalent bond?
2. Describe, in your own words, how a peptide bond is formed.
3. Why is a wet-dry cycle necessary for the formation of proteins?
4. Which of the two pictures of abiogenesis is this method of protein assembly more consistent with?

STATION 2: METABOLISM

Materials:

• Safety goggles
• Baking soda (3 tbsp)
• Vinegar (½ cup)
• Funnel
• One balloons
• One small, round bottle (or a soda bottle)
• A ruler

Astrobiologists believe that the source of the first metabolism was the energy released when basic (i.e. not acidic, or “alkaline”) water from deep within the Earth met acidic ocean water. This hypothesis is consistent with life evolving around deep sea vents.

An acid is a material that has too many protons. A base is a material that does not have enough. When they come into contact, a lot of energy is generated in the exchange of protons.

Water deep inside the Earth is not necessarily alkaline when it comes up from those reservoirs. Along the way, it passes through a material called olivine. Olivine is sometimes cut and polished into a gemstone called peridot. When water comes into contact with olivine on its way up through the crust, it becomes alkaline.

Instructions:

1. Every group member should put safety glasses on.
2. Using the funnel, place the baking soda into the balloon.
3. Pour the vinegar into the bottle.
4. Stretch the balloon securely around the opening of the bottle.
5. Shake the baking soda from the balloon into the bottle and watch the balloon inflate.
6. Let the balloon inflate until it is large, but not in danger of popping. Remove it from the bottle and tie the bottom shut.
7. Measure the diameter of the balloon with the ruler in centimeters. Write it here: D = ________________ cm
8. Divide that number by 100 to obtain the balloon’s diameter in meters: D =  ______________ m
9. Divide that number by two to find the radius of the balloon: r = ________________________ m
10. Use the equation below to calculate the volume of the balloon.

V = 4/3 * 3.14 * r^3

V = ______________ (0.00214) m^3

1. Calculate the mass of the carbon dioxide in the balloon by multiplying V by 1.98 kg/m3 (the density of CO2 gas).             m = _____________ kg
2. The “specific heat” of carbon dioxide gas is c = 840 J/kg*C.
3. You may have noticed that the balloon feels colder. That is because this reaction is “endothermic”, or takes heat from the environment. Assume that the balloon has dropped 10º Celcius in temperature. T = -10º C
4.  Use the equation below to calculate how much energy, in Joules, was generated by this reaction (q). The amount will come out to roughly -20 – -50 J of energy.

q = -m * c * T

q = __________________ J

1.  One Joule (J) is equal to .00024 kCal, which is the calorie we are familiar with on food labels. Multiple your answer (q) by 0.00024 to calculate how many calories of energy this reaction produced. qkCal = _________________
2.  A donut is about 300 calories. How many times would you have to perform this experiment in order to use one donut worth of calories? (divide 300 by qkCal) N = ___________________.
3. A single cell in the human body uses 0.17 micro-Joules every day (.00000017 J). How many cells could be powered by the energy made in this reaction? (divide qKcal by 0.00000017) N = _______________________

Questions:

1. An endothermic reaction is when a reaction takes energy from its environment. An exothermic reaction is when a reaction produces energy. Which type happened when you dumped the baking soda into the vinegar? How do you know?
2. The balloon is full of CO2 gas. Why does it fall so quickly when you drop it?
3. Which of the two pictures of abiogenesis is the more likely place for this kind of reaction to play a role?

STATION 3: MEMBRANES

Materials:

• Flat, shallow container
• Water
• Dish soap
• Straws

One of the most essential parts of a cell is the boundary between itself and its environment. In modern cells, this membrane looks like the image below:

Membranes are made of molecules called lipids. Lipids are special in that they have one end which hates water (hydrophobic), and one end that loves water (hydrophilic). This membrane is a double layer, where the hydrophilic ends point out to the environment and in toward the cell, and the hydrophobic ends point toward each other.

Not only does this membrane need to exist, but it also plays the very important function of allowing helpful molecules in and keeping harmful molecules out.

The cells in your body are more complex than the membrane seen in the first picture. The image below is more accurate. Notice that there are specialized “channel proteins” that allow for the passage of molecules in and out.

In this activity, we will learn about how dish soap bubbles mimic this behavior, but reversed: with the hydrophobic ends out, and the hydrophilic ends in.

Instructions: 

1. Fill the shallow dish with about an inch of water.
2. Squirt in about a teaspoon of dish soap and mix around with the straw.
3. Use the straw to blow bubbles air under the surface of the water and watch bubbles form.
4. Push the soapy end of the straw through the surface of a bubble and see what happens.
5. Touch a bubble with your finger and see what happens.

Questions:

1. What happens when two bubbles get close to one another? Describe the geometry.
2. Draw a single lipid molecule and label the hydrophobic and hydrophilic ends.
3. Draw a double lipid membrane as it appears in a cell in our body.
4. Draw a double lipid membrane as it appears in a soap bubble; that is, with the hydrophobic and hydrophilic ends reversed. In the case of the soap bubble, the interior hydrophilic ends mean that there is a thin layer of water in between the double membrane layers.
5. There is a thin layer of oil on the tips of our fingers. Dish soap was invented to break down oils, because it is full of free-floating lipids. When wet, the hydrophobic ends of the dish soap lipids seek the dry space that exists between the membranes of cells. They wedge themselves into the membrane like a crowbar and break it up. This is why we use soap to wash our hands (it breaks up the membranes of surface germs and kills them), and also why washing dishes by hand can hurt your skin after a while. Using this information, explain why the soapy end of the straw can go through a bubble without popping it, but touching your finger to a bubble will pop it.