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Biochemistry: A Short Course, Second Edition Test Bank

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    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) uridine b) cytoplasm c) protein d) thymine e) carbohydrate f) sugar – phosphate units g) cell wall h) transcription i) glycogen j) lipid k) three l) two m) endoplasmic reticulum n) translation o) prokaryotes p) eukaryotes q) lysozome 1. DNA is made from the building blocks adenine, guanine, cytosine, and ____________. Ans: d Section: 1.2 2. ____________ : Unbranched polymer that, when folded into its three - dimensional shape, performs much of the work of the cell. Ans: c Section: 1.2 3. ____________ : The number of hydrogen bonds formed between A and T. Ans: l Section: 1.2 4. ____________ : The number of hydrogen bonds formed between G and C. Ans: k Section: 1.2 5. The transfer of information from DNA to RNA is called ____________. Ans: h Section: 1.3 6. ____________ are cells which are composed of multiple specialized compartments . Ans: p Section: 1.4

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    Chapter 1 Biochemistry and the Unity of Life 2 7. ____________ : C lass of biological macromolecules w ith many functions such as forming barriers between cell organelles, serving as a metabolic fuel , and cell - to - cell signaling. Ans: j Section: 1.2 8. ____________ : Highly organized region of the cell where glycolytic metabolism occurs. Ans: b Section: 1.4 9. ____________ : Responsible for protein processing and xenobiotic metabolism. Ans: m Section: 1.4 10. ____________ : Filled with proteases and other digestive enzymes. Ans: q Section: 1.4 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 _______________. Ans: carbon Section : 1.1 13. A chemical that can dissolve in water is said to be _______________. Ans: hydrophilic Section : 1.2 14. A nucleotide consists of one or more _______________ groups, a 5 - carbon ribose sugar , and a nitrogen - containing aromatic ring group. Ans: phosphate Section : 1.2 15. The most common carbohydrate fuel is _______________. Ans: glucose Section: 1.2 16. Heritable information is packaged into discrete units called _______________. Ans: genes Section: 1.3 17. A group of enzymes called _______________ catalyze replication. Ans: DNA polymerase Section: 1.3 18. Although all cells in an organism have the same DNA, tissues differ due to selective _______________. Ans: expression Section: 1.3 19. The basic unit of life is considered the _______________. A ns: cell Section: 1.4 20. Large particles of extracellular material are taken into the cell via : Ans: phagocytosis Section: 1.4

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    Chapter 1 Biochemistry and the Unity of Life 3 Multiple - Choice Questions 2 1. 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. Ans: E Section: 1.2 22 . In higher organisms, w hich of the following is composed of a polymer with double - stranded phosphodiester - linked monomers? A) RNA B) DNA C) protein D) carbohydrate E) None of the above. Ans: B Section 1.2 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. Ans: D Section: 1.2 24 . Proteins are chiefly composed of which of the following? A) c arbohydrate and amino acids B) l ong unbranched amino acid polymers C) p eptide bonds formed between lipid moieties D) a ggregated amino acids E) A and B Ans: B Section 1.3 25 . How a protein folds is determined by : A) w hether the environment is hydrophobic or hydrophilic . B) t he location in the cell in which the protein is located . C) t he pH of the cytoplasm . D) t he order of the amino acids found in the sequence . E) All of the a bove . Ans: D Section: 1.2

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    Chapter 1 Biochemistry and the Unity of Life 4 26 . The half - life of which of the following is likely to be shortest ? A) p rotein B) l ipid C) c arbohydrate D) DNA E) RNA Ans: E Section: 1.2 27 . The central dogma describes : A) t he formation of cells from individual components . B) t he selective expression of genes . C) t he flow of information between DNA, RNA , and protein . D) t he work of polymerases on RNA and DNA . E) All of the above . Ans: C Section: 1.3 28 . Translation takes place on/in the : A) r ibosomes . B) s mooth endoplasmic reticulum . C) n ucleus . D) DNA polymerases . E) DNA parent strand . Ans: A Section: 1.3 29 . Which of the following organelles has a double membrane ? A) n ucleus B) e ndoplasmic reticulum C) m itochondria D) p lasma membrane E) A and C F) All of the above . Ans: E Section: 1.4 30 . The main function of the plasma membrane is to : A) p rovide the interior of the cell an enclosed environment which no molecules may cross . B) p rovide a selectively permeable barrier with the aid of transport proteins . C) g ive eukaryote and prokaryote cells structural strength . D) a llow only the free passage of water in and out of the cell . E) None of the above . Ans: B Section: 1.4 31 . The structural components (filaments and tubules) are organelles called the: A) c hloroplast . B) c ytoplasm . C) c ytoskeleton . D) c ell wall . E) B and D . Ans: C Section: 1.4

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    Chapter 1 Biochemistry and the Unity of Life 5 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) m itochondria B) c ytoskeleton C) c ytoplasm D) e ndoplasmic r eticulum E) n ucleus Ans: A Section: 1.4 33 . A secreted protein would be processed through organelles in the following order : A) n ucleus; secretory vesicle; G olgi complex B) c ytoplasm; G olgi complex; cytosol; secretory vesicle C) e ndoplasmic reticulum; cytoplasmi c reticulum; G olgi complex D) n ucleus; cyt oplasm; endoplasmic reticulum; G olgi complex; secretory vesicle E) None of the above . Ans: E Section: 1.4 34 . Extracellular material is taken into the cell via which process ? A) e ndocytosis B) p hagocytosis C) l ysosome - mediated indocytosis D) r everse secretory mechanism E) p hago - cytosolic internalization Ans: B Section 1.4 35 . The rigid material which provides structural support to a plant cell is /are called the : A) p lant cytoskeleton B) p lasma membrane C) c ell wall D) c hloroplast anchor proteins E) m icrofilaments and microtubules Ans: C Section: 1.4 Short - Answer Questions 36 . What are the four key classes of biomolecules? Ans: Proteins, DNA/RNA, l ipids, c arbohydrates. These are the larger, monomer or biopolymer molecules which perform many functions to maintain cellular life. Each has a different biochemical make - up. Section: 1.2 37 . How do eukaryotic cells differ from prokaryotic cells? Ans: The simplest answer is defined by the existence of organelle. Eukaryotic cells contain organelles including a nucleus, while prokaryotic cells do not have such compartments. Section: 1.4

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    Chapter 1 Biochemistry and the Unity of Life 6 38 . Describe the central dogma and why i t i s important for cell life . Ans: T his is the phrase coined by Franc is Crick and is the overview of how a cell uses the information from DNA to produce RNA, protein, and more DNA . Much of the fate of a cell (metabolism, survival, growth, movement , and cell differentiation) is based on the control of the central dogma. Which genes are transcribed and translated define s the function of a cell. Section: 1.3 39 . Define an organelle. Ans: An organelle is often , but not always , enclosed by a membrane. Examples include the nucleus, mitochondria , and chloroplasts. However, the cytoplasm is defined as that area surrounded by the plasma membrane, excluding the organelles. Section: 1.4 40 . What is the role of the endoplasmic reticulum (ER) ? Ans: The endoplasmic reticulum is series of membrane tubes or sacs. When studded with proteins (ribosome s) , the endoplasmic reticulum is considered rough ER and is involved with the processing of nascent protein. Smooth ER is involved in maturing proteins and carbohydrates , and is responsible for xenophobic metabolism of foreign compounds. Section: 1.4 41 . Of the biochemical macromolecules, which class is chiefly responsible for catalysis of cellular processes? Ans: Proteins. Section: 1.2 42 . DNA and RNA are composed of what basic biochemical compounds? Ans: Both RNA and DNA are nucleotides. Central to nucleotides is a carbohydrate molecule called a ribose or deoxyribose . Bonded to the ribose is one of several aromatic nitrogen - containing organic compounds which are generically called “bases . ” One or more phosphate groups are also bonded to the ribose or deoxyribose . Section: 1.2 43 . What are the important functions of carbohydrates? Ans: Structural, energy storage, modify proteins, cell – cell recognition, lipid modification. Section: 1.2 44. What is significant about the base pairing found in the helix? Ans: It provides a mechanism for copying the DNA from one generation to the next. Section: 1.4 45 . Which property of lipids drives the formation of membranes? Ans: T he dual chemical nature of lipids allows them to self - organize into membranes . Section: 1. 2

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    Chapter 2 Water, Weak Bonds, and the G eneration 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) zwit t erion j) amphipathic k) positive l) dielectric constant m) negative 1. ____________ : T he t ype of bond found between an oxygen o n one water molecule and hydrogen on a different water molecule. Ans: d Section: 2.2 2. Movement of particles due to the random fluctuations of energy content of the environment is known as ____________ . Ans: b Section: 2.1 3. Electrostatic interactions between atoms with opposite electrical charges are also called ____________ . Ans: a Section: 2.3 4. Water weaken s the electrostatic interaction of ions due to its high ____________. Ans: l Section: 2.3 5. The distance when two atoms no longer repulse each other yet have the strongest attraction is known as the____________ radii or contact distance. Ans: g Section: 2.3

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    Chapter 2 Water, Weak Bonds, and the Generation of Order Out of Chaos 2 6. ____________ : Thermodynamic force that drives hydrophobic interactions . Ans: h Section: 2.4 7. ____________ : A molecule with two distinctive chemical properties or characteristics. Ans: j Section: 2.4 8. Which type of amino acids are responsible for increasing entropy as a protein folds ? Ans: f Section: 2.4 9. ____________ : The charge of the side group of a sp artate when the pH is more than one pH unit above the p K a. Ans: m Section: 2.5 10. ____________ : The charge of an amino group when the pH is one pH unit below the pKa . Ans: k Section: 2.5 Fill - in - the - Blank Questions 11. Molecules that are readily soluble in water are considered ____________ . Ans: polar Section 2.2 12. The force that is quantified by Coulomb’s law is called the ____________. Ans: ionic or electrostatic interaction Section 2.3 13. A solvent with a low dielectric constant would be a ____________ solvent for salts. Ans: poor Section 2.3 14. The transient force which , while weak, still has a large impact on how macromolecules interact is the ____________. Ans: Van der Waals interaction Section 2.3 15. Hydrophobic molecules are driven together by ____________ , not because the y have an affinity for each other. Ans: entropy Section 2.4 16. Lipid s that interact with both the water and the hydrophobic regions of the membrane are considered ____________. Ans: amphipathic Section 2.4 17. An acid ionizes to form a proton and its ________________. Ans: base or conjugate base Section 2.5

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    Chapter 2 Water, Weak Bonds, and the Generation of Order Out of Chaos 3 18. When the pH is more than two pH units above the pKa of a carboxyl group, the acid i s ____________ . Ans: unprotonated Section 2.5 19. Buffers are critical in maintaining proper ____________ levels in biological systems. Ans: pH Section 2.5 20. The source of the key buffering component of blood is ____________ . Ans: carbon dioxide Section 2.5 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) 10 6 M D) 10 − 14 M E) 8 M Ans: A Section: 2.5 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. Ans: D Section: 2.3 23. What charged group(s) are present in glycine at a pH of 7? A) – NH 3 + B) – COO − C) – NH 2 + D) A and B E) A, B, and C Ans: D Section: 2.5 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 Ans: E Section: 2.3 & 2.4

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    Chapter 2 Water, Weak Bonds, and the Generation of Order Out of Chaos 4 25 . What pairs of atoms in bases are involved in hydrogen bonds? A) N – H and O – H B) N – H and S – H C) O – H and P – O D) All of the above. E) None of the above. Ans: A Section: 2.3 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. Ans: B Section: 12.3 27 . What two properties of water are important for biological interactions? A) the polarity of water B) the density of water C) the cohesive properties of water D) A and C E) B and C Ans: D Section: 2.2 28 . List atoms commonly found in biological molecules that are often hydrogen - bond acceptors. A) carbon B) oxygen C) nitrogen D) B and C E) All of the above. Ans: D Section: 1.3 2 9 . What happens to nonpolar molecules in water? A) They dissolve independently. B) They agg regate together. C) They precipitate. D) All of the above. E) None of the above. Ans: B Section: 1.3 3 0 . What is the [A − ]/[HA] ratio when the weak acid is in a solution one pH unit above its p K a ? A) 1:1 B) 1:10 C) 10:1 D) 2: 1 E) None of th e above. Ans: C Section 1.3

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    Chapter 2 Water, Weak Bonds, and the Generation of Order Out of Chaos 5 31 . What are the primary chemical components present in a phosphate buffer at pH 7.4? A) H 3 PO 4 and PO 4 − 3 B) H 2 PO 4 − and PO 4 − 3 C) HPO 4 - 2 and PO 4 - 3 D) H 2 PO 4 − and HPO 4 − 2 E) H 3 PO 4 and HPO 4 − 2 Ans: D Section 1.3 32 . What is the c oncentration of acetic acid in 250 ml of a 100 mM acetate buffer at pH 4.76? A) 250 mM B) 100 mM C) 50 mM D) 75 mM E) There is n ot enough information to tell. Ans: C Section 2.5 Short - Answer Questions 33 . Using Coulomb’s law, describe how water is an ideal solvent for the ions found in cells? Ans: The force which attracts two oppositely charged ions is measured by a constant a kq 1 q 2 Kq1q2 divided the dielectric constant of the solvent × R. This means that a solvent such as water, with a high dielectric constant , will result in a lowered attractive force. Section: 2.4 34 . What is the significance of hydrogen bonding in biochemical structures such as DNA? Ans: The bonds are weak enough to be easily disrupted; yet when many are present, they provide the stabilization necessary for larger structures such as DNA. Section: 2.3 35 . What is an electrostatic interaction? Give an example. Ans: It is the attractive force of two oppositely charged atoms. Salts (such as NaCl) are a common example. Section: 2.3 36 . How is water able to be a solvent for so many biological molecules? Ans: Many biological molecules have polar characteristics. Water is extremely polar and is capable of competing with other polar molecules by weakening their electrostatic and hydrogen bonds. The oxygen can act as a hydrogen - bond acceptor, and the hydrogen can act as a donor. Section: 2.2 37 . What is the net effect of many van der Waals interactions? Ans: At the interface of two large molecules, the numerous van der Waals interactions can substantially affect and stabilize the interaction. Section: 2.3

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    Chapter 2 Water, Weak Bonds, and the Generation of Order Out of Chaos 6 38 . How is protein folding driven ? Ans: Nonpolar amino acids associate with each other , forming the interior of folded proteins. This causes an increase in the entropy of water and thermodynamically drives protein folding. Se ction: 2.4 39 . If noncovalent bonds are so much weaker than covalent bonds, how do they stabilize large biochemical structures? Ans: There is stability in numbers. Section: Introduction 40 . What thermodynamic and free - energy changes participate in protein folding? Ans: A combination of hydrogen bonds and van der Waals forces affect enthalpy and the entropy associated with hydrophobic interactions. Section: 2.4 41 . How do hydrophobic int eractions aid in membrane formation ? Ans: Hydrophobic interaction causes the nonpolar tails to aggregate and form the interior of the membrane . This results in a net re lease of heat and a favorable change in the system enthalpy. Section: 2.4 42 . Give examples of key functional groups found in biochemistry. Ans: Hydrophobic, hydroxyl, aldehyde, keto, carboxyl, amino, phosphoryl, sulfhydryl Section: 2.5 , Table 2.1 43 . Draw a titration curve for the ionization of acetic acid . Ans: The c urve should look like F igure 2.12. Section: 2.5 44 . Why are conjugate acid – base pairs so important in biological systems? Ans: The conjugate acid – base pairs in biological systems act as buffers. Many metabolic activities release protons, and these can combine with the conjugate base and so have little effect on the pH. Section: 2.5

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    Chapter 3 Amino Acids 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) L amino acids b) water c) protons d) zwitterions e) leucine f) serine g) tyrosine h) cysteine i) glutamate j) histidine k) proline l) asparagine m) D amino acids 1. ____________ : Chiral type of amino acids found in proteins. Ans: a Section: 3.1 2. ____________ : Another name for dipolar molecules. Ans: d Section: 3.1 3. ____________ : Disulfide bonds are formed by pairs of th is amino acid . Ans: h Section: 3.2 4. ____________ : The amino acid with a p K a near neutral pH. Ans: j Section: 3.2 5. ____________: The amino acid with whose side group has a terminal carboxamide . Ans: l Section: 3.2 6. ____________ : The amino acid with an imidazole side chain. Ans: j Section: 3.2 7. ____________ : An amino acid that must be supplied by the diet. Ans: j Section: 3.3

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    Chapter 3 Amino Acids 2 8. ____________ : The amino acid with a negative ly charged side chain at neutral pH. Ans: i Section: 3.2 9. ________ ____ : The amino acid with a sulfhydryl side chain. Ans: h Section: 3.2 10. ____________: The amino acid with the abbreviation Ser. Ans: f Section: 3.2 Fill - in - the - Blank Questions 11. The amino acid that contains a weakly acidic “phenolic” group is __________ . Ans: tyrosine Section 3.2 12. __________ are amino acid s with neutral R groups containing an electronegative atom that hoards electrons . Ans: Polar amino acids Section 3.2 13. The amino acid with the smallest - size side chain allowing great est flexibility in a protein is __________. Ans: glycine Section 3.2 14. The charge of glycine when the pH is < 2.0 is __________ . Ans: +1 Section 3.1 15. Between the amino and the carboxyl functional group, the ________ has the lowest affinity for a proton . Ans: carboxyl Section: 3.1 16. The amino acid with an indol ring is __________ . An s: tryptophan Section: 3.2 17. __________ is a n amino acid with a hydrophobic side chain containing a thioether . Ans: Methionine Section: 3.2 18. The ____________ group is the functional group that makes an amino acid more reactive than nonpolar amino acids such as valine, alanine , and phenylalanine. Ans: hydroxyl Section: 3.2 19. The group of amino acids that can be supplied by an organism under a defined condition are the ______ amino acids. Ans: Nonessential Section: 3.3 20. ____________ is often seen in a child with a protein - deficient diet. Ans: E dema Section: 3.3

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    Chapter 3 Amino Acids 3 Multiple - Choice Questions 21. What charged group(s) is / are present in glycine at a pH of 7? A) – NH 3 + B) – COO − C) – NH 2 + D) A and B E) A, B, and C Ans: D Section: 3. 2 22. At a pH of 12, what charged group(s) is / are present in glycine? A) – NH 3 + B) – COO − C) – NH 2 + D) A and B E) A, B, and C Ans: B Section: 3.2 23. I n what pH range is zwitterionic a lanine the predominate structure? A) 0 – 2 B) 9 – 14 C) 8 – 10 D) 2 – 4 E) 2 – 9 Ans: E Section 3.2 24. Which amino acids contain reactive aliphatic hydroxyl groups? A) serine and methionine B) serine and threonine C) methionine and threonine D) cysteine and methionine E) cysteine and threonine Ans: B Section: 3.2 25. Name three amino acids that are positively charged at a neutral pH. A) lys ine and arg inine B) his tidine and arg inine C) cys teine and arg inine D) lys ine and pro line E) glu tamine and his tidine Ans: A Section: 3.2 26. Interactions between side chains of and Asp artate and Arg inine at neutral pH would be? A) hydrophobic B) ionic C) hydrogen bonding D) steric E) covalent Ans: B Section: 3.2

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