C. If the pH of a cytoplasmic compartment falls from 7.0 to 6.0 then: 14) the gloves must fit

1. Name ____________________ BCOR 011 Vayda/Stratton Sept 14, 2005 • PRACTICE EXAM QUESTIONS • Lectures 1, 2 & 3 (Bonding & Functional Groups, Water, pH & Hydrophobicity, Carbohydrates, Lipids, Nucleic Acids &n Proteins, Cell Tour) • NOTE: MEMBRANE STRUCTURE AND FUNCTION WILL BE ON THE EXAM • These are “dry-runs” for the Exams you will take. The questions here ARE exam questions from previous years (that’s why the jokes are so out of date). You will see questions similar to these on Sept 23 (with fresher jokes). • Section I. MULTIPLE, Multiple Choice. • Rarely is there just one right answer in life. These questions are designed to explore the different characteristics of individual things, processes or properties. Practice looking for ALL possible characteristics of an item while you are studying your notes. • Indicate all of the answers below that correctly relate to the questions in bold type. Note: there is frequently more than one right answer! Sometimes there IS only one correct choice, other times none of the choices are correct, or all may be correct. Think of this as a type of “true-false” choice for each possible answer to the question. When you fill out the “bubble” answer sheet column 1 will be “true”, column 2 will be ”false”. On the the practice exam • below, you have 200 answer choices: so each choice is worth 0.5 pt; that is, if you say it is correct and it is, you get 0.5 pt; if you don’t say it is correct and it is, you lose 0.5 pt, etc. We the actual exam will probably be shorter (have less answer choices, like 150), so each choice will be worth more (like 0.67 pt). You only have 50 min for the 9/23 exam. A. The structure at right: 1) is a -sheet (beta) 2) is a base pair 3) is a micelle 4) is a starch grain 5) is an polysaccharide 3 B. The tertiary structure of a protein is: 6) the overall 3-D structure of the protein. 7) dictated by interactions of amino acid R-groups with one another. 8) dictated by interactions of the N-terminus with the C-terminus of the polypeptide. 9) influenced by the presence of disulfide bonds. 10) influenced by hydrophobic interactions. 11) the interaction of two or more polypeptide chains to form a protein complex. 12) the interaction of individual amino acids with one another to form a polypeptide. 13) dictated by how the surfaces of secondary structures interact with one another. 6 7 9 10 13 C. If the pH of a cytoplasmic compartment falls from 7.0 to 6.0 then: 14) the gloves must fit 15) the amount of H+ (hydronium) ions has increased 16) the amount of -OH (hydroxide) ions has increased 17) an acid with a pKa of 4.2 will lose its negative charge 18) a base with a pKb of 6.8 will become positively charged 19) phosphate functional groups will become positively charged 15 18

2. D. Which of the following biologically-important linkages are the result of condensation/dehydration reactions: 20) peptide bonds 21) ester linkages 22) phosphodiester bond 23) James Bond 24) hydrogen bonds 25) Van der Waal’s interactions 26) Glycosidic bonds 20 21 22 26 E. Covalent bonds: 27) are formed when two atoms share electrons. 28) enable atoms to form molecules with stable, precise spatial configurations 29) give the molecule a positive charge at high pH 30) can be purchased through your stockbroker. 27 28 F. Atoms interact to attain chemical stability by: 31) sharing electrons to form covalent bonds 32) sharing the Oval Office 33) “stealing” electrons to complete a stable outer electron shell 34) forming micelles 35) sharing intimate secrets with Linda Tripp 31 33 G. Chiral carbons: 36) are found in carbohydrate polymers 37) are found in amino acids 38) are found in polypeptides 39) were found at Rockingham 40) are found in saturated fatty acids 41) are found in water 42) are found in DNA 43) have 4 different functional groups attached to them 44) cannot interact with water 36 37 38 42 43 H. Amino acids: 45) as monomers, can be expected to be ions at pH 7.0 46) with non-polar “R” groups include alanine, valine and leucine. 47) can be joined in linear polymers to form polypeptides. 48) were allegedly used by Nicole and Faye Resnick 49) with alcohols for “R” groups include threonine and serine 45 46 47 49

3. Intracellular membrane-bound organelles: • 50) Are typically observed in Prokaryotes • 51) Comprise distinct compartments within the cytoplasm • 52) Are the cell’s lock boxes • 53) Include “mitochondria” • 54) are typically observed in Eukaryotes • 55) include the “Golgi Apparatus” • 56) include the “endoplasmic reticulum” • 57) include “ribosomes” • 58) include “nuclei” (plural of “nucleus”) • 59) contain “phospholipids” in their membranes • 60) allow different functions to occur in a cell at the same time • 61) allow different microcompartments within the cell to have distinct internal pH’s • 62) allow the cell to maximize effective surface area 51 53 54 55 56 58 59 60 61 62 • J. Water has a tendency to : • 63) Form hydrogen bonds with polar molecules • 64) Form hydrogen bonds with non-polar molecules • 65) Form four oxygen bonds with carbon molecules • 66) ionize and form the charged species –OH and H+ • 67) Form hydrogen bonds with hydrocarbon chains (R-CH2-CH2-CH2-CH3) • 68) Form hydrogen bonds with amino groups (R-NH2) • 69) Bomb Iraq • 70) Let the weapons inspectors do their job 63 66 68 K. A Carbon atom always makes this number of covalent bonds: 71) one 72) two 73) four 74) eight 73 L. Eukaryotic cells differ from prokaryotic cells in that eukaryotic cells: 75) are typically much larger than prokaryotic cells 76) contain internal membranes and membrane bound organelles whereas prokaryotic cells typically do not 77)) store their genetic information in the DNA whereas prokaryotic cells use RNA to store genetic information 78) have nuclei whereas prokaryotic cells do not 79) have viruses whereas prokaryotic cells do not 75 76 78

4. Which of the following is a membrane-bound organelle? • 80) ribosome • 81) nucleus • 82) triglyceride • 83) microtubule 80 N. A covalent bond between a carbon and a hydrogen atom is considered: 84) nonpolar 85) polar 86) ionic 87) ironic 88) romantic 84 O. A solution with a pH of 5 : 89) has a hydrogen ion concentration of 1x10-9M 90) has a water concentration of 5 M 91) has a hydrogen ion concentration of 0.00001M 92) cannot form hydrogen bonds 91 • P. A carboxylic acid group with a pKa of 5.5: • 93) Will be ionized at pH 7.0 • 94) Will be uncharged at pH 7.0 • 95) Will be uncharged at pH 4.0 • 96) Will be uncharged at pH 8.8 • 97) Will bear a negative charge in a solution that has 1x10-10 M –OH ions • 98) Can form a condensation reaction with an alcohol group to form an ester bond • 99) Is hydrophilic 93 95 98 99 Q. Which of the following components are found in prokaryotes (bacteria and cyanobacteria)? 100) plasma membrane 102) nucleus 103) endoplasmic reticulum 104) golgi apparatus 105) ribosomes 106) DNA 107) bloody gloves 108) mitochondria 109) chloroplasts 110) lysosomes 111) Bruno Magli shoes 100 105 106

5. R. Carbohydrate polymers are polar molecules which tend to: 112) be insoluble in water. 113) hydrogen bond with themselves rather than water. 114) form micelles which are great for cleaning greasy dishes. 115) be slimy, gooey or gelatinous when forced to be fully hydrated by water. 116) serve as recognition markers on external surfaces of membrane proteins. 117) hydrolyze peptide bonds. 112 113 115 116 S. Which of the following components are usually found in DNA: 118) phosphatidyl Choline 119) Glutamic acid 120) the preservative EDTA 121) Adenosine monophosphate 122) phosphatidyl Inositol 123) Threonine 124) deoxyRibose 121 124 T. Phospholipids tend to: 125) form aromatic rings. 126) be solids at room temperature if comprised of unsaturated fatty acids. 127) form cholesterol. 128) be hydrolyzed to cholesterol and wax. 129) form bilayers and vesicles. 130) bear a negative charge at pH 7.0. 129 130 U. Which of the following structures represents a monosaccharide? 131) C12H22O11 132) 133) HO – C = O | H – C – OH | H – C – OH | H 132 134) V. An alpha helix ( a-helix ) : 135) Is a “primarystructure” that a polypeptide can adopt 136) Is formed when one polar peptide bond hydrogen bonds with another peptide bond further down the chain 137) is held together by disulfide bonds 138) Is the covalent bonding arrangement that holds two polypeptides into a quaternary structure 139) Is a secondary structure of DNA and other polynucleotide chains 136

6. W. Which of the following are considered “hydrophobic” aminoacids with “hydrophobic” R groups 140) glucose 144) serine 148) palmitic acid   141) leucine 145) valine   142) phenylalanine 146) glutamine   143) adenine 147) lysine 141 142 145 1. X. The molecule below : 149) is the L form of an amino acid 150) is likely to be a liquid oil 151) is a pentose 152) is likely to bear a negative (-) charge at pH 7.0 153) is a trisaccharide 154) is comprised of one or more unsaturated fatty acids 155) is hydrophobic 156) was found on Monica Lewinski’s dress 150 154 155 156 Among other things Note: will never take off for a “joke” answer Y.The SECONDARY STRUCTURE of DEOXYRIBONUCLEIC ACID (DNA) polymer: 157) Is formed by linking ATP mononucleotides together 158) Is a double-helix of anti-parallel strands 159) Is an alpha (a) helix of two parallel strands 160) Is a beta (b) helix of two anti-parallel strands 161) Is stabilized by precise hydrogen bonding of complementary “bases” trapped in a non-polar microenvironment; A with T, G with C 162) Is driven by the need for hydrophobic bases to stack on top of one another 163) Is driven by the insatiable desire for Bill Clinton to stack… (let’s not go there) 164) Is driven by the political motives of Kenneth Starr 165) Has the negatively (-) charged phosphate groups on the outside, exposed to water 166) is maintained “fluid” by the presence of unsaturated fatty acids in the polymer 158 161 162 165

7. BB. Which of the following amino acids has a hydrophilic R-group ? 181) isoleucine 182) threonine 183) arginine 184) glutamic acid Z. The monomers which make up a polypeptide are: 167) held together by phosphodiester bonds 168) chiral 169) nitrogenous bases 170) unsaturated 171) nucleotides 172) amino acids 173) monosaccharides 174) interns 168 172 AA. Cellulose and Amylose (starch): 175) both contain the exact complement of amino acids but arranged in different orders 176) are both polymers of D-glucose but monomers of one are bound together by a1-4 glycosidic linkages whereas the other is bound together by b1-4 glycosidic linkages 177) are both polysaccarides, but one is hydrophobic and the other is hydrophilic 178) are polymers comprised of glucose but have very different 3-D shapes 179) are amphipathic molecules 180) are buffers which can bind ATP 176 178 182 183 184

8.  CC. Familiarity with the properties of water is important to understand: • 185) Why polymers adopt the secondary and tertiary structures they do • 186) How soap works • 187) What chirality is • 188) What a “lock box” is • 189) Why we need a tax cut (didn’t Reagan try this already?) • 190) Why some hydronium (H+) ions and hydroxide (-OH) ions are always present for reactions in water • 191) Why hydrophilic polymers tend to hydrogen bond with themselves rather than water • 192) Who this Chad guy is • 193) How Chad got pregnant. • 194) Why membranes form in water • 195) Why carbon atoms can form covalent bonds with 4 other atoms 185 186 190 191 194 DD. A molecule that is Chiral has : 196) an unshared pair of electrons 197) a pH of 7 198) hydrophobic character 199) a left-handed and right-handed form 200) at least one carbon with four different functional groups bonded to it 199 200 2. The fluid mosaic model of membranes predicts that: a) O.J. did it. b) phospholipids are free to move laterally in membranes. c) proteins are free to move laterally in membranes. d) fluids are free to pass through membranes but solid particles cannot. e) polypeptides are embedded in a sea of phospholipids. f) polymers of a-D-glucose are soluble in water whereas polymers of b-D-glucose are not. B C E