Name__________________________________________________________PD___________DATE_________________ Biology Topic 2 Worksheet Packet: Life’s Chemical Basis Every compound, molecule, or element you come across will be made of atoms. For example, trees are made of atoms. Air is made of atoms. Your pencil is made of atoms. Everything is made of atoms. In order to understand how living things work in biology, we must understand what they are made of. At the most basic level, all living things, and indeed everything in the universe, are made of atoms. Atoms are the basic units of all matter. Atoms can also be broken down into their smaller parts, which are called subatomic particles (“smaller than an atom particles”). These subatomic particles include: • • • Neutrons – which have no charge Protons – which are positively charged Electrons – which are negatively charged The protons and neutrons can be found in the nucleus of the atom, while the electrons orbit around the outside of the nucleus. See the figure above to better understand the structure of all atoms. 1. The basic unit of all matter is called a(n) ____________________________ 2. Describe the nucleus of an atom. 3. Complete the table below about subatomic particles Particle Charge Location in Atom Positive Neutral Negative Elements and Isotopes All atoms on Earth make up pure substances called elements. If you’ve ever looked at the Periodic Table of Elements, then you probably already know the names of some elements, such as copper, nitrogen, oxygen, and gold. Elements are pure substances that cannot be broken down any further by chemical reactions. Gold is an element. If you were to hold a bar of gold in your hand, you would be holding a pure element, made of many billions of the same type of atom. If you were to cut the bar of gold in half, then in half again, and again, and again… eventually you would be left with only a single atom of gold. This gold atom cannot be broken down any further without a nuclear reaction to release the protons and neutrons from the nucleus. Each element on the Periodic Table has a different number of protons. The number of protons is what determines the element. For example, all gold atoms in the universe have 79 protons. The number that tells you the number of protons is the element’s atomic number. Carbon has the atomic number 6, so all carbon atoms have 6 protons. Pure elements generally have the same number of protons and electrons, making them neutral in charge. While all atoms of the same element have the same number of protons (which is determined by the atomic number), not all atoms of an element have the same number of neutrons. The different versions of an element that have different numbers of neutrons are called isotopes. For example, all carbon atoms have 6 protons, but there are different isotopes of carbon that could have either 6 neutrons, 7 neutrons, or 8 neutrons. Isotopes are useful in biology, because some isotopes are radioactive. The radioactivity found in these special atoms can be used to scan living organisms for cancer or to see how the heart is pumping, to be used as tracers, and for radiation to kill microorganisms. In biology and all living things on Earth, the 6 most important elements are sulfur, phosphorous, oxygen, nitrogen, carbon, and hydrogen (SPONCH). All of the most important molecules in our body (such as our DNA, sugars, fats, and proteins) are made up of a combination of these 6 elements. In fact, a squirrel or a bird, or an earthworm, are also made up of about the same percentage and quantity of these 6 elements as we are. All living things also need other elements, but only in very small amounts. These elements are called trace elements (because you only need “trace” amounts of them). For example, our bodies, and all living organisms require tiny amounts of iron in our body. Calcium, lithium, and iodine are other examples of trace elements that living organisms require to live, but only in very small amounts. 4. What is a chemical element? 5. What does the atomic number of an element tell you about the atom of that element? 6. If oxygen has the atomic number 8, how many protons does it have? _________________ 7. What are the 6 most common elements in biology? 8. What are trace elements? 9. What is an isotope? How are isotopes used in biology? Molecules and Chemical Compounds Individual atoms can also come together to form molecules. A molecule is a group of 2 or more atoms held together by a chemical bond. A compound, is a molecule containing at least 2 different elements. For example, carbon dioxide, CO2, is a molecule and a compound. It consists of 2 oxygen atoms bonded to a carbon atom and its molecular structure is shown to the right. The molecular formula tells you how many of each atom is bonded together to form the molecule. There are three different types of chemical bonds that are important in biology: Covalent bonds – when electrons are shared between atoms; the strongest type of bond - nonpolar covalent bonds –when electrons are shared equally between atoms - polar covalent bonds – when electrons are shared unequally between atoms Ionic bonds – when electrons are traded between atoms; a medium strength bond Hydrogen bonds – an electromagnetic attraction between two polar molecules due to electron attraction; the weakest type of bond Notice that all three of the types of chemical bonds involve electrons. The reason atoms tend to form bonds with other atoms is to fill their electron shells. When an atom has a full electron shell, it is the most stable. The electrons found in the outer energy shell of an atom are called the valence electrons. The valence electrons are the ones participating in chemical reactions, either being shared, traded, or attracted to through an electromagnetic attraction. 10. What is a chemical compound? 11. A. What does the formula for table salt (NaCl) indicate about the compound? (Think about what a chemical formula tells you about the compound) B. What does the chemical formula for water (H2O) indicate about that compound? 12. Complete the table below about the main types of chemical bonds Type Formed when ... Relative Strength Covalent bond Ionic bond Hydrogen bond 13. What are valence electrons? 14. Why do atoms want to fill their valence electron shells? Ionic bonds Ionic bonds involve the transfer of electrons between atoms. In this case, one atom will give one or two electrons to another atom. The trading of electrons will form charged atoms called ions. Generally, the atom giving away electrons is trying to get rid of extra electrons, so that is has a full valence shell of electrons. This atom becomes positively charged because it is giving away negatively charged electrons. This atom is called a cation. The other atom is therefore receiving electrons. It is generally receiving electrons to fill up a partially filled valence shell, to become the most stable. This atom becomes negatively charged because it is gaining negatively charged electrons, and is called the anion. Ionic bonds between atoms generally form compounds called salts. Ionic compounds dissolve easily when interacting with water. When these ionic compounds are dried out, what’s left is a crystal, in which the cations and anions line up in a regularly repeating lattice structure. 15. What is an ion? 16. When an atom loses an electron, does it become positively or negatively charged? Why? 17. When ionic compounds are dried out, what do they form? 18. What happens when ionic compounds interact with water? Covalent bonds Covalent bonds involve the sharing of electrons between atoms. Generally, the atoms involved in a covalent compound are trying to obtain more electrons to fill their valence shell, making them the most stable. When atoms in a covalent bond share electrons, they form a very strong chemical connection that is difficult to break. There are two types of covalent bonds. When atoms in a covalent molecule share electrons equally, this is called a nonpolar covalent bond. When atoms in a covalent molecule share electrons unequally, this is called a polar covalent bond. Molecules formed using a polar covalent bond have oppositely charged ends (positive and negative) of the molecule due to the unequal sharing. The reason that some molecules form polar covalent bonds, and therefore polar molecules, has to do with each atom’s electronegativity. Electronegativity describes how hard a certain element of the Periodic Table pulls on electrons. Some elements pull harder than others, and therefore don’t share electrons equally when they form a polar covalent bond. 19. Why do atoms in a covalent bond share electrons? What are they trying to accomplish? 20. How are polar and nonpolar covalent bonds different? 21. What is meant by an atom’s electronegativity? Hydrogen bonds Hydrogen bonds form between polar covalent molecules. A hydrogen bond is a weak attraction between the positive pole of a polar molecule, and the negative pole of another polar molecule. In biology, hydrogen bonds are most important when discussing the chemistry of water, but hydrogen bonds also hold the two strands of a DNA double helix together. In water molecules, the oxygen atom has a higher electronegativity than the two hydrogen atoms. This means that the oxygen pulls harder on the electrons shared between them, forming a polar covalent bond. The oxygen side of a water molecule is partially negative, while the hydrogen sides of the water molecule are partially positive. This makes water molecule like little magnets. The magnetic attraction between the positive side of one water molecule, and the negative side of another water molecule forms a hydrogen bond. These hydrogen bonds are what makes water sticky, and leads to all of the properties of water that we will soon discuss in biology! 22. What is a hydrogen bond? 23. Why does the oxygen atom in a water molecule have a slightly negative charge? 24. Draw one water molecule below. Label the charges of the hydrogen and oxygen atoms. 25. Hydrogen bonds between water molecules make water ______________!!!! This causes all of the properties of water that we see! The Properties of Water The structure of the water molecule gives water unique properties. Water is a polar molecule, which means that it has a region with a slight negative charge (the oxygen atom), and a region with a slight positive charge (the hydrogen atoms). The oppositely charged regions of water molecules interact to form hydrogen bonds. Hydrogen bonds are responsible for several important properties of water. Cohesion: The attraction among molecules of a substance is called cohesion. Cohesion due to hydrogen bonds makes water molecules “stick” together strongly. So cohesion is when water molecules stick to water molecules. This can be observed in large raindrops, where water molecules tend to group together. Adhesion: The attraction among molecules of different substances is called adhesion. Water molecules “stick” to many other materials because of hydrogen bonds attracting them to those substances. So adhesion is when water sticks to other substances. This can be observed when drops of water stick to the surface of your car, or the liquid condensation sticking to the side of a cold drinking glass. High surface tension: Surface tension describes the strength of the bonds at the surface of a liquid and how hard it is to break the surface by breaking these bonds. Water has a very high surface tension due to the hydrogen bonds holding the water molecules at the surface together. This is what allows certain insects to “walk on water” of streams or ponds. Capillary action: Capillary action is defined as the ability of water to move through porous surfaces due to its cohesion, adhesion, and surface tension properties. Really, this describes the ability of water to absorbed naturally up small tubes, or into small holes. This is particularly important when considered the ability of plants to suck water from the ground without a heart to pump the fluid against gravity. Capillary action allows water to move from the soil vertically all the way to the top of a tree through tiny tubes in the plant. High specific heat: The specific heat of a substance describes its ability to absorb heat energy without changing temperature. Water has a high specific heat, and therefore resists changes in temperature; it must absorb a large amount of heat energy to increase in temperature. This is helpful for life on Earth because the lakes, streams, ponds, and oceans of the world can absorb a lot of heat without changing temperature, keeping a stable environment for the aquatic organisms that live in them. Low density of ice: Ice is less dense than liquid water, so it floats. When water freezes, each molecule forms a stable hydrogen bond with four neighbors. These stable hydrogen bonds cause more empty space between molecules of frozen water, when compared with liquid water, making the ice less dense. Very few substances on Earth have this property, for example frozen vegetable oil will sink in its liquid self! The frozen layer of ice on the surface of a lake or pond allows the ice to insulate the water below, keeping it warm for those organisms living in the water. The universal solvent: Water is a good solvent due to its polarity. Many compounds that are important for life dissolve in water. Water is the largest component of cells’ interiors (the cytoplasm), and chemical reactions in the cell take place in this water. When one substance dissolves in another, a solution is formed. The substance present in the greatest amount is called the solvent. Substances that are present in lower amounts and dissolve in the solvent are called solutes. Polar solvents, such as water, dissolve polar molecules and ions. 26. The hydrogen and oxygen atoms of one water molecule are held together by ______________ bonds. 27. Oxygen attracts more electrons than Hydrogen because it is more __________________________. 28. The electrons of water are not shared equally creating a _________________ molecule. 29. Hydrogen bonds form between two adjacent water molecules because the ___________________ charged hydrogen end of one water molecule attracts the ______________________ charged oxygen end of another water molecule. 30. Water molecules stick to other water molecules which is called _____________________. 31. Water molecules stick to other materials which is called __________________________. 32. __________________ _______________________ creates the skin-like surface formed due to the polar nature of water. 33. The ability for water to climb up small tubes against gravity is known as _________________________ ____________________________. 34. It takes a lot of energy to heat 1 gram of water. This describes water’s __________________________ ____________________. 35. The polarity of water allows it to _____________________ most substances. Because of this it is referred to as the universal solvent. 36. Explain how ice floats on the molecular level. 37. Draw and arrange three water molecules, showing dotted lines where the hydrogen bonds would be located, and signify which areas of the atoms are positive (+) and which ones are negative (-). The pH Scale: Acids and Bases What is pH? When certain substances called solutes, are dissolved in water, they can change the pH level of the water and create an acidic or basic solution. pH is a measurement of how acidic or how basic a solution is. The pH scale starts at 0 and goes to 14. Halfway between 0 and 14 is 7, which is neutral. Pure water has a neutral pH of 7. Compounds are acidic if they have a pH lower than 7. Compounds with a pH higher than 7 are said to be basic or alkaline. Exactly what makes a compound an acid or a base? To understand this you must understand water. Water is a molecule made up of three atoms covalently bonded together. Think of water as HOH instead of H20. Some compounds can cause water molecules to break apart into H+ and OH- ions. The H+ ion is called a hydrogen ion. It is actually a proton with no electrons. The OH- ion is called a hydroxide ion. If you mixed hydroxide and hydrogen ions together, they would immediately pair up and make water molecules. This is called a neutralization reaction. Hydroxide ions neutralize hydrogen ions. If, after a neutralization reaction is complete, there are H+ ions left over, then the solution is acidic. If, after a neutralization reaction is complete, there are OH- ions left over, then the solution is basic. Why is pH important to biology? Most cells can only survive within a certain range of pH. For example, human blood has a pH of about 7.2, which is slightly basic. Any higher or lower and the blood cells would be injured or killed. So you could say that a healthy person’s blood has a pH range of between 6.9 and 7.2 on the pH scale. Acids denature, or change the shape of proteins. As a matter of fact, strong acids like vinegar and lemon juice can be used to actually cook meats like fish and eggs. Ceviche is a dish made by mixing raw fish and lime juice and letting it sit for a few hours, actually cooking the fish using acid instead of heat. Acids are used by your digestive system to break down food molecules into simpler parts (called monomers). Bases cause oils and fats to fall apart. Your digestive system uses bile, a basic compound to help in the digestion of fats and grease. Oven cleaners and drain cleaners contain lye, a strong base that dissolves baked on grease and burned fats. Buffers are weak acids or bases that can react with strong acids or bases to prevent sharp sudden changes in pH. This is very important for maintaining homeostasis and pH balance. In your blood, and other fluids of your body, buffers help keep your pH levels balanced. When a buffer (such as a weak base) reacts with a strong acid, the buffer keeps the pH stable and the pH of the buffered solution will not change. 38. A student mixes strawberry Kool-Aid and water. A pH meter is used to measure pH of 5.4. What kind of solution is strawberry Kool-Aid? 39. In the Kool-Aid mixture, what must there be more of, hydrogen ions or hydroxide ions? 40. Sodas and fountain drinks contain dissolved carbon dioxide. Carbon dioxide, when dissolved in water, forms carbonic acid. This is why sodas are bad for your teeth. What might be the pH of soda? Explain. 41. A student adds an Alka-Seltzer to the Kool-Aid and it starts to bubble. After the bubbling, the pH meter now reads 8.3. What was released by the Alka-Seltzer tablet to cause this change? (OH- or H+ ions?) 42. Baking soda is a weak base. When dissolved in water, baking soda creates a buffered solution. Hydrochloric acid is a strong acid. What would happen if hydrochloric acid was added to the baking soda solution? 43. Bromothymol blue is a chemical indicator that is blue in basic and neutral solutions, and turns yellow as the solution becomes more and more acidic. Fill in what color you think Bromothymol blue would be in each of the situations in the chart. Situation Water directly from the tap Water after exhaled air is blown through a straw into it for 5 minutes. Water after a snail has lived in it for 3 days Water with 2mL of bleach added Water with instant coffee added Water after an aquatic plant is grown in it for 3 days in bright sunlight pH Bromothymol blue indicator color 7.2 5.1 5.8 9.4 5.0 7.7 44. Based on the table above, what effect does carbon dioxide (the gas you exhale) have on tap water? 45. This gas is also found in sodas and pop. What is in the list of ingredients to indicate this? (Find a can of pop and read it!!!) 46. Is bleach an acid or a base? Would bleach contain more hydrogen or hydroxide ions? 47. Is coffee an acid or a base? Would coffee contain more hydrogen or hydroxide ions?
