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medical sciences
biochemistry
Fundamentals of biochemistry Life at the Molecular Level 4th edition Donald Voet, Judith G. Voet, Charlotte W. Pratt - Solutions
When the reaction A + B ΔC is at equilibrium, the concentrations of reactants are as follows: [A] = 2 mM, [B] = 3 mM, and [C] = 9 mM. What is the standard free energy change for the reaction?
Calculate ΔG°, for the reaction A + B ΔC + D at 25°C when the equilibrium concentrations are [A] = 10 μM, [B] = 15 μM, [C] = 3 μM, and [D] = 5 μM. Is the reaction exergonic or endergonic under standard conditions?
Calculate the equilibrium constant for the reaction
ΔG°, for the isomerization reaction glucose-1-phosphate (GIP) glucose-6-phosphate (G6P) is -7.1 kj ˆ™ mol-1. Calculate the equilibrium ration of [GIP] to [G6P] at 25°C.
The equilibrium constant for the reaction Q → R is 25. (a) If 50 μM of Q is mixed with 50 μM of R, which way will the reaction proceed: to generate more Q or more R? (b) Calculate the equilibrium concentrations of Q and R.
At 10°C, Keq for a reaction is 100. At 30°C, Keq = 10. Does enthalpy increase or decrease during the reaction?
Two biochemical reactions have the same Keq = 5 x 108 at temperature T1= 298 K. However, Reaction 1 has ΔH° = -28 kJ ∙ mol-1 and Reaction 2 has ΔH° =-28 kJ∙mol-1. The two reactions utilize the same reactants. Your lab partner has proposed that you can get more of the reactants to proceed
A spheroidal bacterium with a diameter of 1 m contains two molecules of a particular protein. What is the molar concentration of the protein?
How many glucose molecules does the cell in Problem 3 contain when its internal glucose concentration is 1.0 mM?
Consider a reaction with ΔH = 15 kJ and ΔS = 50 J ∙ K-1. Is the reaction spontaneous (a) at 10°C, (b) at 80°C?
For the reaction A → B at 298 K, the change in enthalpy is -7 kJ ∙ mol-1 and the change in entropy is -25 J ∙ K-1 ∙ mol-1. Is the reaction spontaneous? If not, should the temperature be increased or decreased to make the reaction spontaneous?
For the conversion of reactant A to product B, the change in enthalpy is 7 kJ ∙ mol-1 and the change is entropy is 20 J ∙ K-1 ∙ mol-1. Above what temperature does the reaction become spontaneous?
Draw a 3-dimensional structure of a water molecule, including any lone pairs of electrons, and indicate the dipole moment. What is the name of the geometrical figure have you drawn?
What is the [OH-] in a 0.05 M HCl solution? What is the pH?
A solution of 0.1 M HCl has a pH of 1. A solution of 0.1 M acetic acid has a pH of 2.8. How much 1 M NaOH is needed to titrate a 100 mL sample of each acid to its respective equivalence point?
A 0.01 M solution of a weak acid in water is 0.05% ionized at 25°C. What is its pK?
What is a buffer? How does it work? What compounds act as buffers in cells?
What is the pH of a 0.1 M solution of cacodylic acid (pK = 6.27)?
A 0.02 M solution of lactic acid (pK = 3.86) is mixed with an equal volume of a 0.05 M solution of sodium lactate. What is the pH of the final solution?
You need a KOAc solution at pH 5, which is 3 M in K+. Such a solution is used in bacterial plasmid DNA isolation. How many moles of KOAc and acetic acid (HOAc) do you need to make 500 mL of this solution?
A beaker of pure distilled water sitting out on your lab bench is slightly acidic. Explain.
Which gas in each of the following pairs would you expect to be more soluble in water? Why? (a) Oxygen and carbon dioxide (b) Nitrogen and ammonia (c) Methane and hydrogen sulfide
What is the pH of a solution of 10-12M of HCl? Explain.
Mammalian erythrocytes contain the enzyme carbonic anhydrase, which catalyzes the equilibrium CO2 + H2O ⇆ HCO3- + H+ with no carbonic acid intermediate. Hence, we have the following acid-base equilibrium: CO2 + H2O ⇆ HCO3- + H+ (a) Describe how this equilibrium is affected in the lungs. What
The last two columns of the table (labeled 'pH of environment' and '[A-]/[HA]') have been partially completed for you. The 'pH of environment' column lists a hypothetical pH at which the weak acid is poised, while the '[A-]/[HA]' is the ratio of conjugate base-to-weak acid at that particular pH.
Are the weak acids listed in this table in order from top to bottom as strongest (at the top) to weakest (at the bottom) or weakest to strongest? Why?
Which weak acid on the table has the highest affinity for protons? Which weak acid on the table has the lowest affinity for protons?
If the glass gets cold to the touch as the dissolving process occurs, what can we say about the enthalpy changes (ΔH) as the process occurs?
What could be happening at the molecular level to account for the endothermic nature of this process? Try to be as complete as possible in your answer.
Given your answer to question #4, what must be true about the magnitude and value of TΔS and ΔG for this process?
What other strategy could one use other than stirring to increase the ability of the sucrose to go into solution?
What purpose does stirring have in the process of dissolving sucrose in water? Is it absolutely necessary?
Why do bottles of beer break when placed in a freezer?
Distinguish between hydrophilic, hydrophobic, and amphipathic substances.
Mixing olive oil with vinegar creates a salad dressing that is an emulsion, a mixture of vinegar with many tiny oil droplets. However, in a few minutes, the olive oil separates entirely from the vinegar. Describe the changes in entropy that occur during the initial mixing and the subsequent
Below is a beaker that contains a solution of 0.1 M NaCl. Floating inside is a cellulose bag that is permeable to water and small ions like Na+ and Cl- but is impermeable to protein. The bag contains 1 M NaCl and 0.1 M protein. Describe the movement of solutes and solvent.
In the most general definition of an acid and a base, a Lewis acid is a compound that can accept an electron pair, and a Lewis base is a compound that can donate an electron pair. Which of the following compounds can be classified as Brønsted-Lowry acids and bases and which as Lewis acids and
Define pK and pH, and write the Henderson-Hasselbalch equation that relates the two.
The pK's of trichloroacetic acid and acetic acid are 0.7 and 4.76, respectively. Which is the stronger acid? What is the dissociation constant of each?
Identify the potential hydrogen bond donors and acceptors in the following molecules:(a)(b)
You have a 5 mL sample of a protein in 0.5 M NaCl. You place the protein/salt sample inside dialysis tubing and place the bag in a large beaker of distilled water. If your goal is to remove as much NaCl from the sample as possible, which would be more effective: (1) placing the dialysis bag in 4 L
Patients with kidney failure frequently develop metabolic acidosis. If such patients undergo dialysis, the dialysate includes sodium bicarbonate at a concentration higher than that of the blood. Explain why this would benefit the patient.
Draw the structures of the conjugate bases of the following acids:(a)(b)
Draw the structures of the conjugate bases of the following acids:(a)(b)
Calculate the pH of a 200 mL solution of pure water to which has been added 50 mL of 1 mM HCl.
Calculate the pH of a 1 L solution containing (a) 10 mL of 5 M NaOH, (b) 10 mL of 100 mM glycine and 20 mL of 5 M HCl, and (c) 10 mL of 2 M acetic acid and 5 g of sodium acetate (formula weight 82 g ∙ mol-1).
A solution is made by mixing 50 mL of 2.0 M K2HPO4 and 25 mL of 2.0 M KH2 PO4. The solution is diluted to a final volume of 200 mL. What is the pH of the final solution?
Occasionally, a C----H group can form a hydrogen bond. Why would such a group be more likely to be a hydrogen bond donor group when the C is next to N?
What is the pK of the weak acid HA if a solution containing 0.1 M HA and 0.2 M A- has a pH of 6.5?
How many grams of sodium succinate (formula weight 140 g ∙mol-1) and disodium succinate (formula weight 162 g ∙mol-1) must be added to 1 L of water to produce a solution with pH 6.0 and a total solute concentration of 50 mM?
Estimate the volume of a solution of 5 M NaOH that must be added to adjust the pH from 4 to 9 in 100 mL of a 100 mM solution of phosphoric acid.
Calculate the standard free energy change for the dissociation of HEPES.
You need a buffer at pH 7.5 for use in purifying a protein at 4°C. You have chosen Tris, pK 8.08, = H° = 50 kJ ∙ mol-1. You carefully make up 0.01 M Tris buffer, pH 7.5 at 25°C, and store it in the cold box to equilibrate it to the temperature of the purification. When you measure the pH of
Glycine hydrochloride (Cl-H3N+ CH2 COOH) is a diprotic acid that contains a carboxylic acid group and an ammonium group and is therefore called an amino acid. It is often used in biochemical buffers. (a) Which proton would you expect to dissociate at a lower pH, the proton of the carboxylic acid
Explain why water forms nearly spherical droplets on the surface of a freshly waxed car. Why doesn't water bead on a clean windshield?
Describe what happens when a dialysis bag containing pure water is suspended in a beaker of seawater. What would happen if the dialysis membrane were permeable to water but not solutes?
(a) Assuming the cell membrane is permeable to water but not to ions, describe what will happen to the cell in terms of osmosis.(b) If the membrane were permeable to ions, in which direction would solutes diffuse: into or out of the cell?
A segment of DNA containing 20 base pairs includes 7 guanine residues. How many adenine residues are in the segment? How many uracil residues are in the segment?
Draw the tautomeric form of adenine.
Indicate which of the following are purine or pyrimidine bases, nucleosides, or nucleotides: (a) Uracil (b) Deoxythymidine (c) Guanosine monophosphate (d) Adenosine (e) Cytosine (f) Guanylic acid (g) UMP (h) Guanine
An automated DNA sequencing system using chain-terminator sequencing technology can identify ~ 550,000 bases per day. A sequencing center has 15 such systems running simultaneously. How many days would it take to obtain a single read of human DNA on both strands (assuming no maintanence is
Assume that the average gene size in a prokaryotic genome (listed in Table 3-3) is about 1000 bases pairs in the smaller prokaryotic genomes and 1400 base pairs in the larger bacterial genomes. What is the average number of genes in the smallest and largest prokaryotic genomes shown in the table if
Using the data in Table 3-3, compute the average chromosome length in humans. Assuming that the length of ten base pairs of DNA found in one turn of the helix is 34Å, what is the average length of a human chromosome in centimeters? Does your calculation lead to a surprising result?
Outline a procedure for identifying E. coli cells that contain a recombinant pUC18 plasmid in which a foreign gene has been inserted at the polylinker site.
The size of the human haploid genome is about 3.2 × 106 kb. Using human sperm DNA and bacteriophage λ as a cloning vector, you have made a human genome library containing 105 clones. Each clone has a 10-kb insert on average. What is the probability that a particular 10-kb single-copy gene is
The amplification of DNA by PCR is exponential for many rounds and then becomes linear. What factors are likely to become rate limiting so that rate of DNA accumulation becomes linear?
During PCR, which cycle of DNA replication results in a double-stranded, unit-length DNA product? How does the rate of accumulation of this product differ from that of the DNA product wherein only one strand is of unit length?
DNA synthesized using RNA as a template is known as cDNA. In the technique called subtractive hybridization cloning, small amounts of cDNA from all the mRNA of tissue A is hybridized to all the RNA from tissue B. The unhybridized cDNA is then cloned. What has been cloned?
During DNA replication in vitro, two populations of DNA will be produced. What are they? What problem is faced by the molecular biologist once she transforms bacteria with this DNA?
What key sets of data were used to build the Watson-Crick model of DNA?
Define or explain the following terms: (a) Antiparallel; (b) Complementary base pairing.
The base compositions of samples of genomic DNA from several different animals are given below. Which samples are likely to come from the same species? (a) 27.3% T (b) 29.5% G (c) 13.1% C (d) 36.9% A (e) 22.7% C (f) 19.9% T
A certain gene in one strain of E. coli can be cleaved into fragments of 3 kb and 4 kb using the restriction endonuclease PstI, but it is unaffected by PvuII. In another strain of bacteria, the same gene cannot be cleaved with PstI, but treatment with PvuII yields fragments of 3 kb and 4 kb.
You have inserted a 5-kb piece of eukaryotic DNA into a 3.5-kb plasmid at the BamHI site. When you digest the recombinant DNA with various restriction enzymes, you obtain the fragments listed below. Draw a circular map of the recombinant plasmid showing all the restriction sites. Is it possible to
T7 DNA polymerase is less sensitive to dideoxynucleotides than the E. coli DNA polymerase I fragment described in Section 3-4C. (a) For a given concentration of dideoxynucleotides, which enzyme is more likely to give a longer "ladder" on the sequencing gel? (b) Which enzyme is best used for
You are interested in the sequence of a 15-base segment of a gene. Using the chainterminator procedure, you obtain the following results after gel electrophoresis. What is the sequence of the gene segment?
Draw the tautomeric form of cytosine.
The adenine derivative hypoxanthine can base-pair with cytosine. Draw the structure of this base pair.
Hypoxanthine can also base-pair with adenine. Draw the structure of this base pair.
Explain why increasing the NaCl concentration increases the temperature at which the two strands of DNA "melt" apart.
How many different amino acids could theoretically be encoded by nucleic acids containing four different nucleotides if (a) Each nucleotide coded for one amino acid; (b) Consecutive sequences of two nucleotides coded for one amino acid; (c) Consecutive sequences of three nucleotides coded for
The recognition sequence for the restriction enzyme TaqI is TTCGA. Indicate the products of the reaction of TaqI with the DNA sequence shown.
Describe the outcome of a chain-terminator sequencing procedure in which (a) Too little ddNTP is added or (b) Too much ddNTP is added.
The 13-Mb genome of the green alga Ostreococcus tauri contains~8000 genes. Compare the gene density in this eukaryote to that of E. coli (4300 genes) and that of A. thaliana (~25,500 genes).
Describe how to select recombinant clones if a foreign DNA is inserted into the polylinker site of pUC18 and then introduced into E. coli cells.
Calculate the number of clones required to obtain with a probability of 0.99 a specific 5-kb fragment from C. elegans.
You are attempting to clone a 250-kb segment of mouse DNA in a yeast artificial chromosome. You obtain 5000 similar-sized clones representing the entire mouse genome. How confident are you that you have cloned the DNA you are interested in?
Why is a genomic library larger than a cDNA library for a given organism?
Describe the possible outcome of a PCR experiment in which (a) one of the primers is inadvertently omitted from the reaction mixture and (b) one of the primers is complementary to several sites in the starting DNA sample.
Describe the possible outcome of a PCR experiment in which (a) There is a single-stranded break in the target DNA sequence, which is present in only one copy in the starting sample, and (b) There is a double-stranded break in the target DNA sequence, which is present in only one copy in the
In many organisms, DNA is modified by methylation. Draw the structure of 5-methylcytosine, a base that occurs with high frequency in inactive DNA.
A blood stain from a crime scene and blood samples from four suspects were analyzed by PCR using fluorescent primers associated with three STR loci: D3S1358, vWA, and FGA. The resulting electrophoretograms are shown below. The numbers beneath each peak identify the allele (upper box) and the height
A diploid organism with a 45,000-kb haploid genome contains 21% G residues. Calculate the number of A, C, G, and T residues in the DNA of each cell in this organism.
Without consulting the text, draw a generic L-α-amino acid using the Fischer convention.
Using the pK values in Table 4-1, identify the amino acids that have the titration curves shown below.
Which of the following tripeptides contain peptide bonds NOT commonly found in proteins? Provide a name for tripeptide B.
Why is the pK of the carboxyl group of glycine (pK = 2.3) less than that for acetic acid (pK = 4.76)?
Calculate the pI's of aspartate, lysine and serine.
Calculate the pI of the tripeptide Asp-Lys-Ser. Is it simply the average of the pI's of the individual amino acids?
In proteins, the pK of the C-terminus is about 3.8, while that of the N-terminus is about 7.8. Rationalize these differences from the pK values of the α-carboxyl and the α-amino groups in free amino acids.
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