Course Introduction
Advanced Biochemistry Exam
Solutions
Advanced Biochemistry delves into the molecular mechanisms underlying complex biological processes, building upon foundational biochemical principles. The course explores enzyme kinetics, regulation, and mechanisms, as well as advanced topics in metabolic pathways, signal transduction, membrane dynamics, and macromolecular structure-function relationships. Emphasis is placed on the application of modern biochemical techniques and tools, such as spectroscopy, chromatography, and structural biology methods. Students will critically analyze primary literature and case studies to understand the integration of biochemical processes in health and disease, fostering analytical skills necessary for cutting-edge research in the biochemical sciences.
Recommended Textbook
Biochemistry 1st Edition by Roger L. Miesfeld
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Page 2
Chapter 1: Principles of Biochemistry
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Q1) Differentiate between germ-line cell mutations and somatic cell mutations. Answer: Although both are mutations in DNA,if the mutation is passed from the parent to the offspring,then the mutation is contained within the DNA of a germ-line cell.If the DNA mutation occurs during the lifetime of the organism in a somatic cell,then this disease is limited to that individual organism.
Q2) Evaluate the following statement: Two amino acid sequences with high sequence conservation must have the same function in an organism.
Answer: Although two amino acid sequences with high sequence conservation may have the same structure,it does not mean that those two proteins will perform the same function in a body.As is shown in Figure 1.30,similar structures may have different function.
Q3) What is an advantage of using polypeptides for storage and information transmission?
Answer: The complexity of monomeric units forms a stable arrangement that is perfect for information storage and transmission.
Q4) What functions can polysaccharides perform?
Answer: They provide structural support to cells and energy storage.
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Chapter 2: Physical Biochemistry: Energy
Conversion,water,and Membranes
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Q1) Compare a catabolic pathway versus an anabolic pathway.
Answer: Anabolic pathways synthesize biomolecules,whereas catabolic pathways extract energy from metabolic fuels.Catabolic pathways also generate ATP and reduced coenyzmes.
Q2) List the three chemical properties of ATP that account for the large standard free energy change that occurs when a phosphoanhydride bond is cleaved.
Answer: 1.Electrostatic repulsion between the charged phosphoryl groups destabilizes ATP.Repulsion is reduced on hydrolysis,and therefore the products of ATP hydrolysis are more stable than ATP itself,which favors the hydrolysis reaction.
2.The released phosphate ion has more possible resonance forms than when it is covalently attached to adenylate.Entropically,this favors the free phosphate ions compared to ATP or ADP.
3.The phosphate ion and ADP have a greater degree of solvation than ATP.This means that the phosphate ion and ADP form hydration layers and are more stable than ATP.
Q3) 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) The DNA of a bacteria was isolated and it was determined that 15% of the DNA is composed of cytosine.What percentage of the DNA is guanine?
A) 15%
B) 30%
C) 35%
D) 70%
Answer: A
Q2) Predict how type II topoisomerases change the supercoil region.
A) Lk = 2
B) Lk = 1
C) Lk = -1
D) Lk = -2
Answer: D
Q3) Why does the T<sub>m</sub> increase as the G-C content increases?
Answer: G-C base pairs have more favorable base stacking interactions than A-T base pairs.Therefore,it takes more heat energy to disrupt the base stacking interactions of the G-C base pairs.
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Chapter 4: Protein Structure
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Q1) Which amino acid side chain from the list below is the most polar?
A) Gln
B) Ala
C) Leu
D) Phe
Q2) Draw the resonance structures that stabilize the peptide bonds found in proteins.
Q3) Of the three proposed models of globular protein folding,which one describes the initial formation of all secondary structures,followed by the arrangement of those secondary structures into a final tertiary structure?
A) mutant globule
B) hydrophobic collapse model
C) framework model
D) nucleation model
Q4) Which stabilizing force in protein tertiary structures is a covalent bonding force?
A) ionic bonding
B) disulfide bonding
C) hydrophobic interactions
D) van der Waals bonding
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Chapter 5: Methods in Protein Biochemistry
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Q1) Which method uses mass to charge ratios as well as a bioinformatics approach to determine the amino acid composition of a protein?
A) X-ray crystallography
B) nuclear magnetic resonance
C) tandem mass spectrometry
D) size exclusion chromatography
Q2) Explain the difference between polyclonal and monoclonal antibodies.
Q3) In an ELISA,the detection antibody is a __________ antibody.
A) monoclonal primary
B) polyclonal tertiary
C) monoclonal secondary
D) polyclonal secondary
Q4) How can the mass of an unknown protein can be determined using gel electrophoresis?
Q5) Why is X-ray crystallography more commonly used than NMR spectroscopy when determining protein structure?
Q6) Describe how an ELISA detects antigenic proteins.
Q7) Compare and contrast the three MOST commonly used homogenization techniques to prepare a cell extract.
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Chapter 6: Protein Function
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Q1) If a metabolic enzyme __________ the energy of activation of a reaction,the rate of product formation will __________.
A) increases; decrease B) decreases; increase C) increases; increase D) decreases; decrease
Q2) Explain the relationship between P<sub>50</sub> of oxygen binding and K<sub>d</sub> for oxygen binding to myoglobin.
Q3) Which of the following is NOT a passive transporter protein?
A) porin
B) Cl<sup>-</sup> channel
C) Ca<sup>2+</sup>-ATPase transporter protein
D) Ca<sup>2+</sup> channel
Q4) A reduction in the catalytic ability of carbonic anhydrase may lead to __________ efficient oxygen delivery by hemoglobin as a result of a(n)__________ Bohr effect. A) less; increased B) more; increased C) less; reduced D) more; reduced
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Chapter 7: Enzyme Mechanisms
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Q1) Which of the following is NOT a function of the Mg<sup>2+</sup> ions in the mechanism of enolase?
A) orientation of substrate in the active site
B) stabilizing the intermediate
C) making the proton at the C-2 position more acidic
D) electrophilic attack on the scissile bond
Q2) Which of the following is true of a coenzyme but NOT true of a prosthetic group?
A) It contains an organic component.
B) It is loosely associated with the enzyme.
C) It is necessary for enzyme function.
D) It is present in a holoenzyme but not an apoenzyme.
Q3) Define the term zymogen.
Q4) An enzyme can increase the rate of a reaction inside a cell by __________ the energy of the __________.
A) lowering; transition state
B) increasing; product
C) lowering; substrate
D) increasing; transition state
Q5) What three amino acids are targeted for phosphorylation by kinases?
Q6) What is Henry Eyring's transition state theory?
Page 9
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Chapter 8: Cell Signaling Systems
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Q1) Which of the following is a metabolite receptor?
A) aldosterone receptor
B) glucocorticoid receptor
C) progesterone receptor
D) thyroid hormone receptor
Q2) What characteristic is true for both RTKs and GPCRs?
A) The receptor binds to intracellular proteins only when activated.
B) When activated, the receptor has enzymatic activity.
C) The receptor transmits ions.
D) The receptor undergoes a conformational change on activation.
Q3) Define the main characteristics of a signal transduction pathway and give a specific example of such a pathway.
Q4) Which of the following list includes ONLY first messengers?
A) cortisol, insulin, prostaglandins
B) nitric oxide, estradiol, heme
C) insulin, glucagon, glucose
D) Ca<sup>2+</sup>, testosterone, protein kinase A
Q5) Activation of caspases ultimately leads to the programmed death of the cell.What is this process known as? Explain why this may be a beneficial outcome to the organism.
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Chapter 9: Glycolysis: a Paradigm of Metabolic Regulation
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Q1) Glucokinase is a molecular sensor for which molecule?
A) glucose
B) lactose
C) galactose
D) maltose
Q2) Describe galactose metabolism.If a person has galactosemia,what does that indicate about his or her galactose metabolic pathway?
Q3) List the 10 enzymes required for glycolysis.
Q4) Which of the following is an energy conversion pathway?
A) urea cycle
B) citrate cycle
C) nitrogen fixation and assimilation
D) fatty acid degradation and synthesis
Q5) What is the fate of pyruvate in the presence of yeast,Saccharomyces cerevisiae?
A) converts to CO<sub>2</sub> and ethanol
B) converts to H<sub>2</sub>O and CO<sub>2</sub>
C) converts to lactate and ethanol
D) converts to lactate and glucose
Q6) Benedict's test is a redox reaction between glucose and copper.Draw the reaction between glucose and copper.
Page 11
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Chapter 10: The Citrate Cycle
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Q1) Which of the following is a reactant in the net reaction of the citrate cycle?
A) CO<sub>2</sub>
B) H<sub>2</sub>O
C) GTP
D) CoA
Q2) What is the purpose of the first 3 steps in the pyruvate dehydrogenase reaction?
A) regenerate the oxidized form of lipoamide
B) form NADH
C) transfer electrons
D) form acetyl-CoA
Q3) Compare and contrast the functions of NAD<sup>+</sup><sup> </sup>and FAD in the citrate cycle.
Q4) You exercise vigorously for 30 minutes.Which chemical compounds would you expect to be elevated that would affect the regulation of pyruvate dehydrogenase? State the substances and explain how they would affect the regulation.
Q5) Briefly describe the eight reactions from the citrate cycle,including the identity of the organic reactions and the energetic products.
Q6) Predict what happens to citrate in a cell when ATP and NADH concentrations are high.
Page 12
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Chapter 11: Oxidative Phosphorylation
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Q1) ATP synthesis occurs
A) on the outer mitochondrial membrane.
B) at the ATP synthase complex after ADP and P<sub>i</sub> are transported into the mitochondria.
C) as a result of the leakage of H<sup>+</sup> back out of the mitochondria.
D) from the electron transfer reactions through complex IV.
Q2) What would happen to a mutated ATP synthase enzyme where the proton binding aspartate residue on the c subunits was mutated to an alanine?
A) The enzyme would make ATP as normal in the presence of a proton gradient.
B) The enzyme would not make ATP in the presence of a proton gradient.
C) The enzyme would make ATP without the need for a proton gradient.
D) The rotor would rotate in response to a proton gradient, but no ATP would be made.
Q3) Approximately how many more ATPs are made from one glucose molecule under aerobic conditions with oxidative phosphorylation than under anaerobic conditions?
A) 0
B) 2
C) 30
D) 104
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Chapter 12: Photosynthesis
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Q1) Where do electrons from photosystem II (PSII)come from to re-reduce the oxidized P680<sup>+</sup> state?
A) O<sub>2</sub>
B) NADPH
C) plastocyanin
D) H<sub>2</sub>O
Q2) Which is a way that light controls the Calvin cycle activity?
A) Calvin cycle enzymes are inhibited by the lower H<sup>+</sup>, which is pumped out of the stroma by light reactions.
B) Reduced ferredoxin from the light reactions keeps thioredoxin reduced, which keeps Calvin cycle enzymes in an active form.
C) High levels of ATP and NADPH from the light reactions inhibit the Calvin cycle enzymes. D) Calvin cycle or dark reaction enzyme activators are present at higher levels in the dark.
Q3) Draw the path of electrons in the cyclic photophosphorylation pathway showing the main enzymes and electron carriers involved and demonstrating its cyclic nature.
Q4) At what stage of plant growth is the glyoxylate cycle most common,and why?
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Chapter 13: Carbohydrate Structure and Function
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Q1) The growth rate of nonruminating animals often decreases when they eat feed containing __________ because of the inability to digest it.
A) glucose
B) lactose
C) starch
D) raffinose
Q2) Why can cows digest grass but humans cannot?
Q3) Which glucose homopolymer would be used if a person had to sprint quickly?
A) sucrose
B) galactose
C) starch
D) glycogen
Q4) Which of the following is classified as a monosaccharide?
A) sucrose
B) glucose
C) lactose
D) maltose
Q5) Explain how penicillin functions.
Q6) Compare the mechanisms of resistance that bacteria have developed with penicillin and methicillin.
Page 15
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Chapter 14: Carbohydrate Metabolism
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Q1) Which enzyme uses cellular NADPH to regenerate reduced glutathione?
A) glucose-6-phosphate dehydrogenase
B) glutathione peroxidase
C) glutathione reductase
D) hemoglobin
Q2) Which of the following metabolites is NOT a gluconeogenesis substrate in humans?
A) pyruvate
B) lactate
C) oxaloacetate
D) acetate
Q3) In the glycogenesis pathway,what is the leaving group in the last step where glucose is added to the growing glycogen chain?
A) UDP-glucose
B) pi
C) glucose-1-phosphate
D) UDP
Q4) von Gierke disease is a common glycogen storage disease caused by a deficiency in glucose-6-phosphatase.Explain how a deficiency in this gluconeogenesis enzyme leads to glycogen storage issues.
Q5) Name each of the distinct catalytic activities of the debranching enzyme.
Page 16
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Chapter 15: Lipid Structure and Function
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Q1) Which steroid hormone is synthesized in the ovaries?
A) cortisol
B) progesterone
C) testosterone
D) estradiol
Q2) A wax is defined as
A) long chain fatty alcohols esterified to hydrocarbon chains.
B) three fatty acids linked to a glycerol backbone.
C) a long hydrocarbon chain with a carboxylate group at the end.
D) two fatty acids and a phosphate group linked to a glycerol backbone.
Q3) Which of the following membranes would have the greatest fluidity based on the following percentage of cholesterol in the membrane?
A) 10%
B) 25%
C) 30%
D) 40%
Q4) Compare and contrast the enzyme deficiencies that result in Tay-Sachs disease,Fabry disease,and Niemann-Pick disease.
Q5) Compare and contrast chylomicrons and VLDLs.
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Chapter 16: Lipid Metabolism
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Q1) What is the cellular location of the fatty acid oxidation pathway?
A) cytoplasm
B) peroxisome
C) mitochondrial matrix
D) smooth endoplasmic reticulum
Q2) About __________ more ATPs can be obtained from one 16:0 fatty acid than from one glucose molecule.
A) 32
B) 106
C) 2
D) 75
Q3) The acetyl-CoA for fatty acid synthesis comes from the
A) breakdown of fats.
B) TCA cycle.
C) mitochondria via the citrate shuttle.
D) breakdown of cytoplasmic pyruvate.
Q4) Describe the roles of the citrate shuttle with regards to the fat synthesis pathway.
Q5) Draw the structure of malonyl-CoA,the activated form of acetyl-CoA for fatty acid synthesis.
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Chapter 17: Amino Acid Metabolism
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Q1) Aminotransferase reaction is an example of what kind of kinetics?
A) ternary
B) ping-pong
C) cooperative
D) reversible
Q2) Which intermediate is shared by the urea cycle and the citric acid cycle?
A) citrulline
B) argininosuccinate
C) aspartate
D) malate
Q3) Why does carbamoyl phosphate synthetase I require two equivalents of ATP?
Q4) Which metabolic process is the cause of albinism?
A) inefficient production of dopamine
B) the enzyme tyrosinase working inefficiently
C) overproduction of NADPH
D) low levels of ATP available in the cell
Q5) Explain the mechanism by which glyphosate inhibits the production of aromatic amino acids in plants.
Q6) Summarize the synthesis of the catecholamines.
Q7) Compare and contrast the known porphyrias.
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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 transformation of ribose-5-phosphate to AIR in the first stage of purine biosynthesis in E.coli consumes the equivalent of 5 ATP.The second stage consumes
A) an additional 5 ATP.
B) more than 5 ATP.
C) less than 5 ATP and generates 1 ATP.
D) less than 5 ATP.
Q3) Which of the following is NOT a general role of nucleotides in cells?
A) energy conversion reactions
B) signal transduction pathways
C) genetic information storage
D) proteolysis
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Chapter 19: Metabolic Integration
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Q1) What are the concentrations of glucose that would be expected of a healthy individual after an 8-hour fast and after consuming a large soft pretzel?
A) 80 mg/dL; 130 mg/dL
B) 130 mg/dL; 180 mg/dL
C) 75 mg/dL; 100 mg/dL
D) 125 mg/dL; 75 mg/dL
Q2) Most fad diets do not work because
A) they cost too much.
B) 40% of people do not "stick to it."
C) they increase caloric intake.
D) they slow metabolism because of a lack of micronutrient consumption.
Q3) The blood-brain barrier results from __________,which allow glucose and __________ to enter the brain.
A) astrocytes; ketone bodies
B) astrocytes; triacylglycerols
C) hepatocytes; ketone bodies
D) hepatocytes; triacylglycerols
Q4) What are the two aspects of energy within an organism that must be considered to determine the energy balance?
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Chapter 20: Dna Replication, repair, and Recombination
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Q1) The complete complex that contains the enzymes and proteins required to replicate DNA is called the
A) primase.
B) polymerase.
C) replisome.
D) DNA gyrase.
Q2) How is Dam methylase able to be a control mechanism for DNA replication initiation?
Q3) What is the specific site on the E.coli genome where DNA replication can initiate?
A) oriC
B) DnaA
C) primase
D) SeqA
Q4) If a strand of DNA has a large lesion that distorts the helical nature of the DNA,what would be the mechanism of repair?
A) mismatch repair
B) abasic repair
C) base excision
D) nucleotide excision
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Chapter 21: Rna Synthesis, processing, and Gene Silencing
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Q1) miRNA is
A) involved in stimulating gene expression.
B) derived from degraded mRNA.
C) expressed in the nucleus and is involved in regulating gene expression.
D) derived from degraded virus RNA strands.
Q2) The spliceosome
A) is a cis-acting ribozyme.
B) resembles group II introns in its mechanism and product.
C) performs the same function in prokaryotes and eukaryotes.
D) is a protein enzyme.
Q3) What prokaryotic promoter would most likely control a housekeeping gene?
A) weak promoter
B) -10 and -35 box
C) TATA box
D) strong promoter
Q4) Cis-acting enzymes are
A) self-operating enzymes.
B) enzymes that operate on a target molecule.
C) intermolecular-operating enzymes.
D) enzymes that operate on other enzymes.
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Chapter 22: Protein Synthesis, posttranslational
Modification, and Transport
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Q1) Describe the steps of the mechanism of aminoacyl-tRNA synthetase.Clarify the role of ATP in the process.
Q2) An experiment with bacteria that has been exposed to an antibiotic reveals that the translocation step has been inhibited.Which antibiotic was likely used?
A) chloramphenicol
B) erythromycin
C) tetracycline
D) streptomycin
Q3) Enzyme-mediated protein modification in eukaryotic cells is a means of regulating the activity of the protein.Which of the following is UNLIKELY to result from such a modification?
A) phosphorylation
B) methylation
C) glycosylation
D) hydration
Q4) Radioactively labeled aminoacyl-tRNAs were used in the Nirenberg-Leder experiment to assign triplet codons to specific amino acids.Why was this important in the experimental design?
Q5) Explain what is meant by the statement,"The genetic code is universal."
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Chapter 23: Gene Regulation
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Q1) List the chain of events that occurs after a pioneer factor binds to a cis-acting sequence.
Q2) The function of the lac operon is to provide
A) the enzymes needed to utilize the disaccharide lactose.
B) the enzymes needed to produce lactose.
C) lactose.
D) glucose and galactose to make lactose.
Q3) How does entropy drive protein-DNA complex formations?
Q4) What are the two key protein complexes recruited to the preinitiation complex by activator proteins?
A) mediator complex and DNA polymerase
B) mediator complex and TFIID
C) TFIID and RNA polymerase
D) TFIID and DNA polymerase
Q5) What are the four transcription factors involved in the eve stripe 2 enhancer region?
Q6) Compare negative and positive autoregulation.
Q7) Describe the three biochemical consequences of histone acetylation.
Q8) How can pluripotency be induced?
Q9) Compare the two mechanisms used for control of the trp operon.
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