What region of an enzyme is responsible for its specificity?
> Why is the genetic code said to be mutation-resistant?
> What is meant by a triplet code?
> What is the function of the cap structure on eukaryotic mRNA?
> What is the purpose of the poly(A) tail on eukaryotic mRNA?
> What are snRNPs? How do they facilitate RNA splicing?
> What is the function of each of the classes of RNA molecules?
> The following is the unspliced transcript of a eukaryotic gene: What would the structure of the final mature mRNA look like, and which of the above sequences would be found in the mature mRNA? exon 1 intron A exon 2 intron B exon 3 intron C exon 4
> Distinguish among the four plasma lipoproteins in terms of their composition and their function.
> If an RNA strand has the nucleotide sequence 59-AUGCCAUAACGAUACCCAGUC-39 what was the sequence of the DNA strand that was transcribed?
> On what molecule is the codon found?
> What is the binding site of an enzyme active site?
> Define the term active site.
> What does a graph of enzyme activity versus substrate concentration tell us about the nature of enzymecatalyzed reactions?
> What is occurring at the replication fork?
> If the sequence of a double-stranded DNA molecule is what would the sequence of the two daughter DNA molecules be after DNA replication? Indicate which strands are newly synthesized and which are parental. 5'-CATAAGTCGAGACCGTTACTCACTACTGGAC-3' 3'-G
> If an enzyme does not alter the equilibrium constant of a reaction, how does it speed up the reaction?
> Define the term product.
> Write the structure that results when adenosine-59- monophosphate is linked by a −3−−9− → 59 phosphodiester bond to uridine-59-monophosphate.
> Using the periodic table, write the electron configuration and orbital diagram of each of the following atoms: a. V b. Cd c. Te
> Draw the guanine-cytosine base pair and indicate the hydrogen bonds that link them.
> What is the most common characteristic used to classify enzymes?
> List three differences between DNA and RNA.
> One of the energy-harvesting steps of the citric acid cycle results in the production of GTP. What is the structure of the GTP nucleotide?
> a. Draw the ring structure of the pyrimidines. b. In a nucleotide, which nitrogen atom of pyrimidine rings is bonded to the sugar?
> Heating is an effective mechanism for killing bacteria on surgical instruments. How does elevated temperature result in cellular death?
> What is the relationship between pepsin and pepsinogen?
> Repeat Question 19.95 for the peptide trp-pro-gly-tyr. Question 19.95: Draw the complete structural formula for the peptide tyrlys- ala-phe. Show which bond would be broken when this peptide is reacted with chymotrypsin.
> What properties are shared by chymotrypsin, trypsin, and elastase?
> The addition of phenylthiourea to a preparation of the enzyme polyphenoloxidase completely inhibits the activity of the enzyme. a. Knowing that phenylthiourea binds all copper ions, what conclusion can you draw about whether polyphenoloxidase requires a
> As you increase the temperature of an enzyme-catalyzed reaction, the rate of the reaction initially increases. It then reaches a maximum rate and finally dramatically declines. Keeping in mind that enzymes are proteins, how do you explain these changes i
> Why are irreversible enzyme inhibitors often called poisons?
> Fibrinogen and prothrombin are both involved in formation of blood clots when they are converted into proteolytic enzymes. However, they are normally found in the blood in an inactive form. Develop an explanation for this observation.
> Three proenzymes that are involved in digestion of proteins in the stomach and intestines are pepsinogen, chymotrypsinogen, and trypsinogen. What is the advantage of producing these enzymes as inactive peptides?
> What is the transition state in an enzyme-catalyzed reaction?
> How do sickled red blood cells hinder circulation?
> Why do extremes of pH inactivate enzymes?
> Describe the structure of myoglobin.
> An increase in temperature will increase the rate of a reaction if a nonenzymatic catalyst is used; however, an increase in temperature will eventually decrease the rate of a reaction when an enzyme catalyst is used. Explain the apparent contradiction of
> Define the optimum pH for enzyme activity.
> Explain why a-keratins that have many disulfide bonds between adjacent polypeptide chains are much less elastic and much harder than those without disulfide bonds.
> Draw the Lewis structure of NO2-.
> How does a coenzyme function in an enzyme-catalyzed reaction?
> If an enzyme catalyzed a reaction by modifying the local pH, what kind of amino acid R groups would you expect to find in the active site?
> What is the relationship between an enzyme active site and its substrate?
> Describe the transition state.
> Provide an example of an enzyme with stereochemical specificity and explain the advantage of stereochemical specificity for that particular enzyme.
> Provide an example of an enzyme with linkage specificity and explain the advantage of linkage specificity for that particular enzyme.
> What is meant by the term stereochemical specificity?
> What is meant by the term linkage specificity?
> Why is the induced fit model of enzyme-substrate binding a much more accurate model than the lock-and-key model?
> What is the net ATP yield for degradation of each of the amino acids listed in Question 22.85? Question 22.85: Into which citric acid cycle intermediate is each of the following amino acids converted? a. Alanine b. Glutamate c. Aspartate d. Phenylal
> If enzyme active sites are small, why are enzymes so large?
> What chemical reaction is mediated by each of the enzymes in Question 19.3? Question 19.3: What is the substrate for each of the following enzymes? a. Sucrase b. Pyruvate decarboxylase c. Succinate dehydrogenase
> How does the rate-limiting step influence an enzymecatalyzed reaction?
> Why doesn’t the rate of an enzyme-catalyzed reaction increase indefinitely when the substrate concentration is made very large?
> What is the effect of an enzyme on the activation energy of a reaction?
> List the six classes of enzymes based on the type of reaction catalyzed. Briefly describe the function of each class, and provide an example of each.
> Give a systematic name for the enzyme that would act on each of the following substrates: a. Alanine b. Citrate c. Ampicillin d. Ribose e. Methylamine
> Draw the structural formula of the peptide trp-val-lys-ala-ser. Show which bonds would be cleaved by trypsin, chymotrypsin, and elastase.
> What is the IUPAC name for each of the fatty acids in Question 17.1? (Hint: Review the naming of carboxylic acids in Section 14.1, and Table 17.1.) Question 17.1: Draw formulas for each of the following fatty acids: a. Oleic acid b. Lauric acid c. Li
> Draw the structural formulas of the following peptides, and show which bond would be cleaved by chymotrypsin. a. trp-val-gly b. phe-ala-pro
> By comparing two solutions: 0.50 M sodium chloride (an ionic compound) and 0.50 M sucrose (a covalent compound). Calculate the boiling temperature of each solution. Assume that the molality of each solution is 0.50 m. (The molar and molal concentrations
> How can structural analogs serve as enzyme inhibitors?
> Explain the difference between an irreversible inhibitor and a reversible, competitive inhibitor.
> What are the coenzymes formed from each of the following vitamins? What are the functions of each of these coenzymes? a. Pantothenic acid b. Niacin c. Riboflavin
> Name some ethnic foods that apply the principle of mixing vegetable proteins to provide all of the essential amino acids.
> Write an equation representing the action of the proteolytic enzyme trypsin. (Hint: In order to write the structure of a dipeptide that would be an appropriate reactant, you must consider what is known about where trypsin cleaves a protein chain.)
> Define the term incomplete protein.
> Define the term nonessential amino acid.
> Wine is made from the juice of grapes by varieties of yeast. The yeast cells produce ethanol as a by-product of their fermentation. However, when the ethanol concentration reaches 12–13%, all the yeast die. Explain this observation.
> Where in the body do you find glycogen stored?
> What are the possible side effects of cortisone treatment?
> In step 10 of glycolysis, phosphoenolpyruvate is converted to pyruvate, and ATP is produced by substrate level phosphorylation. How is this reaction bypassed in gluconeogenesis?
> How is oxygen efficiently transferred from mother to fetus?
> The blood of the horseshoe crab is blue because of the presence of a protein called hemocyanin. What is the function of hemocyanin?
> Write an equation representing the binding to and release of oxygen from hemoglobin.
> What is the function of myoglobin?
> Why are glycosidic bonds acetals?
> Draw the structure of a lecithin molecule in which the fatty acyl groups are derived from arachidic acid.
> What is a prosthetic group?
> What weak interactions are responsible for maintaining quaternary protein structure?
> Write a complete equation for the acid hydrolysis of butyl acetate. Write the IUPAC name for each of the organic reactants and products.
> Why is the amino acid proline often found in the random coil hinge regions of the tertiary structure?
> a. Calculate the boiling temperature of 1.50 m urea, N2H4CO. Urea is a covalent compound. b. Calculate the boiling temperature of 1.50 m LiBr, an ionic compound.
> What is the role of cystine in maintaining protein structure?
> What is a Haworth projection?
> Compare a parallel b-pleated sheet to an antiparallel b-pleated sheet.
> What is the relationship between the structure of fibrous proteins and their functions?
> Describe the forces that maintain the two types of secondary structure: a-helix and b-pleated sheet.
> What are the two most common types of secondary structure?
> Write a balanced equation showing peptide bond formation between threonine and aspartate.
> Explain the relationship between the primary structure of a protein and the gene for that protein.
> What type of bond joins the amino acids to one another in the primary structure of a protein?
> Write the structure of each of the following peptides at pH 7: a. Glycyl-valyl-serine b. Threonyl-cysteine c. Isoleucyl-methionyl-aspartate
> Of what value are restriction enzymes in recombinant DNA research?
> Using line formulas, write an equation for the hydrogenation of all cis-4,7,10,13,16,19-docosahexaenoic acid.
> Draw the resonance hybrids that represent the peptide bond.
> Write an equation for the acid hydrolysis of a triglyceride containing three capric acid molecules.
> Write the structures of the positively charged amino acids. Indicate whether you would expect to find each on the surface or buried in a globular protein.
> What are the common and IUPAC names of each of the following fatty acids? a. CH3(CH2)5CH ——CH(CH2)7COOH b. CH3(CH2)7CH ——CH(CH2)7COOH
