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The Chemistry of Life Atoms • All matter is made up of elements, which are substances that cannot be broken down into smaller substances in a chemical reaction. • An atom, the fundamental unit of matter, is the smallest unit of an element that displays all of that element’s characteristics. Continue… • Atoms contain the following subatomic particles: – Protons: positively charged particles located with the atomic nucleus, or core of the atom – Neutrons: Electrically neutral particles located within the atomic nucleus. – Electrons: Negatively charged particles orbiting in a cloud around the atomic nucleus electron neutron proton Continue… • Atoms are described by their atomic number and mass number – Atomic number: indicates the number of protons in an atom. – Mass number: indicates the combined number of protons and neutrons in an atom • Atom’s chemical symbol, the written representation of an atom includes atomic number, mass number, any charge on the atom. Atomic Behavior • Is largely determined by the number and arrangement, or electron structure, of electrons orbiting its nucleus. • Electrons move about in regions called orbitals located at varying distances from the nucleus. Electron Shells • All of an atom’s electrons are arranged in orbitals located at different energy levels, called electron shells, around the nucleus. • Shells further away from the nucleus requires more energy. • Electrons tend to move toward lower energy positions and will fill orbitals in the lowest electron shells before filling orbitals in electrons shells farther out. Continue… • Each electron shell has a maximum number of orbitals, and therefore electrons that it can hold: – First electron shell – maximum one orbital- 2 electrons – Second electron shell- maximum 4 orbitals- 8 electrons – Third electron shell- maximum 4 orbitals – 8 electrons – Four electron shell- maximum 4 orbitals- 8 electrons Valence Electrons • Occupy the energy shell farthest from the nucleus. • Atoms with a full complement of electrons in their outermost shell are more stable and less reactive. • These valence electrons will help in the forming of chemical bonds. Example: Valence Electrons • Sodium 11Na has 11 electrons. Two electrons in the first shell, 8 in the second shell and 1 in the last (3rd shell). To create a full outer shell electrons, a sodium atom loses the single valence electron from the third shell. • In contrast, chlorine, 17Cl has seventeen electrons. Two in the first orbital, 8 in the second orbital, 7 in the third orbital. To create a full outer shell electrons, a chlorine atom gains one electron. Ions • An ion is an atom that has acquired a positive or negative electric charge by gaining or losing electrons. • There are two types of ions: – Cation: is an atom that has lost electrons and acquired a positive charge (Example: Sodium) – Anion: is an atom that has gained electrons and acquired a negative charge (Example: Chlorine) Example: Potassium (K) can lose an electron to become a cation, K+. Sulfur (S) can lose two electrons to become an anion, S-2 Isotopes • Are atoms of the same element that have different number of neutrons and therefore different atomic masses. • Example: There are three naturally occurring carbon isotopes, each with a different atomic number: Carbon -12, Carbon-13, and Carbon-14. As represented in the atomic number, carbon-14 has one more neutron than carbon-13 and two more neutrons than carbon-12 Radioactive Isotopes • Are highly unstable and spontaneously decay by losing protons or neutrons along with energy. The rate of decay is constant for any given isotopes • Half-life: is a measure of the amount of time it takes for half of the atoms in that substance to decay Continue… • All living organisms are composed of carbon14 and carbon-12 in a certain ratio, designated by the variable x. – Half life of carbon-14 is 5, 730 years and will decay to nitrogen-14 • Scientist measure the ratio of radioactive isotopes such as carbon-14 against other elements present in a fossil to determine the approximate age of the fossil. Example of radioactive isotopes • The age of a bone fossil that contains carbon14 and carbon-12 in a ratio of 1/8 x can be dtermined using the half-life of carbon-14. Because one-eighth is (1/2)3, three half-lives have passed for carbon-14 presnet in this fossil. Three times 5,730 equals 17, 190; therefore the fossil is approximately 17, 190 years old Chemical Bonds • Are the interactions between the electrons of two or more atoms. • Electronegativity- is the strength of the attraction an atom has for its electrons, helps determine the nature of the chemical bonds that atom can form. – The more attraction electronegative an atom is, the greater the strength of its attraction for electrons. Covalent Bond • Two or more atoms share valence electrons. • Covalent bonds result in the formation of molecules, which are strong, stable associations between two or more atoms • Atoms joined by covalent bonds may share one, two, or three electrons resulting in single, double, or triple bonds. Continue… • The distribution of shared atoms in a covalent bond depends on the electronegativities of the atoms. • Two terms to describe the way electrons are shared: – Nonpolar covalent bonds: form between atoms that have similar electronegativity. The electrons in a nonpolar covalent bond are shared equal between the two atoms. – Polar covalent bonds: form between atoms that have different electronegativities. Valence electrons in a polar covalent bond will be more attracted to the atom of higher electronegativity, resulting in a partial negative charge on that atom and partial positive charge on the other atom. Polar Vs. Nonpolar Ionic Bonds • Form when electrons are transferred from an atom of low electronegativity to an atom of high electronegativity. • The atom that lost an electron becomes positively charged anion, while the atom that has gained an electron becomes a negatively charged cation. • Cations and anions are mutually attracted to one another by their charges. • This mutual attraction results in the formation of a crystal, which is a highly regular and ordered solid whose atoms are arranged in repeating units. Hydrogen Bond • The weakest of all chemical attractions, form when a hydrogen atoms that is covalently bonded to an electronegative atom is attracted to another electronegative atom, generally either oxygen (O) or nitrogen (N). • Hydrogen bonds are one of the main forces that give proteins their 3-D shapes Water • Water is the most abundant molecule present in all living organisms. • All chemical reactions within an organism take place in the presence of water. • Several characteristics unique to water contribute to its vital importance in the processes of life, such as its properties as a solvent and tendency to form ions. Water as a Solvent • Solution is a homogeneous mixture of molecules (Evenly distributed mixture) – Example: Kool-Aid • Parts of a solution: – Solvent: Substances that dissolves other molecules. • Water – Solute: Substance that is being dissolved • Kool-aid Continue… • The hydrogen bonds that hold water molecules make water a versatile solvent that can form a solutions with a polar (hydrophilic: a molecule that is attracted to water) molecules. Water can form solutions with nonpolar (hydrophobic: a molecule that repelled from water) molecules. • Example: In an aqueous solution of NaCl and water, the solvent is water and the solute is NaCl. NaCl is ionic, and therefore hydrophilic and forms an aqueous solution in which water is the solvent and NaCl is the solute. Oil nonpolar, and therefore hydrophobic. Oil will not dissolve in water. Water Ionization • Water molecules spontaneously ionize, or break down, into hydroxide ion (OH-) and hydrogen ions (H+). • Chemical equation illustrates the explanation: H2O OH- + H+ pH Scale • Ranges 0 to 14, expresses the concentration of hydrogen and hydroxide ions in a solution. – This determines if a solution is Neutral, Acidic, or Basic • Neutral Solution: Have equal number of –OH and H+ ions in the solution – pH of 7 • Acidic Solution: have a greater concentration of H+ ions in the solution – pH of less than 7 • Basic Solution: have a greater concentration of – OH –pH of greater than 7 Continue… • A buffer solution : a solution containing either a weak acid and a conjugate base or a weak base and a conjugate acid, used to stabilize the pH of a liquid upon dilution. • Buffers are substances that reduce the effect of acids and bases on the pH of a solution Calculating pH • The pH of a given solution expresses the negative logarithm of the hydrogen ion concentration • Equation: pH = -log [H+] Isomers • Are organic compounds that have the same molecular formula but different structure – There are three types • Structural Isomers: differ in their covalent arrangement • Geometric isomers: differ in their spatial arrangement around a double bond • Enantiomers or optical isomers: are mirror images of each other Reactions • There are five types of reactions you should know for this exam: • 1- Hydrolysis reaction: a reaction that breaks down compounds by the addition of H2O • 2- Dehydration synthesis reaction: A reaction in which two compounds are brought together with H2O released as a product. • 3- Endergonic Reaction: A reaction that requires input of energy to occur A + B + energy C Continue… • 4- Exergonic Reaction: A reaction that gives off energy as a product. A + B energy + C 5- Redox reaction: A reaction involving the transfer of electrons Biological Macromolecules • Compounds that contains Carbon and usually Hydrogen. • Four types of macromolecules – Nucleic Acid – Proteins – Carbohydrate – Lipds Continue… • Most biological macromolecules are polymers, which are long chains composed of many monomers, similarly structured subunits bonded together Nucleic Acid • Form polymers of nucleotides, molecules composed of a phosphate group, a five-carbon sugar, and a nitrogenous bases (Four nitrogenouos bases: adenine, guanine, cytosine, thymine, uracil) • DNA and RNA are nucleic acids that function in protein synthesis and the storage and transmission of genetic transmission Proteins • Proteins consist of one or more polypeptides, polymers of amino acids (building blocks of proteins) folded into complex 3-D shapes. • An amino acid is a small molecule made up of a central carbon atom, an amino group, a carboxyl group, a hydrogen atom, and functional group labled “R” • Twenty different amino acids exist, each formed with a different R group. Proteins Continued… • Polypeptides form when amino acids bond together in long chains. • The twenty different amino acids can produce a diverse range of proteins, including enzymes, hormones, cell receptors, antibodies, transport proteins, storage proteins, motor proteins, and structural proteins. Proteins Continue… • All proteins have either 3 or 4 structural levels – Primary Structure: Refers to the sequence of amino acids that form the polypeptides – Hydrogen bonds single groups in a polypeptide chain result in a folded region referred as the secondary structure. Secondary structure includes helices (coils) and sheets (pleated folds) – Tertiary structure describes the folding of an entire polypeptide chain. Interactions between the R groups of the polypeptide chain determine the overall shape of the tertiary structure. Continue…Protein • Quaternary structure: Interactions between two or more polypeptides Enzymes • Are proteins that act as organic catalyst – Catalyst: speeds up reactions by lowering the activation energy needed for the reaction to take place but are not used in the reaction. – Substrate: substance that enzymes act on • Enzymes are selective; they interact only with particular substrates. It is the shape of the enzyme that provide the specificy. – Active Site: The part of the enzyme that interacts with the substrate Induced-fit Model • Of the enzyme-substrate interaction describes the active site of an enzyme as specific for a particular substrate that fist its shape (Often times called the lock and key model) Enzyme Activate Energy Graph Enzyme Continue… • Every enzyme effectiveness (reaction taking place) This will – Temperature – pH – Concentration of substrate – Concentration of the enzyme involved be helpful to know for both the AP Exam and the Enzyme Lab Competitive Inhibition and Noncompetitive Inhibition • Competitive Inhibition: an inhibitor molecule resembling the substrate binds to the active site and physically blocks the substrate from attaching. Continue… • Noncompetitive inhibition: an inhibitor molecule binds to a different part of an enzyme, causing change in the shape of the active site so that it can no longer interact with the substrate Carbohydrates • Macromolecule that contains Carbon, Hydrogen, and Oxygen – Ratio of 1:2:1 • Provides energy for organisms Monosaccharide • Simple sugar or simple carbohydrates – Examples: Glucose (used for cellular respiration), fructose, and lactose – provides energy for cells Disaccharide • Sugar consisting of two monosacharides bound together – Sucrose: Table sugar • Major sugar in plants • Fructose and glucose bonded together – Lactose • Found in diary products • 2 glucose molecules bonded together Polysaccharide • Carbohydrate of bonding three or more monosaccharide molecules • Two important molecules for storing energy are: – Starch : Made up of solely of glucose • Energy storage for plants • Corn, Potatoes, Beans – Glycogen: linking many glucose molecules together • Animals store their energy • Found in liver and muscle cells Continue… Polysaccharides • Two important structural polysaccharides – Cellulose: composed of glucose molecules • Used for in the formation of the their cell walls – Chitin: Important part of the exoskeletons of arthropods– such as insects, lobsters, and crabs Lipids • Organic compounds used by cells as long-term energy stores or building blocks • Hydrophobic and insoluble in water because they contain a hydrocarbon tail Fats • Which are lipids made up of combining glycerol and three fatty acids • Used as long term energy stores in cells • Are not easily metabolized as carbohydrates Saturated vs. Unsaturated • Saturated: Contain no double bonds (means it can be easily broken) – Associated with heart disease and atherosclerosis • Unsaturated: contain one (mono-) or more (poly-) double bonds Steroids • Act as chemical messengers in an organisms • Cholesterol: Component found in cell membranes • Steroids: the sex hormones (testosterone, progesterone, and estrogen) Phospholipds • Combining a glycerol with two fatty acids and a phosphate group • Phospholipds are bilayered structures they have both hydrophobic tail and hydrophilic head • Major component of cell membranes Functional Groups • Commonly found in biological macromolecules • Share the same chemical properties Functional Groups Functional Group Class of Compounds Macromolecule Amino Amines Proteins Carbonyl Ketones & aldehydes Lipids Carboxyl Carboxylic acid Proteins Alcohols Carbohydrates Phosphate Phosphate Nucleic Acids Sulfhydryl Thiols Proteins Hydroxyl Structural Formula Notice the -OH Functional Group • Quiz on: ____________________________________ The End