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Biochemistry Concepts And Connections By Appling, Anthony – 
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Biochemistry: Concepts and Connections (Appling et al.)

Chapter 1   Biochemistry and the Language of Chemistry

 

1) The water content in the human body is approximately:

  1. A) 90%.
  2. B) 80%.
  3. C) 70%.
  4. D) 60%.
  5. E) 50%.

 

 

2) The four most abundant chemical elements in living systems are:

  1. A) hydrogen, oxygen, sulfur and phosphorus.
  2. B) hydrogen, carbon, nitrogen and oxygen.
  3. C) sodium, potassium, carbon and oxygen.
  4. D) sodium, potassium, nitrogen and sulfur.
  5. E) carbon, nitrogen, oxygen and potassium.

 

 

 

3) Nearly all proteins contain:

  1. A) cobalt.
  2. B) phosphorus.
  3. C) selenium.
  4. D) sulfur.
  5. E) none of the above.

 

 

 

 

4) Which of the following statements is FALSE?

  1. A) Proteins can be structural components of cells.
  2. B) Proteins can transmit signals between cells.
  3. C) Proteins can transport molecules within cells and between cells.
  4. D) Proteins can be both hormones and hormone receptors.
  5. E) Proteins are the only biological polymer that can catalyze biochemical reactions.

 

 

 

 

 

5) Which of the following is NOT classed as a lipid?

  1. A) Cholesterol
  2. B) Palmitic acid
  3. C) Glycerol
  4. D) Phosphatidyl serine
  5. E) Triacylglycerol

 

 

 

6) Amino acids and simple organic compounds like carbon dioxide and hydrogen cyanide cannot be produced without the use of enzymes.

 

 

 

 

7) Oxidation-reduction reactions, which are the basis of many biochemical reactions and pathways, cannot take place in the absence of oxygen.

 

 

 

 

8) Many biochemical reactions that form biopolymers from monomeric units involve the removal of water.

 

 

 

 

9) The principle component of a biological membrane is a triglyceride.

 

 

 

 

10) The chemical element ________ has a role in both transfer of energy as well as in the structure of nucleic acids.

 

 

 

11) List the four major classes of biological macromolecules.

 

 

 

 

12) An amphipathic molecule provides the foundation for biological membranes because they have both ________ and ________ functional groups.

 

 

 

13) Genomics is concerned with the entire ________, while ________ is focused on identifying all of the proteins of a cell.

 

=========================================

 

Biochemistry: Concepts and Connections (Appling et al.)

Chapter 2   The Chemical Foundation of Life: Weak Interactions in an Aqueous Environment

 

1) Each of the following is a noncovalent interaction EXCEPT:

  1. A) a hydrogen bond.
  2. B) a carbon-hydrogen bond.
  3. C) the interaction between an amino and a carboxylate group.
  4. D) a van der Waals interaction.
  5. E) an interaction between —NH3+and a water molecule.

 

Objective:  2.1

 

 

2) The most important noncovalent interaction in biochemistry is the ________ bond.

 

 

3) Which of the following is FALSE when considering van der Waals interactions?

  1. A) The van der Waals radius represents the most stable distance between two interacting centers.
  2. B) Van der Waals radii can determine molecular surfaces.
  3. C) Molecules that interact by van der Waals forces do not interpenetrate.
  4. D) The total interaction energy is the sum of the attractive and repulsive forces.
  5. E) They are not important in determining the stability of three-dimensional structures of proteins.

 

Objective:  2.2

 

 

4) Which of the following in biological compounds are sufficiently electronegative to serve as strong donors in a hydrogen bond?

  1. A) Hydrogen and oxygen
  2. B) Oxygen and nitrogen
  3. C) Nitrogen and hydrogen
  4. D) Hydrogen and carbon
  5. E) Nitrogen and carbon

 

Objective:  2.2

 

 

5) Hydrogen bonds share features of both covalent and noncovalent bonds.

 

Objective:  2.2

 

 

6) Which of the following is TRUE of hydrophobic molecules?

  1. A) They have limited solubility in water.
  2. B) Water forms a cage-like structure around them.
  3. C) Dissolving in water decreases the entropy of the mixture.
  4. D) They self-associate by releasing some of the surrounding water molecules.
  5. E) All of the above

 

 

 

 

7) Water is both a hydrogen bond donor and acceptor.

 

 

 

 

8) Amphipathic molecules are not able to interact via van der Waals forces.

 

 

 

 

9) Ionic compounds can be readily dissolved in water because the high dielectric constant of water screens and decreases the ________ force between the oppositely charged ions.

 

 

 

10) The ________ describes the tendency for hydrophobic molecules to aggregate because of the exclusion of water with the consequent increase of entropy of the solvent.

 

 

 

11) Glycine cannot serve as a buffer because it has two ionizable groups.

 

Objective:  2.4

 

 

12) The average charge on an amino acid below its pI will be positive.

 

Objective:  2.4

 

 

13) Calculate the acid dissociation constant Ka of a 0.2 M solution of weak acid that is 0.1% ionized.

 

14) Calculate the pH of a 0.1 M phosphate buffer (pKa = 6.86) that contains equal amounts of acid and conjugate base.

 

15) Calculate the pH of a 0.2 M acetate buffer (pKa = 4.77) that contains twice as much acid as conjugate base.

 

16) The pKa of each amino acid residue in a protein will not be influenced by the adjacent residue.

 

 

 

17) Calculate the pH at the end of an enzyme-catalyzed reaction if it were carried out in a 0.1 M phosphate buffer, pH 6.86 and 0.005 M of acid was produced during the reaction?

 

 

18) If hydroxide is added to an amino acid it will become increasingly ________ charged.

 

 

19) Calculate the pH of a weak acid that is 0.2% ionized in a 0.2 M solution.

 

 

20) The net charge on an amino acid at its isoelectric point (pI) is ________.

 

21) Many proteins interact with DNA at physiological pH because:

  1. A) proteins are naturally attracted to DNA regardless of the pH.
  2. B) the negatively charged DNA is electrostatically attracted to positively charged regions on proteins.
  3. C) the positively charged DNA is electrostatically attracted to negatively charged regions on proteins.
  4. D) proteins and DNA interact using mainly hydrophobic interactions.
  5. E) both proteins and DNA are at their isoelectric points at physiological pH and tend to aggregate.

 

Objective:  2.8

 

22) Small ions in biological fluids:

  1. A) encourage strong electrostatic interactions between oppositely charged macroions at low ionic strengths.
  2. B) encourage strong electrostatic interactions between oppositely charged macroions at high ionic strengths.
  3. C) have no effect on the interactions between oppositely charged macroions.
  4. D) tend to cluster around macroions of the same charge.
  5. E) have large effects on pH.

 

Objective:  2.8

 

Biochemistry: Concepts and Connections (Appling et al.)

Chapter 3   The Energetics of Life

 

1) Which of the following statements is FALSE?

  1. A) Organisms are open systems as they can exchange both energy and materials with their environments.
  2. B) In an open system energy can be converted from one form into another.
  3. C) Organisms are open systems as they can create energy from their environments.
  4. D) Energy can be transferred between a system and the surroundings.
  5. E) In biochemical processes, energy can neither be created or destroyed.

 

Objective:  3.1

 

 

2) Which of the following statements is FALSE?

  1. A) Entropy is a measure of disorder.
  2. B) The entropy of an isolated system will tend to increase to a maximum value.
  3. C) Biological systems are highly ordered so entropy changes are not relevant.
  4. D) Biological systems expend energy to overcome entropy.
  5. E) The entropy of a biological system can decrease.

 

Objective:  3.2

 

 

3) A biochemical reaction will proceed in the direction as written if:

  1. A) △G = zero.
  2. B) G > 0.
  3. C) △G < 0.
  4. D) △H > 0.
  5. E) △H < 0.

 

Objective:  3.2

 

 

4) Life is an irreversible process, such that it never comes to equilibrium.

 

Objective:  3.2

 

 

 

5) The equilibrium constant of a reaction:

  1. A) is not related to the change in free energy of the reaction.
  2. B) is the same as the mass action ratio when the reaction is displaced from equilibrium.
  3. C) can change if the concentration of reactants and products are changed.
  4. D) is related to the change in free energy of the reaction.
  5. E) cannot be used to determine whether a reaction will proceed in the direction as written under non-standard conditions.

 

Objective:  3.3

 

6) The change in enthalpy (△H) for the complete oxidation of a fatty acid is different depending on whether it occurs via a biochemical pathway or combustion to CO2 and H2O.

 

Objective:  3.3

 

 

7) A reaction at its lowest energy state for the system and with equal rates in the forward and reverse directions is said to be at ________.

 

 

8) A reaction at equilibrium can be driven in one direction or the other by changing the ________ of reactants or products.

 

 

9) A thermodynamically unfavorable reaction can become favorable if the mass action ratio is ________ than the equilibrium mass action ratio.

 

 

10) Calculate the equilibrium constant for the enzymatic hydrolysis of 0.1 M glucose-6-phosphate to glucose and inorganic phosphate given that 0.05% of the original glucose-6-phosphate remained after reaching equilibrium and the activity of water is unity.

 

11) The △Go of a reaction:

  1. A) will change if the temperature of the reaction is changed.
  2. B) will change if the concentration of reactants and products are changed.
  3. C) is not related to the equilibrium constant.
  4. D) can be used to calculate whether a reaction is thermodynamically favorable under defined non-standard conditions.
  5. E) can predict whether a reaction will be thermodynamically favorable under standard conditions.

 

Objective:  3.5

 

 

12) Calculate the △G∘’ for the reaction

 

fructose-6-phosphate → glucose-6-phosphate

 

given the equilibrium constant is 1.97 and the physiological relevant temperature is 37∘C.

 

13) A thermodynamically unfavorable reaction can become favorable when coupled to a highly endergonic reaction.

 

 

 

14) A reaction with a large negative free energy of hydrolysis can be coupled to the synthesis of ATP from ADP and Pi.

 

 

 

15) In a general redox reaction, the reductant becomes oxidized and the oxidant becomes reduced.

 

Objective:  3.8

 

 

16) The standard reduction potential is a measure of the ability of a reductant to ________ an electron.

 

17) The standard reduction potentials for the following reactions are given below.

 

Pyruvate + 2H+ + 2e- → lactate  E∘ = -0.190 V

 

NAD+ + 2H+ + 2e- → NADH/H+ E∘ = -0.320V.

 

Calculate △G∘ for the overall spontaneous reaction making use of the relationship between △E∘ and △G∘.

=

 

Biochemistry: Concepts and Connections (Appling et al.)

Chapter 4   Nucleic Acids

 

1) The difference between a nucleoside and a nucleotide is:

  1. A) the presence of uracil.
  2. B) a phosphate group.
  3. C) a phosphodiester bond.
  4. D) a 2′ —H group.
  5. E) methylated cytosine.

 

Objective:  4.1

 

 

2) Which statement is CORRECT?

  1. A) Both phosphodiester and glycosidic bonds in RNA and DNA are hydrolyzed in acid solution.
  2. B) Both RNA and DNA are hydrolyzed in mild alkaline solution.
  3. C) DNA is more unstable when dehydrated than when in solution
  4. D) RNA is not hydrolyzed in mild alkaline solution.
  5. E) Both A and B

 

Objective:  4.1

 

 

3) Nucleotides are all weak acids.

 

Objective:  4.1

 

 

4) The nucleotide sequence of a polynucleotide chain is called the ________ structure.

 

 

5) Which of the following does NOT describe the secondary structure of DNA as proposed by Watson and Crick?

  1. A) The two strands of the double helix are stabilized by hydrogen-bonding between A and T and between G and C.
  2. B) The two strands of the double helix run in opposite directions.
  3. C) The distance between the 1′ carbons of the deoxyribose units is the same between the A-T and the G-C base pair.
  4. D) The phosphate deoxyribose backbones of the helix are on the outside.
  5. E) The base pairs are stacked on one other with their planes at 180o to the helix axis.

 

Objective:  4.5

 

 

 

6) An important observation that assisted in the elucidation of the secondary structure of DNA was that the mole percent adenine was almost always the same as the mole percent of thymine.

 

Objective:  4.5

 

7) The mode of replication of DNA is BEST described as ________.

 

8) Which of the following statements about nucleic acid secondary structure is FALSE?

  1. A) The width of the major and minor grooves is more equal in the A-from of DNA than in the B-form.
  2. B) Triple helices and G-quadruplexes can form at specific sequences in DNA.
  3. C) DNA can form cruciform structures at palindromic sequences.
  4. D) The A-form of DNA exists at high humidity, whereas the B-form exists at low humidity.
  5. E) Some nucleic acids can form a zig-zag structure or Z form.

 

Objective:  4.7

 

 

9) Supercoiled DNA has a lower mobility than relaxed DNA with the same number of base pairs when subjected to gel electrophoresis.

 

Objective:  4.8

 

 

10) Single-stranded RNA molecules can have extensive regions of intramolecular base pairing leading to defined secondary and tertiary structure.

 

Objective:  4.8

 

 

11) DNA in vivo is normally ________ supercoiled.

 

 

12) Calculate the superhelix density of a circular DNA molecule with 210 base pairs and two negative supercoils, assuming that there are 10.5 bp per turn of the double helix.

 

13) Calculate the linking number in vivo for a plasmid that is 4200 bp in size if there is normally 1 negative supercoil in every 20 base pairs of a circular DNA. Assume there are 10.5 bp per turn of the double helix.

Answer:   190

Objective:  4.8

 

 

14) Nucleic acids absorb light strongly in the ultraviolet region of the spectrum because they have ________ double-bond systems.

Objective:  4.10

 

15) The melting temperature of DNA ________ with increasing G plus C content.

 

 

16) Expression of genetic information involves first ________ then ________.

 

 

17) Restriction endonucleases are useful in gene cloning because:

  1. A) they can cut DNA at specific sequences.
  2. B) they can join DNA molecules that have been cut at specific sequences.
  3. C) they all make cohesive ends when they cut DNA.
  4. D) they all make 5′ phosphate extensions and recessed 3′ OH groups that can be rejoined by DNA ligase.
  5. E) they can both cut and rejoin DNA molecules.

 

Objective:  4.12

 

 

18) Viral genomes cannot be used as vectors for making recombinant DNA molecules.

 

Objective:  4.12

 

 

19) Dideoxynucleotide sequence analysis is a template-directed method that makes use of chain terminators that stop DNA synthesis because they lack a 2’OH group.

 

Objective:  4.12

 

 

20) Which of the following is a feature of X-diffraction?

  1. A) Radiation passing through a structure will be scattered only if the structure contains repeating units.
  2. B) Scattered radiation from repeating units in a structure will be weakened by interference.
  3. C) Scattered radiation from repeating units in a structure will be strengthened by interference.
  4. D) Short spacings in repeating structures will result in short spacings in diffraction patterns.
  5. E) The wavelength of radiation used to generate diffraction patterns must be slightly longer than the spacings between the repeating units of the structure.

 

Objective:  4.13

 

Biochemistry: Concepts and Connections (Appling et al.)

Chapter 5   Introduction to Proteins: The Primary Level of Protein Structure

 

1) Which of the following amino acids would most likely be found on the surface of a protein?

  1. A) Aspartic acid
  2. B) Leucine
  3. C) Proline
  4. D) Valine
  5. E) Phenylalanine

 

Objective:  5.1

 

 

2) Protein biosynthesis uses only L-amino acids.

 

Objective:  5.1

 

 

3) All amino acids have a chiral α-carbon EXCEPT ________.

 

 

4) The side chain of ________ has a pKa in the physiological pH range and is therefore often involved in proton transfer during enzymatic catalysis.

 

 

5) At physiological pH, the carboxylic acid group of an amino acid will be ________, while the amino group will be ________, yielding the zwitterion form.

 

 

6) At pH=0, the net charge on a polypeptide will be negative.

 

7) Which of the following modified amino acids is incorporated during translation rather than being modified post-translationally?

  1. A) Phosphoserine
  2. B) Selenocysteine
  3. C) γ-carboxyglutamate
  4. D) N-ε-acetyllysine
  5. E) 4-hydroxyproline

 

Objective:  5.11

 

8) An amide bond between the α-carboxylic acid group of one amino acid and the α-amino group on another is called a ________.

 

 

9) The chemical ________ can cleave amide bonds on the C-terminal side of methionine residues.

 

10) Which of the following is FALSE when considering the standard genetic code?

  1. A) Three separate codons encode translation stop signals.
  2. B) There are 64 possible codons to represent 20 common amino acids.
  3. C) AUG serves as the translation start codon in most cases.
  4. D) Apart from methionine, the only other amino acid with a single codon is tryptophan.
  5. E) Each of the three stop codons can also encode rare modified amino acids.

 

Objective:  5.16

 

 

11) Which of the following statements about insulin is INCORRECT?

  1. A) In the active form it has two polypeptide chains joined by disulphide bonds.
  2. B) It is synthesized as a random coil single chain on membrane-bound ribosomes.
  3. C) The leader sequence is cleaved off after membrane transport.
  4. D) The disulphide bonds form after the final proteolytic cleavage to yield mature insulin.
  5. E) It is stored in the pancreas in an inactive form.

 

Objective:  5.17

 

 

12) Most proteins have blocked amino and carboxyl terminals.

 

Objective:  5.17

 

 

13) Conservative amino acid changes never affect stability or function of a protein.

 

Objective:  5.18

 

 

14) When referring to the amino acid sequences of proteins, sequence homology is the same as sequence similarity.

 

Objective:  5.18

 

 

15) Several homologous proteins can be aligned to provide a ________ sequence.

 

16) Recombinant proteins containing a ________ can be purified using immobilized metal affinity chromatography and eluted by the addition of imidazole, a low pH buffer or a buffer containing EDTA.

 

17) Applications of mass spectrometry include:

  1. A) determination of the mass of a protein.
  2. B) determining the primary structure of proteins.
  3. C) detection of post-translational modifications on proteins.
  4. D) A and B.
  5. E) A, B, and C.

 

Objective:  5.21

 

 

18) In size exclusion chromatography, the smallest proteins are eluted last.

 

Objective:  5.21

 

 

19) ________ chromatography is used to separate proteins based on their surface charge.

Answer:  Ion exchange

Objective:  5.21

 

Biochemistry: Concepts and Connections (Appling et al.)

Chapter 6   The Three-Dimensional Structure of Proteins

 

1) In considering protein secondary structure which of the following is INCORRECT?

  1. A) An α helix repeats after 18 residues and has 3.6 residues per turn.
  2. B) A network of main-chain hydrogen bonds connect β strands in a β sheet.
  3. C) The most common structures are the α helix and the β sheet.
  4. D) The 310helix is right-handed and often contains proline residues.
  5. E) The β strands can be in either parallel or antiparallel configuration.

 

Objective:  6.1

 

 

2) The amino acid side chain residues in an α helix point outwards away from the center of the helix.

 

Objective:  6.1

 

 

3) ________ between amide protons and carbonyl oxygens is necessary to stabilize a regular folding of protein secondary structure.

Answer:  Hydrogen bonding

Objective:  6.1

 

 

4) A ________ plot describes which structures in a polypeptide are sterically possible and which are not based on the angles of rotation about the backbone Namide —Cα and Cα-Ccarbonyl bonds.

 

 

5) Which of the following statements about α-keratins is FALSE?

  1. A) They include a major class of protein that comprises hair, fingernails and animal skin.
  2. B) Individual molecules are α-helical.
  3. C) There is a strip of contiguous hydrophobic surface making a shallow spiral around the helix.
  4. D) They include a small globular regions covalently linked to the surface.
  5. E) Pairs of α-helices twist about each other in a coiled-coil structure held together entirely by hydrophobic interactions.

 

6) The protein that makes up about a third of the total protein mass in animals is:

  1. A) β-keratin.
  2. B) collagen.
  3. C) hemoglobin.
  4. D) myoglobin.
  5. E) α-keratin.

 

Objective:  6.4

 

 

7) Fibroin is a β-sheet protein, with a high proportion of glycine.

 

Objective:  6.4

 

 

8) Tropocollagen is a double helix of two left-handed polypeptide chains.

 

Objective:  6.4

 

 

9) Scurvy results in weakness in collagen fibres because the enzymes that catalyze ________ of proline and lysine residues in collagen require Vitamin C.

4

 

 

10) Which of the following is CORRECT when considering the tertiary structure of globular proteins?

  1. A) β sheets are usually twisted or wrapped into barrel structures.
  2. B) Hydrophobic residues are normally on the inside and hydrophilic residues are on the outside.
  3. C) The amino acid proline never occurs in a region where the polypeptide chain bends or turns.
  4. D) All parts of the proteins can be classified as helix, β sheet or turns.
  5. E) None of the above.

 

Objective:  6.6

 

 

11) Proteins cannot self-assemble into a functional conformation after they have been denatured.

 

Objective:  6.6

 

 

12) Protein folding is a random process, whereby a vast number of possible conformations are tested to find the desired most stable state.

 

Objective:  6.7

 

13) The folded conformation of proteins can be stabilized by the binding of a metal ion or cofactor.

 

Objective:  6.9

 

 

14) The interactions that stabilize multisubunit complexes are different to those that stabilize tertiary structure.

 

Objective:  6.9

 

 

15) Protein folding is a thermodynamically favorable process under physiological conditions because:

  1. A) there is an increase in entropy associated with protein folding.
  2. B) there is a decrease in entropy of the solvent by burying hydrophobic groups within the molecule.
  3. C) of the large negative enthalpy change associated with many noncovalent interactions.
  4. D) no intermediate stage disulphide bonds form during the folding process.
  5. E) all of the above.

 

Objective:  6.10

 

 

16) The cavity in the GroEL-GroES complex from E. coli provides a favorable environment that prevents ________ and mis-folding.

 

 

17) Bovine spongiform encephalopathy is an infectious disease caused by a prion protein, which undergoes a ________ change to become pathogenic.

 

 

18) Proteins have an asymmetrical tertiary structure, while multisubunit proteins can exhibit several types of symmetry.

 

Objective:  6.14

 

 

19) The functional organization of proteins where specific complexes of two or more polypeptides are formed is called ________ structure.

 

20) Which technique is able to investigate secondary structural features of proteins?

  1. A) Infrared spectroscopy
  2. B) Ultraviolet spectroscopy
  3. C) Fluorescence spectroscopy
  4. D) Circular dichroism
  5. E) All of the above

 

Objective:  6.15

 

 

21) ________ spectroscopy can be used to study dynamic processes in solution.

 

 

22) SDS gel electrophoresis can be used to determine:

  1. A) whether subunits in a protein complex are identical or not.
  2. B) the molecular mass of a native protein complex.
  3. C) the overall charge on a polypeptide.
  4. D) the molecular mass of denatured protein subunits.
  5. E) none of the above.

 

 

 

Biochemistry: Concepts and Connections (Appling et al.)

Chapter 7   Protein Function and Evolution

 

1) Which of the following is NOT true of immunoglobulin molecules?

  1. A) They consist of four polypeptide chains held together by disulphide bridges.
  2. B) They have two identical heavy chains and two identical light chains.
  3. C) Antigenic determinants reside only in the variable region of the light chains.
  4. D) Proteolytic cleavage can generate fragments containing the antigen-binding site.
  5. E) Some are membrane bound.

 

Objective:  7.3

 

 

2) The immunoglobulin domain is a stable scaffold containing two antiparallel β- sheets upon which to display hypervariable loops.

 

Objective:  7.3

 

 

3) The specific interaction between an antibody and antigen occurs by virtue of both shape and ________ complementarity.

 

 

4) Which of the following statements is FALSE?

  1. A) Myoglobin is a single polypeptide chain folded about a heme prosthetic group.
  2. B) Hemoglobin is a tetramer, each of which binds a heme group.
  3. C) In both hemoglobin and myoglobin, iron is chelated by a tetrapyrole ring system.
  4. D) The iron in both hemoglobin and myoglobin has two coordination sites that bind to oxygen.
  5. E) Hydrogen bonding to a histidine residue assists stabilization of the Fe2+-O2complex in both hemoglobin and myoglobin.

 

Objective:  7.9

 

 

5) Both myoglobin and hemoglobin exhibit cooperative binding to oxygen.

 

Objective:  7.9

 

 

6) The conserved residues in the hemoglobins and myoglobins include the ________ proximal and distal to the heme iron.

 

7) The ________ binding of oxygen to hemoglobin is facilitated by changes in protein conformation upon oxygen binding to one subunit that affect the binding of oxygen to another subunit.

 

 

8) Which of the following observations helps to explain the conformational changes that occur in hemoglobin upon binding to oxygen?

  1. A) The four heme groups are positioned close to the surface of the molecule.
  2. B) An αβ dimer rotates and slides with respect to the other dimer upon binding oxygen.
  3. C) Neither the heme nor the iron ion in the deoxy conformation is in a planar conformation.
  4. D) All of the above
  5. E) B and C

 

Objective:  7.14

 

 

9) Fetal hemoglobin has a higher affinity for oxygen than does maternal hemoglobin because it has a higher affinity for the allosteric regulator 2,3-bisphosphoglycerate.

 

Objective:  7.16

 

 

10) The production of carbon dioxide during respiration in aerobic tissues lowers the pH in erythrocytes, which in turn ________ the affinity of oxygen binding to hemoglobin.

 

 

11) Comparison of globin sequences from many different species suggests that myoglobin and hemoglobin have evolved from a single myoglobin-like protein.

 

Objective:  7.21

 

 

12) The sickle cell mutation causes oxyhemoglobin molecules to ________ due to hydrophobic interactions because a glutamate residue is replaced with a valine.

 

13) Which of the following statements about muscle contraction is TRUE?

  1. A) ATP hydrolysis releases myosin from actin.
  2. B) ATP hydrolysis results in strong binding of myosin to actin.
  3. C) ATP hydrolysis causes a conformational change in the myosin head.
  4. D) Muscle contraction occurs as ATP is hydrolyzed.
  5. E) ATP hydrolysis must occur before the actin-binding site closes.

 

Objective:  7.23

 

14) The heavy chain of the muscle form of myosin:

  1. A) forms a coiled-coil structure with a globular head domain.
  2. B) contains the motor domain within the C-terminal region.
  3. C) is a complex of 540 kDa.
  4. D) binds ATP near the C-termini.
  5. E) has two covalently bound light chains.

 

Objective:  7.24

 

 

15) F-actin is a polymer of G-actin monomers and exhibits symmetry.

 

Objective:  7.24

 

 

16) The A band of skeletal muscle is formed by noncovalent cross-bridges between the thin filaments that are mainly ________ and the thick filaments that are mainly ________.

 

 

17) The most critical substance in stimulating muscle contraction is:

  1. A) ATP.
  2. B) Ca2+.
  3. C) tropomyosin.
  4. D) troponin C.
  5. E) troponin T.

 

Objective:  7.27

 

 

 

18) Calcium regulates muscle contraction by binding to:

  1. A) actin.
  2. B) myosin.
  3. C) tropomyosin.
  4. D) troponin C.
  5. E) troponin T.

 

Objective:  7.27

 

 

19) The greatest conformational change in the neck piece of myosin occurs during ATP hydrolysis.

 

Objective:  7.27

 

 

20) The concentration of Ca2+ in the myoplasm can increase as much as 10,000 fold in response to a motor nerve impulse.

 

Objective:  7.27

 

21) Antibodies cannot be used to purify proteins because the antibody-antigen interaction is too strong.

 

Objective:  7.28

 

 

22) Enzyme-linked immunosorbent assay, western blotting and immunofluorescent light microscopy all make use of the specific interaction between an antigen and an ________.

 

==

 

Biochemistry: Concepts and Connections (Appling et al.)

Chapter 8   Enzymes: Biological Catalysts

 

1) Which of the following statement is FALSE?

  1. A) The free energy barrier in a chemical reaction must be overcome in order for products to form.
  2. B) An increase in temperature can result in an increased reaction rate.
  3. C) Lowering the free energy of the transition state can increase a reaction rate.
  4. D) At a given temperature and time all molecules in a solution or a sample will have the same energy.
  5. E) An enzyme can increase a reaction rate by lowering the activation energy.

 

Objective:  8.1

 

 

2) In a favorable reaction the free energy of the products is ________ than the free energy of the reactants.

 

 

3) Catalysts affect the thermodynamic f of a chemical reaction.

 

Objective:  8.1

 

 

4) Pyruvate carboxylase is an example of the ligase class of enzymes.

 

Objective:  8.2

 

 

5) In an enzyme-catalyzed reaction, the lifetime of the transition state is similar to the vibrational frequencies of covalent bonds.

 

Objective:  8.2

 

 

6) Non-catalyzed biochemical reactions always occur at physiological useful timescales.

 

Objective:  8.2

 

 

7) Electrostatic catalysis proceeds via covalent bonding interactions.

 

Objective:  8.2

 

8) A second-order reaction:

  1. A) occurs when one substrate is converted into one product.
  2. B) is characterized by two molecules coming together to form a product.
  3. C) is the rate-limiting step of a reaction.
  4. D) has a rate constant with units of (time)-1.
  5. E) only occurs in multistep processes.

 

Objective:  8.3

 

 

9) The equilibrium constant for a first-order ________ reaction is equivalent to the ratio of the rate constant for the forward and reverse reactions.

 

 

10) Enzymes can accelerate reactions by:

  1. A) binding a substrate or substrates.
  2. B) promoting the removal or addition of protons.
  3. C) correctly positioning a metal ion for catalysis.
  4. D) lowering the energy for activation.
  5. E) all of the above.

 

Objective:  8.4

 

 

11) The equilibrium state of a biochemical reaction is approached ________ in the presence of a catalyst.

 

12) The lock and key model of substrate binding and enzymatic catalysis explains:

  1. A) the release of product.
  2. B) substrate specificity.
  3. C) formation of a transition state.
  4. D) the catalytic mechanism.
  5. E) structural changes that occur on substrate binding.

 

13) Which of the following amino acid residues are often involved in proton transfers in enzyme-catalyzed reactions?

  1. A) Histidine, aspartate, serine, and cysteine
  2. B) Serine, tyrosine, arginine, and cysteine
  3. C) Glutamine, asparagine, lysine, and tyrosine
  4. D) Histidine, aspartate, lysine, and serine
  5. E) Histidine, aspartate, glutamate, arginine, and lysine

 

Objective:  8.5

 

14) The ________ hypothesis suggests that an enzyme can induce distortion of the substrate or the substrate can induce conformational changes in the enzyme that stabilize the transition state.

 

15) The formation of an enzyme-substrate complex tends to be thermodynamically favorable due to ________ interactions between the substrate and enzyme.

 

 

16) Which of the following statements about the proposed mechanisms of action for hen egg white lysozyme does NOT support either model?

  1. A) Glycosidic bond cleavage occurs by general acid/base catalysis.
  2. B) A covalent intermediate is formed between an active site aspartate and C1 of the substrate.
  3. C) A water molecule is deprotonated, which then attacks C1 of the substrate.
  4. D) The active site aspartic acid changes between being protonated and deprotonated.
  5. E) The active site glutamic acid changes between being protonated and deprotonated.

 

Objective:  8.6

 

 

17) A Lineweaver-Burk plot for a first order enzyme-catalyzed reaction gives values of 1/KM = 2.5 × 104 (M)-1 and 1/Vmax of 1.25 × 10-2 (µmolL-1 sec-1)-1. Calculate the rate constant k.

 

 

18) Serine proteases make use of covalent catalysis as well as electrostatic stability of the transition state to achieve rate enhancement.

 

19) A common feature of serine proteases is the catalytic triad consisting of a nucleophile, a general base and an acid. In chymotrypsin these amino acid residues are ________, ________, and ________ respectively.

 

20) The cofactor NAD+ is:

  1. A) a reductant.
  2. B) an oxidant.
  3. C) oxidized to NADH/H+ in dehydrogenase reactions.
  4. D) able to accept 2 electrons and 2 protons.
  5. E) covalently linked to enzymes in whose catalytic activity it assists.

 

Objective:  8.8

 

 

21) Coenzymes or cofactors are irreversibly changed during catalysis.

 

Objective:  8.8

 

 

22) Which of the following statements applies to metalloenzymes?

  1. A) Some metal ions assist in ATP binding.
  2. B) Amino acid residues in the enzyme are never covalently linked to the metal ion.
  3. C) The metal does not bind at the catalytic site.
  4. D) Many are oxido-reductases.
  5. E) A and D

 

Objective:  8.9

 

 

23) Metal ions are often required for catalytic efficiency but they may not remain permanently bound to the protein or take part in the catalytic process.

 

Objective:  8.9

 

 

 

24) Which of the following statements BEST describes the Michaelis-Menton constant KM?

  1. A) It is numerically equal to the affinity between the enzyme and its substrate.
  2. B) It is numerically equal to the substrate concentration required to reach half maximal velocity for an enzyme-catalyzed reaction.
  3. C) It is a measure of the rate of a catalytic process.
  4. D) It is a measure of enzyme efficiency.
  5. E) It has units of concentration.

 

Objective:  8.11

 

 

25) A mutation causing an amino acid change in an enzyme that affects the turnover number kcat will always affect the KM as well.

 

Objective:  8.12

 

26) A Lineweaver-Burk plot can be used to determine KM using initial-rate data for an enzyme-catalyzed reaction.

 

Objective:  8.12

 

 

27) A graph of initial velocity vs substrate concentration will be ________ for an enzyme that obeys Michaelis-Menton kinetics.

 

 

28) Random substrate binding, ordered substrate binding and the ping-pong mechanism are all features of ________ enzyme-catalyzed reactions.

 

 

29) Which of the following statements about inhibitors of enzyme-catalyzed reactions is TRUE?

  1. A) An uncompetitive inhibitor typically affects KMbut not kcat.
  2. B) A competitive inhibitor does not affect Vmax.
  3. C) An uncompetitive inhibitor will always bind at the active site.
  4. D) A competitive inhibitor binds irreversibly to the enzyme at the active site.
  5. E) Reversible inhibitors bind to either free enzyme or the enzyme-substrate complex but not both.

 

Objective:  8.14

 

 

 

30) A reversible ________ inhibitor is one that binds to the active site of an enzyme but cannot undergo the chemical conversion step of the reaction.

 

 

31) Which of the following is NOT a feature of substrate-level enzyme regulation?

  1. A) A high substrate concentration will speed up the rate of reaction.
  2. B) A high product concentration will slow the rate of reaction.
  3. C) The product can be a competitor.
  4. D) It is sufficient for regulation of most enzyme-catalyzed reactions.
  5. E) Sometimes products can be competitive or uncompetitive.

 

Objective:  8.15

 

 

32) Almost all irreversible enzyme inhibitors bind noncovalently to the enzyme.

 

Objective:  8.15

 

33) Feedback regulation of a metabolic pathway can either be activation or inhibition.

 

Objective:  8.16

 

 

34) Which of the following is a feature of allosteric regulation of enzyme activity?

  1. A) Ligand binding causes a conformation change in the enzyme.
  2. B) Allosteric enzymes often have multiple active sites.
  3. C) Cooperativity in substrate binding.
  4. D) There is often a range of different effectors for a single enzyme.
  5. E) All of the above

 

Objective:  8.17

 

 

35) Covalent modification can either activate or inhibit enzymes.

 

Objective:  8.18

 

 

36) Protein kinases add a phosphoryl group to the —OH group of a ________, ________, or ________ residue of the target protein.

 

 

37) Proteolytic cleavage is an example of an ________ post-translational modification.

 

 

38) Catalytically inactive enzyme precursors are called ________.

 

 

39) A ribonucleic acid that can act as a biological catalyst is called a ________.

 

 

40) A stopped-flow apparatus is used to measure rates of pre-steady state slow enzymatic reactions.

 

 

 

Biochemistry: Concepts and Connections (Appling et al.)

Chapter 9   Carbohydrates: Sugars, Saccharides, Glycans

 

1) Carbohydrates are components of the following:

  1. A) the membrane of red blood cells.
  2. B) nucleic acids.
  3. C) the hormone erythropoietin.
  4. D) the bacterial cell wall.
  5. E) all of the above.

 

Objective:  9.1

 

 

2) Which of the following is an example of a monosaccharide?

  1. A) Galactose
  2. B) Lactose
  3. C) Amylose
  4. D) Maltose
  5. E) None of the above

 

Objective:  9.1

 

 

3) Glyceraldehyde has a chiral carbon so has two stereoisomers, which are called diastereomers.

 

Objective:  9.2

 

 

4) Pentoses and hexoses can form stable ring structures by internal hemiacetal formation.

 

Objective:  9.2

 

 

5) Which of the following is considered to be the smallest carbohydrate?

  1. A) Glucose
  2. B) Dihydroxyacetone
  3. C) Ribose
  4. D) Xylose
  5. E) Formaldehyde

 

Objective:  9.3

 

 

6) D-ribose can form a ring structure with either four or five carbons in the ring.

 

Objective:  9.3

 

 

7) Maltose has a (1→4) α linkage between glucose and ________.

 

8) Synthesis of sugar polymers is enzyme catalyzed and requires activated monomers like ________ in lactose biosynthesis.

 

 

9) Amylose and amylopectin are the principle storage polysaccharides of:

  1. A) bacteria.
  2. B) plants.
  3. C) animals.
  4. D) mollusks.
  5. E) insects.

 

Objective:  9.6

 

 

10) The storage polysaccharides are ________ in plants and ________ in animals.

 

 

11) N-linked glycans are attached to proteins through N-acetylglucosamine or N-acetyl galactosamine to the amide side chain of:

  1. A) glutamine.
  2. B) histidine.
  3. C) asparagine.
  4. D) arginine.
  5. E) lysine.

 

Objective:  9.7

 

 

12) Glycosaminoglycans are polysaccharides composed of repeating disaccharide units in which one of the sugars is always N-acetylgalactosamine.

 

13) Proteins are marked for secretion from the cell by the post translational addition of oligosaccharides.

 

Objective:  9.7

 

 

14) Heparin is a highly sulphated glycosaminoglycan that act as an ________.

 

15) O-linked glycans are attached to proteins through the hydroxyl group of serine or ________ and sometimes ________.

 

Biochemistry: Concepts and Connections (Appling et al.)

Chapter 10   Lipids, Membranes, and Cellular Transport

 

1) Saturated fatty acids are different to unsaturated fatty acids because they:

  1. A) have an even number of carbon atoms.
  2. B) have short hydrophobic tails.
  3. C) have no C=C double bonds.
  4. D) exhibit free rotation about the carbon carbon bonds in the hydrocarbon tail.
  5. E) mostly have cis double bonds.

 

Objective:  10.1

 

 

2) Which of the following statements is FALSE?

  1. A) The longer the chain length of a saturated fatty acid, the higher the melting temperature.
  2. B) The difference in melting temperature between a saturated fatty acid and an unsaturated fatty acid with the same chain length is only a few degrees C.
  3. C) Most types of fat in many animals is used in energy production.
  4. D) Some unsaturated fatty acids are liquid at physiological temperatures.
  5. E) Fatty acids exist in the anionic form (RCOO-) at physiological pH.

 

Objective:  10.1

 

 

3) Linolenic acid has cis double bonds with the formula CH3CH2CH=CHCH2CH=CHCH2CH=CH(CH2)7COOH. Write out the abbreviated systematic numbering for this fatty acid.

 

4) Which of following lipids can be a major component of biological membranes?

  1. A) Phosphatidic acid
  2. B) Phosphatidylcholine
  3. C) Phosphatidylinositol
  4. D) Cholesterol
  5. E) B and D

 

Objective:  10.2

 

 

5) Sphingomyelin contains a fatty acid linked by an ________ bond and phosphocholine linked via the C-3 hydroxyl group of sphingosine.

 

6) Which of the following is unlikely to be a characteristic of a membrane protein?

  1. A) Largely hydrophobic transmembrane segments
  2. B) α-helical membrane-spanning motifs.
  3. C) Covalently attached lipid moities
  4. D) Symmetric orientation across the membrane
  5. E) β-sheet membrane-spanning motifs

 

Objective:  10.3

 

 

7) In an aqueous environment the hydrocarbon tails of lipids tend to associate by entropy-driven ________ and by Van der Waals interactions.

 

 

8) Raft platforms in membranes have functional roles in cell signaling and sorting of proteins into specific ________ in the cell.

 

 

9) Which of the following statements about biological membranes is FALSE?

  1. A) They are composed of a mixture of lipids and proteins in which lateral diffusion of components is possible.
  2. B) Lipids and proteins move laterally at approximately the same rate within the membrane.
  3. C) The faces of biological membranes are distinct and usually different in both composition and structure.
  4. D) Phospholipids often require a specialized enzyme to facilitate movement across (flipping) the membrane.
  5. E) They are often organized into smaller regions of specific function.

 

Objective:  10.4

 

 

10) Integral membrane proteins can be inserted into the membrane and folded into the normal 3D structure during translation.

 

Objective:  10.4

 

 

11) Lipid rafts are small long-lived structures that respond to stimuli to transiently associate with each other to form larger raft platforms.

 

Objective:  10.4

 

12) Which of the following is NOT relevant to facilitated transport across biological membranes?

  1. A) An ionophore is a carrier protein that increases the permeability of a membrane to ions.
  2. B) Some permeases can transport their substrates in both directions.
  3. C) A symport will transport two molecules in the same direction across a membrane.
  4. D) ATP hydrolysis is required.
  5. E) An antiport will move substrates in opposite directions across a membrane.

 

Objective:  10.5

 

 

13) Which of the following mechanisms is responsible for the selectivity of aquaporins for water?

  1. A) Size exclusion
  2. B) Electrostatic repulsion
  3. C) Dynamic hydrogen bonding
  4. D) Prevention of ion gradient formation
  5. E) All of the above

 

Objective:  10.5

 

 

14) Mediated transport or diffusion will ultimately result in the concentration of diffusing substance being the same on both sides of the membrane.

 

Objective:  10.5

 

 

15) Passive facilitated cotransport can move some substrate across a membrane against its concentration gradient.

 

Objective:  10.5

 

 

16) The rate of nonmediated diffusion tends to increase as the ________ character of the diffusing substance increases.

 

 

17) Active transport can move a substance across a membrane ________ its concentration gradient.

 

 

18) The standard free energy that is required for the sodium-potassium ATPase to pump two K+ ions into the cell and three Na+ ions is +43.8 kJ/mol but the standard free energy change of hydrolysis of ATP is only -32 kJ/mol. This apparent imbalance of free energy can be accounted for because:

  1. A) the movement of Na+ions is down the concentration gradient.
  2. B) the movement of K+ ions is down the concentration gradient.
  3. C) the membrane potential favours the flow of ions.
  4. D) more than one ATP is hydrolyzed.
  5. E) the free energy provided from the hydrolysis of one ATP is sufficient under physiological conditions.

 

Objective:  10.6

 

 

19) Digitoxin can act as a short term cardiac stimulant by inhibiting the Na+-K+ pump.

 

Objective:  10.7

 

 

20) The sodium-glucose cotransport system is an example of:

  1. A) an antiport transporter.
  2. B) passive transport.
  3. C) facilitated transport.
  4. D) an ATP-dependent transporter.
  5. E) none of the above.

 

Objective:  10.9

 

 

21) The Na+-K+ ATPase uses the free energy of ATP hydrolysis in an active transport process to move Na+ and K+ across a membrane. What would the rate of nonmediated transport be given that the permeability coefficient for K+ through a human erythrocyte membrane is 2.4 × 10-10 cm/s. K+ ions must be moved from a concentration of 4 mM on the outside of the cell to 155 mM inside the cell?

Answer:  3.62 × 10-8 cm/s

Objective:  10.9

 

 

22) Action potentials are propagated along a nerve axon by sequentially opening and closing a series of voltage-gated potassium and sodium channels.

 

 

 

Biochemistry: Concepts and Connections (Appling et al.)

Chapter 11   Chemical Logic of Metabolism

 

1) Calculate the amount of ATP in kg that is turned over by a resting human every 24 hours. Assume that a typical human contains ~50g of ATP (Mr 505) and consumes ~8000 kJ of energy in food each day. The energy stored in the terminal anhydride bond of ATP under standard conditions is 30.6 kJmol-1. Assume also that the dietary energy is channeled through ATP with an energy transfer efficiency of ~50%.

 

 

2) The anabolic and catabolic processes of cellular metabolism can be coupled by ATP.

 

Objective:  11.3

 

 

3) Catabolic processes involve degradation of complex molecules into simpler molecules with the net release of chemical energy.

 

Objective:  11.3

 

 

4) Name the type of reaction that involves reversible electron transfer from a donor to an acceptor.

 

 

5) Which of the following produces the largest number of reducing equivalents when oxidized?

  1. A) Glucose
  2. B) NADPH
  3. C) NADH
  4. D) Palmitic acid
  5. E) A hydrogen atom

 

6) ATP has a high phosphoryl group transfer potential because:

  1. A) it is chemically unstable.
  2. B) it has a high rate of spontaneous hydrolysis at physiological pH and temperature.
  3. C) it exhibits resonance stabilization prior to hydrolysis.
  4. D) it has three phosphate groups.
  5. E) cleavage of either of its two phosphoanhydride bonds proceeds with a large negative △Go’of hydrolysis.

 

Objective:  11.6

 

7) Substrate-level phosphorylation is a term given to the loss of free energy when ATP is hydrolyzed.

 

Objective:  11.6

 

 

8) The main energy-coupling compound in biochemical reactions that allows thermodynamically unfavorable processes to become favorable is ________.

 

 

9) Under physiological conditions the complete oxidation of glucose to carbon dioxide and water in the presence of oxygen has a △G of -2900 kJ/mol glucose. This process can be coupled to the synthesis of ~32 mol ATP. The △G of the coupled reactions to make ATP is -1300 kJ/mol glucose. Calculate the △G for the synthesis of ATP from ADP.

 

 

10) Which of the following can be used as a metabolic control mechanism?

  1. A) Enzyme compartmentation
  2. B) Action of hormones
  3. C) Covalent modification of an enzyme
  4. D) Regulation of enzyme degradation
  5. E) All of the above

 

11) A futile cycle is:

  1. A) the citric acid cycle.
  2. B) two reactions or pathways that share substrates and products, and result in no net gain of ATP.
  3. C) two opposing cellular reactions that are independently controlled.
  4. D) an endergonic reaction that uses up ATP.
  5. E) the reoxidation of NAD+from NADH.

 

Objective:  11.7

 

 

12) Enzyme-catalyzed sequential reactions that make up a metabolic pathway are normally separated in the cell for equal access to reactants.

 

Objective:  11.7

 

 

13) Reactions in metabolic pathways that are subject to regulation are those that are displaced far from ________.

 

14) An enzyme that catalyzes a committed step in a metabolic pathway has a high ________.

 

 

15) The standard free energy change in physiological conditions (△G∘’) for the reaction catalyzed by malate dehydrogenase in the citric acid cycle

malate + NAD+ oxaloacetate + NADH + H+

is ~+29 kJmol-1

Calculate the actual △G’ at 37∘C if Keq’ is 1.02 × 10-5

 

 

Biochemistry: Concepts and Connections (Appling et al.)

Chapter 12   Carbohydrate Metabolism: Glycolysis, Gluconeogenesis, Glycogen Metabolism, and the Pentose Phosphate Pathway

 

1) Anaerobic glycolysis can produce ATP at a much faster rate than aerobic oxidative phosphorylation.

 

Objective:  12.2

 

 

2) Which of the following types of reaction does NOT occur in glycolysis?

  1. A) Isomerization
  2. B) Nucleophilic attack
  3. C) Aldol condensation
  4. D) Oxidation
  5. E) Dehydration

 

Objective:  12.3

 

 

3) The standard free energy change of the glycolytic pathway to pyruvate is -79.9 kJ/mol, while the standard free energy change associated with gluconeogenesis from pyruvate is -42.7 kJ/mol.  What would the standard free energy change be for a direct reversal of the glycolytic pathway.

 

 

4) Glycolysis is regulated primarily by:

  1. A) the availability of glucose-6-phosphate.
  2. B) three strongly endergonic, nonequilibrium reactions.
  3. C) three strongly exergonic, nonequilibrium reactions.
  4. D) allosteric effectors of pyruvate kinase.
  5. E) phosphorylation of phosphofructokinase.

 

Objective:  12.4

 

 

5) Which of the following statements about regulation of phosphofructokinase is FALSE?

  1. A) AMP is an activator.
  2. B) ADP is an activator.
  3. C) Citrate is an inhibitor.
  4. D) Fructose 2,6-bisphosphate is an activator.
  5. E) ATP decreases the apparent Km for fructose-6-phosphate.

 

Objective:  12.4

 

 

6) Liver pyruvate kinase is activated by dephosphorylation in response to glucagon.

 

Objective:  12.4

 

7) Hexokinase, phosphofructokinase and pyruvate kinase are each subject to ________ control.

 

 

8) Fructose-1,6-bisphosphate is a feedforward ________ activator of liver pyruvate kinase.

 

 

9) The oxidation of glucose to lactate has a standard free energy change of approximately -196 kJ/mol. Calculate the efficiency of energy conversion if the standard free energy change for the production of ATP from ADP and inorganic phosphate is +32.2 kJ/mol.

 

 

10) All of the reactions of both glycolysis and gluconeogenesis occur in the cytosol.

 

Objective:  12.8

 

 

11) The flux rate through the gluconeogenic pathway is directly proportional to the amount of carbohydrate in the diet.

 

Objective:  12.8

 

 

12) Much of the regulation of gluconeogenesis is a result of the inhibition of glycolysis.

 

Objective:  12.8

 

 

13) Which of the following cannot be used as a precursor for gluconeogenesis?

  1. A) Glycerol
  2. B) Pyruvate
  3. C) Lactate
  4. D) Leucine
  5. E) Alanine

 

Objective:  12.10

 

 

14) Flux through the pentose phosphate pathway is controlled mainly by the NADP+/NADPH ratio in the cell.

 

Objective:  12.10

 

15) The primary gluconeogenic organ in animals is:

  1. A) skeletal muscle.
  2. B) kidney medulla.
  3. C) kidney cortex.
  4. D) liver.
  5. E) heart muscle.

 

Objective:  12.11

 

 

16) ________ from muscle working anaerobically is released to blood and can be taken up by liver where it is converted to pyruvate by the enzyme lactate dehydrogenase.

Answer:  Lactate

Objective:  12.11

 

 

17) The Pasteur effect describes the observation that yeast-metabolizing glucose anaerobically will dramatically increase their rate of glucose utilization when provided with air.

 

Objective:  12.12

 

 

18) Both glycolysis and gluconeogenesis are controlled by fructose 2,6-bisphosphate in response to hormones.

 

Objective:  12.13

 

 

19) Pyruvate carboxylase and phosphoenolpyruvate carboxykinase catalyze reactions of gluconeogenesis that bypass the reaction of glycolysis that is catalyzed by ________.

 

 

20) Glycogen is a major energy source for skeletal muscle contraction.

 

21) Polysaccharide digestion and glycogen breakdown involve sequential cleavage from ________ ends of glucose polymers.

 

 

22) The major product from the action of glycogen phosphorylase and the debranching enzyme glucantransferase is ________.

 

23) Which of the following is NOT involved in glycogen synthesis?

  1. A) UDP-glucose
  2. B) Glycogenin
  3. C) Amylo-(1,4 to 1,6)-transglycosylase
  4. D) Glycogen synthase
  5. E) Glycogen phosphorylase

 

Objective:  12.19

 

 

24) Which statement about control of glycogen metabolism is INCORRECT?

  1. A) Epinephrine signals glycogen breakdown in muscle.
  2. B) Glucagon signals glycogen breakdown in liver.
  3. C) Glycogen phosphorylase is activated by phosphorylation.
  4. D) Glycogen synthase is phosphorylated at only one site.
  5. E) Glycogen synthase is activated by dephosphorylation.

 

Objective:  12.20

 

 

25) Phosphorylases and phosphatases catalyze the same reaction, the removal of a phosphate group.

 

Objective:  12.20

 

 

26) The pentose phosphate pathway provides ________ for reductive biosynthesis and ________ for nucleic acid biosynthesis.

==

 

 

Biochemistry: Concepts and Connections (Appling et al.)

Chapter 13   The Citric Acid Cycle

 

1) Which of the following techniques can be used to quantify protein-protein interactions?

  1. A) Co-immunoprecipitation
  2. B) Affinity chromatography
  3. C) Chemical cross-linking
  4. D) Surface plasmon resonance
  5. E) The two-hybrid system

 

 

 

2) Oxaloacetate is replenished via the ________ in plants and bacteria.

 

 

3) The glyoxylate cycle in plants and bacteria can be used for net carbohydrate synthesis from fat because isocitrate lyase yields glyoxylate and ________ without the loss of two carbons as occurs in the citric acid cycle.

 

 

4) All of the enzymes of the citric acid cycle are located in the mitochondrion.

 

 

5) Which of the following does NOT apply to the reaction catalyzed by the pyruvate dehydrogenase complex?

  1. A) The process is highly exergonic and essentially irreversible in vivo.
  2. B) Each intermediate in the five step reaction is able to diffuse to the next active site in a sequential manner.
  3. C) It takes place in the mitochondrion.
  4. D) It is an oxidative decarboxylation.
  5. E) The product is acetyl CoenzymeA.

 

Objective:  13.2

 

 

6) NAD+, coenzyme A, thiamine pyrophosphate, lipoic acid and FAD are all cofactors used in the reaction catalyzed by pyruvate dehydrogenase.

 

7) The citric acid cycle is classed as a reductive pathway as it produces reduced electron carriers.

 

Objective:  13.4

 

8) The two carbon atoms that are lost as CO2 in the third and fourth steps of the citric acid cycle are the same as the two carbon atoms of acetyl CoA because of the stereochemistry of the isocitrate dehydrogenase reaction.

 

Objective:  13.4

 

 

9) Which of the following enzymes catalyzes a reaction of the citric acid cycle that does NOT produce reduced electron carriers?

  1. A) Malate dehydrogenase
  2. B) Succinate dehydrogenase
  3. C) α-ketoglutarate dehydrogenase
  4. D) Isocitrate dehydrogenase
  5. E) Succinyl —CoA synthetase

 

Objective:  13.5

 

 

10) Arsenic poisoning acts by inhibiting the citric acid cycle at the point of both pyruvate dehydrogenase and α-ketoglutarate dehydrogenase because it makes a stable adduct with the ________ groups of the dihydrolipoamide intermediate.

 

 

11) One substrate level phosphorylation occurs in the citric acid cycle in the reaction catalyzed by:

  1. A) α-ketoglutarate dehydrogenase.
  2. B) succinate dehydrogenase.
  3. C) succinyl —CoA synthetase.
  4. D) isocitrate dehydrogenase.
  5. E) citrate synthase.

 

12) Taking one mole of glucose through glycolysis and the citric acid cycle generates:

  1. A) 6C02, 8 NADH/H+, 1FADH2and 1 ATP.
  2. B) 6C02, 8 NADH/H+, 1FADH2and 2 ATP.
  3. C) 6C02, 10 NADH/H+, 2FADH2and 2 ATP.
  4. D) 6C02, 10 NADH/H+, 2FADH2and 4 ATP.
  5. E) 6C02, 8 NADH/H+, 2FADH2and 4 ATP.

 

Objective:  13.7

 

13) Which of the following does NOT regulate flux through the citric acid cycle?

  1. A) Substrate availability
  2. B) The ratio of [NAD+]/[NADH]
  3. C) Allosteric inhibition of isocitrate dehydrogenase by ADP
  4. D) Inhibition of α-ketoglutarate dehydrogenase by succinyl CoA
  5. E) Ca2+activation of isocitrate dehydrogenase

 

Objective:  13.8

 

 

14) The malate dehydrogenase reaction has a strongly positive standard free energy change but it proceeds in the direction of oxaloacetate because the concentration of ________ is maintained at exceedingly low levels.

 

 

15) Transamination reactions can be used to provide intermediates for the citric acid cycle.

 

Objective:  13.11

 

 

16) The citric acid cycle can be considered both a ________ and anabolic pathway as it is used to oxidise acetyl CoA to carbon dioxide as well as to provide precursors for other ________ pathways.

 

 

17) Acetyl CoA is a feed forward activator of the enzyme ________ ensuring sufficient oxaloacetate for the citric acid cycle to continue.

 

=

 

Biochemistry: Concepts and Connections (Appling et al.)

Chapter 14   Electron Transport, Oxidative Phosphorylation, and Oxygen Metabolism

 

1) Electrons are transferred through the respiratory chain from reduced NADH or FADH2 to oxygen in small steps with each step in the pathway associated with a slightly more ________ reduction potential.

 

 

2) Calculate the standard free energy change for the reactionFADH2 + 1/2O2  → FAD + H2O given that the standard reduction potential for the reduction of oxygen to water is +0.82 V and for the reduction of FAD to FADH2 is +0.03 V.

 

 

3) Which of the following statements is FALSE?

  1. A) All of the protein complexes of the mitochondrial respiratory chain are bound in the inner mitochondrial membrane.
  2. B) Cytochrome c and coenzyme Q are both soluble electron carriers that are loosely attached to the outside of the inner mitochondrial membrane.
  3. C) Oxygen is reduced to water at complex IV of the mitochondrial respiratory chain.
  4. D) The citric acid cycle is linked directly to the mitochondrial respiratory chain at the site of complex II.
  5. E) During electron transport protons are pumped across the inner mitochondrial membrane from the matrix to the intermembrane space.

 

Objective:  14.3

 

 

4) Which of the following is NOT an electron acceptor in the mitochondrial respiratory chain?

  1. A) FMN
  2. B) FAD
  3. C) Fe3+
  4. D) Cu2+
  5. E) CoQH2

 

Objective:  14.3

 

 

5) All of the cytochromes in the mitochondrial respiratory chain contain the same heme moiety as found in hemoglobin.

 

Objective:  14.3

 

6) CoQ carries electrons from NADH-Coenzyme Q reductase and succinate dehydrogenase as well as other flavoproteins to CoQ:Cytochrome c oxidoreductase.

 

Objective:  14.4

 

 

7) Which of the following statements about oxidative phosphorylation by ATP synthase is FALSE?

  1. A) The electrochemical gradient across the inner mitochondrial membrane generated by electron flow is used to synthesize ATP.
  2. B) Uncouplers dissipate the electrochemical gradient but electron transport continues without ATP production.
  3. C) Inhibitors disrupt electron flow as well as ATP synthesis.
  4. D) A proton gradient alone without a corresponding energy input is not sufficient to drive the synthesis of ATP.
  5. E) ATP synthesis occurs via simultaneous conformational changes in protein subunits containing catalytic sites.

 

Objective:  14.5

 

 

8) Electron transport through NADH-Coenzyme Q reductase (Complex I) is accompanied by transfer of ________ protons from the matrix to the intermembrane space.

 

 

9) The Q cycle is responsible for transferring electrons from a two-electron donor ________ to a one-electron acceptor ________ at the point of complex III of the mitochondrial respiratory chain.

 

 

10) Calculate the free energy change associated with transporting one proton from the matrix to the intermembrane space at 37∘C where the electrical potential across the membrane is ~ = 170 mV and the △pH is +0.75.

 

 

11) Proton-driven rotation of the c-ring of the F0 unit of the F1F0 ATP synthase is required for complete passage of protons from the intermembrane space to the matrix.

 

Objective:  14.8

 

12) Oligomycin is an inhibitor of ADP phosphorylation because it blocks the flow of protons through the ________.

 

 

13) Which of the following is NOT true of respiratory control?

  1. A) Oxidative phosphorylation is absolutely dependent on the continued flow of electrons from substrates to oxygen.
  2. B) Oxidative phosphorylation is regulated by allosteric mechanisms.
  3. C) The stimulation of respiration by addition of ADP is stoichiometric.
  4. D) The rate of respiration is controlled by the balance between the △G’s for phosphorylation of ADP, electron transport and proton pumping.
  5. E) Maintenance of respiratory control depends on the structural integrity of the mitochondrial inner membrane.

 

Objective:  14.9

 

 

14) Energy derived from oxidation of acetyl-CoA in the citric acid cycle is used for the production of ________ in brown adipose tissue because the mitochondria are rich in UCP1.

 

 

15) In animal cells the mitochondrial electron transport chain is responsible for reoxidizing most of the NADH produced by oxidative pathways regardless of the cellular compartment in which it was produced.

 

Objective:  14.11

 

 

16) The ATP yield from NADH transported across the mitochondrial inner membrane by the glycerol phosphate shuttle is the same as if the malate/aspartate shuttle were used.

 

Objective:  14.11

 

 

17) Calculate the efficiency of energy conversion from glucose under aerobic conditions assuming that 32 moles of ATP are produced for each mole of glucose and given that △G0′ for glucose oxidation is -2870kJ/mol and the △G0′ for ATP hydrolysis is -32.2 kJ/mol.

 

18) Which of the following is NOT involved in the enzymatic inactivation of reactive oxygen species?

  1. A) Superoxide dismutase
  2. B) Catalase
  3. C) Vitamin C
  4. D) Peroxiredoxin
  5. E) Peroxidase

 

Objective:  14.17

 

 

19) ________, which are potentially damaging, are generated because the interactions between one electron and two electron carriers are not 100% efficient.

 

 

 

Biochemistry: Concepts and Connections (Appling et al.)

Chapter 15   Photosynthesis

 

1) Which of the following statements about photosynthesis is FALSE?

  1. A) The light reactions occur within or on the thylakoid membranes.
  2. B) The dark reactions occur in the stroma of the chloroplast.
  3. C) The light reactions oxidise water to oxygen, reducing NADP+to NADPH in the process.
  4. D) The dark reactions use the NADPH and ATP formed in the light reactions in reductive synthesis of carbohydrate from CO2and water.
  5. E) In plants much of the carbohydrate formed is stored as sucrose.

 

Objective:  15.1

 

 

2) Photosynthesis is the major source of oxygen in Earth’s atmosphere.

 

 

3) Calculate the amount of energy required to make one mole of hexose from CO2 and water by photosynthesis if the average photon has an energy of 2.77 × 10-19 J and 48 photons are required for each 6C sugar. Assume the efficiency of photosynthesis is ~35%.

 

 

4) Upon which region of the light spectrum does photosynthesis mainly depend?

  1. A) Visible
  2. B) Ultraviolet
  3. C) Infrared
  4. D) Visible and infrared
  5. E) Visible and ultraviolet

 

Objective:  15.2

 

 

5) Photons with any energy value are able to cause transitions in the electronic states of organic molecules to drive reactions and thus capture light energy in chemical form.

 

Objective:  15.2

 

 

6) Chlorophylls, carotenes and xanthophylls absorb light in the visible part of the spectrum because they contain large ________ double-bond systems.

 

7) The energy of a photon absorbed by an antenna molecule of the photosystem finds it way to a chlorophyll molecule in the reaction center of a light-harvesting complex by a process of:

  1. A) electron transfer.
  2. B) fluorescence re-radiation.
  3. C) resonance transfer.
  4. D) resonance transfer and electron transfer.
  5. E) electron transfer and fluorescence re-radiation.

 

Objective:  15.3

 

 

8) Which of the following represents the CORRECT order of events in the two-photosystem light reactions of photosynthesis?

  1. A) Photosystem I is the first to receive a photon of light.
  2. B) Photosystem II receives electrons from plastocyanin at the end of the electron transfer chain from the excited reaction center of photosystem I.
  3. C) Photosystem I receives electrons from plastocyanin at the end of the electron transfer chain from the excited reaction center of photosystem II.
  4. D) Photosystem I receives electrons from ferredoxin at the end of the electron transfer chain from the excited reaction center of photosystem II.
  5. E) The final electron acceptor, NADP+, receives electrons from plastocyanin at the end of the electron transfer chain from the excited reaction center of photosystem I.

 

Objective:  15.3

 

 

9) Water is oxidized to oxygen at the oxygen-evolving complex of photosystem II and released into the lumen of the thylakoid and diffuses out of the chloroplast.

 

Objective:  15.3

 

 

10) A proton gradient is formed across the thylakoid membrane with the stroma becoming more acidic than the lumen.

 

 

 

11) The plastoquinones associated with photosystem II proteins are structurally and functionally similar to ________ in the mitochondrial respiratory chain.

 

12) Which of the following intermediates of the Calvin cycle is NOT used directly to regenerate ribulose-1,5-bisphosphate?

  1. A) Glyceraldehyde 3-phosphate
  2. B) Dihydroxyacetone phosphate
  3. C) Fructose 6-phosphate
  4. D) Fructose 1,6-bisphosphate
  5. E) Both C and D

 

Objective:  15.6

 

 

13) Which of the following is NOT true considering the regulation of photosynthesis?

  1. A) Rubisco is activated by high pH.
  2. B) Rubisco is activated by 2-carboxy-D-arabinitol-1-phosphate, which is synthesized in the dark.
  3. C) Rubisco activase removes 2-carboxy-D-arabinitol-1-phosphate in the presence of light.
  4. D) Several of the Calvin cycle enzymes respond to redox state.
  5. E) Xylulose-1,5-phosphate inhibits Rubisco.

 

Objective:  15.7

 

 

14) The C4 photosynthesis pathway helps to provide CO2 to the carboxylase active site of Rubisco in conditions of high O2 concentration.

 

Objective:  15.8

 

 

15) Cyclic electron flow through photosystem one and its associated electron transfer chain can be used to produce ATP when levels of ________ are very low.

 

 

16) As well as acting as a carboxylase, Rubisco can act as an oxygenase under normal environmental conditions initiating a pathway known as ________ which produces 3-phosphoglycerate and 2-phosphoglycolate.

 

 

Biochemistry: Concepts and Connections (Appling et al.)

Chapter 16   Lipid Metabolism

 

1) Free fatty acids are released from the adipocyte after mobilization of fat stores by:

  1. A) hormone sensitive lipase.
  2. B) monoacylglycerol lipase.
  3. C) adipose triglyceride lipase.
  4. D) lipoprotein lipase.
  5. E) A, B, and C.

 

Objective:  16.1

 

 

2) The liver is the central organ in animals for processing lipoproteins whether they are derived from the diet or from biosynthetic pathways.

 

Objective:  16.2

 

 

3) Clathrin is a self-associating protein, which is able to form cage-like structures, which facilitate receptor-mediated endocytosis.

 

Objective:  16.2

 

 

4) Propionyl-CoA, the end product of β-oxidation of odd-chain fatty acids can enter the citric acid cycle after being converted to ________.

 

 

5) Which of the following statements is FALSE?

  1. A) Chylomicrons are lipoproteins that transport dietary fat from intestine to peripheral tissues.
  2. B) VLDL transports triacylglycerol synthesized in the liver to peripheral tissues.
  3. C) Some fatty acids become complexed with serum albumin for transport in the blood to peripheral cells.
  4. D) LDL is the main form in which cholesterol is transported to tissues.
  5. E) The cholesterol ester content of HDL is generally less than that of chylomicrons.

 

Objective:  16.3

 

 

6) Excess cholesterol is metabolically degraded in the liver.

 

Objective:  16.4

 

7) ________ is taken up by cells using receptor-mediated endocytosis, which involves the recognition of the B-100 apolipoprotein component of LDL.

 

 

8) Which of the following statements about β-oxidation of fatty acids is CORRECT?

  1. A) Both dehydrogenation reactions produce a C=C double bond.
  2. B) Both dehydrogenation reactions use FAD as the electron acceptor.
  3. C) Thiolytic cleavage releases acetyl-CoA and a free fatty acid in the final step of the cycle.
  4. D) Fatty acids of any length are oxidized by exactly the same enzymes.
  5. E) All fatty acids must be activated to acyl-CoAs before entering the pathway.

 

Objective:  16.8

 

 

9) The overall net synthesis of palmitate starting from acetyl CoA requires:

  1. A) 8 acetyl-CoA, 8 ATP and 16 NADPH and 16H+.
  2. B) 8 acetyl-CoA, 7 ATP and 14 NADPH and 14 H+.
  3. C) 8 acetyl-CoA, 7 ATP and 14 NADPH and 7 H+.
  4. D) 8 acetyl-CoA, 7 ATP and 16 NADPH and 8 H+.
  5. E) 8 acetyl-CoA, 8 ATP and 14 NADPH and 7 H+.

 

Objective:  16.8

 

 

10) Long-chain fatty acyl-CoAs are transported across the mitochondrial inner membrane using the carrier ________.

 

 

11) β-oxidation of unsaturated fatty acids yields the same amount of energy as saturated fatty acids with the same number of carbons.

 

Objective:  16.9

 

 

12) Mono- and poly-unsaturated fatty acids are produced in the endoplasmic reticulum by desaturase enzymes.

 

13) While a number of hormones can stimulate lipolysis, the primary hormonal effects in adipose tissue are mediated by ________ in response to stress and by ________ during fasting.

 

14) Ketone bodies can be used as an alternative fuel source by the liver.

 

Objective:  16.12

 

 

15) ________ are formed (primarily in the liver) when acetyl CoA accumulates beyond its capacity to be oxidized or used for fatty acid synthesis.

 

 

16) The shuttle system for transfer of acetyl-CoA generated in the mitochondrial matrix to the cytosol includes:

  1. A) citrate from the citric acid cycle.
  2. B) citrate lyase in the cytosol.
  3. C) the production of NADPH by malic enzyme.
  4. D) ATP hydrolysis.
  5. E) all of the above.

 

Objective:  16.13

 

 

17) The reduced cofactor used in fatty acid synthesis is ________.

 

 

18) All of the fatty acid synthase reactions are carried out on substrates attached to acyl carrier protein via a ________ linkage.

 

19) Elongation of fatty acids from palmitate occurs only in the mitochondrion.

 

20) The first committed step in fatty acid synthesis is the formation of ________ in a reaction catalyzed by acetyl CoA carboxylase.

21) Insulin stimulates fatty acid synthesis by which of the following mechanisms?

  1. A) Stimulation of a glucose transport across the plasma membrane
  2. B) Dephosphorylation of acetyl-CoA carboxylase
  3. C) Stimulation of dephosphorylation of pyruvate dehydrogenase
  4. D) Activation of citrate lyase
  5. E) All of the above

 

Objective:  16.15

 

 

22) HMG-CoA reductase, the major control point of cholesterol biosynthesis is regulated by transcriptional and post-transcriptional mechanisms mediated by Insig proteins bound in the endoplasmic reticulum membrane.

 

Objective:  16.20

 

 

23) Which of the following compounds is NOT derived from cholesterol?

  1. A) Glycocholate
  2. B) 1,25-dihydroxycholecalciferol
  3. C) α-tocopherol
  4. D) Aldosterone
  5. E) Cortisol

 

Objective:  16.21

 

 

24) The prostaglandins, leukotrienes and thromboxanes belong to a family of local acting signaling molecules, all of which are derived from ________ acid.

 

=

 

Biochemistry: Concepts and Connections (Appling et al.)

Chapter 17   Interorgan and Intracellular Coordination of Energy Metabolism in Vertebrates

 

1) The heart is a completely aerobic tissue that can make use of fatty acids, lactate, glucose and ketone bodies as fuel sources.

 

Objective:  17.1

 

 

2) Which of the following fuel reserves can be used by skeletal muscle?

  1. A) Protein
  2. B) Glycogen
  3. C) Creatine phosphate
  4. D) Fatty acids
  5. E) All of the above

 

Objective:  17.2

 

 

3) The primary factor that controls metabolism is:

  1. A) post-translational modification of enzymes.
  2. B) substrate availability.
  3. C) enzyme turnover.
  4. D) hormone signaling.
  5. E) compartmentalization of metabolic pathways.

 

Objective:  17.3

 

 

4) Which of the following organs both uses and exports fatty acids as a fuel source?

  1. A) Resting skeletal muscle
  2. B) Liver
  3. C) Adipose tissue
  4. D) Heart muscle
  5. E) B and C

 

Objective:  17.3

 

 

5) The main organ that monitors and stabilizes blood glucose is the ________.

 

 

6) Which of the following statements is FALSE?

  1. A) Glucagon increases cAMP levels in the liver in response to the fasting state.
  2. B) Epinephrine causes mobilization of triacylglycerols from adipose tissue in response to stress.
  3. C) Insulin decreases gluconeogenesis in the liver and increases glucose uptake and glycolysis in muscle.
  4. D) Glycogen phosphorylase is an enzyme target of insulin but not of glucagon.
  5. E) Phosphofructokinase-1 is an enzyme target of glucagon.

 

Objective:  17.4

 

 

7) Which of the following is NOT an effect of glucagon?

  1. A) Hydrolysis of fructose-2,6-bisphosphate
  2. B) Inhibition of glycogenolysis
  3. C) Inhibition of pyruvate kinase
  4. D) Phosphorylation of hormone-sensitive lipase
  5. E) Phosphorylation of glycogen synthase

 

Objective:  17.4

 

 

8) Which of the following is an endocrine regulator that inhibits food intake?

  1. A) Ghrelin
  2. B) Adiponectin
  3. C) Leptin
  4. D) Insulin
  5. E) Both C and D

 

Objective:  17.4

 

 

9) Insulin and glucagon are both synthesized by the same cell types in the pancreas.

 

Objective:  17.4

 

 

10) Epinephrine has a longer term effect on metabolism than does glucagon.

 

Objective:  17.4

 

 

11) AMPK and mTOR play opposing roles in regulating metabolic activity in response to energy status.

 

Objective:  17.5

 

12) Sirtuins are deacetylases that are ________-dependent and therefore can respond to the redox state of the cell.

 

 

13) A side effect of diabetes is the production of acetone from the decarboxylation of acetoacetate due to ketoacidosis.

 

Objective:  17.7

 

 

14) One of the metabolic adaptations that occurs with prolonged starvation is the increased production of ________ because there is insufficient oxaloacetate for oxidation of all the acetyl CoA produced from fat breakdown.

 

 

 

15) Calculate the approximate weight gain per annum if energy intake exceeds energy expenditure by 5 g (1 teaspoon) of sugar per day. Assume that 120 g sugar yields ~1760 kJ of energy and adipose tissue contains ~30 MJkg-1.

 

 

Biochemistry: Concepts and Connections (Appling et al.)

Chapter 18   Amino Acid and Nitrogen Metabolism

 

1) N2 gas can be converted to NH3 by:

  1. A) most organisms.
  2. B) mammals.
  3. C) all plants.
  4. D) all bacteria.
  5. E) legumes.

 

Objective:  18.1

 

 

2) Nitrate can be reduced to ammonia by virtually all organisms.

 

Objective:  18.1

 

 

3) Which of the following enzymes is NOT involved in the conversion of NH3 to an organic nitrogen-containing compound?

  1. A) Glutamate dehydrogenase
  2. B) Carbamoyl phosphate dehydrogenase
  3. C) Glutamate-oxaloacetate transaminase
  4. D) Glutamine synthetase
  5. E) Asparagine synthetase

 

Objective:  18.2

 

 

4) Nitrogen fixation requires the hydrolysis of 8 ATPs to produce 2 NH3 molecules from 1 N2.

 

Objective:  18.2

 

 

5) The proteasome is a large multisubunit ATP-dependent protease that degrades proteins that have been modified by the attachment of ________.

 

 

6) Pyridoxal phosphate is a versatile coenzyme as it is capable of forming a stable ________ base between an amino acid substrate and the coenzyme.

 

7) Tetrahydrofolate is a coenzyme involved in the mobilization and utilization of single carbon functional units in the:

  1. A) metabolism of serine, glycine, methionine, and histidine.
  2. B) biosynthesis of purine nucleotides.
  3. C) biosynthesis of thymine.
  4. D) biosynthesis of formylmethionyl-tRNA.
  5. E) all of the above.

 

Objective:  18.7

 

 

8) In the degradation of amino acids in muscle NH4+ is carried to the liver for conversion into urea by:

  1. A) glutamine.
  2. B) asparagine.
  3. C) alanine.
  4. D) either alanine or glutamine.
  5. E) any amino acid.

 

Objective:  18.8

 

 

9) Transamination reactions can be used to degrade or synthesize amino acids because they have an ________ that has a value close to one.

 

 

10) With appropriate nutrition, animals maintain nitrogen intake and excretion at equivalent rates.

 

Objective:  18.9

 

 

11) The Krebs-Henseleit urea cycle takes place in liver cells entirely within the mitochondrion.

 

Objective:  18.10

 

 

12) In mammals excess dietary protein is degraded with amino acid nitrogen being excreted as ________.

 

13) ________ high energy phosphates from ATP are consumed in each turn of the urea cycle.

 

14) Which of the following amino acids is both glucogenic and ketogenic?

  1. A) Lysine
  2. B) Leucine
  3. C) Tryptophan
  4. D) Cysteine
  5. E) Arginine

 

Objective:  18.11

 

 

15) Which of the following amino acids cannot be used to provide an intermediate of the citric acid cycle?

  1. A) Histidine
  2. B) Proline
  3. C) Phenylalanine
  4. D) Lysine
  5. E) Tyrosine

 

Objective:  18.11

 

 

16) The H2S produced by metabolism of cysteine is a waste product with no physiological or biochemical function.

 

Objective:  18.11

 

 

17) The oxidation of branched chain amino acids shares a similar chemical strategy with β-oxidation of fatty acids.

 

Objective:  18.11

 

 

18) The common degradation product of lysine, tryptophan, phenylalanine and tyrosine is ________.

 

19) Arginine and methionine can be synthesized by mammals but are generally classed as essential amino acids.

 

Objective:  18.14

 

20) All amino acids can be synthesized from intermediates of the:

  1. A) glycolytic pathway alone.
  2. B) glycolytic pathway and the pentose phosphate pathway.
  3. C) citric acid cycle alone.
  4. D) the glycolytic pathway and citric acid cycle.
  5. E) the glycolytic pathway, the pentose phosphate pathway and citric acid cycle.

 

Objective:  18.15

 

 

21) Folate deficiency results in increased risk of cardiovascular disease associated with abnormally high levels of serum ________ due to decreased levels of tetrahydrofolate cofactors required for the methionine synthase reaction.

 

 

22) Apart from in the synthesis of methionine, S-adenosylmethionine is the only biological ________ group donor.

 

 

23) Tyrosine is the precursor of serotonin which has a number of roles in the nervous system.

 

Objective:  18.21

 

 

24) The catecholamine neurotransmitters are derived from ________.

=================================================

 

 

Biochemistry: Concepts and Connections (Appling et al.)

Chapter 19   Nucleotide Metabolism

 

1) Which of the following enzymes is NOT primarily used in salvage of nucleic acids because the pyrophosphate product is rapidly hydrolyzed?

  1. A) Endonuclease
  2. B) Phosphodiesterase
  3. C) Nucleotidase
  4. D) Phosphoribosyltransferase
  5. E) None of the above

 

Objective:  19.1

 

 

2) Nucleoside phosphorylase cleaves a glycosidic bond to yield a base and either ribose-1-phosphate or deoxyribose-1-phosphate.

 

Objective:  19.1

 

 

3) 5-phosphoribosyl-α-D-1-pyrophosphate is a key intermediate in de novo synthesis of nucleotides but not in salvage pathways.

 

Objective:  19.1

 

 

4) Which of the following compounds is NOT a precursor for nucleotide biosynthesis?

  1. A) Aspartate
  2. B) Glutamine
  3. C) Glycine
  4. D) Fumarate
  5. E) Carbamoyl phosphate

 

Objective:  19.2

 

 

5) Which of the following statements about purine biosynthesis in vertebrates is FALSE?

  1. A) Many of the proteins are multifunctional in that they have more than one active site.
  2. B) Six proteins form a multienzyme complex with covalent linkages.
  3. C) The multienzyme complex is called a purinosome.
  4. D) Two enzymes of single carbon metabolism are associated with the multifunctional enzyme complex.
  5. E) One of the enzymes that contributes to the formation of 10-formyl-tetrahydrofolate is a multifunctional enzyme.

 

Objective:  19.2

 

 

6) The initial end products of purine nucleotide biosynthesis are monophosphates.

 

Objective:  19.2

 

7) Inosine 5′-monophosphate, which contains the base hypoxanthine, is a common intermediate for ________ nucleotide biosynthesis.

 

 

8) Formyltransferases, which are ________ dependent, are involved in several steps of purine nucleotide biosynthesis.

 

 

9) The end product of purine catabolism in humans is:

  1. A) xanthine.
  2. B) uric acid.
  3. C) allantoin.
  4. D) urea.
  5. E) hypoxanthine.

 

Objective:  19.3

 

 

10) Humans and great apes do not make the enzyme urate oxidase and are hence prone to gout from the crystallization of ________ in synovial fluid of joints.

 

 

11) All six atoms in the pyrimidine ring are derived from two amino acids.

 

Objective:  19.5

 

 

12) While purines are assembled as nucleotides early in their biosynthetic pathway, the pyrimidine ring is assembled as a ________.

 

13) Glutamine amidotransferases require ATP hydrolysis to make the ________ of glutamine biosynthetically active.

 

14) Which statement about nucleotides is FALSE?

  1. A) Most cells contain 5 to 10 times more RNA than DNA.
  2. B) Ribonucleotides have a number of different metabolic roles.
  3. C) The only role of deoxyribonucleotides is as constituents of DNA.
  4. D) The electrons for reduction of ribonucleotides to the corresponding deoxyribonucleotides ultimately come from NADPH.
  5. E) dTTP can only be synthesized from dCDP.

 

Objective:  19.7

 

 

15) All of the dNTPs are produced in approximately the same amounts because the first step in each pathway is catalyzed by the same ribonucleotide reductase enzyme.

 

Objective:  19.8

 

 

16) The mechanism of action of dihydrofolate reductase inhibitors used for chemotherapy is based on their ability to block the synthesis of dTMP.

 

Objective:  19.9

 

 

17) 5-fluorouracil and 5-fluorodeoxyuridine are both prodrugs and potent inhibitors of DNA synthesis because they can be converted in the cell to 5-fluorodeoxyuridine monophosphate, an irreversible inhibitor of ________.

 

 

18) Ganciclovir or Acyclovir can be used treat herpes virus infections because they are nucleoside analogues that become phosphorylated by the viral thymidine kinase and interfere with viral ________.

 

Biochemistry: Concepts and Connections (Appling et al.)

Chapter 20   Mechanisms of Signal Transduction

 

1) Which of the following is an extracellular messenger involved in signal transduction?

  1. A) Cyclic GMP
  2. B) Ca2+
  3. C) Epinephrine
  4. D) Rhodopsin
  5. E) Diacylglycerol

 

Objective:  20.1

 

 

2) Hormone action is ultimately controlled by the cells that secrete the hormone.

 

Objective:  20.1

 

 

3) Which of the following compounds can act as second messengers in signal transduction pathways?

  1. A) Cyclic AMP
  2. B) Phospholipase C
  3. C) Adenylate cyclase
  4. D) Phosphotidylinositol 4,5-bisphosphate
  5. E) Both A and D

 

Objective:  20.2

 

 

4) G proteins are membrane-bound proteins that bind GDP when inactive.

 

Objective:  20.2

 

 

5) The membrane-bound receptor in G protein-coupled signal transduction is quite separate to the effector enzyme which catalyses the formation of an intracellular ________.

 

) Which of the following does NOT belong to a receptor tyrosine kinase family?

  1. A) Platelet-derived growth factor receptor
  2. B) Insulin receptor
  3. C) Fibroblast growth factor receptor
  4. D) Thyroid receptor
  5. E) Epidermal growth factor receptor

 

Objective:  20.4

 

7) Receptor tyrosine kinases are membrane-spanning proteins with an intrinsic tyrosine kinase domain on the extracellular side of the membrane.

 

Objective:  20.4

 

 

8) The end result of a signal transduction pathway is often a change in gene expression.

 

Objective:  20.5

 

 

9) Nuclear receptors:

  1. A) reside on the nuclear membrane.
  2. B) do not bind to hormones.
  3. C) reside only within the nucleus of a cell.
  4. D) are DNA rather than proteins.
  5. E) are transcriptional regulators.

 

Objective:  20.6

 

 

10) Name the amino acid residue that is used to complex zinc ions in the zinc finger motif of steroid receptors.

 

 

11) The drug tamoxifen can be used as an anti-cancer drug in some breast tumors as it binds to the ________ but does not activate estrogen-responsive genes.

 

 

12) Steroid hormones are cytosolic ligands for a class of nuclear receptors that exert their effects by binding to specific sites on ________.

 

 

13) The protein products of viral ________ are often components of signal transduction pathways that result in tumorigenesis.

 

 

14) Most synaptic transmission events are mediated electrically through gap junctions between cells.

 

 

 

Biochemistry: Concepts and Connections (Appling et al.)

Chapter 21   Genes, Genomes, and Chromosomes

 

1) A bacterial genome is packaged into a nucleoid, which is organized mainly by:

  1. A) interactions with protein.
  2. B) being bound within a nuclear membrane.
  3. C) supercoiling of the DNA.
  4. D) having many attachment points to the cell membrane.
  5. E) being wrapped around histone proteins.

 

Objective:  21.1

 

 

2) Approximately how much of the human genome has a biological function?

  1. A) 90%
  2. B) 80%
  3. C) 60%
  4. D) 50%
  5. E) 40%

 

Objective:  21.2

 

 

3) Heterochromatin is transcriptionally active.

 

Objective:  21.2

 

 

4) The human genome contains one gene for every protein that can be translated from the mRNA.

 

Objective:  21.2

 

 

5) The linker histone H1 has a high proportion of the following amino acid residue.

  1. A) Leucine
  2. B) Lysine
  3. C) Isoleucine
  4. D) Asparagine
  5. E) Histidine

 

6) In eukaryotic cells, chromosomes are organized into a DNA-protein complex known as chromatin.

 

Objective:  21.3

 

7) The post-translational modifications of histone proteins have functional roles in gene expression.

 

 

 

8) The repeating unit of chromatin is known as the ________.

 

 

9) Nucleosomal core particles contain ________ bp of DNA wrapped around a histone octamer.

 

 

10) If 10.4 bp of DNA represents a linear length of 3.4 nm, how long (in meters) would one copy of the human genome (~3 × 109 bp) be if all of the DNA was placed end to end in a linear fashion?

 

 

11) Restriction-modification systems:

  1. A) exist in all organisms as a protection against foreign DNA invasion.
  2. B) include a site-specific exonuclease to degrade foreign DNA.
  3. C) modify DNA by acetylation.
  4. D) include a DNA methylase and an endonuclease.
  5. E) include three types of endonuclease all of which cleave within a specific DNA target sequence.

 

Objective:  21.4

 

 

12) The ________ activity associated with restriction-modification systems is able to flip out the target base from the DNA.

 

 

 

13) Random variations among human genome sequences can result in gain or loss of ________ endonuclease cleavage sites.

 

 

14) Calculate the number of times a recognition site for a 4 bp restriction endonuclease is likely to occur in the diploid human genome

 

15) Southern blotting and hybridization is a technique that uses specific probes to analyze:

  1. A) restriction fragment length polymorphisms.
  2. B) complex mixtures of any nucleic acid.
  3. C) centromeres or telomeres on condensed chromosomes.
  4. D) DNA fingerprints.
  5. E) both A and D.

 

Objective:  21.5

 

 

16) If a PCR reaction starts out with 20 double-stranded DNA targets, how many specific PCR products could be formed after 35 cycles of denaturation, annealing and extension.

 

 

Biochemistry: Concepts and Connections (Appling et al.)

Chapter 22   DNA Replication

 

1) Both type I or type II topoisomerases carry out their catalytic activity via a covalent phosphodiester intermediate between a phosphate group on the DNA and a tyrosine hydroxyl group on the enzyme.

 

Objective:  22.1

 

 

2) DNA gyrase is able to relax supercoils as well as introduce negative supercoils in DNA.

 

Objective:  22.1

 

 

3) The DNA polymerase reaction is a nucleophilic substitution facilitated by:

  1. A) the 3’OH group being a weak nucleophile.
  2. B) the 3’OH group being a strong nucleophile.
  3. C) the pyrophosphate being a good leaving group.
  4. D) the reaction being irreversible.
  5. E) none of the above.

 

Objective:  22.2

 

 

4) Which of the following statements about E. coli DNA polymerase I is FALSE?

  1. A) It can copy a circular DNA template but cannot join the ends.
  2. B) It can extend a gapped duplex from a 3’OH group and displace a preexisting 5′ end.
  3. C) The 3′ exonuclease site is some distance from the polymerase active site.
  4. D) It has 3′ exonuclease activity that resides in a small N-terminal fragment that can be cleaved off by limited proteolysis.
  5. E) It has 5′ exonuclease activity that resides in a small N-terminal fragment that can be cleaved off by limited proteolysis.

 

5) Which of the following statements about E. coli DNA replication is INCORRECT?

  1. A) The β subunit of DNA polymerase III is the sliding clamp essential for processivity.
  2. B) The clamp-loading complex uses exchange between ADP and ATP to eject the clamp loader and close the clamp.
  3. C) Single-stranded DNA-binding protein promotes denaturation of DNA by lowering the melting temperature.
  4. D) Helicases are multimeric proteins that bind preferentially to one strand and rely on ATP-hydrolysis to unwind the duplex.
  5. E) Topoisomerases are responsible for relieving torsional stress ahead of the replication fork generated by unwinding the duplex.

 

Objective:  22.2

 

6) The specificity of DNA polymerase activity is determined by the shapes of the substrate molecules as well as their ________ capacity.

 

 

7) Evidence supporting E.coli DNA polymerase III having the major role in nucleotide incorporation during replication includes:

  1. A) DNA polymerase III has a high Vmax.
  2. B) There are ten or fewer molecules of enzyme per cell.
  3. C) Replication is blocked at high temperatures in temperature sensitive mutants with a thermolabile form of DNA polymerase III.
  4. D) A point mutation can inactivate DNA pol III and inhibit replication.
  5. E) All of the above.

 

Objective:  22.3

 

 

8) E. coli DNA polymerase III makes extensive contacts with the ________ in duplex DNA.

 

 

9) A null mutant in the ________ activity of DNA polymerase I will be defective in DNA replication because it will be unable to carry out primer removal.

 

 

10) Okazaki fragments are initiated with ________ primers by a primase enzyme.

 

 

11) DNA ligase can join Okazaki fragments after activation by ________ of a lysine residue in the active site.

 

 

12) E. coli DNA polymerase I in vitro requires a template and primer, which must always be separate nucleic acids.

 

Objective:  22.5

 

 

13) The individual proteins of the E. coli replisome complex dissociate and reassociate in a dynamic manner.

 

Objective:  22.5

 

14) The replicative E. coli DNA polymerase is a symmetrical dimer, with each part of the dimer being responsible for replicating one strand of the DNA duplex.

 

Objective:  22.5

 

 

15) Which of the following is NOT a requirement of E. coli DNA ligase?

  1. A) A nick in the DNA strand must have a 3′ OH group.
  2. B) A nick in the DNA strand must have a 5′ phosphate group.
  3. C) The nucleotides being linked must be adjacent in the duplex structure.
  4. D) The nucleotides being linked must be properly based-paired.
  5. E) ATP

 

Objective:  22.6

 

 

16) Which of the following statement about eukaryotic DNA replication is INCORRECT?

  1. A) Only one DNA polymerase is required to propagate a replication fork.
  2. B) The same polymerase in humans is involved in proofreading and primer removal as well as lagging strand elongation.
  3. C) The main DNA polymerase that elongates the leading strand has an intrinsic processivity factor.
  4. D) Eukaryotes require two enzymes to remove RNA primers.
  5. E) Chromatin must be dismantled in advance of replication forks and reassembled on daughter strands after the fork has passed through.

 

Objective:  22.7

 

 

17) The initiation of DNA replication in E. coli can occur anywhere on the genome that has repeat sequence elements and requires the interaction of DnaA proteins that results in stretching and bending of DNA causing tension that leads to local unwinding.

 

Objective:  22.8

 

 

18) Eukaryotes solve the problem of replicating the ends of their linear chromosomes by:

  1. A) terminal redundancy whereby each end of the chromosome is duplicated allowing recombination.
  2. B) using a protein as a primer.
  3. C) by covalently linking the two strands at each end of the linear chromosome to form a circle.
  4. D) enzyme activity that uses an RNA template and reverse transcription in a series of repeat cycles.
  5. E) all of the above.

 

Objective:  22.9

 

19) Replication of linear genomes is problematic because primer removal at the ________ leaves a gap in the duplex.

 

 

20) Fidelity of DNA replication is determined solely by the 3′ exonucleolytic proofreading activity of the DNA polymerase.

 

Objective:  22.10

 

 

21) A single-stranded RNA virus makes a DNA copy of itself by the use of a viral multifunctional enzyme called ________.

 

 

Biochemistry: Concepts and Connections (Appling et al.)

Chapter 23   DNA Repair, Recombination, and Rearrangement

 

1) O6-methylguanine has a high probability of base pairing with thymine to result in a post replication mutation from a GC base pair to:

  1. A) TA.
  2. B) AT.
  3. C) CG.
  4. D) GT.
  5. E) TC.

 

Objective:  23.1

 

 

2) The only function of Uracil-DNA N-glycosylase is to remove dUMP residues in DNA that have been arisen by deamination of cytosine.

 

Objective:  23.1

 

 

3) Which of the following types of DNA damage cannot be repaired by base excision repair?

  1. A) Depurination
  2. B) Cytosine deamination
  3. C) Thymine dimer
  4. D) Single-strand break
  5. E) Base oxidation

 

Objective:  23.2

 

 

4) Nucleotide excision repair:

  1. A) involves a multisubunit enzyme.
  2. B) preferentially repairs genes that are being actively transcribed.
  3. C) involves making nicks on either side of a DNA lesion.
  4. D) uses helicase, polymerase and ligase to repair the DNA.
  5. E) all of the above.

 

Objective:  23.2

 

 

5) Photoreactivation using DNA photolyase is responsible for direct repair of thymine dimers in all organisms.

 

6) ________ and bulky adducts on DNA can be repaired using the nucleotide excision repair process.

 

7) The direct DNA repair enzymes DNA photolyase and O6-alkyguanine alkytransferase are unusual in that they are ________ after one catalytic cycle.

 

 

8) Base excision repair starts with cleavage of the ________ between the damaged base and the deoxyribose.

 

 

9) Which of the following enzyme activities is NOT used in base excision repair?

  1. A) Glycosylase
  2. B) Apyriminidic endonuclease
  3. C) Deoxyribose-5′-phosphatase
  4. D) DNA polymerase
  5. E) Helicase

 

Objective:  23.3

 

 

10) The SOS response to DNA damage in bacteria is error-prone because:

  1. A) it uses DNA polymerase that lacks 5′ exonuclease activity.
  2. B) it is an inducible system.
  3. C) the polymerases used lack 3′ exonuclease activity.
  4. D) more than one polymerase can be used to repair the damage.
  5. E) it is stimulated by ultraviolet light that causes mutations.

 

Objective:  23.3

 

 

11) Transcription-coupled repair usually repairs the template strand.

 

12) The dam methylase has a role in which of the following DNA repair systems?

  1. A) Base-excision repair
  2. B) Nucleotide excision repair
  3. C) Non-homologous end-joining
  4. D) Mismatch repair
  5. E) Homologous recombination

 

Objective:  23.4

 

13) Strand-displacement in homologous recombination in E. coli is facilitated by:

  1. A) the RecBCD complex.
  2. B) ss-binding protein.
  3. C) RecA.
  4. D) RuvC.
  5. E) the chi

 

Objective:  23.5

 

 

14) Which of the following mechanisms is NOT involved in the generation of antibody diversity?

  1. A) Recombination with excision of DNA between a V gene sequence and a J sequence
  2. B) Splicing out of RNA sequences between a J region and a C region
  3. C) Somatic hypermutation
  4. D) Non-homologous end joining and DNA repair
  5. E) Transposition

 

Objective:  23.5

 

 

15) Bacteria cannot use homologous recombination for DNA repair as they only have a single copy of their genome.

 

Objective:  23.5

 

 

16) Site-specific recombination generally requires longer homologous sequences than does homologous recombination.

 

17) Homologous recombination occurs by nicking followed by strand invasion, ligation then branch migration.

 

Objective:  23.5

 

 

18) The λ genome is inserted into the E. coli genome in the lysogenic pathway by the use of ________ recombination.

 

19) Which of the following is a feature of bacterial transposition?

  1. A) Homologous recombination
  2. B) DNA synthesis
  3. C) Target site duplication
  4. D) Deletions or inversions
  5. E) All of the above

 

Objective:  23.6

 

 

20) Gene amplification occurring as a result of specific metabolic stress will always be reversed once the stress has been removed.

 

Objective:  23.6

 

 

21) The movement of transposable genetic elements within a genome is essentially ________.

 

 

22) Retroviruses are characterized by the presence of ________ that flank the viral structural genes.

 

 

23) One mechanism that could result in gene duplication involves ________ sister-chromatid exchange.

 

 

Biochemistry: Concepts and Connections (Appling et al.)

Chapter 24   Transcription and Post-transcriptional Processing

 

1) RNA polymerase transcribes all DNA sequences at an equal rate.

 

Objective:  24.2

 

 

2) Which of the following is FALSE when comparing DNA pol III and RNA polymerase?

  1. A) There are many more copies of RNA polymerase in the cell.
  2. B) DNA pol III is much more processive.
  3. C) RNA polymerase makes more errors.
  4. D) RNA polymerase has a much slower kcat.
  5. E) RNA polymerase does not need a primer.

 

Objective:  24.3

 

 

3) Which of the following statements about E. coli RNA polymerase is INCORRECT?

  1. A) It has five different subunits.
  2. B) The σ subunit can be dissociated easily from the rest of the enzyme.
  3. C) The σ subunit is responsible for accurate determination of transcription start sites.
  4. D) Without the σ subunit the enzyme has no RNA polymerase activity.
  5. E) The σ subunit has a role in regulation of transcription.

 

Objective:  24.4

 

 

4) Which of the following is NOT correct when considering the initiation of transcription in E. coli?

  1. A) The σ subunit of RNA polymerase makes strong contacts with the -10 region of promoters.
  2. B) Only the -10 region of the promoter is required.
  3. C) DNA melting near the transcription start site is essential for promoter recognition.
  4. D) The phosphodiester bonds that are formed are not stable until about 10 nucleotides have been incorporated.
  5. E) The RNA polymerase contacts about 50 bp of DNA.

 

Objective:  24.4

 

 

5) Alignment of conserved sequences in promoters recognized by E. coli RNA polymerase revealed two ________ sequences upstream of the transcribed region, which are separated by similar lengths of DNA.

 

 

6) In bacteria, mRNA, tRNA and rRNA are all transcribed by the same RNA polymerase.

 

Objective:  24.5

 

7) Rho-dependent termination of transcription makes use of a hexameric protein, which has RNA-DNA helicase activity.

 

Objective:  24.6

 

 

8) Most ________ of transcription in prokaryotes is based on a weakened interaction due to ________ base pairing between the template and the transcript as well as a stable stem loop structure in the nascent transcript which eliminates base pairing between the template and transcript upstream of the AU interaction.

 

 

9) In eukaryotes RNA polymerase I transcribes all of the ribosomal RNA components.

 

Objective:  24.7

 

 

10) The different sensitivities to the toxin ________ revealed that eukaryotes have three distinct RNA polymerases for synthesis of mRNA, rRNA and small RNAs including tRNA and the 5S species of rRNA.

 

 

11) All the tRNA genes are transcribed by ________ in eukaryotes.

 

12) Which of the following statements is FALSE?

  1. A) RNA polymerase II is responsible for the transcription of genes encoding protein-coding sequences only.
  2. B) Many promoters recognized by RNA polymerase II contain regulatory elements several kbp upstream of the initiation site.
  3. C) TFIIB has a role in converting a closed-promoter into an open-promoter complex.
  4. D) The C-terminal domain of the largest subunit of RNA pol II undergoes extensive phosphorylation prior to transcription elongation.
  5. E) A multiprotein complex is involved in communication between upstream control elements and proteins bound at the promoter.

 

Objective:  24.9

 

13) After promoter clearance by RNA polymerase II:

  1. A) all associated factors remain bound to the polymerase for elongation.
  2. B) a subset of factors remain at the promoter region.
  3. C) no further elongation factors are acquired by the polymerase.
  4. D) no further chromatin remodeling is required.
  5. E) transcription continues until the polymerase reaches the poly (A) tail.

 

Objective:  24.9

 

 

14) In eukaryotes genes encoding enzymes for metabolic pathways often exist as operons of several genes with a single regulatory region to provide coordinate regulation of all genes required for the pathway.

 

Objective:  24.9

 

 

15) Eukaryotic transcription normally takes place on a chromatin template at nuclease-accessible sites.

 

Objective:  24.9

 

 

16) In eukaryotes a set of ________ function in a comparable manner to the σ subunit of E. coli RNA polymerase.

 

 

17) High levels of histone ________ correlate with high levels of transcriptional activity.

 

 

18) Degradation of bacterial mRNAs occurs:

  1. A) from the 3′ end.
  2. B) largely by the activity of non-specific nucleases.
  3. C) from the 5′ end.
  4. D) relatively slowly.
  5. E) from both 3′ and 5′ ends at the same time.

 

Objective:  24.12

 

19) Which of the following types of post-transcriptional processing does NOT occur for bacterial tRNAs?

  1. A) Exonuclease cleavage
  2. B) Endonuclease cleavage
  3. C) Non-template directed addition of bases
  4. D) Methylation of bases
  5. E) Addition of a phosphate group to the 5′ end

 

Objective:  24.12

 

 

20) In bacteria post-transcriptional processing of pre-rRNA species can yield mature tRNAs.

 

Objective:  24.12

 

 

21) All processing of eukaryotic mRNAs takes place in the nucleus after transcription has been completed.

 

Objective:  24.13

 

 

22) The 5′ cap added to eukaryotic mRNA serves to stabilize the mRNA and assists in the efficiency of ________.

 

23) Alternative splicing can:

  1. A) be tissue-specific.
  2. B) produce proteins with different functions from the same gene.
  3. C) contribute to temporal control of gene expression.
  4. D) produce mRNAs that are nonfunctional.
  5. E) all of the above.

 

Objective:  24.14

 

 

24) Splicing of mRNA occurs in spliceosomes and chemically is a series of ________ reactions.

 

 

25) DNA microarrays can be used for gene ________ profiling, starting with RNA and using the enzyme ________ to synthesize cDNA and simultaneously incorporate nucleotides labeled with fluorescent dyes.

 

26) Which of the following is the first step in chromatin immunoprecipitation?

  1. A) Extraction of chromatin from cells
  2. B) Cross-linking with formaldehyde
  3. C) Shearing by sonication
  4. D) Addition of antibodies to recognize proteins that bind to DNA
  5. E) PCR to amplify the target sites

 

 

 

Biochemistry: Concepts and Connections (Appling et al.)

Chapter 25   Information Decoding: Translation and Post-translational Protein Processing

 

1) Which of the following statements about initiation of translation in bacteria is FALSE?

  1. A) fMet-tRNAfMetis the only charged tRNA that can bind to the 30S subunit on its own.
  2. B) The formyl group is transferred to Met-tRNAfMetfrom 10-formyl-tetrahydrofolate.
  3. C) Three initiation factor proteins are required to bind the mRNA and the initiator tRNA to the 30S ribosome.
  4. D) Pairing between mRNA and rRNA places the initiation codon next to the P site in the ribosome.
  5. E) The complete 70S initiation complex ready to receive a second charged tRNA is assembled without any GTP hydrolysis.

 

Objective:  25.1

 

 

2) Which of the following statements about translation elongation in bacteria is TRUE?

  1. A) Charged amino acids are escorted to the A site of the ribosome by an initiation factor.
  2. B) The growing polypeptide chain is moved from the A site to the P site before peptide bond formation.
  3. C) GTP hydrolysis occurs after moving the aminoacyl-tRNA into the A site and before peptide bond formation.
  4. D) The entire peptidyl-tRNA is translocated from the P site to the A site during peptide bond formation.
  5. E) The uncharged tRNA leaves from the E site as the ribosome moves one codon in the 5′ direction.

 

Objective:  25.1

 

 

3) Termination of translation requires GTP hydrolysis and direct interaction of a release factor with a termination codon.

 

Objective:  25.1

 

 

4) Translation is an RNA-directed process whereby amino acids are specified by ________ on the mRNA, which are complementary to ________ on aminoacyl tRNAs.

 

5) An ________ is a sequence within an mRNA that is bounded by stop and start codons that can be continuously translated.

 

6) In the secondary structure of ribosomal RNA, the regions of self-complementarity are highly ________.

 

 

7) The anticodon ends of tRNAs contact the ________ subunit and the acceptor ends contact the ________ subunit of the ribosome.

 

8) Termination of translation occurs when a stop codon is translocated into the ________ site of the ribosome.

 

Objective:  25.1

 

 

9) Which of the following BEST explains the “wobble” hypothesis proposed by Francis Crick?

  1. A) The genetic code is degenerate in that most amino acids have more than one codon.
  2. B) The genetic code is ambiguous in that each codon can specify more than one amino acid.
  3. C) The anticodon can pair with any part of the corresponding codon.
  4. D) The 5′ base of the anticodon can make non Watson-Crick hydrogen bonds with several different bases at the 3′ position of the codon.
  5. E) Inosine can pair up with A, U, or C.

 

Objective:  25.2

 

 

10) Which of the following statements is FALSE?

  1. A) There does not need to be as many different tRNA types as there are codons.
  2. B) The modified bases in the tRNAs are added during transcription.
  3. C) The amino acid is attached at the 3′ terminus of the tRNA.
  4. D) The 3D structures of all tRNA molecules are such that they fit equally well into the ribosome.
  5. E) tRNA exhibits unusual base pairing including single bases pairing with two others.

 

11) The genetic code is universal for all organisms and organelles.

 

Objective:  25.2

 

 

12) Aminoacyl-tRNA synthetases do not contribute to the fidelity of translation.

 

Objective:  25.3

 

13) Peptide bond formation requires GTP hydrolysis.

 

Objective:  25.3

 

 

14) Differences between eukaryote and prokaryote translation include the 40S ribosome recognizing the ________ rather than a Shine-Dalgarno sequence and the N-terminal amino acid is ________.

 

 

15) The bacterial Shine-Dalgarno sequence aligns the mRNA with the 16S rRNA to start translation at the correct position.

 

Objective:  25.5

 

 

16) Antibiotics that inhibit translation are useful because:

  1. A) the translational machinery of eukaryotes is sufficiently different to that of bacteria.
  2. B) microorganisms can develop resistance to other antibiotics.
  3. C) antibiotic resistance genes are often carried on plasmids rather than the bacterial chromosome.
  4. D) different antibiotics can inhibit different steps of translation.
  5. E) they do not cross the cell membrane in higher animals.

 

17) Which of the following applies only to prokaryotic proteins?

  1. A) Secreted proteins have signal sequences in their N-terminal regions.
  2. B) Some proteins are covalently modified after translation.
  3. C) Hydrophilic proteins are able to either traverse or become embedded in hydrophobic membranes.
  4. D) Some proteins are synthesized on polyribosomes.
  5. E) Translation is coupled to transcription.

 

Objective:  25.10

 

 

18) Which of the following BEST describes the transport of nuclear proteins across the nuclear membrane?

  1. A) Simple diffusion
  2. B) An N-terminal targeting sequence that is cleaved during transport
  3. C) A targeting sequence that interacts with a carrier protein
  4. D) Vesicular transport followed by delivery via fusion with the nuclear membrane
  5. E) Co-translational transport using ribosomes attached to the membrane

 

Objective:  25.10

 

19) Which of the following does NOT apply to proteins synthesized on the rough endoplasmic reticulum?

  1. A) Signal recognition particle
  2. B) Vesicular transport
  3. C) Signal sequence cleavage
  4. D) Continuous translation
  5. E) Docking protein

 

Objective:  25.10

 

 

20) Glycosylated proteins are synthesized on rough endoplasmic reticulum.

 

Objective:  25.10

 

 

21) Nuclear encoded proteins destined for ________, chloroplasts or nuclei are synthesized in the cytoplasm.

 

22) The fusion of vesicles, from the Golgi complex, with specific membranes is facilitated by ________ protein pairs called t-SNARES and v-SNARES on membranes as well as cytosolic fusion proteins.

 

Biochemistry: Concepts and Connections (Appling et al.)

Chapter 26   Regulation of Gene Expression

 

1) Which of the following BEST describes transcriptional regulation of the lac operon in E. coli?

  1. A) On in the presence of lactose
  2. B) On in the presence of lactose and presence of glucose
  3. C) Off in the presence of glucose
  4. D) On in the absence of lactose and presence of glucose
  5. E) On in the presence of lactose and absence of glucose

 

 

 

 

2) A partial diploid containing a wild type allele for lacI and a lacI mutant that was unable to bind the inducer would:

  1. A) always show low levels of β-galactosidase gene expression.
  2. B) show normal induction in the presence of an inducer.
  3. C) express β-galactosidase at all times.
  4. D) only show normal induction in the presence of an inducer in the absence of glucose.
  5. E) show induction in the presence of an inducer in the presence of glucose.

 

 

 

 

3) Which of the following is INCORRECT when considering the lac repressor?

  1. A) It is tetramer of two dimers.
  2. B) Binding to the operator site is cooperative.
  3. C) Binding of each dimer is to different regions of the operator.
  4. D) Binding of inducer forces the DNA-binding helices apart so they cannot contact the DNA-binding sites.
  5. E) It is an allosteric protein.

 

 

 

 

4) Which of the following BEST describes catabolite repression of the lac operon?

  1. A) The operon is transcriptionally inactive in the absence of lactose.
  2. B) The operon is transcriptionally inactivated by a repressor protein, which binds to glucose.
  3. C) The operon is transcriptionally active when an activator protein binds to the promoter in the absence of glucose.
  4. D) Glucose is the preferred energy source for coli.
  5. E) The operon is repressed by its protein products.

 

5) A partial diploid containing a wild type allele for lacO and a lacO mutant that was unable to bind to the lac repressor would always express β-galactosidase.

 

 

 

6) Catabolite or glucose repression of the lac operon is a regulatory system, which depends on the levels of cAMP in the cell.

 

 

 

 

7) The λ repressor can act as a transcriptional activator as well as a repressor.

 

 

 

 

8) The physiological inducer of the lac operon is ________.

 

 

 

9) ________ mutants of the lac operon express β-galactosidase at high levels in the absence of an inducer, while ________ mutants of the lac operon express only very low levels of β-galactosidase even in the presence of inducer.

 

 

 

10) The affinity of the lac repressor for DNA ________ markedly when the inducer binds to the lac repressor.

 

 

 

11) Conformational changes in the cAMP receptor protein upon binding to cAMP trigger ________ of the lac operon in the presence of lactose.

 

 

 

12) The λ repressor is inactivated by proteolytic cleavage stimulated by the ________ protein.

 

 

 

 

13) The helix-turn-helix is a common protein motif that is able to interact with DNA in the major grooves by both electrostatic and specific interactions between amino acids of the helix and the bases of the DNA.

 

 

 

14) Which of the following BEST describes the SOS response?

  1. A) DNA damage by UV light causes a λ lysogen to be induced to the lytic life cycle.
  2. B) It is an error prone DNA repair system.
  3. C) Activation of RecA by sensing DNA damage and single-stranded DNA.
  4. D) Coordinated activation of a set of unlinked genes whose protein products will collectively help the cell to respond to environmental damage.
  5. E) Transcriptional depression by proteolytic cleavage of the LexA

 

 

 

15) Which of the following BEST describes attenuation of the trp operon?

  1. A) The ribosome will stall at adjacent trp codons if tryptophan levels in the cell are low.
  2. B) High levels of tryptophan result in continued translation by the ribosome.
  3. C) A transcription termination sequence forms in the leader mRNA because the ribosome reaches a translation stop codon if tryptophan levels are high.
  4. D) The structural genes are not expressed if tryptophan levels in the cell are high.
  5. E) Regulation of trp operon expression by transcriptional repression by the trp repressor when tryptophan levels in the cell are high.

 

 

 

16) A set of linked genes regulated by a common mechanism is called a regulon.

 

 

 

17) The trp operon is transcribed when the trp repressor is bound to tryptophan.

 

 

 

18) The greater complexity of humans compared to worms and flies is due to:

  1. A) a greater number of genes.
  2. B) higher levels of alternative splicing.
  3. C) a much greater number of transcription factors.
  4. D) chromatin structure.
  5. E) combinatorial regulation by a greater number of transcription factors.

 

Objective:  26.4

 

 

19) Nucleosomes very close to the transcription start site in eukaryotes tend to have a high proportion of the histone variants H3.3 and H2A.Z.

 

Objective:  26.4

 

20) All chromatin remodelling complexes are associated with activation of transcription.

 

Objective:  26.4

 

 

21) Nucleosome remodeling complexes use ________ to drive changes in chromatin structure.

 

 

22) Which of the following is NOT part of initiation of transcription in eukaryotes?

  1. A) Phosphorylation of Ser-5 in the heptad repeats in the C-terminal domain of RNA polymerase II by TF-IIH.
  2. B) Unwinding of the DNA template by TF-IIH
  3. C) Non-specific interactions of general transcription factors at promoters
  4. D) Phosphorylation of Ser-2 in the heptad repeats in the C-terminal domain of RNA polymerase II by P-TEFb.
  5. E) The binding of upstream regulatory proteins

 

 

 

23) In eukaryotes RNA polymerase is only bound at promoters that are carrying out active transcription.

 

 

 

 

24) Chromatin modifications that tend to inhibit transcription include:

  1. A) methylation at lysine 9 or 27 of histone H3.
  2. B) methylation at lysine 4 of histone H3.
  3. C) ubiquitylation at lysine 119 of histone H3.
  4. D) A, B, and C.
  5. E) A and C.

 

Objective:  26.7

 

 

25) DNA methylation in eukaryotes:

  1. A) is part of the epigenetic process.
  2. B) occurs only on cytosine residues.
  3. C) is maintained by specific DNA methyl transferases.
  4. D) is inhibited by 5′-azacytidine.
  5. E) all of the above.

 

 

26) Transcriptionally active chromatin usually contains ________ histones, while ________ is normally inhibitory to transcription.

 

 

27) ATPase domains of chromatin remodelers associated with transcriptionally active chromatin can contain a bromodomain that interacts specifically with ________ lysines or a chromodomain that interacts specifically with ________ histones.

 

 

28) Epigenetics is the heritable transmission of gene ________ patterns that does not involve a change in the DNA base sequence.

 

29) miRNAs are used in gene regulation to:

  1. A) block translation.
  2. B) target mRNA for degradation.
  3. C) cause ribosomes to stall.
  4. D) promote degradation of polyA tails.
  5. E) all of the above.

 

 

 

30) RNA interference can be a mechanism of defense against viral infection as well as for regulation of gene expression.

 

 

 

31) ________ are alternative mRNA structures that are produced by binding of a ________ which is often a product of a specific metabolic pathway.

 

 

32) ________ of specific RNA nucleotides in a process known as RNA editing is a mechanism of altering the protein product encoded by some genes in mammals.