Category - Definitions

Query - What definition best describes the term below?

Reversal

Category - Term Recognition

Query - What term does the description below refer to?

(Terms are shown on left, descriptions in middle, figures on right)

30S | A name for the small prokaryotic ribosomal subunit. The name arises from its size -S is a unit of centrifugal force related to size. This subunit contains 21 unique proteins and the 16S rRNA. |  | 50S | A name for the large prokaryotic ribosomal subunit. The name arises from its size -S is a unit of centrifugal force related to size. This subunit contains 32 unique proteins and the 23S and 5S rRNAs. |  | A site | A tRNA binding site found on the 50S ribosomal subunit. During translation it holds the incoming tRNA with the amino acid to be added to the growing peptide chain. | Figure 27.22 | Acceptor Stem | The portion of a tRNA where the amino acid is covalently attached. | Figure 27.6 | Aminoacyl-tRNA synthetase | A group of enzymes that catalyze attachment of a specific amino acid to each tRNA molecule. |  | Anticodon | A three nucleotide base sequence in the anticodon loop of a tRNA complementary to the codon of a messenger RNA. During translation, this structure base pairs with the codon to bring the appropiate amino acid into the place where protein synthesis is occurring. |  | Anticodon Loop | The part of the tRNA where the anticodon is located. | Figure 27.6 | Codon | A sequence in a messenger RNA of three nucleotide bases that specify either an amino acid for incorporation into a protein or a stop signal to terminate protein synthesis at that point. |  | D-Loop | The loop of a tRNA nearest the 5' end. | Figure 27.6 | Deformylase | A prokaryotic enzyme that removes the formyl group from the N-formyl-methionine at the end of bacterial polypeptides. |  | E site | A tRNA binding site found on the 50S ribosomal subunit. During translation, the tRNA that has just transferred its peptide to the next tRNA moves to this site briefly before exiting. | Figure 27.22 | EF-G | A translational elongation factor that is necessary for translocation | Table 27.4 | EF-TS | A translational elongation factor that participates in recharging EF-Tu with GTP | Table 27.4 | EF-Tu | A translational elongation factor that carries tRNA into A site | Table 27.4 | Frame Shift Mutation | A mutation in the region of a gene coding for protein that results in insertion or deletion of a number of bases not divisible by three. |  | Genetic Code | The code by which the nucleotide sequence of a DNA or RNA molecule specifies the amino acid sequence of a polypeptide. It consists of three-nucleotide codons that either specify a particular amino acid or tell the ribosome to stop translating and release the polypeptide. With a few minor exceptions, all living things use the same code. | Figure 27.3 | IF1 | A translational initiation factor that promotes dissociation of the 70S ribosome | Table 27.4 | IF2 | A translational initiation factor that helps attach initiator tRNA to the initiation complex | Table 27.4 | IF3 | A translational initiation factor that promotes dissociation of the 70S ribosome | Table 27.4 | Intergenic Mutation | A suppressor mutation that occurs in a second gene apart from the original mutation. | Fiugre 27.27 | Missense Mutation | A mutation in the region of a gene coding for protein that results in a change of amino acid inserted at a particular point. |  | N-formylmethionine | A modified form of methionine used by prokaryotic organisms as the first amino acid in a polypeptide. It is the only place the amino acid is used in a polypeptide. Everywhere else that the AUG codon appears, methionine is used. |  | Nonsense Mutation | A mutation that converts a codon for an amino acid to a stop codon. |  | Operon | A set of contiguous prokaryotic structural genes that are transcribed as a unit, along with the adjacent regulatory elements that control their expression. |  | P site | A tRNA binding site found on the 50S ribosomal subunit. During translation it holds the tRNA that is attached to the growing peptide chain. The initiator tRNA also occupies this site at the initiation of translation. | Figure 27.22 | Peptide Bond | The bond that links successive amino acids in a peptide; it consists of an amide bond between the #-carboxyl group of one amino acid and the #-amino group of the next. |  | Peptidyltransferase | An enzymatic activity that is an integral part of the 50S ribosomal subunit. It catalyzes formation of a peptide bond as the growing peptide chain is transferred to the amino acid on the tRNA in the A site of the ribosomal subunit. |  | Polycistronic Messages | The form by which messages are often carried in prokaryotic organisms- multiple polypeptide coding sequences located on a single mRNA. |  | Resistance Gene | A term for a gene in a bacterium that enables it to grow in the presence of an antibiotic designed to kill it. |  | RF1 | A translational release factor for UAA, UAG | Table 27.4 | RF2 | A translational release factor for UAA, UGA | Table 27.4 | RF3 | A GTPase that promotes release of the polypeptide chain. | Table 27.4 | Ribosome | The multiprotein-RNA complex on which translation occurs in the cell. | Figure 27.13, Figure | Ribozyme | An RNA that catalyzes a reaction. In the 50S ribosomal subunit, the rRNA in it acts l this way. |  | SecA | An ATPase involved in secretion of E. coli proteins. It binds to the secretory pore and uses both ATP hydrolysis and the electrochemical potential gradient across the membrane to drive translocation of the protein out of the cell. |  | SecB Protein | A molecular chaperone involved in secretion of prokaryotic polypeptides. | Figure 27.30 | Selenocysteine | A rare amino acid that occasionally is incorporated into proteins according to the UGA codon, which normally specifies STOP. |  | Shine-Dalgarno Sequence | A common, conserved sequence in prokaryotic mRNAs that helps orient the ribosome to begin translation. The sequence is located just before the AUG start codon and is complementary to the 3' end of the 16S rRNA in the ribosome. |  | Signal Sequence | A stretch of highly hydrophobic amino acids at the amino terminus of bacterial genes that target the polypeptide for secretion (export across the cell membrane) | Figure 27.30 | Start Codon | The first codon that is translated in making a protein. It is almost always AUG, which codes for methionine. | Figure 27.3 | Stop Codon | A codon that, when encountered by the ribosome during translation of an mRNA, causes translation to stop. In the universal code, this is specified by UAA, UAG, and UGA. | Figure 27.3 | Suppressor Mutation | A mutation occurring elsewhere in the genome that overcomes the effect of a primary mutation. For example, if a nonsense mutation occurs, it can be suppressed by a mutation in another gene that causes the gene containing the premature stop codon to still make full length proteins. | Fiugre 27.27 | TC loop | The loop of a tRNA nearest the 3' end. | Figure 27.6 | Transfer RNA | The form of RNA that provides translation between the three base codon sequence in the mRNA and amino acid corresponding to it. |  | Transformylase | An enzyme that catalyzes transfer of a formyl group to methionine after the methionine is linked to the tRNA. |  | Translation | A process carried out by the ribosomes in which the genetic code in mRNA is converted to amino acids in polypeptide. The process of making polypeptides in a cell. |  | Universal Genetic Code | The version of the genetic code that is used by almost all organisms. |  | Variable Loop | A tiny loop that varies considerably from one tRNA to another. | Figure 27.6 | Wobble Position | In a codon, the third nucleotide is often referred to as this because the first two bases are the most important ones in specifying an amino acid and the third position can vary (in many cases) to some extent. In an anticodon, the wobble position is the first nucleotide, due to the antiparallel nature of base pairing of nucleic acids. | Figure 27.4

Chaperone Proteins | Proteins that are involved in managing the folding of other proteins. Some of them help proteins to fold correctly; some prevent premature folding; and some prevent polypeptides from associating with other polypeptides until they have folded properly. |

Polyribosome | A structure in which many ribosomes may be found on a single mRNA, simultaneously translating the message. |

Category - General

Query - Is contained in the left column below, solution in middle, figure on right

Reversal - there is no reversal

After a polypeptide is synthesized, what must happen for it to be active? | It must be folded into the proper three-dimensional structure and it may have to associate with other subunits. |  | At which terminus of a tRNA is the amino acid attached? | 3' end | Figure 27.6 | Compared to other RNA molecules, what is different about the composition of the tRNAs? | The high content of unusual and modified bases in tRNAs. |  | Evolutionarily, what is interesting about the structure of the 16S rRNA? | Though the sequence of 16S rRNAs vary between organisms, the overall secondary structure is fairly well conserved. | Figure 27.15 | How are ribosomal proteins named? | L' designates they are from the large (50S) subunit and 'S' designates they are from the small subunit. A number uniquely identifies each protein in each subunit. |  | How can a mutation in a tRNA gene suppress a mutation in a gene coding for protein? | If the mutation occurs in the anticodon loop such that it alters the tRNA that will pair with the mutation, the mutation in the protein sequence will be suppressed, because the correct amino acid is inserted at the point of the mutation. | Fiugre 27.27 | How do aminoacyl tRNA synthetases insure that an amino acid is linked to its proper tRNA? | With a proofreading activity. |  | How do aminoacyl-tRNA sythetase classes I and II differ | In amino acid sequence, the ways in which they bind their cognate tRNAs, and in their quaternary structure. |  | How do bacteria sometimes bypass using a glutamine-specific aminoacyl tRNA-synthetase | The synthetase for glutamate is used and glutamine is created by transamination |  | How does the growing peptide chain exit from the 50S ribosomal subunit? | Through a tunnel |  | How does the wobble position work? | In many tRNAs, the third position is occupied by the uncommon nucleoside, inosine. It is capable of base-pairing with either A or U or C. In addition, in RNA duplexes, G can base pair with U. |  | How is the cell able to read all 61 codons that code for amino acids without having all 61 tRNAs? | The wobble position pairings (G-U or I with A or U or C) allow all possible pairings to occur with a smaller number of tRNAs. |  | How is the polypeptide released from the ribosome at the end of translation? | The peptidyltransferase transfers the C-terminal residue of the polypeptide chain from the P-site tRNA to a water molecule, releasing the polypeptide chain from the ribosome. |  | How many amino acids must be linked in translation before the end of the polypeptide chain begins to emerge from the ribosome? | About 30 |  | How many aminoacyl-tRNA synthetases are present in E. coli? | 20 - one for each amino acid. Each one is capable of reading one or more tRNAs. |  | How many different proteins are found in each of the prokaryotic ribosomal subunits? | 50S - 32 unique proteins; 30S - 21 unique proteins. | Figure 27.13 | How many major folding domains does a 16S rRNA have? | Four | Figure 27.15 | How many nucleotides specify a codon? | Three |  | How many ribosomes are found in an E. coli cell? | About 15,000 |  | How many ribosomes may be found on a single bacterial mRNA? | 50 |  | In a polycistronic mRNA, what happens to the 30S ribosomal subunit at the end of translation of the first message? | It may simply slide along the mRNA until the next Shine-Dalgarno sequence and initiation codon are encountered and begin a new round of translation. |  | In what direction does translation always occur? | 5' to 3' |  | Is the sequence of the anticodon loop used to identify the correct tRNA in which to put an amino acid onto? | Sometimes, but not always. Other portions of the tRNA may be used as well. | Figure 27.11 | The 3' end of the coding region of a messenger RNA corresponds to which end of the polypeptide chain made from it? | The carboxyl end. |  | The 5' end of the coding region of a messenger RNA corresponds to which end of the polypeptide chain made from it? | The amino end |  | The wobble position is which nucleotide of the anticodon? | First |  | The wobble position is which nucleotide of the codon? | Third |  | Translocation during translational elongation is dependent on which translational factor? | EF-G |  | What are some modified bases commonly found in tRNAs? | Pseudouridine (), ribothymidine, and dihydrouridine | Figure 27.7 | What are the rare codons that prokaryotes used to initiate protein synthesis? | GUG, UUG, or AUU |  | What are the three stages of translation? | Initiation, elongation, and termination. |  | What are the two E. coli transmembrane proteins involved in secretion of proteins? | SecY and SecE | Figure 27.30 | What are the two ribosomal subunit sizes in prokaryotic organisms? | 50S and 30S |  | What does the peptidyltransferase activity of the 50S ribosomal subunit arise from? | Ribosomal proteins and the ribosomal RNA, acting as a ribozyme. |  | What energy source is used to covalently link an amino acid to a tRNA? | ATP is hydrolyzed to AMP | Figure 27.10 | What factor binds to EF-Tu to help it release GDP and bind another GTP? | EF-Ts | Figure 27.23 | What factors are required to bind in forming the translational initiation complex? | IF1, IF2, and IF3 | Figure 27.20 | What functions do the first proteins that bind to a ribosomal RNA seem to perform? | They help fold the RNA to provide sites for the rest of the proteins to bind. |  | What ion favors formation of the 70S ribosome? | Magnesium |  | What ionic condition favors dissociation of the 70S ribosome? | High concentrations of monovalent cations. |  | What is a common sequence feature of the 3' end of all tRNAs? | It terminates in the sequence 5'C-C-A-'3 | Figure 27.6 | What is the covalent linkage between an amino acid and a tRNA? | Amino acids are linked to tRNA molecules by a covalent bond between the carboxyl group of the amino acid and a ribose hydroxyl group of the 3' (or 2') adenosine of the acceptor stem of the tRNA. | Figure 27.10 | What is the energy cost to the cell, per peptide bond? | About 160 kJ of free energy |  | What is the error frequency in putting amino acids on tRNAs? | One error per 10,000 |  | What is the evidence that protein folding (at least for some proteins) begins during translation and is nearly complete by the time the chain is released? | Antibodies against the tertiary structure (that is, folded) of the -galactosidase protein will bind to polyribosomes in the midst of translation. |  | What is the fate of the formyl group on methionine (of prokaryotic messages) after translational initiation? | It is almost always removed during chain elongation. |  | What is the fate of the leader sequence in prokaryotic protein secretion? | The leader peptide is cleaved by a membrane-bound protease. | Figure 27.30 | What is the function of the chaperone protein in bacterial protein secretion? | Keep the protein from folding prematurely, which would prevent it from passing through the secretory pore. |  | What is the length of the 16S rRNA? | 1542 nucleotides. |  | What is the length of the 23S rRNA? | 2904 nucleotides. |  | What is the length of the 5S rRNA? | 120 nucleotides. |  | What is the primary energy source used in translation? | Hydrolysis of GTP |  | What is the rate of protein synthesis for a bacterial cell? | About 750 protein molecules of 300 residues in length per second, at full capacity. |  | What is the rate of translation in E. coli at 37C? | 15 amino acids per second |  | What is the signal for termination of translation? | When one of the stop codons (UAA, UAG, or UGA) appears in the A site of the ribosome. |  | What is the size of the prokaryotic ribosome when the two subunits are put together? | 80S |  | What powers translocation in translation? | Hydrolysis of GTP by EF-G |  | What step in prokaryotic translation is the primary regulatory one? | Initiation |  | What term is used to describe the aspect of the genetic code that multiple codons can specify a single amino acid? | Redundancy | Figure 27.3 | When a prokaryote uses an unusual codon, such as GUG, UUG, or AUU to initiate protein synthesis, what amino acid is inserted into the protein as the first amino acid? | N-formylmethionine |  | When can deformylation of a bacterial polypeptide occur? | As soon as the N-terminus emerges from the ribosome. |  | When does translational proofreading occur? | After the charged tRNA is put into the A site of the ribosome during elongation. It is checked both before and after EF-Tu hydrolyzes GTP and is rejected from the site if the wrong tRNA is in place. |  | Where does the protease usually cleave an E. coli protein during secretion? | Between a small amino acid (glycine or alanine) and an acidic or basic residue. |  | Where is the universal genetic code not used? | Generally the only places where the universal code is not used are in mitochondria and in certain protozoans. |  | Which are the rRNAs associated with each prokaryotic ribosomal subunit? | 50S - 23S rRNA and 5S rRNA; 30S - 16S rRNA | Figure 27.13 | Which codons are the stop codons in the universal genetic code? | UAA, UGA, and UAG | Figure 27.3 | Which end of a polypeptide chain is made last? | The carboxyl end. |  | Which end of the polypeptide chain is made first? | The amino end. |  | Which end of the tRNA contacts the 30S subunit of the ribosome during translation? | Anticodon |  | Which prokaryotic ribosomal subunit is involved in positioning the ribosome for initiating translation? | 30S, because the 16S rRNA within it pairs with the Shine-Dalgarno sequence. |  | Which protein is found in both the large and small ribosomal subunits? | L26 in the large subunit is the same as S2 0 in the small subunit. |  | Which ribosomal RNA is the Shine-Dalgarno complementary to the 3' end of? | 16S |  | Which ribosomal subunit is the first one to come apart from the mRNA? | 50S | Figure 27.26 | Which rRNA contains many regions of self-complementarity capable of creating a complicated secondary structure for the molecule? | 16S | Figure 27.15 | Which rRNA contains the complementary sequence to the Shine-Dalgarno sequence of prokaryotic mRNAs? | 16S |  | Which rRNA is used to trace evolutionary relationships between organisms? | 16S |  | Which tranlsational subunit hydrolyzes GTP as the proper tRNA is put into the A site of the ribosome during elongation? | EF-Tu |  | Which translational factor bind close to the A site when it contains a stop codon? | RF1 (for UAA or UAG) or RF2 (for UAA or UGA) | Figure 27.26 | Which translational factors bind GTP? | IF2, EF-Tu, EF-Ts, EF-G, and RF3 | Table 27.4 | Why are many antiobiotic drugs designed for use as translational inhibitors? | Because the process of translation is sufficiently different in prokaryotes than in humans. |  | Why do suppressor mutations in tRNAs have other effects in cells? | Because the mutated tRNAs are not confined in action only to the mutated gene. |  | Why is the amino end of a polypeptide chain so named? | Because it is the only -amino group in the polypeptide that is not involved in a peptide bond. |  | Why is the carboxyl end of a polypeptide chain so named? | Because it is the only -carboxyl group in the polypeptide that is not involved in a peptide bond. |  | Why is the free energy of peptide bond formation in cells (160 kJ/bond) considerably higher than the free energy of peptide formation in dilute solutions (20 kJ/bond)? | Because peptide bond synthesis in the cell is not random. It is making a defined sequence and that specification comes with an energy cost. |

What are three mechanisms of translational initiation control? | 1. mRNA tertiary structure may prevent attachment to the 30S ribosomal unit. 2. Proteins may bind to the mRNA, blocking initiation. For example, ribosomal proteins bind to their own mRNAs. 3. Antisense RNA may block initiation. |  | What are the steps in prokaryotic translation initiation? | 1. mRNA and the initiator tRNA (N-formylmethionine-tRNA) are bound to a free 30S subunit, forming a 30S initiation complex. 2. The 50S subunit binds to the 30S initiation complex. 3. GTP carried by IF2 is hydrolyzed, and IF2-GDP, Pi, and IF1 are all released. The 70S initiation complex is ready to accept a second charged tRNA and begin elongation | Figure 27.20 | What are the steps in elongation of prokaryotic translation? | 1. The nascent polypeptide chain is attached to a tRNA in the P site and the A and E sites are empty. Aligned with the A site is the mRNA codon corresponding to the next amino acid to be incorporated. 2. A charged tRNA is escorted to the A site in a complex with the protein elongation factor EF-Tu, which also carries a molecule of GTP.

3. When the appropriate charged tRNA is depositied into the A site, the GTP is hydrolyzed and the EF-Tu GDP is released.

4. Peptide bond formation - The polypeptide chain that was attached to the tRNA in the P site is transferred to the amino group of the amino acid carried by the A-site tRNA.

5. Translocation - The uncharged tRNA remaining in the P site is transferred to the E site and the tRNA in a hybrid P/A state (that has the nascent polypeptide chain attached to it) is moved to the P site. At the same time, the ribosome moves the mRNA by three nucleotides in the 3' direction, placing a new codon adjacent to the now empty A site.

6. As the old tRNA is released from the E site, the empty A site gains high affinity and accepts the aminoacyl tRNA corresponding to the next codon.

Figure 27.22, Figure 27.23
What are the steps in termination of prokaryotic translation?

1. RF1 or RF2 binds to the ribosome near the A site. RF3 binds elsewhere.

2. The peptidyltransferase transfers the C-terminal residue of the polypeptide chain from the P-site tRNA to a water molecule, releasing the polypeptide chain from the ribosome.

3. The RF factors and GDP are released.

4. The tRNA is released.

5. The now unstable 70S ribosome in the presence of the protein ribosome recycling factors, IF3, and IF1, dissociates to 50S and 30S subunits for another round of translation.

Category - General

Query - Given the 5' base below of the anticodon, what base(s) at the 3' end of the codon can pair with it?

Reversal - there is no reversal

(5' anticodon base on left, base on 3' end of codon in middle, figure on right)

G | C or U | Table 27.3 | C | G | Table 27.3 | A | U | Table 27.3 | U | A or G | Table 27.3 | I | A,U, or C | Table 27.3

Category - General

Query - What is the function of the protein factor below in prokaryotic translation?

Reversal - there is no reversal

(protein factor on left, function in middle, figure on right)

IF1 | Promotes dissociation of 70S ribosome |  | IF2 | Helps attach initiator tRNA |  | IF3 | Promotes dissociation of 70S ribosome |  | EF-Tu | Carries tRNA into A site |  | EF-TS | Participates in recharging EF-Tu with GTP |  | EF-G | Necessary for translocation |  | RF1 | Release factor for UAA, UAG |  | RF2 | Release factor for UAA, UGA |  | RF3 | A GTPase that promotes release |

Category - General

Query - What is the effect of the antibiotic below on translation?

Reversal - there is no reversal

(antibiotic on left, effect in middle, figure on right)

Tetracycline | Inhibits binding of aminoacyl tRNAs to the ribosome and thereby blocks continued translation | Figure 27.28 | Streptomycin | Interferes with normal pairing between aminoacyl tRNAs and message codons, causing misreading, and thereby producing aberrant proteins. | Figure 27.28 | Erythromycin | Binds to a specific site on the 23S RNA and blocks elongation by interfering with the translocation step. | Figure 27.28 | Chloramphenicol | Blocks elongation, apparently by acting as competitive inhibitor for the peptidyltransferase complex. The amide link in the molecule resembles a peptide bond. | Figure 27.28 | Puromycin | Causes premature chain termination. Part of the molecule resembles the 3' end of the aminoacylated tRNA. It will enter the A site and transfer to the growing chain, causing premature chain release. | Figure 27.28