Deck 27: Protein Metabolism

Question 1

In bacteria the elongation stage of

A)aminoacyl-tRNAs.
B)EF-Tu.
C)GTP.
D)IF-2.
E)peptidyl transferase.

Answer 1

IF-2.

Question 2

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.

Answer 2

are amino acid-specific;there is at least one enzyme specific for each amino acid.

Question 3

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.

Answer 3

"recognize" specific tRNA molecules and specific amino acids.

Question 4

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 "wobble" occurs only in the third base of the anticodon.

Question 5

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' $\rightarrow$ 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.

Question 6

Which one of the following statements about the elongation phase of

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.

Question 7

Which one of the following is true about

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 two or three different codons.
E)The first position of the tRNA anticodon is always adenosine.

Question 8

Formation of the ribosomal initiation complex for bacterial

A)EF-Tu.
B)formylmethionyl tRNA^fMet.
C)GTP.
D)initiation factor 2 (IF-2).
E)mRNA.

Question 9

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.

Question 10

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 + PP_i.
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.

Question 11

Which one of the following is not true about RNA editing?

A)RNA editing occurs mostly in mitochondria and chloroplasts.
B)RNA editing requires guide RNAs that have sequences complementary to the edited mRNA.
C)Deamination of G is a common reaction in RNA editing.
D)Deamination of A is common reaction in RNA editing.
E)RNA editing allows for the synthesis of two different proteins from one gene.

Question 12

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 specifically 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.

Question 13

In the "activation" of an amino acid for

A)leucine can be attached to tRNA^Phe,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.

Question 14

Which of the following is not one of the five steps of

A)Termination and ribosome degradation
B)Elongation of the peptide chain
C)Initiation of peptide synthesis
D)Activation of the amino acids
E)Protein folding and posttranslational processing

Question 15

Which of the following is/are true for

A)All proteins are initially synthesized with methionine at their C-terminus.
B)All proteins are initially synthesized with methionine at their N-terminus.
C)All proteins are initially synthesized with tryptophan at their C-terminus.
D)All proteins are initially synthesized with a multiple of 3 amino acids in their sequence.
E)None of the above

Question 16

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 + P_i.

Question 17

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.

Question 18

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.

Question 19

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 ribosomes in an E.coli cell.
D)There are two major ribosomal subunits,each with multiple proteins.
E)Ribosomes are relatively small,with molecular weights less than 10,000.

Question 20

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.

Question 21

Explain how insertions and deletions were used to provide evidence that the genetic code was a triplet code.

Question 22

The large structure consisting of a mRNA molecule being translated by multiple copies of the macromolecular complexes that carry out

A)lysosome.
B)polysome.
C)proteosome.
D)ribosome.
E)synthosome.

Question 23

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
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 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.

Question 24

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:

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. 27-7, p. 1107.)

Question 25

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

Question 26

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

Question 27

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

Question 28

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.
___Ribosomes contain many different RNAs.
___The three ribosomal RNAs in a bacterial ribosome are distributed in three separate, large ribosomal subunits.
___The catalytic machinery of the ribosome is protein-based.
___There are four binding sites for aminoacyl-tRNAs on a ribosome.

Question 29

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.

Question 30

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.

Question 31

Consider the following hypothetical short mRNA;what would be the sequence of the protein produced if this were translated in an E.coli cell?
5'-AUAGGAGGUUUGACCUAUGCCUCGUUUAUAGCC-3'

Question 32

The template strand of a segment of double-stranded DNA contains the sequence:
(5')-CTT TGA TAA GGA TAG CCC TTC-(3')
(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?
(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?

Question 33

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.

Question 34

Approximately how many NTPs must be converted to NDPs to incorporate one amino acid into a protein?

A)0
B)1
C)2
D)4
E)8

Question 35

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

Question 36

Posttranslational glycosylation of proteins is inhibited specifically by:

A)chloramphenicol.
B)cycloheximide.
C)puromycin.
D)streptomycin.
E)tunicamycin.

Question 37

Which of the following is not utilized for protein degradation in eukaryotes?

A)ATP
B)Ubiquitin ligases
C)Deubiquitinases
D)Lon protease
E)Proteasome

Question 38

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.

Question 39

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

Question 40

It is possible to convert the Cys that is a part of Cys-tRNA^Cys to Ala by a catalytic reduction.If the resulting Ala-tRNA^Cys 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-tRNA^Cys 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

Question 41

In no more than three sentences,describe a nonsense suppressor tRNA and how it differs from a normal tRNA.

Question 42

A new antibiotic was recently discovered that inhibits prokaryotic protein synthesis. In the presence of the antibiotic, protein synthesis can be initiated, but only dipeptides that remain bound to the ribosome are formed. What specific step of protein synthesis is likely to be blocked by this antibiotic?

Question 43

A given mRNA sequence might be translated in any of three reading frames.Describe how prokaryotes and eukaryotes determine the correct reading frame.

Question 44

Describe the role of ubiquitin in mediating intracellular protein breakdown.

Question 45

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.

Question 46

What are the stages in targeting of nuclear proteins,and why are the targeting sequences not removed upon arrival of the protein in the nucleus?

Question 47

The ribosome does not have a comparable protease proofreading function like the exonuclease activity found in DNA polymerase.What is the "technical difficulty" that perhaps prevented the easy evolution of such an activity?

Question 48

Polypeptide chain elongation in E.coli occurs by the cyclical repetition of three steps.What are these steps and what cellular components are necessary for each of them to occur?

Question 49

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.

Question 50

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?

Question 51

Describe the sequence of events between the transcription of an mRNA for a secreted protein and the arrival of that protein in the lumen of the endoplasmic reticulum.

Question 53

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) tRNAf^Met

Question 54

Number the following steps in the proper order with regard to protein synthesis.
___ Aminoacyl-tRNA binds to the A site.
___ Deacylated tRNA is released from ribosome.
___ Peptide bond formation shifts the growing peptide from the P to the A site.
___ The 50S subunit binds to the initiation complex of the 30S subunit and mRNA.

Question 55

Indicate whether each of the following statements is true (T)or false (F).
___ Bacterial mRNA is broken down within a few minutes of its formation in E.coli.
___ Bacterial mRNA consists only of the bases that code for amino acids.
___ Polysomes do not necessarily contain mRNA.
___ Bacterial mRNA normally occurs as a double-stranded structure,with one strand containing codons,the other containing anticodons.
___ Bacterial mRNA can be translated while it is still being synthesized.

Question 56

Following the synthesis of their polypeptide chain,many proteins require further posttranslational modifications before they attain their full biological activity or function.List and describe briefly at least four possible types of modification that can occur.

Question 57

The process of charging tRNAs with their cognate amino acids involves multiple proofreading steps to increase the overall fidelity.Briefly describe these steps.

Question 58

Regarding translation in eukaryotes versus that in prokaryotes (bacteria),indicate whether each of the following statements is true (T)or false (F).
___ In eukaryotes,the 3' end of the mRNA is associated with the 5' end during initiation,whereas in prokaryotes,it is not.
___ In prokaryotes,it is initiated at an AUG near a Shine-Dalgarno sequence in the mRNA,whereas in eukaryotes,it is initiated at an AUG near the 3' end of the mRNA.
___ In prokaryotes,it is initiated with Met,whereas in eukaryotes,it is initiated with fMet.
___ In prokaryotes,translation and transcription are coupled,whereas in eukaryotes,they are not.

Question 59

When first synthesized,proinsulin has an additional leader or signal peptide at its amino terminus.This complete molecule is called preproinsulin and the signal peptide is cleaved off to give proinsulin.Briefly,what is the likely function of the signal peptide?

Question 60

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 GTP hydrolysis.
___Termination of translation requires release factors,but no NTP hydrolysis.