Molecular Models in Biology

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1 Molecular Models in Biology Objectives: After this lab a student will be able to: 1) Understand the properties of atoms that give rise to bonds. 2) Understand how and why atoms form ions. 3) Model covalent, ionic and hydrogen bonds. 4) Be able to predict which type of bond (if any) an atom is likely to form. 5) Model a carbon chain 6) Model the functional groups: hydroxyl, amino, and carboxyl 7) Understand basic carbohydrate structure. 8) Understand basic organic acid structure. 9) Model glucose, fatty acids and amino acids. Introduction: The properties of chemical compounds are directly related to the ways in which atoms are bonded together into molecules. Molecules are 3-dimensional entities that we often discuss in on a 2-dimensional surface (in our notes). Lewis dot structures and structural formulas of molecules are both examples of 2-D models. Using a ball and stick modelling kit, you will be able to see how atoms form molecules in 3-D. Atoms: Before you can begin forming models, you need to be able to predict the atomic structure of atoms of various elements. Atoms are made up of 3 parts (as discussed in lecture). Fill in the table below with your knowledge of the basic structure of an atom: Particle Location in the atom Electrical Charge Mass Proton Neutron Electron 1

2 Using the Periodic Table of Elements attached to this worksheet, complete the following chart: Element Oxygen Chemical Symbol Number of Protons Number of Neutrons Number of Electrons Atomic Mass Carbon Hydrogen Nitrogen Phosphorous Sulfur Sodium Chlorine Iodine Neon Draw a Bohr model for each of an atom of each of the following elements: O, C, H, N, P, S, Na, Cl, I, Ne 2

3 Valence electrons are those located in the outermost orbital (shell). Indicate how many valence electrons each of the following elements has and represent an atom using a Lewis dot structure. Element Number of valence electrons Lewis dot structure Oxygen Carbon Hydrogen Nitrogen Phosphorous Sulfur Sodium Chlorine Iodine Neon Models of Covalently Bonded Molecules A covalent bond occurs when 2 atoms share a pair of electrons. By sharing electrons, each atom can satisfy meeting a full valence shell and thus be stable. For each molecule below, draw both a Lewis Dot Structure and a structural formula H2O (water) CH4 (methane) NH3 (ammonia) 3

4 Now model each of the above molecules using your ball and stick model kit. Color code for the kit Atom Color and size Hole pattern Hydrogen White, very small No holes; ball and stick unit Carbon Black, large 4 holes equally spaced Oxygen Red, small 2 holes spaced far apart Nitrogen Blue, small 3 holes spaced far apart Sodium Orange, large 1 hole Chlorine Green, large 1 hole Question: What do the sticks between the balls represent? Look at your model of methane. If you drew a line connecting each hydrogen to each other, you could visualize a tetrahedron. Question: Water and ammonia also form tetrahedrons. For each of those molecules, describe what is located at the points that do not have a hydrogen. 4

5 The Polar Covalent Nature of Water and Hydrogen Bonds Because water has electrons at 2 of the 4 corners of the tetrahedron, those corners have concentrated a negative charge on that side of the molecule. Likewise, the hydrogen atoms at the other 2 corners have concentrated the positive charge of the protons on the opposite side of the molecule. The unequal distribution of charge means that water is polar. Polar molecules form hydrogen bonds. The negative side of one molecule aligns with the positive side of another molecule and forms a weak electrical attraction. You can experience these bonds with water when you watch a water strider walking on water. The insect is not heavy enough to break the hydrogen bonds that link the water molecules together. Water Strider 5

6 Make a couple of water molecules with your ball and stick set. Trace them in the space below. Show how hydrogen bonds would form between them. Ions and Ionic Compounds Ions form when an atom gains or loses electrons in order to complete a valence shell. Atoms that have gained electrons are called anions; those that have lost electrons are called cations. What charge to anions and cations have? Fill in the table below: Ion Anion Cation Charge Complete the following table indicating whether the element would readily become an anion or cation. Draw the Lewis dot structure for the ion. Element Number of Valence Electrons Becomes an anion or a cation? Lewis dot structure for the ion Sodium Chlorine Potassium Magnesium Calcium 6

7 For the following ionic compounds, indicate which atom is the anion and which is the cation. Compound Anion Cation NaCl (sodium chloride) CaCl2 (calcium chloride) KI (potassium iodide) HCl (hydrogen chloride) Use your ball and stick model to form NaCl. Question: Should you use the sticks provided? Why or why not? If not, can you think of a better way to model this compound? Ionic compounds dissociate in polar solvents (like water). This happens because the polarity of water surrounds each ion and separates it from its partner ion. Make a few ball and stick models of water. Model how water dissolves NaCl. Question: In your own words, explain why water is an excellent solvent and why ionic compounds dissociate in water. 7

8 Organic Compounds Organic molecules contain the elements C and H. Question: Which organic molecule have you modeled in this lab? In organic molecules, carbon forms chains. In the simplest structure, the other available bonding sites on each C are H. Methane Ethane Propane Make a ball and stick model of each of these compounds. Notice how they are not flat 2- dimensional structures. 8

9 Functional Groups In organic molecules important to biology, some of the H atoms on the C-chain are replaced by groups of atoms called functional groups. Functional Group Hydroxyl Carboxyl Chemical Formula -O-H O -C-OH Amino Phosphate -NH2 -PO4 Modelling glucose. Glucose (C6H12O6) is a typical carbohydrate. The molecule is a 6 carbon chain. Each carbon is connected to another carbon. Each C has two other bonding sites (besides those connected to the neighboring C). One of those sites has an H, and the other has a hydroxyl group (OH). Notice that H + OH = H2O. Carbo hydrate means that each carbon has the components of water (hydration) attached to it. Using the information above, make a ball and stick model of glucose. Question: Using that ball and stick model. Draw a 2-D structural formula of glucose below. Question: How many hydroxyl groups are in glucose? Circle them in your diagram above. 9

10 Modelling Fatty Acids All organic acids have a carboxyl group. Fatty acids are just a long chain of carbon atoms with a carboxyl group at one end. In saturated fatty acids, all other bonding sites on each C in the chain are filled with hydrogen. Use your ball and stick model to create a saturated fatty acid that is 6 C s long. Question: Using that model as a guide, draw the structural formula of your saturated fatty acid below. Circle the carboxyl group. Modelling Amino Acids Like fatty acids, amino acids are organic acids. Question: What functional group must an amino acid have if it is an organic acid? In addition to that carboxyl group, amino acids have an amino group. Both the carboxyl group and amino group are attached to the same carbon. The generalized structural formula for an amino acid is: The R indicates the rest of the molecule. 10

11 Question: There are 20 different amino acids. How many different R configurations do you think there are? Using your ball and stick model, create a model of this basic amino acid structure. Leave the R location unfilled. For the amino acid glycine, the R group is just a hydrogen atom. Add that to your model. Draw the structural formula of glycine below. Circle the amino group and the carboxyl group. For the amino acid alanine, the R group is CH3. Change your model to reflect alanine. Draw the structural formula of alanine below. Circle the amino group and the carboxyl group. You can see that ball and stick models can get complicated fast! Rather than continue making more and more complicated models, we will go back to 2-D representations of molecules. Now you have a basic understanding of the 3-D structure underlying those 2-D models. 11

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