Structural Biochemistry
Mock Exam
Course Introduction
Structural Biochemistry explores the intricate architecture and molecular function of biological macromolecules, such as proteins, nucleic acids, carbohydrates, and lipids. The course delves into the fundamental principles of molecular structure, the methods used to determine these structures (including X-ray crystallography, NMR spectroscopy, and cryo-electron microscopy), and the relationship between structure and biological activity. Emphasis is placed on understanding how alterations in structure can affect function and contribute to disease, as well as discussing contemporary topics such as protein folding, enzyme catalysis, and molecular recognition. This course equips students with the foundational knowledge required to analyze and interpret molecular structures in the context of cellular processes and biotechnology applications.
Recommended Textbook
Biochemistry 1st Edition by Roger L. Miesfeld
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Chapter 1: Principles of Biochemistry
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Q1) What is the function of the chloroplast in a plant cell?
A) detoxification of macromolecules
B) degradation of macromolecules
C) conversion of light energy to chemical energy
D) conversion of glucose to ATP
Answer: C
Q2) Plasmids are small,circular DNA molecules that are used in which of the following?
A) gene cloning
B) production of chromatin
C) cell movement
D) replication of nucleus
Answer: A
Q3) Compare and contrast a transcriptome and a proteome.
Answer: Although both transcriptomes and proteomes are collections of genetic material,a collection of DNA transcripts (RNA products)generated by DNA transcription is called a transcriptome,whereas a proteome is the collection of proteins produced by mRNA translation.
Q4) Which six elements make up 97% of the weight of most organisms?
Answer: Hydrogen,oxygen,carbon,nitrogen,phosphorus,and sulfur
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Chapter 2: Physical Biochemistry: Energy
Conversion,water,and Membranes
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Q1) The fluidity of a membrane depends on
A) the degree of saturation of the phospholipids.
B) the number of phospholipids in the membrane.
C) the size of the polar head group.
D) osmotic pressure.
Answer: A
Q2) Freezing point depression,boiling point elevation,and osmotic pressure are all what kind of properties?
A) intrinsic properties
B) colligative properties
C) state functions
D) hydrophobic effects
Answer: B
Q3) Compare the reaction conditions under which you measure K<sub>eq</sub> versus Q.
Answer: K<sub>eq</sub> is the equilibrium constant,so the reaction is at equilibrium at 1 atm,298 K,and initial concentration of 1 M of all reactants and products.Q is the mass-action ratio measured at nonequilibrium concentrations.
Q4) What are the three major types of membranes?
Answer: Plasma membrane,endomembrane,organelle membranes
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Chapter 3: Nucleic Acid Structure and Function
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Q1) When a gene sequence is cloned using mRNA,the mRNA is isolated from the cell and converted into a double-stranded sequence using which enzyme?
A) DNA methylase
B) restriction endonucleases
C) reverse transcriptase
D) DNA ligase
Answer: C
Q2) In a single RNA transcript,polycistronic prokaryotic genes encode __________ protein(s).
A) one
B) two
C) three
D) multiple
Answer: D
Q3) The DNA double helix is considered to be a __________ structure.
A) primary
B) secondary
C) tertiary
D) quaternary
Answer: B
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Chapter 4: Protein Structure
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Q1) What is the peptide sequence Asp-Gln-Gly-Ser,using one-letter abbreviations for the amino acids?
A) AGYS
B) DNGC
C) DQGS
D) EGYS
Q2) In the multi-subunit protein family called immunoglobulins,the different subunits are held together by both covalent and noncovalent forces.What are the covalent forces that hold subunits together in immunoglobulins?
Q3) It is important for cells to degrade misfolded proteins.If misfolded proteins are not degraded,the misfolded proteins may
A) waste excessive ATP in attempts to refold them.
B) aggregate and interfere with normal cellular function.
C) eventually refold, but not until excessive and sometimes fatal levels of cellular energy are spent.
D) be excreted from the cell rather than recycled for building blocks.
Q4) List reagents and conditions that denature proteins.
Q5) Describe the proposed model of globular protein folding called the nucleation model.
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Chapter 5: Methods in Protein Biochemistry
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Q1) Protein NMR is more useful than X-ray crystallography for studying A) secondary structure elements.
B) large proteins.
C) protein unfolding.
D) static protein structures.
Q2) Epitopes on protein antigens are generally located
A) in the heavy chain domains.
B) on polar surface groups in loop regions.
C) in the light chain domains.
D) in association with variable domain amino acid residues.
Q3) Describe the major difference between the types of protein samples used in X-ray crystallography and NMR spectroscopy.Then explain how this difference limits each method.
Q4) The advantage of using an SDS-PAGE gel compared with a native PAGE gel is that the SDS-PAGE gel
A) separates proteins only based on molar mass.
B) gives information about the charge or conformation of the protein.
C) results in a better separation of small proteins.
D) increases the resolution of large and small proteins.
Q5) Why is protein purification often referred to as an art and a science?
Page 7
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Chapter 6: Protein Function
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Q1) Explain how the five arginine residues found within the channel of Omp32 protein of the bacterium Delftia acidovorans increase the specificity of the channel.
Q2) After __________ induced changes in the structure of thin filament,myosin heads containing __________ in the nucleotide binding site will bind with high affinity to actin subunits.
A) ATP; ADP + P<sub>i</sub>
B) ATP; Ca<sup>2+</sup>
C) Ca<sup>2+</sup>; ATP
D) Ca<sup>2+</sup>; ADP + P<sub>i</sub>
Q3) An increase in sickle cell disease symptoms can occur when a person with the disease is at higher altitudes.Hypothesize how allosteric regulation at high altitudes may be related to sickle cell anemia.
Q4) Describe the two functional units of myoglobin that are responsible for O<sub>2</sub> binding.Include the type of chemical bond involved for each binding interaction (i.e.,hydrogen bond,covalent bond,electrostatic bond,etc.).
Q5) Both SERCA and the Na<sup>+</sup>-K<sup>+</sup> ATPase contain a P domain.Explain the general function of this domain.
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Chapter 7: Enzyme Mechanisms
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Q1) A mutation of Lys<sub>229</sub> in aldolase leads to a loss of enzyme activity.This is most likely because the
A) active site can no longer exclude water.
B) active site can no longer include water.
C) enzyme can no longer hold the intermediate in the correct orientation for catalysis. D) product will remain bound to the enzyme active site.
Q2) The side chains of the amino acids that make up the catalytic triad of chymotrypsin contain all EXCEPT
A) a hydroxyl group.
B) a carboxylic acid.
C) an aromatic group.
D) an imidazole.
Q3) Which answer correctly classifies the compound with its relationship to aspartate transcarbamoylase?
A) ATP; allosteric inhibitor
B) ATP; allosteric activator
C) CTP; allosteric activator
D) CTP; substrate
Q4) What is Henry Eyring's transition state theory?
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Chapter 8: Cell Signaling Systems
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Q1) Oncogenic Ras protein chronically stimulates the MAP kinase pathway.Why is Ras not inactivated in this situation?
Q2) What is the TNF receptor-TRADD-FADD-procaspase 8 adaptor complex also known as?
Q3) An inhibitor of PTEN is accidentally ingested by an infant.The infant displays symptoms of hypoglycemia.How would inhibiting PTEN lead to this outcome?
Q4) Estradiol is secreted by the ovaries,travels through the bloodstream,and interacts with estrogen receptors on breast epithelial cells.In this scenario estradiol is acting through which type of mechanism?
A) synacrine
B) paracrine
C) endocrine
D) autocrine
Q5) Outline the steps that occur in the shared pathway of glucagon and epinephrine signaling in a liver cell.Include the specific receptors,G protein subunits,upstream signaling protein,and second messengers.
Q6) Explain how the conformational organization of a nuclear receptor homodimer allows it to recognize inverted repeat sequences of DNA.
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Chapter 9: Glycolysis: a Paradigm of Metabolic Regulation
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Q1) Define aldose.
A) Only aldose molecules have CH<sub>2</sub>OH.
B) Aldose molecules have ketone functional groups.
C) Aldose molecules have aldehyde functional groups.
D) Aldose molecules are all five-membered rings.
Q2) Using glucose metabolism,justify the following statement: Metabolic pathways are highly interdependent and are exquisitely controlled by enzyme activity levels and substrate bioavailability.
Q3) List the major metabolic pathways in animals and classify each as either an energy conversion pathway or a synthesis/degradation pathway
Q4) List the major metabolic pathways in plants and classify each as either an energy conversion pathway or a synthesis/degradation pathway.
Q5) Fructose-1,6-bisphosphate is cleaved by aldolase.What is required for the reaction to proceed?
A) production of endergonic intermediate
B) substrate phosphorylation
C) cleaving of high-energy phosphate bond
D) formation of Schiff base intermediate
Q6) List three common disaccharides in nature and draw the structures of each.
Page 11
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Chapter 10: The Citrate Cycle
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Q1) An in vitro study shows that isocitrate dehydrogenase is activated in the citrate cycle.What is a possible explanation for the activation?
A) high levels of ATP
B) low levels of ATP
C) high levels of NADH
D) low levels of AMP
Q2) Coenzyme A is derived from which of the following vitamins?
A) thiamine
B) pantothenic acid
C) riboflavin
D) niacin
Q3) Which of the following is the cause of the irreversible blockage of the catalytic activity of lipoamide-containing enzymes?
A) cheilosis
B) pellagra
C) beriberi
D) arsenic poisoning
Q4) Compare and contrast the functions of NAD<sup>+</sup><sup> </sup>and FAD in the citrate cycle.
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Chapter 11: Oxidative Phosphorylation
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Q1) If the mitochondrial ATP synthase were inhibited,but the electron transport chain was allowed to run continuously,the pH of the cytoplasm would A) decrease.
B) increase.
C) remain unchanged.
D) increase immediately and then decrease.
Q2) Studies of the inner mitochondrial membrane reveal its composition to be approximately 20% lipid bilayer and 80% protein.What is true of these proteins?
A) Abundant collagen proteins form connective tissues to strengthen the membrane against the pH gradient.
B) High levels of proteins are required to metabolize glucose in the glycolysis pathway for rapid energy production.
C) The proteins form highly folded cristae structures.
D) The proteins are largely electron transport complexes and ATP synthase enzymes.
Q3) List the common enzyme names of the major enzyme complexes in the oxidative phosphorylation pathway,which are required to couple NADH oxidation with ATP synthesis.
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Chapter 12: Photosynthesis
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Q1) Which is the orange pigment commonly found in plant's light harvesting complexes?
A) chlorophyll
B) phycocyanobilin
C) porphyrin
D) \(\beta\)-carotene
Q2) Heme and chlorophyll have the same porphyrin cofactor,yet they have largely different roles.Compare their color and the metal ions employed by each.
Q3) C<sub>4</sub> plants are thought to be more efficient than C<sub>3</sub> plants because they
A) make larger sugar molecules from CO<sub>2</sub>.
B) can concentrate the CO<sub>2</sub> in chloroplasts and therefore minimize side reactions with O<sub>2</sub>.
C) can produce sugar molecules at night in addition to during the day.
D) can live in dry climates.
Q4) What is the main difference between C<sub>4</sub> and CAM plants?
Q5) Explain how the bundle sheath and mesophyll cells in C<sub>4</sub> plants cooperate to accomplish the delivery of CO<sub>2</sub> to the Calvin cycle.
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Chapter 13: Carbohydrate Structure and Function
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Q1) Which disaccharide can be found in fermented beverages such as beer?
A) sucrose
B) glucose
C) lactose
D) maltose
Q2) Which fluorescent dye is used to label glycans before HPLC?
A) 2-aminobenzamide
B) sodium hydroxide and sodium borohydride
C) sodium cyanoborohydride
D) PNGaseF
Q3) Glycoconjugates are linked to proteins or lipids via A) London forces.
B) ionic bonds.
C) covalent bonds.
D) hydrogen bonds.
Q4) Compare the glycosyltransferase enzyme expression that results in the ABO blood groups.
Q5) What challenges are encountered during the structural characterization of glycans on glycoconjugates? Compare the two approaches used to overcome the characterization challenges presented by glycans.
Page 15
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Chapter 14: Carbohydrate Metabolism
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Q1) Starting from the oxidative phase of the pentose phosphate pathway,how many ATP and high-energy reduced molecules,respectively,are made in going from one glucose molecule to glyceraldehyde-3-phosphate and fructose-6-phosphate?
A) 0; 0
B) 0; 2
C) 2; 0
D) 2; 2
Q2) Which of the following molecules would activate phosphofructokinase 1 (PFK1)?
A) NADH
B) AMP
C) ATP
D) pyruvate
Q3) What is the cellular role of glutathione in red blood cells?
Q4) What is the name of the enzyme that removes phosphate groups from the regulated glycogen metabolism enzymes to reverse their activity?
A) phosphorylase kinase
B) protein phosphatase 1
C) insulin
D) protein kinase A
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Chapter 15: Lipid Structure and Function
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Q1) The inner monolayer and outer monolayer of a plasma membrane have different lipid compositions.Describe the composition and explain the role of the uneven distribution of membrane lipids.
Q2) List and describe the major types of lipids found in a typical plasma membrane.
Q3) Compare and contrast saturated,monounsaturated,and polyunsaturated fatty acids.
Q4) Which particles transport triacylglycerols to adipose tissue for storage?
A) apolipoproteins
B) adipocytes
C) chylomicrons
D) perilipin
Q5) During the process of saponification,fatty acid molecules are released from triacylglycerols by treatment(s)with a strong
A) base.
B) acid.
C) base and heat.
D) acid and heat.
Q6) Outline the six steps required for the absorption and transport of dietary triacylglycerols.
Q8) Define lipid rafts and explain their function. Page 17
Q7) Summarize the conversion of 7-hydroxycholestrol into 1,25-hydroxyvitamin D.
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Chapter 16: Lipid Metabolism
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Q1) By what process are LDL particles removed selectively from the blood serum?
A) through targeted digestion by serum lipases
B) by receptor-mediated endocytosis
C) They are replenished with triacylglycerols and never removed.
D) They form atherosclerotic plaques.
Q2) How many passes through the fatty acid oxidation pathway are required to degrade palmitic acid?
A) 1
B) 7
C) 8
D) 16
Q3) Which one of the following lipoproteins functions to transport cholesterol from the peripheral tissues to the liver?
A) VLDL
B) LDL
C) HDL
D) chylomicron
Q4) Describe the roles of the citrate shuttle with regards to the fat synthesis pathway.
Q5) Describe the metabolic conditions under which ketone bodies are produced.
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Chapter 17: Amino Acid Metabolism
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Q1) Outline the process of protein degradation by the ubiquitin proteasome pathway.
Q2) The nitrogen balance in the biosphere incorporates which of the following processes?
A) nitrogen fixation, nitrogen assimilation, and nitrate reduction
B) nitrogen oxidation and nitrogen reduction
C) nitrogen fixation, nitrification, and nitrate reduction
D) nitrogen oxidation and nitrate assimilation
Q3) The urea cycle's function is to __________ the body of an organism.
A) remove excess sugar from
B) remove excess water-soluble vitamins from
C) remove excess nitrogen from
D) add additional nitrogen to
Q4) Why do angina patients carry nitroglycerine with them?
A) as a rapid source of NO for blood vessel dilation
B) as a source of ammonia for muscle relaxation
C) to inhibit acetylcholine release from neurons
D) to inhibit cGMP phosphodiesterase
Q5) What are the key enzymes,intermediates,and products of heme catalysis?
Q6) Why does carbamoyl phosphate synthetase I require two equivalents of ATP?
Q7) How are Roundup Ready soybeans resistant to the herbicide?
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Chapter 18: Nucleotide Metabolism
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Q1) The importance of stable free radicals in the mechanism of E.coli ribonucleotide reductase was identified in the early 1970s.The existence of stable radicals in a protein had not been previously observed.Which of the following amino acids can exist as a stable radical in ribonucleotide reductase?
A) Cys
B) His
C) Ser
D) Glu
Q2) The biosynthesis of CTP is allosterically regulated at many steps.Which of the following is a major point of regulation?
A) dihydroorotate dehydrogenase
B) UMP kinase
C) nucleoside diphosphate kinase
D) UMP synthase
Q3) A mutation in __________ may alter the rate at which UT is converted to CTP.
A) CTP synthetase
B) UTP dehydrogenase
C) CTP transferase
D) UTP decarboxylase
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Chapter 19: Metabolic Integration
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Q1) The net effect of leptin signaling in humans includes
A) decreased appetite.
B) decreased basal metabolic rates.
C) increased set point.
D) decreased thrifty gene expression.
Q2) Anorexigenic neurons express the __________ receptor.
A) MC4
B) Y1/Y5
C) Y2
D) NPY
Q3) Which list correctly places the foods in order of lowest to highest glycemic index?
A) corn chips < soda < cherries
B) peanuts < donut < skim milk
C) broccoli < soda < corn chips
D) donut < broccoli < pretzel
Q4) Liver and skeletal muscle both respond to insulin by exhibiting an increased metabolic flux through glycolytic and glycogen synthesis pathways.Yet the tissues also exhibit different responses in how glucose is transported into the cells on insulin stimulation.What are these differences?
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Chapter 20: Dna Replication, repair, and Recombination
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Q1) If <sup>15</sup>N DNA replicated using conservative replication in <sup>14</sup>N media,the outcome would be that new DNA has
A) a single intermediate density.
B) a lower density.
C) only the higher density.
D) one high density and one low density strand.
Q2) What role does PARP1 have in repairing a single-strand DNA break?
A) recognizes the break
B) removes the methyl group from guanine
C) replaces the mismatched pair
D) absorbs light to become excited
Q3) Which of the following best describes base excision?
A) removal and replacement of individual bases that have been damaged by various chemical reactions
B) repair of large lesions that distort DNA
C) removal of individual bases that have been phosphorylated
D) repair of small lesions that distort DNA
Q4) What is the difference between a transposon move and a retrotransposon move?
Q5) Describe the HIV infection cycle.
Q6) How is an individual with Lynch syndrome at higher risk for cancer?
Page 23
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Chapter 21: Rna Synthesis, processing, and Gene Silencing
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Q1) Eukaryotic transcription promoters
A) require multiple DNA binding regions.
B) are largely conserved across the genome.
C) can stimulate DNA polymerases by direct binding.
D) control translational as well as transcriptional events.
Q2) Approximately how many different types of RNA promotors are needed in eukaryotic systems?
A) 1
B) 2
C) 3
D) 4
Q3) How are RNA structures different from protein structures?
A) RNA is single stranded, whereas proteins are not.
B) RNA can H-bond with itself, whereas proteins cannot.
C) RNA mutations can lead to nonfunctioning proteins, whereas protein mutations do not.
D) RNA adopts less defined tertiary structures than proteins.
Q4) Describe the composition and processing of the C-terminal domain (CTD)of eukaryotic RNA polymerase II,as well as its role in transcription.
Q5) What reaction is catalyzed by the spliceosome?
Page 24
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Chapter 22: Protein Synthesis, posttranslational
Modification, and Transport
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Q1) All glycoproteins have __________ covalently added posttranslationally.
A) carbohydrates
B) phosphates
C) methyl groups
D) acetyl groups
Q2) Which sequence is MOST likely to be modified with the fatty acid myristoylate in the ER? (The represents additional amino acids N-terminal to those shown.)
A) Cys-Leu-Ala-Ile-Ser-Phe
B) Leu-Gly-Phe-Ala-Ser-Phe
C) Gly-Leu-Phe-Ala-Ile-Ser
D) Phe-Leu-Cys-Gly-Leu-Ile
Q3) The anticodon of tRNA is made up of __________ bases.
A) 2
B) 3
C) 4
D) 5
Q4) How does the wobble hypothesis allow for fewer than 63 tRNAs to effectively recognize 63 codons?
Q5) Describe the function of the SRP receptor.
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Chapter 23: Gene Regulation
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Q1) What are two medical applications that iPS could be used for?
A) type 1 diabetes and Parkinson's
B) type 2 diabetes and Parkinson's
C) Alzheimer's and Parkinson's
D) Alzheimer's and type 2 diabetes
Q2) High concentration of CI protein in the cell __________ expression of the
A) prevents; lytic promoter
B) allows; lytic promoter
C) prevents; trp operon
D) allows; attenuator sequence
Q3) The function of RecA* is to
A) inhibit expression of its own gene.
B) repress SOS genes.
C) stimulate LexA autocleavage.
D) allow LexA to accumulate.
Q4) Compare negative and positive autoregulation.
Q5) Define the different mechanism of positive and negative gene regulation by ligand binding.
Page 26
Q6) Compare and contrast the structures of the lac repressor protein and CRP.
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