kupdf com lehninger principles of biochemistry test bank ch 27pdf

The genetic code Page: 1038 Difficulty: 2 Ans: C Assuming that the average amino acid residue contributes 110 to the peptide molecular weight, what will be the minimum length of the mRNA

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Multiple Choice Questions

1 The genetic code

Page: 1038 Difficulty: 2 Ans: C

A certain bacterial mRNA is known to represent only one gene and to contain about 800 nucleotides

If you assume that the average amino acid residue contributes 110 to the peptide molecular weight, the largest polypeptide that this mRNA could code for would have a molecular weight of about: A) 800

B) 5,000

C) 30,000

D) 80,000

E) An upper limit cannot be determined from the data given

Assuming that the average amino acid residue contributes 110 to the peptide molecular weight, what will be the minimum length of the mRNA encoding a protein of molecular weight 50,000?

A) 133 nucleotides

B) 460 nucleotides

C) 1,400 nucleotides

D) 5,000 nucleotides

E) A minimum length cannot be determined from the data given

Pages: 1039-1044 Difficulty: 3 Ans: D

Which of the following are features of the wobble hypothesis?

A) A naturally occurring tRNA exists in yeast that can read both arginine and lysine codons B) A tRNA can recognize only one codon

C) Some tRNAs can recognize codons that specify two different amino acids, if both are nonpolar D) The “wobble” occurs only in the first base of the anticodon

E) The third base in a codon always forms a normal Watson-Crick base pair

Which one of the following is true about the genetic code?

A) All codons recognized by a given tRNA encode different amino acids

B) It is absolutely identical in all living things

C) Several different codons may encode the same amino acid

D) The base in the middle position of the tRNA anticodon sometimes permits “wobble” base pairing with 2 or 3 different codons

E) The first position of the tRNA anticodon is always adenosine

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5 Protein synthesis

Page: 1045 Difficulty: 1 Ans: D

Which one of the following statements about ribosomes is true?

A) The large subunit contains rRNA molecules, the small subunit does not

B) The RNA in ribosomes plays a structural, not catalytic, role

C) There are about 25 of them in an E coli cell

D) There are two major subunits, each with multiple proteins

E) They are relatively small, with molecular weights less than 10,000

Page: 1049 Difficulty: 2 Ans: A

Which of the following statements about tRNA molecules is false?

A) A, C, G, and U are the only bases present in the molecule

B) Although composed of a single strand of RNA, each molecule contains several short, double-helical regions

C) Any given tRNA will accept only one specific amino acid

D) The amino acid attachment is always to an A nucleotide at the 3' end of the molecule

E) There is at least one tRNA for each of the 20 amino acids

Page: 1050 Difficulty: 2 Ans: E

Which of the following statements about the tRNA that normally accepts phenylalanine is false?

(mRNA codons for phenylalanine are UUU and UUC.)

A) It interacts specificially with the Phe synthetase

B) It will accept only the amino acid phenylalanine

C) Its molecular weight is about 25,000

D) Phenylalanine can be specifically attached to an —OH group at the 3' end

E) The tRNA must contain the sequence UUU

Which of the following is not true of tRNA molecules?

A) The 3'-terminal sequence is —CCA

B) Their anticodons are complementary to the triplet codon in the mRNA

C) They contain more than four different bases

D) They contain several short regions of double helix

E) With the right enzyme, any given tRNA molecule will accept any of the 20 amino acids

Aminoacyl-tRNA synthetases (amino acid activating enzymes):

A) “recognize” specific tRNA molecules and specific amino acids

B) in conjunction with another enzyme attach the amino acid to the tRNA

C) interact directly with free ribosomes

D) occur in multiple forms for each amino acid

E) require GTP to activate the amino acid

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Page: 1051 Difficulty: 2 Ans: B

In E coli, aminoacyl-tRNA synthetases:

A) activate amino acids in 12 steps

B) are amino acid–specific; there is at least one enzyme specific for each amino acid

C) fall into two classes, each of which attaches amino acids to different ends of the tRNA

D) have no proofreading activities

E) require a tRNA, an amino acid, and GTP as substrates

Pages: 1051-1054 Difficulty: 2 Ans: D

Which of the following statements about aminoacyl-tRNA synthetases is false?

A) Some of the enzymes have an editing/proofreading capability

B) The enzyme attaches an amino acid to the 3' end of a tRNA

C) The enzyme splits ATP to AMP + PPi

D) The enzyme will use any tRNA species, but is highly specific for a given amino acid

E) There is a different synthetase for every amino acid

The enzyme that attaches an amino acid to a tRNA (aminoacyl-tRNA synthetase):

A) always recognizes only one specific tRNA

B) attaches a specific amino acid to any available tRNA species

C) attaches the amino acid at the 5' end of the tRNA

D) catalyzes formation of an ester bond

E) splits ATP to ADP + Pi

In the “activation” of an amino acid for protein synthesis:

A) leucine can be attached to tRNAPhe, by the aminoacyl-tRNA synthetase specific for leucine B) methionine is first formylated, then attached to a specific tRNA

C) the amino acid is attached to the 5' end of the tRNA through a phosphodiester bond

D) there is at least one specific activating enzyme and one specific tRNA for each amino acid E) two separate enzymes are required, one to form the aminoacyl adenylate, the other to attach the amino acid to the tRNA

Formation of the ribosomal initiation complex for bacterial protein synthesis does not require:

A) EF-Tu

B) formylmethionyl tRNAfMet

C) GTP

D) initiation factor 2 (IF-2)

E) mRNA

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In bacteria the elongation stage of protein synthesis does not involve:

A) aminoacyl-tRNAs

B) EF-Tu

C) GTP

D) IF-2

E) peptidyl transferase

Which one of the following statements about the elongation phase of protein synthesis is true? A) At least five high-energy phosphoryl groups are expended for each peptide bond formed

B) During elongation, incoming aminoacylated tRNAs are first bound in the P site

C) Elongation factor EF-Tu facilitates translocation

D) Peptidyl transferase catalyzes the attack of the carboxyl group of the incoming amino acid on an ester linkage in the nascent polypeptide

E) Peptidyl transferase is a ribozyme

Which of the following statements about bacterial mRNA is true?

A) A ribosome usually initiates translation near the end of the mRNA that is synthesized last B) An mRNA is never degraded but is passed on to the daughter cells at cell division

C) During polypeptide synthesis, ribosomes move along the mRNA in the direction 5' → 3'

D) Ribosomes cannot initiate internally in a polycistronic transcript

E) The codon signaling peptide termination is located in the mRNA near its 5' end

Bacterial ribosomes:

A) bind tightly to specific regions of DNA, forming polysomes

B) contain at least one catalytic RNA molecule (ribozyme)

C) contain three species of RNA and five different proteins

D) have specific, different binding sites for each of the 20 tRNAs

E) require puromycin for normal function

The large structure consisting of a mRNA molecule being translated by multiple copies of the

macromolecular complexes that carry out protein synthesis is called a:

A) lysosome

B) polysome

C) proteosome

D) ribosome

E) synthosome

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It is possible to convert the Cys that is a part of Cys-tRNACys to Ala by a catalytic reduction If the resulting Ala-tRNACys were added to a mixture of (1) ribosomes, (2) all the other tRNAs and amino acids, (3) all of the cofactors and enzymes needed to make protein in vitro, and (4) mRNA for

hemoglobin, where in the newly synthesized hemoglobin would the Ala from Ala-tRNACys be

incorporated?

A) Nowhere; this is the equivalent of a nonsense mutation

B) Wherever Ala normally occurs

C) Wherever Cys normally occurs

D) Wherever either Ala or Cys normally occurs

E) Wherever the dipeptide Ala-Cys normally occurs

Pages: 1066-1067 Difficulty: 2 Ans: C

Which one of the following antibiotics does not function by interfering with the translational process? A) Chloramphenicol

B) Cycloheximide

C) Penicillin

D) Puromycin

E) Streptomycin

22 Protein targeting and degradation

Which of the following is true about the sorting pathway for proteins destined for incorporation into lysosomes or the plasma membrane of eukaryotic cells?

A) Binding of SRP to the signal peptide and the ribosome temporarily accelerates protein synthesis B) The newly synthesized polypeptides include a signal peptide at their carboxyl termini

C) The signal peptide is cleaved off inside the mitochondria by signal peptidase

D) The signal recognition particle (SRP) binds to the signal peptide soon after it appears outside the ribosome

E) The signal sequence is added to the polypeptide in a posttranslational modification reaction

Pages: 1069-1070 Difficulty: 2 Ans: A

Glycosylation of proteins inside the endoplasmic reticulum does not involve:

A) a His residue on the protein

B) an Asn residue on the protein

C) dolichol phosphate

D) glucose

E) N-acetylglucosamine

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Posttranslational glycosylation of proteins is inhibited specifically by:

A) chloramphenicol

B) cycloheximide

C) puromycin

D) streptomycin

E) tunicamycin

The signal sequences that direct proteins to the nucleus are:

A) always at the amino terminus of the targeted protein

B) cleaved after the protein arrives in the nucleus

C) glycosyl moieties containing mannose 6-phosphate residues

D) not located at the ends of the peptide, but in its interior

E) the same as those that direct certain proteins to lysosomes

Pages: 1072-1074 Difficulty: 3 Ans: C

The pathway for polypeptides exported from E coli includes the following steps, which occur in what

order for correct export?

1 A chaperone, SecA, binds to the polypeptide

2 A chaperone, SecB, binds to the polypeptide

3 ATP is hydrolyzed by Sec A

4 SecA pushes 20 amino acids of the polypeptide into the translocation complex

A) 1, 2, 3, 4

B) 1, 2, 4, 3

C) 2, 1, 4, 3

D) 2, 3, 1, 4

E) 3, 1, 4, 2

Ubiquitin-mediated protein degradation is a complex process, and many of the signals remain

unknown One known signal involves recognition of amino acids in a processed protein that are either stabilizing (Ala, Gly, Met, Ser, etc.) or destabilizing (Arg, Asp, Leu, Lys, Phe, etc.), and are located at:

A) a helix-turn-helix motif in the protein

B) a lysine-containing target sequence in the protein

C) a zinc finger structure in the protein

D) the amino-terminus of the protein

E) the carboxy-terminus of the protein

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Short Answer Questions

Pages: 1035-1036 Difficulty: 2

Outline one of the experimental methods providing evidence that the genetic code was a triplet code

Ans: When one or two nucleotides were added to or deleted from a gene, the resulting mRNA

produced a protein with a different amino acid sequence after the deletion or insertion When three nucleotides were added or deleted, the resulting protein had a normal sequence except for the

insertion or deletion of a single amino acid residue

Page: 1036 Difficulty: 3

Describe, succinctly, two ways in which synthetic polynucleotides were used in solving the genetic code (you need not describe how the synthetic polynucleotides were made)

Ans: (1) When synthetic polymers of only one nucleotide were used as mRNA in vitro, only one of

the 20 amino acids was converted into protein For example, poly(U) (containing only the codon UUU) directed the synthesis of polyphenylalanine, showing that UUU encodes Phe (2)

Trinucleotides of known sequence were used to stimulate aminoacyl-tRNA binding to ribosomes Because only that aminoacyl-tRNA whose anticodon matched the trinucleotide “mRNA” was bound, the coding specificity of each sequence of three bases could be determined by determining which of the 20 aminoacyl-tRNAs bound (3) Random polymers of RNA containing known ratios of

nucleotides (e.g., 70% A and 30% T) generate only certain codons in predictable ratios The

identities and ratios of the amino acids specified by such polymers provided important clues that helped solve the genetic code (4) Additional assignments were made possible using synthetic

oligonucleotides containing repeats of specific two, three, or four base pair sequences

You have isolated a fragment of viral DNA that totally encodes at least two proteins, 120 and 80 amino acids long The DNA fragment is 400 base pairs long (a) Why might you consider this unusual? (b) You sequence the two proteins and find no sequence homology Propose a model to account for these findings

Ans: (a) Two distinct proteins of these sizes should require mRNAs of 360 and 240 base pairs

because each amino acid residue requires 3 base pairs to code for it (b) No homology means that the smaller protein cannot be derived from the larger by proteolysis; if it were, there would be 80 amino acid residues of identical sequence in the two proteins One possible explanation is that the two genes coding for these proteins overlap and are read in different reading frames

The template strand of a segment of double-stranded DNA contains the sequence:

(5')CTT TGA TAA GGA TAG CCC TTC

(a) What is the base sequence of the mRNA that can be transcribed from this strand? (b) What amino acid sequence could be coded by the mRNA base sequence in (a), using only the first reading frame

starting at the 5' end? (Refer to Fig 27-7, p 1038.) (c) Suppose the other (complementary) strand is

used as a template for transcription What is the amino acid sequence of the resulting peptide, again

starting from the 5' end and using only the first reading frame?

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Ans:

(a) (5')GAA GGG CUA UCC UUA UCA AAG(3’)

(b) Glu-Gly-Leu-Ser-Leu-Ser-Lys

(c) The codons translate to Leu-Stop-Stop No peptide would be produced because of the stop

codons

(See also Fig 27-6, p 1038.)

Describe the possible outcomes that could occur because of a single base change in an mRNA

Ans: The most likely result is a single amino acid change in the encoded protein, when a codon is

altered to one of another amino acid However, some nucleotide changes will be “silent” and not change the protein, if the altered codon still specifies the original amino acid Conversion to a

nonsense codon will result in a truncated polypeptide, while alteration of the normal stop codon to a

“sense” codon will result in a lengthened protein Alternation of the initiaton codon may result in the total failure to translate, and result in no protein product Changes in mRNA sequence outside the protein-coding region may affect translational efficiency, splicing, or mRNA turnover rates

The following sequence of four amino acids occurred in the structure of a polypeptide found in a wild-type organism: Leu-Ser-Ile-Arg Several mutants were isolated, each of which carried a single base pair change in the region of DNA that coded for this amino acid sequence Their corresponding amino acid sequences are:

Mutant

1 MET-Ser-Ile-Arg

2 Leu-TRP-Ile-Arg

3 Leu-Ser-ARG-Arg

4 Leu-Ser-Ile-PRO

5 Leu-Ser-Ile-TRP

What was the nucleotide sequence of the region of mRNA that coded for the amino acid sequence in the wild-type organism? (Refer to Fig 27-6, p 1038.)

Ans: (5')C or (5')U UG UCG AUA CGG

In protein synthesis, 61 codons specify the 20 amino acids Base pairing between the codon and the tRNA anticodon assures that the correct amino acid will be inserted into the nascent polypeptide chain Why then does the cell require only 32 different tRNAs to recognize 61 different codons?

Ans: Certain tRNAs have the unusual nucleotide inosinate in the first anticodon position Because

inosinate can base pair with A, U, or C, a tRNA containing hypoxanthine can recognize three

different codons In each recognized codon, there is a standard anticodon-codon base pair with the first two bases of the codon; “wobble” in the third base pair allows one tRNA to read three different codons Similarly, tRNAs with U or G in the first anticodon position also exhibit a wobble effect that permits pairing with two different codons

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Indicate whether the following statements are true (T) or false (F)

_A ribosome is the complex within which protein synthesis occurs

_Ribosomes contain many separate proteins

_The three ribosomal RNAs in a bacterial ribosome are distributed in three separate, large ribosomal subunits

_There are four binding sites for aminoacyl-tRNAs on a ribosome

Ans: T; T; F; F

The process of charging tRNAs with their cognate amino acids involves multiple proofreading steps

to increase the overall fidelity Briefly describe these steps

Ans: There are two main stages of selection: 1) the synthetase strongly favors activation of the

correct amino acid to become aminoacyl-AMP (incorrect amino acids are very poorly activated) and 2) when the correct uncharged tRNA is bound to the enzyme, only the correct aminoacyl-AMP is tolerated in the “proofreading” active site (incorrect aminoacyl-AMPs, though they may become bound, are rapidly hydrolyzed) In addition, for most synthetases, if their tRNA does manage to become acylated by the wrong amino acid, that product is also rapidly hydrolyzed

The recognition of an amino acid by its cognate aminoacyl-tRNA synthetase is said to involve a

“second genetic code” What is meant by this?

Ans: Each of the 20 amino acids has a unique synthetase, but many have multiple cognate tRNAs that

must be charged (aminoacylated) The “second code” refers to features common to all tRNAs that carry the same amino acid, making them specifically recognizable by the correct synthetase These features occur at different places in different tRNA classes, and may be as simple as a single G-U basepair, or require ten or more specific nucleotides throughout the sequence (See Fig 27-16, p 1053.)

In 1961, Howard Dintzis carried out an experiment that defined the direction of polypeptide chain growth during protein synthesis in cells The experiment involved the analysis of hemoglobin

molecules that were being synthesized in reticulocytes in the presence of radioactive amino acids Describe the analysis and how it demonstrated the direction of chain growth

Ans: In the experiment, only completed polypeptides were isolated and analyzed for the amount of

redioactivity in different regions The greatest radioactivity should be located in the region furthest from the initiation point and the least radioactivity in the region closest to the initiation point The opposite is true for the termination point The analysis showed that polypeptide synthesis was

initiated at the amino terminus and terminated at the carboxyl terminus

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Page: 1056-1058 Difficulty: 3

A given mRNA sequence might be translated in any of three reading frames Describe how

prokaryotes and eukaryotes determine the correct reading frame

Ans: In prokaryotes, the Shine-Dalgarno sequence in the mRNA base pairs with a complementary

sequence in the 16S RNA of the ribosome; this positions the correct start codon (AUG) on the 30S ribosomal subunit Thus, the initiating AUG is distinguished by its proximity to the Shine-Dalgarno sequence In eukaryotes, the initiating AUG codon is the first AUG that the ribosome encounters as it

scans the mRNA from its 5' end In both cases the initiating AUG also sets the correct reading frame

Match the factor or enzyme at the right with the stage(s) of protein synthesis at which it acts If a factor or enzyme participates in two stages of protein synthesis, indicate both of them

_ Amino acid activation (a) RF1

_ Initiation (b) EF-Tu

_ Elongation (c) aminoacyl-tRNA

_ Termination (d) Shine-Dalgarno sequence

Ans: c; d; b; a

Indicate whether each of the following statements is true (T) or false (F)

_Assembly of a complete ribosome onto an mRNA requires ATP hydrolysis

_Aminoacylation or “charging” of tRNA requires the formation of an aminoacyl-AMP

intermediate

_Aminoacyl-tRNA binding to the A site of the ribosome requires the accessory factor EF-G and GTP hydrolysis

_Translocation of a growing polypeptide from the A to the P site on the ribosome requires

EF-G and EF-GTP hydrolysis

_Termination of translation requires release factors, but no NTP hydrolysis

Ans: F; T; F; T; T

Briefly describe the role of the following components in bacterial protein synthesis

(a) Initiation factor 2 (IF-2)

(b) 16S RNA

(c) Peptidyl transferase

(d) Release factors

(e) Elongation factor G (EF-G)

(f) N10-formyltetrahydrofolate

(g) ATP

(h) tRNAfMet

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