7 Lab Protocol: Chemistry & pH
Exercise 1: Draw a Bohr Model for a Carbon-12 atom
Read and discuss the pre-activity questions on your data sheet with your group. Complete answering all questions before moving to the next activity.
1. Carbon has an atomic number of six (6). This means all atoms with 6 protons in the nucleus are carbon atoms. How many protons are present in one Carbon-12 atom?
2. Isotopes are different versions of the same element. Two atoms are isotopes of one another if they contain the same number of protons but have different numbers of neutrons. Therefore, different isotopes of the same element will have a different atomic mass = # of protons + # of neutrons (a proton and a neutron are equal in atomic mass). Carbon-12 refers to a carbon atom with an atomic mass of 12. How many neutrons are in one Carbon-12 atom?
3. When thinking about an atom, we will assume that it is uncharged unless we are told otherwise. To be uncharged, the carbon-12 atom must have the same number of electrons as it has protons. How many electrons will be part of the uncharged Carbon-12 atom?
4. Atoms can have multiple electron shells. Each shell has a maximum number of electrons that it can hold: the shell closest to the nucleus is the first shell and can hold a maximum of 2 electrons; the second and third shells can each hold a maximum of 8 electrons. Since electrons prefer to be in their lowest possible energy state, the first shell is filled first followed by shell 2 and then shell 3.
How many electrons will be part of the first shell in a Carbon-12 atom?
How many electrons will be in the second shell?
How many electrons will be in the third shell?
5. The outermost shell containing electrons is called the valence shell of that atom. How many electrons are expected to be in the valence shell of a Carbon-12 atom?
6. The valence number of an atom refers to the number of unpaired electrons in the valence shell. Note that this is not the same as the number of valence electrons. The valence number can be determined by placing one electron at a time into the valence shell. If the second or third shell is the valence shell, consider it to have a north, east, south, and west position. You must put one electron into each of these positions before going back and adding a second electron. After you have done this, the number of electrons that are not part of a pair of electrons is called the valence number. (Remember that before placing any electrons in the valence shell, lower-level shells must be filled.) What is the valence number of an uncharged Carbon-12 atom?
7. The number of bonds that an atom is expected to make is the same as the valence number of that atom. How many bonds is a Carbon-12 atom expected to make?
8. Draw a Bohr model for Carbon-12 atom. Each group member is to draw their own Bohr model and initial next to it. Include the nucleus and electron shells making sure that the number of protons, neutrons, and electrons are correct and can be clearly counted by the instructor. Make sure it is clear which valence electrons are paired and which are unpaired.
Exercise 2: Determine the type of chemical bond
In this activity, you will practice identifying what type of chemical bond two atoms are likely to make depending on the difference in electronegativity between them. Complete the activity labeled Exercise 2 on your data sheet with your group.
Electronegativity difference between atoms | Type of bond between atoms |
< 0.4 | Nonpolar covalent |
0.4 – 1.6 | Polar covalent |
> 2 | Ionic bond |
1.7 – 2.0 | Ionic if metal, polar covalent if not |
Complete the following table in your data sheet.
Element | # of protons | # of electrons | # of valence electrons | electronegativity |
Hydrogen | 2.2 | |||
Oxygen | 3.5 | |||
Fluorine | 4.1 | |||
Lithium | 1.0 | |||
Carbon | 2.5 | |||
Nitrogen | 3.1 | |||
Sulfur | 2.4 | |||
Magnesium | 1.2 |
Complete the following table in your data sheet.
Element pairs | Electronegativity difference | Type of bond |
Hydrogen and Oxygen | ||
Carbon and Hydrogen | ||
Oxygen and Carbon |
Exercise 3: Identify the model elements by color
Now, you will work with the chemistry models provided in lab. The balls in the chemistry model kit represent different elements and the connectors represent covalent bonds. Based on the number of holes per ball (which represent unpaired electrons and the potential to make a bond), indicate which color of ball represents each of the following elements:
Phosphorus:
Carbon:
Hydrogen:
Nitrogen:
Oxygen:
In this model kit, the pieces used to represent single covalent bonds are short and rigid. The pieces used to represent double covalent bonds are long so that they can bend a little bit. Find examples of each in the kit.
Exercise 4: Build functional groups
Build each of the functional groups depicted in the table below using the correct balls and connectors. Then take a photograph of the models and upload it to Canvas. Do not include a ball to represent the R group (rest of the molecule); however, include a connector to show how the functional group would attach to the rest of the molecule. Note that the yellow ball which represents sulfur has six holes. Sometimes sulfur makes six bonds and sometimes only two.
- Methyl
- Hydroxyl
- Carboxyl
- Carbonyl
- Amino
- Phosphate
Below is a table that displays the functional groups to help you accomplish this task. Note that the colors may be different than the model. Focus on the elements used.
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Exercise 5: Build an amino acid using functional groups.
There are four components that make up an amino acid:
- A central carbon, including a covalent bond to one hydrogen.
- An amino group.
- A carboxyl group.
- An R group
Using the functional groups you produced in the previous task and other model parts, build the amino acid valine, isoleucine, serine, or asparagine. Below is a table showing the atomic make-up of all standard amino acids.
As a group of two, build the amino acid assigned to you. We want to build a variety of different amino acids so we can compare them to one another. Follow this procedure:
- 1) Place the amino group that you built in the previous task in front of you.
- 2) Place the carboxyl group that you built in the previous task in front of you.
- 3) Attach a connector to a hydrogen atom.
- 4) Build the R group and include a connector with which you will connect it to the central carbon atom (in blue on diagram).
- 5) Use a carbon atom with four empty holes. Attach items 1 – 4 to the carbon atom. Your amino acid is complete.
Exercise 6: Build various hydrocarbons
Build each of the following hydrocarbons:
- An unbranched chain with 4 carbons and 10 hydrogens (C4H10)
- A branched hydrocarbon with 4 carbons and 10 hydrogens (C4H10)
- Chain with 4 carbons and 8 hydrogens (C4H8) including one double bond between any two carbon atoms
- A ring with 6 carbons and 12 hydrogens (C6H12)
- Two different structural isomers of C4H9OH
Exercise 7: Build Structural and Cis-Trans isomers
1) Structural isomers
Structural isomers have the same chemical formula but differ in the arrangement of the atoms within the molecule. For example, a branched C4H10 is a structural isomer of a straight chain C4H10. Structural isomers will have different chemical properties. Note that to change a molecule into one of its structural isomers, you will need to break at least two bonds.
You may work in pairs to construct the two of four possible structural isomers of C4H9OH at your table. Take a picture of each. One of the two pairs should begin with an unbranched C4H10 and the other group with a branched chain. This should be simple: remove a hydrogen from the hydrocarbon and replace with a hydroxyl group. Two structural isomers are possible with the unbranched hydrocarbon and two with the branched hydrocarbon. Note that structural isomers are different molecules requiring bond breakage to interconvert. A simple rotation of the molecule will not change it into a different structural isomer.
2) Cis-Trans isomers
Cis-Trans isomers are important in fatty acids. Fatty acids are a key component of many lipids. Cis and trans isomers differ in the rotation of the carbon atoms around a double bond. Because double bonds cannot rotate, cis and trans isomers differ in shape as shown in the diagram below.
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Create a cis isomer of C5H10COOH placing the double bond in the center of the molecule.
Create a trans isomer of C5H10COOH placing the double bond in the center of the molecule
Exercise 8: Demonstrate hydrogen bonding
Build five water molecules (H2O).
Lay the water molecules on the table. Line up the water molecules so that the oxygen of one water molecule is pointing toward one of the hydrogens of the other water molecule. Take a picture. Get instructor initials.
What is the name of the attraction between the oxygen of one water molecule and the hydrogen of the other?
Is this a type of covalent bond? Circle one: Yes No
What type of covalent bond is this?
Exercise 9: Evaluating a solution for its buffering capacity
First assess the effect of adding HCl to a known buffer (phosphate buffer, pH = 6) and water (negative control).
- Measure 3 mL of phosphate buffer (known buffer) into one test tube and 3 mL of water (negative control) into another test tube.
- Measure and record the pH of each solution.
- Add 200 μL of 0.1 M HCl to each tube, wrap tube in parafilm and invert to mix.
- Measure and record the pH of each solution.
Based on molecular formulas and reading labels of alka seltzer and other acid indigestion product, predict which of the solutions below will function as buffers. Indicate why you made each prediction.
Now evaluate the buffering capacity of a variety of liquids in the same way as described above.
- Milk
- 0.1 M NaCl
- 0.1 M glucose
- 0.1 M glycine
- Alka Seltzer
- Another product to reduce acid indigestion.
Record pH readings on the data table and indicate if the solution is an effective buffer,
pH before HCl | pH after HCl | Effective buffer | |
Phosphate buffer | yes | ||
water | no | ||
milk | |||
0.1 M NaCl | |||
0.1 M glucose | |||
0.1 M glycine | |||
Alka Seltzer | |||
Second product |
Text adapted from Jacob Broderick