Questions and Answers of Biochemistry Concepts And Connections

What is the relationship between pKa and the useful range of a buffer?
How would you prepare 1 L of a 0.050 M phosphate buffer at pH 7.5 using crystalline K2HPO4 and a solution of 1.0 M HCl?
The buffer needed for Question 35 can also be prepared using crystalline NaH2PO4 and a solution of 1.0 M NaOH. How would you do this?Question 35How would you prepare 1 L of a 0.050 M phosphate buffer
Calculate the pH of a buffer solution prepared by mixing 25 mL of 1.0 M lactic acid and 75 mL of 1.0 M sodium lactate.
If you mix equal volumes of 0.1 M HCl and 0.20 M TRIS (free amine form; see Table 2.8), is the resulting solution a buffer? Why or why not? Table 2.8 Acid and Base Form of Some Useful Biochemical
What would be the pH of the solution described in Question 41?Question 41If you mix equal volumes of 0.1 M HCl and 0.20 M TRIS (free amine form; see Table 2.8), is the resulting solution a buffer?
A catalog in the lab has a recipe for preparing 1 L of a TRIS buffer at 0.0500 M and with pH 8.0: dissolve 2.02 g of TRIS (free base, MW = 121.1 g/mol) and 5.25 g of TRIS hydrochloride (the acidic
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? Table 2.8 Acid and Base Form of Some Useful Biochemical Buffers Name Acid
What would be the pH of the solution in Question 43 if you were to add 3.0 mL more of 1 M HCl?Question 43If 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
What is the ratio of concentrations of acetate ion and undissociated acetic acid in a solution that has a pH of 5.12?
Which of the buffers shown in Table 2.8 would you choose to make a buffer with a pH of 7.3? Explain why. Table 2.8 Acid and Base Form of Some Useful Biochemical Buffers Name Acid
You need to carry out an enzymatic reaction at pH 7.5. A friend suggests a weak acid with a pKa of 3.9 as the basis of a buffer. Will this substance and its conjugate base make a suitable buffer? Why
If the buffer suggested in Question 47 were made, what would be the ratio of the conjugate base/conjugate acid?Question 47You need to carry out an enzymatic reaction at pH 7.5. A friend suggests a
The solution in Question 35 is called 0.050 M, even though the concentration of neither the free base nor the conjugate acid is 0.050 M. Why is 0.050 M the correct concentration to report?Question
In Section 2-4, we said that at the equivalence point of a titration of acetic acid, essentially all the acid has been converted to acetate ion. Why do we not say that all the acetic acid has been
What quality of zwitterions makes them desirable buffers?
Many of the buffers used these days, such as HEPES and PIPES, were developed because they have desirable characteristics, such as resisting pH change with dilution. Why would resisting pH change with
Identify the zwitterions in the list of substances in Question 19.Question 19Identify the conjugate acids and bases in the following pairs of substances: (CH3)3 NH(CH3)
Another characteristic of modern buffers such as HEPES is that their pH changes little with changes in temperature.Why is this desirable?
A frequently recommended treatment for hiccups is to hold one’s breath. The resulting condition, hypoventilation, causes buildup of carbon dioxide in the lungs.Predict the effect on the pH of blood.
How do D-amino acids differ from L-amino acids? What biological roles are played by peptides that contain D-amino acids?
Identify the nonpolar amino acids and the acidic amino acids in the following peptide: Glu-Thr-Val-Asp-Ile-Ser-Ala
Which amino acid is technically not an amino acid? Which amino acid contains no chiral carbon atoms?
Calculate the isoelectric point of each of the following amino acids: glutamic acid, serine, histidine, lysine, tyrosine, and arginine.
An organic chemist is generally happy with 95% yields. If you synthesized a polypeptide and realized a 95% yield with each amino acid residue added, what would be your overall yield after adding 10
Suggest a reason why amino acids are usually more soluble at pH extremes than they are at neutral pH.
In each of the following two groups of amino acids, which amino acid would be the easiest to distinguish from the other two amino acids in the group, based on a titration?(a) Gly, leu, lys (b) Glu,
Could the amino acid glycine serve as the basis of a buffer system? If so, in what pH range would it be useful?
Sketch resonance structures for the peptide group.
How do the resonance structures of the peptide group contribute to the planar arrangement of this group of atoms?
Would the peptide group be planar if the amino group of amino acids was bonded to the β carbon of the amino acid, rather than to the α carbon?
Would you expect the titration curves of the two peptides in Question 28 to differ? Why or why not?Question 28Consider the peptides Ser—Glu—Gly— His—Ala and Gly—His—Ala—Glu—Ser. How
What are the sequences of all the possible tripeptides that contain the amino acids aspartic acid, leucine, and phenylalanine? Use the three-letter abbreviations to express your answer.
Using one-letter designations for the amino acids.
Most proteins contain more than 100 amino acid residues. If you decided to synthesize a “100-mer,” with 20 different amino acids available for each position, how many different molecules could
Why do we not indicate the side chains of the amino acids that form the peptide bond (see Figure 3.10)? :0: X-X H C=N Resonance structures of the peptide group. H Peptide group Peptide bond B The
If the amino acids alanine and glycine react to form a peptide bond, is there more than one reaction product? If so, what products?
Would the presence of a chiral center in an amino acid side chain affect the formation of a peptide bond?
Would the presence of a chiral center in an amino acid side chain affect the formation of a peptide bond?
Suggest a reason why the amino acids thyroxine and hydroxyproline are produced by posttranslational modification of the amino acids tyrosine and proline, respectively.
Consider the peptides Gly—Pro—Ser—Glu—Thr (open chain) and Gly—Pro—Ser—Glu—Thr with a peptide bond linking the threonine and the glycine. Are these peptides chemically the same?
Can you expect to separate the peptides in Question 39 by electrophoresis?Question 39Consider the peptides Gly—Pro—Ser—Glu—Thr (open chain) and Gly—Pro—Ser—Glu—Thr with a peptide bond
Suggest a reason why biosynthesis of amino acids and of proteins would eventually cease in an organism with carbohydrates as its only food source.
You are studying with a friend who draws the structure of alanine at pH 7. It has a carboxyl group (—COOH) and an amino group (—NH2). What suggestions would you make?
Suggest a reason (or reasons) why amino acids polymerize to form proteins that have comparatively few covalent crosslinks in the polypeptide chain.
Suggest the effect on the structure of peptides if the peptide group were not planar.
Speculate on the properties of proteins and peptides if none of the common amino acids contained sulfur.
Speculate on the properties of proteins that would be formed if amino acids were not chiral.
How do the peptide hormones oxytocin and vasopressin differ in function?
What is the role of the disulfide bond in oxytocin and vasopressin?
Is it possible to form cyclic peptides without bonds between side chains of the component amino acids?
Imagine we identify a gene that is directly responsible for the effects of vasopressin on male mammals, including humans—we will call it trust1—that leads to the production of a vasopressin
What types of experiments led to evidence regarding the effect of oxytocin and vasopressin on mammalian behavior?
How has oxytocin been implicated in human behavior?
What types of experiments led to evidence regarding the effect of oxytocin and vasopressin on mammalian behavior?
Define denaturation in terms of the effects of secondary, tertiary, and quaternary structure.
Suggest an explanation for the observation that when proteins are chemically modified so that specific side chains have a different chemical nature, these proteins cannot be denatured reversibly.
Glycine is a highly conserved amino acid residue in proteins (i.e., it is found in the same position in the primary structure of related proteins). Suggest a reason why this might occur.
A biochemistry student characterizes the process of cooking meat as an exercise in denaturing proteins.Comment on the validity of this remark.
List three major differences between fibrous and globular proteins.
What is a β-bulge?
What is a reverse turn? Draw two types of reverse turns
List some of the differences between the α-helix and β-sheet forms of secondary structure.
List some of the possible combinations of α-helices and β-sheets in supersecondary structures.
Why must glycine be found at regular intervals in the collagen triple helix?
Draw two hydrogen bonds, one that is part of a secondary structure and another that is part of a tertiary structure.
Draw a possible electrostatic interaction between two amino acids in a polypeptide chain.
Draw a disulfide bridge between two cysteines in a polypeptide chain.
Draw a region of a polypeptide chain showing a hydrophobic pocket containing nonpolar side chains.
What are the two critical amino acids near the heme group in both myoglobin and hemoglobin?
What is the highest level of organization in myoglobin? In hemoglobin?
Describe the Bohr effect.
How does the oxygen-binding curve of fetal hemoglobin differ from that of adult hemoglobin?
What is the critical amino acid difference between the β-chain and the γ-chain of hemoglobin?
Suggest a reason for the observation that people with sickle-cell trait sometimes have breathing problems during high-altitude flights.
Does a fetus homozygous for sickle-cell hemoglobin (Hb S) have normal Hb F?
Why is proline frequently encountered at the places in the myoglobin and hemoglobin molecules where the polypeptide chain turns a corner?
Assume that you are getting ready to do an amino acid sequencing experiment on a protein containing 100 amino acids, and amino acid analysis shows the following data:Which of the chemicals or enzymes
Why might you expect to find some Hb F in adults who are afflicted with sickle-cell anemia?
What is the direct cause of sicklecell anemia (think primary structure)?
Why do scientists believe that the sickle-cell trait has not evolved out of the human population yet considering how deadly it is to be homozygous for the sickle cell gene?
What is the purpose of treating a sickle-cell patient with hydroxyurea?
What is BCL11A and how is it related to hemoglobin?
You have discovered a new protein, one whose sequence has about 25% homology with ribonuclease A. How would you go about predicting, rather than experimentally determining, its tertiary structure?
What is a chaperone?
What are the protein secondary structures that differ between a normal prion and an infectious one?
What is the nature of the prion mutation that leads to extreme sensitivity to prion disease?
Severe combined immunodeficiency disease (SCID) is characterized by the complete lack of an immune system. Strains of mice have been developed that have SCID. When SCID mice that carry genetic
An isolated strain of sheep was found in New Zealand. Most of these sheep carried the gene for predisposition to scrapie, yet none of them ever came down with the disease. How do these facts relate
What types of homogenization techniques are available for solubilizing a protein?
When would you choose to use a Potter–Elvehjem homogenizer instead of a blender?
What differences between proteins are responsible for their differential solubility in ammonium sulfate?
Can you separate mitochondria from peroxisomes using only differential centrifugation?
Describe a procedure for isolating a protein that is strongly embedded in the mitochondrial membrane.
What is the order of elution of proteins on a gel-filtration column? Why is this so?
What are two types of compounds that make up the resin for column chromatography?
Draw an example of a compound that would serve as a cation exchanger. Draw one for an anion exchanger.
Draw an example of a compound that would serve as a cation exchanger. Draw one for an anion exchanger.
Sephadex G-75 has an exclusion limit of 80,000 molecular weight for globular proteins. If you tried to use this column material to separate alcohol dehydrogenase (MW 150,000) from β-amylase (MW
Referring to Question 19, could you separate β-amylase from bovine serum albumin (MW 66,000) using this column?Question 19Sephadex G-75 has an exclusion limit of 80,000 molecular weight for globular

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