Cell Biology West Final HW Questions
Figure Q7-42 shows an mRNA molecule. Figure Q7-42 A. Match the labels given in the list below with the label lines in Figure Q7-42. (a) ribosome-binding site (b) initiator codon (c) stop codon (d) untranslated 3′ region (e) untranslated 5′ region (f) protein-coding region B. Is the mRNA shown procaryotic or eucaryotic? Explain your answer.
(A) a. 3 b. 3 c. 4 d. 6 e. 1 f. 5 (B) Prokaryotic because it contains regions for more than one protein
The process of generating monoclonal antibodies is labor-intensive and expensive. An alternative is to use polyclonal antibodies. A subpopulation of purified polyclonal antibodies that recognize a particular antigen can be isolated by chromatography. Which type of chromatography is used for this purpose? (a) affinity (b) ion-exchange (c) gel-filtration (d) any of the above
A) affinity
Which of the following statements about the genetic code is correct? (a) All codons specify more than one amino acid. (b) The genetic code is redundant. (c) All amino acids are specified by more than one codon. (d) All codons specify an amino acid.
B) The genetic code is redundant.
Which DNA base pair is represented in Figure Q5-12? (a) A-T (b) T-A (c) G-C (d) C-G
C) G-C
On the phospholipid molecule in Figure Q2-35 label each numbered line with a correct term selected from the list below.
1) D. polar head 2) A. phosphate 3) C. glycerol 4) J. nonsaturated FA 5) I. hydrophilic region 6) H. hydrophobic region 7) E. saturated FA
Because hydrogen bonds hold the two strands of a DNA molecule together, the strands can be separated without breaking any covalent bonds. Every unique DNA molecule "melts" at a different temperature. In this context, Tm, melting temperature, is the point at which two strands separate, or become denatured. Order the DNA sequences listed below according to relative melting temperatures (from lowest Tm to highest Tm). Assume that they all begin as stable double-stranded DNA molecules. Explain your answer. A. GGCGCACC B. TATTGTCT C. GACTCCTG D. CTAACTGG
1. B 2. D 3. C 4. A The more C and G's that are present with bring up the boiling point because of their 3 bonds.
Name three covalent modifications that can be made to an RNA molecule in eucaryotic cells before the RNA molecule becomes a mature mRNA.
1. a poly A tail is added 2. a 5' cap is added 3. introns can be spliced out
Arrange the following molecules in order with respect to their relative levels of oxidation (assign 5 to the most oxidized and 1 to the most reduced). _______ CH2O (formaldehyde) _______ CH4 (methane) _______ CHOOH (formic acid) _______ CH3OH (methanol) _______ CO2 (carbon dioxide)
3 1 4 2 5
Given the sequence of one strand of a DNA helix as 5′-GCATTCGTGGGTAG-3′, give the sequence of the complementary strand and label the 5′ and 3′ ends.
5'-CTACCCACGAATGC-3'
Consider the reaction X→Y in a cell at 37°C. At equilibrium, the concentrations of X and Y are 50 μM and 5 μM, respectively. Using the equations below and your new knowledge, answer the following questions. ΔG° = -0.616 ln Keq ΔG = ΔG° + 0.616 ln [Y]/[X] Recall that the natural log of a number z will have a negative value when z < 1, positive when z > 1, and 0 when z = 1. A. What is the value of Keq for this reaction? B. Is the standard free-energy change of this reaction positive or negative? Is the reaction X→Y an energetically favorable or unfavorable reaction under standard conditions? C. What is the value of the standard free energy? Refer to Table 3-1 in the textbook or use a calculator. D. Imagine circumstances in which the concentration of X is 1000 μM and that of Y is 1 μM. Is conversion of X to Y favorable? Will it happen quickly? E. Imagine starting conditions in which the reaction X→Y is unfavorable, yet the cell needs to produce more Y. Describe two ways in which this may be accomplished.
A) 0.1 B) ΔG°= -0.616 C) 1.42 kcal/mol D) Not necessarily; Most consider energy of activation, this is just thermodynamics E) couple to a favorable reaction; Increase X or Decrease Y
A. What is the pH of pure water? B. What concentration of hydronium ions does a solution of pH 8 contain? C. Complete the following reaction: CH3COOH + H2O ↔ __________. D. Will the reaction in C occur more readily (be driven to the right) if the pH of the solution is high?
A) 1 B) 10-8 C) CH3COO- D) Yes
Isomerization of glucose 1-phosphate to glucose 6-phosphate is energetically favorable. At 37°C, ΔG° = -1.42 log10K. What is the equilibrium constant for this reaction if ΔG° = -1.74 kcal/mole at 37°C? (a) 16.8 (b) 0.09 (c) -0.09 (d) 0.39
A) 16.8
A. How many carbon atoms does the molecule represented in Figure Q2-32 have? B. How many hydrogen atoms does it have? C. What type of molecule is it?
A) 20 B) 31 C) 6 fatty acid
Match the following structures with their names. Figure Q7-4
A) 4 B) 1 C) 2 D) 3
Below is the sequence from the 3′ end of an mRNA. 5′-CCGUUACCAGGCCUCAUUAUUGGUAACGGAAAAAAAAAAAAAA-3′ If you were told that this sequence contains the stop codon for the protein encoded by this mRNA, what is the anticodon on the tRNA in the P-site of the ribosome when release factor binds to the A-site? (a) 5′-CCA-3′ (b) 5′-CCG-3′ (c) 5′-UGG-3′ (d) 5′-UUA-3′
A) 5'-CCA-3'
Larger molecules have hydrogen-bonding networks that contribute to specific, high-affinity binding. Smaller molecules such as urea can also form these networks. How many hydrogen bonds can urea form if dissolved in water? (a) 6 (b) 5 (c) 3 (d) 4
A) 6
During respiration, energy is retrieved from the high-energy bonds found in certain organic molecules. Which of the following, in addition to energy, are the ultimate products of respiration? (a) CO2, H2O (b) CH3, H2O (c) CH2OH, O2 (d) CO2, O2
A) CO2, H2O
The repair of mismatched base pairs or damaged nucleotides in a DNA strand requires a multistep process. Which choice below describes the known sequence of events in this process? (a) DNA damage is recognized, the newly synthesized strand is identified by an existing nick in the backbone, a segment of the new strand is removed by repair proteins, the gap is filled by DNA polymerase, and the strand is sealed by DNA ligase. (b) DNA repair polymerase simultaneously removes bases ahead of it and polymerizes the correct sequence behind it as it moves along the template. DNA ligase seals the nicks in the repaired strand. (c) DNA damage is recognized, the newly synthesized strand is identified by an existing nick in the backbone, a segment of the new strand is removed by an exonuclease, and the gap is repaired by DNA ligase. (d) A nick in the DNA is recognized, DNA repair proteins switch out the wrong base and insert the correct base, and DNA ligase seals the nick.
A) DNA damage is recognized, the newly synthesized strand is identified by an existing nick in the backbone, a segment of the new strand is removed by repair proteins, the gap is filled by DNA polymerase, and the strand is sealed by DNA ligase.
Several experiments were required to demonstrate how traits are inherited. Which scientist or team of scientists first demonstrated that cells contain some component that can be transferred to a new population of cells and permanently cause changes in the new cells? (a) Griffith (b) Watson and Crick (c) Avery, MacLeod, and McCarty (d) Hershey and Chase
A) Griffith
Drawn below are segments of β sheets, which are rigid pleated structures held together by hydrogen bonds between the peptide backbones of adjacent strands (Figure Q4-19). The amino acid side chains attached to the Cα carbons are omitted for clarity.
A) Parallel B) Antiparallel
Transcription in bacteria differs from transcription in a eucaryotic cell because __________________________. (a) RNA polymerase (along with its sigma subunit) can initiate transcription on its own (b) RNA polymerase (along with its sigma subunit) requires the general transcription factors to assemble at the promoter before polymerase can begin transcription (c) The sigma subunit must associate with the appropriate type of RNA polymerase to produce mRNAs (d) RNA polymerase must be phosphorylated at its C-terminal tail for transcription to proceed
A) RNA polymerase (along with its sigma subunit) can initiate transcription on its own
Oligosaccharides are short sugar polymers that can become covalently linked to proteins and lipids through condensation reactions. These modified proteins and lipids are called glycoproteins and glycolipids. Within a protein, which of the amino acids (shown in Figure Q2-30) is the most probable target for this type of modification? Figure Q2-30 (a) serine (b) glycine (c) phenylalanine (d) methionine
A) Serine
Sometimes chemical damage to DNA can occur just before DNA replication begins, not giving the repair system enough time to correct the error before the DNA is duplicated. This gives rise to mutation. If the cytosine in the sequence TCAT is deaminated and not repaired, which of the following is the point mutation you would observe after this segment has undergone two rounds of DNA replication? (a) TTAT (b) TUAT (c) TGAT (d) TAAT
A) TTAT
Which of the following does not occur before a eucaryotic mRNA is exported from the nucleus? (a) The ribosome binds to the mRNA. (b) The mRNA is polyadenylated at its 3′ end. (c) 7-methyl-G is added in a 5′ to 5′ linkage to the mRNA. (d) RNA polymerase dissociates.
A) The ribosome binds to the mRNA.
The amino acids glutamine and glutamic acid are shown in Figure Q2-29. They differ only in the structure of their side chains (circled). At pH 7, glutamic acid can participate in molecular interactions that are not possible for glutamine. What types of interaction are these? Figure Q2-29 (a) ionic bonds (b) hydrogen bonds (c) van der Waals interactions (d) covalent bonds
A) ionic bonds
The classic "beads-on-a-string" structure is the most decondensed chromatin structure possible and is produced experimentally. Which chromatin components are not retained when this structure is generated? (a) linker histones (b) linker DNA (c) nucleosome core particles (d) core histones
A) linker histones
Which of the following expressions accurately describes the calculation of pH? (a) pH = -log10[H+] (b) pH = log10[H+] (c) pH = -log2[H+] (d) pH = -log10[OH-]
A) pH = -log10[H+]
The DNA from two different species can often be distinguished by a difference in the ______________________. (a) ratio of A + T to G + C (b) ratio of A + G to C + T (c) ratio of sugar to phosphate (d) presence of bases other than A, G, C, and T
A) ratio of A + T to G + C
You have two purified samples of protein Y: the wild-type (nonmutated) protein and a mutant version with a single amino acid substitution. When washed through the same gel-filtration column, mutant protein Y runs through the column more slowly than the normal protein. Which of the following changes in the mutant protein is most likely to explain this result? (a) the loss of a binding site on the mutant protein surface through which protein Y normally forms dimers (b) a change that results in the mutant protein's acquiring an overall positive instead of a negative charge (c) a change that results in the mutant protein's being larger than the wild-type protein (d) a change that results in the mutant protein's having a slightly different shape from the wild-type protein
A) the loss of a binding site on the mutant protein surface through which protein Y normally forms dimers
Which of the choices below represents the correct way to repair the mismatch shown in Figure Q6-26?
A.
A. You are measuring the effect of temperature on the rate of an enzyme-catalyzed reaction. If you plot reaction rate against temperature, which of the graphs in Figure Q3-43 would you expect your plot to resemble? B. Explain why temperature has this effect.
A. 1 B. At low temperatures, the reaction is slow because molecular motion is slow. As the temperature is raised, the rate increases until at a critical point at which the protein is destabilized and eventually denatures.
The first reaction in glycolysis is the phosphorylation of glucose: Pi + glucose glucose-6-phosphate This is a thermodynamically unfavorable process, with Go = +14 kJ/mole Note: R = 0.008314 kJ / Degree*mole; T = absolute temperature (Kelvin) a) In a liver cell at 37 degrees Celsius, the concentrations of both phosphate and glucose are normally maintained at about 5mM each. What would the equilibrium concentration of glucose-6-phosphate be, according to the above data? b) This very low concentration of the desired product would be very unfavorable for glycolysis. In fact, the reaction is coupled to ATP hydrolysis to give the overall reaction ATP + water ADP + Pi Given that the Go = -31 kJ/mole for the hydrolysis of ATP to ADP, what is the Go for the net reaction now? c) If, in addition to the constraints on glucose concentration listed above, we have in the liver cell [ATP] = 3mM and [ADP] = 1mM, what is the equilibrium concentration of glucose-6-phosphate? The answer you will obtain is an absurdly high value for the cell and in fact is never approached in reality. Why?
A. 1.1x10-3 mM B. -17 kJ/mol C. [G-6-P]
The human genome comprises 23 pairs of chromosomes found in nearly every cell in the body. Answer the quantitative questions below by choosing one of the numbers in the following list: 23 69 >200 46 92 >109 A. How many centromeres are in each cell? What is the main function of the centromere? B. How many telomeres are in each cell? What is their main function? C. What is the main function of the origins of replication?
A. 46; distribution of chromosomes to daughter cells during mitosis B. 92; protect the ends of the chromosomes and to enable transcription C. >200; direct the intiation of DNA synthesis
One strand of a section of DNA isolated from the bacterium E. coli reads: 5′-GTAGCCTACCCATAGG-3′ A. Suppose that an mRNA is transcribed from this DNA using the complementary strand as a template. What will be the sequence of the mRNA in this region (make sure you label the 5′ and 3′ ends of the mRNA)? B. How many different peptides could potentially be made from this sequence of RNA, assuming that translation initiates upstream of this sequence? C. What are these peptides? (Give your answer using the one-letter amino acid code.)
A. 5'-GUAGCCUACCCAUAGG-3' B. Two C. VAYP; SLPIG
Figure Q4-18 shows a fatty acid binding protein from two different angles. Apart from its two short α helices, its structural elements are extended strands that form a curved β sheet, which is called a β barrel. Draw arrows on the six top strands in panel (A) (those running horizontally) to determine whether the β barrel is made up of parallel or antiparallel strands. Look at panel (B) and predict the relative distribution of polar and nonpolar side chains (inside the barrel or outside the barrel) and explain your answer.
A. Antiparallel B. outside is polar and exposed to aqueous environment; FA binding site is nonpolar and hydrophobic
Your lab director requests that you add new growth medium to the mammalian cell cultures before heading home from the lab on a Friday night. Unfortunately, you need to make fresh medium because all the pre-mixed bottles of medium have been used. One of the ingredients you know you need to add is a mix of the essential amino acids (those that cannot be made by the cells, but are needed in proteins). On the shelf of dry chemicals you find the amino acids you need, and you mix them into your medium, along with all the other necessary nutrients and replace the old medium with your new medium. On Sunday, you come in to the lab just to check on your cells and find that the cells have not grown. You are sure you made the medium correctly, but on checking you see that somebody wrote a note on the dry mixture of amino acids you used: "Note: this mixture contains only D-amino acids." A. What is the meaning of the note and how does it explain the lack of cell growth in your culture? B. Are there any organisms that could grow using this mixture? Justify your answer.
A. D applies to the stereochemistry. Proteins are made from only L-isomers. B. No. All need the L-amino acids to make proteins.
Eucaryotic cells have their DNA molecules inside their nuclei. However, to package the DNA all into such a small volume requires the cell to use specialized proteins called histones. Histones have amino acid sequences enriched for lysines and arginines. A. What problem might a cell face in trying to package DNA into a small volume without histones, and how do these special packaging proteins alleviate the problem? B. Lysine side chains are substrates for enzymes called acetylases. A diagram of an acetylated lysine side chain is shown in Figure Q2-54. How do you think the acetylation of lysines in histone proteins will affect the ability of a histone to perform its role (refer to your answer in part A)?
A. DNA is negatively charged and could get repulsion. Histones have positive charge lysine and arginine that help overcome this. B. When acetylated, they lose positive charge so it can no longer interact as well with the negatively charged DNA.
Indicate whether the following statements are true or false. If a statement is false, explain why it is false. A. Feedback inhibition is defined as a mechanism of down-regulating enzyme activity by the accumulation of a product earlier in the pathway. B. If an enzyme's allosteric binding site is occupied, the enzyme may adopt an alternative conformation that is not optimal for catalysis. C. Protein phosphorylation is another way to alter the conformation of an enzyme and serves exclusively as a mechanism to increase enzyme activity. D. GTP binding proteins typically have GTPase activity, and the hydrolysis of GTP transforms them to the "off" conformation.
A. False; dowstream not earlier B. True C. not exclusively D. True
Indicate whether the following statements are true or false. If a statement is false, explain why it is false. A. The amino acids in the interior of a protein do not interact with the ligand and do not play a role in selective binding. B. Antibodies are Y shaped and are composed of six different polypeptide chains. C. ATPases generate ATP for the cell. D. Hexokinase recognizes and phosphorylates only one of the glucose stereoisomers.
A. False; interior a.a. form scaffold that helps give binding site its shape so play important role in selective binding B. False; four not six C. ATPases cleave ATP D. True
You have made a collection of mutant fruit flies that are defective in various aspects of DNA repair. You test each mutant for its hypersensitivity to three DNA-damaging agents: sunlight, nitrous acid (which causes deamination of cytosine), and formic acid (which causes depurination). The results are summarized in Table Q6-38, where a "yes" indicates that the mutant is more sensitive than a normal fly, and blanks indicate normal sensitivity. Table Q6-38 A. Which mutant is most likely to be defective in the DNA repair polymerase? B. What aspect of repair is most likely to be affected in the other mutants?
A. Mr. Self-Destruct B. Recognition and excision of the damaged base pairs
You have produced a monoclonal antibody that binds to the protein actin. To be sure that the antibody does not cross-react with other proteins, you test your antibody in a western blot assay on whole cell lysates that have been subjected to electrophoresis under nondenaturing conditions (shown in Figure Q4-24A) and denaturing conditions (shown in Figure Q4-24B). Does the antibody cross-react with other proteins? If so, does this explain the results in the two western blots? If not, how do you explain the differences observed?
A. Non-Dentured B. Denatured Antibody does nto appear to cross react since only see one band in each gel Plot A- probably have actin complex; lots of actin monomers assmebled Plot B- denaturing conditions so only see single subunit/monomer of actin
The structures of the four bases in DNA are given in Figure Q5-14. Figure Q5-14 A. Which are purines and which are pyrimidines? B. Which bases pair with each other in double-stranded DNA?
A. Purines-adenine and guanine Pyrimidines-Cytosine and thymine B. C with G and A with T
You wish to produce a human enzyme, protein A, by introducing its gene into bacteria. The genetically engineered bacteria make large amounts of protein A, but it is in the form of an insoluble aggregate with no enzymatic activity. Which of the following procedures might help you to obtain soluble, enzymatically active protein? Explain your reasoning. A. Make the bacteria synthesize protein A in smaller amounts. B. Dissolve the protein aggregate in urea, then dilute the solution and gradually remove the urea. C. Treat the insoluble aggregate with prtease. D. Make the bacteria overproduce chaperone proteins in addition to protein A. E. Heat the protein aggregate to denature all proteins, then cool the mixture.
A. The cell may be overwhelmed by the protein - not enough chaperones making less may help B. Urea is a denaturant. Adding the urea may help denature it and removing it slowly may help C. No D. More chaperones may help E. No
In an attempt to define the protein domains of protein X, you treat it with a protease and use polyacrylamide gel electrophoresis to analyze the peptides produced. In the past, you have used chymotrypsin to perform this experiment, but the stock of this enzyme has been used up . You find a stock of elastase and decide to use it instead of waiting for a new stock of chymotrypsin to arrive. A. Give two reasons why elastase is a good substitute for chymotrypsin in this assay. B. Why might proteolysis of the same substrate by chymotrypsin or elastase yield different results?
A. They are both serine proteases that both cleave proteins with similar mechanisms B. They have different specificities for where they cut so they could get different results
Indicate whether the following statements are true or false. If a statement is false, explain why it is false. A. Each strand of DNA contains all the information needed to create a new double-stranded DNA molecule with the same sequence information. B. All functional DNA sequences inside a cell code for protein products. C. Gene expression is the process of duplicating genes during DNA replication. D. Gene sequences correspond exactly to the respective protein sequences produced from them.
A. True B. False; SOme sequences encode only RNA molecules, some bind to specific regulatory proteins, and others are sites specific chromosomal protein structures are built C. False; Process of going from gene sequence to RNA sequence to protein sequence D. False; genes often contain intron sequences
Indicate whether the following statements are true or false. If a statement is false, explain why it is false. A. Ionizing radiation and oxidative damage can cause DNA double-strand breaks. B. After damaged DNA has been repaired, nicks in the phosphate backbone are maintained as a way to identify the strand that was repaired. C. Depurination of DNA is a rare event that is caused by ultraviolet irradiation. D. Nonhomologous end joining is a mechanism that ensures that DNA double-strand breaks are repaired with a high degree of fidelity to the original DNA sequence.
A. True B. False; sealed by DNA ligase after replication C. False; it is caused by spontaneous hydrolysis of the bond linking the DNA base pair to the deoxyribose sugar D. False; homologous recombination not nonhomologous end joining
Indicate whether the following statements are true or false. If a statement is false, explain why it is false. A. Primase is needed to initiate DNA replication on both the leading strand and the lagging strand. B. The sliding clamp is loaded once on each DNA strand, where it remains associated until replication is complete. C. Telomerase is a DNA polymerase that carries its own RNA molecule to use as a primer at the end of the lagging strand. D. Primase requires a proofreading function that ensures there are no errors in the RNA primers used for DNA replication.
A. True B. False; the lagging needs to unload the clamp C. True D. False; primase does not have a proofreading function
Imagine that an RNA polymerase is transcribing a segment of DNA that contains the following sequence: 5′-AGTCTAGGCACTGA-3′ 3′-TCAGATCCGTGACT 5′ A. If the polymerase is transcribing from this segment of DNA from left to right, which strand (top or bottom) is the template? B. What will be the sequence of that RNA (be sure to label the 5′ and 3′ ends of your RNA molecule)?
A. bottom strand B. 5'-AGUCUAGGCACUGA-3'
For each of the following sentences, choose one of the options enclosed in square brackets to make a correct statement about nucleosomes. A. Nucleosomes are present in [procaryotic/eucaryotic] chromosomes, but not in [procaryotic/eucaryotic] chromosomes. B. A nucleosome contains two molecules each of histones [H1 and H2A/H2A and H2B] as well as of histones H3 and H4. C. A nucleosome core particle contains a core of histone with DNA wrapped around it approximately [twice/three times/four times]. D. Nucleosomes are aided in their formation by the high proportion of [acidic/basic/polar] amino acids in histone proteins. .
A. eukaryotic, prokaryotic B. H2A and H2B C. twice D. basic
Consider the structure of the DNA double helix. A. You and a friend want to split a double-stranded DNA molecule so you each have half. Is it better to cut the length of DNA in half so each person has a shorter length, or to separate the strands and each take one strand? Explain. B. In the original 1953 publication describing the discovery of the structure of DNA, Watson and Crick wrote, "It has not escaped our notice that the specific pairings we have postulated immediately suggest a possible copying mechanism for the genetic material." What did they mean?
A. it is better to separate the strands and take a single strand, because all of the information found in the original molecule is preserved in a full-length single strand not in a half-length double-stranded molecule. B. Watson and Crick meant that the complementary base pairing of the strands allows a single strand to contain all of the information necessary to direct the synthesis of a new complementary strand.
A. Write out the sequence of amino acids in the following peptide, using the full names of the amino acids. Pro-Val-Thr-Gly-Lys-Cys-Glu B. Write the same sequence with the single-letter code for amino acids. C. According to the conventional way of writing the sequence of a peptide or a protein, which is the C-terminal amino acid and which is the N-terminal amino acid in the above peptide?
A. proline-valine-threonine-glycine-lysine-cytesine-glutamate B. PVTGKCE C. C-Temrinal: glu N-Terminal: pro
For each of the pairs A-D in Figure Q3-13, pick the more reduced member of the pair.
B B A B
Use the terms listed to fill in the blanks in Figure Q5-13. A. A-T base pair B. G-C base pair C. deoxyribose D. phosphodiester bonds E. purine base F. pyrimidine base
B E F C D A
Homologous recombination is an important mechanism in which organisms use a "back-up" copy of the DNA as a template to fix double-strand breaks without loss of genetic information. Which of the following is not necessary for homologous recombination to occur? (a) 3′ DNA strand overhangs (b) 5′ DNA strand overhangs (c) a long stretch of sequence similarity (d) nucleases
B) 5′ DNA strand overhangs
Which of the following statements about RNA splicing is false? (a) Conventional introns are not found in bacterial genes. (b) For a gene to function properly, every exon must be removed from the primary transcript in the same fashion on every mRNA molecule produced from the same gene. (c) Small RNA molecules in the nucleus perform the splicing reactions necessary for the removal of introns. (d) Splicing occurs after the 5′ cap has been added to the end of the primary transcript.
B) For a gene to function properly, every exon must be removed from the primary transcript in the same fashion on every mRNA molecule produced from the same gene.
A poison added to an in vitro translation mixture containing mRNA molecules with the sequence 5′-AUGAAAAAAAAAAAAUAA-3′ has the following effect: the only product made is a Met-Lys dipeptide that remains attached to the ribosome. What is the most likely way in which the poison acts to inhibit protein synthesis? (a) It inhibits peptidyl transferase activity. (b) It inhibits movement of the small subunit relative to the large subunit. (c) It inhibits release factor. (d) It mimics release factor.
B) It inhibits movement of the small subunit relative to the large subunit.
Seed oils are often dehydrogenated and added back into processed foods as partly unsaturated fatty acids. In comparison with the original oil, the new fatty acids have additional double carbon-carbon bonds, replacing what were once single bonds. This process could also be described as _____________. (a) isomerization (b) oxidation (c) reduction (d) protonation
B) Oxidation
You have a bacterial strain with a mutation that removes the transcription termination signal from the Abd operon. Which of the following statements describes the most likely effect of this mutation on Abd transcription? (a) The Abd RNA will not be produced in the mutant strain. (b) The Abd RNA from the mutant strain will be longer than normal. (c) Sigma factor will not dissociate from RNA polymerase when the Abd operon is being transcribed in the mutant strain. (d) RNA polymerase will move in a backwards fashion at the Abd operon in the mutant strain.
B) The Abd RNA from the mutant strain will be longer than normal.
Which of the following statements is not an accurate statement about thymidine dimers? (a) Thymidine dimers can cause the DNA replication machinery to stall. (b) Thymidine dimers are covalent links between thymidines on opposite DNA strands. (c) Prolonged exposure to sunlight causes thymidine dimers to form. (d) Repair proteins recognize thymidine dimers as a distortion in the DNA backbone.
B) Thymidine dimers are covalent links between thymidines on opposite DNA strands.
DNA and RNA are different types of nucleic acid polymer. Which of the following is true of DNA but not true of RNA? (a) It contains uracil. (b) It contains thymine. (c) It is single stranded. (d) It has 5′-to-3′ directionality.
B) Thymine
The piece of RNA below includes the region that codes the binding site for the initiator tRNA needed in translation. 5′-GUUUCCCGUAUACAUGCGUGCCGGGGGC-3′ Which amino acid will be on the tRNA that is the first to bind to the A-site of the ribosome? (a) methionine (b) arginine (c) cystine (d) valine
B) arginine
Which of the following is not a feature commonly observed in β sheets? (a) antiparallel regions (b) coiled-coil patterns (c) extended polypeptide backbone (d) parallel regions
B) colied-coil patterns
Enzymes facilitate reactions in living systems. Figure Q3-25 presents an energy diagram for the reaction X→Y. The solid line in the energy diagram represents changes in energy as the product is converted to reactant under standard conditions. The dashed line shows changes observed when the same reaction takes place in the presence of a dedicated enzyme. Which equation below indicates how the presence of an enzyme affects the activation energy of the reaction (catalyzed versus uncatalyzed)? (a) d - c versus b - c (b) d - a versus b - a (c) a + d versus a + b (d) d - c versus b - a
B) d - a versus b - a
Stepwise condensation of linear DNA happens in five different packing processes. Which of the following four processes has a direct requirement for histone H1? (a) formation of "beads-on-a-string" (b) formation of the 30 nm fiber (c) looping of the 30 nm fiber (d) packing of loops to form interphase chromosomes
B) formation of the 30 nm fiber
The N-terminal tail of histone H3 can be extensively modified, and depending on the number, location, and combination of these modifications, these changes may promote the formation of heterochromatin. What is the result of heterochromatin formation? (a) increase in gene expression (b) gene silencing (c) recruitment of remodeling complexes (d) displacement of histone H1
B) gene silencing
Both DNA and RNA are synthesized by covalently linking a nucleotide triphosphate to the previous nucleotide, constantly adding to a growing chain. In the case of DNA, the new strand becomes part of a stable helix. The two strands are complementary in sequence and antiparallel in directionality. What is the principal force that holds these two strands together? (a) ionic interactions (b) hydrogen bonds (c) covalent bonds (d) van der Waals interactions
B) hydrogen bonds
In eucaryotes, but not in procaryotes, ribosomes find the start site of translation by ____________________________. (a) binding directly to a ribosome-binding site preceding the initiation codon (b) scanning along the mRNA from the 5′ end (c) recognizing an AUG codon as the start of translation (d) binding an initiator tRNA
B) scanning along the mRNA from the 5′ end
The classic experiments conducted by Meselson and Stahl demonstrated that DNA replication is accomplished by employing a ________________ mechanism. (a) continuous (b) semiconservative (c) dispersive (d) conservative
B) semiconservative
DNA polymerases are processive, which means that they remain tightly associated with the template strand while moving rapidly and adding nucleotides to the growing daughter strand. Which piece of the replication machinery accounts for this characteristic? (a) helicase (b) sliding clamp (c) single-strand binding protein (d) primase
B) sliding clamp
A mutation in the tRNA for the amino acid lysine results in the anticodon sequence 5′-UAU-3′ (instead of 5′-UUU-3′). Which of the following aberrations in protein synthesis might this tRNA cause? (Refer to the codon table provided above Q7-29.) (a) read-through of stop codons (b) substitution of lysine for isoleucine (c) substitution of lysine for tyrosine (d) substitution of lysine for phenylalanine
B) substitution of lysine for isoleucine
You have a piece of DNA that includes the following sequence: 5′-ATAGGCATTCGATCCGGATAGCAT-3′ 3′-TATCCGTAAGCTAGGCCTATCGTA-5′ Which of the following RNA molecules could be transcribed from this piece of DNA? (a) 5′-UAUCCGUAAGCUAGGCCUAUGCUA-3′ (b) 5′-AUAGGCAUUCGAUCCGGAUAGCAU-3′ (c) 5′-UACGAUAGGCCUAGCUUACGGAUA-3′ (d) none of the above
B)5′-AUAGGCAUUCGAUCCGG AUAGCAU-3′
The kinetics of an enzyme are measured as a function of substrate concentration in the presence and absence of 100 micromolar inhibitor. The data obtained is shown below. [S] velocity velocity with inhibitor micromolar micromoles/min micromoles/minute 3 10.4 2.1 5 14.5 2.9 10 22.5 4.5 30 33.8 6.8 90 40.5 8.1 1.) Draw a lineweaver burke plot of this data. 2.) What are the values of Km and Vmax for the enzyme? 3.) What are the values of Km and Vmax in the presence of inhibitor? 4.) What type of inhibition is this?
B. 10 picoMolar; 45 picoMolar C. 10 picoMolar; 9 picoMolar D. Km same and Vmax different therefore noncompetitive
You mentor just came to you and told you that she needs some enzyme activity assays run by TOMORROW! You have no protocol for designing the buffers for the assay. You know that the active site has an essential histidine whose R group must be fully protonated in order to function. Your first goal is to determine the optimal pH for the assay. Given that the pKa for the imidazole group is 6.0, what pH buffer would you use? Why? Assume no local changes in pH due to other amino acids in the active site.
Buffer is below 6. Here, the imidizole would protonated. Not too low though or protein would denature.
Nucleosomes are formed when DNA wraps _____ times around the histone octamer in a ______ coil. (a) 2.0; right-handed (b) 2.5; left-handed (c) 1.7; left-handed (d) 1.3; right-handed
C) 1.7; left-handed
When the polymer X-X-X... is broken down into monomers, it is "phosphorylyzed" rather than hydrolyzed, in the following repeated reaction: X-X-X... + P → X-P + X-X... (reaction 1) Given the ΔG° values of the reactions listed in the following table, what is the expected ratio of X-phosphate (X-P) to free phosphate (P) at equilibrium for reaction 1? (a) 1:106 (b) 1:104 (c) 1:1 (d) 104:1 (e) 106:1
C) 1:1
Most types of molecule in the cell have asymmetric (chiral) carbons. Consequently there is the potential to have two different molecules that look much the same but are mirror images of each other and therefore not equivalent. These special types of isomer are called stereoisomers. Which of the four carbons circled in Figure Q2-33 is the asymmetric carbon that determines whether the amino acid (threonine in this case) is a D- or an L- stereoisomer? Figure Q2-33 (a) 1 (b) 2 (c) 3 (d) 4
C) 3
The biosynthetic pathway for the two amino acids E and H is shown schematically in Figure Q4-41. You are able to show that E inhibits enzyme V, and H inhibits enzyme X. Enzyme T is most likely to be subject to feedback inhibition by __________________ alone. Figure Q4-41 (a) H (b) B (c) C (d) E
C) C
Which of the following pairs of codons might you expect to be read by the same tRNA as a result of wobble? (a) CUU and UUU (b) GAU and GAA (c) CAC and CAU (d) AAU and AGU
C) CAC and CAU
Which of the following statements is true? (a) Disulfide bonds are formed by the cross-linking of methionine residues. (b) Disulfide bonds are formed mainly in proteins that are retained within the cytosol. (c) Disulfide bonds stabilize but do not change a protein's final conformation. (d) Agents such as mercaptoethanol can break disulfide bonds through oxidation.
C) Disulfide bonds stabilize but do not change a protein's final conformation.
You have discovered a gene (Figure Q7-27A) that is alternatively spliced to produce several forms of mRNA in various cell types, three of which are shown in Figure Q7-27B. The lines connecting the exons that are included in the mRNA indicate the splicing. From your experiments, you know that protein translation begins in exon 1. For all forms of the mRNA, the encoded protein sequence is the same in the regions of the mRNA that correspond to exons 1 and 10. Exons 2 and 3 are alternative exons used in different mRNA, as are exons 7 and 8. Which of the following statements about exons 2 and 3 is the most accurate? Explain your answer. Figure Q7-27 (a) Exons 2 and 3 must have the same number of nucleotides. (b) Exons 2 and 3 must contain an integral number of codons (that is, the number of nucleotides divided by 3 must be an integer). (c) Exons 2 and 3 must contain a number of nucleotides that when divided by 3, leaves the same remainder (that is, 0, 1, or 2). (d) Exons 2 and 3 must have different numbers of nucleotides
C) Exons 2 and 3 must contain a number of nucleotides that when divided
The core histones are small, basic proteins that have a globular domain at the C-terminus and a long extended conformation at the N-terminus. Which of the following is not true of the N terminal "tail" of these histones? (a) It is subject to covalent modifications, (b) It extends out of the nucleosome core. (c) It binds to DNA in a sequence-specific manner. (d) It helps DNA pack tightly.
C) It binds to DNA in a sequence-specific manner.
Biological membranes are composed of specialized lipids that form bilayers. Which of the following is formed by unmodified fatty acids? (a) fat droplets (b) bilayers (c) micelles (d) planar lipid patches
C) Miscelles
Sometimes chemical damage to DNA can occur just before DNA replication begins, not giving the repair system enough time to correct the error before the DNA is duplicated. This gives rise to mutation. If the adenosine in the sequence TCAT is depurinated and not repaired, which of the following is the point mutation you would observe after this segment has undergone two rounds of DNA replication? (a) TCGT (b) TAT (c) TCT (d) TGTT
C) TCT
A strain of yeast translates mRNA into protein inaccurately. Individual molecules of a particular protein isolated from this yeast have variations in the first 11 amino acids compared with the sequence of the same protein isolated from normal yeast cells, as listed in Figure Q7-36. What is the most likely cause of this variation in protein sequence? Figure Q7-36 (a) a mutation in the DNA coding for the protein (b) a mutation in the anticodon of the isoleucine tRNA (tRNAIle) (c) a mutation in the isoleucyl-tRNA synthetase that decreases its ability to distinguish between different amino acids (d) a mutation in the isoleucyl-tRNA synthetase that decreases its ability to distinguish between different tRNA molecules
C) a mutation in the isoleucyl-tRNA synthetase that decreases its ability to distinguish between different amino acids
Which of the following mechanisms best describes the manner in which lysozyme lowers the energy required for its substrate to reach its transition state conformation? (a) by binding two molecules and orienting them in a way that favors a reaction between them (b) by altering the shape of the substrate to mimic the conformation of the transition state (c) by speeding up the rate at which water molecules collide with the substrate (d) by binding irreversibly to the substrate so that it cannot dissociate
C) by speeding up the rate at which water molecules collide with the substrate
You are studying a biochemical pathway that requires ATP as an energy source. To your dismay, the reactions soon stop, partly because the ATP is rapidly used up and partly because an excess of ADP builds up and inhibits the enzymes involved. You are about to give up when the following table from a biochemistry textbook catches your eye. Which of the following reagents are most likely to revitalize your reaction? (a) a vast excess of ATP (b) glucose 6-phosphate and enzyme E (c) creatine phosphate and enzyme A (d) pyrophosphate
C) creatine phosphate and enzyme E
NADH and NADPH are activated carrier molecules that function in completely different metabolic reactions. Both carry two additional ________ and one additional _____________. This combination can also be referred to as a hydride ion. (a) protons, electron (b) electrons, phosphate (c) hydrogens, electron (d) electrons, proton
C) hydrogens, electron
RNA in cells differs from DNA in that ___________________. (a) it contains the base uracil, which pairs with cytosine (b) it is single-stranded and cannot form base pairs (c) it is single-stranded and can fold up into a variety of structures (d) the sugar ribose contains fewer oxygen atoms than does deoxyribose
C) it is single-stranded and can fold up into a variety of structures
In addition to the repair of DNA double-strand breaks, homologous recombination is a mechanism for generating genetic diversity by swapping segments of parental chromosomes. During which process does swapping occur? (a) DNA replication (b) DNA repair (c) meiosis (d) transposition
C) meiosis
Which of the following statements is true? (a) Ribosomes are large RNA structures composed solely of rRNA. (b) Ribosomes are synthesized entirely in the cytoplasm. (c) rRNA contains the catalytic activity that joins amino acids together. (d) A ribosome binds one tRNA at a time.
C) rRNA contains the catalytic activity that joins amino acids together.
The sigma subunit of bacterial RNA polymerase ___________________. (a) contains the catalytic activity of the polymerase (b) remains part of the polymerase throughout transcription (c) recognizes promoter sites in the DNA (d) recognizes transcription termination sites in the DNA
C) recognizes promoter sites in the DNA
The concentration of a particular protein X in a normal human cell rises gradually from a low point, immediately after cell division, to a high point, just before cell division, and then drops sharply. The level of its mRNA in the cell remains fairly constant throughout this time. Protein X is required for cell growth and survival, but the drop in its level just before cell division is essential for division to proceed. You have isolated a line of human cells that grow in size in culture but cannot divide, and on analyzing these mutants, you find that levels of X mRNA in the mutant cells are normal. Which of the following mutations in the gene for X could explain these results? (a) the introduction of a stop codon that truncates protein X at the fourth amino acid (b) a change of the first ATG codon to CCA (c) the deletion of a sequence that encodes sites at which ubiquitin can be attached to the protein (d) a change at a splice site that prevents splicing of the RNA
C) the deletion of a sequence that encodes sites at which ubiquitin can be attached to the protein
5-45 Although the chromatin structure of interphase and mitotic chromosomes is very compact, DNA-binding proteins and protein complexes must be able to gain access to the DNA molecule. Chromatin-remodeling complexes provide this access by __________________. (a) recruiting other enzymes (b) modifying the N-terminal tails of core histones (c) using the energy of ATP hydrolysis to move nucleosomes (d) denaturing the DNA by interfering with hydrogen-bonding between base pairs
C) using the energy of ATP hydrolysis to move nucleosomes
One way in which an enzyme can lower the activation energy required for a reaction is to bind the substrate(s) and distort its structure so that the substrate more closely resembles the transition state of the reaction. This mechanism will be facilitated if the shape and chemical properties of the enzyme's active site are more complementary to the transition state than to the undistorted substrate; in other words, if the enzyme were to have a higher affinity for the transition state than for the substrate. Knowing this, your friend looked in an organic chemistry textbook to identify a stable chemical that closely resembles the transition state of a reaction that converts X into Y. She generated an antibody against this transition state analog and mixed the antibody with chemical X. What do you think might happen?
Created a catalytic antibody that may be able to catalyze the reaction
Which diagram accurately represents the directionality of DNA strands at one side of a replication fork?
D
Motor proteins use the energy in ATP to transport organelles, rearrange elements of the cytoskeleton during cell migration, and move chromosomes during cell division. Which of the following mechanisms is sufficient to ensure the unidirectional movement of a motor protein along its substrate? (a) A conformational change is coupled to the release of a phosphate (Pi). (b) The substrate on which the motor moves has a conformational polarity. (c) A conformational change is coupled to the binding of ADP. (d) A conformational change is linked to ATP hydrolysis.
D) A conformational change is linked to ATP hydrolysis.
Which of the following statements about amino acids is true? (a) Twenty-two amino acids are commonly found in proteins. (b) Most of the amino acids used in protein biosynthesis have charged side chains. (c) Amino acids are often linked together to form branched polymers. (d) All amino acids contain an NH2 and a COOH group
D) All amino acids contain an NH2 and a COOH group
The events listed below are all necessary for homologous recombination to occur properly: A. Holliday junction cut and ligated B. strand invasion C. DNA synthesis D. DNA ligation E. double-strand break F. nucleases create uneven strands Which of the following is the correct order of events during homologous recombination? (a) E, B, F, D, C, A (b) B, E, F, D, C, A (c) C, E, F, B, D, A (d) E, F, B, C, D, A
D) E,F,B,C,D,A
The octameric histone core is composed of four different histone proteins, assembled in a stepwise manner. Once the core octamer has been formed, DNA wraps around it to form a nucleosome core particle. Which of the following histone proteins does not form part of the octameric core? (a) H4 (b) H2A (c) H3 (d) H1
D) H1
Several experiments were required to demonstrate how traits are inherited. Which scientist or team of scientists obtained definitive results demonstrating that DNA is the genetic molecule? (a) Griffith (b) Watson (c) Crick (d) Hershey and Chase
D) Hershey and Chase
You have discovered an "Exo-" mutant form of DNA polymerase in which the 3′-to-5′ exonuclease function has been destroyed but the ability to join nucleotides together is unchanged. Which of the following properties do you expect the mutant polymerase to have? (a) It will polymerize in both the 5′-to-3′ direction and the 3′-to-5′ direction. (b) It will polymerize more slowly than the normal Exo+ polymerase. (c) It will fall off the template more frequently than the normal Exo+ polymerase. (d) It will be more likely to generate mismatched base pairs.
D) It will be more likely to generate mismatched base pairs.
You are examining the DNA sequences that code for the enzyme phosphofructokinase in skinks and Komodo dragons. You notice that the coding sequence that actually directs the sequence of amino acids in the enzyme is very similar in the two organisms but that the surrounding sequences vary quite a bit. What is the most likely explanation for this? (a) Coding sequences are repaired more efficiently. (b) Coding sequences are replicated more accurately. (c) Coding sequences are packaged more tightly in the chromosomes to protect them from DNA damage. (d) Mutations in coding sequences are more likely to be deleterious to the organism than mutations in noncoding sequences.
D) Mutations in coding sequences are more likely to be deleterious to the organism than mutations in noncoding sequences.
You have a segment of DNA that contains the following sequence: 5′-GGACTAGACAATAGGGACCTAGAGATTCCGAAA-3′ 3′-CCTGATCTGTTATCCCTGGATCTCTAAGGCTTT-5′ If you know that the RNA transcribed from this segment contains the following sequence: 5′-GGACUAGACAAUAGGGACCUAGAGAUUCCGAAA-3′ Which of the following choices best describes how transcription occurs? (a) The top strand is the template strand; RNA polymerase moves along this strand from 5′ to 3′. (b) The top strand is the template strand; RNA polymerase moves along this strand from 3′ to 5′. (c) The bottom strand is the template strand; RNA polymerase moves along this strand from 5′ to 3′. (d) The bottom strand is the template strand; RNA polymerase moves along this strand from 3′ to 5′.
D) The bottom strand is the template strand; RNA polymerase moves along this strand from 3′ to 5′.
Telomeres serve as caps at the ends of linear chromosomes. Which of the following is not true regarding the replication of telomeric sequences? (a) The lagging strand telomeres are not completely replicated by DNA polymerase. (b) Telomeres are made of repeating sequences. (c) Additional repeated sequences are added to the template strand. (d) The leading strand doubles back on itself to form a primer for the lagging strand.
D) The leading strand doubles back on itself to form a primer for the lagging strand.
Which of the following statements is false? (a) A new RNA molecule can begin to be synthesized from a gene before the previous RNA molecule's synthesis is completed. (b) If two genes are to be expressed in a cell, these two genes can be transcribed with different efficiencies. (c) RNA polymerase is responsible for both unwinding the DNA helix and catalyzing the formation of the phosphodiester bonds between nucleotides. (d) Unlike DNA, RNA uses a uracil base and a deoxyribose sugar.
D) Unlike DNA, RNA uses a uracil base and a deoxyribose sugar.
The Ras protein is a GTPase that functions in many growth-factor signaling pathways. In its active form, with GTP bound, it transmits a downstream signal that leads to cell proliferation; in its inactive form, with GDP bound, the signal is not transmitted. Mutations in the gene for Ras are found in many cancers. Of the choices below, which alteration of Ras activity is most likely to contribute to the uncontrolled growth of cancer cells? (a) a change that prevents Ras from being made (b) a change that increases the affinity of Ras for GDP (c) a change that decreases the affinity of Ras for GTP (d) a change that decreases the rate of hydrolysis of GTP by Ras
D) a change that decreases the rate of hydrolysis of GTP by Ras
Which of the following might decrease the transcription of only one specific gene in a bacterial cell? (a) a decrease in the amount of sigma factor (b) a decrease in the amount of RNA polymerase (c) a mutation that introduced a stop codon into the DNA that precedes the gene's coding sequence (d) a mutation that introduced extensive sequence changes into the DNA that precedes the gene's transcription start site
D) a mutation that introduced extensive sequence changes into the DNA that precedes the gene's transcription start site
Choose the answer that best fits the statement. Cholesterol is an essential component of biological membranes. Although it is much smaller than the typical phospholipids and glycoplipids in the membrane, it is a(n) _________________ molecule, having both hydrophilic and hydrophobic regions. (a) polar (b) oxygen-containing (c) hydrophobic (d) amphipathic
D) amphipathic
Figure Q3-24 is an energy diagram for the reaction X→Y. Which equation below provides the correct calculation for the amount of free-energy change when X is converted to Y? (a) a + b - c (b) a - b (c) a - c (d) c - a
D) c - a
The complete set of information found in a given organism's DNA is called its ____________. (a) genetic code (b) coding sequence (c) gene (d) genome
D) genome
ΔG° indicates the change in the standard free energy as a reactant is converted to product. Given what you know about these values, which reaction below is the most favorable? (a) ADP + Pi → ATP ΔG° = +7.3 kcal/mole (b) glucose 1-phosphate → glucose 6-phosphate ΔG° = -1.7 kcal/mole (c) glucose + fructose → sucrose ΔG° = +5.5 kcal/mole (d) glucose → CO2 + H2O ΔG° = -686 kcal/mole
D) glucose → CO2 + H2O
Although all protein structures are unique, there are common structural building blocks that are referred to as regular secondary structures. Some have α helices, some have β sheets, and still others have a combination of both. What makes it possible for proteins to have these common structural elements? (a) specific amino acid sequences (b) side-chain interactions (c) the hydrophobic core interactions (d) hydrogen bonds along the protein backbone
D) hydrogen bonds along the protein backbone
Total nucleic acids are extracted from a culture of yeast cells and are then mixed with resin beads to which the polynucleotide 5′-TTTTTTTTTTTTTTTTTTTTTTTTT-3′ has been covalently attached. After a short incubation, the beads are then extracted from the mixture. When you analyze the cellular nucleic acids that have stuck to the beads, which of the following is most abundant? (a) DNA (b) tRNA (c) rRNA (d) mRNA
D) mRNA
Transcription is similar to DNA replication in that ___________________. (a) an RNA transcript is synthesized discontinuously and the pieces are then joined together (b) it uses the same enzyme as that used to synthesize RNA primers during DNA replication (c) the newly synthesized RNA remains paired to the template DNA (d) nucleotide polymerization occurs only in the 5′-to-3′ direction
D) nucleotide polymerization occurs only in the 5′-to-3′ direction
Which of the following chemical groups is not used to construct a DNA molecule? (a) five-carbon sugar (b) phosphate (c) nitrogen-containing base (d) six-carbon sugar
D) six-carbon sugar
In a DNA double helix, _____________________. (a) the two DNA strands are identical (b) purines pair with purines (c) thymine pairs with cytosine (d) the two DNA strands run antiparallel
D) the two DNA strands run antiparallel
The correct folding of proteins is necessary to maintain healthy cells and tissues. Unfolded proteins are responsible for such neurodegenerative disorders as Alzheimer's, Huntington's, and Creutzfeld-Jacob disease (the specific faulty protein is different for each disease). What is the ultimate fate of these disease-causing, unfolded proteins? (a) They are degraded. (b) They bind a different target protein. (c) They form structured filaments. (d) They form protein aggregates.
D) they form protein aggregates
ΔG measures the change of free energy in a system as it converts reactant (Y) into product (X). When [Y] =[X], ΔG is equal to _____________. (a) ΔG° + RT (b) RT (c) ln [X]/[Y] (d) ΔG°
D) ΔG°
Researchers have isolated a mutant strain of E. coli that carries a temperature-sensitive variant of the enzyme DNA ligase. At the permissive temperature, the mutant cells grow just as well as the wild-type cells. At the nonpermissive temperature, all of the cells in the culture tube die within 2 hours. DNA from mutant cells grown at the nonpermissive temperature for 30 minutes is compared with the DNA isolated from cells grown at the permissive temperature. The results are shown in Figure Q6-22, where DNA molecules have been separated by size by means of electrophoresis (P, permissive; NP, nonpermissive). Explain the appearance of a distinct band with a size of 200 base pairs (bp) in the sample collected at the nonpermissive temperature.
DNA ligase has an imprtant role in DNA replication.
The synthesis of DNA in living systems occurs in the 5′-to-3′ direction. However, scientists synthesize short DNA sequences needed for their experiments on an instrument dedicated to this task. B. Although 3′-to-5′ synthesis of DNA is chemically possible, it does not occur in living systems. Why not?
DNA synthesis from 3' to 5' does not allow proofreading. If the last nucleotide added was mispaired and is removed, the last nucleotide on the growing strand is a nucleotide monophosphate and the nucleotide coming in only has a hydroxyl group on the 3' end. Thus, there is no favorable hydrolysis to drive the addition of new nucleotides.
Use the components in the list below to label the diagram of a replication fork in Figure Q6-21. A. DNA polymerase B. single-strand binding protein C. Okazaki fragment D. primase E. sliding clamp F. RNA primer G. DNA helicase
E A D G B C F
Match each term related to the structure of nucleic acids (A-I) with one of the descriptions provided. A. base B. glycosidic bond C. nucleoside D. nucleotide E. phosphoanyhydride bond F. phosphoester bond G. ribose H. phosphodiester bond I. deoxyribose ____ the linkage between two nucleotides ____ the linkage between the 5′ sugar hydroxyl and a phosphate group ____ the nitrogen-containing aromatic ring ____ five-carbon sugar found in DNA ____ sugar unit linked to a base ____ linkage between the sugar and the base ____ linkages between phosphate groups ____ sugar linked to a base and a phosphate ____ five-carbon sugar found in RNA
H. phosphodiester bond F. phosphoester bond A. base I. deoxyribose C. nucleoside B. glycosidic bond E. phosphoanyhydride bond D. nucleotide G. ribose
The amino acid histidine is often found in enzymes. Depending on the pH of its environment, sometimes histidine is neutral and at other times it acquires a proton and becomes positively charged. Consider an enzyme with a histidine side chain that is known to have an important role in the function of the enzyme. It is not clear whether this histidine is required in its protonated or its unprotonated state. To answer this question you measure enzyme activity over a range of pH, with the results shown in Figure Q2-26. Which form of histidine is necessary for the active enzyme?
It would be more protonated at lower pH and more active at lower pH so enzyme needs to be protonated to be active
Aspirin is a weak acid with a pKa of 3.5. It is absorbed into the blood through the cells lining the stomach and the small intestine. Absorption requires passage through the plasma membrane, the rate of which is determined by the polarity of the molecule: charged and highly polar molecules pass slowly, whereas neutral hydrophobic ones pass rapidly. The pH of the stomach contents is about 1.5, and the pH of the contents of the small intestine is about 6. Is more aspirin absorbed into the bloodstream from the stomach or from the small intestine? Clearly justify your choice.
More readily absorbed through the stomach because still mostly protonated and uncharged. It would be chraged at a pH of 6 in intestines.
Some of the enzymes that oxidize sugars to yield usable cellular energy (for example, ATP) are regulated by phosphorylation. For these enzymes, would you expect the inactive form to be the phosphorylated form or the dephosphorylated form? Explain your answer.
Phosphorylation - if they are involved in indirectly generating ATP and ATP is up, then ATP could be used to inactivate them
You are trying to make a synthetic copy of a particular protein but accidentally join the amino acids together in exactly the reverse order. One of your classmates says the two proteins must be identical, and bets you $20 that your synthetic protein will have exactly the same biological activity as the original. After having read this chapter, you have no hesitation in staking your $20 that it won't. What particular feature of a polypeptide chain makes you sure your $20 is safe and that your project will have to be redone.
Protein has directionality. Folds as synthesized. Cannot fold same if synthesized in reverse.
Using terms from the list below, fill in the blanks in the following brief description of the experiment with Streptococcus pneumoniae that identified which biological molecule carries heritable genetic information. Some terms may be used more than once. Cell-free extracts from S-strain cells of S. pneumoniae were fractionated to __________________ DNA, RNA, protein, and other cell components. Each fraction was then mixed with __________________ cells of S. pneumoniae. Its ability to change these into cells with __________________ properties resembling the __________________ cells was tested by injecting the mixture into mice. Only the fraction containing __________________ was able to __________________ the __________________ cells to __________________ (or __________________ ) cells that could kill mice. carbohydrate lipid R-strain DNA nonpathogenic RNA identify pathogenic S-strain label purify transform
Purify R-strain pathogenic S-strain DNA transform R-strain pathogenic/S-strain
Below is a segment of RNA from the middle of an mRNA. 5′-UAGUCUAGGCACUGA-3′ If you were told that this segment of RNA was part of the coding region of an mRNA for a large protein, give the amino acid sequence for the protein that is encoded by this segment of mRNA. Write your answer using the one-letter amino acid code.
SLGT
For each of the following sentences, fill in the blanks with the best word or phrase selected from the list below. Not all words or phrases will be used; each word or phrase should be used only once. The α helices and β sheets are examples of protein __________________ structure. A protein such as hemoglobin, which is composed of more than one protein __________________, has __________________ structure. A protein's amino acid sequence is known as its __________________ structure. A protein __________________ is the modular unit from which many larger single-chain proteins are constructed. The three-dimensional conformation of a protein is its __________________ structure. allosteric ligand secondary domain primary subunit helix quaternary tertiary
Secondary Subunit Quatenary Primary Domain Tertiary
You are digesting a protein 625 amino acids long with the enzymes Factor Xa and thrombin, which are proteases that bind to and cut proteins at particular short sequences of amino acids. You know the amino acid sequence of the protein and so can draw a map of where Factor Xa and thrombin should cut it (Figure Q4-22). You find, however, that treatment with each of these proteases for an hour results in only partial digestion of the protein, as summarized under the figure. List the segments (A-E) of the protein that are most likely to be folded into compact, stable domains.
Stable Domains = B and D
For each of the following sentences, fill in the blanks with the best word or phrase selected from the list below. Not all words or phrases will be used; each word or phrase should be used only once. In eucaryotic cells, general transcription factors are required for the activity of all promoters transcribed by RNA polymerase II. The assembly of the general transcription factors begins with the binding of the factor __________________ to DNA, causing a marked local distortion in the DNA. This factor binds at the DNA sequence called the __________________ box, which is typically located 25 nucleotides upstream from the transcription start site. Once RNA polymerase II has been brought to the promoter DNA, it must be released to begin making transcripts. This release process is facilitated by the addition of phosphate groups to the tail of RNA polymerase by the factor __________________. It must be remembered that the general transcription factors and RNA polymerase are not sufficient to initiate transcription in the cell and are affected by proteins bound thousands of nucleotides away from the promoter. Proteins that link the distantly bound transcription regulators to RNA polymerase and the general transcription factors include the large complex of proteins called the__________________. The packing of DNA into chromatin also affects transcriptional initiation, and histone __________________ is an enzyme that can render the DNA less accessible to the general transcription factors. activator lac TFIIA CAP ligase TFIID deacetylase mediator TFIIH enhancer TATA
TFIID TATA TFIIH mediator deacetylase
The relative strengths of covalent bonds and van der Waals interactions remain the same when tested in a vacuum or in water. However, this is not true of hydrogen bonds or ionic bonds, whose bond strength is lowered considerably in the presence of water in comparison with the bond strength observed in a vacuum. Explain these observations.
Water can conform hydrogen bonds and electrostatic interactions and therefore competes for interactions with molecules with ionic and hydrogen bonds
Which amino acid would you expect a tRNA with the anticodon 5′-CUU-3′ to carry? (a) lysine (b) glutamic acid (d) leucine (d) phenylalanine
a0 lysine
For each of the following sentences, fill in the blanks with the best word or phrase selected from the list below. Not all words or phrases will be used; each word or phrase should be used only once. In eucaryotic __________________, DNA is complexed with proteins to form __________________. The paternal and maternal copies of human Chromosome 1 are __________________, whereas the paternal copy of Chromosome 1 and the maternal copy of Chromosome 3 are __________________. Cytogeneticists can determine large-scale chromosomal abnormalities by looking at a patient's __________________. Fluorescent molecules can be used to paint a chromosome by a technique that employs DNA __________________, and thereby to identify each chromosome by microscopy. bands extended kinetochore chromatin homologous nonhomologous chromosomes hybridization condensation karyotype
chromosomes chromatin homologous nonhomologous karyotype hybridization
The addition of a new deoxynucleotide to a growing DNA chain requires more energy than can be obtained by the hydrolysis of ATP to ADP + Pi. What alternative series of reactions is used, and how does this help overcome the energy barrier for DNA synthesis?
dNTP converts to dNMP and PPi; PPi further cleaved by pyrophosphatase
For each of the following sentences, fill in the blanks with the best word or phrase selected from the list below. Not all words or phrases will be used; each word or phrase should be used only once. Interphase chromosomes contain both darkly staining __________________ and more lightly staining __________________. Genes that are being transcribed are thought to be packaged in a __________________ condensed type of euchromatin. Nucleosome core particles are separated from each other by stretches of __________________ DNA. A string of nucleosomes coils up with the help of __________________ to form the more compact structure of the __________________. A __________________ model describes the structure of the 30 nm fiber. The 30 nm chromatin fiber is further compacted by the formation of __________________ that emanate from a central __________________. 30 nm fiber heterochromatin linker active chromatin histone H1 loops axis histone H3 more beads-on-a-string histone H4 synaptic complex euchromatin less zigzag
heterochromatin euchromatin less linker histone H1 30nm fiber zigzag loops axis
Is this statement true or false? Explain your answer. "Since introns do not contain protein coding information, they do not have to be removed precisely (meaning, a nucleotide here and there should not matter) from the primary transcript during RNA splicing."
it could shift the reading frame
For each of the following sentences, fill in the blanks with the best word or phrase selected from the list below. Not all words or phrases will be used; use each word or phrase only once. Once an mRNA is produced, its message can be decoded on ribosomes. The ribosome is composed of two subunits: the __________________ subunit, which catalyzes the formation of the peptide bonds that link the amino acids together into a polypeptide chain, and the __________________ subunit, which matches the tRNAs to the codons of the mRNA. During the chain elongation process of translating an mRNA into protein, the growing polypeptide chain attached to a tRNA is bound to the __________________-site of the ribosome. An incoming aminoacyl-tRNA carrying the next amino acid in the chain will bind to the __________________-site by forming base pairs with the exposed codon in the mRNA. The __________________ enzyme catalyzes the formation of a new peptide bond between the growing polypeptide chain and the newly arriving amino acid. The end of a protein-coding message is signaled by the presence of a stop codon, which binds the __________________ called release factor. Eventually, most proteins will be degraded by a large complex of proteolytic enzymes called the __________________. A medium proteasome central P RNA DNA peptidyl transferase small E polymerase T large protein ubiquitin
large small P A peptidyl transferase protein proteasome
The following DNA sequence includes the beginning of a sequence coding for a protein. What would be the result of a mutation that changed the C marked by an asterisk to an A? 5′-AGGCTATGAATGGACACTGCGAGCCC.... *
the change causes a stop codon
The length of a particular gene in human DNA, measured from the start site for transcription to the end of the protein-coding region, is 10,000 nucleotides, whereas the length of the mRNA produced from this gene is 4000 nucleotides. What is the most likely reason for this difference?
the gene contains one or more introns
For each of the following sentences, fill in the blanks with the best word or phrase selected from the list below. Not all words or phrases will be used; use each word or phrase only once. For a cell's genetic material to be used, the information is first copied from the DNA into the nucleotide sequence of RNA in a process called __________________. Various kinds of RNA are produced, each with different functions. __________________ molecules code for proteins, __________________ molecules act as adaptors for protein synthesis, __________________ molecules are integral components of the ribosome, and __________________ molecules are important in the splicing of RNA transcripts. incorporation rRNA transmembrane mRNA snRNA tRNA pRNA transcription proteins translation
transcription mRNA tRNA rRNA snRNA