Chapter 3: Gene Function

Multiple-Choice Questions 1. The role of tRNA is A) to serve as an intermediate in the decoding of genes. B) to act as transporters bringing amino acids to the site of protein synthesis. C) to serve as general translational components of the ribosome. D) to facilitate splicing of pre-messenger RNAs. E) to facilitate protein trafficking in protein secretion. 2. Which of the following acts before the others? A) tRNA alignment with mRNA B) Aminoacyl-tRNA synthetase C) RNA polymerase D) Ribosome movement to the next codon E) Amino acid chain elongation 3. Which of the following is not a component of the transcriptional system in cells? A) RNA polymerase B) DNA C) Promoter D) Shine-Dalgarno sequence E) Hairpin loop 5. In a chromosome, which of the following is true? A) RNAs of different genes can be transcribed off either DNA strand, always 5 3. B) RNAs of different genes can be transcribed off either DNA strand, always 3 5. C) The RNAs of all genes are synthesized 5 3 off the same DNA strand. D) The RNAs of all genes are synthesized 3 5 off the same DNA strand. E) Different genes can be transcribed off either strand, some in the 5 3 direction and some in the 3 5 direction.

Evolutionary Genetics

6. The following diagram shows a fragment of transcribed DNA (the upper strand is the template strand): 5-ATTGCC-3 3-TAACGG-5 The transcribed RNA is A) 3-TAACGG-5 B) 5-TAACGG-3 C) 3-AUUGCC-5 D) 5-UAACGG-3 E) 5-GGCAAU-3 7. The following diagram shows a protein-coding gene and specifies the positions of its translational start and stop signals:

Which of the following is correct? A) Upper is template strand, carboxy terminus of protein to right B) Upper is template strand, carboxy terminus of protein to left C) Lower is template strand, carboxy terminus of protein to right D) Lower is template strand, carboxy terminus of protein to left E) Either strand could be template on the basis of this information 8. A protein fragment has the following sequence: NH2 -His-Met-Leu-Ile-Lys-COOH. The DNA template strand sequence (3 5) would be A) GUGUACAAUAUUUUU B) GTGTACAATATTTTT C) GTATACAATTATTTT D) GUAUACAAUUAUUUU E) CATATGTTAATAAAA 11. In a wild-type strain of Drosophila the size of a gene from the start to stop codon is calculated to be 2000 nucleotide pairs. However, the size of the mRNA molecule transcribed from this gene is estimated at 1200 nucleotides. The most likely explanation for this discrepancy in size would invoke the existence of A) a new stop codon introduced by mutation. B) a frameshift mutation. C) mRNA degradation. D) DNA degradation. E) the presence of one or more introns.

Evolutionary Genetics

Open-Ended Questions 1. In the chart below indicate by a + if the characterisic is present in at least some members of the group (bacteria, bacteriophages, eukaryotes). Use a 0 if the characteristic is absent in all members of the group. (b) (c) (d) (e) (f) (g) (h) (i) (j) (k) (l) A membrane-bound nucleus DNA as its genetic material RNA as its genetic material Shine-Dalgarno sequences 5 cap Open reading frames Introns Aminoacyl-tRNA synthetases Ribozyme Spliceosomes mRNAs with poly(A) tails at their 3 ends Bacteria ___ ___ ___ ___ ___ ___ ___ ___ ___ ___ ___ Bacteriophages ___ ___ ___ ___ ___ ___ ___ ___ ___ ___ ___ Eukaryotes ___ ___ ___ ___ ___ ___ ___ ___ ___ ___ ___

2. Shown below is the structure of a Drosophila gene, divided into 10 segments, designated A J. The gene contains three exons, two introns, a promoter, and a site in I for poly(A) addition.

(a) What segment or segments of the gene will be represented in the initial RNA transcript? List the appropriate letter or letters. (b) What segment or segments of the gene will be found in the completely processed transcript? (c) What segment or segments of the gene in the processed transcript will have additional nucleotides added to them? (d) What segment or segments of the gene contain the CCAAT box and TATA box elements? (e) What segment or segments of the gene will possess the translation initiation codon? (f) In a large sample of null alleles, would mutant sites be expected in segments C and D, at the boundary of GH, or both? If mutant sites exist, would the transcript be detected? Would a polypeptide chain be observed? 3. In the silkmoth, a single gene encodes the protein that is the major constituent of the cocoon. (a) The mRNA encoding this protein was isolated from silkmoth larvae and hybridized with silkmoth DNA. The following electron micrograph was obtained:

Evolutionary Genetics

(1) Explain the loops in the DNA strand. (2) Show on the diagram which side of the mRNA is its 5 and which is its 3 end. Explain. (b) A mutant silkmoth was isolated that cannot make the cocoon protein. The mutant makes mRNA encoding the protein at the same concentration as the wild type, but the mRNA molecules are slightly longer than usual. In addition, an electron micrograph of the mRNA-DNA hybridization with mRNA from the mutant organism shows the following:

Suggest a possible explanation for the nature of the mutation. 4. Consider the following piece of messenger RNA: 5-AUGGAGUCGUUAAUUAAACCGGUGCGGAUCGUAUUUAGUCCCCAC-3 (a) Draw both strands of the segment of DNA from which this mRNA was transcribed. (b) State which of the DNA strands the RNA synthesizing enzyme used as template for the transcription process. (c) Using the codon chart, give the amino acid sequence of the protein that would be produced by translation of the mRNA, assuming the ribosome moved along the mRNA from left to right. 5. What would the minimum word (codon) size be if the number of different bases in the mRNA were (a) two? (b) three? (c) five? Give your reasoning. Assume that all other features of the translation of mRNA into protein are the same as what we now know. 6. Code Crackerjacks (a) 5CAU3 is a codon in mRNA that specifies the amino acid histidine (His) in position 58 in the chain of human hemoglobin. (1) What is the corresponding anticodon in tRNA? (2) What is the corresponding triplet in the coding DNA strand? (3) What is the corresponding triplet in the template DNA strand? (b)The following is a pedigree of amino acid substitutions that have been observed in the and chains of human hemoglobin. The direction of change is indicated by an arrow. Using the codon chart, propose codons for these amino acids that would explain the observed substitutions in the form of single nucleotide changes.

Evolutionary Genetics

8. From DNA sequencing studies the nucleotide sequences of three short adjacent fragments (1, 2, 3) that comprise a short bacterial gene were determined. They are shown below, grouped as codons. (a) In the blanks below write out the RNA sequences coded by each template strand sequence and show the polarity of the RNA.

(b) What is the correct order of the three fragments? Explain why there is only one order. (c) Using the codon chart, write out the amino acid sequence, indicating the amino and carboxy termini of the polypeptide chain. (c) NH2MetCysGlyLeuSerArgTyrLysGlyCysGlyCOOH 18. A gene makes a polypeptide 30 amino acids long containing an alternating sequence of phenylalanine and tyrosine. What are the sequences of nucleotides corresponding to this sequence in (a) the DNA strand which is read, assuming phe = UUU and tyr = UAU in mRNA? (b) the DNA strand which is not read? (c) tRNA?