BioChem 384: EXAM 1
Throughout the study of molecular evolution and speciation, many examples of gene duplications have been uncovered. Within humans, two genes that have evolved from one another following a gene duplication are called ___, and when comparing one of these genes in humans to its counterpart in chimpanzees, you are observing ___.
paralogs orthologs
In terms of evolution of these species, ___phylogeny is a more powerful way of measuring genetic relatedness.
molecular
Single-stranded nucleic acid is expected to absorb ___ ultraviolet light than double-stranded nucleic acid of similar size would absorb.
more
Mutations in adenylate kinase have led to a hyperactive enzyme that ultimately ends up elevating ADP levels in a cell. Calculate the EC (energy charge) given the following atypical adenylate concentrations fo the cell containing the mutant adenylate kinase: ATP = 0.5 mM, ADP = 12.2 mM, AMP = 80 uM
0.52
Within the middle base pair, measure the distance from the guanine amide oxygen to the cytosine amine nitrogen. This distance between atomic nuclei is approximately ___ angstroms.
2.61 angstroms
If the hydrophobic part of a membrane is roughly 60 Å thick, how many amino acids are necessary to form the shortest possible transmembrane spanning an α helix? ___ amino acids
40 amino acids
Transmembrane helices are often angled through the membrane. For the same membrane, how many amino acids are necessary if the transmembrane helix is at an angle of 24° from being perpendicular to the plane of the membrane? ___ amino acids
44 amino acids
If a sample of double-stranded DNA is determined to be 20% guanine, what percent of this DNA sample is purine nucleotide chemistry?
50%. All double-stranded DNA is 50% purine and 50% pyrimidine. This logic is consistent with the rules of base pairing nucleotides. The diameter of the double helix is constant along its longitudinal axis.
___ hydrogen bonds would connect these two complementary strands together. This nucleic acid is most likely ___
8 (There are two G-C base pairs -three hydrogen bonds each- and one A-T base pair- two hydrogen bonds- : 3 + 3 + 2 = 8) DNA
These days, treatment of CF symptoms has allowed patients to survive much longer than in prior decades. Based on the information presented in the initial passage, which of the following have likely become increasingly more common for CF patients? A. gene therapy B. lung transplant C. inhaled antibiotics
A, B, C
Given that the approximate bond length of O-H in water is roughly 1 Å, what is the approximate distance each proton "hops" between molecules? A. 1.5 Å (1 × 10-10 m) B. 15 nm (1.5 ×10-8 m) C. 1.5 µM (1.5 × 10-6 m) D. 1.5 fm (1.5 × 10-15 m) E. 15 pm (1 × 10-12 m)
A. 1.5 Å (1 × 10-10 m) (H+ hopping occurs on the order of the length of a typical bond, about 1.5 Å.)
What is the isoelectric point (pI) of lysine, which has pKa values of 2.1 for the α carboxyl group, 9.7 for the α amino group, and 10.5 for the side chain amino group? A. 10.1 B. 5.9 C. 6.3 D. 7.0
A. 10.1
Which statement is correct? A. Both Hsp70 and GroEL-GroES utilize ATP to assist in protein refolding. B. Only GroEL-GroES utilizes ATP to assist in protein refolding. C. Only Hsp70 utilizes ATP to assist in protein refolding. D. Neither Hsp70 nor GroEL-GroES utilizes ATP to assist in protein refolding.
A. Both Hsp70 and GroEL-GroES utilize ATP to assist in protein refolding
Fatty acids are amphipathic, meaning that within the molecular structure, A. One end is polar and the other is non-polar B. Both ends interact with water, they are both hydrophilic C. Both ends repel from water, they are both hydrophobic D. One end is negatively charged and the other end is positively charged
A. One end is polar and the other is non-polar
Which of the following is correct about biological membranes? A. Phospholipid head groups are directed toward the aqueous environment. B. Phospholipid tails are directed toward the aqueous environment. C. Biological membranes are made up of a lipid monolayer. D. Molecules freely pass through the membrane.
A. Phospholipid head groups are directed toward the aqueous environment.
From the partial nucleotide sequence given below, what peptides could be encoded? 5'-GCCUCCAAACCCCUCCA-3' A. Pro-Pro-Asn-Pro-Ser B. Met-Arg-His-Asp-Pro C. Ala-Ser-Lys-Pro-Leu D. Leu-Gln-Thr-Pro-Pro E. Lys-Pro-Ser-Gly-Met
A. Pro-Pro-Asn-Pro-Ser C. Ala-Ser-Lys-Pro-Leu D. Leu-Gln-Thr-Pro-Pro
Which of the following amino acid sequences could form an amphipathic helix? Choose one or more: A. TVVEAIDRLVDT B. TVEERGTDKVST C. TEVEIADRLSDT D. TIVRAKPGGPST
A. TVVEAIDRLVDT
Which of the following is correct about protein folding? Choose one: A. The amino acid sequence of a protein leads to a limited number of possible folding pathways. B. The decrease in possible conformations for a polypeptide is a larger contribution to the entropy of folding than the increased disorder of surrounding water molecules. C. Protein folding in vivo takes place under more dilute conditions than those used in vitro. D. Folding does not begin in vivo until the entire polypeptide chain is synthesized.
A. The amino acid sequence of a protein leads to a limited number of possible folding pathways.
If a mutation occurred in which a codon changed to that for proline, what would you expect if the codon were found in a region that formed an α helix? Choose one: A. The proline would disrupt the α helix. B. The proline would have no effect. C. The proline would form hydrogen bonds to the residue four amino acids ahead (i + 4). D. The proline would cause the α helix to turn into a β sheet.
A. The proline would disrupt the α helix.
Which of the following is expected for DNA that is exposed to increasingly elevated temperature? A. The quantity of light absorbed at wavelength 260nm is expected to increase. B. The quantity of light absorbed at wavelength 260nm is expected to decrease. C. The quantity of light absorbed at wavelength 260nm is expected to remain constant. D. The sample is expected to behave more like DNA with intact base pairs. E. The sample is expected to behave more like DNA with disrupted base pairs.
A. The quantity of light absorbed at wavelength 260nm is expected to increase. E. The sample is expected to behave more like DNA with disrupted base pairs.
If the cytoplasm of a cell were to become a much more oxidizing environment, what do you predict would happen to an existing surface-exposed disulfide bond in a typical cytoplasmic protein? Choose one A. There would be no change since the disulfide bond is already oxidized. B. The proteins would be quickly ubiquitinated and degraded since the disulfide bond would be incorrect. C. The disulfide bond would further oxidize, forming highly reactive sulfur centers. D. The disulfide bond would be more quickly reduced than normally
A. There would be no change since the disulfide bond is already oxidized.
Cancer therapeutics are designed to impact the life of the replicative cell in some way. Some chemotherapy drugs target topoisomerase enzymes. Which of the following statements most accurately describes the effect of these types of anticancer drugs? A. These drugs negatively impact DNA replication so that these cells experience a cell cycle arrest. B. These drugs decrease the ability of the cell to produce ribonucleotides, thereby preventing transcription. C. These drugs prevent the cell from producing plasma membrane lipids so that the cell cannot grow in size. D. These drugs embed pores in the plasma membrane of cells so that cytoplasm leaks out and the cell apoptoses.
A. These drugs negatively impact DNA replication so that these cells experience a cell cycle arrest. (chemotherapy drugs that target topoisomerase enzymes are effective as anticancer agents because they negatively impact DNA replication so that these cells experience a cell cycle arrest. Topoisomerase enzymes alleviate the supercoil that develops during DNA replication, and if inhibited, DNA replication cannot complete.)
Which of the following are properties of water? A. Water is polar and an excellent solvent because of its hydrogen-bonding properties. B. Water freezes more readily when ionic solutes are dissolved in it. C. Water is a strong acid at high temperatures. D. Water is less dense as a solid than as a liquid. E. Water is miscible with oil. F. Water is liquid over a wide range of temperatures.
A. Water is polar and an excellent solvent because of its hydrogen-bonding properties. D. Water is less dense as a solid than as a liquid. F. Water is liquid over a wide range of temperatures.
How much space along the longitudinal axis of DNA does the HindIII enzyme occupy when bound? A. approximately one major groove and one neighboring minor groove, which in total is approximately 40 angstroms B. approximately two major grooves and the two neighboring minor grooves, which in total is approximately 40 angstroms C. approximately three major grooves and the three neighboring minor grooves, which in total is approximately 20 angstroms D. approximately four major grooves and the four neighboring minor grooves, which in total is approximately 20 angstroms
A. approximately one major groove and one neighboring minor groove, which in total is approximately 40 angstroms
The various chemical properties of the amino acid side chains determine the chemical properties and the three-dimensional structures of proteins. What are the four groups that amino acids can be divided into? A. charged; aromatic; hydrophilic or polar uncharged; hydrophobic or aliphatic B. polar; nonpolar; aerobic; hydrophobic or aliphatic C. short-chain Polar; long-chain aliphatic; aromatic; unreactive D. charged; aromatic; lipophilic; sulfur-containing
A. charged; aromatic; hydrophilic or polar uncharged; hydrophobic or aliphatic
Which of the following gene expression assays requires that the sequence of genes be known in advance? A. gene microarray B. RNA-seq analysis C. both RNA-seq analysis and gene microarray D. neither RNA-seq analysis nor gene microarray
A. gene microarray
Which of the following types of chromatin is usually associated with non-coding DNA? A. heterochromatin B. euchromatin
A. heterochromatin
Which of the following types of chromatin is usually associated with the centromere of a chromosome? A. heterochromatin B. euchromatin
A. heterochromatin
Which of the following three terms includes the other two? A. homologous B. orthologous C. paralogous
A. homologs
Based on the molecular phylogeny of these primates, which two are the most related? A. human and chimp B. chimp and gorilla C. human and gorilla
A. human and chimp
Which of the following residues would you likely find in a transmembrane spanning α helices? Choose one or more: A. leucine B. arginine C. isoleucine D. aerine E. aspartate
A. leucine C. isoleucine
What responses are observed in a person experiencing acidosis, a condition defined by the pH of the blood falling below 7.4? A. more CO2 exhaled (hyperventilation) B. less CO2 exhaled (decreased breathing rate) C. diminished HCO3- excretion D. no change in HCO3- excretion E. no change in CO2 exhalation F. elevated excretion of HCO3-
A. more CO2 exhaled (hyperventilation) C. diminished HCO3- excretion
The excess sodium ions are most likely interacting with which chemical component of the nucleotides? A. pentose sugar B. phosphate group C. nitrogenous base
B. phosphate group
If RNase were heated to twice its Tm in the absence of β-mercaptoethanol and then cooled to 4 °C, it would be in what state? Choose one: A. native state B. partially unfolded intermediate C. random coil D. denatured
A. native state Excessive heat denatures proteins. However, since the disulfide bonds are intact, RNaseA will refold. Most proteins cannot do this.
Placed in a hypertonic solution, a living cell will A. shrink as water leaves the cell. B. decrease the pH of the cytoplasm to stop water movement. C. remain unchanged. D. absorb water and get larger.
A. shrink as water leaves the cell.
Which secondary structure elements are stabilized by hydrogen bonds? Choose one or more: A. α helices B. antiparallel β sheets C. parallel β sheets D. random coil
A. α helices B. antiparallel β sheets C. parallel β sheets
Another hexamer is composed of two homotrimers. Using the same letter/number designation as before, indicate its quaternary structure.
A3B3
Given the following common reactions, which are entropically favored? 2 pyruvate —-> glucose ATP —-> ADP + Pi Glucose 6P —> fructose 6P 6CO2 + 6H20 —> C6H12O6 + 6CO2
ATP —> ADP + Pi
Heat shock proteins are A. kinases. B. lipases. C. ligases. D. chaperones.
D. chaperones.
The delta G of ATP hydrolysis is -30.5 kJ/mol. Which of the following reactions are not spontaneous and could be driven by being couple to hydrolysis of ATP (one ATP molecule per individual reaction)? A. Fructose - 6- phosphate <——> fructose + Pi (-15.9 kJ/mol) B. Dihydroxyacetone phosphate (DHAP) <—-> glyceraldehyde 3 phosphate (GAP) (7.5 kJ/mol) C. Pyruvate + Pi <—-> phosphoenolpyruvate (+31.5 kJ/mol) D. Glucose + Pi <—-> glucose 6 phosphate (+13.8 kJ/mol)
B and D
Which of the following biochemical reactions are endergonic? A. ATP —> ADP + Pi ; Delta G = -30.5 kJ/mol B. Glutamate + NH4+ —> Glutamine; Delta G = +14.2 kJ/mol C. L-Malays + NAD+ —> Oxaloacetate + NADH + H+ ; Delta G = +29.7 kJ/mol D. Acetyl-CoA + Oxaloacetate + H2O —> Citrate + CoASH + H+ ; Delta G= -32.2 kJ.mol E. Glutamate + NH4+ + ATP —> Glutamine + ADP + Pi ; Delta G= -16.3 kJ.mol
B, C
How many ATP molecules are hydrolyzed during a full cycle of GroEL-GroES-aided protein folding? Choose one: A. 7 B. 14 C. 21 D. 28
B. 14 The GroEL-GroES complex is made up of seven subunits and each subunit has an ATP binding site. The four-step cycle requires hydrolysis of ATP by each subunit to cause conformational changes to allow for protein folding, as well as hydrolysis of ATP by each subunit to cause conformation changes for protein release. Thus 14 ATP molecules are required.
Given the Second Law of Thermodynamics, how can reactions that create order (which are entropically unfavorable) occur? A. It is not possible. B. A favorable enthalpy change overcomes entropic penalty. C. Energy is absorbed from the surroundings. D. The unfavorable reaction is coupled to a favorable one.
B. A favorable enthalpy change overcomes entropic penalty. D. The unfavorable reaction is coupled to a favorable one.
High-throughout DNA sequencing and bioinformatics have greatly facilitated our ability to study evolutionary history. Which of the following is correctly defined? A. A human receptor gene and a mosquito receptor gene are highly conserved and are called paralogs B. Glucose-6-phosphate gene sequences from a human and a chimpanzee are highly conserved and are called orthologs C. Glucose-6-phosphate gene sequences from a human and a chimpanzee are highly conserved and are called paralogs D. Steroid receptor gene and globin receptor gene sequences in humans are highly conserved and are called orthologs
B. Glucose-6-phosphate gene sequences from a human and a chimpanzee are highly conserved and are called orthologs
What is a major consequence of the partial double bond character? A. Unrestricted rotational freedom B. Greatly reduced rotational freedom compared to the φ (phi)/ψ (psi) torsion angles C. Minimal difference in rotational freedom compared to the φ (phi)/ψ (psi) torsion angles D. Greatly increased rotational freedom compared to the φ (phi)/ψ (psi) torsion angles
B. Greatly reduced rotational freedom compared to the φ (phi)/ψ (psi) torsion angles
Fatty acids are amphipathic, meaning that within the molecular structure, A. one end is negatively charged and the other end is positively charged. B. one end is polar and the other end is nonpolar. C. both ends interact with water; they are both hydrophilic. D. both ends repel from water; they are both hydrophobic.
B. one end is polar and the other end is nonpolar.
to break the base pair, _ energy needs to be invested than is required to break a base pair that consists of two hydrogen bonds
more
DNA methylase enzymes transfer a methyl group to C-5 of a cytosine or to N-6 of an adenine within a DNA sequence recognized by the enzyme. What effect, if any, would this have on the establishment of the HindIII-DNA complex that is shown in this molecular structure? A. If the HindIII target DNA were methylated, then it would increase the probability of binding between HindIII and DNA and would decrease the endonuclease activity at that methylated site. B. If the HindIII target DNA were methylated, then it would decrease the probability of binding between HindIII and DNA and would decrease the endonuclease activity at that methylated site. C. If the HindIII target DNA were methylated, then it would increase the probability of binding between HindIII and DNA and would increase the endonuclease activity at that methylated site. D. If the HindIII target DNA were methylated, then it would decrease the probability of binding between HindIII and DNA and would increase the endonuclease activity at that methylated site. E. If the HindIII target DNA were methylated, then it would not alter the probability of binding between HindIII and DNA and would not alter the endonuclease activity at that methylated site.
B. If the HindIII target DNA were methylated, then it would decrease the probability of binding between HindIII and DNA and would decrease the endonuclease activity at that methylated site.
Which of the following steps is performed when preparing to do both an RNA-seq analysis and a gene microarray? A. Generate fluorescently labeled RNA fragments. B. Isolate mRNA from whole cell lysate. C. Convert RNA to complementary DNA called cDNA. D. Create high-throughput DNA sequencing.
B. Isolate mRNA from whole cell lysate.
Consider the following DNA melting curves and then answer the question. Which conclusion is supported by the data in the figure? A. Longer-length nucleic acid cannot become completely denatured. B. Shorter-length nucleic acid has a lower melting temperature than that of longer-length DNA. C. Shorter-length nucleic acid cannot become completely denatured. D. Longer-length nucleic acid has a lower melting temperature than that of shorter-length DNA.
B. Shorter-length nucleic acid has a lower melting temperature than that of longer-length DNA.
For cells without the hyperactive adenylate kinase mutation, how would you expect the EC to change? A. The EC would remain unchanged B. The EC would increase C. The EC would decrease D. There is no way to predict how the EC would change
B. The EC would increase
What is the molecular geometry of the constituents of the peptide plane? A. The amide nitrogen is tetrahedral and the carbonyl carbon is trigonal planar. B. The amide nitrogen is trigonal planar and the carbonyl carbon is also trigonal planar. C. The amide nitrogen is trigonal bipyramidal and the carbonyl carbon is trigonal planar. D. The amide nitrogen is tetrahedral and the carbonyl carbon is also tetrahedral.
B. The amide nitrogen is trigonal planar and the carbonyl carbon is also trigonal planar. Both are in the same plane
A reaction is always spontaneous if A. The change in free energy, delta G, is positive B. The change in free energy, delta G, is negative C. The change in enthalpy is zero D. Entropy is increased E. Enthalpy is reduced
B. The change in free energy, delta G, is negative
Upon reception of a biochemical signal by a eukaryotic cell, which of the following would change first when the genetic expression pattern of the cell changes? A. The proteome would change first. B. The transcriptome would change first. C. The proteome and transcriptome would change simultaneously. D. The proteome and transcriptome would not change; they are not parts of genetic expression.
B. The transcriptome would change first.
Quaternary structures provide increased functionality to proteins in which of the follow ways? Choose one or more: A. They prevent cooperativity. B. They provide structural properties not present in individual subunits. C. They increase efficiency of biochemical processes. D. They alter the chemical reaction to tolerate more diverse substrates.
B. They provide structural properties not present in individual subunits. C. They increase efficiency of biochemical processes.
Which of the following is an example of a weak acid? A. NaOH B. Vinegar, CH3COOH C. HCl D. Ammonia, NH3
B. Vinegar, CH3COOH (HCl and NaOH completely dissociate in water and are examples of a strong acid and a strong base, respectively. Weak acids and bases only partially dissociate in water. Vinegar, or acetic acid, is an example of a weak acid. Ammonia is an example of a weak base.)
The GroEL-GroES complex is Choose one or more: A. a ligase. B. a chaperone. C. an ATPase. D. a lipase. E. a kinase.
B. a chaperone. C. an ATPase.
Based on the morphological phylogeny of these primates, which two are most related? A. human and chimp B. chimp and gorilla C. human and gorilla
B. chimp and gorilla
What type of chaperone is Hsp70? A. disulfide isomerase B. clamp type C. heat shock protein D. chamber type
B. clamp type C. heat shock protein
Which amino acids contain sulfur? A. proline B. cysteine C. arginine D. glutamine E. methionine
B. cysteine E. methionine
Within a eukaryotic cell, the _________ is the organelle with highly invaginated membrane structures that sequester ribosomes for protein synthesis. A. lysosome B. endoplasmic reticulum C. Golgi apparatus D. peroxisome
B. endoplasmic reticulum
The mobility of lipids in membranes is best described by A. fast lateral diffusion and fast transverse diffusion. B. fast lateral diffusion and slow transverse diffusion. C. slow lateral diffusion and fast transverse diffusion. D. slow lateral diffusion and slow transverse diffusion.
B. fast lateral diffusion and slow transverse diffusion.
an organism that has evolved to grow at significantly high temperatures is most likely to have A. much more uracil content in genomic DNA B. greater G/C content as compared to A/T C. roughly equivalent A/T content as compared to G/C D. greater A/T content as compared to G/C
B. greater G/C content as compared to A/T
Which of the following common functional groups in biomolecules is NOT capable of multiple protonation states? A. Hydroxyl B. Methyl C. Amino D. Sulfhydryl
B. methyl
If the molecular formula of a carbohydrate is C6H12O6, then it is most likely considered to be a A. disaccharide. B. monosaccharide. C. polysaccharide. D. trisaccharide.
B. monosaccharide.
Consider the following data regarding VNTR DNA analysis from a crime scene, the victim, and two suspects. Which suspect(s) should be further pursued? Base your answer on the DNA evidence alone. A. suspect A only B. suspect B only C. both suspects A and B D. neither suspect A nor B
B. suspect B only
the main chemical components of the plasma membrane each contain ___ fatty acids A. one B. two C. three D. four
B. two
If a cell is placed in a hypotonic solution, then A. solutes in the solution will enter the cell. B. water will flow into the cell. C. there will be no net change in flow of water into or out of the cell. D. water will flow out of the cell.
B. water will flow into the cell. (When a cell is placed in a hypotonic solution, the solution contains fewer solutes than the cell. To compensate and relieve the osmotic pressure, water will enter the cell to equilibrate the solute concentrations. The flow of too much water into the cell can lead the cell to burst. Hypertonic solutions lead to water flowing out of the cell to compensate for the unequal solute concentrations. Solutes are not being exchanged as freely as water. An isotonic solution is completely balanced and thus there is no known net change in water volume.)
Every cell is surrounded by a plasma membrane that is comprised of A. nucleic acids B. Triglycerides C. Phospholipids
C
How are changes in enthalpy (H) and entropy (S), related to changes in free energy (G)? A. Delta G = Delta S - T delta H B. Delta G = - Delta H + T delta S C. Delta G = Delta H - T delta S D. Delta G = Delta S + T delta H
C
Which of the following statements is correct? A. The overall free energy of a couple reaction is the difference of the free energies for the individual reactions B. ATP is rarely used in coupled reactions C. An exertion is reaction drives an endergonic reaction in living systems D. An endergonic reaction drives an exertion is reaction in living systems
C
if there are six mRNA codons, none of which is a STOP codon, what is the greatest number of amino acids that they could encode in a sequence? A. two B. eighteen C. six D. three
C
Which of the following nucleotides are parts of these interacting molecular structures? (nucleotides are represented by their single letter symbols) U T G C A
C - G
Consider the following DNA: 5'-AGGCT-3'. If this were serving as the template strand for new polynucleotide polymerization, how would the new strand read? A. 3'-AGGCT-5' B. 5'-AGGCT-3' C. 3'-TCCGA-5' D. 5'-TCCGA-3'
C. 3'-TCCGA-5'
If a sample of double-stranded DNA is determined to be 20% guanine, what percent adenine is the sample? A. 10% B. 20% C. 30% D. 40% E. 50%
C. 30%
What is the quaternary structure of a hexamer made of three different homodimers? Choose one: A. A3B3C3 B. ABC C. A2B2C2 D. A6
C. A2B2C2
Which of the following would be an example of decreasing entropy? A. Ice melting B. Flow of ions through a channel from higher ionic concentration to lower ionic concentration C. An anabolic pathway D. A catabolic pathway
C. An anabolic pathway
Proton hopping allows for the rapid apparent movement of protons (H+) through aqueous solution. From first to last in the figure above, what is the correct chronological order of proton hopping events (B-E) that form the "water wire" between proton A and proton F? A. D → E → B → C B. B → C → D → E C. C → E → B → D D. E → D → C → B
C. C → E → B → D (the H+ hops to the nearest water, allowing displacement and hopping of the next H+ in an iterative fashion. Note that the initial H+ is still bound to the first water, but it has in effect "moved" through the water wire toward the final destination..... H+ hopping occurs in sequential series from the closest water (the initial H+) to the farthest water)
Multiple sea creatures utilize proteins that interact with light. Why would GFP not be a good choice of light-interacting protein for a creature that lives exclusively in a cold, dark sea cave? Choose one: A. GFP requires many other genes to synthesize the chromophore, making it poorly suited for use in organisms other than jellyfish. B. The β barrel of GFP would not fold without light. C. GFP would not emit green light since there is no blue light for it to absorb and re-emit. D. The environment is too cold for GFP to fold.
C. GFP would not emit green light since there is no blue light for it to absorb and re-emit.
Which of the following best describes monocistronic and polycistronic genes? A. Monocistronic genes are multiple genes under a single promoter that are transcribed into a single RNA, while polycistronic genes are encoded in multiple different RNAs. B. Monocistronic genes are only prokaryotic, and polycistronic genes are only eukaryotic. C. Polycistronic genes are multiple genes under a single promoter that are transcribed into a single RNA, while monocistronic genes only encode a single protein. D. Polycistronic gene products are interpreted by the ribosome, and monocistronic gene products are not.
C. Polycistronic genes are multiple genes under a single promoter that are transcribed into a single RNA, while monocistronic genes only encode a single protein.
Which of the following is correct concerning the first law of thermodynamics in biological systems? A. The value of Delta H for a particular reaction depends on the path taken B. Delta H > 0 for exothermic reactions C. Pressure and volume do not change D. Delta H < 0 for endothermic reactions
C. Pressure and volume do not change
Which of the following is categorized as a charged amino acid? A. A B. Q C. R D. M
C. R Charged amino acids have ionizable side chains. Arginine, or R, has a net positive charge at physiological pH.
For Anfinsen's studies of RNaseA folding, which of the following is not correct? A. Removal of β-mercaptoethanol and urea at the same time resulted in active RNaseA. B. Urea was used to disrupt polar interactions within the protein. C. Removal of β-mercaptoethanol, followed by removal of urea, resulted in active RNaseA. D. β-mercaptoethanol was used to reduce disulfide bonds.
C. Removal of β-mercaptoethanol, followed by removal of urea, resulted in active RNaseA. Anfinsen's studies showed that the information needed to fold a protein was in the primary amino acid sequence. Urea and β-mercaptoethanol were used to completely unfold the protein and to disrupt disulfide bonds. By removing both the urea and the β-mercaptoethanol at the same time, the protein was able to refold properly and regained activity. If β-mercaptoethanol is removed first, random disulfide bonds form, which keeps the protein inactive. After removing urea, a small amount of β-mercaptoethanol is necessary to break and reform the appropriate disulfide bonds.
Which of the following is most likely to be found on the exterior of a protein? A. Trp B. Pro C. Ser D. Glu
C. Ser Hydrophilic amino acids are most likely to be found on protein surfaces because the surface will interact with the aqueous environment. Serine, or Ser, is hydrophilic.
It has been observed that in a few cases, the peptide plane is actually bent 4°-5° from being a flat plane. What is the most plausible explanation? A. The fast, dynamic motions in a protein cause the peptide plane to be non-ideal over the lifetime of the protein. B. This is not possible. The apparent skewing of the peptide plane must be due to error in the structural measurement. C. Some other restraint is causing the peptide plane to adopt an unfavorable state. The favorable energetics of the other restraint offset the energetic unfavorability of the skewed peptide plane. D. The skewed peptide plane is a result of misformed disulfide bonds, causing the protein to denature.
C. Some other restraint is causing the peptide plane to adopt an unfavorable state. The favorable energetics of the other restraint offset the energetic unfavorability of the skewed peptide plane.
If a semi-conservative mutation occurred in the GroEL gene that abolished ATP binding, what functional consequence would you predict? Choose one: A. The mutated GroEL subunit would be denatured. B. The seven GroEL subunits would not come together to form the barrel-like structure, but would persist as folded monomers. C. The GroEL complex would form but would not act as a chaperone. D. Activity of the GroEL-GroES chaperone would be greatly elevated, more quickly refolding proteins.
C. The GroEL complex would form but would not act as a chaperone.
The genetic anomaly that leads to Hutchinson-Gilford Progeria Syndrome (HGPS) causes A. too much of a certain nuclear protein to be synthesized by the cell. B. too little of a certain nuclear protein to be synthesized by the cell. C. a shortened version of a certain nuclear protein to be synthesized by the cell. D. an elongated version of a certain nuclear protein to be synthesized by the cell.
C. a shortened version of a certain nuclear protein to be synthesized by the cell.
Fatty acids are important for cell membrane formation because they are A. only hydrophilic B. only hydrophobic C. amphipathic D. only polar.
C. amphipathic
Within the biochemical pathway represented in Part 1 (above), whihc chemical contains completely oxidized carbon atoms? A. ethanol B. glucose C. carbon dioxide
C. carbon dioxide
What type of chaperone is GroEL-GroES? Choose one: A. heat shock protein B. disulfide isomerase C. chamber type D. clamp type
C. chamber type
how would someone that has a G6P dehydrogenase deficiency attempt to mitigate the symptoms of the genetic disease? A. consume more G6P dehydrogenase containing foods B. Consume more glucose containing foods C. Consume more five carbon containing foods
C. consume more five carbon containing foods
Cells that experience a devastating mutation in the gene that encodes G6P dehydrogenase are most likely to experience problems specifically connected to A. protein metabolism B. lipid transport C. Nucleotide biosynthesis D. the Krebs cycle
C. nucleotide biosynthesis
Plant cell shape is determined by the amount of water stored in the central vacuole. What is directly responsible for maintaining turgor pressure in a leaf? A. CO2 B. dew point C. osmotic pressure D. air pressure
C. osmotic pressure
Which of the following protein changes is most likely a result of the CF genetic mutation for the form of CF that is described here? A. a polar amino acid is substituted by another polar amino acid B. a non-polar amino acid is substituted by another non-polar amino acid C. positively charged amino acid is substituted by a non-polar amino acid D. a negatively charged amino acid and is substituted by a non polar amino acid
C. positively charged amino acid is substituted by a non-polar amino acid
Many diseases, including Alzheimer's disease, are associated with Choose one: A. antibodies. B. high ATP levels in the liver. C. protein aggregation. D. dietary deficiencies. E. buildup of uric acid.
C. protein aggregation.
If the same experiment were performed again for the 60 bp DNA, but this time in the presence of 1.5 M NaCl, in what direction would the new curve be positioned compared to the 60 bp DNA that is already in place in this figure? A. directly on top of the current curve B. to the left of the current curve C. to the right of the current curve
C. to the right of the current curve (the presence of 1.5 M NaCl causes an increase in the melting temperature of DNA. If the same experiment with the 60 bp DNA were performed again in the presence of 1.5 M NaCl, then the new curve would appear to the right of the established curve.)
Amino acids are polymerized via a ___ reaction
Condensation. Amino acids are polymerized via a condensation reaction. When amino acids are polymerized, water is released from the reaction; thus, it is considered a condensation reaction.
Which amino acid is able to form disulfide bonds?
Cysteine
Due to its partial double bond character, the peptide bond restricts rotation, constraining atoms to lie within the same peptide plane. Rotation in the peptide backbone is around the two bonds that flank adjacent ___ atoms, between which a peptide plane is formed.
Cα. rotation cannot occur around the peptide bond, only around the backbone Cα.
Which of the following differentiates the biochemical standard state from the standard state when discussing standard free energy changes? A. Temperature of 298K B. Constant pressure of 1atm C. 1 M concentration of all reactant and products D. PH of 7
D
What distance does proton A appear to travel through the water wire to reach the position marked F? A. 1 µM B. 10 fm C. 1 pm D. 1 nm E. 100 pm
D. 1 nm (1 nm or roughly 10 Å is the net distance the H+ has moved in the figure shown.)
What is the concentration of [OH-] in a solution of 0.025 M HCl? A. 1.0 × 10-14 M B. 2.5 × 10-2 M C. 4.1 × 10-13 M D. 4.0 × 10-13 M
D. 4.0 × 10-13 M (HCl is a strong acid, which means it will completely dissociate in water. This means the concentration of H+ will be equal to the concentration of HCl, or 0.025 M in this case. The concentration of OH- is related to the concentration of H+ via the water ionization constant, Kw. The concentration of OH- is equal to Kw/[H+].)
Which of the following is correct concerning a peptide backbone? A. The torsional angle between the Cα and the R group is called ϕ (phi). B. The torsional angle between the amide nitrogen and the Cα is called ψ (psi). C. The peptide bond allows for free rotation due to its single bond character. D. A Ramachandran plot shows the allowable ϕ and ψ angles for a peptide.
D. A Ramachandran plot shows the allowable ϕ and ψ angles for a peptide.
Of all the different bond types found in proteins, which has partial double bond character? Choose one: A. An ionic bond B. A hydrogen bond C. A disulfide bond D. A peptide bond
D. A peptide bond
Which of the following is NOT accurately classified as a motif? Choose one: A. Four-helix bundle B. Greek key fold C. Rossmann fold D. FERM domain fold
D. FERM domain fold Motifs are smaller, defined structural units within protein folds. Domains are independently folding modules within a polypeptide chain. The four-helix bundle, the Greek key fold, and the Rossmann fold are common motifs. The FERM domain fold is larger and contains three distinct subdomains.
Given the nature of hair and fingernails, and knowing both have high levels of keratin, which of the following is true? A. Keratin in hair has fewer cysteines and therefore more disulfide bonds than keratin in fingernails. B. Keratin in hair has more cysteines and therefore more disulfide bonds than keratin in fingernails. C. Keratin in hair has more cysteines and therefore fewer disulfide bonds than keratin in fingernails. D. Keratin in hair has fewer cysteines and therefore fewer disulfide bonds than keratin in fingernails.
D. Keratin in hair has fewer cysteines and therefore fewer disulfide bonds than keratin in fingernails. the less rigid behavior of hair is in part due to fewer disulfide bonds between keratin proteins.
When a protein enzyme folds in an aqueous solution, which of the following is correct? A. A mixture of polar and non-polar amino acids is found in the interior of the protein. B. Water is always excluded from the active site in the interior of the protein. C. Polar amino acids are found in the interior of the protein. D. Non-polar amino acids are found in the interior of the protein.
D. Non-polar amino acids are found in the interior of the protein. (A major driving force for protein folding is the burying of non-polar amino acids in the interior of the protein to avoid interactions between these hydrophobic amino acids and water. Polar amino acids are typically found on the exterior of the protein. Water is not always completely excluded from the interior of a protein and can play an important role in the active site of an enzyme.)
GFP is frequently used as a reporter of expression, being added as a fusion tag to other proteins of interest. What would you expect to observe if you overexpressed a GFP fusion protein in E. coli? Choose one: A. The E. coli would not grow unless they were in a dark environment. B. The E. coli would be no different than a control expressing just the protein of interest without the GFP tag. C. The E. coli would have a blue appearance when observed in white light. D. The E. coli would have a green appearance when observed in white light.
D. The E. coli would have a green appearance when observed in white light.
If all the threonines of an antifreeze protein were changed to valines, what would happen to the protein's ability to bind and form complexes with water? A. The protein would demonstrate no change in water binding. B. The protein would have increased affinity for the phosphate backbone of DNA. C. The protein would bind water more tightly. D. The protein would not bind water and would lose antifreeze properties.
D. The protein would not bind water and would lose antifreeze properties. (the sidechain of threonine forms hydrogen bonds with water, whereas the sidechain of valine does not. Without hydrogen bonding, the protein would lose its ability to prevent freezing)
Biological membranes partition aqueous environments to permit life processes to maintain regions of low entropy within the high entropy state of the surrounding environment. What characteristic do molecules found in biological membranes have that allows this capability? A. highly ordered and forming a physically rigid barrier B. strictly hydrophilic C. strictly hydrophobic D. amphipathic
D. amphipathic
An increase in the cytoplasmic molarity of acetaldehyde would directly correlate with which of the following? A. a decrease in the production of ethanol B. a decrease in the production of pyruvate C. an increase in the production of pyruvate D. an increase in the production of ethanol
D. an increase in the production of ethanol
Locate the adenine nitrogenous base and determine its location within the molecular structure. Which best describes its location? A. not as part of a base pair; at the 3' within one polynucleotide strand B. as part of a base pair; at the 5' end in one polynucleotide strand C. not as part of a base pair; at the 5' end in one polynucleotide strand D. as part of a base pair; at the 3' end in one polynucleotide strand
D. as part of a base pair; at the 3' end in one polynucleotide strand the adenine nitrogenous base is part of a base pair with a complementary thymine. The adenine is 3' within one polynucleotide strand. Adenine is shown as the only aromatic nitrogenous base in the structure, and the pentose sugar attached to this nitrogenous base has a 3'-OH exposed - thus this nucleotide is not 5'.
The type of reaction that forms a peptide bond is A. elimination. B. nucleophilic substitution. C. hydrolysis. D. condensation.
D. condensation. Peptide bonds are formed via a condensation reaction that is catalyzed by the RNA component of ribosomes. The condensation reaction is unfavorable, so energy is required for this reaction to occur. Hydrolysis is the opposite reaction and is catalyzed by proteases to degrade proteins.
The genetic anomaly that leads to HGPS is a cytosine A. amination. B. decarboxylation. C. carboxylation. D. deamination
D. deamination
From the following list, which common substance that you encounter in your daily life has molecular properties similar to the molecules found in biological membranes? A. gasoline B. water C. lemon juice D. detergent
D. detergent
Ovalbumin is the major protein constituent of egg white. What is the folded state of ovalbumin in a cooked egg? Choose one: A. misfolded due to improper disulfide-bond formation B. reversibly denatured C. reversibly refolded to native state D. irreversibly denatured
D. irreversibly denatured
Getting your hair permed must involve which of the following? A. oxidation of disulfide bonds, reshaping, and then reduction of disulfide bonds B. proteolytic digestions of keratin C. irreversible denaturation of keratin D. reduction of disulfide bonds, reshaping, and then oxidation of disulfide bonds
D. reduction of disulfide bonds, reshaping, and then oxidation of disulfide bonds the covalent disulfide bonds holding keratin proteins together must be broken and then re-formed once the desired shape is made.
Which of the following pairs contain terms that would be considered synonyms of one another regarding DNA integrity? A. denatured : renatured B. annealed : melted C. denatured : annealed D. renatured : annealed E. melted : denatured
D. renatured : annealed E. melted : denatured
On this graph, the curves shift to the right as the G-C content increases. This is because G and C are connected by A. three hydrogen bonds; therefore, when DNA contains greater G-C content, the melting temperature is lower. B. two hydrogen bonds; therefore, when DNA contains greater G-C content, the melting temperature is higher. C. two hydrogen bonds; therefore, when DNA contains greater G-C content, the melting temperature is lower. D. three hydrogen bonds; therefore, when DNA contains greater G-C content, the melting temperature is higher.
D. three hydrogen bonds; therefore, when DNA contains greater G-C content, the melting temperature is higher.
If a typical person hydrolysis 100.0 mol of ATP per day; how much does this ATP weigh? (The molecular weight of ATP is 507 g/mol) A. 2.54 tons B. 5.07 kg C. 0.254 mg D. 5.07 g E. 50.7 kg
E. 50.7 kg 507 g/mol X 100 mol = 50,700 grams = 50.7 kg
The sequencing of the human genome has been instrumental toward A. the field of individualized/personalized drug development. B. our understanding of the genetic basis of disease. C. better genetic counseling to prospective parents. D. a more complete understanding of Homo sapiens' molecular inheritance. E. All of these areas were enhanced by the sequencing of the human genome.
E. All of these areas were enhanced by the sequencing of the human genome.
Disulfide bonds are covalent interactions formed between which amino acid residues? Choose one: A. Phe B. Met C. Pro D. Leu E. Cys
E. Cys
Both Hsp70 and the GroEL-GroES complex are chaperones. Hsp70 is a ___ chaperone. GroEL-GroES is a ___ chaperone
Hsp70 = clamp type chaperone GroEL-GroES = chamber type chaperone
Consider the following polynucleotide strand and determine whether this would likely be a single strand of DNA, a single strand of RNA, or if there is not enough information to determine. 5'-AGGGCAACCGGCCGGAAACGACCAGACAAAAAAAAAAGC-3'
Not enough information
For the yeast biochemical pathway, identify fermentative reactants and products by dragging the chemical names to their respective structures. A= Carbon dioxide, B= glucose, C= ethanol
See image
A __________ mutation will not lead to a change in the protein product of a gene.
Silent A missense mutation leads to a single amino acid change in the resulting protein product, which may or may not affect the activity of the protein. A nonsense mutation causes a premature stop codon and a truncated protein product. A frameshift mutation is due to insertion or deletion mutations, which changes the codon register, or the frame. The amino acid sequence is altered by this new reading frame until a stop codon is reached. A silent mutation is a change at the DNA level that does not change the resulting protein product. Due to the degeneracy of the genetic code, multiple codons can lead to the same amino acid.
Which enzymes are directly involved when yeast converts pyruvate into ethanol? phosphofructokinase pyruvate kinase alcohol dehydrogenase pyruvate decarboxylase
alcohol dehydrogenase pyruvate decarboxylase
Which of the following are not standard DNA base pairs? Assess your answer based on traditional DNA Watson-Crick base pairing. uracil-thymine thymine-adenine cytosine-guanine adenine-guanine cytosine-thymine
adenine-guanine cytosine-thymine uracil-thymine
Hydrogen bond donors
all bound to hydrogen, in biochemistry either N or O atoms N-H, O-H (NOT C-H) Strong dipole moment and partial positive charge on the hydrogen
Hydrogen bond acceptor
all electronegative with lone pair electrons and not bonded to hydrogen The atom, ion, or molecule component of a hydrogen bond which does not supply the bridging (shared) hydrogen atom.
On a gene microchip assay that has been prepared to measure gene expression, a ___ level of green fluorescence corresponds to more transcripts present upon cell lysis.
greater
Based on these DNA melting curves, a thermophilic microbe living at >75°C would likely have ___ G-C content as compared to a similar microbe living at 37°C.
higher
Within the graph of the three melting curves, identify the curve where the DNA would be most likely to have sodium ions neutralizing the charge on the DNA. Drag the "charge neutralized" label to that location.
see image
In terms of energy conservation by the cell, direct regulation of synthesis ___ is more efficient.
transcriptome
The genetic anomaly that leads to HGPS is a single-nucleotide polymorphism. This statement is
true
The HindIII-DNA complex that is shown in this molecular structure contains ___ amino terminus/termini and ___ carboxy terminus/termini. An amino terminus sequence KSALEKLLSL is associated with a(n) ___. Use the sequence view from the dropdown menu and determine the location of KSALEKLLSL within the folded polypeptide.
two two alpha helix