Introduction to Biochemistry
Exam Materials
Course Introduction
Introduction to Biochemistry provides a foundational understanding of the chemical processes and substances that occur within living organisms. This course explores the structure and function of biomolecules such as proteins, carbohydrates, lipids, and nucleic acids, as well as essential concepts in metabolism, enzyme activity, and bioenergetics. Students will gain insight into the molecular mechanisms underlying biological functions and the relevance of biochemistry in fields such as medicine, genetics, and biotechnology. The course combines theoretical frameworks with practical laboratory techniques to develop a comprehensive appreciation of how chemical principles govern biological systems.
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 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.
Q2) ATP is an abbreviation for which energy currency molecule?
A) adenosine triphosphate
B) adenosine thymine
C) adenosine dinucleotide
D) amino triphosphate
Answer: A
Q3) Simple sugars are made of which of the following elements?
A) carbon, sulfur, and hydrogen
B) carbon, oxygen, and phosphate
C) carbon, oxygen, and helium
D) carbon, oxygen, and hydrogen
Answer: D
Q4) Which six elements make up 97% of the weight of most organisms?
Answer: Hydrogen,oxygen,carbon,nitrogen,phosphorus,and sulfur
Q5) Name the three components of a nucleotide.
Answer: Nucleotide base,five-carbon ribose,and one or more phosphate groups
Page 3
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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) Hydrogen bonds in liquid water are formed between A) two hydrogen atoms on the same molecule.
B) the oxygen of one molecule and the hydrogen of another. C) protons and hydroxides.
D) two oxygen atoms on different molecules.
Answer: B
Q3) You wish to prepare a solution with a pH of 5.44.If the pKa of the weak acid is 4.74,what ratio of weak base to weak acid should you use?
A) 0.70
B) 0.20
C) 1.4
D) 5.0
Answer: D
4
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Chapter 3: Nucleic Acid Structure and Function
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Sample Questions
Q1) When a gene sequence is cloned using mRNA,which enzyme is used to seal the single-strand gaps left behind in the second strand of DNA?
A) DNA methylase
B) restriction endonucleases
C) reverse transcriptase
D) DNA ligase
Answer: D
Q2) Which enzyme is used to cleave DNA at specific sequences during the production of recombinant DNA?
A) DNA methylase
B) restriction endonucleases
C) reverse transcriptase
D) DNA ligase
Answer: B
Q3) A double helix that crosses itself in a right-handed twist is referred to as a
A) positive supercoil.
B) negative supercoil.
C) topoisomer.
D) linking number.
Answer: B
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Chapter 4: Protein Structure
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Q1) 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.
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) The amino acid with the most hydrophobic side chain is
A) asparagine.
B) aspartate.
C) valine.
D) threonine.
Q4) Draw the resonance structures that stabilize the peptide bonds found in proteins.
Q5) 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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Sample Questions
Q1) Predict the fragments of the following peptide after cleavage by the V-8 protease.
CMVAADGKLEPVS
A) CMVAAD GKLEPVS
B) CMVAADGKLE PVS
C) CMVAADG KLEPVS
D) CMVAAD GKLE PVS
Q2) Calculate the purification of the target protein when there is a 30% decrease in activity and a 55% decrease in total protein after centrifugation.
A) 0.55-fold
B) 0.64-fold
C) 1.6-fold
D) 1.8-fold
Q3) In isoelectric focusing,
A) positively charged proteins migrate toward the cathode.
B) positively charged proteins migrate toward the anode.
C) small proteins migrate the fastest.
D) large proteins migrate the fastest.
Q4) Explain how proteins are separated using isoelectric focusing.
Q5) Explain the differences among the three types of column chromatography.
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Chapter 6: Protein Function
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Q1) A mutation of the N-terminal valine in adult hemoglobin occurs.The amino acid is replaced with an isoleucine.Studies show that the replacement does not alter the overall structure of the protein.Which of the following hemoglobin functions may be altered?
A) affinity for 2,3-BPG
B) ability to transport O<sub>2</sub>
C) ability to transport CO<sub>2</sub>
D) ability to switch from the T state to the R state
Q2) Consider a system where a passive transport channel is available for a neutral molecule X.If RTln(C<sub>2</sub>/C<sub>1</sub>)is zero,then
A) no net transport will occur.
B) the molecule will move from the area where the concentration is C<sub>2 </sub>to the area where the concentration is C<sub>1</sub>.
C) the molecule will move from the area where the concentration is C<sub>1</sub> to the area where the concentration is C<sub>2</sub>.
D) There is no way to determine if or how transport of X will occur given the information provided.
Q3) Explain why ABC transporters are channels and not carriers.
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Chapter 7: Enzyme Mechanisms
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Sample Questions
Q1) Binding of glucose to hexokinase causes a conformational change in the enzyme.This is an example of the __________ model of enzyme catalysis.
A) substrate-induced
B) lock and key
C) induced-fit
D) glove and hand
Q2) Hexokinase catalyzes the phosphorylation of glucose to glucose 6-phosphate.Hexokinase belongs to which enzyme class?
A) transferase
B) ligase
C) oxidoreductase
D) hydrolase
Q3) The substrate binding pocket of __________ is best at accommodating substrates with small side chains.
A) elastase
B) chymotrypsin
C) enolase
D) trypsin
Q4) What three amino acids are targeted for phosphorylation by kinases?
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Chapter 8: Cell Signaling Systems
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Sample Questions
Q1) Define the main characteristics of a signal transduction pathway and give a specific example of such a pathway.
Q2) On insulin binding to the insulin receptor,MAP kinase signaling proteins are activated.Which of the following proteins are part of this signaling pathway?
A) Shc
B) IRS
C) PI-3K
D) GLUT-1
Q3) 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.
Q4) Which of the following is a metabolite receptor?
A) aldosterone receptor
B) glucocorticoid receptor
C) progesterone receptor
D) thyroid hormone receptor
Q5) Differentiate between the caspase in the apoptotic pathway that is activated by autocleavage and the caspase that is activated by another enzyme.Clearly name each caspase.
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Chapter 9: Glycolysis: a Paradigm of Metabolic Regulation
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Q1) Benedict's test is a redox reaction between glucose and copper.Draw the reaction between glucose and copper.
Q2) To produce 4 ATP requires 122 kJ/mol.Which reactions in the glycolytic pathway produce enough energy to be able to overcome this deficit?
A) enolase, phosphofructokinase-1, and pyruvate kinase
B) hexokinase, phosphofructokinase-1, and pyruvate kinase
C) phosphofructokinase-1, aldolase, and pyruvate kinase
D) hexokinase, enolase, and pyruvate kinase
Q3) Which of these cofactors participates directly in MOST of the redox reactions in the fermentation of glucose to lactate?
A) ADP
B) ATP
C) NAD<sup>+</sup>/NADH
D) FAD/FADH<sub>2</sub>
Q4) Galactosemia is deficiency in which enzyme?
A) galactokinase
B) galactose-1-P uridyltransferase
C) UDP-galactose 4-epimerase
D) phosphoglucomutase
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Chapter 10: The Citrate Cycle
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Q1) A low NADH to NAD<sup>+</sup> ratio would activate which enzyme in the citrate cycle?
A) succinyl-CoA synthetase
B) fumarase
C) citrate synthase
D) succinate dehydrogenase
Q2) Where do citrate cycle reactions in eukaryotic cells take place?
A) cytosol
B) mitochondrial matrix
C) endoplasmic reticulum
D) nucleus
Q3) Describe the fate of NADH and FADH<sub>2</sub> produced in the citrate cycle.
Q4) Arsenite affects the lipoamide coenzymes of the pyruvate dehydrogenase reaction by
A) acting as a competitive inhibitor.
B) covalently modifying the coenzyme.
C) being a noncompetitive inhibitor.
D) modifying the coenzyme through electrostatic interactions.
Q5) Explain the effect a high concentration of NADH has on the citrate cycle.
Q6) Compare the two roles of lipoic acid in the pyruvate dehydrogenase reaction.
Page 12
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Chapter 11: Oxidative Phosphorylation
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Q1) Submitochondrial particles are inside-out pieces of the inner mitochondrial membrane formed through the sonication of mitochondria.Draw a diagram of these inside-out particles clearly showing (A)where electron transport from NADH occurs,(B)the direction of proton pumping,(C)the location of ATP synthesis,and (D)where O<sub>2</sub> reacts.
Q2) Draw a diagram of the mitochondrion and indicate which side of the organelle has a net positive charge and which side has a net negative charge as a result of proton pumping.
Q3) Which process or pathway describes the coupling of the oxidation reaction of NADH with the formation of ATP?
A) electron transport system
B) chemiosmotic theory
C) proton motive force
D) oxidative phosphorylation
Q4) The ultimate electron acceptor of the mitochondrial electron transport system is A) O<sub>2</sub>. B) NADH.
C) H<sub>2</sub>O.
D) cytochrome c.
Q5) Explain the origin of the brown color of brown adipose tissue.
Page 13
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Chapter 12: Photosynthesis
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Q1) The three stages of the Calvin cycle are A) (1) fix CO<sub>2</sub>, (2) make a C<sub>3</sub> sugar, and (3) make glucose. B) (1) fix CO<sub>2</sub>, (2) use NADPH and ATP, and (3) regenerate the starting C<sub>5</sub> molecule.
C) (1) use ATP, NADPH, and CO<sub>2</sub>, (2) make a C<sub>3</sub> molecule, and (3) regenerate the starting C<sub>3</sub> molecule.
D) (1) use a C<sub>5</sub> sugar, (2) reduce CO<sub>2</sub> with NADPH, and (3) use ATP to regenerate the starting C<sub>5</sub> molecule.
Q2) Explain why the rubisco enzyme's unproductive side reaction with O<sub>2</sub>,called photorespiration,is a concern even when the O<sub>2</sub> affinity for rubisco is 30 times less than that of CO<sub>2</sub>.
Q3) List the four proteins/enzymes and the one molecule involved in the electron transfers in the photosynthetic Z scheme,and show their positions in the "Z" shape.
Q4) Trace the path of each electron through the photosynthetic pathway,starting from H<sub>2</sub>O and proceeding to the cytochrome b<sub>6</sub>f complex.
Q5) Briefly describe the three stages of the Calvin cycle.
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Chapter 13: Carbohydrate Structure and Function
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Q1) Glycan arrays can be coupled with __________ to qualitatively compare fractionated cell extracts from different sources.
A) MALDI-TOF
B) HPLC
C) size exclusion chromatography
D) mass spectrometry
Q2) Approximately 11 different monosaccharides are used as building blocks of glycan groups in glycoconjugates.However,a predictive sugar code has been difficult to identify.Propose three reasons for this difficulty.
Q3) Type O blood is sometime referred to as a universal donor.Explain what this means.
Q4) What would the predicted enzymatic product be when cellulose is exposed to cellulase?
A) pectin
B) hemicellulose
C) cellotetraose
D) glucose
Q5) Compare the mechanisms of resistance that bacteria have developed with penicillin and methicillin.
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Chapter 14: Carbohydrate Metabolism
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Q1) What molecule activates the pentose phosphate pathway?
A) NADP<sup>+</sup>
B) ribulose-5-phosphate
C) ADP
D) NADH
Q2) Which statement of the debranching enzyme is true?
A) It catalyzes the addition of free glucose to a nonreducing end of glycogen.
B) Its product is glucose-1-phosphate.
C) It evenly distributes branch points across the glycogen polymer.
D) It is one enzyme with three unique catalytic activities.
Q3) 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.
Q4) Give the overall balanced reaction for the gluconeogenesis pathway,beginning from pyruvate.Please include any energy currency molecules required by the pathway.
Q5) Name the four enzymes of the gluconeogenesis pathway that are NOT found in the glycolysis pathway.
Q6) Name the enzymes in the glycolysis or gluconeogenesis pathway that could be inhibited by ATP.
Page 16
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Chapter 15: Lipid Structure and Function
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Q1) Compare glycerophospholipids with sphingolipids.
Q2) 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.
Q3) Define lipid rafts and explain their function.
Q4) Which of the following molecules aid in the absorption of dietary lipids?
A) prostaglandin
B) cortisol
C) glycocholate
D) aldosterone
Q5) The outer layer of the plasma membrane of human erythrocytes contains mostly __________ lipids.
A) phosphatidylinositol
B) phosphatidylserine
C) phosphatidylcholine
D) phosphatidylethanolamine
Q6) Compare and contrast chylomicrons and VLDLs.
Page 17
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Chapter 16: Lipid Metabolism
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Q1) The NADPH required by the fatty acid synthesis pathway comes from the A) pentose phosphate pathway and the shuttle of citrate from the mitochondria.
B) mitochondria.
C) breakdown of glucose.
D) TCA cycle and the shuttle of citrate from the mitochondria.
Q2) Which enzyme catalyzes the modification of a fatty acid,so that it can be transported into the mitochondria for oxidation?
A) acyl-CoA dehydrogenase
B) acetyl-CoA carboxylase
C) fatty acyl-CoA synthetase
D) carnitine acyltransferase I
Q3) Describe the roles of the citrate shuttle with regards to the fat synthesis pathway.
Q4) What molecule is the odd chain fatty acid product propionyl-CoA converted into?
A) butyryl-CoA
B) succinyl-CoA
C) citrate
D) palmitate
Q5) Name the steps involved in converting glycerol into triacylglycerol.
Q6) List the five classes of lipoproteins and briefly state the body origin of each.
Page 18
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Chapter 17: Amino Acid Metabolism
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Q1) A no-protein diet with high doses of L-arginine helps patients with argininosuccinase deficiency because it __________ the concentration of __________.
A) increases; fumerate that is metabolized by the citric acid cycle to lower ammonia levels
B) increases; ammonia in the diet to keep them regulated
C) increases; ornithine that is needed to maintain flux through the urea cycle
D) decreases; citrulline to prevent ammonia toxicity
Q2) Nitrogen balance is best described as when the daily intake of __________ equals the amount of __________ lost by excretion.
A) ammonia; nitrogen
B) nitrogen; nitrogen
C) glucose; glucose
D) nitrogen; ammonia
Q3) Aminotransferase reaction is an example of what kind of kinetics?
A) ternary
B) ping-pong
C) cooperative
D) reversible
Q4) What purpose does nitrogen fixation and assimilation serve in the biosphere?
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Chapter 18: Nucleotide Metabolism
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Q1) 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
Q2) In severe combined immunodeficiency disease (SCID),ribonucleotide reductase activity is __________ because of an overabundance of __________.
A) activated; dATP
B) activated; cAMP
C) inhibited; dATP
D) inhibited; cAMP
Q3) Compare the regulatory effects of ATP and CTP on ATCase in E.coli.
Q4) Contrast the source of the nitrogen required for the conversion of UTP to CTP in humans and bacteria.
Q5) Describe how feedback inhibition by GDP may affect the flux of the ATP synthesis pathway.
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Chapter 19: Metabolic Integration
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Q1) 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.
Q2) Analysis of enzyme activity in both liver and muscle cells on insulin exposure would show a decrease in the activity of
A) glycogen phosphorylase.
B) fructose-1,6-bisphosphatase.
C) pyruvate dehydrogenase complex.
D) phosphofructokinase-1.
Q3) What are the two aspects of energy within an organism that must be considered to determine the energy balance?
Q4) Thrifty genes are __________ during times of starvation and __________ when physical activity is low.
A) beneficial; beneficial
B) beneficial; detrimental
C) detrimental; detrimental
D) detrimental; beneficial
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Chapter 20: Dna Replication, repair, and Recombination
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Q1) The importance of V(D)J recombination is that it gives rise to new A) viruses being formed.
B) DNA combinations.
C) antibodies.
D) RNA combinations.
Q2) 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
Q3) The DNA alkylation of guanine is possible because the __________ of guanine is __________ and reacts rapidly with __________ alkylating agents.
A) N-7; nucleophilic; electrophilic
B) N-5; nucleophilic; electrophilic
C) N-7; electrophilic; nucleophilic
D) N-5; electrophilic; nucleophilic
Q4) Distinguish between base excision and nucleotide excision repair.
Q5) Explain the mechanism of nucleotide excision repair.
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Chapter 21: Rna Synthesis, processing, and Gene Silencing
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Q1) Which enzyme is responsible for adding the poly(A)tail to mRNA?
A) cleavage stimulatory factor (CStF)
B) poly(A) polymerase
C) cleavage and polyadenylation specificity factor (CPSF)
D) poly(A) binding protein
Q2) The enzyme responsible for making siRNA is
A) RISC.
B) snoRNA.
C) exosome.
D) dicer.
Q3) Which enzyme degrades the poly(A)tail in the degradation of mRNA?
A) poly(A) binding protein
B) exosome
C) CCR4
D) DCP1 and DCP2
Q4) Describe two ways that termination can occur in the transcription of prokaryotic genes.
Q5) Describe the composition and processing of the C-terminal domain (CTD)of eukaryotic RNA polymerase II,as well as its role in transcription.
Page 23
Q6) Define RNA interference (RNAi)and name the RNA class responsible for RNAi.
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Chapter 22: Protein Synthesis, posttranslational
Modification, and Transport
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Q1) 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.
Q2) How many GTP are hydrolyzed during a single round of translation elongation in a eukaryote?
A) 0
B) 1
C) 2
D) 6
Q3) The Shine-Dalgarno sequence of mRNA base pairs with the __________ rRNA within the prokaryote __________ ribosomal subunit.
A) 23S; 30S
B) 16S; 50S
C) 16S; 30S
D) 5S; 50S
Q4) Differentiate between type I and type II aminoacyl-tRNA synthetases in how they interact with the tRNA and acceptor stem.
Q5) Relate the importance of the binding of Ran to importin to its role in nuclear import.
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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) Which of the following best describes how trans- and cis-acting factors operate?
A) Cis-acting factors can bind to specific DNA sequences whereas trans-acting sites are DNA sequences.
B) Trans-acting factors can bind to specific DNA sequences whereas cis-acting sites are DNA sequences.
C) Trans- and cis-acting factors can both bind to specific DNA sequences.
D) Trans- and cis-acting factors can both only bind to DNA elements to which they are physically linked.
Q3) How can pluripotency be induced?
Q4) Describe the three biochemical consequences of histone acetylation.
Q5) Differentiate between the lytic and lysogenic stages of bacteriophage \(\lambda\) in terms of what genes are active.
Q6) Describe the three broad classes of nucleosome modifications.
Q7) Explain the expression of the Drosophila even-skipped gene.
Page 25
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