Genetics Chapter 9

non-coding RNA (ncRNA)

-are active as functional RNA's; they are never translated into proteins. - ncRNA involved in protein synthesis include transfer RNAs and ribosomal RNAs.

The genetic code can be thought of as _____ blocks, each containing _____ entries defined by the first _____ nucleotides in a codon

A. 16; 2; 4 B. 16; 4; 2 C. 14; 4; 3 D. 16; 3; 1 ANSWER: B The genetic code encompasses 16 blocks, each block contains four codons, and the amino acid is based on the first two nucleotides in each codon.

Cleopatra's turtle, Nile, seems to be ill. Nothing has changed in his tank; however, she has been giving him new food. She decided to compare his old and new food pellets in the lab and noticed a difference in protein structure in the new food pellet that she did not find in the old food pellets. If the amino acid of the altered protein is N-ALA, GLY, SER, LYS, ARG-C, what is the possible codon sequence?

A. 3′-CCUAUGAGAGAUCUU-5′ B. 5′-GCUGGCUCUAAAAGG-3′ C. 3′-GCUGGCUCUAAAAGG-5′ D. 5′-GCUAUGGGCAAACCU-3′ ANSWER: B This is the codon sequence translated from the amino acid sequence.

In which prokaryotic subunit is the decoding center located?

A. 40S B. 70S C. 50S D. 30S ANSWER: D The decoding center in the 30S subunit ensures that only tRNAs carrying anticodons that match the codon will be accepted into the A site.

What is the sequence found at the very 3′ end of all tRNAs?

A. 5′-CAC-3′ B. 5′-CCA-3′ C. 5′-AUG-3′ D. 5′-UAA-3′ ANSWER: B The sequence 5′-CCA-3′ is found at the very 3′ end of all tRNAs. In bacteria, CCA is generally encoded in tRNA genes, but in eukaryotes, CCA is added post-transcriptionally by an enzyme called nucleotidyltransferase, or CCA-adding enzyme.

Which one these is not a type of post-translational modification?

A. Addition of complex molecules to amino acids B. Addition of chemical groups to amino acids C. Cleavage of peptide bonds to convert inactive precursor proteins into smaller, active proteins (proteolysis) D. Modification of the alpha carbon ANSWER: D . The modifications themselves fall into five broad categories: 1. the addition of chemical groups to amino acids 2. complex molecules to amino acids 3. polypeptides to amino acids 4. the modification of amino acids 5. the cleavage of peptide bonds between amino acids to convert inactive precursor proteins into smaller, active proteins

Which of these statements is TRUE?

A. Chaperones contain caverns into which nascent proteins can enter. These caverns are negatively charged and provide an environment in which proteins can fold. B. Chaperones typically bind hydrophobic regions of incorrectly or incompletely folded proteins. C. Binding and release of the chaperone and protein are driven by peptidyltransferase. D. Chaperones are responsible for the ubiquitination of proteins and are involved in protein degradation. ANSWER: B Chaperones typically bind hydrophobic regions of incorrectly or incompletely folded proteins to arrest folding or promote unfolding and then release them to undergo spontaneous refolding.

If Elsa is looking at the translation of a protein, once an mRNA reaches a ribosome, what would be the next step that takes place?

A. Charged tRNA arrives at the E site and base pairs with the tRNA in the small subunit of the ribosome. B. Charged tRNA arrives at the P site and then base pairs with the tRNA in the large subunit of the ribosome. C. mRNA base pairs with tRNA in the small subunit of the ribosome. D. mRNA base pairs with tRNA in the large subunit of the ribosome. ANSWER: C

Which of these nucleotides is a rare modified base in tRNA, and can base pair to C, U, and A?

A. G B. T C. A D. I ANSWER: D. Inosine (I), a rare modified base in tRNA, can base pair to C, U, and A.

One of your friends is talking to you about phosphorylation. He states that this process is carried out by kinases and is a vital part of protein folding, as it causes a region of a polypeptide to adopt a negative charge and adds a methyl to the end of the protein. Which part of this statement is CORRECT?

A. Kinase carries out phosphorylation causing a region of the polypeptide to become negative. B. In phosphorylation, kinase takes part in protein folding. C. Kinases are responsible for phosphorylation. D. Phosphorylation adds a methyl group to the protein. ANSWER: C

What is a ribosome composed of?

A. One-third of their mass is RNA and two-thirds is protein. B. Two-thirds of a ribosome's mass is RNA and one-third is protein. C. Three-fourths of a ribosome's mass is RNA and one-fourth is protein. D. One-fourth of a ribosome's mass is RNA and three-fourths is protein. ANSWER: B There is more RNA than protein in ribosomes.

Where is the deacylated tRNA located in the ribosome during translation?

A. P site B. decoding center C. A site D. E site ANSWER: D The E site (for exit site) contains a deacylated tRNA (it no longer carries an amino acid) that is ready to be released from the ribosome.

If a mutation inactivated the peptidyltransferase center of a ribosome, what would happen?

A. Peptide bonds would not form between adjacent amino acids and a polypeptide would not be produced. B. Ribosomal subunits would be unable to associate with one another, and translation could not be initiated. C. Charged tRNAs would randomly associate with codons and would not pair to complementary codons. D. Unattached tRNAs that have transferred amino acids to growing polypeptides would be unable to exit the ribosome. ANSWER: A The peptidyltransferase center in the 50S subunit is the site where peptide bond formation is catalyzed.

Philipa is analyzing proteins she found in pond water. Which of these amino acids would Philipa expect to see on the surface of the protein itself?

A. Proline B. Tryptophan C. Lysine D. Leucine ANSWER: C Lysine is a polar/positively charged molecule, and thus it can be found on the surface of a protein.

Arjana is analyzing the behavior of the amino acid proline in a protein. In her observations, she believes to find proline located on the outside of the protein, but not any on the inside of the protein. She finds some proline incorporating their amino group into the side chain. Also, she believes to have located proline in the center of α-helices and β-sheets, in the loops and turns at the ends of α-helices, and in the edge strands of β-strands. Which of Arjana's thoughts is INCORRECT?

A. Proline is a polar amino acid and hence will be found on the surface of proteins. B. Prolines can be found in the middle of α-helices and β-sheets. C. Prolines are often found in turns and loops at the ends of α-helices, and in the edge strands of β-strands. D. Proline is able to incorporate the amino group into the side chain. ANSWER: A Proline is a nonpolar amino acid and will be located inside of the protein.

To get ready for another round of translation, other factors such as: _____, _____, and _____, displace the uncharged tRNAs and dissociate the ribosome subunits from one another and from the mRNA.

A. RRF, EF-G, IF3 B. RF1, RF2, RF3 C. eEF2, eEF3, eEF1α D. eRF1, eRF2, eRF3 ANSWER: A These cofactors play a role when the ribosome is getting ready for another round of translation.

Which of these statements is TRUE?

A. The ribosomes of eukaryotes contain only A and E sites; they lack the P site. As a result, translation occurs more quickly in eukaryotes than prokaryotes. B. The eIF4A and eIF4G initiation factors are unique to eukaryotes and play a role in unwinding eukaryotic mRNA, which can form intricate three-dimensional structures. C. Initiation factors remain attached to eukaryotic ribosomes throughout initiation, elongation, and termination; however, initiation factors are released from prokaryotic ribosomes during elongation. D. Shine-Dalgarno sequences are present in both eukaryotic and prokaryotic mRNA. If these sequences were removed, translation could not proceed normally in either prokaryotes or eukaryotes. ANSWER: B eIF4A has RNA helicase activity that unwinds regions in the 5′ UTR that are double-stranded RNA due to intramolecular base pairing. eIF4G binds poly(A) binding proteins (PABPs) that associate with the mRNA poly(A) tail, thereby bringing together the 5′ and 3′ ends of the mRNA.

Certain charged tRNAs can recognize and bind to several alternative codons—not just the one with a complementary sequence—via a loose base pairing. Such pairing is called _____.

A. a wobble B. a primary structure C. Shine-Dalgarno pairing D. a domain ANSWER: A Some tRNAs can recognize multiple codons through a different kind of base pairing at the third position of a codon, termed the wobble position.

Imagine that from the genetic code of rabbits, scientists discovered that AGG encodes amino acid 1 (aa1), GGU encodes amino acid 2 (aa2), GUA encodes amino acid 3 (aa3), UAC encodes amino acid 4 (aa4), ACG encodes amino acid 5 (aa5), CGA encodes amino acid 6 (aa6), and GAC encodes amino acid 7 (aa7). A scientist identifies an mRNA that contains three codons: 5′-GGUUACACGCGA-3′. What amino acid sequence would be produced from this mRNA?

A. aa1-aa4-aa7-aa3 B. aa2-aa4-aa5-aa6 C. aa1-aa3-aa4 D. aa1-aa2-aa3-aa4-aa5-aa6-aa7 ANSWER: B This codon sequence translates to: GGU, UAC, ACG, and CGA.

What is the main component in protein folding correctly called?

A. chaperones B. globular proteins C. ubiquitins D. proteasomes ANSWER: A

Which of these is not found in a tRNA?

A. codon B. TψC loop C. D loop D. anticodon ANSWER: A

A researcher is studying ribosomes in human cells and bacterial cells. She is likely to find that the human ribosomes:

A. consist only of two large 80S subunits. B. perform very different functions from those of bacterial ribosomes. C. contain fewer protein components than bacterial ribosomes. D. are much larger than bacterial ribosomes. ANSWER: D. Eukaryotic ribosomes are larger than bacterial ribosomes.

Two key sites in ribosomes, the _____ center in the large subunit that carries out peptide bond formation and the _____ in the small subunit that accepts the correct tRNA, are built of rRNA.

A. decoding center; peptidyltransferase B. ribosome-binding site; aminoacyl-tRNA binding site C. peptidyltransferase; decoding center D. aminoacyl-tRNA binding site; decoding center ANSWER: C Two key sites in ribosomes—the peptidyltransferase center in the large subunit that carries out peptide bond formation, and the decoding center in the small subunit that accepts the correct tRNA—are built of rRNA.

A student is studying translation in mutant strains of E. coli. She notices in one colony that the 30S and 50S ribosomal subunits always remain attached to one another, even when not associated with mRNA. These bacteria likely carry a mutation affecting the initiation factor _____.

A. eIF4A B. IF3 C. IF1 D. IF2 ANSWER: B Binding of IF3, with help from IF1, blocks association of the 50S subunit from the 30S subunit.

Ginny discovered that there is a defect in prokaryotic IF1, a component found in translation in bacteria. What would be the result of this defect?

A. it unwinds the mRNA B. the aminoacyl-tRNA will bind to the A site early C. it helps IF3 block association of 50S with the 30S ribosome subunit D. it helps deliver aminoacyl tRNA ANSWER: B This can happen since the purpose of IF1 is to block the A site from the aminoacyl-tRNA.

Proteins destined to be secreted from the cell have an amino-terminal sequence that is rich in _____residues.

A. lysine B. aspartate C. hydrophobic D. hydrophilic ANSWER: C

The first synthetic RNA was made using only uracil nucleotides, producing UUU, which is the amino acid sequence for _____

A. lysine B. glycine C. phenylalanine D. proline ANSWER: C The first synthetic RNA was made using only uracil nucleotides, producing . . . UUUU . . . [poly(U)], and the amino acid sequence of this protein was proved to be polyphenylalanine.

The aminoacyl-tRNA is formed by the _____ attachment of an amino acid to the 3′ end of a tRNA that contains the correct anticodon.

A. peptide B. covalent C. hydrophilic D. hydrophobic ANSWER: B

Which of these is NOT one of the four possible categories of amino acids based on the property of their side chains?

A. polar/positively charged B. polar/nonpolar C. polar/negatively charged D. polar/uncharged ANSWER: B because the 4 possible categories include all of the following and NON-POLAR but not polar/nonpolar

Two graduate students have joined a laboratory. The first student's project is to assess how many α-helices and β-pleated sheets exist in a protein of interest. She will not look at how these structures interact with one another. This student will assess the _____ structure of the protein. The other graduate student will determine whether the protein is actually a complex composed of two or more subunits. He is studying the _____ structure of the protein.

A. primary; secondary B. secondary; tertiary C. secondary; quaternary D. tertiary; secondary ANSWER: C Local regions of the protein fold into specific shapes called secondary structures. The most common secondary structures are α-helices and β-sheets. Quaternary structures refer to how polypeptides interact with one another to form a multi-polypeptide protein complex.

Amino acids that undergo post-translational modification often have a functional group that acts as a _____during an enzymatic modification reaction.

A. proteasome B. electrophile C. nucleophile D. kinase ANSWER: C Amino acids that undergo post-translational modification often have a functional group that acts as a nucleophile during an enzymatic modification reaction.

Which of these would be considered a biological machine?

A. ribosomes B. mRNAs C. codons D. amino acids ANSWER: A Translation is carried out by ribosomes moving along mRNA in the 5′-to-3′ direction. Since ribosomes are translating a code, they are using energy to create a product.

A researcher is studying transcription in cultured human cells. After she treats these cells with a special culture medium, the human cells begin to divide. In these actively dividing cells, genes encoding which of these RNAs will be transcribed the most in the nucleus?

A. siRNAs and miRNAs B. mRNAs C. RISC D. tRNAs and rRNAs ANSWER: D In a typical actively dividing eukaryotic cell, rRNA and tRNA account for almost 95 percent of the total RNA, whereas mRNA accounts for only about 5 percent.

Charles is studying translation and decides he wants to isolate the mRNA and make some modifications to it. If Charles cleaves the mRNA into smaller polypeptides or amino acids using an enzyme, what kind of modification would this be?

A. sumoylation B. acetylation C. deamidation D. proteolysis ANSWER: D Cleavage of peptide bonds to convert inactive precursor proteins into smaller, active proteins is called proteolysis.

A researcher is studying the active site of lipase, an enzyme produced by the pancreas. Since she is focusing on lipase′s active site, what might NOT interest the researcher?

A. the concentration of the substrate B. how lipase binds to a substrate C. how R groups are positioned in lipase D. what types of enzymatic reactions lipase can perform ANSWER: A

Which center in the 30S subunit ensures that only tRNAs carrying anticodons that match the codon will be accepted into the A site?

A. the ribosome-binding site B. the decoding center C. the aminoacyl-tRNA binding site D. the peptidyltransferase center ANSWER: B The decoding center in the 30S subunit ensures that only tRNAs carrying anticodons that match the codon will be accepted into the A site.

The mRNA produced by a wild-type gene, which encodes four amino acids, has this sequence: AUUAUUAUUAUU. The insertion of one or two G RNA nucleotides at the beginning of the second codon enables this mRNA sequence to encode only one amino acid. However, if three G′ nucleotides are inserted at the beginning of the second codon, this sequence is able to encode five amino acids, the four original ones plus one more. What character of the genetic code does this experiment demonstrate?

A. universal B. degenerate C. overlapping D. triplets ANSWER: D. Three nucleotides make up a triplet code.

The A and P sites are situated to facilitate formation of a _____ between their amino acids, disconnecting the P site amino acid from its tRNA.

A.phosphate bond B. hydrogen bond C. ionic bond D. peptide bond ANSWER: D tRNAs begin in the A site, peptide bond formation occurs in the P site, and tRNAs exit from the E site.

What are the two classifications of RNAs?

Messenger RNA (mRNA) or non-coding NcRNA

mRNA (messenger RNA)

Serve as an intermediate in the synthesis of proteins

Ribosomes

are RNA-Protein machines that synthesize proteins in bacteria and eukaryotes

Transfer RNAs

carry out decoding work of translation, associating three-nucleotide sequences in an mRNA with their corresponding amino acids.