Bonds, Molecules, and pH Part I. Molecules and Chemical Reactions with ionic bonds often break apart or dissociate since the bond is of intermediate strength. Definition of a Molecule Molecules are groups of two or more atoms linked together by chemicals bonds. The simplest molecules are diatomic, or two-part molecules, such as oxygen gas (O2) and iodine (I2). In the chemical formula for a molecule, each different element within the molecule is listed alphabetically from left to right. A subscript following the element symbol indicates how many atoms of this type are linked within the molecule. For example, in the formula for water, H2O, there are two atoms of hydrogen and one atom of oxygen. Bonding in Molecules Figure 1. A crystal of sodium chloride (table salt) in which the basic molecule, NaCl, is repeated over and over to form a large solid. Ionic compounds are called salts. Such compounds are composed of a positively charged metal ion (such as Li+, Ca+2, Al+3, Cu+1) and a non-metal ion (such as Cl-, Br-, SO4-2, or NO3-1). Ionic Bonds Chemical reactions are the processes by which atoms lose or gain electrons so that they can adjust the number of electrons in their outermost shell. When electrons are gained or lost, however, the atom becomes unbalanced electrically. The outermost shell may be complete, but the number of protons may not now equal the number of electrons, and so the atom has a net positive or negative charge. Such electrically unbalanced atoms are called ions, where positive ions are cations and negative ions are anions. Ions of opposite charge attract each other, just as the north pole of a magnet is attracted to the south pole of another. When positive and negative ions associate together through ionic attraction, they form a molecule. Two ions (electrically unbalanced atoms) of opposite charge are said to be held together through an ionic bond. Sodium chloride (NaCl), a molecule formed from the association of a positive sodium atom and a negative chloride is held together by an ionic bond. When dissolved in water, compounds ACTIVITY A. – Viewing a model of a sodium chloride crystal 1. Locate a model of a sodium chloride crystal and answer the questions on the report worksheet as you examine it. Answer the questions posed under Part A on the report worksheet. Covalent Bonds Two electrically balanced atoms which have unfilled outer shells may react together to form a very strong bond called a covalent bond. This means that the outer shells of the two atoms get very close together and that electrons are shared. Covalent bonds are almost always made between non-metals like O, H, N, P, Cl, etc. found on the far upper right of the Periodic Table. Covalent bonds are the strongest types of chemical bonds. The nifty thing about sharing electrons is that the electrical balance of each atom is not disturbed. An electrically balanced Science 214 Lab Manual pg. 1 atom therefore retains electrical balance while also fulfilling the need to fill the outer shell. Covalent bonds can be single, double, or triple (nitrogen gas). H H H C C H H H N C OH 2. Using the foregoing as an example, complete the addition of hydrogen atoms to the molecule in Part B on the worksheet. Hydrogen Bonds Figure 2. A cartoon representation of two atoms sharing two electrons in a covalent bond and an atomic diagram of C2H6 showing seven covalent bonds. This is a relatively strong bond. The number of bonds that any non-metal atom can make depends upon the number of electrons in the outermost shell of that atom. Atoms will seek to fill their outermost shells to the maximum capacity. In this way, H forms 1 bond, O forms 2 bonds, N forms 3 bonds, and C forms 4 bonds. Polar covalent bonds are formed when atoms differ in electronegativity or electron pull. This asymmetrical pull causes the molecule to be partially charged at two ends. Non-polar covalent bonds are usually between atoms of the same kind like H2, O2, and N2. When two different molecules contain polar covalent bonds, parts of these two molecules become partially charged. An example of this is found in the water molecule where polar covalent bonds extend between the oxygen and the two hydrogen atoms. The partially positive or partially negatively charged portions of these molecules can be attracted to each other, if they are of opposite charge. In the case of water, the partially negatively charged oxygen of one water molecule can be attracted to the partially positive charge on a hydrogen of another molecule. Such an attraction forms a fairly weak link known as a hydrogen bond. ACTIVITY B – Completing a molecule formed of covalent bonds 1. If you are given a partially completed molecule lacking, say, hydrogen atoms, it is possible to fill out the rest of the molecule based on the rules of how many hydrogen bonds the atoms of H, O, N, and C normally form. For example, in the molecule below, C – C – N=C – O one can add hydrogen atoms to the molecule based on how many bonds each atom already has. This produces the molecule: Figure 3. A hydrogen bond formed between two different water molecules. The Greek letter sigma () is used to indicate a partial charge, not a full charge as seen in an ion. This is a relatively weak bond. ACTIVITY C – Examining the hydrogen bonds in a model of frozen water (ice). 1. Describe the arrangement of individual water molecules (red oxygen with two white hydrogens) in a model of ice. What atoms are involved in making a hydrogen bond from one water molecule to the next? Answer these questions under Part C on the report worksheet. Science 214 Lab Manual pg. 2 ACTIVITY D – Naming the type of bond found within a molecule. 1. In Part D on the worksheet, write in the type of bond seen between the indicated atoms (i.e. is it an ionic, covalent, or hydrogen bond)? ACTIVITY E- Writing out simple chemical reactions Chemical Reactions Chemical reactions (interactions between atoms) are usually a subtraction, addition or exchange of outer shell electrons. Atoms that have incompletely filled outer shells have a tendency to want to fill the shell up to its capacity ( 2 or eight) through the stealing or giving away of electrons. Sulfur (S), for example, is lacking two electrons in its outer shell. What does this mean? This means that sulfur wants to form chemical bonds with other atoms in order to gain 2 more electrons, even if the sulfur atoms has to share those two electrons in a covalent bond with another atom. In the course of a chemical reaction where sulfur acquires two new electrons, chemists show the progress of the reaction using an arrow between the beginning substances, or reactants, and the ending substances, the products. Chemical reactions also tend to occur so the reactants change from high energy to lower energy products. This is explained by the Second Law of Thermodynamics which says all matter will tend to become more disordered (or lower in energy). In the case of sulfur borrowing two electrons from oxygen gas to form a covalent bond, we write: S + O2 (oxidation-reduction reactions); the trading of ionic partners (exchange reactions); the breakdown of carbon-hydrogen molecules with oxygen to produce heat, carbon dioxide, and water (combustion); the breakdown of molecules using water (hydrolysis); and the synthesis of chains of units with the loss of water (condensation). O-S=O (or just SO2) In the chemical reaction equation shown above, the sulfur dioxide product can be written either using a structural formula or a simple molecular formula. The structural formula (OS=O) shows in more detail how the atoms are connected to each other. Some common chemical reactions found in nature involve the transfer of electrons 1. Complete the chemical reactions shown in Part E of the report worksheet. Note that some reactions are very simple, such as the association of two oppositely charged ions to form an ionic bond. Biomolecules Living things are largely composed of molecules that are quite large. These macromolecules are known as biomolecules. The four different types of biomolecules are carbohydrates, lipids, proteins, and nucleic acids. Carbohydrates (the sugars) are used as direct sources of energy in their simple forms and as energy storage molecules or rigid support molecules when in long chains. The most common simple forms are glucose, fructose, sucrose and lactose. The complex or long-chain forms include starch and cellulose. Lipids are water-fearing molecules that serve in a number of roles in living things. Some lipids store energy and provide insulation (fats and oils, like corn oil), others form a barrier envelope around cells (phospholipids) in a structure called the plasma membrane. Still other lipids capture light in photosynthesis (pigments like chlorophyll)or serve as chemical messengers (hormones like estrogen) in a multicellular organism. Proteins also have a wide variety of functions. In simple form, called amino acids, they act as a building blocks for larger molecules. When found in long chains, proteins act to speed up chemical reactions (enzymes), provide insulation (fur and feathers), send Science 214 Lab Manual pg. 3 chemical messages (hormones), carry other molecules around (transport proteins), defend the body from attack (antibodies), hold a multicellular organism together (structural proteins), and act as identification labels on cells (membrane proteins). Nucleic acids are found mostly in their long chain forms where they function to store or transport genetic information. Living things use deoxyribonucleic acid (DNA) to store hereditary information while ribonucleic acid (RNA) allows a cell to utilize the hereditary information. DNA is usually found in the nucleus or nucleoid of a cell, while RNA is found in the nucleus and the cytoplasm. ACTIVITY F. Using molecular models to follow a heat-producing reaction. 1. Get a molecular modeling kit for you and your team. Open it up and study the color coding of the atoms (black for carbon, red for oxygen, blue for nitrogen, white for hydrogen). Note also the medium length connectors which serve as covalent bonds between atoms and the long connectors which are used when double bonds lie between two atoms. We won’t be using the short white connectors. 2. Build the following molecules using medium length bonds for carbon-hydrogen bonds and the longest connectors in forming the double bonds between the oxygen atoms: CH4 + 2O2 5. Please take apart the atoms and bonds of your models and return them to the kit when you are finished with this activity. ACTIVITY G. Using molecular models to follow a protein breakdown reaction. 1. Use the model kit to form the following twopart protein molecule made of two amino acids linked together, glycine and alanine. You’ll need to use the longer bond connectors to form the double bonds between the Cs and the Os. H O O and O O H C O H N and O=C=O + 2 H-O-H 4. The reactants of this equation (CH4 and O2) have a lot of energy stored in the covalent bonds of these molecules. The products have much less energy in their bonds. Since energy can neither be created or destroyed (First Law of Thermodynamics), some of the energy of the reactants must be released when the products form. Answer the questions about this reaction under part F on the report worksheet. H H H C H (CH4) molecule. You should be able to rearrange and rebond the atoms of the three reactant molecules to produce one carbon dioxide (CO2) and two water molecules (H2O). H C H C H O N C H H C H O H or (in 3D): Your model should look something like this: 3. Now you will take these three molecules and perform the following chemical reaction. Note that according to the reaction, two molecules of oxygen react with one methane Science 214 Lab Manual pg. 4 2. The dark bold line at the end of the arrow in the structural formula of the protein shown above is the covalent bond (called a peptide bond) connecting the two amino acids together. The chemical reaction you are about to perform involves the breakage of this bond and the addition of a hydrogen atom to the nitrogen on the right and an OH combination to the carbon atom on the left. This will produce two separated amino acids. 3. Make a molecule of water for use in this reaction (H-O-H). 4. Now perform this “water cutting” or hydrolysis reaction by separating the two amino acids at the peptide bond between them. Break your water molecule apart and add the pieces to the two amino acids as described in Step 2. You should now have two product molecules that look like this: 5. Answer the questions under part G on the report worksheet 6. Please take apart the atoms and bonds of your models and return them to the kit. pH, Acidity and Alkalinity Water is made of molecules each with two hydrogen atoms and an oxygen atom (H2O). A water molecule occasionally breaks down into charged molecules called the hydrogen ion (H+) and the hydroxide ion (OH-). The amount of hydrogen ions and hydroxide ions in pure water and human blood is approximately equal. If the amount of H+ is greater than the amount of OH-, the water is said to be acidic. If the amount of OH-is greater than the amount of H+, the water is said to be alkaline, or basic. A system of measuring the concentration of OH- or H+ in water was invented; it is called the pH scale. The pH scale has values between 0-14, with pH 7 being the value where the concentration of H+ equals the concentration of OH- in a water sample. This is called neutral pH. See the pH scale below. and pH OH->H+ Alkaline Neutral H+>OHAcidic 14 13 12 11 10 9 8 7 6 5 4 3 2 1 Substance Draino, lye household bleach, oven cleaner household ammonia, fertilizer milk of magnesia, soap baking soda, Tums seawater deionized, distilled water; blood rainwater, cow’s milk, urine black coffee tomato juice Coca cola, beer, wine, orange juice, vinegar lemon juice, acid rain stomach acid, battery acid Figure 1. The pH scale and some pH values for common substances Science 214 Lab Manual pg. 5 Most living things require a pH of about 7 to function properly. When the pH drops below 7 (acidic conditions) or rises above 7 (alkaline conditions), a living thing will begin to die because the environmental conditions block or destroy a cell’s important metabolic reactions. Specifically, the enzymes in cells are ruined by high or low pHs. In humans, a variation of just a few tenths of a pH in the blood can be fatal. For this reason, our blood contains bicarbonate buffer, a substance which absorbs extra hydrogen or hydroxide ions. This means that bicarbonate buffer helps to prevent the pH change in our bodies, keeping the pH fairly constant, even if we eat or drink acidic or basic foods. ACTIVITY H. Measuring pH 1. Complete the pH chart on your lab report sheet. 2. pH or phydrion paper allows you to determine the pH of a liquid by dipping the paper briefly into the liquid. To see how this works, dip separate sticks of pH paper into the beakers labeled H2O, HCl and NaOH. Record your data on the lab report sheet. blood cells. Use a graduated cylinder to accurately measure 10 ml. Label this tube “B”. 2. Pour exactly 10 ml of “Pure water” into another beaker. Use a graduated cylinder to accurately measure out this volume. Label this tube “W”. 3. Add 5 drops of Methyl Red solution to both the “B” and “W” tubes. Methyl Red is a substance called a pH indicator. After adding Methyl Red, the liquid should be yellowish in color. If the liquid in the test tube becomes acid, the color will change to red. 4. This step involves working with acid, which can burn your skin and make holes in your clothes. Wash your hands or sleeves immediately if you spill it on yourself. Using the Acid/HCl solution, carefully add drops to the “W” tube, counting the drops as you go. Stop and SWIRL THE WATER in the tube AFTER ADDING EACH DROP to provide constant mixing. Stop adding drops when the liquid turns red. Record the number of drops it took to make pure water acidic in the table on page 10. 3. Locate the set of test tubes containing various mystery liquids. Measure the pH of each liquid using pH paper. Then use the pH chart at the beginning of this lab exercise, other observations, and your own experience to identify each liquid. Do not attempt to taste these liquids and use caution if you try to smell them. 6. Next, use the Acid/HCl solution to make the “B” water acidic. Carefully add drops to the “B” tube, counting the drops as you go. Stop and SWIRL THE WATER in the tube AFTER ADDING EACH DROP to provide constant mixing. Stop adding drops when the water turns red. Record the number of drops it took to make blood plasma acidic in the table on page 10. 4. Record a description, the pH, and the identity of each solution on the lab report sheet. 7. Wash out your B and W tubes and remove any labels from them. Place them upside down in the rack. Please wipe up any spills. 5. Be sure to clean up any spilled liquids and pieces of pH paper. ACTIVITY I. Testing the Buffering Capacity of Blood 1. Pour exactly 10 ml of “Blood Plasma” into a 50 ml beaker. Blood plasma is the clearish liquid in your bloodstream that surrounds the red Science 214 Lab Manual pg 6 Lab Report Bonds, Molecules and pH Name A. Describe the arrangement of the individual ions (green is sodium, silver is chloride) and their spacing in this model of NaCl (sodium chloride). What is the ratio of sodiums to chlorides? Describe the spacing between two sodiums as well as between a sodium and a chloride. B. Describe the arrangement of individual water molecules (red oxygen with two white hydrogens) in a model of ice. What atoms are involved in making a hydrogen bond from one water molecule to the next? C. Complete the following molecule by adding covalent bonds to hydrogen atoms according to the rules of how many bonds each of the different atom types make. C = C—N—O—C—N = C D. Name the type of bond found between the atoms indicated by the arrow. (Ca+2)(SO4-2) (K+) (Br -) H_Cl -CH2-O-H+ H-N- - CH2- _ H OH E. Complete the following chemical reactions by showing what the products of the reaction will be. Ca+2 + CO3-2 forms an ionic bond Science 214 Lab Manual pg 7 (Ag+)(NO3-) + (Na+)(Cl-) Silver (Ag) changes places with sodium (Na) t produce silver chloride and sodium nitrate (an exchange reaction) Li + Br (loses) (gains) Each atom steals or give up a single electron to become ions and then an ionic bond is formed (an oxidation-reduction reaction) F. Concerning the reaction where methane and oxygen react to form carbon dioxide and water as described under Activity F in the text: i. Rewrite this reaction (using chemical formulas) but include heat (written as 890 Calories of heat) as another one of the products of the reaction. ii. Given that this reaction features a carbon-hydrogen molecule breaking down in the presence of oxygen to form carbon dioxide, water, and heat, what type of chemical reaction is this? See the end of the Chemical Reactions section in the foregoing text for this lab. G. Concerning the reaction where a two-part protein (alanine-glycine) was broken apart (with the addition of water) to form two free amino acids: i. What type of chemical reaction is this? See the end of the Chemical Reactions section in the foregoing text for this lab. ii. Given that meats are nearly all protein, describe where in your body you might find this particular reaction taking place. Science 214 Lab Manual pg 8 Measuring pH 1. Complete the following chart. Write in the location of pH 0, 7, and 14 in the appropriate places on the pH line scale below. Also indicate with arrows where a strong acid and a weak base would be. Acidic Neutral Basic 2. Complete the chart below with the pH and type of solution for the three solutions shown. Table 1. The pH of three different solutions. H2O CH3COH NaOH (vinegar) (Draino) pH Acid, Base, or Neutral? 3. Complete the description, the pH, and the probable identity of each of the mystery liquids. Solution A Description: pH= Solution B Description: pH= Solution C Identity of liquid: Description: pH= Solution D Identity of liquid: Identity of liquid: Description: pH= Identity of liquid: Science 214 Lab Manual pg 9 Solution E Description: pH= Solution F Description: pH= Solution G Identity of liquid: Description: pH= Solution K Identity of liquid: Description: pH= Solution J Identity of liquid: Description: pH= Solution I Identity of liquid: Description: pH= Solution H Identity of liquid: Identity of liquid: Description: pH= Identity of liquid: Science 214 Lab Manual pg 10 Buffering Capacity of the Blood Number of drops required to turn acidic (red) Pure water Blood plasma 1. Which solution turned acidic with the fewest drops? 2. Which solution is buffered? 3. What specific chemical do we have in our blood that prevents our blood from becoming acidic whenever we drink vinegar (salad dressing) or Coca Cola? 4. How is the pH change (or lack thereof) of blood an advantage to living things? Science 214 Lab Manual pg 11