Gene Expression: From Gene to Protein

Which of the following can be the final product of an expressed gene? mRNA tRNA rRNA polypeptide Answer: D

Which of the following can be the final product of an expressed gene? mRNA tRNA rRNA polypeptide 3

Which of the following terms does not pertain to translation? anticodon tRNA aminoacyl-tRNA synthetase polypeptide rRNA DNA Answer f. DNA 4

Which of the following terms does not pertain to translation? anticodon tRNA aminoacyl-tRNA synthetase polypeptide rRNA DNA Answer f. DNA 5

The template strand of a given gene includes the sequence 3-G C C A C G T A T C A G-5 What is the sequence of the nontemplate strand? 3-C G G T G C A T A G T-5 5-C G G T G C A T A G T-3 5-C G G U G C A U G U-3 3-C G G U G C A U G U-5 Answer: B Nontemplate: 5-C G G T G C A T A G T-3 6

The template strand of a given gene includes the sequence 3-G C C A C G T A T C A G-5 What is the sequence of the nontemplate strand? 3-C G G T G C A T A G T-5 5-C G G T G C A T A G T-3 5-C G G U G C A U G U-3 3-C G G U G C A U G U-5 7

Which of the following is the best example of gene expression? A frog adapts to variation in its environmental temperature. Mouse fur color results from pigment formed by gene-encoded enzymes. DNA is replicated during the S phase of the cell cycle. The percent of A versus a alleles in a population is altered by natural selection. Mutation alters the sequence of a region of DNA. Answer: B Gene expression is the first concept of Chapter 17 (albino deer example). 8

Which of the following is the best example of gene expression? A frog adapts to variation in its environmental temperature. Mouse fur color results from pigment formed by gene-encoded enzymes. DNA is replicated during the S phase of the cell cycle. The percent of A versus a alleles in a population is altered by natural selection. Mutation alters the sequence of a region of DNA. 9

The ability of genes from one species to be expressed in a different species is possible because of which property of the genetic code? the near universality of the genetic code All species in Eukarya use the same genetic code. Gene expression doesn’t utilize the genetic code. RNA codons are the same in all organisms, but DNA codons are different. Gene expression in the laboratory is tolerant of genetic differences. Answer: A Figure 17.6 10

The ability of genes from one species to be expressed in a different species is possible because of which property of the genetic code? the near universality of the genetic code All species in Eukarya use the same genetic code. Gene expression doesn’t utilize the genetic code. RNA codons are the same in all organisms, but DNA codons are different. Gene expression in the laboratory is tolerant of genetic differences. Answer: A Figure 17.6 11

In the transcription process, as diagrammed in Figure 17 In the transcription process, as diagrammed in Figure 17.7 and below, in which process (1, 2, or 3) does the RNA polymerase bind to the promoter, is the RNA transcript released, and is the RNA transcript extended? 1; 2; 3 2; 3; 1 3; 2; 1 1; 3; 2 Answer: D Figure 17.7 12

In the transcription process, as diagrammed in Figure 17 In the transcription process, as diagrammed in Figure 17.7 and below, in which process (1, 2, or 3) does the RNA polymerase bind to the promoter, is the RNA transcript released, and is the RNA transcript extended? 1; 2; 3 2; 3; 1 3; 2; 1 1; 3; 2 13

Which of the following components doesn’t form part of the transcription complex at a eukaryotic promoter? TATA box start point transfer RNA transcription factors RNA polymerase Answer: C 14

Which of the following components doesn’t form part of the transcription complex at a eukaryotic promoter? TATA box start point transfer RNA transcription factors RNA polymerase Answer: C 15

Which of the following is not a modification made to eukaryotic mRNA before it goes to the cytosol? The 5 end is capped A poly-A tail is added to the 3 end Introns are removed Exons are joined together Spliceosomes are removed Answer: e Figure 17.10 16

Which of the following is not a modification made to eukaryotic mRNA before it goes to the cytosol? The 5 end is capped A poly-A tail is added to the 3 end Introns are removed Exons are joined together Spliceosomes are removed Answer: e Figure 17.10 17

Which of the following is not a difference between prokaryotic and eukaryotic transcription? Part of the RNA polymerase specifically recognizes and binds to the promoter in bacteria; in eukaryotes, transcription factors mediate the binding of polymerase. The RNA transcript is immediately useable as mRNA; in eukaryotes, the RNA transcript is processed. RNA polymerase requires a primer in bacteria; in eukaryotes, it does not. Eukaryotic transcription has a polyadenylation signal sequence; in prokaryotes, a transcription terminator causes the polymerase to detach and release the transcript. Answer: c 18

Which of the following is not a difference between prokaryotic and eukaryotic transcription? Part of the RNA polymerase specifically recognizes and binds to the promoter in bacteria; in eukaryotes, transcription factors mediate the binding of polymerase. The RNA transcript is immediately useable as mRNA; in eukaryotes, the RNA transcript is processed. RNA polymerase requires a primer in bacteria; in eukaryotes, it does not. Eukaryotic transcription has a polyadenylation signal sequence; in prokaryotes, a transcription terminator causes the polymerase to detach and release the transcript. 19

Which of the following is incorrectly identified in the figure (Figure 17.15)? A B D C 5 and 3 ends hydrogen bond amino acid attachment site anticodon loop Answer: C Figure 17.15 20

Which of the following is incorrectly identified in the figure (Figure 17.15)? A B D C 5 and 3 ends hydrogen bond amino acid attachment site anticodon loop Answer: C Figure 17.15 21

Aminoacyl-tRNA synthetase is an enzyme whose function is to ________. link a tRNA to its amino acid remove introns from a pre-RNA transcript cause the RNA polymerase to detach from the DNA join together RNA nucleotides complementary to the DNA template strand Answer: d Figure 17.16 22

Aminoacyl-tRNA synthetase is an enzyme whose function is to ________. link a tRNA to its amino acid remove introns from a pre-RNA transcript Cause the RNA polymerase to detach from the DNA join together RNA nucleotides complementary to the DNA template strand 23

Scientific Skills Exercise To show how sequence logos are made, the potential ribosome-binding regions from 10 Escherichia coli genes are shown in a sequence alignment. The figure to the right is the sequence logo derived from the aligned sequences. In the sequence logo, the horizontal axis shows the primary sequence of the DNA by nucleotide position. Letters for each base are stacked on top of each other according to their relative frequency at that position among the aligned sequences, with the most common base as the largest letter at the top of the stack. The height of each letter represents the relative frequency of that base at that position.

In the sequence alignment (on the previous slide), how many of each base appear at position –9? 5 G, 4 A, 1 T, 0 C 7 G, 2 A, 1 C, 0 T 4 G, 3 T, 3 A, 0 C Answer: B

In the sequence alignment (on the previous slide), how many of each base appear at position –9? 5 G, 4 A, 1 T, 0 C 7 G, 2 A, 1 C, 0 T 4 G, 3 T, 3 A, 0 C

In the sequence alignment, how many of each base appear at position 0? 8 A, 1 G, 1 T, 0 C 4 T, 3 C, 3 A, 0 G 10 T, 0 A, 0 C, 0 G Answer: A

In the sequence alignment, how many of each base appear at position 0? 8 A, 1 G, 1 T, 0 C 4 T, 3 C, 3 A, 0 G 10 T, 0 A, 0 C, 0 G

In the sequence alignment, how many of each base appear at position 1? 10 G, 0 C, 0 A, 0 T 4 T, 3 C, 3 A, and 0 G 10 T, 0 A, 0 C, 0 G Answer: C

In the sequence alignment, how many of each base appear at position 1? 10 G, 0 C, 0 A, 0 T 4 T, 3 C, 3 A, and 0 G 10 T, 0 A, 0 C, 0 G

position 1 (T) and position 2 (G) position –10 (G) and position –7 (A) The height of a stack of letters in a logo indicates the predictive power of that stack (determined statistically). If the stack is tall, we can be more confident in predicting what base will be in that position if a new sequence is added to the logo. For example, at position 2, all 10 sequences have a G; the probability of finding a G there in a new sequence is very high, as is the stack. For short stacks, the bases all have about the same frequency, so it’s hard to predict a base at those positions. Which two positions in the logo sequence have the most predictable bases, and which bases would you predict at those two positions in a newly sequenced gene? position 1 (T) and position 2 (G) position –10 (G) and position –7 (A) position 0 (A) and position 2 (G) position 0 (A) and position 1 (T) Answer: A

The height of a stack of letters in a logo indicates the predictive power of that stack (determined statistically). If the stack is tall, we can be more confident in predicting what base will be in that position if a new sequence is added to the logo. For example, at position 2, all 10 sequences have a G; the probability of finding a G there in a new sequence is very high, as is the stack. For short stacks, the bases all have about the same frequency, so it’s hard to predict a base at those positions. Which two positions in the logo sequence have the most predictable bases, and which bases would you predict at those two positions in a newly sequenced gene? position 1 (T) and position 2 (G) position –10 (G) and position –7 (A) position 0 (A) and position 2 (G) position 0 (A) and position 1 (T)

Which positions in the logo have the least predictable bases Which positions in the logo have the least predictable bases? How can you tell? All positions other than 1 and 2 have equally low predictive power because they have multiple bases in their stacks. The four positions with the shortest stacks of bases have the lowest predictive power (–15, –14, –3, and 3). The 13 positions that are each missing at least one base from the stack have the lowest predictive power (–15, –13, –9, –8, –7, –3, –1, 0, 1, 2, 3, 4, and 7). The 12 positions showing no bases have the lowest predictive power (–18, –17, –16, –12, –11, –6, –5, –4, –2, 5, 6, and 8). Answer: D

Which positions in the logo have the least predictable bases Which positions in the logo have the least predictable bases? How can you tell? All positions other than 1 and 2 have equally low predictive power because they have multiple bases in their stacks. The four positions with the shortest stacks of bases have the lowest predictive power (–15, –14, –3, and 3). The 13 positions that are each missing at least one base from the stack have the lowest predictive power (–15, –13, –9, –8, –7, –3, –1, 0, 1, 2, 3, 4, and 7). The 12 positions showing no bases have the lowest predictive power (–18, –17, –16, –12, –11, –6, –5, –4, –2, 5, 6, and 8).

In the actual experiment, the researchers used 149 sequences to build their sequence logo, as opposed to just 10. Now there is a stack at each position, however short, because the sequence logo includes more data.

Which three positions in the sequence logo in the figure have the most predictable bases? Name the most frequent base at each position. position –18 (T); position –5 (A); position 8 (A) position 0 (A); position 1 (T); position 2 (G) position 0 (T); position 1 (A); position 2 (C) position –11 (G); position –10 (G); position –9 (G) Answer: B

Which three positions in the sequence logo in the figure have the most predictable bases? Name the most frequent base at each position. position –18 (T); position –5 (A); position 8 (A) position 0 (A); position 1 (T); position 2 (G) position 0 (T); position 1 (A); position 2 (C) position –11 (G); position –10 (G); position –9 (G)

What gene feature is represented by the bases in positions 0–2? the translation stop codon the transcription start site ATG the ribosome binding site the translation start codon AUG Answer: D

What gene feature is represented by the bases in positions 0–2? the translation stop codon the transcription start site ATG the ribosome binding site the translation start codon AUG

Based on the logo, what five adjacent base positions in the 5' UTR region (the untranslated region at the 5' end of the mRNA) are most likely involved in ribosome binding? Positions –1 to 3 include the tallest stacks; therefore, they represent the most likely sequence for the ribosome binding site. Positions –12 to –8 have the tallest stacks in the 5' UTR region; therefore, they represent the most likely sequence for the ribosome binding site. Positions –5 to –1 are adjacent to the AUG start codon in the 5' UTR region; therefore, they represent the most likely sequence for the ribosome binding site. Answer: B

Based on the logo, what five adjacent base positions in the 5' UTR region (the untranslated region at the 5' end of the mRNA) are most likely involved in ribosome binding? Positions –1 to 3 include the tallest stacks; therefore, they represent the most likely sequence for the ribosome binding site. Positions –12 to –8 have the tallest stacks in the 5' UTR region; therefore, they represent the most likely sequence for the ribosome binding site. Positions –5 to –1 are adjacent to the AUG start codon in the 5' UTR region; therefore, they represent the most likely sequence for the ribosome binding site.