TEST BANK FOR BIOCHEMISTRY: A SHORT COURSE, 3RD EDITION, JOHN L. TYMOCZKO, JEREMY M. BERG , LUBERT STRYER

TEST BANK FOR BIOCHEMISTRY: A SHORT COURSE, 3RD EDITION, JOHN L. TYMOCZKO, JEREMY M. BERG , LUBERT STRYER Table of Contents PART I: THE MOLECULAR DESIGN OF LIFE Section 1: Biochemistry Chapter 1: Biochemistry and the Unity of Life Chapter 2: Water, Weak Bonds and the Generation of Order Out of Chaos Section 2: Protein Composition and Structure Chapter 3: Amino Acids Chapter 4: Protein Three-Dimensional Structure Chapter 5: Techniques in Protein Biochemistry Section 3: Basic Concepts and Kinetics of Enzymes Chapter 6: Basic Concepts of Enzyme Action Chapter 7: Kinetics and Regulation Chapter 8: Mechanisms and Inhibitors Chapter 9: Hemoglobin, An Allosteric Protein Section 4: Carbohydrates and Lipids Chapter 10: Carbohydrates Chapter 11: Lipids Section 5: Cell Membranes, Channels, Pumps and Receptors Chapter 12: Membrane Structure and Function Chapter 13: Signal-Transduction Pathways PART II: TRANSDUCING AND STORING ENERGY Section 6: Basic Concepts and Design of Metabolism Chapter 14: Digestion: Turning a Meal into Cellular Biochemicals Chapter 15: Metabolism: Basic Concepts and Design Section 7: Glycolysis and Gluconeogenesis Chapter 16: Glycolysis Chapter 17: Gluconeogenesis Section 8: The Citric Acid Cycle Chapter 18: Preparation for the cycle Chapter 19: Harvesting electrons from the cycle Section 9: Oxidative Phosphorylation Chapter 20: The Electron-Transport Chain Chapter 21: The Proton-Motive Force Section 10: The Light Reactions of Photosynthesis and the Calvin Cycle Chapter 22: The Light Reactions Chapter 23: The Calvin Cycle Section 11: Glycogen Metabolism and the Pentose Phosphate Pathway Chapter 24: Glycogen Degradation Chapter 25: Glycogen Synthesis Chapter 26: The Pentose Phosphate Pathway Section 12: Fatty Acid and Lipid Metabolism Chapter 27: Fatty Acid Degradation Chapter 28: Fatty Acid Synthesis Chapter 29: Lipid Synthesis: Storage Lipids, Phospholipids, and Cholesterol Section 13: The Metabolism of Nitrogen-Containing Molecules Chapter 30: Amino Acid Degradation and the Urea Cycle Chapter 31: Amino Acid Synthesis Chapter 32: Nucleotide Metabolism PART III: SYNTHESIZING THE MOLECULES OF LIFE Section 14: Nucleic Acid Structure and DNA Replication Chapter 33: The Structure of Informational Macromolecules: DNA and RNA Chapter 34: DNA Replication Chapter 35: DNA Repair and Recombination Section 15: RNA Synthesis, Processing and Regulation Chapter 36: RNA Synthesis and Regulation in Bacteria Chapter 37: Gene Expression in Eukaryotes Chapter 38: RNA Processing in Eukaryotes Section 16: Protein Synthesis and Recombinant DNA Techniques Chapter 39: The Genetic Code Chapter 40: The Mechanism of Protein Synthesis Chapter 41: Recombinant DNA Techniques Chapter 1 Biochemistry and the Unity of Life Matching Questions Use the following to answer questions 1–10: Choose the correct answer from the list below. Not all of the answers will be used. a) uracil b) cytoplasm c) protein d) thymine e) carbohydrate f) sugar–phosphate units g) cell wall h) transcription i) glycogen j) lipid k) central dogma l) phagocytosis m) endoplasmic reticulum n) translation o) prokaryotes p) eukaryotes q) lysosome 1. DNA is made from the building blocks adenine, guanine, cytosine, and . 2. : Unbranched polymer that, when folded into its three- dimensional shape, performs much of the work of the cell. 3. : Scheme that describes the flow of information from one strand of DNA to a new strand of DNA. 4. : Process where large amounts of material are taken into the cell. 5. The transfer of information from DNA to RNA is called . 6. are cells that are composed of multiple specialized compartments. 7. : Class of biological macromolecules with many functions, such as forming barriers between cell organelles, serving as a metabolic fuel, and cell-to-cell signaling. 8. : Highly organized region of the cell where glycolytic metabolism occurs. 9. : Responsible for protein processing and xenobiotic metabolism. 10.. : Filled with proteases and other digestive enzymes. Fill-in-the-Blank Questions 11. Organisms are known to be highly uniform at the level. Ans: molecular Section: Introduction 12. After hydrogen and oxygen, the next most common element in living systems is . 13. A chemical that can dissolve in water is said to be . 14. A nucleotide consists of one or more groups, a 5-carbon ribose sugar, and a nitrogen-containing aromatic ring group. 15. The most common carbohydrate fuel is . 16. Heritable information is packaged into discrete units called . 17. A group of enzymes called catalyze replication. 18. Although all cells in an organism have the same DNA, tissues differ due to selective . 19. The basic unit of life is considered the . 20. Secretory vesicles fuse with the plasma membrane to release material outside of the cell via . Multiple-Choice Questions 21. The structure of DNA described by Watson and Crick included: A) a double helix. B) the sugar–phosphate backbone aligned in the center of the helix. C) the base pairs that are stacked on the inside of the double helix. D) A and B. E) A and C. ed of a polymer s? E) None of the above. 23. What gives proteins such a dominant role in biochemistry? A) the variation in protein sizes B) the ability to act as a blueprint C) their ability to self-replicate D) their ability to spontaneously fold into complex three-dimensional structures E) All of the above. 24. Proteins are chiefly composed of which of the following? A) carbohydrate and amino acids B) long unbranched amino acid polymers C) peptide bonds formed between lipid moieties D) aggregated amino acids E) A and B Section 1.3 25. How a protein folds is determined by: A) whether the environment is hydrophobic or hydrophilic. B) the location in the cell in which the protein is located. C) the pH of the cytoplasm. D) the order of the amino acids found in the sequence. E) All of the above. 26. The half-life of which of the following is likely to be shortest? A) protein B) lipid C) carbohydrate D) DNA E) RNA 27. The central dogma describes: A) the formation of cells from individual components. B) the selective expression of genes. C) the flow of information between DNA, RNA, and protein. D) the work of polymerases on RNA and DNA. E) All of the above. 28. Translation takes place on/in the: A) ribosomes. B) smooth endoplasmic reticulum. C) nucleus. D) DNA polymerases. E) DNA parent strand. 29. Which of the following organelles has a double membrane? A) nucleus B) endoplasmic reticulum C) mitochondria D) plasma membrane E) A and C F) All of the above. 30. The main function of the plasma membrane is to: A) provide the interior of the cell an enclosed environment that no molecules may cross. B) provide a selectively permeable barrier with the aid of transport proteins. C) give eukaryote and prokaryote cells structural strength. D) allow only the free passage of water in and out of the cell. E) None of the above. 31. Filaments and microtubules are components of a network called the: A) chloroplast. B) cytoplasm. C) cytoskeleton. D) cell wall. E) B and D. 32. Poisons that kill an organism as a result of a loss of high-energy ATP molecules are most likely to target which organelle? A) mitochondria B) cytoskeleton C) cytoplasm D) endoplasmic reticulum E) nucleus 33. A secreted protein would be processed through organelles in the following order: A) nucleus; secretory vesicle; Golgi complex. B) cytoplasm; Golgi complex; cytosol; secretory vesicle. C) endoplasmic reticulum; cytoplasmic reticulum; Golgi complex. D) nucleus; cytoplasm; endoplasmic reticulum; Golgi complex; secretory vesicle. E) None of the above. 34. Extracellular material is taken into the cell via which process? A) exocytosis B) phagocytosis C) lysosome-mediated endocytosis D) reverse secretory mechanism E) phago-cytosolic internalization 35. The rigid material that provides structural support to a plant cell is/are called the: A) plant cytoskeleton. B) plasma membrane. C) cell wall. D) chloroplast anchor proteins. E) microfilaments and microtubules. 36. In studying secreted proteins, you find that Substance X inhibits the secretion of a labeled protein. However, you do find a fully synthesized, folded, and glycosylated proteins in the cell. Where is the most likely site in the synthesis and secretion of proteins for Substance X to act? A) nucleus during translation B) budding of the secretory granule C) translation on the ribosome D) enzyme modification in the Golgi E) All of the above. 37. Below is the scheme known as the central dogma. Each of the arrows (A, B, C) represents a particular process in gene expression. A, B, and C, respectively, are: A) replication, transcription, translation. B) reverse transcription, transcription, translation. C) transcription, translation, replication. D) replication translation, expression. E) None of the above. 38. Match the loss of a particular organelle with the associated disease. A) Hypercholesterolemia – smooth endoplasmic reticulum B) Diabetes – endosome C) Tay-Sachs disease - lysosome D) Muscle degeneration – mitochondria E) Stroke – Golgi body 39. In a biochemistry lab course, you are asked to design an experiment to identify a strain of bacteria. Your lab partner claims that she thinks the bacterium contains a rough endoplasmic reticulum. To verify her claim, which of the following experiments would you preform? A) determine whether the bacterium can synthesize ATP in the presence of fuel molecules and O2 B) determine whether the bacterium can synthesize proteins C) determine whether the bacterium generates CO2 in the presence of fuel molecules D) determine whether the bacterium has an internal membrane-enclosed compartment E) All of these experiments will work. Short-Answer Questions 40. What are the four key classes of biomolecules? 41. How do eukaryotic cells differ from prokaryotic cells? 42. Describe the central dogma and why it is important for cell life. 43. Define an organelle. 44. What is the role of the endoplasmic reticulum (ER)? 45. Of the biochemical macromolecules, which class is chiefly responsible for catalysis of cellular processes? 46. DNA and RNA are composed of what basic biochemical compounds? 47. What are the important functions of carbohydrates? 48. What is significant about the DNA process of replication? 49. Which property of lipids drives the formation of membranes? 50. What data might Monod cite to justify the phrase “Anything found to be true of E. coli must also be true of elephants”? Chapter 2 Water, Weak Bonds, and the Generation of Order Out of Chaos Matching Questions Use the following to answer questions 1–10: Choose the correct answer from the list below. Not all of the answers will be used. a) ionic bonds or salt bridges b) Brownian motion c) hydrophobic d) hydrogen e) polar f) nonpolar g) van der Waals h) entropy i) ion product of water j) amphipathic k) positive l) dielectric constant m) negative 1 : The type of bond found between an oxygen on one water molecule and hydrogen on a different water molecule. 2 Movement of particles due to the random fluctuations of energy content of the environment is known as . 3 Electrostatic interactions between atoms with opposite electrical charges are also called . 4 Water weakens the electrostatic interaction of ions due to its high . 5 The distance when two atoms no longer repulse each other yet have the strongest attraction is known as the contact distance. 6 : Thermodynamic force that drives hydrophobic interactions. 7 : A molecule with two distinctive chemical properties or characteristics. 8 Which type of amino acid is responsible for increasing entropy as a protein folds? 9 : The charge on acetic acid when the pH is more than one pH unit above the pKa. 10 : The charge of an amino group when the pH is one pH unit below the pKa. Fill-in-the-Blank Questions 11 Molecules that are readily soluble in water are considered . 12 The force that is quantified by Coulomb’s law is called . 13 A solvent with a low dielectric constant would be a solvent for salts. 14 The transient force, which while weak, still has a large impact on how macromolecules interact is the . 15 Hydrophobic molecules are driven together by , not because they have an affinity for each other. 16 Lipids that interact with both the water and the hydrophobic regions of the membrane are considered . 17 An acid ionizes to form a proton and its . 18 When the pH is more than two pH units above the pKa of a carboxyl group, the acid is . 19 Buffers are critical in maintaining proper levels in biological systems. 20 The source of the key buffering component of blood is . Multiple-Choice Questions 21 What is the H+ concentration in a urine sample that has a pH of 6? A) 10−6 M B) 10−8 M C) 106 M D) 10−14 M E) 8 M 22 Which of the following is considered a noncovalent bond? A) electrostatic interactions B) hydrogen bonds C) van der Waals interactions D) All of the above. E) None of the above. 23 What charged group(s) is/are present in glycine at a pH of 7? A) –NH + B) –COO C) –NH + D) A and B E) A, B, and C 24 Water can form hydrogen bonds with the of another molecule. A) carbonyl groups B) amine groups C) aromatic rings D) alcohol groups E) A, B, and D 25. What pairs of atoms in nucleotide bases are involved in hydrogen bonds? A) N–H and C═O B) N–H and S–H C) O–H and P–O D) All of the above. E) None of the above. 26. Typical van der Waals energies are about: A) 4–20 kJ/mol. B) 2–4 kJ/mol. C) 200 kJ/mol. D) All of the above. E) None of the above