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CHE 420 Final Study Guide

by: Bethany Shay Edgeworth

CHE 420 Final Study Guide CHE 420

Bethany Shay Edgeworth
GPA 3.2

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Study guide for CHE 420 final exam
Principles of Biochemistry
Vijay Rangachari
Study Guide
50 ?




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This 17 page Study Guide was uploaded by Bethany Shay Edgeworth on Monday December 7, 2015. The Study Guide belongs to CHE 420 at University of Southern Mississippi taught by Vijay Rangachari in Summer 2015. Since its upload, it has received 83 views. For similar materials see Principles of Biochemistry in Chemistry at University of Southern Mississippi.


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Date Created: 12/07/15
1. What is a hydrogen ion donor? *Bronsted-Lowry acid 2. What is a hydrogen ion acceptor? *Bronsted-Lowry base 3. What is an electron acceptor? *Lewis acid 4. What is an electron donor? *Lewis base 5. What is the formula for finding the Ka? *Ka = 10^(-pKa) 6. Acid strength increases with increasing _____ values & decreasing ____ values. *Ka & pKa 7. A buffer solution is made using a weak acid, HA. If the pH of the buffer is 9 and the ratio of A- to HA is 100, what is the pKa of HA? *Use the Henderson-Hasselbalch equation: pH = pKa + log (A-/HA) 9 = pKa + log (100) pKa = 9 – log (100) = 7 8. What does the carboxyl group consist of? O= C – O- 9. What does the amino (amine) group consist of? NH3+ 10. What does the carbonyl (ketone) group consist of? O = C – CH3 11. What does the carbonyl (aldehyde) group consist of? O = C – H 12. What does the hydroxyl (alcohol) group consist of? C – OH 13. What does the ester group consist of? R – C=O – OR 14. What does the ether group consist of? R-O-R' 15. What are the biomolecules of carbohydrates? 1. glucose 2. cellulose 3. glycogen 4. starch 16. What are the biomolecules of lipids? 1. cholesterol 2. testosterone 3. triglycerides 4. waxes 17. What are the biomolecules of nucleic acids? 1. DNA 2. RNA 18. What are the biomolecules of proteins? 1. enzymes 2. antibodies 3. hemiglobins 4. structural proteins – collagen 19. Select the statements that describe the energy cells use to drive cell processes. a. Animals use ATP to generate carbohydrates for quick energy. b. ATP is a form of chemical energy that is used to power cell processes. * c. Plants use energy in sunlight to power cell processes when ATP is not available. d. The energy stored in chemical bonds is a form of potential energy. * 20. What do nucleotides contain? 1. 5-carbon sugar 2. a nitrogenous base 3. phosphate group 21. What are the polymers of amino acids? * proteins or polypeptides (contains COO- group & NH3+ group) 22. Classify each statement about ATP as true or false. a. ATP is a nucleotide containing a base, sugar, and phosphate groups. T b. An ATP molecule contains 3 AMP molecules. F c. ATP has 3 phosphate groups. T d. High-energy phosphate bonds in ATP link the phosphate groups & the base adenine. F e. An ATP molecule contains the nitrogenous base guanine. F f. ATP contains ribose, a 5-carbon sugar. T 23. What are the 3 major components of an ATP molecule? 1. 3 phosphate groups 2. ribose sugar 3. adenine 24. Which of the following are examples of coupled reactions? a. ATP synthesis is driven by a proton gradient formed in the mitochondria. * b. Lactose hydrolysis by water results in glucose and galactose. c. ATP is hydrolyzed by water without the presence of enzymes. d. ATP hydrolysis drives sucrose synthesis from glucose and fructose. * e. In water, sodium chloride (NaCl) dissociates into sodium and chloride ions. 25. Where is the genomic DNA stored in a prokaryotic cell? a. mitochondrion b. nucleoid * c. nucleus d. capsule 26. All prokaryotic and eukaryotic cells have what 4 things? 1. DNA 2. plasma membrane 3. ribosomes 4. cytosol 27. What 6 things are only found in eukaryotic cells? 1. rough ER 2. Golgi apparatus 3. vesicles 4. nuclear membrane with nucleus 5. chloroplasts 6. mitochondria 28. What are the functions of mitochondria? Cellular respiration & ATP synthesis 29. What are the functions of rough ER? Membrane synthesis & protein modification 30. What is the function of ribosomes? Protein synthesis 31. What is the function of the golgi apparatus? Protein transport out of the cell 32. What is the function of the nucleus? Storage of genetic information 33. Which cell components have double membranes and DNA? a. nucleus b. mitochondrion c. chloroplast 34. Which cell components have single membranes and NO DNA? a. golgi apparatus b. lysosome c. vacuole 35. Which cell component LACKS a membrane? *ribosome 36. What are the characteristics of polar bonds? a. bond between oxygen and hydrogen in water (H2O) b. electrons are not equally shared by the atoms in a covalent bond c. 1 atom of a covalent bond has higher EN than other atom in bond 37. What are the characteristics of nonpolar bonds? a. bond between nitrogen atoms in diatomic nitrogen (N2) b. electrons of adjoined atoms are equally distributed between those atoms 38. What are 2 examples of hydrogen bonding in DNA? a. between H in thymine and N in adenine b. between H in adenine and O in thymine 39. Which statements accurately describe the polarity and EN of water? a. Water molecules are polar and thus associate with each other through hydrogen bonds. * b. The atoms of the water molecule are held together by covalent bonds. * c. Strong covalent bonds are formed between 2 or more water molecules. d. The oxygen atom in a water molecule is strongly EN. * e. Water has polar bonds and a linear symmetrical shape, so it is polar. (POLAR BONDS AND A NONPOLAR MOLECULE) 40. What 3 things describe acidic solution? 1. tastes sour 2. releases H+ 3. pH below 7 41. What 3 things describe basic solution? 1. tastes bitter 2. absorbs H+ 3. pH of 10 42. What is a buffer? *releases hydrogen ions when base is added to a solution 43. What are 3 examples of endergonic reactions? 1. generating carbohydrates in photosynthesis 2. pedaling a bike up a steep hill 3. constructing a protein from amino acids 44. What are 3 examples of exergonic reactions? 1. a boulder falling off of a cliff 2. breaking down glucose in cellular respiration 3. metabolizing a protein into amino acids 45. Which of the listed biomolecules are types of proteins? a. actin * b. enzymes * c. lipids d. starch e. RNA 46. Protein function is lost or reduced when a protein is denatured. Which of the environmental factors listed can cause protein denaturation? a. protein-digesting enzymes b. extreme pH * c. exposure to water d. excessive heat * 47. What are the monomers (building blocks) of proteins? *amino acids 48. Which of the following events can result in protein misfolding? a. a mutation in a gene that inserts an amino acid in a protein * b. a protein adopts a stable, but non-functional, tertiary structure * c. the binding of a coenzyme to a protein after normal protein folding d. interaction of a partially folded protein with molecular chaperones e. contact with a misfolded protein with the same amino acid sequence * 49. What is a peptide bond? *a covalent bond formed when the carboxyl group of 1 molecule reacts with an amino group of a different molecule 50. What are the 2 characteristics of alpha helices? 1. a rigid, spring-like structure around a central axis 2. form long, thin structures important for transmembrane proteins 51. What are the 2 characteristics of beta helices? 1. 2 adjacent polypeptide chains hold each other in place with hydrogen bonds 2. flat, zig-zag-like structure 52. How do you calculate the isoelectric point (pH at which alanine will have a net charge of 0)? pI = pK1 + pK2 / 2 pI = 2.3 + 9.7 / 2 pI (pH) = 6.0 53. What does the first law of thermodynamics state about energy? *energy can be transformed, but it cannot be either created or destroyed 54. What is a biological catalyst? Enzyme 55. What is a specific enzyme location that binds with the substrate? Active site 56. What is a substance that the enzyme acts upon? Substrate 57. Where should a drug bind to competitively inhibit the enzyme? Active site of enzyme 58. Which of the following best describes the overall role of enzymes in metabolism? a. enzymes decrease the speed of reactions b. enzymes allow reactions to occur without using ATP c. enzymes increase the speed of reactions * d. enzymes only synthesize large molecules 59. How do enzymes catalyze reactions? *enzymes bind with and change substrates 60. Where should a drug bind to allosterically inhibit the enzyme? *to a site on the enzyme other than the active site 61. How do enzymes recognize their substrates? *a binding site that fits the shape & complements the charge of the substrate 62. How do enzymes lower the activation energy of a reaction? a. by forming a temporary bond between the active site and the substrate * b. by using product molecules in the allosteric site to disable the active site c. by holding 2 substrates in the correct orientation to each other * d. by producing conditions within the active site conducive to the reaction * 63. How do you find the velocity? V0 = Vmax X S / Km + S 64. What is unbranched and important for the structure of bamboo stalks? *cellulose 65. What is moderately branched and used for energy storage in seeds? *starch 66. What is highly branched and used for energy storage in liver cells? *glycogen 67. What are the 5 examples of monosaccharides? 1. glucose 2. galactose 3. fructose 4. ribose 5. deoxyribose 68. What are the 2 examples of disaccharides? 1. lactose 2. sucrose 69. What are the 2 examples of polysaccharides? 1. glycogen 2. starch 70. What is a carbohydrate that enters glycolysis directly? *glucose 71. What is the direct energy source for glycolysis? *ATP 72. What is an end product that is modified to enter the citric acid cycle? *pyruvic acid 73. What is a product that donates electrons to the electron transport chain? *NADH 74. What is a product that can be used directly for energy? *ATP 75. Why does the passage of 1 glucose molecule through glycolysis have a payoff of only 2 ATP molecules? *2 ATP molecules are used in the initial phase of glycolysis, reducing the net gain to 2 ATP 76. What are the 6 steps of glycolysis? 1. Glucose is converted to glucose-6-phosphate by hexokinase. 2. Fructose-6-phosphate is phosphorylated by phosphofructokinase. 3. Aldolase cleaves the 6-carbon sugar into two 3-carbon sugars. 4. Glyceraldehyde-3-phosphate is converted to 1,3-bisphosphoglycerate. 5. 3-phosphoglycerate is formed. 6. Phosphoenolpyruvate is converted to pyruvate. 77. Which statements describe glycolysis? a. It occurs in a cell's mitochondria. b. It occurs only when an animal is breathing. c. It is common to aerobic and anaerobic respiration. * d. It breaks down glucose to 2 pyruvate molecules. * 78. How many molecules of glucose must be oxidized in glycolysis to provide the input for 12 turns of the citric acid cycle? *6 79. Cellular respiration consumes glucose during glycolysis. What product of glycolysis can be subsequently modified to enter the citric acid cycle under aerobic conditions? *pyruvate 80. How many CO2 molecules leave the cycle for each acetic acid molecule that enters? *2 81. How many molecules of CO2 are directly generated by the citric acid cycle from 2 molecules of acetic acid? *2X2 = 4 82. Which step of glycolysis is involved in oxidation-reduction reactions? *step 6 (glyceraldehyde 3-phosphate oxidized to 1,3-bisphosphoglycerate reducing NAD+ and yielding NADH) 83. Which 4 steps are involved in phosphorylation (phosphate group is transferred)? 1. step 1 = glucose to glucose-6-phosphate 2. step 3 = fructose-6-phosphate to fructose-1,6-bisphosphate 3. step 7 = 1,3-bisphosphoglycerate to 3-phosphoglycerate 4. step 10 = phosphoenolpyruvate to pyruvate **ADP is converted into ATP in these steps 84. Which step of the glycolysis pathway is the main control point? *step 3 (fructose-6-phosphate to fructose-1,6-bisphosphate) 85. Which steps in glycolysis are irreversible and require a different enzyme in gluconeogenesis than in glycolysis? 1. step 1 = glucose to glucose-6-phosphate 2. step 3 = fructose-6-phosphate to fructose-1,6-bisphosphate 3. step 10 = phosphoenolpyruvate to pyruvate 86. What negative effector inhibits the enzyme in the main control step (3) of glycolysis? *ATP 87. What positive effector activates the enzyme in step 3 of glycolysis? *AMP 88. List in order the enzymes used in the 10 glycolysis steps. a. step 1 = hexokinase b. step 2 = phosphohexose isomerase c. step 3 = phosphofructokinase-1 d. step 4 = aldolase e. step 5 = triosephosphate isomerase f. step 6 = glyceraldehyde-3-phosphate dehydrogenase g. step 7 = phosphoglycerate kinase h. step 8 = phosphoglycerate mutase I. step 9 = enolase j. step 10 = pyruvate kinase 89. Add coefficients to the following reaction summary to show the net results of glycolysis. 0 glucose + 2 ADP + 2 Pi + 2 NAD+ ---> 2 pyruvate + 2 ATP + 2 NADH 90. Draw the structure of pyruvate. Select carbon that was originally the anomeric carbon (aldehyde carbon in the open-chain form) of glucose. *C*H3 – C = O – C = O – O- 91. What steps of the citric acid cycle use the cofactors NADH + H+? 1. B (step 3 involving CO2) 2. D (step 4 involving CoA) 3. J (step 8) 92. What step(s) of the citric acid cycle use the cofactor FADH2? 1. H (step 6) 93. What step(s) of the citric acid cycle use the cofactor GTP? 1. F (step 5 involving CoA) 94. Each turn of the citric acid cycle produces ___ NADH, ___ FADH2, & ___ GTP. *3, 1, & 1 95. What are the 8 enzymes of the citric acid cycle in order starting with citrate synthase? 1. citrate synthase 2. aconitase 3. isocitrate dehydrogenase 4. a-ketoglutarate dehydrogenase 5. succinyl-CoA synthetase 6. succinate dehydrogenase 7. fumarase 8. malate dehydrogenase 96. Choose all the statements that are true about the citric acid cycle. 1. NADH, GTP, FADH2, and CoA molecule are produced by the citric acid cycle. * 2. Each turn of the citric acid cycle requires 2 molecules of acetyl-CoA. 3. The citric acid cycle is an aerobic process. * 4. In the citric acid cycle, pyruvate is degraded to produce acetyl-CoA. 5. The citric acid cycle occurs in the mitochondria of the cell. * 97. Glucose-1-phosphate, glucose-1,6-bisphosphate, & glucose-6- phosphate involve what enzyme? *isomerase 98. L-amino acid & L-aminoacyl-L-amino acid dipeptide involve what enzyme? *ligase 99. Glutamate, alpha-keto acid, alpha-ketoglutarate, & alpha-amino acid involve what enzyme? *transferase 100. What enzyme involves water being a reactant? *hydrolase 101. What enzyme involves NADH and H+ being reactants? *oxidoreductase 102. What 4 steps of glycolysis use transferase enzyme? 1. step 1 2. step 3 3 step 7 4. step 10 103. What 3 steps of glycolysis use isomerase enzyme? 1. step 2 2. step 5 3. step 8 104. What 2 steps of glycolysis use lyase enzyme? 1. step 4 2. step 9 105. In glycolysis, under what conditions will the free energy change be negative, enabling the reaction to proceed forward? *When there is a high concentration of fructose 1,6-bisphosphate relative to the concentration of the products 106. According to the Lineweaver-Burk plot, what are the slope, y-intercept, and x-intercept formulas? a. slope = Km/Vmax b. y-intercept = 1/Vmax c. x-intercept = -1/Km 107. Transition state analogs are usually what? *competitive inhibitors 108. Which statements are true when talking about inhibitors and substrates? a. A higher substrate concentration is associated with a faster reaction rate if the enzyme is not saturated. * b. A competitive inhibitor decreases the maximum rate at which a reaction can proceed. c. When substrate is present in excess, the maximum reaction rate is unchanged in the presence of a competitive inhibitor. * 109. What intermolecular force is responsible for holding the 2 strands of DNA double helix together? *hydrogen bond 110. What are the 2 characteristics of tRNAs? 1. have a distinct cloverleaf-like structure 2. carry amino acids to the ribosome 111. What are the 2 characteristics of mRNAs? 1. protected by a poly-A tail 2. carry instructions required to generate a protein 112. What are the 2 characteristics of rRNAs? 1. transcribed in the nucleolus and associates with proteins 2. catalyze the formation of peptide bonds 113. What does a purine include? *5 and 6-membered rings (adenine and guanine) 114. What do pyrimidines include? *6-membered ring (cytosine and thymine) 115. What are the 2 characteristics of only DNA? 1. uses thymine 2. double-stranded 116. What are the 2 characteristics of only RNA? 1. uses uracil 2. single-stranded 117. What are the 2 characteristics of both DNA and RNA? 1. made of nucleotides 2. contains codes for proteins 118. What are the monomers (building blocks) of nucleic acids? *nucleotides 119. What is the DNA sequence complementary to GACT? *CTGA 120. What are the 3 key features of a DNA molecule? 1. DNA bases are always paired purine with pyrimidine. 2. DNA strands are antiparallel and include a 5' end and a 3' end. 3. The backbone of DNA is made of a sugar and a phosphate molecule. 121. What are the structures in a cell that group genes together, are composed of chromatin (DNA & protein), and become visible under a light microscope during mitosis? *chromosomes 122. The diagram of a single nucleotide is represented with a phosphate group, nitrogenous base, and deoxyribose sugar. What do these look like on the diagram? *phosphate group = circle *nitrogenous base = 6-carbon ring *deoxyribose = 5-carbon ring 123. Thymine complements ______; cytosine complements ______. *adenine; guanine 124. Identify the statements that describe the DNA structure. 1. The five-carbon sugar of DNA is called deoxyribose. 2. Adenine is paired with thymine, and guanine is paired with cytosine. 3. A DNA double helix contains 2 sugar-phosphate backbones oriented in opposite directions. 125. MRNA involves what 2 statements: 1. moves genetic info out of the nucleus and into the cytoplasm 2. read in codons, 3-base sequences for specific amino acids 126. rRNA involves: 1. joins amino acids by peptide bonds 127. tRNA involves what 2 statements: 1. delivers amino acids to the site of protein synthesis (ribosomes) 2. has a convoluted structure with a 3-base sequence called an anticodon 128. mRNA, rRNA, and tRNA all involve what 2 statements: 1. in eukaryotes, can exist outside the nucleus 2. composed of ribonucleic acid 129. Describe mRNA. *a linear sequence of ribonucleotides transcribed from DNA that carries instructions for protein production 130. Describe tRNA. *a cloverleaf-shaped structure of ribonucleotides that contains an anticodon and is attached to an amino acid 131. What is the function of mRNA? *carries the codons for the polypeptide sequence 132. What is the function of rRNA? *catalyzes peptide bond formation 133. What is the function of tRNA? *bonds with codon *transports amino acids to the ribosomes 134. What are the 6 steps of prokaryotic DNA replication? Bacterium initiating DNA replication 1. The DNAa protein binds to the single origin of replication. 2. The upstream region melts, and helicase binds and unwinds DNA. 3. RNA primers are added to provide a 3' end for elongation. 4. DNA polymerase synthesizes the leading strand and short lagging strands 5' to 3'. 5. DNA replaces RNA and lagging strands are joined. 6. Tus protein stops replication forks form crossing each other and ends synthesis. DNA replication terminated 135. What protein relaxes the supercoiled DNA? *DNA topoisomerase 136. What protein unwinds the DNA double helix? *helicase 137. What protein prevents the reannealing of DNA strands? *SSB protein 138. What protein replaces RNA primers with DNA? *DNA polymerase I 139. What protein synthesizes RNA primers? *primase 140. What are the 6 steps of eukaryotic DNA replication in order? Cell enters gap 1 1. Each genomic origin of replication assembles a prereplication complex. 2. The initiation complex creates an active replication fork as helicase unwinds DNA. 3. RNA primers are added to provide a 3' end for elongation. 4. 5' to 3' synthesis of the leading and lagging strands is carried out by DNA polymerase. 5. RNA is replaced with DNA and lagging strands are joined. 6. Active telomerase can extend the lost telomere region. Cell cycle termination 141. Discontinuous replication is the result of which specific feature of DNA? *antiparallel strands 142. What are the 2 characteristics of transcription? 1. acts on only 1 strand 2. catalyzed by RNA polymerase 143. What are the 2 characteristics of replication? 1. catalyzed by DNA polymerase 2. RNA primase is required 144. Compare transcription and replication. *both are localized in the nucleus in eukaryotic cells 145. Place the steps of eukaryotic transcription in order. RNA polymerase II binds DNA promoter element. 1. RNA polymerase unwinds DNA. 2. Ribonucleotides align with complementary DNA nucleotides. 3. RNA polymerase links triphosphate ribonucleotides together. 4. Guanylyl transferase adds a guanine cap to the 5' end of the mRNA. 5. RNA polymerase is released from DNA. 6. Splicing and polyadenylation events modify the mRNA. Processed mRNA leaves nucleus. 146. What are the 2 characteristics of prokaryotic transcription? 1. can be terminated by rho helicase 2. promoter includes 35 consensus sequence 147. What are the 3 characteristics of eukaryotic transcription? 1. includes 3' polyadenylation 2. requires TFIIB 3. promoter includes a TATA box 148. What is the role of the eukaryotic promoter in transcription? *the site where transcription factors bind and function 149. What term describes the new chain of DNA that begins at the replication fork and is synthesized in discontinuous fragments (Okazaki)? *lagging strand


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