Test Bank of Tymoczko’s Biochemistry A Short Course 3Rd Edition by John L. Tymoczko





Tymoczko’s Biochemistry A Short Course 3Rd Edition by John L. Tymoczko

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.

  1. a) uracil
  2. b) cytoplasm
  3. c) protein
  4. d) thymine
  5. e) carbohydrate
  6. f) sugar–phosphate units
  7. g) cell wall
  8. h) transcription
  9. i) glycogen
  10. j) lipid
  11. k) central dogma
  12. l) phagocytosis
  13. m) endoplasmic reticulum
  14. n) translation
  15. o) prokaryotes
  16. p) eukaryotes
  17. q) lysosome


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. ____________: Scheme that describes the flow of information from one strand of DNA to a new strand of DNA.
  Ans: k
  Section: 1.3


4. ____________: Process where large amounts of material are taken into the cell.
  Ans: l
  Section: 1.3


5. The transfer of information from DNA to RNA is called ____________.
  Ans: h
  Section: 1.3


6. ____________ are cells that are composed of multiple specialized compartments.
  Ans: p
  Section: 1.4


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.
  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: phosphoryl            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      .
  Ans: cell                         Section: 1.4


20. Secretory vesicles fuse with the plasma membrane to release material outside of the cell via      .
  Ans: exocytosis             Section: 1.4


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.
  Ans: E                  Section: 1.2



22. In higher organisms, which 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) 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
  Ans: 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.

  Ans: D                  Section: 1.2




26. The half-life of which of the following is likely to be shortest?
  A) protein

B)  lipid

C)  carbohydrate



  Ans: E                  Section: 1.2


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.

  Ans: C                  Section: 1.3


28. Translation takes place on/in the:
  A)  ribosomes.

B)   smooth endoplasmic reticulum.

C)   nucleus.

D)  DNA polymerases.

E)   DNA parent strand.

  Ans: A                  Section: 1.3


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.

  Ans: E                  Section: 1.4


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.

  Ans: B                  Section: 1.4


31. Filaments and microtubules are components of a network called the:
  A)  chloroplast.

B)   cytoplasm.

C)   cytoskeleton.

D)  cell wall.

E)   B and D.

  Ans: C                  Section: 1.4


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

  Ans: A                  Section: 1.4


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.

  Ans: E                  Section: 1.4


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

  Ans: B                  Section 1.4


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.

  Ans: C                  Section: 1.4


  1. 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?
  2. A) nucleus during translation
  3. B) budding of the secretory granule
  4. C) translation on the ribosome
  5. D) enzyme modification in the Golgi
  6. E) All of the above.

Ans: B                  Section: 1.4


  1. 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:


  1. A) replication, transcription, translation.
  2. B) reverse transcription, transcription, translation.
  3. C) transcription, translation, replication.
  4. D) replication translation, expression.
  5. E) None of the above.

Ans: A                  Section: 1.3



  1. Match the loss of a particular organelle with the associated disease.
  2. A) Hypercholesterolemia – smooth endoplasmic reticulum
  3. B) Diabetes – endosome
  4. C) Tay-Sachs disease – lysosome
  5. D) Muscle degeneration – mitochondria
  6. E) Stroke – Golgi body

Ans: C                  Section: 1.4


  1. 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?
  2. A) determine whether the bacterium can synthesize ATP in the presence of fuel molecules and O2
  3. B) determine whether the bacterium can synthesize proteins
  4. C) determine whether the bacterium generates CO­2 in the presence of fuel molecules
  5. D) determine whether the bacterium has an internal membrane-enclosed compartment
  6. E) All of these experiments will work.

Ans: D                  Section: 1.4


Short-Answer Questions


40. What are the four key classes of biomolecules?
  Ans: Proteins, DNA/RNA, lipids, carbohydrates. 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


41. How do eukaryotic cells differ from prokaryotic cells?
  Ans: The simplest answer is defined by the existence of organelles. Eukaryotic cells contain organelles including a nucleus, while prokaryotic cells do not have such compartments.
  Section: 1.4


42. Describe the central dogma and why it is important for cell life.
  Ans: This is the phrase coined by Francis 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 defines the function of a cell.
  Section: 1.3


43. Define an organelle.
  Ans: An organelle is an intracellular compartment, 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


44. What is the role of the endoplasmic reticulum (ER)?
  Ans: The endoplasmic reticulum is series of membrane tubes or sacs. When studded with ribosomes, 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


45. Of the biochemical macromolecules, which class is chiefly responsible for catalysis of cellular processes?
  Ans: Proteins.
  Section: 1.2


46. 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


47. What are the important functions of carbohydrates?
  Ans: Structural, energy storage, modify proteins, cell–cell recognition..
  Section: 1.2


48. What is significant about the DNA process of replication?
  Ans: It provides a mechanism for copying the DNA from one generation to the next.
  Section: 1.4



49. Which property of lipids drives the formation of membranes?
  Ans: The dual chemical nature of lipids allows them to self-organize into membranes.
  Section: 1.2


  1. What data might Monod cite to justify the phrase “Anything found to be true of E. coli must also be true of elephants”?

Ans: He would most likely describe similarities between eukaryotic and prokaryotic cells. The first is a barrier, a membrane, that separates the cell form its environment such that independent of cell type, the interior of the cell is chemically different that the external environment. The membrane is more than a barrier; it is selectively permeable and directs the flow of molecules into and out of the cell. The second is the structure of the molecule that carries information regarding cell activities as the cell undergoes duplication each generation. Nucleic acids are the information storage molecule for living systems.

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. Answers may be used more than once.

  1. a) l amino acids
  2. b) water
  3. c) protons
  4. d) zwitterions
  5. e) arginine
  6. f) serine
  7. g) tyrosine
  8. h) cysteine
  9. i) glutamate
  10. j) histidine
  11. k) proline
  12. l) asparagine
  13. 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 this amino acid.
  Ans: h
  Section: 3.2


4. ____________: The amino acid with a side-chain pKa just below neutral pH.
  Ans: j
  Section: 3.2


5. ____________: The amino acid with a side group that 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


8. ____________: The amino acid with a negatively 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 acids with neutral R groups containing an electronegative atom.
  Ans: Polar amino acids            Section 3.2


13. The amino acid with the smallest-size side chain allowing greatest 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      .
  Ans: tryptophan                       Section: 3.2


17.        is an 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


  Ans: nonessential         Section: 3.3


20.       is often seen in a child with a protein-deficient diet.
  Ans: Edema                 Section: 3.3


Multiple-Choice Questions


21. What charged group(s) is/are present in glycine at a pH of 7?
  A) –NH3+
  B) –COO
  C) –NH2+
  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) –NH3+
  B) –COO
  C) –NH2+
  D) A and B
  E) A, B, and C
  Ans:  B            Section:  3.2


23. In what pH range is zwitterionic alanine 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) lysine and arginine
  B) histidine and arginine
  C) cysteine and arginine
  D) lysine and proline
  E) glutamine and histidine
  Ans: A             Section: 3.2


26. What would interactions between side chains of aspartate and arginine at neutral pH be?
  A) hydrophobic
  B) ionic
  C) hydrogen bonding
  D) steric
  E) covalent
  Ans: B             Section: 3.2


27. Which amino acid has a side chain with a hydroxyl group?
  A) serine
  B) alanine
  C) tryptophan
  D) histidine
  E) glutamine
  Ans: A             Section: 3.2


28. Which amino acid has a carboxyl group in its side chain?
  A) glutamine
  B) galanine
  C) cysteine
  D) glutamate
  E) None of the above.
  Ans: D             Section: 3.2


29. What would the overall charge of a peptide of the following peptide sequence at pH 1 be (Asp-Gly-Arg-His)?
  A) −1
  B) 0
  C) 1
  D) 2
  E) 3
  Ans: E              Section: 3.2


30. Which of the following amino acids would most likely be soluble in a nonpolar solvent such as benzene?
  A) valine
  B) histidine
  C) glutamine
  D) glycine
  E) All of the above.
  Ans: A             Section: 3.2


31. Below is a list of five tripeptides identified by their single letter codes. They are listed as A, B, C, D, and E. Which tripeptide contains an amino acid capable of forming covalent disulfide bonds?
  A) FNC
  B) RGK
  C) VIL
  D) MDE
  E) SYT
  Ans: A             Section: 3.2


32. Below is a list of five tripeptides identified by their single letter codes. They are listed as A, B, C, D, and E. Which tripeptide is negatively charged at physiological pH?
  A) FNC
  B) RGK
  C) VIL
  D) MDE
  E) SYT
  Ans: D             Section: 3.2


33. Below is a list of five tripeptides identified by their single letter codes. They are listed as A, B, C, D, and E. Which tripeptide has the most polar side chains?
  A) FNC
  B) RGK
  C) VIL
  D) MDE
  E) SYT
  Ans: E              Section: 3.2


34. Where are Trp and Phe found in a globular protein and why?
  A)  exterior due to the hydrophilic effect
  B) interior due to the hydrophobic effect
  C) exterior forming polar H-bonds with water
  D) interior forming ionic bonds with other amino acids
  E) exterior forming ionic-polar bonds with water
  Ans: B             Section: 3.2


35. Amino acids contain all of the following functional groups except:
  A) indole.
  B) thioester.
  C) phenyl.
  D) sulfhydryl.
  E) amine.
  Ans: B             Section: 3.2


Short-Answer Questions


36. What is the advantage of having multiple functional groups in proteins?
  Ans: The rich diversity of functional groups in proteins can contribute independently to protein structure and accounts for the diversity in function as well.
  Section: Introduction


37. What is the advantage of protein interaction and assembly with other proteins?
  Ans: When proteins interact or assemble, new functions and specificity become available. These protein interactions provide multifunctional activity and specificity.
  Section: Introduction


38. Draw the general structure of an amino acid at pH 7.0 with the side group shown as an “R.”
  Ans: The figure should look like either one of the structures shown in the left margin on p. 38.
  Section: 3.1


39. Why is the central carbon on an amino acid so important?
  Ans: This is the chiral center of the molecule and is linked to each important functional group of an amino acid.
  Section: 3.1
40. Draw the structure of alanine, aspartic acid, and histidine when the pH is 1.0, 7.0, and 12.0.
  Ans: Use the figures in your book and the pKa for each functional group to determine the ionization state for each amino acid.
  Section: 3.2


41. What is the net charge of each the following amino acid: alanine, aspartic acid, and histidine when the pH is 1.0, 7.0, and 12.0?
  Ans: For alanine, the charges are: 1, 0, and −1. For aspartic acid, the charges are: 1, −1, and −2. For histidine, the charges are: 2, 0, and −1.
  Section: 3.2


42. A gene is mutated so the amino acids glycine and glutamate are now alanine and leucine, respectively. What are the potential results of each of these mutations? Assume that the mutations are not near each other in the primary sequence and have no impact on the other.
  Ans: The glycine-to-alanine mutations are similar and will have little or no effect. Glutamate and leucine have very different chemistries and will impact the function and structure of the protein, as one is charged and water soluble, and the other is hydrophobic and nonpolar.
  Section: 3.2


43. What are the four ways amino acids can be classified?
  Ans: hydrophobic, polar, positively charged, and negatively charged
  Section: 3.2


44. What are the three aromatic amino acids?
  Ans: phenylalanine, tyrosine, and tryptophan
  Section: 3.2


45. Which amino acid side chains are capable of ionization?
  Ans: The amino acids are aspartate, glutamate, histidine, cysteine, tyrosine, lysine, and arginine.
  Section: 3.2


46. Which are the branched amino acids, and what impact do they have on protein shape?
  Ans: These are the aliphatic, hydrophobic amino acids, valine, leucine, and isoleucine. They are hydrophobic, which drives the hydrophobic interactions in the interior of a protein. These are also bulky amino acids that will lend to steric strain if forced close to each other in a peptide.
  Section: 3.2


47. Draw a titration curve for glycine.
  Ans: Use the information from Section 2.5 and the graph from Figure 3.2.
  Section: 3.2


48. What do serine, threonine, and tyrosine have in common?
  Ans: Each has a hydroxyl (–OH) group, which makes the first two amino acids more water soluble and increases the reactivity of all three amino acids.
  Section: 3.2


49. Which amino acid is responsible for stabilizing the structure of a protein by forming pairs of sulfhydryl groups?
  Ans: cysteine
  Section: 3.2


50. What functions make histadine an important amino acid?
  Ans: The pKa of the imidazole ring is near physiological pH. This means that the side group may be charged and protonated or neutral and deprotonated. This results in an amino acid that can either lend or accept a proton or charge in the active site of an enzyme.
  Section: 3.2


51. Which amino acids have a side chain that includes a modified carboxyl group, carboxaminde?
  Ans: asparagine and glutamine
  Section: 3.2


52. Which ionizable group has the lowest affinity for protons: the terminal a-carboxyl group, the aspartic acid side group, or the terminal a-amino group?
  Ans: the terminal a-carboxyl group
  Section: 3.2


53. Malnourished children with Kwashiorkor display a distended stomach, giving the illusion of being full. Why does this happen?
  Ans: This is a nutritional state where there is an extremely low or poor protein intake in the diet. The osmolar shift of the blood, which is poor in protein content, causes water to flow into the tissues.
  Section: 3.3


54. What is the difference between nonessential and essential amino acids?
  Ans: The former are amino acids that humans can generate de novo, or from scratch. The latter cannot be made and must be ingested for the mature formation of proteins.
  Section: 3.3


55. List the essential amino acids.
  Ans: histadine, isoleucine, leucine, lysine, methionine, phenylalanine, threonine, tryptophan, and valine
  Section: 3.3

Chapter 11   Lipids



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.

  1. a) ether-linked lipid
  2. b) triacylglycerol
  3. c) sterol
  4. d) amphipathic
  5. e) 16 or 18
  6. f) organic solvent
  7. g) cholesterol
  8. h) cysteine
  9. i) phospholipid
  10. j) prokaryotes
  11. k) glycolipid
  12. l) 20 or 24
  13. m) sphingosine
  14. n) serine


1. ____________ The storage form of fatty acids.


  Ans:  b
  Section:  Introduction


2. ____________ This is the number of carbons in most common fatty acids.


  Ans:  e
  Section:  11.1


3. ____________ In addition to phospholipids and glycolipids, this is a major type of membrane lipid.


  Ans:  g
  Section:  11.3


4. ____________ This is a term applied to molecules that have both hydrophilic and hydrophobic moieties.


  Ans:  d
  Section:  11.3


5. ____________ A lipid is defined as a compound soluble in ________________.


  Ans:  f
  Section:  Introduction


6. ____________ Lipids that are bound to carbohydrates.
  Ans:  k
  Section:  Introduction


7. ____________Type of lipid with two acyl chains, a glycerol backbone, and a polar head group.
  Ans:  i
  Section:  11.3


8. ____________ Flat polycylic molecule absent in prokaryotic membranes.


  Ans:  g
  Section:  11.3


9. ____________ These lipids are less resistant to hydrolysis, potentially due to the way the acyl chain is linked to the glycerol backbone.


  Ans:  a
  Section:  11.3


10. ____________ A complex amino alcohol backbone for membrane lipids.


  Ans:  m
  Section:  11.3



Fill-in-the-Blank Questions


11.      is a membrane lipid composed of sphingosine, fatty acid, and a simple sugar.
  Ans:  Cerebroside     Section:  11.3


12. The common name of hexadecanoic acid is      .
  Ans:  palmitic acid     Section:  11.1


13. In phosphoglycerides, the fatty acids are linked to the glycerol backbone by the       linkages.
  Ans:  ester     Section:  11.3


14. The configuration of most fatty acids in biological systems is      .
  Ans:  cis     Section:  11.1


15. Fatty acids are ionized at physiological pH and so are referred to in their      form.
  Ans:  carboxylate     Section:  11.1


16.      The short-hand notation indicating that there are two cis double bonds between carbons 9 and 10 and again between 12 and 13.
  Ans:  cis, cis-912   Section:  11.1


17. The presence of double bonds in fatty acids limits tight packaging and the number of


  Ans:  van der Waals     Section:  11.1


18.       is the type of glycolipid that contains a branched chain of as many as seven sugar residues.
  Ans: Ganglioside   Section:  11.3


19. The reduction in tight packing due to cis double bonds       the melting temperature of a fatty acid.
  Ans: lowers   Section:  11.1


20. One important       is EPA (eicosapentoenoate) and is found in fatty fish and shellfish.
  Ans:  ω-3 fatty acid   Section:   11.1



Multiple-Choice Questions


21. Membrane lipids are primarily comprised of:
  A) phospholipids.     B) glycolipids.     C) cholesterol.     D) A and B.     E) A, B, and C.
  Ans:  E     Section:  11.3


22.  Which of the following is NOT a main function of lipids?
  A) cell signaling
  B) fuel source
  C) structural rigidity of the cytoskeleton
  D) membrane component
  E) All of the above.
  Ans:   C    Section:  Introduction


23.  Octadecatrienoic acid has how many double bonds?
  A) 0
  B) 1
  C) 2
  D) 3
  E) 4
  Ans:    D   Section:   11.1


24.  An w-3 fatty acid ____________.
  A) has a methyl group at the carboxyl end of the fatty acid
  B) has a methyl group on the third carbon of the chain
  C) has a double bond the third carbon in from the carboxyl group
  D) has a triple bond on the third carbon from the methyl end of the fatty acid
  E) None of the above.
  Ans:   E    Section:   11.1


25.  The notation 12:2 indicates which of the following about a fatty acid?
  A) There are 12 carbons in the chain with two double bonds.
  B) There are two 12-carbon chains for this fatty acid.
  C) The second carbon has a fatty acid double bond.
  D) The  12th carbon has a double bond.
  E) There are two trans-double bonds on this 12-carbon fatty acid.
  Ans:   A    Section:   11.1


26. Which of the following is NOT correct concerning the structure given?


  A) It is a component of biological membranes.
  B) It is amphipathic.
  C) It is a sphingolipid.
  D) It is a phosphoglyceride.
  E) It is phosphatidyl choline.
  Ans:  C     Section: 11.3


27.  The longer the fatty acid the ________ the fatty acid.
  A) more oxidized
  B) lower the melting point of
  C) higher the melting point of
  D) more reduced
  E) more double-bond containing
  Ans:   C    Section: 11.1


28.  Palmitate has how many carbons in its chain?
  A) 12
  B) 14
  C) 16
  D) 20
  E) 24
  Ans:      C    Section:   11.1


29.  Unsaturations ________ melting points of fatty acids and their derivatives.
  A) maintain
  B) decrease
  C) increase
  D) are unrelated to
  E) None of the above.
  Ans:  B     Section:   11.1


30.  Eating ____________ increases the w-3 fatty acids decreasing ___________.
  A) arachidonic acid,  cardiovascular disease
  B) a low fat diet, cardiovascular disease
  C) fatty fish, cardiovascular disease
  D) shellfish, lung cancer
  E) vegetable oils, blood pressure
  Ans:     C  Section:   11.1


31.  The backbone of a phospholipid is which of the following?
  A) glucose
  B) cholesterol
  C) fatty acid chain
  D) triacylglycerol
  E) glycerol
  Ans:   E    Section:   11.3



32.  The polar head group of phospholipids is found at which carbon of glycerol?
  A) C1
  B) C2
  C) C3
  D) C1-OH
  E) C2-OH
  Ans:    C   Section:   11.3



33.  Polar-head groups of phospholipids are esterified to what functional group?
  A) methyl
  B) phosphate
  C) ketone
  D) thiol
  E) aldehyde
  Ans:  B     Section:   11.3


34.  A phosphatidate lipid (phosphatidic acid) has which of the following components?
  A) phosphate
  B) glycerol
  C) ester linkage
  D) acyl chain
  E) All of the above.
  Ans:   E    Section:  11.3


35.  Which phospholipid is enriched in neural sheath membranes?
  A) phosphatidic acid
  B) phosphatidylcholine
  C) sphingomyelin
  D) diphophatidylglycerol (cardiolipin)
  E) phosphatidylinositol
  Ans:    C   Section:   11.3


36.  Identify the differences in archaea membrane lipids compared to those of eukaryotes or bacteria and how these differences help them withstand extreme environmental conditions.
  A) The ether linkages are more, readily hydrolyzed by enzymes allowing the membrane to serve as an energy reserve.
  B) The glycerol moiety is esterified to multiple complex carbohydrate chains making them more soluble in low pH environments.
  C) The fatty acid chains are branched, allowing them to pack more tightly, thereby protecting membrane integrity.
  D) There are two phosphate esters instead of only one giving the archaea better solubility in high salt environments.
  E) Omega ω-3 fatty acids are common in membranes and may act as important precursors as they do in eukaryotes.
  Ans:    C   Section:   11.3


37.  You are studying a protein known to be localized to the membrane surface. What protein modifications might you look for to determine how the protein is attached to the membrane?
  A) Determine whether a farnesyl group is attached to a carboxy terminal cysteine residue.
  B) Determine whether a fatty alcohol is attached to a serine residue on the surface of the protein.
  C) Determine whether a glycosylphosphatidylinositol anchor is attached to the carbosy terminus.
  D) A and C only.
  E) All of the above.
  Ans:    D   Section:   11.3


38. Cholesterol and other steroids are not soluble in blood, and therefore must be transported. Predict what chemical modifications must occur for cholesterol to move through the circulatory system.
  A) Cholesterol forms micells in blood, the surface of which is hydrophilic and the interior is hydrophobic.
  B) Cholesterol cannot be transported in blood and so it broken down and resynthesized in all cells.
  C) Cholesterol moves through cell membranes from tissue to tissue.
  D) Cholesterol forms glycolipids with large carbohydrate complexes in order to increase solubility.
  E) Cholesterol is esterified to a fatty acid for transport by lipoprotein particles, the surface of which is hydrophilic and the interior is hydrophobic.
  Ans:    E   Section:   11.3


Short-Answer Questions


39. What does the notation 18:2 for fatty acids imply?
  Ans: In this fatty acid there are 18 carbons, with two double bonds.
  Section:  11.1


40. What are the two systems for naming the positions of the double bonds? Provide examples.
  Ans: Two systems are used. One system refers to the double bond relative to the last, or omega (w), carbon. (An example would be w-3 fatty acids.) The other system uses notation that indicates the position of the double bond relative to the carboxyl carbon, and indicates if the bond is cis or trans. (An example would be cis-D9.)
  Section:  11.1


41. What are some molecules that form the polar-head group of phospholipids? Provide several examples.
  Ans: Examples of head groups include serine, ethanolamine, choline, glycerol, and inositol.
  Section:  11.3


42.  Explain the biochemical nature of why trans bonds do not have the same effect as cis bonds on the melting point of fatty acids.
  Ans: This is due to the order or cis-order when a double bond is introduced.  A trans-double bond maintains the linear shape of the fatty acid, while a cis-double bond creates a kinked or bent shape.  The latter reduces the number of contact points, thus reducing the amount of energy needed to melt the fatty acid lattice.
  Section:  11.1


43.  Explain why fats are an efficient way to store biochemical energy.
  Ans: This has to do with the anhydrous nature of fat (less water means more mass of fat per gram) and with the fact that fatty acid tails are more reduced than carbohydrates or amino acids.  We will learn later, that the transfer of electrons through redox reactions leads to ATP production.
  Section:  11.2


44. Draw and label a typical phospholipid.
  Ans: The phospholipid drawn should resemble Figure 12.5 in the textbook. It should contain a central glycerol molecule, to which two fatty acids are attached in ester linkages at the center and an end. The other end should be linked to a phosphor alcohol group. The phosphate should be shown negatively charged at pH 7.
  Section:  11.3


45.  How are birds that migrate across the Gulf of Mexico able to sustain flight over long distances?
  Ans: The energy source for these migrations are fatty acids, stored as triacylglycerols (TAGs). TAGs are stored in a nearly anhydrous form, and as a result, a gram of fat stores more than six times as much energy as a gram of hydrated glycogen.
  Section:  11.2


46.  What is the difference between a sphingolipid and a glycerolipid?
  Ans: A sphingolipid has an alcohol such as a serine for the backbone and only one fatty acid tail, where as a glycerolipid uses glycerol as the backbone and has two acyl chains esterified to the hydroxyl groups of the glycerol.
  Section:  11.3


47.  Steroid hormones come from what lipid?
  Ans: Cholesterol is the main source of steroid hormones.
  Section:  11.3


48.  Define the different chemical characteristics for the phospholipids, phosphatidylserine, phosphatidylcholine, and phosphadidylinositol.
  Ans: See the figure for each phospholipid and focus on the head group.  Look for charge and hydrophobicity.
  Section:  11.3


49.  How does the structure of cholesterol give it a unique structural quality among the lipids?
  Ans: The flat double-bonded fused ring creates a bulky hydrophobic moiety for several potential modifications.
  Section:  11.3


50.  Based on your knowledge of lipids, guess why some fats from plants are oils (liquid at room temperature) and animal fats are solid at room temperature.
  Ans: Knowing that the longer the fatty acid chain the higher the melting point and that more double bonds lead to lower melting points, plant fats are likely to be shorter and primarily unsaturated or monounsaturated, while animal fats are more often polyunsaturated.
  Section:  11.2



51.  Phosphoglycerides have common but varying structural features. Describe which structural features are common to all phosphoglycerides and which ones vary. Draw correlations between structural variability and membrane function.
  Ans: All phosphoglycerides contain a glycerol backbone with two fatty acid chains attached through ester bonds to two of the hydroxyls. The third hydroxyl is attached by a phosphoester bond to phosphate, which is then attached to one of several alcohols. This amphipathic structure forms a bilayer in aqueous solutions, so that even with the differences identified as follows, phosphoglycerides form a stable hydrophobic barrier between the cell’s interior and its surroundings. The differences are seen in the length and saturation of the fatty acids, and the chemical nature of the alcohol attached to the phosphate. Fatty acid differences affect the fluidity of the membrane and the chemical nature of the alcohol provides multiple functional sites on the membrane surfaces.
  Section:  11.2


52. Draw the structure of sphingomyelin and label the linkages in this structure.
  Ans: See Figure 12.6
  Section:  12.3

Chapter 21   The Proton-Motive Force



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.

  1. a) Peter Mitchell
  2. b) chemiosmotic theory
  3. c) binding-change
  4. d) loose
  5. e) ATP
  6. f) entropy
  7. g) α subunit
  8. h) tight
  9. i) glycerol 3-phosphate shuttle
  10. j) c ring
  11. k) ATP-ADP translocase
  12. l) malate-aspartate shuttle
  13. m) Sir Hans Krebs


1. ____________ The thermodynamic driving force of ATP synthesis due to pumping of protons.


  Ans:  f
  Section:  21.3


2. ____________ first described the chemiosmotic hypothesis.


  Ans:  a
  Section:  21.1


3. ____________ is the mechanism for the proton-driven ATP synthesis.


  Ans:  c
  Section:  21.1


4. ____________ Which form of the ATPase subunits is responsible for phosphorylation of ADP?


  Ans:  h
  Section:  21.1


5. ____________ Rotation of this, driven by proton gradient, powers ATP synthesis.


  Ans:  j
  Section:  21.1


6. ____________ ADP transport into the mitochondria is coupled to the export of __________.
  Ans:  e
  Section:  21.2


7. ____________ Dihydroxyacetone phosphate is part of the ______________  shuttle.


  Ans:  i
  Section:  21.2


8. ____________ This is the name given to the hypothesis proposed by Peter Mitchell to explain how ATP synthesis is coupled to electron transport.


  Ans:  b
  Section:  21.1


9. ____________ Atractyloside inhibits this mitochondrial protein.


  Ans:  k
  Section:  21.3


10. ____________ This is a process by which cytoplasmic NADH can be reoxidized by O2 using the electron-transport system.
  Ans:  l
  Section:  21.2



Fill-in-the-Blank Questions


11. Transfer of electrons from NADH leads to how many ATP?      .
  Ans:  2.5    Section:  21.1


12.       membrane protein couples the entry of ADP into the mitochondrial matrix with the exit of ATP.
  Ans:  ADP-ATP translocase    Section:  21.2


13. The protein involved with thermogenesis by uncoupling electron transport from oxidative phosphorylation is      .
  Ans:  uncoupling protein (UCP-1)    Section:  21.3


14.      is a molecular assembly in the inner mitochondrial membrane that carries out the synthesis of ATP.
  Ans:  F1F0 ATPase, or ATP synthase     Section:  21.1


15. In the glycerol phosphate shuttle, cytoplasmic glycerol phosphate dehydrogenase uses cytoplasmic NADH to reduce      to glycerol-3-phosphate.
  Ans:  dihydroxyacetone phosphate     Section:  21.2


16. Acceptor control of oxidative phosphorylation means that the rate of respiration depends on the level of      .
  Ans:  ADP     Section:  21.3


17.      is a poison because it blocks the flow of electrons from cytochrome c to oxygen.
  Ans:  Carbon monoxide (CO), or Cyanide (CN), or Azide (N3)     Section:  21.3


18. In the presence of      respiration continues but no ATP is formed.
  Ans:  uncouplers     Section:  21.3


19. The antibiotic      inhibits the flow of protons through ATP synthase.
  Ans:  oligomycin     Section:  21.3


20. ATP is transported out of the mitochondria by the antiporter      .
  Ans:  ATP-ADP translocase     Section:  21.2



Multiple-Choice Questions


21. What type of gradient is critical to ATP formation by oxidative phosphorylation?
  A) sodium ion D) potassium ion
  B) chloride ion E) None of the above.
  C) proton    
  Ans:  C     Section:  Introduction


22. When glucose is totally oxidized to CO2 and H2O, how many ATP molecules are made by oxidative phosphorylation relative to the maximum yield?
  A) 12 out of 30
  B) 26 out of 30
  C) 26 out of 32
  D) 12 out of 38
  E) None of the above.
  Ans:  B     Section:  21.3


23. What is the chemical effect of rotenone on aerobic metabolism?
  A) The flow of electrons from NADH to CoQ is blocked.
  B) The flow of electrons from Cyt a-a3 to oxygen is blocked.
  C) Oligomycin blocks the proton transfer through F0 of ATP synthase and therefore blocks the phosphorylation of ADP to form ATP.
  D) The transport of ATP out of and ADP into the mitochondria are blocked.
  E) Oxidative phosphorylation is uncoupled from electron transport and all the energy is lost as heat.
  Ans:  A     Section:  21.3


24.  The subunit of the ATPase embedded in the inner mitochondrial membrane is the __________.
  A)  anchor subunit
  B)  membrane-c ring subunit
  C)  F0 subunit
  D)  F1 subunit
  E)  Fm subunit
  Ans:    C   Section:  21.1


25.  The F1 component of ATP synthase is composed of _________.
  A)  three α subunits
  B)  three β subunits
  C)  a Δ subunit
  D)  All of the above.
  E)  None of the above.
  Ans:   D    Section:  21.1


26. The proton motive force consists of _____________.
  A) a chemical gradient D) A and B.
  B) a proton gradient. E) A, B, and C.
  C) an electron gradient    
  Ans:  D     Section:  21.1


27. Electron flow down the electron-transport chain leads to the
  A) transport of protons across the inner mitochondrial membrane from inside the matrix to the intermembrane space.
  B) transport of protons across the inner mitochondrial membrane from the intermembrane space into the matrix.
  C) coupled synthesis of GTP.
  D) a dangerous imbalance of K+ ions across the mitochondiral membrane.
  E) None of the above.
  Ans:  A     Section:  21.1


28.  How does the rotation of the c ring lead to ATP synthesis?
  A)  The c ring is linked tightly to the gamma and epsilon subunits in the stalk of F1.
  B)  The c ring interacts with the beta subunit.
  C)  The gamma subunit rotates with proton gradient formation inducing the binding-change mechanism.
  D)  All of the above.
  E)  None of the above.
  Ans:    D   Section:  21.1


29.  What are the driving force (energetic) costs for the ATP-ADP translocase?
  A)  entropy – concentration gradient of ATP
  B)  membrane potential from electron transport
  C)  active transport by Na-K ATPase
  D)  All of the above.
  E)  None of the above.
  Ans:   B    Section:  21.1



30.  A diet pill that acts to increase oxygen consumption and a high amount of electron transport without ATP production is likely what kind of compound?
  A)  uncoupler
  B)  ATP synthase activator
  C)  site I inhibitor
  D)  site II activator
  E)  cyanide
  Ans:    A   Section:  21.3


31. What is the reaction of ATP synthase?
  A) AMP3 + 2 HPO42 + H+ Û ATP4 + H2O
  B) ADP3 + HPO42 + H+ Û ATP4 + H2O
  C) ADP3 + HPO42 + 2H+ Û ATP4 + H2O
  D) AMP3 + 2 HPO42 + 2H+ Û ATP4 + H2O
  E) None of the above.
  Ans:  B     Section:  21.1


32. What is the net ATP obtained from one cytoplasmic NADH when it is oxidized by the electron-transport chain using the glycerol 3-phosphate shuttle?
  A)  2.5.     B)  1.5.     C)  2.0.     D)  1.0.     E)  None of the above.
  Ans:  B     Section:  21.3


33. In the malate-aspartate shuttle, electrons from NADH are transferred to ________, forming malate.
  A) oxaloacetate D) glutamate
  B) aspartate E) None of the above.
  C) acetate    
  Ans:  A     Section:  21.3


34.  Suppose there is a mutation in the c subunit of ATP synthase, such that the glutamate found in the middle of one of the membrane spanning helices is converted to a valine. What is likely to be the effect on ATP synthesis and why?
  A) No effect. The middle of the helix is in contact with the hydrophobic center of the lipid bilayer and the valine is readily soluble in lipid.
  B) No effect. The valine side chain is shorter than the glutamate side chain, so it causes no change in the secondary structure of the helix.
  C) Inhibit ATP synthesis. Valine cannot bind a proton, so there will be no proton flow through the inner membrane.
  D) Inhibit ATP synthesis. Because valine is hydrophobic, the α subunit will move in the reverse direction, causing the hydrolysis of ATP, not synthesis.
  E) Increase ATP synthesis. Because the valine side chain is hydrophobic, the α subunit can move easily without regard to oxidative processes.
  Ans:  C     Section:  21.1


35.  Why is it not surprising that substances such as intermediates for the citric acid cycle, protons, inorganic phosphate, nucleotide phosphates, and many others have their transport across the inner membrane regulated?
  A) Regulated transport allows for more effective substrate cycling.
  B) Ultimately all electrons flow into the electron-transport chain, which regulates electron flow from the matrix to the inner membrane space.
  C) The experiment where bacteriorhodopsin and ATP synthase were inserted into reconstituted vesicles showed that biochemically, membranes control the movement of electrons in the respiratory chain.
  D) Many of the reactions in the citric acid cycle and ATP synthesis are driven by accessibility of substrates and differential gradients across the inner membrane.
  E) It is necessary to segregate the enzymes capable of substrate level phosphorylation during anaerobic respiration.
  Ans:    D   Section:  21.3



Short-Answer Questions


36. Provide a brief description of oxidative phosphorylation.
  Ans: It is the process in which ATP is formed due to the transfer of electrons from NADH or FADH2 to O2 by a series of electron carriers in the inner membrane of the mitochondria.
  Section:  Introduction


37. What additional free energy driven processes are powered by a proton gradient?
  Ans: Active transport, flagellar rotation, NADPH synthesis, and heat production are all driven by a proton gradient.
  Section:  21.3 and Figure 21.21


38. Explain why less ATP is made from the reoxidation of FADH2 as compared to NADH.
  Ans: Complex II is not a proton pump.  When electrons flow from FADH2 to oxygen, as catalyzed by complex II, complex III, and complex IV, fewer protons are pumped out of the matrix as compared to NADH.  Thus, fewer ATP molecules are ultimately made.
  Section:  21.3


39. What is the actual function of the protons in the synthesis of ATP by F0F1 ATP synthase?
  Ans: The proton gradient is necessary for ATP synthesis because the binding of a proton to the enzyme causes a conformational change that releases the bound ATP.  The role of the proton gradient is not to form ATP but to release it from the synthase.
  Section:  21.1


40. What was the proof that the ATP synthase was rotating?
  Ans: Using cloned a3b3g subunits, with the b subunits tagged with a histidine that attached it to a nickel coated slide, and using another fluorescent tag linked to the g subunit, the rotation could be observed using a fluorescent microscope.
  Section:  21.1 and Figure 21.7


41. How does the glycerol 3-phosphate shuttle function?
  Ans: Electrons from NADH are transferred to DHAP, to form glycerol-3-P, a reaction that occurs in the cytosol. Glycerol 3-phosphate diffuses through the outer membrane and then transfers the electrons to FAD of glycerol-3-phosphate dehydrogenase located in the inner membrane.  The FADH2 then transfers the electrons to Q.
  Section:  21.3


42. In the malate-aspartate shuttle, how is oxaloacetate regenerated even though there is no transporter for oxaloacetate across the inner membrane?
  Ans: Inside the mitochondria, the malate is converted to oxaloacetate by malate dehydrogenase.  The oxaloacetate is converted to aspartate, which can be transported out of the mitochondria.  The aspartate can then be converted to oxaloacetate. The aspartate-oxaloacetate reactions require glutamate and a-ketoglutarate.
  Section:  21.3


43. How is oxidative phosphorylation regulated?
  Ans: The electrons do not flow unless ADP is available to be simultaneously phosphorylated to ATP. Thus, the synthesis of ATP does not occur unless ADP levels are high.  This is referred to as acceptor control.
  Section:  21.3


44. What are uncouplers? Provide an example of when this might be useful.
  Ans: Uncouplers destroy the proton gradient across the inner membrane by carrying protons back into the matrix.  This disrupts the coupling of electron transport to oxidative phosphorylation, and the energy is released as heat instead of being used to drive phosphorylation of ADP. Nonshivering thermogenesis, to generate heat for newborns, is one example provided (due to the uncoupler UCP-1).
  Section:  21.3


45. Explain why carbon monoxide is toxic.
  Ans: Carbon monoxide binds to the ferrous ion of cytochrome a3 of cytochrome c oxidase.  The result is that the electron flow to oxygen is blocked and the proton-motive force can no longer be generated.  Without the proton gradient, the phosphorylation of ADP cannot occur.  Thus, energy production ceases.
  Section:  21.3


46. What is the mechanism for nonshivering thermogenesis?
  Ans: Tissues rich in brown fat mitochondria have large amounts of uncoupling protein 1 (UCP-1). UCP-1 generates heat by uncoupling respiration and ATP synthesis.
  Section:  21.3



47. What is the relationship between obesity and UCP-1?
  Ans: Obesity leads to a decrease in brown fat adipose, a tissue rich in UCP-1.
  Section:  21.3


48. What is the IF1 protein and what is its protective role in tissues?
  Ans: IF1 or inhibitory factor 1, specifically inhibits the potential hydrolytic activity of the F0F1 ATPase. In the case of ischemia, the electron-transport chain will be unable to generate the proton gradient. ATP in the matrix would by hydrolyzed by the synthase working in reverse. It is IF1’s role to prevent wasteful hydrolysis of ATP by inhibiting this hydrolytic activity.
  Section:  21.3



49. Would you expect polar bears to have a rich store of brown adipose? Why or why not?
  Ans: Brown adipose, found mainly in newborn animals, generates heat and actually consumes energy. In polar bears, it is found in adults and plays an important role in survival. Species that hibernate experience a drop in body temperature and a slowing of metabolism during winter dormancy, which allows them to conserve energy. Brown adipose, by consuming energy, releases heat, which is vital for awakening and emergence from dormancy.
  Section:  21.3



50. What is the difference between a respiratory inhibitor and a decoupling agent? Describe an experiment that could determine the difference.
  Ans: Respiratory inhibitors inhibit electron transport at one of the four complexes in the respiratory chain. Uncouplers allow for electron transport, but allow protons to flow back into the matrix via another mechanism that ATP synthesizes. In an experiment containing a mitochondrial preparation, ADP and inorganic phosphate, ATP synthesis, and O2 consumption are monitored. In the presence of a respiratory inhibitor, both ATP synthesis and O2 consumption stop; however, in the presence of a decoupling agent, only ATP synthesis stops.
  Section:  21.3


Chapter 31         Amino Acid Synthesis



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.

  1. a) atmospheric nitrogen (N2)
  2. b) 3-phosphoglycerate
  3. c) cumulative
  4. d) nitrogen fixation
  5. e) B12
  6. f) histidine
  7. g) tetrahydrofolate
  8. h) committed
  9. i) pyridoxal phosphate
  10. j) enzyme multiplicity
  11. k) MoFe cofactor
  12. l) ammonia (NH3)


1. _______________ is the original nitrogen source for the nitrogen found in amino acids.
  Ans: a
  Section: Introduction


2. The process of converting N2 to NH3 is called _______________.
  Ans: d
  Section: Introduction


3. _______________ is the site of nitrogen fixation by nitrogenase enzymes.
  Ans: k
  Section: 31.1


4. The precursor for serine, cysteine, and glycine amino acid biosynthesis is _______________.
  Ans: b
  Section: 31.2


5. A versatile carrier of one-carbon units is _______________.
  Ans: g
  Section: 31.2


6. Methylcobalamine is derived from vitamin _______________.
  Ans: e
  Section: 31.2


7. _______________ is a cofactor for transamination reactions.
  Ans: i
  Section: 31.2


8. The final product pathway that inhibits an enzyme that catalyzes its production typically takes place at the _______________ step.
  Ans: h
  Section: 31.3


9. Glutamine synthesis is inhibited by _______________ feedback inhibition.
  Ans: c
  Section: 31.3


10. Isozymes, or multiple enzymes with the same identical catalytic properties but with different regulation, are an example of _______________.
  Ans: j
  Section: 31.3



Fill-in-the-Blank Questions


11. Only a few prokaryotes, such as _____, are able convert N2 to ammonia.
  Ans: nitrogen-fixing bacteria                           Section: Introduction


12. _____ ATP molecules are hydrolyzed for each N2 reduced.
  Ans: At least 16                                                           Section: 31.1


13. The α-amino group found in most amino acids comes from _____ through a transamination reaction.
  Ans: glutamate                                                 Section: 31.1


14. Glutamine synthase adds NH3 to _____ to make glutamine.
  Ans: glutamate                                                 Section: 31.1


15. Glutamate is the precursor for the amino acids glutamine, proline, and _____.
  Ans: arginine                                                   Section: 31.2


16. Methyl, methylene, and _____ units can be carried by tetrahydrofolate.
  Ans: formyl                                                     Section: 31.2


17. Homocysteine is an intermediate in the synthesis of cysteine and _____.
  Ans: methionine                                              Section: 31.2


18. The enzyme _____ is regulated by cumulative feedback inhibition.
  Ans: glutamine synthase                                  Section: 31.3


19. The binding of serine to 3-phosphoglycerate dehydrogenase induces a _____ in Vmax.
  Ans: reduction                                                 Section: 31.3


20. Metabolic pathways that have alternate products are often regulated by _____ and _____.
  Ans: feedback inhibition; activation                Section: 31.3



Multiple-Choice Questions


21. Amino acid synthesis is generally regulated by
  A) turnover.
  B) diet.
  C) feedback and allosteric enzyme regulation.
  D) A and B.
  E) A, B, and C.
  Ans: C             Section: 31.3


22. Organisms capable of carrying out reduction of atmospheric nitrogen include
  A) some bacteria and archaea.
  B) higher eukaryotic organisms, such as mammals.
  C) all plants.
  D) All of the above.
  E) None of the above.
  Ans: A             Section: 31.1


23. The electrons for the reduction of molecular nitrogen are donated by
  A) proteins.
  C) ferredoxin.
  D) None of the above.
  E) All of the above.
  Ans: C             Section: 31.1


24. The carbon skeletons for amino acids are intermediates found in
  A) glycolysis.
  B) the citric acid cycle.
  C) the pentose phosphate pathway.
  D) All of the above.
  E) None of the above.
  Ans: D             Section: 31.2


25. Essential amino acids differ from nonessential amino acids in that
  A) nonessential amino acids are synthesized in simple reactions compared to many for most essential amino acids.
  B) essential amino acids are generally synthesized directly from citric acid cycle intermediates, but nonessential amino acids are not.
  C) microorganisms and animals cannot synthesize essential amino acids but plants can.
  D) animals cannot synthesize essential amino acids because they have lost the ability to carry out transamination reactions.
  E) None of the above.
  Ans: A             Section: 31.2.


26. S-adenosylmethionine carries which groups?
  A) methyl
  B) CO2
  C) ammonia
  D) None of the above.
  E) All of the above.
  Ans: A             Section: 31.2


27. This amino acid, in high levels, is correlated with the damage of cells lining the blood vessels.
  A) serine
  B) cysteine
  C) S-adenosylmethionine
  D) citrulline
  E) homocysteine
  Ans: E              Section: 31.2


28. Essential amino acids are synthesized by:
  A) microorganisms.
  B) humans.
  C) plants.
  D) A and B.
  E) A and C.
  Ans: E              Section: 31.2


29. Which amino acid is added to indole to form tryptophan?
  A) glutamine
  B) serine
  C) tyrosine
  D) All of the above.
  E) None of the above.
  Ans: B             Section: 31.2


30. Erythrose 4-phosphate is a precursor to the amino acids
  A) tryptophan, tyrosine, and phenylalanine.
  B) tryptophan and phenylalanine.
  C) tyrosine and phenylalanine.
  D) tryptophan, tyrosine, phenylalanine, and serine.
  E) None of the above.
  Ans: A             Section: 31.2


31. Through what process might feedback inhibition processes have evolved?
  A) duplication of genes encoding catalytic domains
  B) evolution of homologous subunits in the enzyme catalyzing the committed step
  C) linking specific regulator domains to catalytic domains
  D) linking of multiple regulatory domains
  E) All of the above.
  Ans: C             Section: 31.3


32. An example of a reaction controlled by enzyme multiplicity is
  A) phosphorylation of asparagine by aspartokinases.
  B) phosphorylation of aspartate by aspartokinases.
  C) phosphorylation of glutamine by glutamine synthetase.
  D) All of the above.
  E) None of the above.
  Ans: B             Section: 31.3


33. Which gaseous plant hormone is involved in triggering ripening?
  A) melanin
  B) epinephrine
  C) ethylene
  D) A and B.
  E) A and C.
  Ans: C             Section: 31.2


34. The activated methyl cycle involves the production and use of
  A) glutamine.
  B) glycine.
  C) heterocysteine.
  D) homocysteine.
  E) methanol.
  Ans: D             Section: 31.2


35. The rates of synthesis of amino acid metabolic pathways often depends on the
  A) committed step.
  B) allosteric regulation.
  C) feedback inhibition.
  D) All of the above.
  E) None of the above.
  Ans: D             Section: 31.3


36. The making of carbon-carbon bonds requires energy. How does the activated methyl cycle provide energy for methyl group transfer to a wide variety of acceptors?
  A) The side-chain methylene group of serine is transferred to tetrahydrofolate, a carrier of one-carbon units.
  B) The fully oxidized one-carbon unit, CO2, is carried by biotin.
  C) The most reduced form of one-carbon groups carried by tetrahydrofolate is the methyl group.
  D) Transmethylation reactions are carried out by pyricoxal phosphate-dependent methyltransferases.
  E) The methyl group of methionine is activated by the transfer of an adenosyl group to the sulfur atom of methionine.
  Ans:     E          Section: 31.2



37. Increased synthesis of which of the following amino acids might affect DNA production?
  A) histidine and tryptophan
  B) aspartate and glutamate
  C) threonine and methionine
  D) cysteine and glycine
  E) valine and leucine
  Ans:     A         Section: 31.2



38. Insufficient amounts of this amino acid would not only inhibit protein synthesis, but also phostidylcholine and phostidylethanolamine.
  A) glutamine
  B) histidine
  C) phenylalanine
  D) methionine
  E) alanine
  Ans:     D         Section: 31.2



39. In Chapter 22, we learned that ferredoxin is a strong reductant in the ferredoxin-NADP+ reductase. Where else is ferredoxin’s reducing power required?
  A) glutamine synthetase
  B) reductase (Fe protein)
  C) nitrogenase (MoFe protein)
  D) glutamate dehydrogenase
  E) aspartate transaminase
  Ans:     B          Section: 31.1



40. Enzymes that catalyze the same reaction but are regulated differently is a strategy known as
  A) sequential feedback inhibition.
  B) end-product inhibition.
  C) substrate-limited inhibition.
  D) enzyme multiplicity.
  E) cumulative feedback inhibition.
  Ans:     D         Section: 31.3




Short-Answer Questions


41. What is significant about many of the intermediates in amino acid biosynthesis?
  Ans: Many of the biosynthetic intermediates can also be found in energy-forming pathways, and thus are critical to anabolic and catabolic paths. In this way, intermediates can play a dual role, depending on the energy status of the organism.
  Section: 31.2


42. What determines the range of one-carbon units carried by tetrahydrofolate?
  Ans: One-carbon units bind to the pteridine ring of tetrahydrofolate and exist in one of three states. The most reduced form carries methyl groups, while the intermediate form carries a methylene group. The most oxidized form carries multiple units, including formyl, formimino, or methenyl groups.
  Section: 31.2


43. Describe the process and proteins involved in nitrogen fixation.
  Ans: Electrons are provided by ferredoxin, transferred to the reductase, and then to the nitrogenase. In this process, electrons are provided by the reductase to the nitrogenase to use. The reaction is driven by the hydrolysis of ATP. See Figure 31.1 for further details.
  Section: 31.1


44. What is the MoFeco factor?
  Ans: This unusual redox center is the site of nitrogen reduction in nitrogenase. It appears to bind the N2 in the central cavity, and forms multiple Fe–N interactions, weakening the N-to-N bond, and lowering the activation barrier for reduction. Each cofactor contains seven nitrogen atoms, a molybdenum atom, and nine sulfides, as well as homocitrate. Each nitrogenase heterotetramer binds two cofactors via amino acid links.
  Section: 31.1


45. What is a major difference between the amino acid biosynthetic capacity of prokaryotic organisms and humans?
  Ans: Whereas microorganisms can make most of the amino acids, humans cannot. At least nine of the amino acids must be obtained through diet. In part, the dietary need depends on the individual. For example, children cannot synthesize enough arginine to meet their own needs and must have it supplied in their diet.
  Section: 31.2


46. What do S-adenosylmethionine and fruit ripening have in common?
  Ans: S-adenosylmethionine is a precursor to the compound ethylene. Ethylene is critical in the ripening, and often premature spoiling, of fruits.
  Section: 31.2


47. Draw homocysteine.
  Ans: SH–CH2–CH2 CH–NH3+



  Section: 31.2


48. Describe the regulation of the enzyme threonine deaminase.
  Ans: This enzyme is inhibited by isoleucine, a product of the path in which the enzyme participates. In contrast, the enzyme is inhibited by valine, which is synthesized by an independent pathway. Thus, this mechanism helps to adjust the amounts of the amino acids made and helps balance the relative amounts.
  Section: 31.3


49. What is enzyme multiplicity?
  Ans: This is a strategy for regulation in which several enzymes that carry out the same step, but differ somewhat in structure and sequence, are regulated by different molecules. In this way, various biomolecules can influence the overall amount of a product made.
  Section: 31.3


50. What is the advantage of the cumulative enzymatic regulation of glutamine synthetase activity?
  Ans: It allows fine-tuning and amplification of signals, such as in E. coli, where it regulates the flow of nitrogen. Allosteric control is increased and each activator or inhibitor can specifically contribute to regulation.
  Section: 31.3


51. What would be the result of a pathway such as that shown in Figure 31.12 if only one enzyme catalyzed the first reaction? What if there was inhibition only by X and not by Y?
  Ans: The shunting of metabolites between the two branches would be limited to diffusion and other enzyme rates, not limited to the cellular needs of each product. The primary product of inhibition only by X would be Y and not X.
  Section: 31.3


52. Describe the effect of cumulative inhibition.
  Ans: This describes a situation in which several allosteric inhibitors can act on a single enzyme or metabolic pathway. In this case, the addition of another inhibitor will still have an effect, even in the presence of the other inhibitors.
  Section: 31.3




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