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ESSENTIAL CELL BIOLOGY, FOURTH EDITION CHAPTER 7: FROM DNA TO PROTEIN © 2014 GARLAND SCIENCE PUBLISHING 7-1

For each of the following sentences, fill in the blanks with the best word or phrase selected from the list below. Not all words or phrases will be used; use each word or phrase only once. The instructions specified by the DNA will ultimately specify the sequence of proteins. This process involves DNA, made up of ____ different nucleotides, which gets _________________ into RNA, which is then _________________ into proteins, made up of _____ different amino acids. In eukaryotic cells, DNA gets made into RNA in the _________________, while proteins are produced from RNA in the _________________. The segment of DNA called a _________________ is the portion that is copied into RNA; this process is catalyzed by RNA _________________. 4 20 109 128 cytoplasm exported

7-2

gene Golgi kinase nuclear pore nucleus polymerase

proteasome replisome sugar-phosphate transcribed transferase translated

Use the numbers in the choices below to indicate where in the schematic diagram of a eukaryotic cell (Figure Q7-2) those processes take place.

Figure Q7-2 1. 2. 3.

transcription translation RNA splicing Page 1 of 29

4. 5.

polyadenylation RNA capping

From DNA to RNA 7-3

Consider two genes that are next to each other on a chromosome, as arranged in Figure Q7-3.

Figure Q7-3 Which of the following statements is true? (a) The two genes must be transcribed into RNA using the same strand of DNA. (b) If gene A is transcribed in a cell, gene B cannot be transcribed. (c) Gene A and gene B can be transcribed at different rates, producing different amounts of RNA within the same cell. (d) If gene A is transcribed in a cell, gene B must be transcribed. 7-4

RNA in cells differs from DNA in that ___________________. (a) it contains the base uracil, which pairs with cytosine. (b) it is single-stranded and cannot form base pairs. (c) it is single-stranded and can fold up into a variety of structures. (d) the sugar ribose contains fewer oxygen atoms than does deoxyribose.

7-5

Transcription is similar to DNA replication in that ___________________. (a) an RNA transcript is synthesized discontinuously and the pieces are then joined together. (b) it uses the same enzyme as that used to synthesize RNA primers during DNA replication. (c) the newly synthesized RNA remains paired to the template DNA. (d) nucleotide polymerization occurs only in the 5′-to-3′ direction.

Figure Q7-6 is to be used with Questions 7-6, 7-7, and 7-8. These three questions can be used separately or together.

Figure Q7-6

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7-6

Figure Q7-6 shows a ribose sugar. RNA bases are added to the part of the ribose sugar pointed to by arrow _____. (b) (c) (d)

4. 5. 6.

7-7

Figure Q7-6 shows a ribose sugar. The part of the ribose sugar that is different from the deoxyribose sugar used in DNA is pointed to by arrow ____. (a) 1. (b) 4. (c) 5. (d) 6.

7-8

Figure Q7-6 shows a ribose sugar. The part of the ribose sugar where a new ribonucleotide will attach in an RNA molecule is pointed to by arrow ____. (a) 1. (b) 3. (c) 4. (d) 5.

7-9

For each of the following sentences, fill in the blanks with the best word or phrase selected from the list below. Not all words or phrases will be used; use each word or phrase only once. For a cell’s genetic material to be used, the information is first copied from the DNA into n_____. Various kinds the nucleotide sequence of RNA in a process called ___ mRNA of RNA are produced, each with different functions. __________________ molecules tRNA code for proteins, __________________ molecules act as adaptors for protein synthesis, rRNA __________________ molecules are integral components of the ribosome, and SnRNA __________________ molecules are important in the splicing of RNA transcripts. incorporation mRNA pRNA proteins

7-10

rRNA snRNA transcription

Match the following structures with their names.

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translation transmembrane tRNA

4

1

2

3 Figure Q7-10

7-11

Which of the following statements is false? (a) A new RNA molecule can begin to be synthesized from a gene before the previous RNA molecule’s synthesis is completed. (b) If two genes are to be expressed in a cell, these two genes can be transcribed with different efficiencies. (c) RNA polymerase is responsible for both unwinding the DNA helix and catalyzing the formation of the phosphodiester bonds between nucleotides. (d) Unlike DNA, RNA uses a uracil base and a deoxyribose sugar.

7-12

Unlike DNA, which typically forms a helical structure, different molecules of RNA can fold into a variety of three-dimensional shapes. This is largely because ___________________. (a) RNA contains uracil and uses ribose as the sugar. (b) RNA bases cannot form hydrogen bonds with each other. (c) RNA nucleotides use a different chemical linkage between nucleotides compared to DNA. (d) RNA is single-stranded.

7-13

Which of the following molecules of RNA would you predict to be the most likely to fold into a specific structure as a result of intramolecular base-pairing? (a) 5′-CCCUAAAAAAAAAAAAAAAAUUUUUUUUUUUUUUUUAGGG-3′ (b) 5′-UGUGUGUGUGUGUGUGUGUGUGUGUGUGUGUGUGUGUGUG-3′ (c) 5′-AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA-3′ (d) 5′-GGAAAAGGAGAUGGGCAAGGGGAAAAGGAGAUGGGCAAGG-3′

7-14

Which one of the following is the main reason that a typical eukaryotic gene is able to respond to a far greater variety of regulatory signals than a typical prokaryotic gene or operon? (a) Eukaryotes have three types of RNA polymerase. (b) Eukaryotic RNA polymerases require general transcription factors. (c) The transcription of a eukaryotic gene can be influenced by proteins that bind far

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(d) 7-15

from the promoter. Prokaryotic genes are packaged into nucleosomes.

Match the following types of RNA with the main polymerase that transcribes them. 1 3 3 2 2

7-16

List three ways in which the process of eukaryotic transcription differs from the process of bacterial transcription.

7-17

For each of the following sentences, fill in the blanks with the best word or phrase selected from the list below. Not all words or phrases will be used; each word or phrase should be used only once. In eukaryotic cells, general transcription factors are required for the activity of all promoters transcribed by RNA polymerase II. The assembly of the general transcription TFIIID factors begins with the binding of the factor __________________ to DNA, causing a marked local distortion in the DNA. This factor binds at the DNA sequence called the tata __________________ box, which is typically located 25 nucleotides upstream from the transcription start site. Once RNA polymerase II has been brought to the promoter DNA, it must be released to begin making transcripts. This release process is facilitated by the addition of phosphate groups to the tail of RNA polymerase by the factor TFIIIH __________________. It must be remembered that the general transcription factors and RNA polymerase are not sufficient to initiate transcription in the cell and are affected by proteins bound thousands of nucleotides away from the promoter. Proteins that link the distantly bound transcription regulators to RNA polymerase and the general transcription mediator factors include the large complex of proteins called the__________________. The packing of DNA into chromatin also affects transcriptional initiation, and histone deacetylase __________________ is an enzyme that can render the DNA less accessible to the general transcription factors. activator CAP deacetylase enhancer

7-18

lac ligase Mediator TATA

TFIIA TFIID TFIIH

You have a piece of DNA that includes the following sequence: 5′-ATAGGCATTCGATCCGGATAGCAT-3′ 3′-TATCCGTAAGCTAGGCCTATCGTA-5′

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Which of the following RNA molecules could be transcribed from this piece of DNA? (a) 5′-UAUCCGUAAGCUAGGCCUAUGCUA-3′ (b) 5′-AUAGGCAUUCGAUCCGGAUAGCAU-3′ (c) 5′-UACGAUAGGCCUAGCUUACGGAUA-3′ (d) none of the above 7-19

The following segment of DNA is from a transcribed region of a chromosome. You know that RNA polymerase moves from left to right along this piece of DNA, that the promoter for this gene is to the left of the DNA shown, and that this entire region of DNA is made into RNA. 5′-GGCATGGCAATATTGTAGTA-3′ 3′-CCGTACCGTTATAACATCAT-5′ Given this information, a student claims that the RNA produced from this DNA is: 3′-GGCATGGCAATATTGTAGTA-5′ Give two reasons why this answer is incorrect.

7-20

You have a segment of DNA that contains the following sequence: 5′-GGACTAGACAATAGGGACCTAGAGATTCCGAAA-3′ 3′-CCTGATCTGTTATCCCTGGATCTCTAAGGCTTT-5′ You know that the RNA transcribed from this segment contains the following sequence: 5′-GGACUAGACAAUAGGGACCUAGAGAUUCCGAAA–3′ Which of the following choices best describes how transcription occurs? (a) the top strand is the template strand; RNA polymerase moves along this strand from 5′ to 3′ (b) the top strand is the template strand; RNA polymerase moves along this strand from 3′ to 5′ (c) the bottom strand is the template strand; RNA polymerase moves along this strand from 5′ to 3′ (d) the bottom strand is the template strand; RNA polymerase moves along this strand from 3′ to 5′

7-21

Imagine that an RNA polymerase is transcribing a segment of DNA that contains the following sequence: 5′-AGTCTAGGCACTGA-3′ 3′-TCAGATCCGTGACT-5′ A.

If the polymerase is transcribing from this segment of DNA from left to right,

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B.

which strand (top or bottom) is the template? What will be the sequence of that RNA (be sure to label the 5′ and 3′ ends of your RNA molecule)?

7-22

The sigma subunit of bacterial RNA polymerase ___________________. (a) contains the catalytic activity of the polymerase. (b) remains part of the polymerase throughout transcription. (c) recognizes promoter sites in the DNA. (d) recognizes transcription termination sites in the DNA.

7-23

Which of the following might decrease the transcription of only one specific gene in a bacterial cell? (a) a decrease in the amount of sigma factor (b) a decrease in the amount of RNA polymerase (c) a mutation that introduced a stop codon into the DNA that precedes the gene’s coding sequence (d) a mutation that introduced extensive sequence changes into the DNA that precedes the gene’s transcription start site

7-24

There are several reasons why the primase used to make the RNA primer for DNA replication is not suitable for gene transcription. Which of the statements below is not one of those reasons? (a) Primase initiates RNA synthesis on a single-stranded DNA template. (b) Primase can initiate RNA synthesis without the need for a base-paired primer. (c) Primase synthesizes only RNAs of about 5–20 nucleotides in length. (d) The RNA synthesized by primase remains base-paired to the DNA template.

7-25

You have a bacterial strain with a mutation that removes the transcription termination signal from the Abd operon. Which of the following statements describes the most likely effect of this mutation on Abd transcription? (a) The Abd RNA will not be produced in the mutant strain. (b) The Abd RNA from the mutant strain will be longer than normal. (c) Sigma factor will not dissociate from RNA polymerase when the Abd operon is being transcribed in the mutant strain. (d) RNA polymerase will move in a backward fashion at the Abd operon in the mutant strain.

7-26

Transcription in bacteria differs from transcription in a eukaryotic cell because __________________________. (a) RNA polymerase (along with its sigma subunit) can initiate transcription on its own. (b) RNA polymerase (along with its sigma subunit) requires the general transcription factors to assemble at the promoter before polymerase can begin transcription. (c) the sigma subunit must associate with the appropriate type of RNA polymerase to produce mRNAs. (d) RNA polymerase must be phosphorylated at its C-terminal tail for transcription to

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proceed. 7-27

Which of the following does not occur before a eukaryotic mRNA is exported from the nucleus? (a) The ribosome binds to the mRNA. (b) The mRNA is polyadenylated at its 3′ end. (c) 7-methylguanosine is added in a 5′-to-5′ linkage to the mRNA. (d) RNA polymerase dissociates.

7-28

Total nucleic acids are extracted from a culture of yeast cells and are then mixed with resin beads to which the polynucleotide 5′-TTTTTTTTTTTTTTTTTTTTTTTTT-3′ has been covalently attached. After a short incubation, the beads are then extracted from the mixture. When you analyze the cellular nucleic acids that have stuck to the beads, which of the following is most abundant? (a) DNA (b) tRNA (c) rRNA (d) mRNA

7-29

Name three covalent modifications that can be made to an RNA molecule in eukaryotic cells before the RNA molecule becomes a mature mRNA.

7-30

Which of the following statements about RNA splicing is false? (a) Conventional introns are not found in bacterial genes. (b) For a gene to function properly, every exon must be removed from the primary transcript in the same fashion on every mRNA molecule produced from the same gene. (c) Small RNA molecules in the nucleus perform the splicing reactions necessary for the removal of introns. (d) Splicing occurs after the 5′ cap has been added to the end of the primary transcript.

7-31

The length of a particular gene in human DNA, measured from the start site for transcription to the end of the protein-coding region, is 10,000 nucleotides, whereas the length of the mRNA produced from this gene is 4000 nucleotides. What is the most likely reason for this difference?

7-32

Why is the old dogma “one gene—one protein” not always true for eukaryotic genes?

7-33

Genes in eukaryotic cells often have intronic sequences coded for within the DNA. These sequences are ultimately not translated into proteins. Why? (a) Intronic sequences are removed from RNA molecules by the spliceosome, which works in the nucleus. (b) Introns are not transcribed by RNA polymerase. (c) Introns are removed by catalytic RNAs in the cytoplasm. (d) The ribosome will skip over intron sequences when translating RNA into protein.

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7-34

snRNAs ___________________. (a) are translated into snRNPs. (b) are important for producing mature mRNA transcripts in bacteria. (c) are removed by the spliceosome during RNA splicing. (d) can bind to specific sequences at intron–exon boundaries through complementary base-pairing.

7-35

Is this statement true or false? Explain your answer. “Since introns do not contain protein-coding information, they do not have to be removed precisely (meaning, a nucleotide here and there should not matter) from the primary transcript during RNA splicing.”

7-36

You have discovered a gene (Figure Q7-36A) that is alternatively spliced to produce several forms of mRNA in various cell types, three of which are shown in Figure Q736B. The lines connecting the exons that are included in the mRNA indicate the splicing. From your experiments, you know that protein translation begins in exon 1. For all forms of the mRNA, the encoded protein sequence is the same in the regions of the mRNA that correspond to exons 1 and 10. Exons 2 and 3 are alternative exons used in different mRNA, as are exons 7 and 8. Which of the following statements about exons 2 and 3 is the most accurate? Explain your answer.

Figure Q7-36 (a) (b)

Exons 2 and 3 must have the same number of nucleotides. Exons 2 and 3 must contain an integral number of codons (that is, the number of nucleotides divided by 3 must be an integer). 3,

(d)

Exons 2 and 3 must have different numbers of nucleotides.

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From RNA to Protein 7-37

Which of the following statements about the genetic code is correct? (a) All codons specify more than one amino acid. (b) The genetic code is redundant. (c) All amino acids are specified by more than one codon. (d) All codons specify an amino acid. NOTE: The following codon table is to be used for Problems Q7-38 to Q7-49.

7-38

The piece of RNA below includes the region that codes for the binding site for the initiator tRNA needed in translation. 5′-GUUUCCCGUAUACAUGCGUGCCGGGGGC-3′ Which amino acid will be on the tRNA that is the first to bind to the A site of the ribosome? (a) methionine (b) arginine (c) cysteine (d) valine

7-39

The following DNA sequence includes the beginning of a sequence coding for a protein. What would be the result of a mutation that changed the C marked by an asterisk to an A? 5′-AGGCTATGAATGGACACTGCGAGCCC… *

7-40

Which amino acid would you expect a tRNA with the anticodon 5′-CUU-3′ to carry? (a) lysine (b) glutamic acid

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(d) (d)

leucine phenylalanine

7-41

Which of the following pairs of codons might you expect to be read by the same tRNA as a result of wobble? (a) CUU and UUU (b) GAU and GAA (c) CAC and CAU (d) AAU and AGU

7-42

Below is a segment of RNA from the middle of an mRNA. 5′-UAGUCUAGGCACUGA-3′ If you were told that this segment of RNA was part of the coding region of an mRNA for a large protein, give the amino acid sequence for the protein that is encoded by this segment of mRNA. Write your answer using the one-letter amino acid code.

7-43

Below is the sequence from the 3′ end of an mRNA. 5′-CCGUUACCAGGCCUCAUUAUUGGUAACGGAAAAAAAAAAAAAA-3′ If you were told that this sequence contains the stop codon for the protein encoded by this mRNA, what is the anticodon on the tRNA in the P site of the ribosome when release factor binds to the A site? (a) 5′-CCA-3′ (b) 5′-CCG-3′ (c) 5′-UGG-3′ (d) 5′-UUA-3′

7-44

One strand of a section of DNA isolated from the bacterium E. coli reads: 5′-GTAGCCTACCCATAGG-3′ A.

B. C.

7-45

Suppose that an mRNA is transcribed from this DNA using the complementary strand as a template. What will be the sequence of the mRNA in this region (make sure you label the 5′ and 3′ ends of the mRNA)? How many different peptides could potentially be made from this sequence of RNA, assuming that translation initiates upstream of this sequence? What are these peptides? (Give your answer using the one-letter amino acid code.)

A strain of yeast translates mRNA into protein inaccurately. Individual molecules of a particular protein isolated from this yeast have variations in the first 11 amino acids compared with the sequence of the same protein isolated from normal yeast cells, as listed in Figure Q7-45. What is the most likely cause of this variation in protein

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sequence?

Figure Q7-45 (a) (b) (c) (d)

a mutation in the DNA coding for the protein a mutation in the anticodon of the isoleucine-tRNA (tRNAIle) a mutation in the isoleucyl-tRNA synthetase that decreases its ability to distinguish between different amino acids a mutation in the isoleucyl-tRNA synthetase that decreases its ability to distinguish between different tRNA molecules

7-46

A mutatio...