Molecular Biology Problem Set Answers

Molecular Biology Problem Set Answers

ATP is an important molecule in metabolism because

  • It is readily obtained from an organism’s environment


  • It is extremely stable
  • It contains valuable nutrients
  • It has high-energy phosphate bonds
  • Its phosphate bonds are very easily formed but not easily broken


All of the following processes involve hydrogen bonding except:

  1. DNA replication
  2. Formation of ice crystals


  1. Binding of enzyme and substrate
  2. Protein folding
  3. All of the above


In Pompe’s disease, the liver is damaged due to the accumulation of glycogen. What organelle is most


likely malfunctioning?

  1. endoplasmic reticulum


  1. golgi apparatus
  2. lysosome
  3. nucleus
  4. vacuole


Transport of which nutrient across the intestinal epithelium is by passive diffusion?

  1. alanine
  2. fructose


  1. glucose
  2. glutamine
  3. all of the above



Listed are three statements about lipids.

  1. Lipids are made up of polymers of fatty acids
  2. Lipids are hydrophobic


  1. Lipids that are made up of fatty acids with a high degree of saturation are more likely to be solids at room temperature


Choose the most accurate statement from below: A. Statements 1 and 2 are true


  1. Statements 1 and 3 are true
  2. Statements 2 and 3 are true D. Only statement 2 is true


  1. All three statements are true


Of the cellular compartments listed below, which has the lowest pH?

  1. Mitochondrial matrix
  2. Endoplasmic reticulum
  3. Lysosome
  4. Cytoplasm
  5. Nucleus



Terminally differentiated cells are most often found in which phase of the cell cycle?

  1. G0
  2. G1
  3. G2


  1. M
  2. S


A mutation in the gene encoding cyclin D:

  1. may cause the production of a mutated protein
  2. may cause the production of a non-mutated protein
  3. may prevent transcription of the cyclin D gene
  4. A and B only


  1. A, B or C


The velocity of carrier-mediated diffusion across cellular membranes:

  1. can increase up to a maximum value
  2. is always proportional to substrate concentration
  3. is greater in uniporters than symporters
  4. does not depend on saturation of the carrier
  5. varies with substrate concentration in the same way as that observed for simple diffusion



What is the concentration of hydrogen ions at pOH 8.3? (You do NOT need a calculator.)


  1. 0 x 10-5 M H+
  2. 0 x 10-6 M H+
  3. 0 x 10-5 M H+
  4. 0 x 10-6 M H+
  5. 0 x 10-5 M H+


An amphipathic molecule is a molecule that has

  • 2 different forms that are mirror images of each other
  • An amino group
  • A hydrophilic end and a hydrophobic end
  • A positively charged end and a negatively charged end


The quaternary structure of a protein is determined by


  • Interactions between distant amino acids of the same polypeptide
  • Interactions between close amino acids of the same polypeptide
  • Interactions between amino acids of different polypeptide chains
  • The arrangement of the alpha helices and beta sheets in the protein
  • Binding of a coenzyme or cofactor to the protein
















The molecular weight of fumarate is 160.0. How many grams of fumarate are there in 200 mL of a 0.1 M fumarate solution?


  1. 0.32 grams
  2. 3.20 grams
  3. 8.00 grams
  4. 80.00 grams
  5. 3.20 kg


Replacement of a lysine with a glycine in a protein could result in all of the following EXCEPT:

  1. a change in the quaternary structure of the protein


  1. a change in the secondary structure of the protein
  2. a loss of catalytic activity of the protein
  3. a loss of a negatively charged side chain
  4. a loss of the protein’s ability to interact with other proteins


A strain of bacteria living in a hospital is found to have a plasmid containing two genes: one for sex pilus construction, and one for tetracycline resistance. If these bacteria were to undergo conjugation with bacteria lacking this plasmid, and thereby transferred the plasmid to the other bacteria, the most likely result would be:


  1. a genetically identical clone of bacteria containing the same plasmid.
  2. a possible spread of tetracycline resistance to other bacteria in the hospital.
  3. the subsequent loss of tetracycline resistance in the initially resistant strain.
  4. production of endospores in the bacterial progeny.
  5. temporary tetraploidy of the conjugating bacteria.



The function of a molecular chaperone is to

  • Act as an energy source during the polymerization of amino acids into a polypeptide
  • Act as a carrier molecule and bring “activated” monomers to a polymer for incorporation
  • Bind to specific structures on the polypeptide in order to assist the folding of a protein into its correct threedimensional



  • Unfold proteins with the incorrect three-dimensional shape and refold them into the proper shape


  • Transport rRNA from the nucleus to the cytoplasm



Ethidium Bromide is used in electrophoresis of DNA fragments because:

  • It makes the fragments visible under UV light
  • It makes the DNA fragments more mobile in the gel
  • It increases the conductivity of electricity through the gel
  • It helps determine the size of the fragments


  • It maintains a stable pH


Suppose the lac repressor of E. coli is mutated so that it never binds to the operator. Which of the following is true?


  • Glucose digesting enzymes are never produced
  • Lactose digesting enzymes are never produced
  • Lactose digesting enzymes are always produced
  • The result depends on the concentration of glucose



[e] The result depends on the concentration of lactose





Tobacco mosaic virus has RNA rather than DNA as its genetic material. If the RNA genome from a tobacco mosaic virus is mixed with proteins from a human rhinovirus, the result is a mixed virus. If that virus could infect a cell and reproduce, what would you expect the resulting viruses to be like?

  • A hybrid including genetic material from tobacco mosaic virus and proteins from the rhinovirus
  • A hybrid including proteins from tobacco mosaic virus and genetic material from the rhinovirus
  • Rhinovirus
  • Tobacco mosaic virus
  • No viruses would result because no viral DNA was present


A protein is usually tagged for degradation by proteasome activity by which of the following proteins?


  • Caspase
  • Kinase
  • Protease
  • Ubiquinone
  • Ubiquitin


Insulin injected by diabetics to control blood sugar levels is derived from bacteria whose DNA has been modified by the addition of the human gene for insulin, which is then produced by the prokaryotes. This is an example of:


  1. acid therapy
  2. cloning
  3. genetic engineering
  4. gene therapy
  5. pluripotency


Isolated RNA molecules are generally less stable than DNA at physiological pH because:

  1. RNA has ribose
  2. RNU is always linear
  3. RNA has U instead of T
  4. RNA is usually single stranded
  5. there are many more RNAse enzymes


Which of the following would act as an “uncoupler” of electron transport and ATP synthesis in the mitochondrion?


  1. NH4Cl
  2. Urea
  3. The F0 base piece of the ATP synthase (without the F1 subunit)
  4. All of the above
  5. A and C only



If the rate constant of a first order reaction that converts substrate S into product P is


0.693 min-1 then what is the half life of the reaction?


  1. 0.346 min



  1. 0.693 min
  2. 1.000 min
  3. 1.440 min


Suppose a plant cell had a mutation that prevented the Golgi apparatus from functioning. Which of the following processes would not occur in the cell?


  1. Cellular respiration
  2. Photosynthesis
  3. DNA replication
  4. Mitosis
  5. Cell wall formation



The local swimming pool is contaminated with an organism that is causing “swimmers itch.” You think you have identified cyanobacteria in your sample. Which features would you expect this organism to LACK?


  1. chlorophyll
  2. cell membrane
  3. differentiated cell types such as spores, vegetative cells, and heterocysts
  4. nucleoid


  1. nucleolus


Suppose radioactive thymine was added to an actively dividing culture of E.coli bacteria. What would happen if a cell replicated once in the presence of this radioactive base?


  1. one of the daughter cells, but not the other, would have radioactive DNA B. neither of the two daughter cells would be radioactive C. all four bases of the DNA would be radioactive


  1. radioactive thymine would pair with nonradioactive guanine


  1. DNA in both daughter cells would be radioactive



Which of the following molecules is able to cross the lipid bilayer?

  1. antibodies
  2. ATP
  3. insulin
  4. Na+


  1. steroid hormones

Amino acids and nucleotides form complex polymers. Select ALL the statements that are TRUE (Select all that apply).


  1. Both contain peptide bonds
  2. Both contain nitrogen
  3. Both may form helical structures
  4. Nucleotides and amino acids form branched polymers


  1. Both contain phosphate groups


You extract RNA from liver cells and then carry out an agarose gel electrophoresis of the liver RNA. The RNA fragments are then transferred to an RNA-binding membrane (nitrocellulose or nylon) using capillary action. Next, you hybridize a probe for gene X to the RNA on the membrane. Which of the following statements regarding your experiment is true?


  • You are trying to determine how many copies of Gene X are in liver cells
  • You are trying to determine if the Gene X protein is present in liver cells



  • You are trying to determine if Gene X is expressed in liver cells
  • You are trying to determine the chromosomal location of Gene X
  • You are trying to determine whether Gene X has a mutant sequence


Which of the following would be most effective for sequencing the exact 5’- end of an mRNA transcript?


  1. PCR
  2. Primer extension
  3. Cloning
  4. Southern blot
  5. Linkage mapping


A toxin exists that inhibits the enzyme succinate dehydrogenase. If this were used in an experiment to stop respiration, how many net NADH+ and ATP molecules would be generated from each glucose molecule up to that stage?


  • 4, 4
  • 4, 6
  • 4, 8
  • 6, 2
  • 6, 4


  • Mistyped answer choice, the correct answer should be 8,4


If radioactive sulfur (35S) is used in the culture medium of bacteria that harbor bacteriophage viruses, it will later appear in:

  1. bacterial RNA
  2. bacterial cell walls


  1. viral DNA
  2. viral RNA
  3. viral coats


Which of the following would probably be LEAST DAMAGED by a lipid-dissolving enzyme (lipase)?


  1. endoplasmic reticulum
  2. mitochondria


  1. ribosomes
  2. nuclei
  3. plasma membrane


Five events occur in a cell constituting a cause-and-effect sequence:

  1. an enzyme is manufactured at the ribosomes
  2. cellulose is deposited in a cell wall
  3. a molecule of RNA is transcribed


  1. a carbohydrate polymer is synthesized
  2. a nucleic acid migrates from nucleus to ribosome The order in which these events occur is:


  1. 1,3,5,4,2
  2. 2,1,4,5,3
  3. 3,5,1,4,2
  4. 4,2,1,3,5
  5. 5,3,4,1,2




The concentration of ions inside an amoeba is expressed below as ion-units per milliliter. The composition of the extracellular environment (ECE) is given for comparison. Assume the amoeba has been in the environment for some time.



Na+ K+ Cl- HCO3-
Amoeba 1 42 3 119
ECE 21 16 41 119


As the number of (+) and (-) ions in the amoeba and in the ECE are not equal, one might assume that:


  1. the amoeba and the ECE are very acidic
  2. the amoeba and the ECE are very basic


  1. either K+ or Na+ has a different valence


  1. a mistake in measurements had been made
  2. other ions are also involved


The differences in concentration of K+ and Na+ inside and outside of the amoeba indicate that:


  1. diffusion is not occurring
  2. energy has been increased
  3. energy has been expended
  4. osmosis has occurred


When bacterial cells multiply maximally during the logarithmic phase, the total number of cells (b) after some time interval (t) is equal to the original number of cells (B) multiplied by 2n, where n is the number of generations formed during the time interval: n = t/g and b = (B)(2n). The generation time (g) for type A cells is 28 minutes (assume no cell death).


Estimate the LEAST amount of time required for a population of type A cells to increase by 300 percent.


  1. approximately 42 minutes
  2. approximately 48 minutes
  3. approximately 52 minutes
  4. approximately 58 minutes


  1. more than 62 minutes


Researchers found that the arginine code AGG is poorly represented in genes of E.coli. Interestingly, they also found that this triplet, when present, binds to the ribosome 7-9 base pairs upstream from the starting ATG triplet (methionine). What does this information suggest in regard to the AGG codon?


  1. it is a codon rarely found in this bacterium
  2. it is conserved in most prokaroytic organisms


  1. it may have a regulatory function in the cell
  2. both B and C
  3. A, B and C









The strongest evidence for the endosymbiotic origin of eukaryotic organelles is the similarity between:


  1. eukaryotic and prokaryotic ribosomes
  2. prokaryotic and eukaryotic flagella


  1. prokaryotic and eukaryotic cell walls
  2. some prokaryotes and mitochondria
  3. some prokaryotes and ribosomes


The fluidity of a lipid bilayer is enhanced with:

  1. decreased temperature
  2. increased unsaturation in fatty acid tails
  3. increased unsaturation in polar head groups


  1. increased saturation in fatty acid tails
  2. increased fatty acid chain length


Which of the following are NOT imbedded in the thylakoid membrane?

  1. Enzymes associated with carbon dioxide fixation
  2. Molecules of chlorophyll a and chlorophyll b
  3. P700 and P680 molecules
  4. Proton channels of the ATP synthase


  1. Ferredoxin-NADP+


In the actual USABO exams, E may also be accepted, but A must be marked.


Which of the following fibers binds to the cytoplasmic site of the cell-matrix adherens junctions?

  1. Elastin
  2. Actin
  3. Tubulin


  1. Reticular
  2. Collagen


Which of the following statements about the energy yield of aerobic respiration is NOT true? A. Less than 50% of the chemical energy stored in glucose is converted to ATP.


  1. Glycolysis and pyruvate oxidation together provide more NADH per glucose molecule than does the Krebs cycle.


  1. Each pair of electrons donated by an FADH2 or NADH molecule during electron transport results in the synthesis of more than one molecule of ATP.
  2. ATP is needed to transport NADH produced during glycolysis into the mitochondria.
  3. Most of the ATP derived during aerobic respiration results from the utilization of an electrochemical gradient.


















In the transcription of DNA to RNA the nitrogenous base cytosine will pair with: (note: the answers A, B, C, D, E are listed in columns.)




















C is the correct answer.



























Which of the following is NOT a second messenger?

[a] Calcium ion

[b] Magnesium ion

  • Diacyl glycerol


  • Inositol trisphosphate (IP3)
  • Cyclic AMP


Hemoglobin, an iron-containing protein in erythrocytes, binds oxygen molecules. Myoglobin, a protein in muscle cells, is used for oxygen storage. What can be deduced about the relative oxygen affinities of hemoglobin and myoglobin?


  • Myoglobin has greater oxygen affinity than hemoglobin
  • Hemoglobin has greater oxygen affinity than myoglobin


  • Both have roughly the same oxygen affinity
  • Neither has a significant oxygen affinity


A spectrophotometer is used to measure concentrations of proteins, DNA and many other chemical compounds. Assume the input light intensity at a particular wavelength λ is I0, and the intensity of the light transmitted through the second cuvette is I1. If the concentration is doubled which of the following statements are TRUE.














  1. The percent transmission of the first sample will be two times greater than the second sample
  2. The absorbance, Aλ, of the second sample will be twice the absorbance of the first sample
  3. The increase in concentration will shift the wavelength of maximum absorbance to a longer wavelength
  4. The percent transmission of the second sample will be twice the first sample
  5. There is insufficient information to determine the correct answer


A variety of different techniques are used to separate, analyze, and purify different chemical compounds. Select ALL of the following techniques that can be used to estimate the molecular weight of a protein? (Select all that apply)



  1. Isoelectric focusing.
  2. Size exclusion gel chromatography.


  1. Ion-exchange chromatography.
  2. Affinity chromatography.











Both amino acids and nucleotides form complex chains. Select all the answers below that are accurate.


  1. The chains formed by both have polar phosphate groups.
  2. Both contain peptide bonds.
  3. Both contain nitrogen.
  4. The chains formed by both can be lysed by trypsin.
  5. The sequence of chains both form from preexisting templates.




Which of the following is NOT an accurate description of protein synthesis and folding? A. All protein synthesis is initiated in the cytoplasm.


  1. Many copies of a protein can be synthesized simultaneously from the same mRNA.
  2. The 3D shape of a protein is determined largely by its amino acid sequence.
  3. The entire chain of amino acids exits the ribosome before it begins folding into its 3D shape.
  4. The first encoded amino acid in every protein is methionine.



Which of the following carbohydrates contain α-1, 4-linkages?


  1. amylose
  2. Cellulose
  3. Deoxyarabinose
  4. Glucose
  5. Hexose


Which of the following would act as an “uncoupler” of electron transport and ATP synthesis in the mitochondrion?


  1. dinitrophenol
  2. urea
  3. the F0 base piece of the ATP synthase (without the F1 subunit)
  4. all of the above
  5. A and C only



Using accelerator mass spectrometry, the 14C atoms in a 2 mg bone fragment were directly counted and found to be 1/8 of those that would be present in a 2 mg bone fragment in 1950. What is the approximate age of this specimen? The half-life of 14C is 5,730 years.


  1. 1,540 years BP (before present)
  2. 5,730 years BP
  3. 17,190 years BP
  4. 22,920 years BP


  1. 45,840 years BP










The membrane potential across a cell membrane is determined by the relative permeabilities and concentration gradients of electrolytes across its cell membrane. The intracellular/extracellular concentration of sodium ions is 14 mM/140 mM.


The intracellular/extracellular concentration of potassium ions is 120 mM / 4 mM.


The chemical potential or equilibrium potential = (RT/zF) ln ([x]o/[x]i).

Given the gas constant, R = 8.31 JK-1mol-1, the temperature, T, needs to be in Kelvin, °K.

The Faraday constant, F = 9.65 coulombs mol-1m, and z is the valency of the cation or ion.

At 25°C, the ___________________ equals +58 mVs.

  1. calcium equilibrium potential
  2. chloride equilibrium potential
  3. membrane potential
  4. potassium equilibrium potential


  1. sodium equilibrium potential


Sunflower chromosomes have been isolated and their DNA/NT analyzed. It was found that chromosome 2 has unusually high content of Adenine (40%). How many percent of Guanine is present in chromosome 2?


  1. 10%
  2. 20%
  3. 30%


  1. 40 %
  2. 50%


Assume that the entire sequence of the chromosome is transcribed. Which of the following is true for the content of Adenine in the transcribed RNA?


  1. Adenine is 40% of the RNA.
  2. Adenine is 20% of the RNA.
  3. Adenine is at least 20% of the RNA.


  1. Adenine is at least 40% of the RNA.
  2. The content of Adenine is not possible to determine based on the information provided.


A strain of bacteria living in a hospital is found to have a plasmid containing two genes: one for sex pilus construction, and one for tetracycline resistance. If these bacteria were to undergo conjugation with bacteria lacking this plasmid, and thus transferred the plasmid to the other bacteria, the most likely result would be:


  1. a genetically identical clone of bacteria containing the same plasmid


  1. rapid spread of tetracycline resistance to other bacteria in the hospital
  2. the subsequent loss of tetracycline resistance in the initially resistant strain
  3. production of endospores in the bacterial progeny
  4. temporary diploidy of the conjugating bacteria



Why can glycolysis proceed under anaerobic or aerobic conditions while the citric acid cycle only proceeds under aerobic conditions?


  1. Oxygen is a byproduct of the conversion of the glycolytic intermediate glucose-6-phosphate to fructose-6-phosphate.


  1. Enzymes of glycolysis do not use oxygen as cofactors, while enzymes of the citric acid cycle require oxygen for proper folding.


  1. Enzyme catalysis during the citric acid cycle is regulated by allosteric effectors, which include oxygen.
  2. NAD+ is produced during three steps of glycolysis and only one step of the citric acid cycle.
  3. Under anaerobic conditions, NAD+ (for glycolysis) can be regenerated through the conversion of pyruvate into lactate.





If a strand of coding DNA has the following nucleotide sequence —ATTCGCTAGACC — what will be the nucleotide sequence of micro RNA (miRNA) be?


  5. None of the above




Use the pathway for the next two questions. Many metabolic pathways involve multi -step reactions. Consider the following pathway, where E represents different enzymes, and A, B, C, D and F represent substrates and products of the pathway.


E1    E2   E3    E4




Feedback inhibition of this pathway may involve

  1. The product of the final reaction, F, interacting with and inhibiting E1
  2. F interacting with and inhibiting product B
  3. Product B interacting with and inhibiting E4
  4. Product C interacting with and inhibiting E4
  5. E3 interacting with and inhibiting E2


In the example above, assume that D is an allosteric inhibitor of the enzyme E2. D would


  1. Compete with B for binding to the E2 active site
  2. Compete with F for binding with E2
  3. Bind directly to the substrate B and prevent it from entering the E2 active site
  4. Bind E2 at a site different from the active site but change the shape of the active site so B can no longer bind


  1. Bind E2 at the active site, change its shape and prevent B from binding the active site


The primary energy source of the brain is


  1. L-serine.


Glycogenesis and glycogenolysis are controlled primarily by two hormones.

  1. Fructose kinase and glucose hydrolyase
  2. Glucagon and glucose hydrolyase
  3. Glycogen synthetase and insulin
  4. Insulin and glucagon
  5. Pentose kinase and insulin






Eukaryotic transcription seems to be a wasteful process because so many proteins need to assemble on a large array of DNA sequences to initiate transcription. What might be the evolutionary advantage that allows such a complex process to be maintained throughout all eukaryotic organisms?


  1. Since eukaryotes are larger than prokaryotes, you need a larger transcription process for initiation.


  1. There are more genes that need to be transcribed in a eukaryote than in a prokaryote.


  1. The use of large number of proteins and regulatory sequences in DNA is essential for alternative splicing in eukaryotes.


  1. The use of large numbers of proteins and regulatory sequences in DNA opens many possibilities for sophisticated gene regulation by eukaryotes.


  1. Since transcription happens in the cytoplasm, you need so many proteins to prevent it from being broken up.


The chemical EDTA is routinely used in many experiments. For example, EDTA is used in electrophoresis buffer solutions. Which of the following statements is not true?


  1. EDTA has a strong binding affinity for divalent and some trivalent cations.


  1. EDTA is a catalyst for polymer formation and essential for protein and nucleic acid polymerization.


  1. EDTA is a chelator.


  1. EDTA is used to help denature proteins and weaken cell membranes.


  1. EDTA protects DNA from restriction enzymes by removing magnesium ions from the solution.



Positive cooperativity is an emergent property of what type of enzymatic regulatory mechanism? A. Allosteric interactions.


  1. Cellular compartmentalization.


  1. Genetic regulatory mechanisms.


  1. Second messenger systems.


  1. None of the above.



Select ALL of the following associations that are accurate.

  1. Tryptophan, tyrosine and phenylalanine – aromatic amino acids which absorb UV light.
  2. L-Isoleucine – most hydrophobic.
  3. L-Histidine – side chain can shift pKs, at physiologic pH can act as either an acid or a base.
  4. L-Lysine -amphipathic
  5. L-Proline is known as an “a-helix breaker” and is found in tight turns.


All of the above statements are indeed true.


Select ALL statements that are true concerning the Photosynthesis Reaction Center (Photosystem II)?


  1. The Photosynthesis Reaction Center contains chlorophyll and sometimes Fe-heme groups.


  1. It is a globular protein found in the cytoplasm where it acts as an antenna protein.
  2. It oxidizes carbon dioxide and produces H2O.


  1. It transfers high-energy electrons to an acceptor nearby in the thylakoid membrane.
  2. The Photosynthesis Reaction Center is usually a heterotetramer, but may be a heterotrimer in some species of cyanobacteria.





Rank the following biological molecules in order of how readily they diffuse across the plasma membrane from the most diffusible to the least diffusible.


  1. CO2 II. Cl-

III. Sucrose IV. Glycerol A. I, III, IV, II B. II, IV, III, I C. III,II, IV, I


  1. I, IV, III, II E. II, I, III, IV


Ciprofloxacin is an antibiotic frequently prescribed for traveler’s diarrhea and urinary tract E. coli infections. It acts by binding to and interfering with bacterial topoisomerases. Which of the following is the most accurate explanation of ciprofloxacin’s mechanism of action?


  1. Ciprofloxacin prevents the unwinding of double-stranded DNA and thus both DNA transcription and replication.


  1. Ciprofloxacin prevents the relief of supercoiling caused by unwinding of double-stranded DNA and thus DNA replication.


  1. Ciprofloxacin prevents the conversion of RNA primers to DNA and thus accurate DNA replication.


  1. Ciprofloxacin prevents replication of the lagging strand.


  1. Ciprofloxacin prevents the binding of DNA polymerases to DNA and thus both DNA transcription and replication.


Due to the widespread use of ciprofloxacin, many bacterial populations are now resistant to ciprofloxacin. You are studying a ciprofloxacin-resistant clinical isolate of E. coli. You have a hunch that this population does not harbor any plasmids. Given this information, which of the following best explains your isolate’s resistance mechanism?


  1. Your resistant bacteria pump ciprofloxacin out of the cell and thus minimize its effect.


  1. Your resistant bacteria produce an enzyme that modifies the binding site of ciprofloxacin.


  1. Your resistant bacteria have mutant topoisomerases that have less affinity for ciprofloxacin.


  1. Your resistant bacteria produce a chemical compound that reacts with ciprofloxacin and reduces its affinity for topoisomerases.


  1. Your resistant bacteria do not require the activity of topoisomerases


All amino acids except lysine and leucine can be broken down into precursors for gluconeogenesis. What are the products produced by the breakdown of lysine and leucine that prevent them from functioning in that pathway?


  1. Oxaloacetate and acetyl-CoA


  1. Pyruvate and succinate


  1. Acetyl-CoA and acetoacetate
  2. Succinyl-CoA and acetoacetate


  1. Acetaldehyde and pyruvate


Pollen grains were treated with colchicine in culture. The resulting plants were

  1. No more than large calluses
  2. Dihaploid and fertile
  3. Dihaploid and sterile
  4. Haploid and sterile



  1. Haploid and fertile


The presence of which of the following amino acids in the channel region of aquaporins contributes to the electrostatic selectivity to allow water, but not other molecules, to pass through?


  1. Valine
  2. Tryptophan
  3. Asparagine
  4. Methionine
  5. Leucine


Select the chemical property that is shared by all types of lipids forming the plasma membrane. A. Polar head

  1. Sugar component
  2. Glycerol backbone
  3. Phosphate group
  4. Hydrophobic region


The following photograph shows filamentous growth of a kind of cyanobacteria, Nostoc sp. The bacteria form heterocysts (thick-walled cells), when nitrogen sources such as ammonia or nitrates are deficient in the environment.















Which of the following statements describing these heterocysts is/are true?

  1. Nitrogen is fixed in the heterocyst.
  2. Photosystem I does not function in the heterocyst.

III. Photosystem II does not function in the heterocyst.



  1. Only I


  1. Only II
  2. Only I and II
  3. Only I and III
  4. Only II and III


When a mammal ingests a carbohydrate-rich meal after a long fast, the metabolic behavior of its hepatocytes undergoes many changes. Which of the following responses would not occur after a large influx of glucose?


  1. Dephosphorylation and activation of PFK-2


  1. Increased glucokinase activity


  1. Glycogen phosphorylase R → T transition


  1. Decreased phosphoglucomutase activity



  1. Rise in concentration of NADPH


The mitochondrion has more than three stop codons. Which biological principle does this violate? A. Central dogma


  1. Endosymbiotic theory


  1. Conservation DNA replication


  1. Complementary base-pairing


  1. Universal genetic code


A1. Endorphin is a natural analgesic secreted by the pituitary gland. Upon binding to its receptor in brain cells, endorphin can relieve pain and create a sense of euphoria. Morphine can achieve similar pain relief effects by binding to the endorphin receptor. Why do both endorphin and morphine bind to the endorphin receptors in brain cells?


  • Sizes of both molecules are similar.
  • Molecular weights of both molecules are similar.


  • Both are isomers.
  • Shapes of both molecules are similar.
  • Net charges of both molecules are identical.



Most biological macromolecules are made by the polymerization of small principal components. The major structural polysaccharide of the insect exoskeleton is a polymer. Which of the following statements regarding this kind of polysaccharide is NOT correct?


  • It is made by polymerization of glucose.
  • It contains C, H, O and N atoms.
  • Its structure is similar to that of cellulose.
  • It can be used to produce chitosan and glucosamine in industry.


  • This polymer can also been found in the cell wall of fungi.


In some cells, synthesis of isoleucine from threonine is catalyzed by the sequential action of five enzymes a, b, c, d and e which produce 4 intermediates A, B, C, D, and the end product isoleucine, respectively. What is most likely to happen when isoleucine is overproduced and there is an ample supply of threonine in cells?


  • Isoleucine associates with threonine to inhibit the activity of enzyme a.
  • Isoleucine associates with intermediate D to inhibit the activity of enzyme e.
  • Isoleucine binds to enzyme a and inhibits its activity.
  • Isoleucine binds to enzyme e and inhibits its activity.
  • Threonine is converted into isoleucine continuously through the 5 enzymes.


In some prokaryotic organisms, SO42- is used as the final electron receptor at the end of electron transport chain during cellular respiration. Which of the following statements regarding cellular respiration in these prokaryotic organisms is NOT correct?

  • It is anaerobic respiration.
  • The reception of electron by SO42- is accompanied by the production of H2O.
  • Operation of the electron transport chain builds up a proton motive force.
  • ATP can be produced.
  • Production of ATP is correlated with the mobility of H+.










Three stages in bacteria growth are:

  1. Lag phase


  1. Log phase

III. Stationary phase

In which phase or phases can penicillin inhibit the synthesis of the bacterial cell wall?

  • Only I
  • Only II
  • Only III
  • Only I and II
  • Only I and III


  • I, II and II


Which structural or physiological feature of bacteria can be used as a target for developing drugs to kill bacteria effectively but with no harm to human cells?


  • Glycolysis
  • Components of plasma membrane


  • Components of ribosome
  • Components of the electron transport chain in aerobic respiration
  • Requirement of oxygen



Histones are small basic proteins that assemble with DNA molecules to form chromosomes. There are five histones, including H1, H2A, H2B, H3 and H4, in eukaryotic cells. Which of the following structural features of chromosomes is associated with Histone H1?

  • Telomere
  • Nucleosome fiber (10-nm fiber)
  • 30-nm fiber


  • Looped domains
  • Centromere



DNA is a double helix molecule containing four different types of nitrogen bases. Which of the following statements regarding both the replication and chemical composition of DNA is correct?


  • Base sequences of both strands are the same.
  • The amount of purine is equal to that of pyrimidine in a double-stranded DNA.
  • Both strands are synthesized continuously in 5’→3’ direction.
  • The first base of the newly synthesized DNA is catalyzed by DNA polymerase.
  • The proof-reading activity of DNA polymerase proceeds in the 5’→3’ direction.



Miss Ling-Ling conducts DNA synthesis and transcription reactions in two separate test tubes. Which of the following substances needs to be added to both reactions?


  • ATP
  • DNA template
  • RNA primer
  • DNA polymerase
  • DNA ligase







The Nobel Prize in Physiology or Medicine 2009 was awarded jointly to Blackburn, Greider and Szostak for the discovery that chromosomes are protected by telomeres and the enzyme telomerase is highly correlated with aging and cancer in animals. Which of the following statements regarding telomere and telomerase is correct?


  • Telomerase is a DNA exonuclease.
  • Telomerase is an RNA polymerase.
  • Embryonic cells possess long telomeres and high telomerase activity.
  • Telomeres are longer and telomerase is inactive in cancer cells.


  • Telomeres are longer and telomerase is highly active in somatic cells.



EcoRI restriction enzyme is a DNA endonuclease that can recognize the sequence GAATTC. It was first discovered in E. coli, therefore it was named EcoRI. To produce a large quantity of the endonuclease, the DNA fragment encoding the gene was subcloned into an expression plasmid and the resultant recombinant plasmid was transformed into E. coli cells to produce recombinant enzyme for a study. Why is the host DNA not cleaved by the recombinant EcoRI?


  • The host DNA does not contain EcoRI cleavage sites.
  • EcoRI is secreted out of the host cells.


  • Environmental factors such as temperature and pH value inhibit EcoRI activity.
  • The coli host produces inhibitors to block EcoRI activity.
  • The EcoRI cleavage sites within the host DNA are modified.


Which of the following structures and processes can exist in eukaryotic cells and in all prokaryotic cells?


  1. Nuclear envelope


  1. Ribosomes III. Introns
  2. ATP synthesis V. rRNA 18S


  1. Cell membrane VII. DNA polymerase VIII. Cytoskeletal elements


  1. I, II, III and VIII


  1. II, IV, VI and VIII
  2. I, III, V and VII


  1. II, IV, V and VI


  1. II, III, VI and VIII



Comparing the effect of an inhibitor with an uncoupler of oxidative phosphorylation, the:

  1. inhibitor would allow electrons to pass through the electron transport chain


  1. inhibitor would increase the pumping of protons by the electron transport chain C. uncoupler would increase heat production by the mitochondria


  1. uncoupler would inhibit the reduction of oxygen by the electron transport chain E. uncoupler would stop the oxidation of NADH by the electron transport chain



A yeast extract contains all the enzymes required for alcohol production. The extract is incubated under anaerobic conditions in 1 liter of media containing: 200 mM glucose, 20 mM ADP, 40 mM ATP, 2 mM NADH, 2 mM NAD+ and 20 mM Pi (inorganic phosphates). What is the maximum amount of ethanol that can be produced in these conditions?


  • 2 mM
  1. 20 mM C. 40 mM D. 200 mM E. 400 mM


Three different genes (B, D, and W) are found on a small region of chromosome 1. Each gene has two alleles. In order to determine the recombination frequency between these three genes, sperm were isolated from a male heterozygous for all three genes. The male had all dominant alleles on his maternal copy of chromosome 1, but only recessive alleles on his paternal copy of chromosome 1. Each sperm was isolated individually and PCR amplified in the BDW region. The amplified products were spotted on a nitrocellulose membrane and radioactive allele specific probes were hybridized with the samples. The resulting audioradiograph is shown below where a dark spot indicates successful hybridization of the probe with the membrane.






















What is the recombination frequency between B and W?

  1. 1:2


  1. 1:3


  1. 1:4


  1. 5:6


  1. 1:1



The function of an electron in the electron transport chain is to:

  1. transfer energy from complex II to complex I.
  2. pump hydrogen ions using complex II.
  3. use its free energy to pump protons against the concentration gradient.


  1. combine with phosphate when ATP is synthesized.
  2. react with ATP synthase.





Fatigue in iron deficiency anemia may be explained in part by all of the following EXCEPT:

  1. a lack of functional hemoglobin in the blood.
  2. an inability to transport oxygen.
  3. a lack of functional cytochromes in the electron transport chain.
  4. the inability to synthesize ATP.
  5. a lack of functional Coenzyme Q.


Concerning the generation of ATP by oxidative phosphorylation, all of the following are true


  1. NADH produced in the cytosol of the cell will generate approximately 2.5 ATPs.
  2. NADH produced in the mitochondria will generate approximately 2.5 ATPs.
  3. NADH produced by the succinate thiokinase reaction will generate approximately 1.5 GTPs.
  4. FADH2 produced in the mitochondria will generate approximately 1.5 ATPs.
  5. acetyl CoA entering the TCA cycle will produce approximately 10 ATPs.


Some pathogens produce exotoxins that can cause human diseases. One type of exotoxins consists of two polypeptides, subunits A and B. Subunit B can bind to surface receptors on the target cells and cause the transport of the subunit A or associated molecules across the plasma membrane into the cell. Once the subunit A enters the cell, it inhibits protein synthesis and destroys the cells. Which of the following statements regarding exotoxins is/are correct?


  • Subunit A alone can cause disease.


  • Subunit B alone can bind to target cells.


  • Subunit A may carry other molecules to kill target cells.
  • Subunit B may carry other molecules and assist these molecules to enter target cells.


  • When conjugated with an antibody against breast cancer cells, subunit A can kill breast cancer cells.


B5. Tom isolated phagocytes from a blood sample. He cultured these phagocytes in a test tube for a period of time. To observe phagocytosis, E. coli was co-cultured with phagocytes. What will be the consequence if an antacid is added to the culture?


  • Phagocytes can ingest and kill E. coli.
  • Ingestion of E. coli by phagocytes is inhibited.
  • coli is viable in phagolysosome.


  • If phagolysosomes are formed, the digestive enzymes in them are inactive.


  • Phagocytes can secrete ingested debris out of the cells.



What enzyme does a retrovirus primarily rely on to create a copy of its genome that is ready for integration into the host genome?


  1. DNA gyrase
  2. RNA polymerase
  3. Reverse transcriptase


  1. DNA polymerase
  2. DNA helicase









Integral transmembrane proteins are proteins embedded in the cell membrane. Which of the following amino acids would you MOST expect to find in the transmembrane region of such proteins?


  1. Tryptophan


  1. Lysine
  2. Arginine


  1. Serine
  2. Glutamate


A gene regulatory protein X controls cell proliferation. Protein X is found in the cytosol and has

no typical nuclear localization signal (NLS). When cells are treated with a specific growth hormone, protein X re-localizes from the cytoplasm into the nucleus where it activates the transcription factors involved in cell proliferation.


Recently, a protein (Y) that interacts with protein X has been identified in unstimulated cells. To investigate the function of protein Y, a mutant lacking the gene encoding protein Y was generated. Fractionation of cells from the wild type and mutant produced membrane (M), cytoplasmic (C), and nuclear (N) fractions for each cell type. Proteins extracted from each fraction were separated by SDS-PAGE and analyzed by Western blotting for the presence of proteins X and Y.













On the basis of the results shown above, which of the following statements is the most plausible characterization of protein Y?


  1. In the absence of growth hormone, protein Y associates with protein X, and the X/Y complex is subjected to a degradation pathway.


  1. In the presence of growth hormone, protein Y interacts with protein X, and the complex remains in the cytoplasm.
  2. Protein X interacts with protein Y in the absence of growth hormone. Upon growth hormone treatment, protein X is released from protein Y and re-localizes to the nucleus.
  3. Protein Y is a membrane-associated protein and re-localizes with protein X to the nucleus upon the growth hormone treatment.


  1. Protein Y is one of the nuclear import proteins and the growth hormone does not induceprotein Y to translocate protein X to the nucleus.


The expansion of plant cells occurs differently from that of animal cells. The primary reason for this difference is associated with:


  1. the presence of a central vacuole in a plant cell.


  1. the presence of a cell wall in plant cells.


  1. a difference in protein synthesis in plant cells.
  2. the absence of golgi apparati in plant cells.
  3. a difference in microtubular organization in plant cells.




One reason phospholipids are well suited to be the main structural component of membranes is:

  1. they are completely insoluble in water.
  2. they provide energy for transport through the membrane.


  1. they form a structure in which the hydrophobic portion faces outward.
  2. they form a single sheet in water.
  3. they form a selectively permeable structure.


Certain amino acids are considered essential in an animal’s diet because they cannot be produced within the organism. Which of the following cellular processes would be most DIRECTLY affected by a dietary deficiency in essential amino acids?


  1. Cell division


  1. Cellular respiration
  2. Translation of mRNA
  3. Replication of DNA
  4. Oxygen transport


Cancer is a collective disease associated with uncontrollable cell growth. Mutation in which of the following types of genes is LEAST likely to result in higher chances of developing cancer. A. Tumor necrosis factor gene


  1. Tumor suppressor gene
  2. Oncogene
  3. Proto-oncogene
  4. Anti-oncogene


Which of the following cell types would you expect to be abundant in ER and Golgi Bodies?

  1. Adipose cells
  2. Islet of Langerhans cells III. Plasma B cells


  1. Red blood cells


  1. I only


  1. III only
  2. I and II only
  3. II and III only


  1. I, II, III, and IV


A day in the sun will expose your skin to UV light. Which is not true about the resulting DNA damage/repair pathway?


  1. UV exposure will cause single bonded cross-linked thymine-thymine dimers which severely distort the phosphate backbone.


  1. UV exposure will cause double bonded perpendicular thymine-thymine dimers which kink the phosphate backbone.


  1. Photolyase will repair DNA damage by using energy from UV light to break open thymine dimers.
  2. During replication of damaged DNA, a single base pair deletion will be found on the newly synthesized DNA strand opposite to the thymine dimer site.










Which of the following interactions is most responsible for the structural stability of soluble globular proteins?


  1. Dipole-dipole interactions.
  2. Electrostatic interactions.
  3. Hydrogen bonds.


  1. The Hydrophobic Effect.
  2. Van der Waal force.


This is indeed the correct answer; the folding of all proteins is primarily determined by the hydrophobic effect.


For the next four questions use the data in the two diagrams below. You identify a mutant protein of transferrin. After purifying both mutant and wild-type proteins, you run two SDS PAGE gels loading equal amounts of protein. One gel is stained with Cerulean Blue, the other is blotted and hybridized with an antibody to transferrin.






























Mutant transferrin is _____ than wild-type transferrin. (1 point)

  1. longer
  2. shorter


What is the approximate molecular weight of mutant tranferrin? (2 points)

  1. About 180 KDa
  2. About 130 KDa
  3. About 300 KDa


  1. About 90 KDa
  2. Impossible to determine from the information provided.




The sample in lane 4 is called a _____ marker. (1 point)

  1. reference
  2. rate of diffusion


  1. molecular weight
  2. degree of polarity
  3. degree of bonding


Which of the following reasons most likely explains why the transferrin band in lane 2

is darker than the band in lane 3? (2 points)

  1. The mutant band in lane 3 is not transferrin.
  2. HRP binds more efficiently to wild-type transferrin than to mutant transferrin.


  1. Mutant transferrin has a similar, but not identical epitope to the primary antibody.
  2. You added too much HRP in lane 2.
  3. There is less mutant transferrin than wild-type transferrin.



You develop your western blot and see purple coloring covering the entirety of the nitrocellulose. Which step in the western blotting procedure probably was forgotten? Why? (2 points)


  1. Improper buffer used thus causing a secondary reaction that colored the nitrocellulose. B. Contamination during separation with SDS-PAGE by a purple-colored compound


  1. Milk proteins not added thus no protective coating formed over the nitrocellulose D. Primary antibodies not added thus the specific protein is not bound


  1. Secondary antibody-enzyme conjugate not added thus the primary antibody is not recognized.



Use the the following answers for the next question. A choice is used only once.

  1. neurons


  1. liver cells
  2. cardiac myocytes
  3. neutrophils
  4. sperm cell midpiece





In terms of interaction between function and structure, in which cells would you expect the greatest number/amount of:


rough endoplasmic reticulum-C


gap junctions-A







Which of the following is(are) part of RNA processing and synthesis? Select Acceptable (A) or

Unacceptable (B)

Polyadenylation -A

Transport to the nucleolus-A

Catalytic function of small nuclear RNA -A















Consider the following data for a green plant


Maximum photosynthesis rate @ 20 mg glucose/dm-2/hr-1 Glucose heat of combustion @ 686 Kc/mole


Glucose gram molecular weight = 180gm

How much energy (Kcal/m) could be made over a 12-hr lighted period by a green plant having a


total leaf surface area of 2000 dm-2?

  1. 183.2 Kc


  1. 1832 Kc
  2. 1524.4 Kc


  1. 916 Kc


  1. 9.16 Kc


There is a large difference in pH across the thylakoid membrane between the thylakoid compartment and the stroma. From the list given below, choose those that are appropriate in explaining the difference. (Choose A, B, C, or D) 3 points


  1. the transport of protons into the thylakoid compartment by the electron transfer system
    1. the transport of protons out of the thylakoid compartment into the stroma by the electron transfer system


  • protons splitting from water remaining in the thylakoid compartment


  1. protons splitting from water exiting the thylakoid compartment
  2. the removal of hydrogen from the stroma during the reduction of NADP to NADPH
  3. the retention of hydrogen in the stroma during the reduction of NADP to NADPH


  1. i, iv, and vi only


  1. ii, iv and vi only


  1. i, iv and v only


  1. i, iii and v only


Why is it necessary to store harvested fruits in ventilated packaging?


  1. Cells from harvested fruit need oxygen, because they are alive and still undergoing respiration.
  2. Cells from harvested fruit need oxygen, because they are alive and still undergoing fermentation.


  1. Cells from harvested fruit need atmospheric nitrogen, because they are alive and still synthesizing amino acids.


  1. Cells from harvested fruit need atmospheric nitrogen, because they are alive and still synthesizing nucleic acids.


  1. Cells from harvested fruit need atmospheric nitrogen, because they are alive and still undergoing respiration.





Photosynthesis is a process in which light energy is converted to chemical energy and used to produce organic compounds within the chloroplasts. It consists of two stages, the light reactions and the dark reactions. Which of the following processes would NOT occur if carbon dioxide was removed from a plant’s growth chamber?


  1. ATP energy forms from the conversion of light energy B. NADP+ is reduced to NADPH


  1. 5-carbon sugars, RuBP, is produced
  2. photons are absorbed by photosynthetic pigments


  1. oxygen is produced


How do polypeptides find their way from the site of synthesis on the cytoplasmic ribosome to the place of their destination in the peroxisome?


  1. Without signals


  1. By specific transport along the cytoskeleton


  1. By specific carboxy-terminal targeting signals
  2. By specific vesicular transport


  1. By transport within the ER


In the lab, you are running an SDS-PAGE, but you realize that you forgot to add DTT, a reducing agent, when you were loading the gel. Which amino acid residue will this affect?


  1. Cysteine
  2. Serine


  1. Glutamate


  1. Lysine


  1. Methionine


You are given an unknown organism to study. Upon examination, you find that it does not have a nuclear membrane or mitochondria, which structure(s) below would it possess?


  1. Chloroplast


  1. Endoplasmic reticulum


  1. Ribosomes
  2. Lysosome


  1. 9+2 Cilia



A human liver cell and a plant cell from the cortex of a root are placed in a beaker of distilled water. What will most likely occur?


  1. Both cells will be in osmotic balance with the water and neither will swell or shrink


  1. The liver cell will shrivel, while the plant cell will become flaccid and the plasma membrane will pull away from the cell wall


  1. The liver cell will shrivel, while the plant cell will become very turgid


  1. The plant cell will become flaccid and the plasma membrane will pull away from the cell wall, while the liver cell will swell and may even burst


  1. The plant cell will become very turgid, while the liver cell will swell and may even burst


The majority of proteins exist as homo-oligomers rather than hetero-oligomers. That is, their quaternary structure is composed of two or more identical polypeptides rather than two or more different polypeptides. Which of the following is not a reason that quaternary structures are homo-oligomers?


  1. Aggregation of identical subunits gives rise to symmetry and possible allosteric interactions.



  1. A slow post-translational process favors a quaternary structure with the homo-oligomers held together by covalent bonds.


  1. Homodimers may increase binding specificity and stability.


  1. Homo-oligomerization results in a genetic savings with lower energy demand.


  1. The presence of two identical catalytic subunits in a single protein may lower the activation energy of the reaction.








Some bacteria possess an additional mechanism to regulate the production of enzymes involved in tryptophan (Trp) biosynthesis. The (Trp) operon possesses, prior to the actual genes (trpA- E), a leader sequence (trpL), coding for a leader peptide. trpL contains two tryptophan codons next to each other.


At high tryptophan concentrations, the ribosome translates the mRNA of the leader peptide and stalls at its stop codon, thereby masking segment 2 of the mRNA and allowing segments 3 and 4 to form a stem loop. A stem loop followed by poly-U is a termination signal for the RNA polymerase (RNA pol), which falls off the DNA.


However, at low tryptophan concentrations, the ribosome gets stalled at the tryptophan codons allowing 2 and 3 to form a stem loop. The whole tryptophan operon can be transcribed by the RNA polymerase.


Indicate if each of the following statements is true or false.


  • The same regulation mechanism also works for nuclear genes in eukaryotes.


  • With reduced concentration of the aminoacyl-tRNA synthetase (attaches tryptophan to tRNATrp), transcription of the trpA-E genes will be inactivated at a lower tryptophan concentration.


  • After deletion of one of the two tryptophan codons in the gene coding for the leader peptide, transcription of the trpA-E genes will be inactivated at a lower tryptophan concentration.


  • In the case of a mutation destabilizing the stem loop 2-3, transcription of the trpA-E genes will be inactivated at a lower tryptophan concentration.








In a living organism, cells die either through apoptosis (programmed cell death) or necrosis (cells swell and burst).


Indicate if each of the following statements is true or false.


  • Apoptosis is induced in immature T-cells that recognize self-antigens.




  • Intestinal epithelial cells losing contact with the basal lamina undergo apoptosis.


  • Neural stem cells undergoing apoptosis expose on their surface a signal promoting phagocytosis.


  • Necrosis often induces an inflammatory immune response.












Some substances need to be transported (actively or passively) from their site of synthesis to the location where they are active.



Indicate for each of the following substances if they are transported from the cytoplasm to the nucleus.


  • tRNAs
  • Histone proteins


  • Nucleotides
  • ATP-synthase subunits




High levels of triglycerides in the bloodstream have been linked to higher risks of heart diseases. An agonist (activating molecule) S of receptor Y was observed to reduce the triglycerides levels.


How could one convincingly prove that the effect of S is mediated specifically via receptor Y?


  • Generate genetically modified mice which overexpress (more than physiological) receptor Y.


  • Generate genetically modified mice in which receptor Y is knocked out (deleted).


  • Treat the mice with an antagonist (inactivating molecule) specific for receptor Y.


  • Treat the mice with an antibody that sequesters (removing from circulation) S.





In genetic engineering, it is often desired to increase the yield of secreted proteins.




Indicate if each of the following strategies is expected to increase the yield in a mammalian cell.


  • Overexpression of chaperones (proteins assisting others to fold) present in the endoplasmatic reticulum.


  • Deletion of the genes coding for glycosylating enzymes present in the endoplasmatic reticulum.


  • Overexpression of proteins facilitating the fusion of secretory vesicles with the cell membrane.


  • Duplicating the gene encoding the desired protein.







Which of the following is the primary interaction accounting for the majority of proteins in aqueous solution?



  1. Salt bridges


  1. Hydrogen bonding


  1. Dipole-dipole


  1. Disulfide bonds


  1. Hydrophobic interactions – Hydrophobic interactions determine the structure of all proteins, including globular ones.


You are given four unlabeled samples of polysaccharides and told that each contains either

amylopectin, amylose, cellulose, or glycogen, (one of each). Given the following information, which

sample contains which type of polysaccharide?

Sample #1: Many 1-6 linkages of α-glucose monomers

Sample #2: Composed of β-glucose monomers

Sample #3: Many 1-4 linkages of α-glucose monomers


Sample #4: Some 1-6 linkages of α-glucose monomers

  1. #1 – amylose, #2 – cellulose, #3 – amylopectin, #4 – glycogen B. #1 – cellulose, #2 – glycogen, #3 – amylose, #4 – amylopectin


  1. #1 – amylopectin, #2 – cellulose, #3 – amylopectin, #4 – glycogen D. #1 – glycogen, #2 – amylopectin, #3 – cellulose, #4 – amylase
  2. #1 – glycogen, #2 – cellulose, #3 – amylose, #4 – amylopectin


Which of the following amino acids has an R-group that can “shuttle” hydrogen ions?

  1. Alanine


  1. Leucine


  1. Valine


  1. Histidine


  1. Isoleucine



You attempt to isolate two different subunits from a protein by running a denaturing protein gel electrophoresis. To your dismay, you only find one band on the gel that corresponds roughly to the total size of the protein. What did you most likely forget to add?


  1. an oxidizing agent



  1. a reducing agent


  1. loading dye


  1. polyacrylamide


  1. SDS, a detergent



In an experiment, mice were injected intravenously with uniformly


labeled [14C] – glucose. The molecules in the body where the 14C would be found are:


  1. essential amino acids and proteins.
  2. lipids and all vitamins.
  3. proteins and lipids.
  4. proteins and all vitamins



A given DNA sample has 60% purines. The source of this DNA is most likely to be:


  1. a eukaryotic cell.
  2. a bacterial cell.
  3. a bacteriophage with double-stranded DNA.
  4. a bacteriophage with single-stranded DNA.







Which of the primer pairs is the correct one to amplify the gene sequence below with PCR?










Equal concentrations of urea, ethyl urea, and dimethyl urea were

separately added to a suspension of red blood cells (RBC). The relative rates of diffusion of these molecules into RBCs will be:








  1. 1 > 2 > 3
  2. 1 > 2 = 3
  3. 3 > 2 > 1



  1. 3 = 2 > 1


























There are some rare organisms that do not have lipid bilayers, but instead have lipid monolayers. Which of these is a plausible structure for the lipids they use to make up their lipid monolayers?








































D is the correct answer, has


hydrophilic groups on both sides.












A highly mutated protein is isolated from a line of lab rats. A number of charged amino acids are shown to have been replaced by non-polar amino acids in its polypeptide sequence when compared to the wild-type protein. Which of the following changes in the protein might have occurred as a result?


  1. There is a greater amount of α-helix found in the mutated protein.


  1. The mutated protein does not fold at all because some of the charged amino acids that were replaced were very important to the shape of the wild-type protein.


III. The mutated protein has a very different quaternary structure compared to the wild-type.


  1. When inserted into a cell membrane, a smaller portion of the mutated protein is found inside the lipid bilayer.


  1. I only.


  1. III only.


  1. I and III only.


  1. I, II, and IV only.


  1. I, III, and IV only.


For a constant concentration of an enzyme, which of the following is true of a noncompetitive inhibitor?


  1. km is lowered; vmax remains constant
  2. km is increased; vmax remains constant
  3. km remains constant; vmax is lowered
  4. km remains constant; vmax is increased
  5. km remains constant; vmax remains constant


While preparing to teach an organic chemistry class, Professor Dacb has managed to mix up several beakers. He has taken samples from each beaker and enlisted your help in identifying them. Below are the results of a series of reagent tests.


Which of the following correctly matches each beaker to its possible contents?



Beaker Biuret Benedict’s Ninhydrin Iodine Sudan
1 Blue Blue Blue Orange Rather Pale
2 Blue Blue Pale yellow Red-orange Red-orange
3 Purple Blue Pale yellow Orange Rather pale
4 Blue Red Precipitate Pale yellow Orange-yellow Rather Pale
5 Blue Blue Pale yellow Orange Rather Pale


  1. 1: Gelatin, 2: Corn oil, 3: A solution of asparagine, 4: A solution of glucose, 5: A solution of sucrose


  1. 1: Gelatin, 2: Triglycerides, 3: A solution of asparagine, 4: A solution of sucrose, 5: A solution of glucose


  1. 1: A solution of asparagine, 2: Triglycerides, 3: Gelatin, 4: A solution of glucose, 5: A solution of sucrose
  2. 1: A solution of sucrose, 2: Corn oil, 3: A solution of glucose, 4: A solution of asparagine, 5:


  1. 1: A solution of glucose, 2: Triglycerides, 3: A solution of sucrose, 4: A solution of

asparagine, 5: Gelatin



































You have been hired as a consultant for a halitosis support group. Assume that stinky breath is an autosomal recessive disorder whose gene has been cloned and is expressed in the blood. You obtain blood samples from affected individuals and controls, and send them off to the lab for analysis. The results come back, with the diagnoses and raw data for each person but the autoradiographs have been mixed up. Many of your clients in the support group are scientists who want to see the raw data, so you have to figure out what goes with what. Assume that each halitosis patient is homozygous for one of four restriction endonucleases. The map shows



the location of each mutation, how the normal sequence is altered, and diagnostic probes and oligos used.

Use the above diagram the following 15 questions.


















Of the three tests above, one represents a Southern blot, one a Northern blot, and one a gel of the PCR products of a PCR reaction . Each has two specimens, one from a patient and one of control.




What is the allele detected in test result I?


  1. W
  2. X
  3. Y


What lane represents the patient in test result I?

  1. Left
  2. Right


What material is being analyzed in test result I?

  1. DNA
  2. RNA
  3. DNA and RNA
  4. Protein


What type of analysis is represented in test I?

  1. Northern


  1. Southern
  2. PCR gel


What probe(s) or primer(s) could have been used for the analysis of test result I?

  1. Probe J
  2. Probe K
  3. Primers A and C
  4. Primers A and B


  1. Primers B and C


What is the allele detected in test result II?

  1. W
  2. X



  1. Y


What lane represents the patient in test result II?

  1. Left


  1. Right


What type of analysis is represented in test II?

  1. Northern
  2. Southern
  3. PCR gel


What material is being analyzed in test result II?


  1. DNA
  2. RNA
  3. DNA and RNA
  4. Protein


What probe(s) or primer(s) could have been used for the analysis of test result I?

  1. Probe J
  2. Probe K


  1. Primers A and C
  2. Primers A and B
  3. Primers B and C


What is the allele detected in test result III?

  1. W
  2. X
  3. Y



  1. Left
  2. Right


What type of analysis is represented in test result III?

  1. Northern
  2. Southern


  1. PCR gel



  1. DNA
  2. RNA
  3. DNA and RNA
  4. Protein


What probe(s) or primer(s) could have been used for the analysis of test result III?

  1. Probe J
  2. Probe K
  3. Primers A and C
  4. Primers A and B
  5. Primers B and C


You perform a Western blot on two proteins of similar molecular weights (~50kDa) and find


only one band developed on your SDS-PAGE gel. How would you modify your assay to distinguish the two proteins?


  1. Use a lower concentration of acrylamide to raise the resolution of your gel
  2. Use a non-ionic detergent to denature your protein


  1. Focus your sample isoelectrically on a pH gradient
  2. Remove reducing agents like mecaptoethanol or dithiothreitol
  3. Switch the anode and cathode on your gel


In classical Michaelis-Menten enzyme kinetics, the two constants Vmax and Km determine the activity of an enzyme that acts on one substrate. You are studying the effects of various chemicals on these constants for your favorite enzyme, and find one molecule that increases its Km but leaves Vmax constant. Your molecule is most likely to be:


  1. a substrate analog
  2. the enzyme’s substrate


  1. a coenzyme that increases catalytic efficiency


  1. an allosteric inhibitor that decreases the enzyme’s affinity for the substrate E. an allosteric enhancer that increases the enzyme’s affinity for the substrate






The tiny hairs on a gecko’s toes enable it to climb walls. The hairs are made of hydrophobic keratin and adhere to surfaces via van der Waals interaction. At the tiny interface where the gecko’s toe hairs touch the surface it climbs, which amino acid are you LEAST likely to find?


  1. Isoleucine


  1. Leucine


  1. Phenylalanine


  1. Serine
  2. Alanine


When found on the extracellular side of the cell, which of the following classes of membrane molecules is a marker for the phagocytosis of apoptotic cells?


  1. Glycolipid
  2. Sphingomyelin
  3. Phosphatidylethanolamine
  4. Phosphatidylserine
  5. Phosphatidylcholine


A rare genetic disease is characterized by immuno-deficiency, developmental and growth delay, and microcephaly. Suppose you extract DNA from a patient with this syndrome and find almost equal quantities of long and very short DNA strands, which enzyme is likely to be defective in this patient?


  1. DNA ligase
  2. Topoisomerase
  3. DNA polymerase


  1. Helicase





You perform a western blot for a 42kD peptide. To your surprise, you find the protein running at the speed of an 84kD protein. What reagent did you leave out?


Beta mercaptoethanol



Acetaldehyde dehydrogenase is an enzyme required for the oxidation of acetaldehyde to acetic acid. Given that acetaldehyde exhibits no cooperativity and functions as a monomer, what is the most likely inheritance pattern of a loss of function allele for acetaldehyde dehydrogenase?





Collagen consists of three identical peptides wound in a triple helix. On the peptide, each third residue is glycine, which is small enough to fit in the center of the triple helix. What is the most likely inheritance pattern of a G837W mutant allele?






A scientist has suggested that a homolactic fermenting organism grows anaerobically on glycerol 3-phosphate as the sole source of carbon, exclusively using the following pathway:





























However, the scientific community rejected this suggestion because:


  1. the number of ATP molecules produced is insufficient to support growth.
  2. the number of NAD+ that are reduced is not same as the number of NADH



that are oxidized in the pathway.

  1. the carbon source is not as reduced as glucose and hence, cannot support growth.


  1. the number of negative charges on lactic acid (which is being produced) is not the same as that on glycerol 3-phosphate (which is being consumed). .





If active transport is inhibited, the passive sodium and potassium ion fluxes across the plasma membrane are still coupled. What makes these two passive ion fluxes dependent on each other?


  1. The membrane potential.


  1. The potassium channels.
  2. The pumping ratio of the Na+/K+ ATPase.
  3. The ratio of cholesterol to phospholipids in the membrane.
  4. The ratio of the extracellular sodium ion concentration to the intracellular potassium ion concentration.










The Henderson Hasselbalch equation describes the relationship between pH, pK and the ratio of base to acid concentration, pH = pK + log ([B]/[A]). It is useful when determining the amount of weak acid and weak base to weigh out for a buffer system. It is also useful to determine percent of a functional group in it’s ionized state. If a carboxylic acid has a pK of 3.9, what percentage of the functional group will carry a negative charge at pH 4.9?


  1. 10%
  2. 9%
  3. 09%
  4. 50%



With proofreading, which of the following is the error rate of DNA polymerase?


  1. One error in 1x 101 bases.
  2. One error in 1 x 102 bases.
  3. One error in 1 x 103 bases.
  4. One error in 1 x 106 bases.
  5. One error in 1 x 109 bases.


Use the gel diagram below to answer Questions 62 and 63. The positively-charged electrode of the electrophoresis gel is shown at the bottom of the diagram; the negatively-charged electrode is at the top. The mixture in each well included the original DNA fragment, all four dNTPs, one type of ddNTP as labeled in the diagram, and other necessary components of the dideoxy chain-termination reaction. The results are below.








































What is the sequence of the template strand? (Short Answer)




According the ABC model of flower development, if the B gene is knocked out, the development of which flower parts would be interrupted? Check all that apply.




  1. Corolla
  2. Gynoecium
  3. Androecium

Imagine that you are a molecule of RNA polymerase that is sliding along DNA and encountering a gene with typical structure (promoter, coding sequence and terminator) depicted below. Which of the choices below presents the most accurate order of DNA segments (labeled 1, 2, 3……) in which

the affinity of the RNA polymerase binding to DNA progressively diminishes?













3’1                           2             3                  4                                                           5    6




During translation in prokaryotes, the ribosome binds to

  • The TATA box
  • The mRNA cap
  • The terminator sequence
  • An enhancer sequence
  • The Shine-Dalgarno sequence


Compartmentalization is a hallmark of eukaryotic cells. For each metabolic pathway, choose the intracellular compartment or organelle from the list below in which it takes place.


  1. Cytosol


  1. Mitochondrial Matrix


  1. Mitochondrial Membranes


  1. Peroxisomes


  1. Endoplasmic Reticulum



Beta-Oxidation -B

Pentose Phosphate Pathway-A

Glyoxylate Cycle -D

Steroid Synthesis-E







A macrophage cell notifies other cells of an immunological invader by:

  1. Up-regulating expression of MHC I molecules upon activation.


  1. Up-regulating expression of MHC II molecules upon activation.


III. Interacting with the complement system.


  1. Acting as an antigen presenting cell.


  1. Inactivating viruses through release of antibodies.


  1. Decreasing enzymatic production.


VII. Increased cytokine production.


  1. I, III, IV, and VI


  1. I, IV, V, and VII
  2. II, III, IV, and VII
  3. II, III, IV, and V
  4. I, II, IV, and VI


A confluent layer of macrophage cells are grown in two 25 cm2 tissue culture flasks with appropriate medium containing 10% plasma serum. For the experiment all medium is removed from the flask and the cells are washed with appropriate buffers to remove all traces of serum and media. E. coli bacteria, suspended in serum free media, are then added or “fed” to the macrophages. The process of E. coli death from phagocytosis was then studied. It is necessary in a phagocytosis study to remove the serum because:



  1. The complement proteins could have independently killed the bacteria.
  2. The B cells could have independently killed the bacteria.
  3. The natural killer cells could have independently phagocitized the bacteria.
  4. Serum proteins could have inhibited the Membrane Attack Complex (MAC).


After 30 minutes the cells in tissue culture Flasks 1 and 2 are washed with appropriate buffers to remove all free E. coli. Serum free media is added and the flasks incubated. During incubation the macrophages and microbes are at war. Which statement is true?


  1. The macrophage digests the E. coli through the oxidative burst.


  1. The E. coli protects itself through the oxidative burst.


  1. The oxidative burst is characterized by an increased production of hydrogen peroxide.


  1. The oxidative burst results in the formation of a membrane attack complex.


  1. A and C


After 45 minutes, the macrophages in Flask 1 are lysed by adding ice cold water. The macrophages and water are centrifuged and the bacteria isolated from the macrophage debris. The bacteria are suspended, diluted and plated on agar. After 90 minutes, the same procedure was followed for tissue culture Flask 2 and these bacteria were plated. Bacterial Plates 1 and 2 were incubated for 24 hours. What would be your prediction of the bacterial growth on Plate 1 (45 minutes) compared to the bacterial growth on Plate 2 (90 minutes)?


  1. Plates 1 and 2 have equal colonies


  1. Plate 1 has no colonies


  1. Plate 2 has no colonies


  1. Plate 1 has more colonies than Plate 2


  1. Plate 2 has more colonies than Plate 1




Which of the following cellular proteins make direct contact with chromosomes?

  1. Centrosomes and microtubule-associated proteins


  1. Kinesins, myosins, and actin microfilaments


  1. Histones, condensins, and synaptonemal complexes


  1. All of the above


  1. None of the above


Your colleague’s PCR reaction failed to amplify the human rhodopsin gene. Her lab notebook indicates that she added dNTPs, the Rhodopsin template gene, complementary DNA primers, buffer, and an E. coli DNA polymerase and ran the reaction under the proper conditions. How would you advise her to fix the reaction?


  1. Add a bacterial promoter to the Rhodopsin template


  1. Add extra ATP so there is enough energy to catalyze the reaction C. Add dNTPs to facilitate elongation


  1. Use a different polymerase


  1. Use RNA primers instead


Redsoxase catalyzes the reaction WI2N2 -> L(OSS)3. The reaction progress can be measured by the loss of red color


If the reaction is progressing forward, over time you would expect optical density (OD) readings to:

  1. Increase



  1. Decrease


You have a mutant of Redoxase that does not bind substrate as well as the wuild type. Which of the following do you expect to change?


  1. Vmax
  2. Km
  3. kcat
  4. Both A and C
  5. All of the above


You have an additional mutant which does not convert WI2N2 to L(OSS)3 as efficiently. Which of the following do you expect to change?


  1. Vmax
  2. Km
  3. kcat
  4. Both A and C
  5. All of the above


You calculate the Vmax and Km for a 0.5M Redsoxase at 37 degree Celsius in 10 mM NaCl, pH 8.5 using a Michaelis-Menten plot. You want to use these constants for comparison in future experiments. Which of the following parameters does NOT need to be kept constant in your new experiments for your comparisons to remain valid?


  1. Constant pH
  2. Constant concentration of substrate
  3. Constant temperature
  4. Constant salt
  5. Constant concentration of enzyme



Use the following Lineweaver-Burke plot to calculate Km and Vmax(Short Answer).






























The Vmax is 50 while Km is 25


Many proteins are transported around cells in vesicles. Which of the following determines the specificity or directionality of vesicle transport?


  1. Clathrin coat proteins.
  2. v-SNARES and t-SNARES.
  3. Hydrophobic domains.


Which one of the following graphs shows the relative change in the amount of mitochondrial DNA of a cell undergoing mitosis?


















A is the correct answer, mitochondria divide constantly.


A GFP (green fluorescent protein) tagged form of protein P was expressed in fibroblast cells. The subcellular distribution of protein P can be observed using fluorescence microscopy. To determine the precise movement mechanism of protein P in the cells, fluorescence recovery after photobleaching (FRAP) was performed. As shown below, protein P is expressed in the nucleus (ROI


  • and in the cytoplasm (ROI 2). Protein P in the ROI 1 area was photobleached using a laser beam. Photobleaching causes an irreversible loss of flouorescence. Changes in the fluorescence intensity of protein P in ROI 1 and ROI 2 following photobleaching are shown in the graph and figures below.
























































Which of the following is the best explanation for the distribution and movement of protein P?



  1. P is a nuclear membrane protein.
  2. P is imported to the nucleus through a nuclear pore.
  3. P binds to the nuclear pore complex.
  4. P is imported to the nucleus via vesicular trafficking through Golgi and ER.
  5. P is capable of moving from the nucleus to the cytoplasm.











You use dideoxy termination sequencing to sequence a short fragment of DNA. The results are shown in the gel below, visualized using ethidium bromide.









































Read 5’ to 3’, what is the sequence immediately following the primer? Write X for each base pair which can’t be determined. What reagent was most likely left out in the reaction for G? What reagent was most likely left out in the reaction for C?



GTXXAXTAXAXXTTTAX. G was missing dGTP, and always terminated at the first G. C was missing ddCTP, so elongation continued to the end of the DNA fragment. Note this means the band we see in lane C doesn’t necessarily indicate that the last base is C.
























Protein A is expressed in the brain, but not the lung. Proteins B and C iare expressed in the lung, but not the brain. You perform a western blot for proteins A, B, and C to study their regulation. Based on the data below, how are proteins AB, and C regulated?



























Protein A is polyubiquitinated in lung and degraded, B is phosphorylated and activated in lung, protein

C is cleaved and inactivated in brain.



You extract a plasmid known to contain a single BamHI from E. coli. Bacteria normally maintain plasmids in slightly negatively supercoiled states. You run on a gel: unaltered plasmid, DNAse 1 digest (nicks DNA), BamHI digest, gyrase incubated (supercoils DNA). Draw the expected results.



From fastest to slowest: gyrase, unaltered, BamHI, DNAse 1























You wish to express p53, the product of the TP53 gene, using an expression vector. You currently have a cloning vector containing cDNA for TP53. The cloning and expression vectors are shown below.























The expression vector also codes for penicillin resistance, while the cloning vector doesn’t. You digest both plasmids with EcoRI, transfect into E. coli, and plate with penicillin. You select a resulting colony, and perform a western blot for p53. Unfortunately, you detect no p53. What might be wrong?


No insert, backwards insert, wrong insert (e.g. other half of cloning vector), p53 misfolded and degraded in E. coli.



You decide to use PCR to determine if your expression vector has the cDNA inserted properly. Which primers should you use, so that PCR yields product only if the TP53 cDNA is inserted properly?

A and D or B and C
























You do a complete digest of Plasmid IH7JX with BamHI and EcoRI separately and together.

Determine the restriction enzyme map of the plasmid.


























































Check with me on your picture of the restriction graph, it is very difficult to insert a picture with the correct answer.




Your labmate was given a piece of DNA and told to make a map of the BamHI restriction enzyme sites. The labmate digested the DNA with BamHI to completion and also did a partial digest. He then isolated fragments specifically created by the partial digest. These fragments were digested with BamHI to completion and the resulting products were run on a new gel. Below are pictures of the two gels (note: the size of each band in kilobases is indicated above the band), visualized with ethidium bromide. Help your labmate interpret the gel by drawing the resulting map. Show the relative location of each of the restriction enzyme sites, the number of nucleotides between the sites and indicate if the DNA molecule is circular or linear.



BamHI 5.0 2.7 2.5 3.2 7.0
BamHI digest uncut fragment fragment fragment fragment fragment


7.0 7.7
4.5 4.5 4.5 4.5
2.0 2.0 2.0 2.0 2.0 2.0






0.7 0.7 0.7 0.7
0.5 0.5 0.5 0.5 0.5







4.5 kb 0.5 kb 2.0 kb 0.7 kb















































































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