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Honors Biology Basic Chemistry Notes Mrs. Miriello This note packet is in large part a basic review.

If you are having any difficulty with this material, please make plans to see me as soon as possible. These concepts will be the building blocks for the year and it is essential that you understand them. Why do we study chemistry in biology? A human being has been defined as 20 gallons of water and $5 worth of assorted chemicals. All living matter essentially is built from basic chemical components. This is our starting point to understand biology. The chemistry of living things has two basic features. 1. Living things are composed mostly of water. 2. The backbone of living structures is based on carbon skeletons. Atom the smallest particle of matter that can exist and still retain the properties of that particular type of matter. Example an iron atom can still retain all of the properties of iron. Atoms are electrically neutral when the number of protons equals the number of electrons. Subatomic particles Proton positively charged, found in the nucleus, each with the atomic weight value of 1. Neutron neutrally charged, found in the nucleus, each with the atomic weight value of 1. Electron negatively charges, found in the electron cloud surrounding the nucleus, each with the atomic weight value of 0. An electron has 1/1890th the weight of a proton or neutron. We will refer to electron shells or valence shells to identify the location of the outermost layer where the electrons can be found. Remember the order 2, 8, 8 or 18, 32, etc.

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Elements is a substance that cannot be broken down into other kinds of substances except by extraordinary means (radioactive decay). An element contains only one kind of atom. There are approx. 118 different elements each with their own unique set of chemical properties. Living organisms use only about 20 of these elements they are not the most common elements, but those that are of the most use to living organisms. 97% of the compounds present in organisms contain only 6 elements O C H N P and S. Chemical elements are presented on a periodic chart identified by their symbol. This is a one or two letter designation for the element. The first letter is always capitalized and the second is lower case.

Subscript is a number written below and after the atomic symbol that represents the number of atoms of a particular element in a compound or molecule. If no number is written it is implied as one.

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Atomic Number this is equal to the number of protons Atomic Mass this is equal to the number of protons + neutrons Atomic Weight this is equal to the number of protons and neutrons, however this number is not always a whole number it is an average taking into account for the presence and relative abundance of isotopes found in nature. When using a periodic table and given a decimal atomic weight round up or down before calculating. Isotopes two or more forms of an element differing in terms by the numbers of neutrons in the nuclei of their atoms. This provides varying isotopes with varying atomic weights. The best example is carbon 12 and carbon 14. Carbon 14 is radioactive unstable and will eventually decompose. Ions atoms or groups of atoms that have become electrically charged when the individual atom or groups of atoms has lost or gained one or more electrons. Atoms that lose electrons become positively charged and are also called cations. They are represented by plus signs to the upper right hand portion of the symbol or group of atoms. Atoms that gain electrons become negatively charged and are called anions. They are represented by minus signs to the upper right hand portion of the symbol or groups of atoms. How do we know which atoms will form cations and which will form anions? How do we know the charge to expect?

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Chemical Bonds attraction, sharing or transfer of outer shell electrons from one atom to another. Chemical Reaction change in chemical bonds that produce one or more new substances. The original bonds are broken and rearranged to form new bonds. The reactions are represented by chemical equations. Remember the nucleus of the atom and the inner electrons are not involved in this process. Cells are the basic unit of life and chemical reactions are very important to the cell used for growth and energy changes. Energy is required to break bonds and then it can be released when new bonds are formed. Electric energy 2H2O 2H2 + O2 Why do the number of atoms on each side of the equation equal? The answer lies in the Law of Conservation of Matter. The number in front of each compound or molecule is the coefficient it represents the whole number of molecules in that reaction. The arrow represents the direction of the equation. Activation energy start up energy required to get the chemical reaction to occur. All chemical reactions require some amount of activation energy. Other vocabulary you should remember: reactant and product. Covalent bond a link between two atoms that share a pair or more than one pairs of electrons. Maximum sharing between individual atoms is three. This allows electrons to have complete outer shells. This is the goal of the sharing of electrons Single covalent bond a link between atoms that share one pair of electrons one electron from each element are shared. Double covalent bond a link between atoms that share two pair of electrons two electrons from each element are shared. Triple covalent bond a link between atoms that share three pair of electrons three electrons from each element are shared.

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Electrons, when sharing, can be fair or unfair. Non-polar covalent bonds - Even sharing Each atom gets the shared electron 50% of the time. There are no areas of partial charge, the atoms are equally electronegative. Electronegativity refers to the ability of the atom to attract electrons more strongly or less strongly. Examples methane CH4 Polar Covalent bonds uneven sharing of electrons This occurs when one atom is more electronegative than another. Although the electrons are shared between that atoms and the entire molecule is electrically neutral, the electrons orbit around one of the atoms more than 50% of the time. This results in areas of partial charge. The atom is electrically lopsided. Often this occurs between hydrogen and oxygen, hydrogen and nitrogen. The hydrogen will have a partial positive charge and the oxygen and nitrogen will have a partial negative charge. This becomes very important as molecules grow.

Ionic Bonds this is a force of attraction between charged atoms based on opposite charges. The cations are attracted to the anions. This powerful electrical attraction holds the atoms together. As a result, the outer full shells are attracted to other outer full shells and the overall combination is electrically neutral while together. Example sodium and chlorine. Look at figure 1.7 in your text. Remember it is not the transfer of electrons that forms the ionic bonds it is the fact that a positive ion is attracted to a negative ion.

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Hydrogen bonds this is a weak and often fleeting electrical attraction between two atoms with opposite partial electric charges. One partner is a hydrogen atom, bearing a partial positive charge because it is linked to a nitrogen or oxygen by a polar bond. Because of the partial positive charge, the hydrogen is attracted to a third atom with a partial negative charge. This is what forms a hydrogen bond. Hydrogen bonds can form between atoms in different molecules or between atoms on different parts of a large molecule.

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Now we get to the good stuff the impact of polar covalent bonding, water and the resulting hydrogen bonds. This makes life on Earth possible. Water and the Environment its unique behavior is related to the structure and interactions of its molecules. Water is polar because of hydrogen bonding. Due to oxygens higher electronegativity as compared to hydrogen, oxygen essentially hogs hydrogens electrons almost 75% of the time. This results in a partial positive charge on the hydrogen atom during the time that oxygen is hogging the electrons and a partial negative charge around the oxygen atom while it is hogging the electrons. The molecule as a whole is electrically neutral as the total number of protons equals the total number of electrons. The molecule ends up shaped like a wide V because of the opposite ends having partial positive charges. Remember, this partial positive charge repels each other. All of the special properties of water arise out of the interactions and hydrogen bonds between the water molecules and its environment. Life on Earth is based on water and these properties,

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Cohesion by definition it is the binding together of like molecules, usually by hydrogen bonds. As a result of water molecules all having partial areas of charge, hydrogen bonds form between different water molecules. These hydrogen bonds are not very strong, in liquid water, they are about as strong as 1/20th the strength of a covalent bond. The breaking and reforming occurs in the trillionth of seconds. This is definitely too brief a time to conceptualize. Their strength is in the sheer total numbers of bonds that are being formed. This is important is transporting water against gravity upward in plants. ( OPPOSITE OF COHESION) Adhesion the attraction between different kinds of molecules. This is important as the polar water molecule is attracted to the polar xylem, the transport vessel in plants. Surface tension this is a measure of how difficult it is to break the surface of a liquid. Due to the hydrogen bonds and resulting cohesion, water has a higher surface tension than many other liquids. It makes the water behave as if there is an invisible film. This is how it appears that some organisms are able to walk on the top of water. Water moderates temperature on Earth. Both air and water temperatures are stabilized, they resist changes due to the special properties of water. This is very important to maintain a stable environment. Recall kinetic energy, is the energy of motion. Heat is a measure of the total kinetic energy the total movement of the molecules in a body of matter. Temperature by definition is the average kinetic energy of the molecules. This is important to consider the relationship of the temperature of the water and the rate of movement of the molecules of water. Heat always flows from the warmer matter to the cooler matter. A calorie is a unit of heat it is the amount of heat energy it takes to raise one gram of water one degree Celsius. Joules is another unit 1 calorie = 4.184 joules.

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High Specific Heat The specific heat of a substance is the defined as the amount of heat that must be absorbed or lost for 1 gram of that substance to change its temperature 1 degree Celsius. The higher the specific heat, the more resistant to change in temperature the matter is. Water resists change. To raise the temperature of water, you need to make the molecules move faster. To make the molecules move faster, you need to first break the hydrogen bonds between the water molecules then move the molecules faster. When the temperature of the water drops, hydrogen bonds form. This formation of hydrogen bonds releases energy in the form of heat, thus maintaining the temperature of the water. Large bodies of water absorb and store this energy; the temperature changes minimally during the daytime. At night, as the water cools, the air is warmed. Think about going to the shore, it doesnt seem as hot in the summer or as cold in the winter. This high specific heat allows the oceans to be a stable environment for all that lives in the water. Evaporative Cooling Evaporation or vaporization is the change in state from a liquid to a gas. Remember back to 9th grade, solid liquids and gases. Gases have molecules moving the fastest. The heat of vaporization is the quantity of heat that must be absorbed for 1 gram of that liquid to be converted from liquid to gas. Water at 25 degrees C needs 580 cal to evaporate 1 gram of water. Alcohol and ammonia only need half as much. Why? Back to hydrogen bonds, the energy must first break those hydrogen bonds before the kinetic energy of the molecules can change. Why is this important? It again goes to moderating temperature. Your body temperature is maintained with the assistance of evaporative cooling. As one molecule moves off to the gas state, the average kinetic energy or temperature of the remainder is lower. The Earths climate is assisted, tropical seas absorb the energy and as the current circulate it is released. Density of Water Water is less dense as a solid than as a liquid. Think about ice cubes floating in a glass, if this were another substance, solid in liquid; this would be unlikely to happen. As water changes from a liquid to a solid, it expands. Water is at its most dense at 4 C. Why? Hydrogen bonds again. Water will freeze when the movement of the water molecules does not allow the hydrogen bonds to break. They get locked into a lattice structure with each water molecule bonded to up to four other molecules. This makes them about 10% less dense. Why is this important? This again goes to the stability of the environment. When ice floats on the top surface, life continues below. Ice also acts an insulator for the water below.

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Water is the Universal Solvent Remember your 9th grade science again solution, solute and solvent. An aqueous solution is one in which water is the solvent. The polar nature of water allows both ionic compounds and polar molecules to dissolve in it. A hydration shell is the sphere of water molecules around each dissolving substance. Hydrophilic refers to substances that have an affinity for water. A substance can be hydrophilic if it dissolves in water or if it is a larger molecule, can absorb water like cotton. Hydrophobic refers to substances that do not have an affinity for water, they repel it. This would be a nonpolar substance, such as oil.

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This is a picture of a water soluble protein being dissolved by water. Dissociation of Water Molecules Again, back to the hydrogen bonds sometimes when the bond breaks it does not break evenly and one water molecule is left with oxygen and three hydrogens and the other water molecule is left with an oxygen and a hydrogen. This would be a hydronium ion and a hydroxide ion. This is a reversible reaction.

When we simplify this we speak of the dissociation of one water molecule in to a hydrogen ion and hydroxide ion. This reaction will reach a dynamic equilibrium in pure water only one water molecule in every 554 million is dissociated at 25 C. This is 10-7 M. Acid a substance that increases the hydrogen ion concentration in solution. A strong acid will dissociate readily and not reform. HCl is an example of a strong acid. Carbonic acid is a weak acid. It dissociates into the bicarbonate ion and hydrogen ion and readily reforms. Another way of identifying an acidic solution, is one in which the [H+] is greater than [OH-]. Base a substance that reduces the hydrogen ion concentration in solution. Some bases are bases because when they dissociate they release hydroxide ions, NaOH. Other substances act as bases because they accept hydrogen ions readily from solution. Ammonia accepts hydrogen ions and becomes the ammonium ion. Another way of identifying a basic solution is one in which the [OH-] is greater than [H+].

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The pH scale In aqueous solution the product of hydrogen ions and hydroxide ions is 10-14 [H+] [OH-] = 10-14 The pH scale was named pH originally for the power of hydrogen. Today we define pH as the negative log of the hydrogen ion concentration. This is where the 0 -14 scale comes from. -log 10-7 = -(-7) =7 This is most important to understand that for every numerical change in pH there is a tenfold change in the concentration of hydrogen ions. Living systems are extremely sensitive to changes in pH.

Buffers substances that minimize changes in concentration of H+ and OH- in a solution. Buffers accept hydrogen ions if the solution becomes too acid and donate hydrogen ions if it becomes too basic. Most are weak acids and matched bases. Blood pH is maintained in the human body in a very close range 7.35 -7.45. Much below 7.25 and above 7.7, you cannot live. Write the equation listed on the board.

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Application The Process of Science Acid Rain Normal rain pH of 5.6, it is slightly acid because of the formation of carbonic acid from carbon dioxide and water. If the pH is lower than 5.6, it is considered to be acid precipitation. Where does it come from? Usually it is due to sulfur oxides and nitrogen oxides that mix in the air to form strong acids. The burning of fossil fuels and power plants disperse these pollutants. The wind then carries the chemicals and rain far from the source of pollution. Upstate NY, rainfall averages pH 4.2, considering the pH scale this is many more hydrogen ions than normal. When the acid precipitation is snow, it accumulates and then when it melts it enters the water supply all at once the pH can be as low 3 this hits the water at the same time young are being hatched and can damage stream life. Ultimately, these hydrogen ions end up affecting soil pH.

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