SAT II Biology Episode 1 Part 3 doc

statistical statement, placing it somewhere in a “cloud” surrounding the nucleus, depending on its energy state. C. Atomic Number The number of protons in an atom. D. Atomic Mass The number of protons and neutrons in the nucleus of an atom. Electrons are not considered in this number. The actual number on the periodic table is an average of the abundance of all the isotopes of each element. E. Isotope Different form of an atom due to a different number of neutrons. Carbon 12 has six neutrons, while Carbon 14 has eight neutrons. Different isotopes of an element have slightly different properties that are sometimes biologically important. F. Ion Electrically charged atom due to a loss (1 ion) or gain (− ion) of electrons. An ionic bond is an attractive force of oppositely charged ions by virtue of the loss/gain of electrons that takes place between them. As atoms lose electrons and thus become positive, attraction occurs with the atoms that gain electrons and thus become negative. CHEMISTRY—ATOMS AND COMPOUNDS 37 Peterson’s n SAT II Success: Biology E/M www.petersons.com Some essential atoms A. Hydrogen Simplest element that has one proton and one neutron. It combines with oxygen to form water, an essential abiotic substance for living things. B. Carbon Ubiquitous element on this planet that forms the basis for all living things. It can form the most number of bonds in chemical combina- tions. C. Nitrogen Essential component of proteins and nucleic acids. D. Oxygen Necessary for aerobic respiration to take place and in the formation of many organic molecules. E. Phosphorous Necessary for nucleic acid structure and in energy transformations. Also important in membrane structure. F. Sulfur Forms sulfide bridges that are found in proteins. CHAPTER 1 38 Peterson’s n SAT II Success: Biology E/Mwww.petersons.com MOLECULES Molecules are a group of chemically combined atoms that are the smallest form of a compound and have the properties of that com- pound. Compounds Compounds are chemically combined atoms that form discreet particles in which the atoms lose their individual physical properties, and the compound, as a combined unit, takes on new properties. Molecular bonds Molecular bonds are the attractive forces of atoms by sharing elec- trons or by gaining or losing electrons. A. Covalent Sharing of pairs of electrons between atoms that may result in single, double, or triple bonds. A single bond, for example, results from the sharing of one pair, thus the reference to “single.” 1. Nonpolar covalent—Covalent sharing is distributed symmetri- cally within the molecule. 2. Polar covalent—Covalent sharing is distributed nonsymmetrically within the molecule, resulting in weak positive and weak negative charges. B. Hydrogen bonds Caused by polar covalent bonding, hydrogen bonds are the weak attractions between slightly positive hydrogen atoms of a molecule and slightly negative atoms, such as oxygen and nitrogen, of another molecule. CHEMISTRY—ATOMS AND COMPOUNDS 39 Peterson’s n SAT II Success: Biology E/M www.petersons.com C. Ionic bonds Caused by electrons being pulled off one atom and bonded to the atom that was attracting them. Molecular forces Molecular forces are forces that affect molecules, including the following: A. Van der Waals Attractive forces that occur between electrically neutral molecules because they are so close to each other. B. Hydrophobic Clumping together of molecules that are insoluble in water because they are nonpolar. Some molecules essential to life A. Carbon Dioxide Carbon and two oxygens bonded in a nonpolar, covalent orientation. This is a highly oxidized, low energy form of carbon. B. Oxygen molecule Two atoms of oxygen bonded covalently. Molecular oxygen allows a maximum oxidation of organic molecules in aerobic respiration. C. Water One oxygen and two hydrogen atoms bonded polar covalently. Supplies the hydrogen and electrons to initiate the photosynthesis process. WATER Water is the essential abiotic molecule for sustaining life. It is essential in photosynthesis, in the maintenance of membranes, and as the solvent for all of life’s molecules. CHAPTER 1 40 Peterson’s n SAT II Success: Biology E/Mwww.petersons.com Structure Two hydrogens with two single, covalent bonds with an oxygen atom forming a polar molecule. A. Shape Orientation of the unbonded electrons in the oxygen and the protons in the hydrogen orient them on “opposite sides of the molecule with respect to each other.” The bond angles are approximately 105 degrees. B. H1 bonds Weak associations between the negative side of the water molecule oxygen and the positive side that the hydrogens create; bonds that hold water molecules together and result in high specific heat; good solvent properties and cohesion that results in a substantial surface tension. Properties Water has several unique properties. A. Polar The covalent bond orientation results in the slightly positive hydro- gens being on one side of the molecule and the unequally unshared electrons from oxygen more often on the other side of the molecule. B. Cohesion The dipole nature of the molecule produces bonds between the positive hydrogens and the negative oxygen that, in sum, can be substantial. The result is that water molecules tend to stick together, resulting in a very high surface tension. C. High Specific Heat Because of the hydrogen bonds, water absorbs a large amount of heat before it vaporizes. CHEMISTRY—ATOMS AND COMPOUNDS 41 Peterson’s n SAT II Success: Biology E/M www.petersons.com D. Weak acid/base Water has a neutral pH of 7.0 and normally dissociates into equal amounts of H1 ions and OH − ions. It can, therefore, be a weak proton donor (an acid) or a weak proton acceptor (a base). ACIDS/BASES Acids Proton donor; when dissociated in aqueous solutions, acids become sources of protons donated to the reaction. Bases Proton acceptor; when dissociated in aqueous solutions, bases become proton acceptors in a reaction. CHAPTER 1 42 Peterson’s n SAT II Success: Biology E/Mwww.petersons.com pH pH is the measure of concentration of hydrogen ions in a solution. The term stands for the percent concentration of hydrogen ions and is the negative log of the concentration of hydrogen ions. Thus a lower pH means a higher concentration of H1. (NOTE: Hydrogen ions (H1) and protons are the same thing.) One may also take the inverse of this concentration and thereby arrive at the concentration of hydroxyl ions in solution. CHEMISTRY—ATOMS AND COMPOUNDS 43 Peterson’s n SAT II Success: Biology E/M www.petersons.com BIOCHEMISTRY CARBON Carbon is the atom that is the basis for life on earth, owing to its versatility. Carbon has four bonding electrons that make it capable of forming many complex molecules. The chemistry of life is the chemistry of carbon. The macro molecules of life are carbohydrates, lipids, proteins, and nucleic acids. Carbohydrates Carbohydrates are macro molecules that organisms create for energy storage, such as glycogen, or as structural components, such as cellulose. Their basis is carbon, hydrogen, and oxygen in a 1:2:1 ratio, thus the original term of hydrated carbon or carbohydrate. CHAPTER 1 44 Peterson’s n SAT II Success: Biology E/Mwww.petersons.com A. Monosaccharides Simple sugars made up of a backbone of usually three to seven carbons with the formula of CH 2 O. When combined to produce polysaccharides, they give off water at each bonding site in a reaction known as dehydration synthesis. 1. Glucose—Preferred energy molecule of life. It is produced in chloroplasts in the process of photosynthesis that stores energy from the sun in organic molecules and is broken down in the process of aerobic respiration that releases energy. 2. Fructose—Fruit sugar with the same molecular formula as glucose but different structural formula. When combined with glucose in a dehydration synthesis reaction, the two form sucrose. B. Disaccharide Complex sugars formed from the union of two monosaccharides in a condensation reaction. Condensation Condensation is also called dehydration synthesis. When two monosaccharides bond together to form a disaccharide and a water molecule is produced, then two hydrogens and one oxygen are removed from the two simple sugars and form into a water molecule in the process. Complex organic molecules are created by assembling a small number of simple subunits in many different ways, analogous to forming many words from the 26 letters of the alphabet. The assembly of complex molecules from simple subunits is by so-called “dehydration synthesis” or “condensation reactions” (the same thing). When the small subunits are combined, a hydrogen atom (H) is removed from one and a hydroxyl group (OH) from the next. These atoms combine to make a water molecule (HOH), and the subunits become covalently bonded. The opposite process is called hydrolysis (water splitting) and releases the simple subunits from the molecule. This occurs, for example, during digestion. Hydrolysis Hydrolysis is the opposite of condensation; it occurs when carbohy- drates, for example, are metabolized. Two hydrogens and one oxygen are ultimately inserted into the polysaccharide to cleave it into two simpler carbohydrates. For each cleavage, one water molecule is needed. CHEMISTRY—ATOMS AND COMPOUNDS 45 Peterson’s n SAT II Success: Biology E/M www.petersons.com A. Polysaccharide Carbohydrate formed from a number of simple sugars; the typical storage and structural form of carbohydrate in autotrophs. Polysaccha- rides are less diverse than DNA or proteins and are often long chains of a single monosaccharide, such as glucose (e.g., starch, cellulose, and glycogen). 1. Starch—Plant polysaccharide that is almost insoluble in water. In autotrophs, glucose may be quickly converted to starch in order to conserve glucose, which is soluble in water. 2. Cellulose—Largest carbohydrate molecule is insoluble in water and can be metabolized primarily by bacteria and fungi. An autotroph structural molecule, it is nonetheless important to heterotrophs in that it aids in digestion. 3. Glycogen—The heterotroph analog to starch, it is used to store energy in animals. Proteins One of the main structural as well as functional molecules in living systems, protein comes from chains of amino acids bonded together. It is found embedded in plasma membranes, acting as a catalyst, or as part of the structural integrity of many parts of living systems. In addition to the C, H, N, and O mix of living systems, they also contain S. Proteins are assembled from 20 different amino acids. A. Amino acids Main building block of polypeptides. 1. Backbone—Amino acids are built around a carbon center that has a hydrogen attached to one of the four covalent bonds of the central carbon. 2. R-group—Occupies a second of the four covalent bonds of the central carbon and can be as simple as a hydrogen or a complex ringed structure. There are 20 R-groups on the 20 amino acids that combine to form proteins. CHAPTER 1 46 Peterson’s n SAT II Success: Biology E/Mwww.petersons.com [...]... of a substance into its component parts; it is the opposite of synthesis Single replacement One part of a substance is replaced by another Double replacement Similar to single replacement, except the exchange results in two new compounds as a result of the replacement in two substances, not one Peterson’s n SAT II Success: Biology E/M 51 www.petersons.com CHAPTER 1 Equilibrium Results when conditions... hydrogen bonds (B) electrostatic interactions (C) covalent bonds (D) ionic bonds (E) both (A) and (B) www.petersons.com 54 Peterson’s n SAT II Success: Biology E/M CHEMISTRY—ATOMS AND COMPOUNDS 9 Which arrow(s) point to a peptide bond? (A) 1 (B) 1 and 4 (C) 2 (D) 3 (E) 2 and 5 10 A polypeptide that is ten amino acid units long is split into several small fragments, and the sequences of some of the fragments... covalent bond (B) Van der Waals bond (C) hydrophobic bond (D) electrostatic bond (E) hydrogen bond 3 The element found in all amino acids that is NOT found in carbohydrates is (A) sulfur (B) carbon (C) oxygen (D) hydrogen (E) nitrogen Peterson’s n SAT II Success: Biology E/M 53 www.petersons.com CHAPTER 1 4 Which of the following would NOT have hydrophilic properties? (A) OH (B) molecules in aqueous... systems; also made up of C, H, and O that are not in a 1: 2 :1 ratio Lipids are insoluble in water but soluble in nonpolar substances Fats are examples that have three fatty acid residues attached to a glycerol backbone Lipids are often assembled from fatty acids and an alcohol Peterson’s n SAT II Success: Biology E/M 47 www.petersons.com CHAPTER 1 A Fats Three fatty acids bonded at their carboxyl site... www.petersons.com 52 Peterson’s n SAT II Success: Biology E/M CHEMISTRY—ATOMS AND COMPOUNDS MULTIPLE-CHOICE QUESTIONS 1 In the reaction rate versus substrate concentration graph below, the curve plateaus because (A) a noncompetitive inhibitor is present (B) a competitive inhibitor is present (C) all the substrate has been converted to product (D) the active site is saturated with substrate (E) the cofactor... enzyme molecules available to bind to an added substrate At high substrate concentration, the reaction rate reaches a plateau as the enzyme active sites become Peterson’s n SAT II Success: Biology E/M 55 www.petersons.com CHAPTER 1 saturated with substrate The enzyme-substrate complex and no free enzymes are available to bind the added substrate 2 The correct answer is (A) All of the choices except choice... phosphate group, and a nitrogenous base Their almost infinite variability lies in the unique sequences of their nucleotides RNA and DNA are two types of nucleic acids Peterson’s n SAT II Success: Biology E/M 49 www.petersons.com CHAPTER 1 - A DNA (double helix) Nucleic acid that contains the 5-carbon sugar known as deoxyribose, which denotes less oxygen than the ribose sugar This molecule is the basis for... layers of molecules (bilayer) www.petersons.com 48 Peterson’s n SAT II Success: Biology E/M CHEMISTRY—ATOMS AND COMPOUNDS where the hydrophobic ends are oriented to both the inside of the bilayer and the outside of the bilayer Nucleic Acids Nucleic acids control molecules of life that contain or carry the codes for all the molecules that a particular cell needs In addition, they carry the code for making... basis for genes and chromosomes DNA is assembled from only four nucleotides (adenine, thymine, cytosine, guanine), but the code is millions of nucleotides long www.petersons.com 50 Peterson’s n SAT II Success: Biology E/M CHEMISTRY—ATOMS AND COMPOUNDS B RNA (single stranded) Nucleic acid that contains the 5-carbon sugar known as ribose, which denotes more oxygen than the deoxyribose sugar It is the molecule... lys-trp-arg-pro-gln-his-lys-asp-ala-gly (E) gly-ala-asp-lys-his-gln-pro-arg-trp-lys EXPLANATION OF ANSWERS FOR MULTIPLE-CHOICE QUESTIONS 1 The correct answer is (D) A reaction in which the enzyme is the catalyst may be written as follows: Enzyme 1 Substrate ↔ Enzyme-Substrate complex ↔ Enzyme 1 Product The substrate binds to a specific site on the surface of the enzyme, known as the active site, after which product . both (A) and (B) CHAPTER 1 54 Peterson’s n SAT II Success: Biology E/Mwww.petersons.com 9. Which arrow(s) point to a peptide bond? (A) 1 (B) 1 and 4 (C) 2 (D) 3 (E) 2 and 5 10 . A polypeptide that. basis is carbon, hydrogen, and oxygen in a 1: 2 :1 ratio, thus the original term of hydrated carbon or carbohydrate. CHAPTER 1 44 Peterson’s n SAT II Success: Biology E/Mwww.petersons.com A. Monosaccharides Simple. solution. CHEMISTRY—ATOMS AND COMPOUNDS 43 Peterson’s n SAT II Success: Biology E/M www.petersons.com BIOCHEMISTRY CARBON Carbon is the atom that is the basis for life on earth, owing to its versatility. Carbon has