Questions and Answers of Biochemistry Concepts And Connections

What is the importance of pyrophosphatase in the synthesis of nucleic acids?
What would happen to the replication process if the growing DNA chain did not have a free 3' end?
Suggest a reason for the rather large energy “overkill” in inserting a deoxyribonucleotide into a growing DNA molecule. (About 15 kcal mol–1 is used in forming a phosphate ester bond that
Why is it not surprising that the addition of nucleotides to a growing DNA chain takes place by nucleophilic substitution?
Is it unusual that the β-subunits of DNA polymerase III that form a sliding clamp along the DNA do not contain the active site for the polymerization reaction? Explain your answer.
List the substances required for replication of DNA catalyzed by DNA polymerase.
What are the functions of the gyrase, primase, and ligase enzymes in DNA replication?
Single-stranded regions of DNA are attacked by nucleases in the cell, yet portions of DNA are in a single-stranded form during the replication process. Explain.
Describe the role of DNA ligase in the replication process.
What is the primer in DNA replication?
How does the replication process take place on a supercoiled DNA molecule?
Why is a short RNA primer needed for replication?
What was the recent change in the estimated number of Pol III enzymes that are associated with the replisome?
What experiments led to the change in our understanding of the stoichiometry regarding the replisome
Why is a clamp loader necessary in replication?
How does proofreading take place in the process of DNA replication?
How does proofreading take place in the process of DNA replication?
Describe the excision repair process in DNA, using the excision of thymine dimers as an example.
Of what benefit is it for DNA to have thymine rather than uracil?
Your book contains about 2 million characters (letters, spaces, and punctuation marks). If you could type with the accuracy with which the prokaryote E. coli incorporates, proofreads, and repairs
E. coli incorporates deoxyribonucleotides into DNA at a rate of 250 to 1000 bases per second. Using the higher value, translate this into typing speed in words per minute.
Given the typing speed from Question 37, how long must you type, nonstop, at the fidelity shown by E. coli before an uncorrected error would be permitted?Question 37E. coli incorporates
Can prokaryotes deal with drastic DNA damage in ways that are not available to eukaryotes?
What is a direct way of repairing double-stranded DNA breaks?
What proteins are used in NHEJ?
Why is NHEJ an error-prone mechanism?
What is the role of Ku70/80 in direct repair of DSBs?
What is homologous recombination?
How has the use of DNA labeled with heavy isotopes been instrumental in our understanding of replication?
What is the Holliday Model?
Do eukaryotes have fewer origins of replication than prokaryotes, or more origins, or the same number?
How does DNA replication in eukaryotes differ from the process in prokaryotes?
What role do histones play in DNA replication?
(a) Eukaryotic DNA replication is more complex than prokaryotic replication. Give one reason why this should be so.(b) Why might eukaryotic cells need more kinds of DNA polymerases than bacteria?
How do the DNA polymerases of eukaryotes differ from those of prokaryotes?
Would it be advantageous to a eukaryotic cell to have histone synthesis take place at a faster rate than DNA synthesis?
Outline a series of steps by which reverse transcriptase produces DNA on an RNA template.
Name an important difference in the replication of circular DNA versus linear double-stranded DNA.
Why is it reasonable that eukaryotes have a DNA polymerase (Pol γ) that operates only in mitochondria?
What is meant by the “RNA world”?
Why are scientists excited to find that RNA molecules can be made that are self-replicating?
A friend who is enthusiastic about health foods and organic gardening asks you whether urea is “organic” or “chemical.” How do you reply to this question?
An earlier mission to Mars contained instruments that determined that amino acids were present on the surface of Mars. Why were scientists excited by this discovery?
Common proteins are polymers of 20 different amino acids. How big a protein (how many amino acid residues) would be necessary to have an Avogadro’s number of possible sequences?
Nucleic acids are polymers of just four different monomers in a linear arrangement. How many different sequences are available if one makes a polymer with only 40 monomers?How does this number
RNA is often characterized as being the first “biologically active” molecule. What two properties or activities does RNA display that are important to the evolution of life?
Why is the development of catalysis important to the development of life?
What are two major advantages of enzyme catalysts in living organisms when compared with other simple chemical catalysts such as acids or bases?
Why was the development of a coding system important to the development of life?
Do the sites of protein synthesis differ in prokaryotes and eukaryotes?
Draw an idealized animal cell, and identify the parts by name and function.
Draw an idealized plant cell, and identify the parts by name and function.
Which organelles are surrounded by a double membrane?
Which organelles contain DNA?
Which organelles are the sites of energy-yielding reactions?
List the five kingdoms into which living organisms are divided, and give at least one example of an organism belonging to each kingdom.
Which of the five kingdoms consist of prokaryotes? Which consist of eukaryotes?
How does the five-kingdom classification differ from the one based only on plants and animals?
Mitochondria and chloroplasts contain some DNA, which more closely resembles prokaryotic DNA than (eukaryotic) nuclear DNA. Use this information to suggest how eukaryotes may have originated.
Fossil evidence indicates that prokaryotes have been around for about 3.5 billion years, whereas the origin of eukaryotes has been dated at only about 1.5 billion years ago. Suggest why, in spite of
Which processes are favored: those that require energy or those that release energy?
Does the thermodynamic term spontaneous refer to a process that takes place quickly?
For the process Nonpolar solute + H2O → Solution what are the signs of ΔSuniv, ΔSsys, and ΔSsurr? What is the reason for each answer? (ΔSsurr refers to the entropy change of the surroundings,
In which of the following processes does the entropy increase? In each case, explain why it does or does not increase.(a) A bottle of ammonia is opened. The odor of ammonia is soon apparent
Why is it necessary to specify the temperature when making a table listing ΔG values?
Why is the entropy of a system dependent on temperature?
A reaction at 23°C has ΔG = 1 kJ mol–1. Why might this reaction become spontaneous at 37°C?
Urea dissolves very readily in water, but the solution becomes very cold as the urea dissolves. How is this possible? It appears that the solution is absorbing energy.
Would you expect the reaction ATP → ADP + Pi to be accompanied by a decrease or increase in entropy? Why?
The existence of organelles in eukaryotic cells represents a higher degree of organization than that found in prokaryotes. How does this affect the entropy of the Universe
Why is it advantageous for a cell to have organelles? Discuss this concept from the standpoint of thermodynamics.
Which would you expect to have a higher entropy: DNA in its well-known double-helical form, or DNA with the strands separated?
How would you modify your answer to Question 29 in light of the material on thermodynamics?
Would it be more or less likely that cells of the kind we know would evolve on a gas giant such as the planet Jupiter?
What thermodynamic considerations might enter into finding a reasonable answer to Question 46?Question 46Would it be more or less likely that cells of the kind we know would evolve on a gas giant
If cells of the kind we know were to have evolved on any other planet in our solar system, would it be more likely to have happened on Mars or on Jupiter? Why?
The process of protein folding is spontaneous in the thermodynamic sense. It gives rise to a highly ordered conformation that has a lower entropy than the unfolded protein.How can this be?
Why is water necessary for life?
Contemplate biochemistry if atoms did not differ in electronegativity.
What is a van der Waals force?
What is an induced dipole?
What is a salt bridge?
Under what circumstance is a molecule that has a dipole not a polar molecule?
List the three types of van der Waals forces in decreasing order of strength.
A hydrogen bond is a special case of what type of intermolecular force?
What are some macromolecules that have hydrogen bonds as a part of their structures?
How are hydrogen bonds involved in the transfer of genetic information?
Rationalize the fact that hydrogen bonding has not been observed between CH4 molecules.
Draw three examples of types of molecules that can form hydrogen bonds.
What are the requirements for molecules to form hydrogen bonds?
Many properties of acetic acid can be rationalized in terms of a hydrogen-bonded dimer. Propose a structure for such a dimer.
How many water molecules could hydrogenbond directly to the molecules of glucose, sorbitol, and ribitol, shown here?
Both RNA and DNA have negatively charged phosphate groups as part of their structure. Would you expect ions that bind to nucleic acids to be positively or negatively charged? Why?
Identify the conjugate acids and bases in the following pairs of substances: (a) (CH3)3 NH(CH3) 3N (c) (b) *HgN-CH₂COOH/*H3N-CH₂-COO H₂N-CH₂-COO7H₂N-CH₂-COO (d)
Look at Figure 2.17. If you did this titration using TRIS instead of phosphate, how would the titration curve look compared to the figure? Explain. Figure 2.17 Buffering. Acid is added to the two
Aspirin is an acid with a pKa of 3.5; its structure includes a carboxyl group. To be absorbed into the bloodstream, it must pass through the membrane lining the stomach and the small intestine.
Why does the pH change by one unit if the hydrogen ion concentration changes by a factor of 10?
List the criteria used to select a buffer for a biochemical reaction.
Calculate the pH of a buffer solution that contains 0.10 M acetic acid (Table 2.6) and 0.25 M sodium acetate. Table 2.6 Acid Pyruvic acid Formic acid Lactic acid Benzoic acid Acetic acid Dissociation
Calculate the pH of a buffer solution prepared by mixing 75 mL of 1.0 M lactic acid (see Table 2.6) and 25 mL of 1.0 M sodium lactate. Table 2.6 Acid Pyruvic acid Formic acid Lactic acid Benzoic

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