Chapter 27 Protein Metabolism

Multiple Choice Questions

1. The genetic code Page: 1038 i!!icult": 2 #ns: 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. $ 000. &0 000. 80 000. An upper limit cannot be determined from the data given.

2. The genetic code Page: 1038 i!!icult": 2 #ns: C 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 $0 000) A" #" %" '" (" 1&& nucleotides *+0 nucleotides 1 *00 nucleotides $ 000 nucleotides A minimum length cannot be determined from the data given.

3. The genetic code Pages: 103$%10&& i!!icult": 3 #ns: ,hich of the following are features of the wobble hypothesis) A" #" %" '" (" A naturally occurring tRNA e-ists in yeast that can read both arginine and lysine codons. A tRNA can recogni.e only one codon. /ome tRNAs can recogni.e codons that specify two different amino acids if both are nonpolar. 0he 1wobble2 occurs only in the first base of the anticodon. 0he third base in a codon always forms a normal ,atson3%rick base pair.

&. The genetic code Page: 103$ i!!icult": 2 #ns: C ,hich one of the following is true about the genetic code) A" #" %" '" All codons recogni.ed by a given tRNA encode different amino acids. It is absolutely identical in all living things. /everal different codons may encode the same amino acid. 0he base in the middle position of the tRNA anticodon sometimes permits 1wobble2 base pairing with 4 or & different codons. (" 0he first position of the tRNA anticodon is always adenosine.

'8

Chapter 27 Protein Metabolism

'. Protein s"nthesis Page: 10&' i!!icult": 1 #ns: ,hich one of the following statements about ribosomes is true) A" #" %" '" (" 0he large subunit contains rRNA molecules the small subunit does not. 0he RNA in ribosomes plays a structural not catalytic role. 0here are about 4$ of them in an E. coli cell. 0here are two ma5or subunits each with multiple proteins. 0hey are relatively small with molecular weights less than 10 000.

(. Protein s"nthesis Page: 10&$ i!!icult": 2 #ns: # ,hich of the following statements about tRNA molecules is false) A" A % 6 and 7 are the only bases present in the molecule. #" Although composed of a single strand of RNA each molecule contains several short double3 helical regions. %" Any given tRNA will accept only one specific amino acid. '" 0he amino acid attachment is always to an A nucleotide at the & ' end of the molecule. (" 0here is at least one tRNA for each of the 40 amino acids. 7. Protein s"nthesis Page: 10'0 i!!icult": 2 #ns: ) ,hich of the following statements about the tRNA that normally accepts phenylalanine is false) 8mRNA codons for phenylalanine are 777 and 77%." A" #" %" '" (" It interacts specificially with the 9he synthetase. It will accept only the amino acid phenylalanine. Its molecular weight is about 4$ 000. 9henylalanine can be specifically attached to an :;< group at the & ' end. 0he tRNA must contain the se=uence 777.

8. Protein s"nthesis Page: 10'1 i!!icult": 2 #ns: ) ,hich of the following is not true of tRNA molecules) A" #" %" '" (" 0he &'3terminal se=uence is :%%A. 0heir anticodons are complementary to the triplet codon in the mRNA. 0hey contain more than four different bases. 0hey contain several short regions of double heli-. ,ith the right en.yme any given tRNA molecule will accept any of the 40 amino acids.

$. Protein s"nthesis Page: 10'1 i!!icult": 2 #ns: # Aminoacyl3tRNA synthetases 8amino acid activating en.ymes"! A" #" %" '" 1recogni.e2 specific tRNA molecules and specific amino acids. in con5unction with another en.yme attach the amino acid to the tRNA. interact directly with free ribosomes. occur in multiple forms for each amino acid.

Chapter 27 Protein Metabolism

'$

(" re=uire 609 to activate the amino acid. 10. Protein s"nthesis Page: 10'1 i!!icult": 2 #ns: * In E. coli aminoacyl3tRNA synthetases! A" #" %" '" (" activate amino acids in 14 steps. are amino acid>specific? there is at least one en.yme specific for each amino acid. fall into two classes each of which attaches amino acids to different ends of the tRNA. have no proofreading activities. re=uire a tRNA an amino acid and 609 as substrates.

11. Protein s"nthesis Pages: 10'1%10'& i!!icult": 2 #ns: ,hich of the following statements about aminoacyl3tRNA synthetases is false) A" #" %" '" (" /ome of the en.ymes have an editing@proofreading capability. 0he en.yme attaches an amino acid to the &' end of a tRNA. 0he en.yme splits A09 to AA9 B 99i. 0he en.yme will use any tRNA species but is highly specific for a given amino acid. 0here is a different synthetase for every amino acid.

12. Protein s"nthesis Page: 10'1 i!!icult": 2 #ns: 0he en.yme that attaches an amino acid to a tRNA 8aminoacyl3tRNA synthetase"! A" #" %" '" (" always recogni.es only one specific tRNA. attaches a specific amino acid to any available tRNA species. attaches the amino acid at the $' end of the tRNA. cataly.es formation of an ester bond. splits A09 to A'9 B 9i.

13. Protein s"nthesis Page: 10'1 i!!icult": 2 #ns: In the 1activation2 of an amino acid for protein synthesis! A" #" %" '" (" leucine can be attached to tRNA9he by the aminoacyl3tRNA synthetase specific for leucine. methionine is first formylated then attached to a specific tRNA. the amino acid is attached to the $' end of the tRNA through a phosphodiester bond. there is at least one specific activating en.yme and one specific tRNA for each amino acid. two separate en.ymes are re=uired one to form the aminoacyl adenylate the other to attach the amino acid to the tRNA.

1&. Protein s"nthesis Page: 10'( i!!icult": 2 #ns: # Cormation of the ribosomal initiation comple- for bacterial protein synthesis does not re=uire! A" #" %" '" (" (C30u. formylmethionyl tRNAfAet. 609. initiation factor 4 8IC34". mRNA.

(0

Chapter 27 Protein Metabolism

1'. Protein s"nthesis Page: 10'8 i!!icult": 2 #ns: In bacteria the elongation stage of protein synthesis does not involve! A" #" %" '" (" aminoacyl3tRNAs. (C30u. 609. IC34. peptidyl transferase.

1(. Protein s"nthesis Page: 10'8 i!!icult": 2 #ns: ) ,hich one of the following statements about the elongation phase of protein synthesis is true) A" #" %" '" At least five high3energy phosphoryl groups are e-pended for each peptide bond formed. 'uring elongation incoming aminoacylated tRNAs are first bound in the 9 site. (longation factor (C30u facilitates translocation. 9eptidyl transferase cataly.es the attack of the carbo-yl group of the incoming amino acid on an ester linkage in the nascent polypeptide. (" 9eptidyl transferase is a ribo.yme. 17. Protein s"nthesis Page: 10'$ i!!icult": 2 #ns: C ,hich of the following statements about bacterial mRNA is true) A" #" %" '" (" A ribosome usually initiates translation near the end of the mRNA that is synthesi.ed last. An mRNA is never degraded but is passed on to the daughter cells at cell division. 'uring polypeptide synthesis ribosomes move along the mRNA in the direction $ ' &'. Ribosomes cannot initiate internally in a polycistronic transcript. 0he codon signaling peptide termination is located in the mRNA near its $ ' end. #ns: *

18. Protein s"nthesis Page: 10'$ i!!icult": 2 #acterial ribosomes! A" #" %" '" ("

bind tightly to specific regions of 'NA forming polysomes. contain at least one catalytic RNA molecule 8ribo.yme". contain three species of RNA and five different proteins. have specific different binding sites for each of the 40 tRNAs. re=uire puromycin for normal function.

1$. Protein s"nthesis Page: 10(2 i!!icult": 1 #ns: * 0he large structure consisting of a mRNA molecule being translated by multiple copies of the macromolecular comple-es that carry out protein synthesis is called a! A" #" %" '" lysosome. polysome. proteosome. ribosome.

Chapter 27 Protein Metabolism

(1

(" synthosome. 20. Protein s"nthesis Page: 10(1 i!!icult": 3 #ns: C It is possible to convert the %ys that is a part of %ys3tRNA %ys to Ala by a catalytic reduction. If the resulting Ala3tRNA%ys were added to a mi-ture of 81" ribosomes 84" all the other tRNAs and amino acids 8&" all of the cofactors and en.ymes needed to make protein in vitro and 8*" mRNA for hemoglobin where in the newly synthesi.ed hemoglobin would the Ala from Ala3tRNA %ys be incorporated) A" #" %" '" (" Nowhere? this is the e=uivalent of a nonsense mutation ,herever Ala normally occurs ,herever %ys normally occurs ,herever either Ala or %ys normally occurs ,herever the dipeptide Ala3%ys normally occurs

21. Protein s"nthesis Pages: 10((%10(7 i!!icult": 2 #ns: C ,hich one of the following antibiotics does not function by interfering with the translational process) A" #" %" '" (" %hloramphenicol %yclohe-imide 9enicillin 9uromycin /treptomycin

22. Protein targeting and degradation Page: 10($ i!!icult": 2 #ns: ,hich of the following is true about the sorting pathway for proteins destined for incorporation into lysosomes or the plasma membrane of eukaryotic cells) A" #" %" '" #inding of /R9 to the signal peptide and the ribosome temporarily accelerates protein synthesis. 0he newly synthesi.ed polypeptides include a signal peptide at their carbo-yl termini. 0he signal peptide is cleaved off inside the mitochondria by signal peptidase. 0he signal recognition particle 8/R9" binds to the signal peptide soon after it appears outside the ribosome. (" 0he signal se=uence is added to the polypeptide in a posttranslational modification reaction. 23. Protein targeting and degradation Pages: 10($%1070 i!!icult": 2 #ns: # 6lycosylation of proteins inside the endoplasmic reticulum does not involve! A" #" %" '" (" a <is residue on the protein. an Asn residue on the protein. dolichol phosphate. glucose. N3acetylglucosamine.

(2

Chapter 27 Protein Metabolism

2&. Protein targeting and degradation Page: 1070 i!!icult": 2 #ns: ) 9osttranslational glycosylation of proteins is inhibited specifically by! A" #" %" '" (" chloramphenicol. cyclohe-imide. puromycin. streptomycin. tunicamycin.

2'. Protein targeting and degradation Page: 1071 i!!icult": 2 #ns: 0he signal se=uences that direct proteins to the nucleus are! A" #" %" '" (" always at the amino terminus of the targeted protein. cleaved after the protein arrives in the nucleus. glycosyl moieties containing mannose +3phosphate residues. not located at the ends of the peptide but in its interior. the same as those that direct certain proteins to lysosomes.

2(. Protein targeting and degradation Pages: 1072%107& i!!icult": 3 #ns: C 0he pathway for polypeptides e-ported from E. coli includes the following steps which occur in what order for correct e-port) 1. 4. &. *. A" #" %" '" (" 1 1 4 4 & 4 4 1 & 1 & * * 1 * * & & * 4 A chaperone /ecA binds to the polypeptide. A chaperone /ec# binds to the polypeptide. A09 is hydroly.ed by /ec A. /ecA pushes 40 amino acids of the polypeptide into the translocation comple-.

27. Protein targeting and degradation Page: 107( i!!icult": 3 #ns: 7bi=uitin3mediated protein degradation is a comple- process and many of the signals remain unknown. ;ne known signal involves recognition of amino acids in a processed protein that are either stabili.ing 8Ala 6ly Aet /er etc." or destabili.ing 8Arg Asp Deu Dys 9he etc." and are located at! A" #" %" '" (" a heli-3turn3heli- motif in the protein. a lysine3containing target se=uence in the protein. a .inc finger structure in the protein. the amino3terminus of the protein. the carbo-y3terminus of the protein.

Chapter 27 Protein Metabolism

(3

+hort #ns,er Questions

28. The genetic code Pages: 103'%103( i!!icult": 2 ;utline one of the e-perimental methods providing evidence that the genetic code was a triplet code. #ns: ,hen one or two nucleotides were added to or deleted from a gene the resulting mRNA produced a protein with a different amino acid se=uence after the deletion or insertion. ,hen three nucleotides were added or deleted the resulting protein had a normal se=uence e-cept for the insertion or deletion of a single amino acid residue. 2$. The genetic code Page: 103( i!!icult": 3 'escribe succinctly two ways in which synthetic polynucleotides were used in solving the genetic code 8you need not describe how the synthetic polynucleotides were made". #ns: 81" ,hen synthetic polymers of only one nucleotide were used as mRNA in vitro only one of the 40 amino acids was converted into protein. Cor e-ample poly87" 8containing only the codon 777" directed the synthesis of polyphenylalanine showing that 777 encodes 9he. 84" 0rinucleotides of known se=uence were used to stimulate aminoacyl3tRNA binding to ribosomes. #ecause only that aminoacyl3tRNA whose anticodon matched the trinucleotide 1mRNA2 was bound the coding specificity of each se=uence of three bases could be determined by determining which of the 40 aminoacyl3tRNAs bound. 8&" Random polymers of RNA containing known ratios of nucleotides 8e.g. E0F A and &0F 0" generate only certain codons in predictable ratios. 0he identities and ratios of the amino acids specified by such polymers provided important clues that helped solve the genetic code. 8*" Additional assignments were made possible using synthetic oligonucleotides containing repeats of specific two three or four base pair se=uences. 30. The genetic code Page: 103( i!!icult": 3 Gou have isolated a fragment of viral 'NA that totally encodes at least two proteins 140 and 80 amino acids long. 0he 'NA fragment is *00 base pairs long. 8a" ,hy might you consider this unusual) 8b" Gou se=uence the two proteins and find no se=uence homology. 9ropose a model to account for these findings. #ns: 8a" 0wo distinct proteins of these si.es should re=uire mRNAs of &+0 and 4*0 base pairs because each amino acid residue re=uires & base pairs to code for it. 8b" 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 se=uence in the two proteins. ;ne possible e-planation is that the two genes coding for these proteins overlap and are read in different reading frames. 31. The genetic code Page: 1038 i!!icult": 2 0he template strand of a segment of double3stranded 'NA contains the se=uence! 8$'"%00 06A 0AA 66A 0A6 %%% 00% 8a" ,hat is the base se=uence of the mRNA that can be transcribed from this strand) 8b" ,hat amino acid se=uence could be coded by the mRNA base se=uence in 8a" using only the first reading frame starting at the $' end) 8Refer to Cig. 4E3E p. 10&8." 8c" /uppose the other 8complementary" strand is used as a template for transcription. ,hat is the amino acid se=uence of the resulting peptide again starting from the $' end and using only the first reading frame)

(&

Chapter 27 Protein Metabolism

#ns: 8a" 8$'"6AA 666 %7A 7%% 77A 7%A AA68&H" 8b" 6lu36ly3Deu3/er3Deu3/er3Dys 8c" 0he codons translate to Deu3/top3/top. No peptide would be produced because of the stop codons. 8/ee also Cig. 4E3+ p. 10&8." 32. The genetic code Page: 1038 i!!icult": 3

'escribe the possible outcomes that could occur because of a single base change in an mRNA #ns: 0he most likely result is a single amino acid change in the encoded protein when a codon is altered to one of another amino acid. <owever some nucleotide changes will be 1silent2 and not change the protein if the altered codon still specifies the original amino acid. %onversion to a nonsense codon will result in a truncated polypeptide while alteration of the normal stop codon to a 1sense2 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. %hanges in mRNA se=uence outside the protein3coding region may affect translational efficiency splicing or mRNA turnover rates. 33. The genetic code Page: 1038 i!!icult": 3 0he following se=uence of four amino acids occurred in the structure of a polypeptide found in a wild3type organism! Deu3/er3Ile3Arg. /everal mutants were isolated each of which carried a single base pair change in the region of 'NA that coded for this amino acid se=uence. 0heir corresponding amino acid se=uences are! Autant 1 4 & * $ A(03/er3Ile3Arg Deu30R93Ile3Arg Deu3/er3AR63Arg Deu3/er3Ile39R; Deu3/er3Ile30R9

,hat was the nucleotide se=uence of the region of mRNA that coded for the amino acid se=uence in the wild3type organism) 8Refer to Cig. 4E3+ p. 10&8." #ns: 8$'"% or 8$'"7 76 7%6 A7A %66 3&. The genetic code Pages: 103$%10&& i!!icult": 2 In protein synthesis +1 codons specify the 40 amino acids. #ase pairing between the codon and the tRNA anticodon assures that the correct amino acid will be inserted into the nascent polypeptide chain. ,hy then does the cell re=uire only &4 different tRNAs to recogni.e +1 different codons) #ns: %ertain tRNAs have the unusual nucleotide inosinate in the first anticodon position. #ecause inosinate can base pair with A 7 or % a tRNA containing hypo-anthine can recogni.e three different codons. In each recogni.ed codon there is a standard anticodon3codon base pair with the first two bases of the codon? 1wobble2 in the third base pair allows one tRNA to read three different codons. /imilarly tRNAs with 7 or 6 in the first anticodon position also e-hibit a wobble effect that

Chapter 27 Protein Metabolism

('

permits pairing with two different codons. 3'. Protein s"nthesis Pages: 10&'%10&$ i!!icult": 1 Indicate whether the following statements are true 80" or false 8C". IIIA ribosome is the comple- within which protein synthesis occurs. IIIRibosomes contain many separate proteins. III0he three ribosomal RNAs in a bacterial ribosome are distributed in three separate large ribosomal subunits. III0here are four binding sites for aminoacyl3tRNAs on a ribosome. #ns: 0? 0? C? C 3(. Protein s"nthesis Pages: 10'1%10'3 i!!icult": 2 0he process of charging tRNAs with their cognate amino acids involves multiple proofreading steps to increase the overall fidelity. #riefly describe these steps. #ns: 0here are two main stages of selection! 1" the synthetase strongly favors activation of the correct amino acid to become aminoacyl3AA9 8incorrect amino acids are very poorly activated" and 4" when the correct uncharged tRNA is bound to the en.yme only the correct aminoacyl3AA9 is tolerated in the 1proofreading2 active site 8incorrect aminoacyl3AA9s though they may become bound are rapidly hydroly.ed". In addition for most synthetases if their tRNA does manage to become acylated by the wrong amino acid that product is also rapidly hydroly.ed. 37. Protein s"nthesis Pages: 10'3%10'& i!!icult": 2 0he recognition of an amino acid by its cognate aminoacyl3tRNA synthetase is said to involve a 1second genetic code2. ,hat is meant by this) #ns: (ach of the 40 amino acids has a uni=ue synthetase but many have multiple cognate tRNAs that must be charged 8aminoacylated". 0he 1second code2 refers to features common to all tRNAs that carry the same amino acid making them specifically recogni.able by the correct synthetase. 0hese features occur at different places in different tRNA classes and may be as simple as a single 637 basepair or re=uire ten or more specific nucleotides throughout the se=uence. 8/ee Cig. 4E31+ p. 10$&." 38. Protein s"nthesis Page: 10'' i!!icult": 3 In 1J+1 <oward 'int.is carried out an e-periment that defined the direction of polypeptide chain growth during protein synthesis in cells. 0he e-periment involved the analysis of hemoglobin molecules that were being synthesi.ed in reticulocytes in the presence of radioactive amino acids. 'escribe the analysis and how it demonstrated the direction of chain growth. #ns: In the e-periment only completed polypeptides were isolated and analy.ed for the amount of redioactivity in different regions. 0he 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. 0he opposite is true for the termination point. 0he analysis showed that polypeptide synthesis was initiated at the amino terminus and terminated at the carbo-yl terminus.

((

Chapter 27 Protein Metabolism

3$. Protein s"nthesis Page: 10'(%10'8 i!!icult": 3 A given mRNA se=uence might be translated in any of three reading frames. 'escribe how prokaryotes and eukaryotes determine the correct reading frame. #ns: In prokaryotes the /hine3'algarno se=uence in the mRNA base pairs with a complementary se=uence in the 1+/ RNA of the ribosome? this positions the correct start codon 8A76" on the &0/ ribosomal subunit. 0hus the initiating A76 is distinguished by its pro-imity to the /hine3'algarno se=uence. In eukaryotes the initiating A76 codon is the first A76 that the ribosome encounters as it scans the mRNA from its $' end. In both cases the initiating A76 also sets the correct reading frame. &0. Protein s"nthesis Pages: 10'(%10(1 i!!icult": 1 Aatch the factor or en.yme at the right with the stage8s" of protein synthesis at which it acts. If a factor or en.yme participates in two stages of protein synthesis indicate both of them. III III III III Amino acid activation Initiation (longation 0ermination 8a" RC1 8b" (C30u 8c" aminoacyl3tRNA 8d" /hine3'algarno se=uence

#ns: c? d? b? a &1. Protein s"nthesis Pages: 10'(%10(1 i!!icult": 2 Indicate whether each of the following statements is true 80" or false 8C". IIIAssembly of a complete ribosome onto an mRNA re=uires A09 hydrolysis. IIIAminoacylation or 1charging2 of tRNA re=uires the formation of an aminoacyl3AA9 intermediate. IIIAminoacyl3tRNA binding to the A site of the ribosome re=uires the accessory factor (C36 and 609 hydrolysis. III0ranslocation of a growing polypeptide from the A to the 9 site on the ribosome re=uires (C3 6 and 609 hydrolysis. III0ermination of translation re=uires release factors but no N09 hydrolysis. #ns: C? 0? C? 0? 0 &2. Protein s"nthesis Pages: 10'(%10(1 i!!icult": 3 #riefly describe the role of the following components in bacterial protein synthesis. 8a" Initiation factor 4 8IC34" 8b" 1+/ RNA 8c" 9eptidyl transferase 8d" Release factors 8e" (longation factor 6 8(C36" 8f" N103formyltetrahydrofolate 8g" A09 8h" tRNAfAet

Chapter 27 Protein Metabolism

(7

#ns: 8a" IC34 is a protein factor that when bound to 609 brings the fAet3tRNA fAet to the initiation comple-. 8b" 1+/ RNA is a component of the small 8&0/" subunit. It contains a se=uence complementary to the /hine3'algarno se=uence in the mRNA and helps to line up the mRNA initiation A76 codon on the ribosome. 8c" 9eptidyl transferase is a ribo.yme in the $0/ ribosomal subunit. It cataly.es formation of each peptide bond as the ribosome moves along the mRNA. 8d" Release factors are proteins that bring about the release of the finished polypeptide when the ribosome encounters a termination codon in the mRNA. 8e" (C36 participates in the translocation of the ribosome down the mRNA by one codon after each peptide bond is formed. 8f" N103formyl3 tetrahydrofolate is the cofactor that donates a methyl group in the conversion of tRNA3bound Aet to fAet. 8g" A09 is the substrate for aminoacyl3tRNA synthetases? it donates an AA9 residue in the formation of aminoacyl adenylate which donates the aminoacyl group to tRNA. 8h" tRNA fAet is the transfer RNA that initiates protein synthesis by inserting the first amino acid 8fAet" in every prokaryotic protein. &3. Protein s"nthesis Pages: 10'(%10(1 i!!icult": 2 Number the following steps in the proper order with regard to protein synthesis. III Aminoacyl3tRNA binds to the A site. III 'eacylated tRNA is released from ribosome. III 9eptide bond formation shifts the growing peptide from the 9 to the A site. III 0he $0/ subunit binds to the initiation comple- of the &0/ subunit and mRNA. #ns: 4? *? &? 1 &&. Protein s"nthesis Pages: 10'(%10(2 i!!icult": 2 Indicate whether each of the following statements is true 80" or false 8C". III #acterial mRNA is broken down within a few minutes of its formation in E. coli. III #acterial mRNA consists only of the bases that code for amino acids. III 9olysomes do not necessarily contain mRNA. III #acterial mRNA normally occurs as a double3stranded structure with one strand containing codons the other containing anticodons. III #acterial mRNA can be translated while it is still being synthesi.ed. #ns: 0? C? C? C? 0 &'. Protein s"nthesis Pages: 10'7%10'8 i!!icult": 2 #ns: * Regarding translation in eukaryotes versus that in prokaryotes 8bacteria" indicate whether each of the following statements is true 80" or false 8C". III In eukaryotes the &' end of the mRNA is associated with the $' end during initiation whereas in prokaryotes it is not. III In prokaryotes it is initiated at an A76 near a /hine3'algarno se=uence in the mRNA whereas in eukaryotes it is initiated at an A76 near the & ' end of the mRNA. III In prokaryotes it is initiated with Aet whereas in eukaryotes it is initiated with fAet. III In prokaryotes translation and transcription are coupled whereas in eukaryotes they are not.

(8

Chapter 27 Protein Metabolism

#ns: 0 C C 0 &(. Protein s"nthesis Pages: 10'8%10(1 i!!icult": 2 9olypeptide chain elongation in E. coli occurs by the cyclical repetition of three steps. ,hat are these steps and what cellular components are necessary for each of them to occur) #ns: 0he three steps are! 81" An aminoacyl3tRNA is brought to the A site by (C30u with bound 609? 84" peptidyl transferase 8a ribo.yme" cataly.es peptide3bond formation? 8&" the ribosome translocates three nucleotides down the mRNA helped by (C36 8translocase". 0his shifts the peptidyl3tRNA to the A site and the deacylated tRNA to the ( site. &7. Protein s"nthesis Page: 10(0 i!!icult": 2 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. ,hat specific step of protein synthesis is likely to be blocked by this antibiotic) #ns: 0he antibiotic probably blocks translocation. &8. Protein s"nthesis Page: 10(2 i!!icult": 1 #ns: * 0he large structure consisting of a mRNA molecule being translated by multiple copies of the macromolecular comple-es that carry out protein synthesis is called a! A" #" %" '" (" lysosome. polysome. proteosome. ribosome. synthosome.

&$. Protein s"nthesis Pages: 10(2%10(' i!!icult": 2 Collowing the synthesis of their polypeptide chain many proteins re=uire further posttranslational modifications before they attain their full biological activity or function. Dist and describe briefly at least four possible types of modification that can occur. #ns: 1" Amino3terminal modification 8N3acetylation or deacetylation" 4" removal of signal se=uences used for targeting &" side3chain modification 8phosphorylation carbo-ylation methylation etc." *" attachment of N3linked 8to Asn" or O3linked 8to /er or 0hr" oligosaccharide moieties $" isoprenylation of %ys side3chains +" incorporation of prosthetic groups 8heme biotin etc." E" processing of proen.ymes or .ymogens and 8" formation of disulfide crosslinks. '0. Protein s"nthesis Page: 10(' i!!icult": 3 In no more than three sentences describe a nonsense suppressor tRNA and how it differs from a normal tRNA. #ns: A suppressor tRNA has one or more altered bases in its anticodon which allows it to base pair with one of the stop codons. 0his allows the insertion of an amino acid instead of the chain termination that would normally have occurred at the point of a nonsense 8stop" codon.

Chapter 27 Protein Metabolism

($

'1. Protein targeting and degradation Page: 10(8%10($ i!!icult": 2 ,hen first synthesi.ed proinsulin has an additional leader or signal peptide at its amino terminus. 0his complete molecule is called preproinsulin and the signal peptide is cleaved off to give proinsulin. #riefly what is the likely function of the signal peptide) #ns: 0he leader peptide in proinsulin is a signal se=uence directing it to the endoplasmic reticulum from which it enters the 6olgi comple- and is packaged into a secretory vesicle for secretion by e-ocytosis. '2. Protein targeting and degradation Page: 10($ i!!icult": 2 'escribe the se=uence 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. #ns: 81" 0he mRNA forms an initiation comple- with a cytoplasmic ribosome and transcription begins. 84" 0he amino3terminal portion of the nascent chain containing a signal se=uence binds to an /R9 8signal recognition particle" interrupting polypeptide elongation. 8&" 0he /R93ribosome3 nascent chain comple- binds to the ribosome and /R9 receptors on the cytosolic face of the (R? the /R9 then dissociates. 8*" %hain elongation continues with the newly synthesi.ed polypeptide crossing into the (R lumen as it grows. 8$" 0he signal se=uence is cleaved. '3. Protein targeting and degradation Pages: 1071%1073 i!!icult": 2 ,hat are the stages in targeting of nuclear proteins and why are the targeting se=uences not removed upon arrival of the protein in the nucleus) #ns: In the cytoplasm where eukaryotic protein synthesis occurs proteins carrying nuclear locali.ation signal 8ND/" se=uences are bound by a comple- of importin and which is then bound to a nuclear pore. Ran 609ase mediates translocation of this comple- into the nucleus where importin dissociates from importin and importin releases the nuclear protein. Importin and are then e-ported from the nucleus and available for another cycle of import. 0he nuclear envelope of higher eukaryotes breaks down at each cell division distributing the nuclear contents throughout the cell. ,hen the nuclear envelope is reestablished ND/3carrying proteins can be reimported to fulfill their function. '&. Protein targeting and degradation Page: 107' i!!icult": 3 'escribe the role of ubi=uitin in mediating intracellular protein breakdown. #ns: 7bi=uitin a protein found in all eukaryotic cells is covalently 5oined to proteins targeted for degradation. 0he carbo-yl3terminal residue of ubi=uitin is first activated by the formation of a thioester with the first en.yme in the pathway in an A093dependent reaction. After displacement of the first en.yme by a second also yielding a thioester link ubi=uitin is finally 5oined through its carbo-yl terminus to a lysine 3amino group in the protein to be degraded. 0he presence of ubi=uitin targets the protein for degradation by cellular proteases.