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1) Describe in detail one method that utilizes antibodies as a tool.
2) What is the objective of this method?
State why the following terms are important in biochemistry: polymer, protein, nucleic acid, catalysis, genetic code.
Identify the functional groups in the following compounds.
Biochemical connecTions For the process
Which of the following are spontaneous processes?
Explain your answer for each process.
(a) The hydrolysis of ATP to ADP and Pi
(b) The oxidation of glucose to CO2 and H2O by an organism
(c) The phosphorylation of ADP to ATP
(d) The production of glucose and O2 from CO2 and H2O in photosynthesis
In 1828, Wöhler was the first person to synthesize an organic compound (urea, from ammonium cyanate). How did this contribute, ultimately, to biochemistry?
In biochemistry, the exergonic process of converting glucose and oxygen to carbon dioxide and water in aerobic metabolism can be considered the reverse of photosynthesis, in which carbon dioxide and water are converted to glucose and oxygen. Do you expect both processes to be exergonic, both endergonic, or one exergonic and one endergonic? Why? Would you expect both processes to take place in the same way? Why?
Does biochemistry differ from organic chemistry? Explain your answer. (Consider such features as solvents, concentrations, temperatures, speed, yields, side reactions, and internal control.)
Comment on RNA’s role in catalysis and coding in theories of the origin of life.
Do you consider it a reasonable conjecture that cells could have arisen as bare cytoplasm without a cell membrane?
List five differences between prokaryotes and eukaryotes.
Assume that a scientist claims to have discovered mitochondria in bacteria. Is such a claim likely to prove valid?
Match each entry in Column a with one in Column b; Column a shows the names of some important functional groups, and Column b shows their structures.
What are the differences between the photosynthetic apparatus of green plants and photosynthetic bacteria?
State how the following organelles differ from each other in terms of structure and function: Golgi apparatus, lysosomes, peroxisomes, glyoxysomes. How do they resemble each other?
What are the advantages of being eukaryotic (as opposed to prokaryotic)?
Why do you think that most textbooks do not consider a hydrogen bond to be an example of a van der Waals force?
Identify the conjugate acids and bases in the following pairs of substances:
(a) (CH3)3 NH +/ (CH3)3 N
Identify conjugate acids and bases in the following pairs of substances:
Mathematical Calculate the hydrogen ion concentration, [H1],for each of the following materials:
(a) Blood plasma, pH 7.4
(b) Orange juice, pH 3.5
(c) Human urine, pH 6.2
(d) Household ammonia, pH 11.5
(e) Gastric juice, pH 1.8
Mathematical Calculate the hydrogen ion concentration, [H1], for each of the following materials:
(a) Saliva, pH 6.5
(b) Intracellular fluid of liver, pH 6.9
(c) Tomato juice, pH 4.3
(d) Grapefruit juice, pH 3.2
Mathematical Calculate the hydroxide ion concentration, [OH−], for each of the materials used in Question 24.
Define the following:
(a) Acid dissociation constant
(b) Acid strength
(d) Buffering capacity
(e) Equivalence point
Look at Figure 2.17 and Table 2.8. Which compound in the table would give a titration curve the most similar to the one shown in the figure? Why?
Mathematical What is the [CH3COO−] / [CH3COOH] ratio in an acetate buffer at pH 5.00?
Mathematical What is the [CH3COO−] / [CH3COOH] ratio in an acetate buffer at pH 4.00?
Mathematical What is the ratio of TRIS/TRIS-H1 in a TRIS buffer at pH 8.7?
Mathematical What is the ratio of HEPES / HEPES-H1 in a HEPES buffer at pH 7.9?
Mathematical If you have 100 mL of a 0.10 M TRIS buffer at pH 8.3 (Table 2.8) and you add 3.0 mL of 1 M HCl, what will be the new pH?
Mathematical Show that, for a pure weak acid in water, pH 5 (pKa 2 log [HA])/2.
Biochemical connections Suggest a suitable buffer range for each of the following substances:
(a) Lactic acid (pKa 5 3.86) and its sodium salt
(b) Acetic acid (pKa 5 4.76) and its sodium salt
(c) TRIS (pKa 5 8.3; see Table 2.8) in its protonated form and its free amine form
(d) HEPES (pKa 5 7.55; see Table 2.8) in its zwitterionic form and its anionic form
Mathematical Define buffering capacity. How do the following buffers differ in buffering capacity? How do they differ in pH?
Buffer a: 0.01 M Na2HPO4 and 0.01 M NaH2PO4
Buffer b: 0.10 M Na2HPO4 and 0.10 M NaH2PO4
Buffer c: 1.0 M Na2HPO4 and 1.0 M NaH2PO4
Biochemical connections If you wanted to make a HEPES buffer at pH 8.3, and you had both HEPES acid and HEPES base avail-able, which would you start with, and why?
Biochemical connections We usually say that a perfect buffer has its pH equal to its pKa. Give an example of a situation in which it would be advantageous to have a buffer with a pH 0.5 unit higher than its pKa.
Which would you think would be a stronger interaction and why: an interaction between a sodium ion and the partial negative charge on the oxygen in ethanol (CH3CH2OH), or the interaction between two ethanol molecules?
MatheMatical Sketch a titration curve for the amino acid cysteine, and indicate the pKa values for all titratable groups. Also indicate the pH at which this amino acid has no net charge.
MatheMatical Sketch a titration curve for the amino acid lysine, and indicate the pKa values for all titratable groups. Also indicate the pH at which the amino acid has no net charge.
MatheMatical Sketch a titration curve for aspartic acid, and indicate the pKa values of all titratable groups. Also indicate the pH range in which the conjugate acid–base pair +1 Asp and 0 Asp will act as a buffer.
Write equations to show the ionic dissociation reactions of the following amino acids: aspartic acid, valine, histidine, serine, and lysine.
Based on the information in Table 3.2, is there any amino acid that could serve as a buffer at pH 8? If so, which one?
If you were to have a mythical amino acid based on glutamic acid, but one in which the hydrogen that is attached to the g-carbon were replaced by another amino group, what would be the predominant form of this amino acid at pH 4, 7, and 10, if the pKa value were 10 for the unique amino group?
Identify the charged groups in the peptide shown in Question 4 at pH 1 and at pH 7. What is the net charge of this peptide at these two pH values?
Consider the following peptides: Phe! Glu! Ser! Met and Val! Trp! Cys! Leu. Do these peptides have differ-ent net charges at pH 1? At pH 7? Indicate the charges at both pH values.
Can a peptide act as a buffer? If so, why?
Consider the peptides Ser! Glu! Gly! His! Ala and Gly! His! Ala! Glu! Ser. How do these two pep-tides differ?
For each of the following, name an amino acif in which the R group contains it: a hyfroxyl group, a sulfur atom, a seconf chiral carbon atom, an amino group, an amife group, an acif group, an aromatic ring, anf a branchef sife chain.
If you knew everything about the properties of the 20 common (proteinous) amino acids, would you be able to predict the properties of a protein (or large peptide) made from them?
Identify the polar amino acids, the aromatic amino acids, and the sulfur-containing amino acids, given a peptide with the following amino acid sequence:
Val! Met! Ser! Ile! Phe! Arg! Cys! Tyr! Leu
What are the structural differences between the peptide hormones oxytocin and vasopressin?
Are amino acids other than the usual 20 amino acids found in proteins? If so, how are such amino acids incorporated into proteins? Give an example of such an amino acid and a protein in which it occurs.
MatheMatical Predict the predominant ionized forms of the following amino acids at pH 7: glutamic acid, leucine, threonine, histidine, and arginine.
MatheMatical Draw structures of the following amino acids, indicating the charged form that exists at pH 4: histidine, aspara-gine, tryptophan, proline, and tyrosine.
MatheMatical Predict the predominant forms of the amino acids from Question 8 at pH 10.
Match the following statements about protein structure with the proper levels of organization.
(i) Primary structure (ii) (iii) Tertiary structure (iv) Quaternary structure
(a) The three-dimensional arrangement of all atoms
(b) The order of amino acid Secondary structure residues in the polypeptide chain
(c) The interaction between subunits in proteins that consist of more than one polypeptide chain
(d) The hydrogen-bonded arrangement of the polypeptide backbone.
What are Ramachandran angles?
You hear the comment that the difference between wool and silk is the difference between helical and pleated- sheet structures. Do you consider this a valid point of view? Why or why not?
Woolen clothing shrinks when washed in hot water, but items made of silk do not. Suggest a reason, based on information from this chapter.
The terms configuration and conformation appear in descriptions of molecular structure. How do they differ?
Theoretically, a protein could assume a virtually infinite number of configurations and conformations. Suggest several features of proteins that drastically limit the actual number.
What is the highest level of protein structure found in collagen?
List two similarities and two differences between hemoglobin and myoglobin.
Suggest a way in which the difference between the functions of hemoglobin and myoglobin is reflected in the shapes of their respective oxygen-binding curves.
What is the nature of “random” structure in proteins?
Describe the effect of 2,3-bisphosphoglycerate on the binding of oxygen by hemoglobin.
In oxygenated hemoglobin, pKa 5 6.6 for the histidines at position 146 on the b-chain. In deoxygenated hemoglobin, the pKa of these residues is 8.2. How can this piece of information be correlated with the Bohr effect?
You are studying with a friend who is describing the Bohr effect. She tells you that in the lungs, hemoglobin binds oxygen and releases hydrogen ion; as a result, the pH increases. She goes on to say that in actively metabolizing muscle tissue, hemoglobin releases oxygen and binds hydrogen ion and, as a result, the pH decreases. Do you agree with her reasoning? Why or why not?
How does the difference between the b-chain and the g-chain of hemoglobin explain the differences in oxygen binding between Hb A and Hb F?
What is the effect of the altered amino acid sequence in Hb S that causes the cells to form sickle shapes?
Given the purpose of hemoglobin, what could one envision as a downside to having all our hemoglobin as Hb F instead of Hb A?
Comment on the energetics of protein folding in light of the information in this chapter.
Rationalize the following observations.
(a) Serine is the amino acid residue that can be replaced with the least effect on protein structure and function.
(b) Replacement of tryptophan causes the greatest effect on protein structure and function.
(c) Replacements such as Lys S Arg and Leu S Ile usually have very little effect on protein structure and function.
What are the known diseases caused by abnormal prions?
What are some diseases caused by misfolded proteins?
What causes protein aggregates to form?
What other possible organizations of the globin gene could exist if there were no need for a globin chaperone?
What aspects of the transmission of scrapie or other spongiform encephalopathies act like genetic diseases? What aspects act like transmittable diseases?
Describe what happens according to the “amyloid cascade hypothesis.”
A mutation that changes an alanine residue in a protein to an isoleucine leads to a loss of activity. Activity is regained when a further mutation at the same site changes the isoleucine to a glycine. Why?
If you had a mixture of proteins with different sizes, shapes, and charges and you separated them with electrophoresis, which proteins would move fastest toward the anode (positive electrode)?
Why is the order of separation based on size opposite for gel filtration and gel electrophoresis, even though they often use the same compound to form the matrix?
Show by a series of equations (with structures) the first stage of the Edman method applied to a peptide that has leucine as its N-terminal residue.
Why can the Edman degradation not be used effectively with very long peptides?
You are in the process of determining the ami-no acid sequence of a peptide. After trypsin digestion followed by the Edman degradation, you see the following peptide fragments:
What is abnormal concerning these results? What might have been the problem that caused it?
Amino acid compositions can be determined by heating a protein in 6 M HCl and running the hydrolysate through an ion-exchange column. If you were going to do an amino acid sequencing experiment, why would you want to get an amino acid composition first?
How could you isolate mitochondria from liver cells using differential centrifugation?
Which enzymes or chemicals would you choose to use to cut the protein from Question 50? Why?
With which amino acid sequences would chy-motrypsin be an effective reagent for sequencing the protein from Question 50? Why?
What is the basis for the technique called ELISA?
What are some ways that the antibody-protein complex can be visualized in ELISA or western blots?
What are the main procedures involved in a western blot?
Where did western blot get its name?
What is an advantage of using an ELISA in-stead of a protein microarray to study a proteome? What is a disad-vantage?
What is the advantage to transferring proteins bands form a gel to nitrocellulose during the western blot?
What is the point to labeling a secondary an-tibody with a marker that can be visualized instead of just labeling the primary antibody?
What is the purpose of the tag on the bait protein described in figure 5.26?
What are some of the assumptions behind the logic of the experiment described in figure 5.26?
Give an example of a scenario in which you could partially isolate a protein with differential centrifugation using only one spin.
You are purifying a protein for the first time. You have solubilized it with homogenization in a blender followed by differential centrifugation. You wish to try ammonium sulfate pre-cipitation as the next step. Knowing nothing beforehand about the amount of ammonium sulfate to add, design an experiment to find the proper concentration (% saturation) of ammonium sulfate to use.