Biology 11A Lab #2
Molecular Motion
Pre-Lab Exercise- Hand in the typed (double-spaced) answers to these questions on a separate piece
of paper at the beginning of lab. Please use complete sentences. The sentence should make sense on
its own, even if the question is not present.
1. What do the balls and sticks in the model kit described below represent?
2. What is a valence shell?
3. What do the number of holes in each ball in the model kit represent?
4. What amino acid molecules will you use to build a dipeptide? Include the formula.
5. What disaccharide will you build in today’s lab? Include the formula.
Bring your textbook to lab this week.
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Biology 11A Lab #2 Molecular Modeling
Questions in bold print are for you to answer and hand in during next lab. Copy the question,
respond to the question in complete sentences and type them.
Activity 1 Water - Liquid Awesome: Crash Course Biology #2 (Hank
Greene)
We will watch the You Tube Liquid Awesome video while in class and you will discuss the following
questions as a team. Type the answers to these questions 1-10, for next lab, along with the rest of the
questions (11-18) given later in this handout. You will also include a hand-written concept map. These
three things are due on your next lab.
Q1. What did Rover discover on Mars?
Q2. Draw a molecule of water.
Q3. What kind of bond does a water molecule form between H and O?
Q4. Add a charge to the molecule you drew in Q2. Explain why the charge exists.
Q5. What kind of bond links many water molecules together?
Q6. What is the difference between cohesion, adhesion, and surface tension?
Q7. Explain capillary action.
Q8. Compare a hydrophilic substance to a hydrophobic substance.
Q9. Why is solid water less dense than liquid water?
Q10. How does evaporative cooling work?
For this next section. work in groups of 3-4. Each group uses two model kits. Bring your textbook to
class. Refer to chapter 2.
One of the difficulties of studying molecular bonding is that you cannot see atoms and molecules. It is
difficult to visualize the shape of a molecule based on a two-dimensional drawing in a textbook. In this
lab you will use ball and stick models to construct molecules that are important to living cells.
You will be making covalent bonds by joining various colored “balls”
(representing different atoms) with various “sticks” (representing single, double
or triple bonds) that hold the balls together. The “sticks” represent a pair of
valence electrons shared between two atoms. The number of holes in each ball
represents the number of shared electron pairs that the atom normally requires to
become stable (i.e. a full valence shell).
Objectives
1. Build molecules that are biologically important.
2. Perform the chemical reactions of dehydration synthesis and hydrolysis with the
molecules that you and your classmates build.
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Activity 2: Small Molecules and Monomers
Atoms are usually composed of a nucleus of protons and neutrons with electrons in constant motion
around the nucleus in “electron shells” Each shell can hold a certain number of electrons before the shell
becomes full. Additional electrons then form new shells further away from the nucleus.
• The first shell can hold only two electrons.
• The second and third shells can each hold 8 electrons.
A periodic table arranges atoms in rows by the number of electrons in a particular shell. If the
outer- most shell in an atom has space for additional electrons, it is called a valence shell. A covalent
bond between two atoms are formed when those atoms share a pair of valence shell electrons.
Materials:
Carbon (C): use black balls with 4 holes
Single bond: white short connector
Hydrogen (H): white balls with 1 hole
Multiple bond: gray longer connector
Oxygen (O): red balls with 2 holes
Nitrogen (N): blue balls with 4 holes (these should have only 3 holes)
Procedure: Build the molecules 1-12 listed below using the structural formulas provided. Remember
single lines connecting atoms indicate single bonds, double lines indicate a double bond and triple
lines indicate a triple bond. Use the longer gray connectors in your model kit to form double or
triple bonds. Each connector represents one pair of shared valence electrons, so you use two long
connectors to make a double bond and three to make a triple bond.
Building molecules using your model kits.
1. Water: H20
2. Ammonia: NH3
4. Ethanol: C2H50H
Take those 4 apart now and you will build some carbohydrates.
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3. Oxygen gas: O2
Carbohydrate molecules range from small sugar molecules (you will build some below) to large
polysaccharides, which are long polymers of sugar molecules. Simple sugars have molecular formulas
that are some multiple of CH20. For example, glucose and fructose are six-carbon sugars so they have the
formula C6H1206. You should confirm this by counting the numbers of the different atoms in each
molecule.
5. Fructose (fruit sugar):
C6H1206
Notice where the double bond is on the molecule.
(Don’t undo this molecule)
6. Glucose (blood sugar): C6H1206
The double bond is in a different location
than in the molecule above.
(Don’t undo this molecule)
7. Fructose Ring Form Convert your fructose molecule from a linear molecule (from step 5) to a
ring. See diagram attached. Once you have built it, don’t take it apart.
8. Glucose Ring Form Convert your glucose molecule from a linear molecule to a ring. See diagram
attached. Once you have built it, don’t take it apart.
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Activity 3: Larger Molecules: Building a Disaccharide
Chemical reactions occur when atoms within molecules are rearranged to produce new molecules. Take
your fructose molecule and then combine it with your glucose molecule to make the disaccharide
sucrose. A chemical reaction that combines two molecules into one while producing water is called
dehydration synthesis. Dehydration means water loss, synthesis means building; you are building
sucrose.
9. Sucrose C12H22O11 ( a disaccharide) molecule as seen below. Convert your two monosaccharides into one
disaccharide. Notice what molecule you lost.
Hydrolysis is the “breaking of water”. Break the water molecule and convert your dissacharide BACK into two
monosaccharides. You essentially put an -OH back on one monosaccharide, and an –H back on the other.
Activity 4:
Building a Protein
10. Glycine is an amino acid: NH2CH2COOH
Build TWO of these molecules using Nitrogen (blue ball).
11. Making a protein
Glycine+Glycine: a dipeptide:
•
•
•
•
Remove one H atom from one nitrogen atom.
Remove an OH from the carbon end of the second glycine molecule.
Combine the two amino acids together at the free bonding sites. You now have a dipeptide.
Combine your dipeptide with one from another group to form a polypeptide.
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12. Making your own molecule!
Make your own organic molecule using at least 5 C atoms, and a combination of as many H, O, and N
atoms as you would like. (Remember to keep it simple and to follow the rules of bonding; C forms 4
bonds, N forms 3, O forms 2 and H forms 1). Record the molecular formula and the structural formula in
your notes.
13. Link the following words in a Concept Map:
covalent bond
hydrogen bond
cohesion
hydrophilic
hydrophobic
charge
polar
solvent
Make a drawing on your map and be ready to present it to the class via Elmo (projector).
14. Putting the boxes back together again.
When you are finished, please be sure that the models have all been returned to the proper kits. Each kit
should contain:
14 carbons (black)
40 linkers
28 hydrogens (white)
8 oxygens (red)
4 nitrogens (blue)
12 multiple bond connectors.
Some Background on Hydrocarbons
Hydrocarbons are organic molecules consisting entirely of carbon and hydrogen, such as methane
(CH4). Hydrocarbons are often used as fuels: the propane in a gas grill or the butane in a lighter.
The many covalent bonds between the atoms in hydrocarbons store a great amount of energy,
which is released when these molecules are burned (oxidized). Methane, an excellent fuel, is the
simplest hydrocarbon molecule, with a central carbon atom bonded to four different hydrogen
atoms.
The geometry of the methane molecule, where the atoms
reside in three dimensions, is determined by the shape of its
electron orbitals. The carbon and the four hydrogen atoms
form a shape known as a tetrahedron, with four triangular
faces; for this reason, methane is described as having
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tetrahedral geometry.
Methane has a tetrahedral geometry, with each of the four hydrogen atoms spaced 109.5° apart.
As the backbone of the large molecules of living things, hydrocarbons may exist as linear carbon
chains, carbon rings, or combinations of both. Furthermore, individual carbon-to-carbon bonds
may be single, double, or triple covalent bonds; each type of bond affects the geometry of the
molecule in a specific way. This three-dimensional shape or conformation of the large molecules
of life (macromolecules) is critical to how they function.
Hydrocarbon Chains
Hydrocarbon chains are formed by successive bonds between carbon atoms and may be branched
or unbranched. The overall geometry of the molecule is altered by the different geometries of
single, double, and triple covalent bonds. Double and triple bonds change the geometry of the
molecule: single bonds allow rotation along the axis of the bond, whereas double bonds lead to a
planar configuration. These geometries have a significant impact on the shape a particular
molecule can assume.
When carbon forms single bonds with other atoms, the shape is tetrahedral. When two carbon
atoms form a double bond, the shape is planar, or flat.
Hydrocarbon Rings
The hydrocarbons can be aliphatic hydrocarbons, which consist of linear chains of carbon atoms.
Another type of hydrocarbon, aromatic hydrocarbons, consists of closed rings of carbon atoms.
Ring structures are found in hydrocarbons, sometimes with the presence of double bonds.
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Lab Report Due Next Lab
This week the lab report consists of answering questions 1-10 on Hank Green’s video, answering
the questions 11-18 below in complete sentences, and your concept map. Type the answers up
and hand in during next lab. Hand-write the concept map on your report too. Not answering in
complete sentences will not get you any points. Zero points. Answers to the questions must make
sense on their own without the question present.
Q11. Why do Hydrogen atoms form only single bonds with other atoms and not double or triple
bonds like Carbon atoms?
Q12. What effect do double and triple bonds have on the rotation within molecules as compared
to single bonds?
Q13. How is it possible to change the shape of your molecular models without breaking any of the
covalent bonds? (Hint: shape depends only on the relative position of atoms within the molecule)
Q14. If a carbohydrate molecule contained 48 H atoms, how many atoms of C and O will it
contain? (Remember the formula for carbohydrate molecules is CH20).
Q15. What molecule did you lose in that reaction? What is that reaction called?
Q16. Why is a reaction that links monomers together into a polymer called a dehydration
synthesis?
Q17. What is the molecular formula of your made-up synthesized molecule?
Q18. Draw a two-dimensional model of your made-up molecule.
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