Structural Biology
Final Test Solutions
Course Introduction
Structural Biology explores the molecular architecture and functional mechanisms of biological macromolecules such as proteins, nucleic acids, and complexes. The course covers fundamental principles of structure determination techniques including X-ray crystallography, nuclear magnetic resonance (NMR) spectroscopy, and cryo-electron microscopy (cryo-EM), and discusses how these structures elucidate the biochemical activities and interactions essential for life. Through case studies and practical examples, students will gain an understanding of how structural data advances our knowledge of health, disease, drug design, and molecular evolution.
Recommended Textbook
Biochemistry 8th Edition by Mary K. Campbell
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Chapter 1: Biochemistry and the Organization of Cells
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Q1) A spontaneous reaction is
A) exergonic.
B) endergonic.
C) at equilibrium.
D) none of the above.
Answer: A
Q2) Which of the following organelles does not have a double membrane?
A) mitochondrion
B) nucleus
C) endoplasmic reticulum
D) chloroplast
Answer: C
Q3) How are the majority of elements thought to have been formed?
A) By thermonuclear reactions that normally take place in stars.
B) In explosions of stars.
C) By the action of cosmic rays outside the stars since the formation of the galaxy.
D) All of the choices are true
E) None of the choices; all the elements were present from the initial Big Bang.
Answer: D
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Page 3
Chapter 2: Water: the Solvent for Biochemical Reactions
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Q1) A solution at pH 7 contains a weak acid, HA. The pK<sub>a</sub> of the acid is 6.5. What is the ratio of [A ]:[HA]?
A) 1:3
B) 1:1
C) 3:1
D) 10:1
Answer: C
Q2) Which substance would be the best buffer at pH 8 if it had to be able to buffer against either acid or base?
A) one with a pK<sub>a</sub> of 7
B) one with a pK<sub>a</sub> of 8
C) one with a pK<sub>a</sub> of 9
D) The pK<sub>a</sub> of a substance doesn't tell you whether it would be a good buffer at this pH.
Answer: B
Q3) Hydrogen bonds can only form when the hydrogen atom is involved in a polar bond. A)True
B)False
Answer: True
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Page 4
Chapter 3: Amino Acids and Peptides
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Sample Questions
Q1) Which amino acid has a basic R group?
A) Glutamic Acid
B) Histidine
C) Isoleucine
D) Serine
E) Tyrosine
Answer: B
Q2) Refer to Exhibit 3A. Which one has a pI of 5.0?
A) Alanine
B) Arginine
C) Histidine
D) Cysteine
E) Glutamic acid
Answer: D
Q3) What is the charge on the tetrapeptide lys-lys-his-glu at pH 7?
A) 0
B) +1
C) +2
D) 1
Answer: B
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Chapter 4: The Three-Dimensional Structure of Proteins
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Q1) Which of the following statements regarding hemoglobin (Hb) and myoglobin (Mb) is true?
A) Mb transports oxygen while Hb stores it.
B) Mb has quaternary structure but Hb does not.
C) Mb displays simple kinetics of binding while Hb displays cooperativity.
D) Mb binds Fe(II) while Hb binds heme.
Q2) Variations in the structure of hemoglobin
A) do not always have an adverse effect on health
B) can alter the binding of heme to the protein
C) can occur on the surface of the protein
D) all of these
Q3) Assuming the oligopeptide ALPHAHELICKS forms one continuous -helix, the carbonyl oxygen of the glutamic acid residue is hydrogen bonded to the amide nitrogen of A) leucine.
B) isoleucine.
C) cysteine.
D) lysine.
E) serine.
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Chapter 5: Protein Purification and Characterization Techniques
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Q1) Which of the following is NOT true concerning a western blot?
A) it is usually performed in a 96 well microtiter plate
B) it involves the use of primary antibodies
C) it involves the use of secondary antibodies
D) it involves electrophoresis
Q2) Which of the following happens as a protein is purified?
A) the percent recovery and the fold purification both increase
B) the percent recovery and the fold purification both decrease
C) the percent recovery increases and the fold purification decreases
D) the percent recovery decreases and the fold purification increases
Q3) The purity of an enzyme at various stages of purification is best measured by A) total protein.
B) total enzyme activity.
C) specific activity of the enzyme.
D) percent recovery of the protein.
E) percent recovery of the enzyme.
Q4) It is impossible to sequence a protein if you do not have overlapping sequences to work with.
A)True
B)False
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Chapter 6: The Behavior of Proteins: Enzymes
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Q1) Which of the following is implied by induced fit between the enzyme's active site and the substrate?
A) The enzyme is a flexible molecule.
B) An enzyme will work equally well with different substrates.
C) An active site can bind to different substrates.
D) The enzyme is a flexible molecule so different substrates can bind.
E) All of these are correct
Q2) A rate constant is
A) the rate of a reaction at standard temperature and pressure.
B) the rate of a reaction at equilibrium.
C) a proportionality constant relating the rate of a reaction to the concentration(s) of the reactant(s).
D) a kind of transition state.
Q3) The rate of a reaction depends on
A) the free energy change
B) the activation energy
C) the enthalpy change
D) the entropy change
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Chapter 7: The Behavior of Proteins: Enzymes, Mechanisms, and Control
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Sample Questions
Q1) Which of the following is not true about B vitamins?
A) They are usually fully active in the form we eat them
B) They are usually water soluble
C) Niacin and riboflavin are examples
D) They are important in many metabolic reactions
Q2) The active site of chymotrypsin contains all of the following, except:
A) Histidine residue.
B) A magnesium ion.
C) Hydrophobic pocket to bind the substrate.
D) Serine residue.
E) All of these are in the active site of chymotrypsin.
Q3) ATP is a negative allosteric effector for glycogen phosporylase. This is an example of A) feedback inhibition.
B) positive cooperativity.
C) negative cooperativity.
D) competitive inhibition.
Q4) The term K<sub>0.5</sub> is analogous to the K<sub>M</sub>
A)True
B)False
Page 9
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Chapter 8: Lipids and Proteins Are Associated in Biological Membranes
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Q1) Refer to Exhibit 8A. Which protein might help to identify the cell type?
A) 1
B) 2
C) 3
D) 4
E) More than one could help identify the cell type.
Q2) The distribution of lipids in membranes is
A) uneven, with bulkier molecules on the exterior
B) characterized by even distribution of molecules
C) distinguished by the absence of cholesterol
D) not well understood
Q3) Glycolipids are characterized by containing the following non-lipid component:
A) Sugars
B) Glycerol
C) Phosphate
D) Sphingosine
E) More than one of these characterize glycolipids.
Q4) Glycolipids on the surface of cells are especially important as cell markers.
A)True
B)False
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Chapter 9: Nucleic Acids: How Structure Conveys Information
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Q1) Which is the dominant form of DNA found in the cell?
A) A
B) B
C) Z
D) H
E) All forms of DNA are found in equal amounts
Q2) Transfer RNA molecules are characterized by all the following, except:
A) They are one of the largest of the RNAs.
B) Cloverleaf shape.
C) Many modified bases.
D) Extensive secondary and tertiary structure.
E) All of these characterize transfer RNA molecules.
Q3) The three-dimensional structure of transfer RNA has been determined by
A) analytical ultracentrifugation
B) gel electrophoresis
C) ultraviolet spectroscopy
D) x-ray crystallography
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Page 11
Chapter 10: Biosynthesis of Nucleic Acids: Replication
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Q1) In E. coli,
A) the leading strand is synthesized in one piece while the lagging strand is synthesized discontinuously.
B) the leading strand is synthesized discontinuously while the lagging strand is synthesized in one piece.
C) both the leading and lagging strands are synthesized in one piece.
D) both the leading and lagging strands are synthesized discontinuously.
Q2) The direction of synthesis of a DNA strand is
A) from the 5' end to the 3' end on both strands.
B) from the 3' end to the 5' end on both strands.
C) from the 5' end to the 3' end on one strand and from the 3' end to the 5' end on the other strand.
D) none of the above.
Q3) A special protein called proliferating cell nuclear antigen serves the purpose of the clamp in eukaryotes.
A)True
B)False
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Chapter 11: Transcription of the Genetic Code: Biosynthesis of RNA
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Sample Questions
Q1) The end of the new mRNA molecule in E. coli. usually terminates in a string of A's
A)True
B)False
Q2) Which of the following is not a characteristic of catabolite activator protein (CAP)?
A) it is a positive regulator of the lac operon
B) when the cell has sufficient glucose and lactose, CAP will not be bound to the CAP binding site
C) CAP binding near the promoter site depends on CAP complexation with cAMP
D) the binding of CAP to DNA requires ATP hydrolysis
Q3) Inducers allow for a system in which an enzyme is not made unless it is needed.
A)True
B)False
Q4) Which of the following best describes the order of events at the promoter?
A) open complex closed complex transcription initiation
B) closed complex open complex transcription initiation
C) open complex transcription initiation closed complex
D) transcription initiation open complex closed complex
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Chapter 12: Protein Synthesis: Translation of the Genetic Message
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Q1) A Shine-Dalgarno Sequence is a
A) sequence of nucleotides in the DNA that interacts with the -subunit of RNA polymerase to begin transcription.
B) sequence of nucleotides in an mRNA that interacts with the small subunit of a ribosome to begin translation.
C) sequence of nucleotides in the DNA that interacts with -protein to terminate transcription.
D) sequence of nucleotides in an mRNA that functions to terminate translation.
Q2) The formylation of methionine in prokaryotes
A) depends on two different tRNAs, where methionine can be formylated when bound to one form and not the other.
B) depends on two different tRNAs, where methionine can be formylated when bound to either one.
C) depends on one tRNA, where methionine is formylated after binding.
D) takes place before methionine is bound to tRNA.
Q3) The initiation of eukaryotic translation can be a control point in overall gene expression?
A)True
B)False
Page 14
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Chapter 13: Nucleic Acid Biotechnology Techniques
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Q1) A transcriptome is
A) an mRNA-based vector.
B) three-dimensional mRNA structure.
C) a collection of all the genes being transcribed in a given cell or tissue at a given time.
D) the mRNA transcribed to produce a fusion protein.
Q2) If mRNA is converted to DNA, digested with restriction enzymes, and cloned into suitable vectors, the resultant library is called a:
A) DNA library
B) cDNA library
C) mRNA library
D) none of these
Q3) Fluorescence works because the fluorescent molecule
A) absorbs light at one wavelength and emits light at a longer wavelength.
B) absorbs light at one wavelength and emits light at a shorter wavelength.
C) absorbs light at one wavelength and emits light at the same wavelength.
D) absorbs light at many wavelengths and emits light at many wavelengths.
Q4) Antibiotic-resistance genes in vectors are often used as selectable markers.
A)True
B)False
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Chapter 14: Viruses, Cancer, and Immunology
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Q1) A virus life cycle that involves the incorporation of the viral DNA into the host chromosome is
A) lysogeny.
B) lytic.
C) oncogenic.
D) non-existent.
Q2) The term antibody is essentially interchangeable with A) immunoglobulin.
B) reverse transcriptase.
C) allergen.
D) vaccine.
Q3) Ebola virus is an example of a ________ virus
A) non-enveloped DNA containing B) enveloped DNA containing C) non-enveloped RNA containing D) enveloped RNA containing E) none of these
Q4) Viruses can be genetically engineered to specifically target cancer cells. A)True B)False
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Chapter 15: The Importance of Energy Changes and
Electron Transfer in Metabolism
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Q1) Which of the following is not true?
A) Molecular oxygen is always a substrate in oxidation reactions.
B) Oxidation reactions involve the movement of electrons from one molecule to another
C) When a molecule is oxidized, it loses electrons
D) Reduction involves the gain of electrons
Q2) Which of the following are examples of endergonic processes?
A) protein synthesis and active transport
B) protein synthesis and oxidation of carbohydrates
C) active transport and oxidation of carbohydrates
D) oxidation of fats and of carbohydrates
Q3) "Metabolism" refers to
A) the breakdown of larger molecules into smaller ones.
B) the production of larger molecules from smaller ones.
C) both of these
D) none of these
Q4) The oxidation of nutrients supplies the energy to produce ATP.
A)True
B)False
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Chapter 16: Carbohydrates
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Q1) Which of the following monosaccharides is a ketose?
A) arabinose
B) ribose
C) xylose
D) lyxose
E) none of them
Q2) The following sugar is also called milk sugar:
A) Fructose
B) Glucose
C) Lactose
D) Sucrose
E) Maltose
Q3) Which of the following monosaccharides is an aldose
A) glucose
B) galactose
C) mannose
D) ribose
E) all of them
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18
Chapter 17: Glycolysis
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Q1) The phosphorylation of fructose 6-phosphate to fructose-1,6-bisphosphate is the committed step in glycolysis because
A) it is the rate-limiting step.
B) it is the most strongly exergonic step in the pathway.
C) fructose 1,6-bisphosphate can undergo no other reactions than those of glycolysis.
D) two phosphate groups are involved.
Q2) What is the relationship between glycolysis and cancer?
A) cancer cells lack a glycolytic pathway
B) cancer cells use a modified version of glycolysis
C) cancer cells exhibit a much higher level of anaerobic glycolysis than normal cells
D) none of these
Q3) Which of the following glycolytic enzymes forms a mixed anhydride from phosphoric acid?
A) hexokinase.
B) phosphofructokinase.
C) glyceraldehyde-3-phosphate dehydrogenase.
D) phosphoglycerate kinase.
E) pyruvate kinase.
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Chapter 18: Storage Mechanisms and Control in Carbohydrate Metabolism
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Q1) Which of the following reactions occur when a single glucose residue is transferred from UDP-glucose to a growing glycogen molecule?
A) UDP is released.
B) The glucose can be attached to a #4 carbon atom in the glycogen molecule.
C) UDP is released and the glucose is attached to a #4 carbon.
D) All of these events can occur when a single glucose residue is added.
Q2) Glycogen loading is particularly advantageous for providing energy for long distance athletic events, such as running the marathon.
A)True
B)False
Q3) There is as much energy used to add a phosphate group by means of phosphorolysis, as the energy required adding a phosphate using ATP.
A)True
B)False
Q4) When glycogen phosphorylase is phosphorylated
A) its activity decreases.
B) its activity increases.
C) its activity is unaffected.
D) none of these because that enzyme doesn't get phosphorylated.
Page 20
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Chapter 19: The Citric Acid Cycle
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Q1) Which of the following reactions involves substrate-level phosphorylation?
A) isocitrate -ketoglutarate
B) citrate isocitrate
C) succinate fumarate
D) succinyl-CoA succinate
E) acetyl-CoA + oxaloacetate citrate
Q2) In which cellular location do the majority of the reactions of the citric acid cycle take place?
A) the cytosol.
B) the mitochondrial matrix.
C) the endoplasmic reticulum.
D) lysosomes.
E) none of these
Q3) Which of the following does not play a role in the overall aerobic metabolism of glucose?
A) citric acid cycle
B) electron transport
C) oxidative phosphorylation
D) urea cycle
E) all of these play a role in overall aerobic metabolism of glucose
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Chapter 20: Electron Transport and Oxidative
Phosphorylation
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Q1) What is the net yield of ATP per glucose molecule that passes through all of aerobic respiration (glucose CO<sub>2</sub> + H<sub>2</sub>O)?
A) 2
B) 4
C) 6
D) 30 32, dependent on the shuttle system used.
Q2) Which of the following is not true of the process of oxidative phosphorylation?
A) protons flow into the mitochondrial matrix through ion channels in the ATP synthase
B) the F<sub>0</sub> part of the ATP synthase serves as a proton channel
C) the F<sub>1</sub> part of the ATP synthase is the site of ATP formation
D) iron-sulfur proteins bind to the ATP synthase
Q3) Complex IV of the electron transport chain oxidizes ____, reduces ____, and ____ protons in the process.
A) coenzyme Q; cytochrome c; pumps
B) cytochrome c; coenzyme Q; pumps
C) cytochrome c; O<sub>2</sub>; doesn't pump
D) cytochrome c; O<sub>2</sub>; pumps
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Page 22
Chapter 21: Lipid Metabolism
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Q1) Of the processes listed below, which is not an important source of acetyl-CoA?
A) pentose phosphate pathway
B) amino acid degradation
C) glycolysis
D) fatty acid oxidation
Q2) The acyl carrier used in fatty acid synthesis is similar to coenzyme A.
A)True
B)False
Q3) Carnitine acyltransferase is located in the mitochondrial
A) intermembrane space.
B) outer membrane.
C) inner membrane.
D) matrix.
Q4) Which of the following is true concerning phospholipases?
A) Many snake venoms contain phospholipases
B) Phospholipase D is a component in some spider venoms
C) Phospholipases in snake venoms can lead to the lysing of blood cells
D) All of these
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Chapter 22: Photosynthesis
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Q1) A specialized pair of chlorophylls exists at
A) the antenna complexes.
B) the accessory pigments.
C) the reaction centers.
D) the stroma.
E) the bottom of the roots in most plants
Q2) Which of these statements concerning the Calvin Cycle is false?
A) There is significant overlap between these reactions and glycolysis.
B) During the process, ATP is used with an ADP product.
C) Fructose 1,6 bisphosphate is an intermediate in this pathway.
D) NADP<sup>+</sup> is converted to NADPH during this pathway.
E) At least one reduction reaction occurs during this pathway.
Q3) The earliest photosynthetic organisms most likely used water as an electron source. A)True
B)False
Q4) Rubisco is a rare example of an enzyme whose genetic information is found in two different cellular compartments.
A)True
B)False
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Chapter 23: The Metabolism of Nitrogen
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Q1) High protein foods are not advisable for the long distance runner during a race because they increase the need for water and for urination.
A)True
B)False
Q2) Orotic acid is synthesized from
A) glycine and carbamoyl phosphate.
B) arginine and carbamoyl phosphate.
C) aspartic acid and carbamoyl phosphate.
D) aspartic acid and glutamine.
Q3) Carbamoyl phosphate is made in both the mitochondria and the cytosol, because it is used in the synthesis of several different molecules which are made in either of the compartments.
A)True
B)False
Q4) Deoxyribonucleotides are formed
A) by a pathway entirely different from that of ribonucleotides
B) exclusively by hydrolysis of the DNA of the organism
C) as monophosphates by reduction of ribonucleoside monophosphates
D) as diphosphates by reduction of ribonucleoside disphosphates
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Chapter 24: Integration of Metabolism: Cellular Signaling
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Q1) Which of the following best describes protein kinases?
A) Protein kinases act by transferring a phosphate from a protein to ADP to make ATP.
B) Protein kinases act by transfering a phosphate from a donor molecule, like ATP, to a protein molecule, thereby changing its activity
C) Protein kinases phosphorylate enzymes and activate them
D) Protein kinases phosphorylate key tyrosine residues on receptors
Q2) Which of the following is NOT true?
A) obese individulas are more likely to get cancer
B) diabetic individuals are more likely to get cancer
C) when obese or diabetic patients get cancer, they are more likely to die from it
D) cancer strikes lean and healthy people with the same odds as it strikes obese and diabetic people
Q3) Which of the following is not a potential mechanism to activate protein kinases?
A) Cyclic AMP binding to regulatory subunits on the protein kinase.
B) Binding of a calcium complex to the protein kinase.
C) Binding of inositol phosphate to the protein kinase.
D) All three of these mechanisms activate protein kinase.
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