Biological Sciences
Final Exam
Course Introduction
Biological Sciences is an interdisciplinary course that explores the fundamental principles of life and living organisms, including their structure, function, growth, evolution, and interactions with the environment. Students will study key concepts across molecular biology, genetics, physiology, ecology, and evolution, while gaining practical skills through laboratory experiments and fieldwork. The course provides a foundation for advanced study and diverse career paths in healthcare, research, environmental management, and biotechnology, emphasizing the critical role biology plays in addressing global challenges such as disease, biodiversity loss, and climate change.
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) Which two functional groups are involved in producing a peptide bond?
A) alcohol and amino
B) amino and thiol
C) methyl and amino
D) amino and carboxyl
Answer: D
Q2) What process converts DNA to RNA?
A) DNA transcription
B) DNA replication
C) DNA translation
D) RNA transcription
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
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Chapter 2: Physical Biochemistry: Energy
Conversion,water,and Membranes
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Q1) For a reaction to be spontaneous,the change in the entropy of the universe must be A) greater than zero.
B) less than zero.
C) equal to zero.
D) equal to 1.
Answer: A
Q2) If serum pH falls blow pH 7.4,a condition called acidosis,how does the body respond?
Answer: The equilibrium of the carbonic acid-bicarbonate reaction is shifted toward H<sub>2</sub>CO<sub>3</sub> formation to decrease H<sup>+</sup> concentration and thereby increase the pH.This is done by lowering CO<sub>2</sub> through hyperventilation and decreasing excretion of HCO<sub>3</sub><sup>-</sup> by the kidneys.
Q3) Hydrophobic interactions between nonpolar molecules result from the A) tendency to maximize water's interaction with nonpolar molecules.
B) strong attractions between nonpolar molecules.
C) water becoming more ordered around the nonpolar molecule.
D) water ionically bonding to the nonpolar molecule.
Answer: C
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Chapter 3: Nucleic Acid Structure and Function
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Sample Questions
Q1) The ability to monitor the denaturation of DNA using absorbance is referred to as A) annealing.
B) supercoiling.
C) melting temperature.
D) hyperchromic effect.
Answer: D
Q2) How does the organization of prokaryotic genes differ from the organization of eukaryotic genes?
Answer: Prokaryotic genes can either be monocistronic (code for a single protein)or polycistronic (code for multiple proteins).Eukaryotic genes contain exons (coding regions)separated by introns (noncoding sequences).
Q3) What is the benefit of comparing a human disease gene to similar genes in other organisms using a bioinformatics tool such as BLAST?
Answer: The comparison can lead to insight into the function of the encoded protein based on evolutionary conservation.The biochemical characterization of the protein can lead to further understanding of the biochemistry,resulting in a potential drug or treatment for the disease.
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Chapter 4: Protein Structure
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Q1) Which of the following statements about the chamber-type chaperone protein GroEL-GroES is correct?
A) GroEL-GroES requires the hydrolysis of multiple ATPs to assist in the folding of a protein.
B) GroEL-GroES recycles misfolded proteins by recovering individual amino acids.
C) GroEL-GroES assists in protein unfolding by hydrolyzing and remaking the protein peptide bonds.
D) GroEL-GroES uses GroEL as a cap, trapping an unfolded protein in the GroES chamber.
Q2) After analyzing all the structures of proteins found in the Protein Data Bank,scientists have found that four general classes of protein structures exist,based on their secondary structure themes.Name the four classes of general protein structures.
Q3) The chirality of naturally occurring amino acids in proteins is
A) R.
B) L.
C) D.
D) the same as glyceraldehyde.
Q4) List reagents and conditions that denature proteins.
Q5) Draw the reaction by which a protein disulfide bond forms.
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Chapter 5: Methods in Protein Biochemistry
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Q1) How does the directionality of synthesis differ with in vivo polypeptide synthesis compared to solid-phase peptide synthesis?
Q2) When preparing to isolate proteins from plant cells,the first step in preparing the cell homogenate would be
A) sonication.
B) using a French press.
C) treatment with mild detergents.
D) enzymatic treatment.
Q3) Compare and contrast the three MOST commonly used homogenization techniques to prepare a cell extract.
Q4) Biochemical assays are important in the process of isolating proteins because they A) uniquely identify one protein.
B) separate proteins based on polarity.
C) isolate proteins based on size.
D) determine the molecular weight of proteins.
Q5) Compare and contrast electrospray ionization (ESI)and matrix-assisted laser desorption/ionization (MALDI).
Q6) Explain the differences among the three types of column chromatography.
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Chapter 6: Protein Function
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Sample Questions
Q1) Which of the following directly requires ATP to carry out its function?
A) Cl<sup>-</sup>ion channel
B) malate dehydrogenase
C) myoglobin
D) protein kinase A
Q2) As 18 Na<sup>+</sup> ions are exported out of the cell by the Na<sup>+</sup>-K<sup>+</sup> ATPase membrane transport protein,__________ K<sup>+</sup> ions are imported into the cell.
A) 2
B) 12
C) 18
D) 24
Q3) Explain the relationship between P<sub>50</sub> of oxygen binding and K<sub>d</sub> for oxygen binding to myoglobin.
Q4) 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.
Q5) Explain why ABC transporters are channels and not carriers.
Q6) Explain how a mutation in Asp351 of SERCA might alter Ca<sup>2+</sup> transport.
Page 8
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Chapter 7: Enzyme Mechanisms
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Sample Questions
Q1) The conversion of 2-phosphoglycerate to phosphoenolpyruvate is an example of which type of reaction?
A) hydrolysis
B) dehydration
C) isomerization
D) condensation
Q2) What three amino acids are targeted for phosphorylation by kinases?
Q3) On a plot of [product] versus time for an enzyme-catalyzed reaction,the v<sub>0</sub> is equal to the
A) slope of the line / [S].
B) [P] at the lowest time point.
C) slope of the line.
D) y-intercept.
Q4) What is Henry Eyring's transition state theory?
Q5) The regulation of a biomolecule through the addition or removal of a molecular tag involves __________ reactions.
A) coenzyme-dependent redox
B) reversible covalent modification
C) metabolite transformation
D) isomerization
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Chapter 8: Cell Signaling Systems
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Sample Questions
Q1) Illustrate how a conformational change is critical in the two-step model of EGF function.
Q2) Explain how the conformational organization of a nuclear receptor homodimer allows it to recognize inverted repeat sequences of DNA.
Q3) Liver cells were monitored for changes in metabolic enzymatic activity after exposure to glucagon.The enzymes that showed changes in activity were then analyzed to assess if they had been covalently modified.Which of the following results were likely observed?
A) Enzymes that showed lower activity were not phosphorylated.
B) Enzymes that showed higher activity were methylated.
C) Enzymes that showed altered activity (higher or lower) were phosphorylated.
D) Enzymes that showed altered activity (higher or lower) were methylated.
Q4) Phosphorylation of which of the following is necessary for the increased expression of antiapoptotic genes?
A) RIP
B) TNF receptor
C) FADD
D) IKK
Q5) What is a protein that promotes GDP-GTP exchange in G proteins known as?
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Chapter 9: Glycolysis: a Paradigm of Metabolic Regulation
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Q1) What is the potential metabolic fate of pyruvate under aerobic conditions?
A) produce lactate
B) produce ethanol
C) produce carbon dioxide and water
D) produce glucose
Q2) 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
Q3) Which of following is an anomeric pair?
A) D-glucose and D-fructose
B) D-glucose and L-fructose
C) D-glucose and L-glucose
D) \(\alpha\)-D-glucose and b-\(\beta\)-glucose
Q4) Glucokinase is a molecular sensor for which molecule?
A) glucose
B) lactose
C) galactose
D) maltose
11
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Chapter 10: The Citrate Cycle
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Sample Questions
Q1) Predict the fate of acetyl-CoA and oxaloacetate when the citrate cycle is inhibited.
Q2) How would an increase in Ca<sup>2+</sup> be expected to affect the pyruvate dehydrogenase reaction?
A) The pyruvate dehydrogenase kinase enzyme activity would increase, resulting in an inhibition of pyruvate dehydrogenase activity.
B) The last step of the pyruvate dehydrogenase reaction is blocked, resulting in a decrease in activity.
C) The E1 subunit is phosphorylated by pyruvate dehydrogenase kinase, and the catalytic activity of pyruvate dehydrogenase decreases.
D) The pyruvate dehydrogenase phosphatase-1 enzyme would increase, resulting in pyruvate dehydrogenase activation at an accelerated rate.
Q3) Compare and contrast the anaplerotic nature of the pyruvate carboxylase reaction and the phosphoenolpyruvate carboxylase reaction.
Q4) Describe the fate of NADH and FADH<sub>2</sub> produced in the citrate cycle.
Q5) Briefly describe the eight reactions from the citrate cycle,including the identity of the organic reactions and the energetic products.
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Chapter 11: Oxidative Phosphorylation
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Q1) For each molecule below,list the number of ATP obtained assuming that the electron transport chain and oxidative phosphorylation are active.
NADH (from the TCA cycle)
FADH<sub>2</sub> (from the TCA cycle)
NADH (from the cytoplasm,malate aspartate shuttle)
NAD<sup>+</sup> (from the mitochondria)
Q2) Which of the following is an electron carrier in the mitochondrial electron transport system?
A) proton
B) water
C) quinone
D) ATP
Q3) What is the effect of oligomycin,an ATP synthase inhibitor,on the mitochondrial oxidative phosphorylation pathway?
A) The mitochondria cannot reduce NADH or make ATP.
B) No proton gradient is formed, and no ATP is synthesized.
C) Protons leak back into the cytoplasm.
D) The proton gradient is formed, but no ATP synthesis can occur.
Q4) Why are 2,4-dintrophenol and thermogenin referred to as uncouplers?
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Chapter 12: Photosynthesis
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Q1) What is a reason for keeping photosystem I (PSI)and photosystem II (PSII)separate in the chloroplasts?
A) They are involved in different pathways and not involved with each other.
B) They would quench each other by energy transfer.
C) They have different sunlight exposure requirements.
D) They have different ATP consumption requirements.
Q2) Which two proteins do electrons move between in the PQ cycle?
Q3) In the five steps used by photosynthetic organisms to convert solar energy into chemical energy,which molecules store the solar energy before sugar synthesis?
A) chlorophylls
B) NADH and FADH<sub>2</sub>
C) H<sub>2</sub>O and O<sub>2</sub>
D) ATP and NADPH
Q4) The final product that is formed by the enzyme rubisco is
A) 3-phosphoglycerate.
B) ATP.
C) ribulose-1,5-bisphosphate.
D) glyceraldehyde-3-phosphate.
Q5) 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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Sample Questions
Q1) Give an example of a mono-,di-,and polysaccharide and explain the biological importance of each.
Q2) A person who only expresses the GTB enzyme and not the GTA enzyme will have which blood type?
A) O
B) A
C) B
D) AB
Q3) Explain the difference between simple sugars,polysaccharides,and glycoconjugates.
Q4) What type of inhibitor is penicillin classified as?
A) reversible
B) competitive C) suicide
D) uncompetitive
Q5) How do the antibacterial properties of penicillin compare with methicillin?
Q6) Compare and contrast the structure of glycogen,amylose,and amylopectin.
Q7) What are the biological implication of the increased branching in glycogen compared with amylopectin and amylose?
Page 15
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Chapter 14: Carbohydrate Metabolism
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Q1) Explain how the Cori cycle leads to the regeneration of NAD<sup>+</sup> for muscles with an active glycolysis pathway.
Q2) What class of enzymes in the oxidative phase of the pentose phosphate pathway is responsible for the production of NADPH?
Q3) The hormone insulin activates phosphofructokinase 2 (2PFK2).This leads to a(n)__________ in concentration of fructose 2,6 bisphosphate,which favors the __________ pathway.
A) increase; glycolysis
B) increase; gluconeogenesis
C) decrease; glycolysis
D) decrease; gluconeogenesis
Q4) Which enzyme in the glycolysis pathway catalyzes a reaction that requires two enzymes to reverse in the gluconeogenesis pathway?
A) pyruvate kinase
B) phosphofructokinase I
C) pyruvate dehydrogenase
D) glycogen phosphorylase
Q5) Name the enzymes in the glycolysis or gluconeogenesis pathway that could be inhibited by ATP.
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Chapter 15: Lipid Structure and Function
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Q1) The addition of phosphocholine to ceramides generates
A) glycerophospholipids.
B) gangliosides.
C) cerebrosides.
D) sphingomyelin.
Q2) Compare and contrast the structure of a wax to that of a fatty acid.
Q3) The outer layer of the plasma membrane of human erythrocytes contains mostly __________ lipids.
A) phosphatidylinositol
B) phosphatidylserine
C) phosphatidylcholine
D) phosphatidylethanolamine
Q4) Which of the following amino alcohols act as the functional group attached to a phosphate in a glycerophospholipid?
A) methanolamine
B) ethanolamine
C) propanolamine
D) butanolamine
Q5) List and describe the major types of lipids found in a typical plasma membrane.
Page 17
Q6) Compare glycerophospholipids with sphingolipids.
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Chapter 16: Lipid Metabolism
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Q1) How many more enzymes does the oxidation of oleoyl-CoA (18:1)require than the oxidation of stearoyl-CoA (18:0)?
A) 0
B) 1
C) 2
D) 3
Q2) Which of the following causes inhibition of fatty acid synthesis?
A) increased insulin
B) increased AMP-activated protein kinase (AMPK)
C) decreased cytoplasmic acyl-CoA
D) increased cytoplasmic acetyl-CoA
Q3) As in glycolysis and the degradation of glucose,the degradation of fatty acids also requires an initial investment of ATP energy.State the reaction or reactions where ATP energy is needed before fatty acids can be oxidized.
Q4) During the conversion of VLDL to IDL,the
A) IDL becomes increasingly enriched in cholesterol.
B) core of IDL becomes increasingly enriched in TAGs.
C) LDL intermediate is formed.
D) IDL becomes depleted in protein.
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Chapter 17: Amino Acid Metabolism
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Q1) A person who has alkaptonuria is easily diagnosed from his or her black urine.What causes the black color?
A) oxidation of phenylalanine
B) oxidation of homogentisate
C) reduction of acetoacetyl-CoA
D) dehydration
Q2) Which intermediates of the Krebs bicycle would be found in the cytosol?
A) fumerate and argininosuccinate
B) citrulline and malate
C) arginine and oxaloacetate
D) urea and ammonia
Q3) Summarize the synthesis of the catecholamines.
Q4) Which of the following is the key regulated enzyme in urea synthesis?
A) carbamoyl phosphate synthetase I
B) glutamate dehydrogenase
C) arginase
D) argininosuccinase
Q5) What are the six steps of the nitrogenase reaction?
Q6) Outline the process of protein degradation by the ubiquitin proteasome pathway.
Q7) Why does carbamoyl phosphate synthetase I require two equivalents of ATP?
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Chapter 18: Nucleotide Metabolism
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Q1) Explain how a general inhibitor of endonucleases would alter the homeostasis of mRNA and affect the nucleotide salvage pathway.
Q2) Contrast the energy required to drive the synthesis of AMP from IMP with that required to drive the synthesis of GMP from IMP.
Q3) 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
Q4) How many PRPP are required to synthesize two UMP and two CTP from carbamoyl aspartate?
A) 0
B) 2
C) 4
D) 8
Q5) Contrast the source of the nitrogen required for the conversion of UTP to CTP in humans and bacteria.
Q6) Compare the regulatory effects of ATP and CTP on ATCase in E.coli.
Page 20
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Chapter 19: Metabolic Integration
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Q1) When AMPK is bound by AMP and is phosphorylated at Thr172,__________ activity will __________.
A) glycogen synthase; increase
B) phosphofructokinase-2; decrease
C) acetyl-CoA carboxylase; increase
D) hormone-sensitive lipase; decrease
Q2) A patient has been diagnosed with metabolic syndrome.To establish the diagnosis,the doctor likely performed several tests.A test that the doctor was UNLIKELY to perform would be
A) an assessment of abdominal obesity.
B) fasting followed by glucose tolerance test to establish insulin sensitivity.
C) monitoring of blood pressure.
D) a blood test for lipid levels.
Q3) The exchange of fatty acids and triacylglycerols between the liver and adipose tissue is an ongoing process that helps maintain metabolic homeostasis.What is the name of this process?
Q4) Differentiate the roles of the two different phosphorylation sites of insulin receptor substrate 1 (IRS1).Include the specific amino acids that are phosphorylated as well as the signaling pathway involved in your answer.
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Chapter 20: Dna Replication, repair, and Recombination
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Q1) Methenyltetrahydrofolate (MTHF)absorbs light to form *MTHF.What does the star on MTHF signify?
A) radical
B) excited
C) cation
D) anion
Q2) Compare the two different outcomes of cytosine deamination as replication proceeds.
Q3) 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.
Q4) Tus-Ter terminates DNA synthesis by
A) breaking the single-strand DNA and preventing further synthesis.
B) forcing the primase to dissociate.
C) blocking the opening of helicase.
D) methylating the DNA strand.
Q5) How do Holliday junctions work in DNA recombination?
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Chapter 21: Rna Synthesis, processing, and Gene Silencing
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Q1) The C-terminal domain (CTD)of the eukaryotic RNA polymerase II is involved in the transcriptional process of
A) addition of a poly(A) tail.
B) removal of exons.
C) directing RNA to the cytoplasm.
D) product phosphorylation.
Q2) 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.
Q3) Many noncoding RNAs are involved in gene silencing.Gene silencing refers to A) the splicing of mRNA into alternative transcripts.
B) defense mechanisms against RNA viruses.
C) mechanisms inhibiting gene expression.
D) the modification of genes through RNA-mediated mutation.
Q4) List the three main ways that eukaryotic mRNA molecules are processed before translation,which prokaryotic organisms to do not require.
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Chapter 22: Protein Synthesis, posttranslational
Modification, and Transport
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Q1) Describe the function of the SRP receptor.
Q2) In an iteration of the Nirenberg-Leder experiment to assign triplet codons to specific amino acids,radioactively labeled aminoacyl-tRNA with the anticodon of CUG was used.The radioactivity was retained on the filter at the end of the experiment.Which mRNA was used in this iteration of the experiment?
A) CAG
B) GAC
C) CTG
D) GTC
Q3) In the ER,prenylation can occur.Prenylation is the attachment of an isoprenoid group to a __________ residue via a(n)__________.
A) lysine; amide
B) cysteine; thioester
C) threonine; ester
D) serine; ester
Q4) How was the selectivity of the nitrocellulose filter essential in the Nirenberg-Leder experiment,which was able to assign triplet codons to specific amino acids?
Q5) Explain what is meant by the statement,"The genetic code is universal."
Page 24
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Chapter 23: Gene Regulation
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Q1) iPS cells can be defined as __________ cells.
A) differentiated
B) dedifferentiated
C) embryonic stem
D) somatic stem
Q2) Compare the two mechanisms used for control of the trp operon.
Q3) Bromodomain-containing complexes bind to __________ lysines in histones.
A) methylated
B) acetylated
C) brominated
D) chlorinated
Q4) What are the two main approaches being considered for treatment using iPS cell technology?
Q5) Explain the expression of the Drosophila even-skipped gene.
Q6) Name the key elements of the lac operon.
Q7) Draw the four combinations of nucleotides and label the major groove in each as either an H-bond donor,an H-bond acceptor,or hydrophobic.
Q8) How does entropy drive protein-DNA complex formations?
Page 25
Q9) How can the lac promoter and IPTG be used to produce large amounts of a specific protein?
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