Advanced Biochemistry Practice Exam
Course Introduction
Advanced Biochemistry delves into the complex molecular mechanisms that underpin cellular processes, building upon foundational biochemical principles. Students explore in-depth topics such as enzyme kinetics and regulation, protein structure and function, metabolic pathways, bioenergetics, and molecular signaling. Emphasis is placed on current research methodologies, experimental techniques, and data interpretation within the field. The course also discusses the biochemical basis of disease and integrates recent advancements in topics like genomics, proteomics, and systems biology, preparing students for research or professional applications in biomedical and biochemical sciences.
Recommended Textbook
Biochemistry 1st Edition by Roger L. Miesfeld
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Chapter 1: Principles of Biochemistry
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Q1) Who received the Nobel Prize in 1962 for elucidating the molecular structure of DNA?
A) Albert Einstein
B) Linus Pauling
C) John Kendrew and Max Perutz
D) Maurice Wilkins, James Watson, and Francis Crick
Answer: D
Q2) What process describes using mRNA templates to produce proteins?
A) DNA transcription
B) DNA replication
C) DNA translation
D) mRNA translation
Answer: D
Q3) Which of the following is the correct formula for glucose?
A) C<sub>5</sub>H<sub>10</sub>O<sub>5</sub>
B) C<sub>6</sub>H<sub>12</sub>O<sub>6</sub>
C) C<sub>5</sub>H<sub>12</sub>O<sub>6</sub>
D) C<sub>6</sub>H<sub>10</sub>O<sub>6</sub>
Answer: B
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Chapter 2: Physical Biochemistry: Energy
Conversion,water,and Membranes
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Q1) The lateral mobility of lipids with membrane depends on temperature as well as other factors.What would be expected to happen to the lateral mobility if the temperature was decreased?
A) Mobility would be unaffected.
B) Mobility would increase.
C) Mobility would decrease.
D) The membrane would decompose.
Answer: C
Q2) The interaction between an amino group and a carboxylate group is best characterized as
A) hydrogen bonds.
B) ionic interactions.
C) van der Waals interactions.
D) a covalent bond.
Answer: B
Q3) What are the three major types of membranes?
Answer: Plasma membrane,endomembrane,organelle membranes
Q4) Differentiate between autotrophs and heterotrophs.
Answer: Autotrophs convert solar energy to chemical energy,whereas heterotrophs cannot.
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Chapter 3: Nucleic Acid Structure and Function
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Q1) The mixing and matching of novel genes in eukaryotic cells occurs through A) operons.
B) exon shuffling.
C) promoter regions.
D) untranslated regions.
Answer: B
Q2) 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
Q3) In the eukaryotic cell,the coding sequences on a gene are referred to as A) exons.
B) operons.
C) introns.
D) promoter.
Answer: A
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Chapter 4: Protein Structure
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Q1) Which of the following statements about the clamp-type chaperone protein Hsp70 is correct?
A) Hsp70 uses ATP binding and hydrolysis energy to assist in the folding of a protein.
B) Hsp70 is a multi-subunit protein shaped like a large barrel, inside of which the folding protein is protected.
C) Hsp70 is most active during cell division phases.
D) Hsp70 assists in protein unfolding by hydrolyzing and remaking the protein peptide bonds.
Q2) A polypeptide has a high pI value.Which amino acids might comprise it?
A) arginine and lysine residues
B) aspartate and glutamate residues
C) the large nonpolar amino acids
D) a mixture of aspartate and arginine residues
Q3) Which amino acid has the highest pKa?
A) glutamate
B) asparagine
C) cysteine
D) lysine
Q4) List the levels of protein structure and give a brief description of each.
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Chapter 5: Methods in Protein Biochemistry
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Q1) What is the advantage of using monoclonal antibodies compared with polyclonal antibodies?
A) They are less labor intensive to generate.
B) They can recognize more than one epitope.
C) The process used to produce the antibodies provides unlimited supplies.
D) They can be generated without using animals.
Q2) Describe how polyclonal antibodies are generated.
Q3) How does NMR spectroscopy differ from X-ray crystallography when determining the structure of a protein?
Q4) Which technique can be combined with mass spectrometry to identify protein antigens in large cellular complexes?
A) immunofluorescence
B) Western blot
C) immunoprecipitation
D) ELISA
Q5) Polyclonal antibodies are
A) derived from B cells isolated from the spleen.
B) isolated from hybridoma cells.
C) a heterogeneous mixture.
D) a homogenous mixture.
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Chapter 6: Protein Function
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Q1) An E.coli strain is discovered that has a mutation in the gene encoding RecBCD.The mutation causes RecBCD to not function as effectively as the wild-type RecBCD.Hypothesize how the growth rate of this strain would compare with that of the wild type.
Q2) What is the clinical term for reduced O<sub>2</sub> transport efficiency from the lungs to the tissues,arising from altered hemoglobin function or reduced numbers of red blood cells per unit of blood? Provide an example of a specific type of anemia that is caused by a single point mutation.
Q3) A new protein has been discovered that may be allosterically regulated.The protein is purified and analyzed by SDS-PAGE followed by staining with Coomassie blue.A single band at 42 kDa is seen on the gel.Explain how these data may or may not support the belief that the protein is an allosterically regulated protein.If they do support an allosterically regulated protein,propose the most likely model of allostery followed by the protein.
Q4) Which of the following is NOT considered part of the thin filament?
A) actin
B) myosin
C) troponin
D) tropomyosin
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Chapter 7: Enzyme Mechanisms
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Q1) In a reversible covalent modification reaction involving the phosphorylation of a target protein,which of the following amino acids is LEAST likely to be modified with a phosphate group?
A) Ser
B) Phe
C) Tyr
D) Thr
Q2) 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.
Q3) Justify how an enzyme that catalyzes a hydrolysis reaction does not contradict the concept that enzyme active sites are microenvironments that exclude excess water.
Q4) What three amino acids are targeted for phosphorylation by kinases?
Q5) Define the term zymogen.
Q6) What is Henry Eyring's transition state theory?
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Chapter 8: Cell Signaling Systems
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Q1) Some breast cancers express estrogen receptors and are estrogen dependent.Tamoxifen is a chemotherapy agent used in the treatment of estrogen-responsive breast cancers.What is tamoxifen in relation to the estrogen receptor and why does it have this effect?
Q2) Which of the following is true of active NF\(\kappa\)B?
A) It is a dimer.
B) It is phosphorylated.
C) It is in a complex with a DD.
D) It has been proteolytically activated.
Q3) 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.
Q4) The PI-3K signaling pathway is activated by the binding of __________ to its receptor.This leads to an increase in glucose uptake and in __________ synthesis.
Q5) A caspase is a
A) protease.
B) kinase.
C) phosphatase.
D) transmembrane receptor.
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Chapter 9: Glycolysis: a Paradigm of Metabolic Regulation
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Q1) List three common disaccharides in nature and draw the structures of each.
Q2) A shared intermediate can be defined as a molecule that is
A) a reactant in a pathway.
B) the final product of a pathway.
C) the final product of a pathway and the reactant of the next pathway.
D) favorable to produce.
Q3) What does glycolysis accomplish for the cell?
A) It generates ADP for the cell to be used in other cycles.
B) It generates ATP and pyruvate for the cell to be used in other cycles.
C) It generates glucose to be used for storage.
D) It generates CO<sub>2</sub> that is exhaled.
Q4) Metabolism is best defined as a collection of
A) biochemical reactions that convert chemical energy into work.
B) biochemical reactions that convert mechanical energy into work.
C) enzymes that convert glucose into carbon dioxide.
D) enzymes that convert amino acids into proteins.
Q5) Illustrate both the Fisher and Haworth projections for glucose and fructose
Q6) Distinguish between the energy investment of stage 1 and stage 2 of glycolysis.
Q7) List the major metabolic pathways in plants and classify each as either an energy conversion pathway or a synthesis/degradation pathway.
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Chapter 10: The Citrate Cycle
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Q1) High levels of ATP would result in the inhibition of which enzyme in the citrate cycle?
A) succinate dehydrogenase
B) isocitrate dehydrogenase
C) malate dehydrogenase
D) fumarase
Q2) Explain why riboflavin is critical to the citrate cycle.
Q3) 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
Q4) The disease beriberi is a result of which vitamin deficiency?
A) thiamine
B) pantothenic acid
C) riboflavin
D) niacin
Q5) What two features of the citrate cycle make it unique compared with linear metabolic pathways?
Q6) Describe the fate of NADH and FADH<sub>2</sub> produced in the citrate cycle.
Page 12
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Chapter 11: Oxidative Phosphorylation
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Q1) During transfer of ATP,ADP,and P<sub>i</sub>,some of the proton gradient is lost in the
A) movement of ATP into the mitochondria by the ATP/ADP translocase.
B) movement of ATP out of the mitochondria.
C) transport of ADP into the mitochondria by the ADP translocase.
D) transport of P<sub>i</sub> into the mitochondria by the phosphate translocase.
Q2) What is the primary fuel metabolized by the mitochondria in brown adipose tissue of hibernating animals?
A) glucose
B) NADH
C) lipid
D) ATP
Q3) For one electron entering the electron transport chain at complex I,how many times is it handed off between redox active cofactors on its way through the enzyme complexes to end up on O<sub>2</sub>?
A) ~2000
B) ~200
C) ~20
D) ~2
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Chapter 12: Photosynthesis
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Q1) 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.
Q2) List the five steps of photosynthesis,whereby solar energy is converted into chemical energy.
Q3) Which enzyme in the photosynthetic Z scheme catalyzes the PQ cycle,which is analogous to Complex III and the Q cycle in the mitochondrial electron transport chain?
A) photosystem II
B) plastocyanin
C) cytochrome b<sub>6</sub>f
D) photosystem I
Q4) Which of the following groups of molecules are found in the shuffling reactions of stage 3 of photosynthesis?
A) C<sub>1</sub>, C<sub>2</sub>, C<sub>3</sub>, C<sub>4</sub>, C<sub>5</sub>, C<sub>6</sub>, and C<sub>7</sub> sugars
B) NADPH and ATP
C) erythrose-4-phosphate, glyceraldehyde-3-phosphate, and xylulose-5-phosphate
D) 3-phosphoglycerate, 1,3-bisphosphoglycerate, and glyceraldehyde-3-phosphate
Q5) What is the main difference between C<sub>4</sub> and CAM plants?
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Chapter 13: Carbohydrate Structure and Function
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Q1) Differentiate Gram-positive bacteria and Gram-negative bacteria.
Q2) Which glycan is a major component of plant cell walls?
A) cellulose
B) chitin
C) starch
D) glycogen
Q3) Which fluorescent dye is used to label glycans before HPLC?
A) 2-aminobenzamide
B) sodium hydroxide and sodium borohydride
C) sodium cyanoborohydride
D) PNGaseF
Q4) Explain the connection the disaccharide lactose has to lacto-N-tetraose and lacto-N-fucopentaose I that is found in human breast milk.
Q5) Which amino acid does penicillin form a complex with on transpeptidase?
A) aspartic acid
B) lysine
C) alanine
D) serine
Q6) Compare and contrast the structure of chitin and cellulose.
Q7) Compare and contrast the structure of glycogen,amylose,and amylopectin.
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Chapter 14: Carbohydrate Metabolism
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Q1) Gluconeogenesis would most likely be allosterically activated simultaneously along with which other metabolic process?
A) glycolysis
B) pentose phosphate pathway
C) glycogen synthesis
D) TCA cycle
Q2) 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.
Q3) Name the four enzymes of the gluconeogenesis pathway that are NOT found in the glycolysis pathway.
Q4) In the elongation of glycogen,activated glucose units are attached to which hydroxyl of the terminal residue of the growing glycogen chain?
A) C-1
B) C-3
C) C-4
D) C-6
Q5) State how glucagon functions to increase blood glucose levels.
Q6) What is the cellular role of glutathione in red blood cells?
Page 16
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Chapter 15: Lipid Structure and Function
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Q1) How do cholesterol concentrations affect membrane fluidity?
Q2) Define lipid rafts and explain their function.
Q3) One of the functions of the lipid rafts is to
A) act as a storage mechanism for fatty acids.
B) control fluidity of the membrane.
C) coordinate cell signaling.
D) maintain sodium levels in the cell.
Q4) Cortisol is a glucocorticoid that regulates A) blood pressure.
B) ion transport in the kidneys.
C) testosterone.
D) liver metabolism.
Q5) List the three major lipases in human adipocytes and explain the regulatory mechanism for one of the lipases.
Q6) Compare and contrast saturated,monounsaturated,and polyunsaturated fatty acids.
Q7) One disadvantage of using partial hydrogenation in the food industry is that
A) the shelf life of the oils is not as long.
B) trans fats are formed during the process.
Page 17
C) the oils tend to become rancid and have foul odors.
D) the oils cost more than animal fats.
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Chapter 16: Lipid Metabolism
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Q1) Membrane phospholipids are synthesized in which cellular location?
A) cytoplasm
B) mitochondrial intermembrane space
C) mitochondrial matrix
D) smooth endoplasmic reticulum
Q2) Which enzyme is responsible for assembly of palmitate from activated acetyl-CoA fragments?
A) acyl-CoA dehydrogenase
B) acetyl-CoA carboxylase
C) fatty acyl-CoA synthetase
D) fatty acid synthase
Q3) Why is less ATP obtained from the average carbon in a sugar molecule than from a carbon in a fat molecule?
A) The sugar carbons require more water weight during cellular storage.
B) The carbons in fatty acids are a more reduced form of carbon than those in sugars.
C) The sugar carbons yield more NADH than ATP.
D) The sugar carbons are derived from CO<sub>2</sub>.
Q4) List in order the three most abundant molecule types found in an HDL.
Q5) What are the known components of atherosclerotic plaques?
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Chapter 17: Amino Acid Metabolism
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Q1) Compare and contrast the known porphyrias.
Q2) Diseases affecting heme biosynthesis as a result of deficiencies in the heme biosynthetic pathway are called
A) porphyrias.
B) albinism.
C) shikimate.
D) alkaptonuria.
Q3) Adenylylation of Try397 regulates glutamine synthetase by A) lowering activation energy.
B) inhibiting activity.
C) increasing activation energy.
D) increasing rate of reaction.
Q4) What are the six steps of the nitrogenase reaction?
Q5) Nitrogen in biological compounds ultimately comes from what source?
A) ammonia
B) nitrate
C) nitrogen gas
D) bacteria
Q6) How can individuals with urea cycle deficiencies be treated with sodium phenylbutyrate?
Page 19
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Chapter 18: Nucleotide Metabolism
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Q1) Contrast the binding of nucleotides to the activity site and specificity site on the R1 subunit of E.coli ribonucleotide reductase by choosing the nucleotide that can bind to the specificity site but NOT the activity site.
A) ATP
B) dTTP
C) dATP
D) dCDP
Q2) A person wishes to determine the role of PRPP synthetase in a newly discovered organism.He or she decides that a good way to do this would be to see what happens when PRPP synthetase is inhibited.Which of the following could be added to a cell from this organism to inhibit PRPP synthetase?
A) GDP
B) AMP
C) ATP
D) GTP
Q3) Relate the broad substrate specificity of nucleoside diphosphate kinase to its role in the consumption and synthesis of nucleoside triphosphates.
Q4) Compare the regulatory effects of ATP and CTP on ATCase in E.coli.
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Chapter 19: Metabolic Integration
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Q1) Whipple surgery,sometimes carried out on patients battling pancreatic cancer,is one of the most demanding surgeries to perform.It involves removing parts of the pancreas and rerouting aspects of the digestive track.A complication of the surgery can be the development of diabetes.Why could this complication develop? Include the types of cells and hormones that are involved.
Q2) Which tissue participates in the Cori cycle in order to maintain metabolic homeostasis?
A) skeletal muscle
B) adipose tissue
C) kidney
D) brain
Q3) Metabolic homeostasis relies on maintaining
A) maximum ATP synthase activity.
B) optimal metabolite concentrations.
C) maximum flux through the citric acid cycle.
D) minimal inhibition of gluconeogenesis.
Q4) What is the process of maintaining optimal metabolic concentrations and managing chemical energy reserves in tissues? Describe the three primary factors that influence this process.
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Chapter 20: Dna Replication, repair, and Recombination
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Q1) What is the mechanism by which replication errors are fixed in E.coli?
A) degrading of the entire DNA strand to start over
B) base excision
C) mismatch repair
D) abasic repair
Q2) The function of Dam methylase in DNA synthesis is to methylate the
A) new DNA strand.
B) old DNA strand.
C) RNA primer.
D) primase.
Q3) How is an individual with Lynch syndrome at higher risk for cancer?
Q4) Describe the Meselson-Stahl experiment and how it provided biochemical evidence that DNA replication is semiconservative.
Q5) An advantage of viral DNA using LTR to produce a four-nucleotide overhang on the 3' end is to
A) start replication.
B) help with alignment of the viral DNA to the host DNA.
C) start a base mismatch repair sequence.
D) help with cell meiosis.
Q6) Describe the Ames test.
Page 22
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Chapter 21: Rna Synthesis, processing, and Gene Silencing
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Q1) Which of the following is a coding RNA molecule?
A) short interfering RNA.
B) TERC RNA.
C) small nucleolar RNA.
D) messenger RNA.
Q2) Different mRNAs can be obtained from the same gene by
A) terminating transcription at different stop codons.
B) splicing the mRNA with different exons.
C) adding the 7-methylguanosine cap at different sites.
D) alternate folding of mRNA.
Q3) Prokaryotic mRNA is commonly processed through A) splicing by RNaseP enzymes.
B) immediate translation during transcription.
C) addition of 7-methylguanylate cap.
D) removal of exons.
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) Which of the following is considered the adaptor molecule in protein synthesis?
A) mRNA
B) DNA
C) tRNA
D) rRNA
Q2) During the import of one protein from the cytosol to the nucleus via Ran-dependent nuclear import,__________ high-energy phosphate molecule(s)are hydrolyzed.
A) 2 ATP
B) 1 GTP
C) 1 GTP and 1 ATP
D) 2 GTP
Q3) Differentiate among the trafficking of vesicles coated with COPI,COPII,or clathrin.
Q4) Aminoacyl-tRNA synthetase contains two binding sites.Describe the consequence of a mutation that changed the specificity of the amino acid binding site of an aminoacyl-tRNA synthetase from Glu to Asp.
Q5) Contrast both the structure and function of a prokaryotic initiator tRNA with a prokaryotic Met-tRNA<sup>Met</sup>.
Q6) Describe the function of the SRP receptor.
Page 24
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Chapter 23: Gene Regulation
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Q1) What is the function of the SOS regulatory system in the cell?
A) DNA repair
B) DNA translation
C) lactose degradation
D) glucose inhibition
Q2) Allolactose acts as a(n)
A) repressor by causing the lac repressor to bind.
B) inducer by binding to the lac repressor and causing it to dissociate.
C) repressor by increasing the binding affinity of the lac repressor.
D) inducer by binding to CRP.
Q3) In yeast,the sugar galactose is converted to what molecule to enter glycolysis?
A) glucose
B) fructose
C) glucose-6-phosphate
D) fructose-6-phosphate
Q4) When trp operon is attenuated,what does that mean for the trp operon?
A) inhibition of transcriptional initiation by RNA polymerase
B) disruption of transcriptional elongation by RNA polymerase
C) initiation by RNA polymerase
D) enhancement of transcriptional elongation by RNA polymerase
Page 25
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