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Chapter 17: From Gene to Protein

This is going to be a very long journey, but it is crucial to your understanding of biology. Work on this chapter a single concept at a time, and expect to spend at least 6 hours to truly master the material. To give you an idea of the depth and time required, we spent over 5 hours writing this Reading Guide! You will need even longer to complete it and learn the information. Good luck, and take your time. Overview 1. What is gene expression? Gene expression is the process by which information encoded in DNA directs the synthesis of proteins or, in some cases, RNAs that are not translated into proteins and instead function as RNAs. Concept 17.1 Genes specify proteins via transcription and translation 2. What situation did Archibald Garrod suggest caused inborn errors of metabolism? A persons inability to make a particular enzyme 3. Describe one example Garrod used to illustrate his hypothesis. Garrod gave as one example the hereditary condition called alkaptonuria. In this disorder, the urine is black because it contains the chemical alkapton, which darkens upon exposure to air. Garrod reasoned that most people have an enzyme that metabolizes alkapton, whereas people with alkaptonuria have inherited an inability to make that enzyme. 4. State the hypothesis formulated by George Beadle while studying eye color mutations in Drosophila. The hypothesis stated that in Drosophila, each of the various mutations affecting eye color blocks pigment synthesis at a specific step by preventing production of the enzyme that catalyzes that step. 5. What strategy did Beadle and Tatum adopt to test this hypothesis? Beadle and Tatum bombarded the bread mold Neurospora with X-rays, and then looked among the survivors for mutants that differ in their nutritional needs from the wild-type bread mold. 6. Which organism did Beadle and Tatum use in their research? Neurospora. How did this organisms nutritional requirements facilitate this research? Wild-type Neurospora has modest food requirements. It can grow in the laboratory on a simple solution of inorganic salts, glucose, and the vitamin biotin, and incorporated into agar, a support medium. From this minimal medium, the mold cells use their metabolic pathways to produce all other molecules they need. Beadle and Tatum identified mutants that could not survive on minimal medium, apparently because they were unable to synthesize certain essential molecules
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from the minimal ingredients. 7. How were Neurospora spores treated to increase the mutation rate? Neurospora spores were treated with X-rays to increase the mutation rate. 8. Study Figure 17.2 in your text carefully. On the following unlabeled figure, describe the technique used to identify and isolate mutant fungi. See page 327 in your text for the labeled figure. 9. Cite two significant findings that resulted from the research of Beadle and Tatum. One, that metabolic defects are linked to defective genes, and two, support for the one geneone enzyme hypothesis 10. What revision of detail (but not of basic principle) did this hypothesis undergo as more information was gained? Write this restatement and then box or highlight it. This is an important concept! Because not all proteins are enzymes, and because each protein consists of two or more different polypeptide chains, each specified by its own gene, the hypothesis was revised. Beadle and Tatums idea was restated as the one geneone polypeptide hypothesis. Basic Principles of Transcription and Translation This section will introduce you to the processes and associated terminology in the form of an overview. Once you have the big picture, you will take a closer look in the next few concepts. 11. From the first paragraph in this section, find three ways in which RNA differs from DNA. 1. RNA contains ribose instead of deoxyribose as its sugar. 2. RNA has the nitrogenous base uracil rather than thymine. 3. An RNA molecule usually consists of a single strand rather than DNAs double strand 12. What are the monomers of DNA and RNA? The four types of nucleotides, which differ in their nitrogenous bases Of proteins? Amino acids 13. Define each of these processes that are essential to the formation of a protein: transcription: The synthesis of RNA using a DNA template translation: The synthesis of a polypeptide using the genetic information encoded in an mRNA molecule. There is a change of language from nucleotides to amino acids. 14. Complete the following table to summarize each process.
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Template Transcription Translation DNA mRNA

Product Synthesized RNA Polypeptide Primary transcript

Location in Eukaryotic Cell Nucleus Cytoplasm

15. In eukaryotes, what is the pre-mRNA called?

16. Write the central dogma of molecular genetics, as proclaimed by Francis Crick, in the box below. DNA RNA Protein 20

17. How many nucleotide bases are there? 4 How many amino acids?

18. How many nucleotides are required to code for these 20 amino acids? 3 19. So, the language of DNA is a triplet code. How many unique triplets exist? 64

20. DNA is double-stranded, but for each protein, only one of these two strands is used to produce an mRNA transcript. What is the coding strand called? Template strand

21. Here is a short DNA template. Below it, assemble the complementary mRNA strand.

3'A C G A C C A G T A A A 5' 5' U G C U G G U C A U U U 3'

22. How many codons are there above? 4 Label one codon.

Answers may vary; see page 329 in your text for the labeled figure. 23. Describe Nirenbergs experiment in which he identified the first codon. Nirenberg synthesized an artificial mRNA by linking identical RNA nucleotides containing uracil as their base. 24. What was the first codonamino acid pair to be identified? UUU (poly-U)-phenylalanine 25. Of the 64 possible codons, how many code for amino acids? 61 26. What event is coded for by UAA, UAG, and UGA? 27. What is the start codon? AUG 28. Why is the genetic code said to be redundant but not ambiguous? Although more than one codon may specify a particular amino acid, neither codon specifies any
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other amino acid. 29. Explain the concept of reading frame. On an mRNA, the reading frame is the triplet grouping of ribonucleotides used by the translation machinery during polypeptide synthesis. 30. Now here is an important idea: DNA is DNA is DNA. By this we mean that the code is nearly universal, and because of this, jellyfish genes can be inserted into pigs, or firefly genes can make a tobacco plant glow. Enjoy a look at Figure 17.6 in your text . . . and no question to answer here! Concept 17.2 Transcription is the DNA-directed synthesis of RNA: A closer look 31. Name the enzyme that uses the DNA template strand to transcribe a new mRNA strand. RNA polymerase 32. Recall from Chapter 16 that DNA polymerase III adds new nucleotides to the template DNA strand to assemble each new strand of DNA. Both enzymes can assemble a new polynucleotide only in the 5' direction. Which enzyme, DNA polymerase III or RNA polymerase, does not require a primer to begin synthesis? RNA polymerase 33. What is a transcription unit? A transcription unit is a region of DNA that is transcribed into an RNA molecule. 34. Figure 17.7 in your text will require a bit of study. Use it to label the following elements on the figure below: promoter, RNA polymerase, transcription unit, DNA template, nontemplate DNA, and RNA transcript. Then, to the right of the figure, name the three stages of transcription and briefly describe each stage. See page 332 in your text for the labeled figure and description of each stage. 35. Lets now take a closer look at initiation. Read the paragraph titled RNA Polymerase Binding and Initiation of Transcription carefully. List three important facts about the promoter here. 1. Promoter of a gene includes within it the transcription start point. 2. Promoter typically extends several dozen of more nucleotide pairs upstream from the start point. 3. RNA polymerase binds in a precise location and orientation on the promoter. 36. Use Figure 17.8 in your text to label the following elements of the figure that follows: TATA box, RNA polymerase II, transcription factors, template DNA strand, start point, 5' and 3', and mRNA transcript. To the right of the figure, explain the three stages of initiation that are shown.
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See page 333 of your text for the labeled figure and description of each stage. 37. What is the TATA box? How do you think it got this name? The TATA box is a DNA sequence in eukaryotic promoters crucial in forming the transcription initiation complex. The name TATA box is from the thymine (T) and adenine (A) that make it up. 38. What comprises a transcription initiation complex? The completed assembly of transcription factors and RNA polymerase bound to a promoter 39. Now it is time to put all of the elements of transcription together. Write an essay below to describe the process by which mRNA is formed. Use these terms correctly in your essay, and highlight (or underline) each one: TATA box, gene, terminator, promoter, elongation, 5' to 3', termination, initiation RNA, polymerase RNA nucleotides, template, start point, termination signal, and transcription factors. This essay is typical of what you might be asked to write on the AP Biology exam. Answers will vary. Concept 17.3 Eukaryotic cells modify RNA after transcription 40. RNA processing occurs only in eukaryotic cells. The primary transcript is altered at both ends, and sections in the middle are removed. a. What happens at the 5' end? The 5' end is synthesized first; it receives a 5' cap, a modified form of a guanine (G) nucleotide added onto the 5' end after transcription of the first 2040 nucleotides. b. What happens at the 3' end? The 3' end of the pre-mRNA molecule is also modified before the mRNA exits the nucleus. An enzyme adds 50250 more adenine (A) nucleotides, forming a poly-A tail. 41. What are three important functions of the 5' cap and poly-A tail? 1. They seem to facilitate the export of mature mRNA from the nucleus. 2. They help protect the mRNA from degradation by hydrolytic enzymes. 3. They help ribosomes attach to the 5' end of the mRNA once the mRNA reaches the cytoplasm. 42. Distinguish between introns and exons. Perhaps it will help to remember this: Exons are expressed. Introns are the noncoding segments of nucleic acid that lie between coding regions, also called intervening sequences Exons are the segments of nucleic acid that are eventually expressed by being translated into amino acid sequences.
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43. On the following figure label: pre-mRNA, 5' cap, poly-A tail, introns, and exons. See page 335 of your text for the labeled figure. 44. What are snRNPs? What two types of molecules make up a snurp? (We like the word snurp! It reminds us of little cartoon characters that wore blue hoods and were called smurfs.) snRNPs are small nuclear ribonucleoproteins. snRNPs are made up of RNA and protein molecules. 45. You will be introduced to a number of small RNAs in this course. What type is the RNA in a snRNP? Small nuclear RNA

46. Snurps band together in little snurp groups to form spliceosomes. How do spliceosomes work? The spliceosome interacts with certain sites along an intron, releasing the intron, which is rapidly degraded, and joining together two exons that flanked the intron. 47. On the figure below, label the following: pre-mRNA, snRNPs, snRNA, protein, spliceosomes, intron, and other proteins. See page 335 of your text for the labeled figure. 48. Study the figure and text carefully to explain how the splice sites are recognized. snRNAs, part of the spliceosome complex, recognize specific nucleotide sequences on the intron and catalyze the process of intron removal. This is an excellent example of catalytic function in snRNA. 49. What is a ribozyme? An RNA molecule that functions as an enzyme, such as an intron that catalyzes its own removal during RNA splicing 50. What commonly held idea was rendered obsolete by the discovery of ribozymes? The idea that all biological catalysts are proteins 51. What are three properties of RNA that allow it to function as an enzyme? a. Because RNA is single-stranded, a region of an RNA molecule may base-pair with a complementary region elsewhere in the same molecule, which gives the molecule a particular three-dimensional structure. A specific structure is essential to the catalytic function of ribozymes, just as it is for enzymatic proteins. b. Like certain amino acids in an enzymatic protein, some of the bases in RNA contain functional groups that may participate in catalysis. -6-

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c. This ability of RNA to hydrogen-bond with other nucleic acid molecules (either RNA or DNA) adds specificity to its catalytic activity. 52. What is the consequence of alternative splicing of identical mRNA transcripts? The number of different protein products an organism produces can be much greater than its number of genes. Concept 17.4 Translation is the RNA-directed synthesis of a polypeptide: A closer look 53. You may need to read on in this section in order to answer this question, as well as think back to earlier information about mRNA. Come back to this question later if you wish. Three types of RNA are needed for protein synthesis. Complete the chart below. Type of RNA mRNA Description Messenger RNA Single-stranded tRNA Transfer RNA About 75 nucleotides long; folds into a clover-leaf shape. rRNA Ribosomal RNA Together with proteins, makes up ribosomes; the most abundant type of RNA Function Carries genetic material from the DNA to the protein-synthesizing machinery of the cell Transfers amino acids from the cytoplasmic pool of amino acids to a growing polypeptide in a ribosome

54. What is an anticodon? A nucleotide triplet at one end of a tRNA molecule that base-pairs with a particular complementary codon on an mRNA molecule 55. Transfer RNA has two attachment sites. What binds at each site? Sketch tRNA to indicate the two attachment sites, and note where complementary base pairing and hydrogen bonding occur to give it shape. A specific anticodon binds at one end of tRNA, and a corresponding amino acid at the other end. See page 337 of your text for the labeled figure. 56. How many different aminoacyl-tRNA synthetases are there? 20

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57. Scientists expected to find one aminoacyl-tRNA synthetase per codon, but far fewer have been discovered. How does wobble explain this? Wobble is flexibility in the base-pairing rules in which the nucleotide at the 5' end of a tRNA anticodon can form hydrogen bonds with more than one kind of base in the third position (3' end) of a codon. This flexibility explains why there are only about 45 tRNAs. 58. Use the following figure to explain the process of a specific amino acid being joined to a tRNA. Also add these labels: aminoacyl-tRNA synthetase, ATP, amino acid, and tRNA. See page 338 of your text for the labeled figure. 59. Describe the structure of a eukaryotic ribosome. A ribosome consists of a large subunit and a small subunit, each made up of proteins and one or more rRNAs. 60. How does a prokaryotic ribosome differ from a eukaryotic ribosome? What is the medical significance of this difference? Eukaryotic ribosomes are slightly larger in structure and differ somewhat from bacterial ribosomes in their molecular composition. Certain antibiotic drugs can inactivate bacterial ribosomes without inhibiting the ability of eukaryotic ribosomes to make proteins. These drugs, including tetracycline and streptomycin, are used to combat bacterial infections. 61. On the following figure, label the large subunit, small subunit, A, P, and E sites, mRNA binding site. To the right of the figure, explain the functions of the A, P, and E sites. See page 339 of your text for the labeled figure. 62. Much like transcription, we can divide translation into three stages. List them. a. initiation b. elongation c. termination 63. Summarize the events of initiation. Include these components: small ribosomal subunit, large ribosomal subunit, mRNA, initiator codon, tRNA, Met, initiation complex, P site, and GTP. The figure below may help you. See page 340 in your text for the labeled figure. A small ribosomal subunit binds to a molecule of mRNA. In a bacterial cell, the mRNA binding site on this subunit recognizes a specific nucleotide sequence on the mRNA just upstream of the start codon. An initiator tRNA, within the anticodon UAC, base-pairs with the start codon, AUG. This tRNA carries the amino acid methionine (Met). The arrival of a large ribosomal subunit completes the initiative complex. Proteins called initiation factors are required to bring all the translation components together. Hydrolysis of GTP provides the
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energy for the assembly. The initiator tRNA is in the P site; the A site is available to the tRNA bearing the next amino acid. 64. What is always the first amino acid in the new polypeptide? methionine 65. Now, summarize the events of elongation. Include these components: mRNA, A site, tRNA, codon, anticodon, ribozyme, P site, and E site. Again, the figure may help you. See page 341 in your text for the labeled figure. The anticodon of an incoming aminoacyl tRNA base-pairs with the complementary mRNA codon in the A site. Hydrolysis of GTP increases the accuracy and efficiency of this step. An rRNA molecule of the large ribosomal subunit catalyzes the formation of a peptide bond between the amino group of the new amino acid in the A site and the carboxyl end of the growing polypeptide in the P site. This step removes the polypeptide from the tRNA in the P site and attaches it to the amino acid on the tRNA in the A site. The ribosome translocates the tRNA in the A site to the P site. At the same time, the empty tRNA in the P site is moved to the E site, where it is released. The mRNA moves along with its bound tRNAs, bringing the next codon to be translated into the A site. 66. What is a release factor? By what mechanism is termination accomplished? A release factor is a protein shaped like an aminoacyl tRNA, which binds directly to the stop codon in the A site.Hydrolyzation is the mechanism by which termination is accomplished, releasing the polypeptide through the exit tunnel of the ribosomes large subunit. 67. What is a polyribosome? A polyribosome is a group of several ribosomes attached to, and translating, the same messenger RNA molecule. 68. What are some of the things that will result in a final-form functional protein? Modifications of a protein after translation include protein folding, chemical modification of amino acids, enzymatic removal or rearrangement of amino acids, or the formation of quaternarylevel proteins as in the case of hemoglobin. 69. Describe at least three types of post-translational modifications. 1. Certain amino acids may be chemically modified by the attachment of sugars, lipids, phosphate groups, or other additions. 2. Enzymes may remove one or more amino acids from the leading (amino) end of the polypeptide chain. 3. Two or more polypeptides that are synthesized separately may come together, becoming the subunits of a protein that has quaternary structure. 70. Use the following figure to explain how proteins are targeted for the ER. See page 343 in your text for the labeled figure. Polypeptide synthesis begins on a free ribosome in the cytosol. An SRP binds to a receptor protein in the ER membrane. This receptor is part of a protein complex that has a membrane pore and a
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signal-cleaving enzyme. The SRP leaves, and the polypeptide synthesis resumes, with simultaneous translocation across the membrane. The signal-cleaving enzyme cuts off the signal polypeptide. The rest of the completed polypeptide leaves the ribosome and folds into its final conformation. Concept 17.5 Mutations of one or a few nucleotides can affect protein structure and function 71. Define a mutation in terms of molecular genetics. A change in the nucleotide sequence of an organisms DNA or in the DNA or RNA of a virus 72. Define point mutations. A point mutation is a change in a single nucleotide pair of a gene. 73. What are frameshift mutations? A frameshift mutation is a mutation occurring when nucleotides are inserted in or deleted from a gene and the number inserted or deleted is not a multiple of three, resulting in the improper grouping of the subsequent nucleotides into codons. 74. Identify two mechanisms by which frameshifts may occur. Insertion and deletion 75. What is the difference between a nonsense and missense mutation? A nonsense mutation changes an amino acid codon to one of the three stop codons, resulting in a shorter and usually nonfunctional protein. A missense mutation is a nucleotide-pair substitution that results in a codon that codes for a different amino acid. 76. How can a nucleotide-pair substitution result in a silent mutation? A change in the nucleotide pair may transform one codon into another that is translated into the same amino acid. This mutation has no observable effect on the phenotype. 77. What are the two categories of mutagens? Physical and chemical 78. Describe the action of different types of chemical mutagens. 1. Chemicals that are similar to normal DNA nucleotides but that pair incorrectly during DNA replication 2. Chemicals that interfere with correct DNA replication by inserting themselves into the DNA and distorting the double helix 3. Chemicals that cause chemical changes in bases that change their pairing properties
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Concept 17.6 While gene expression differs among the domains of life, the concept of a gene is universal 79. Describe two important ways in which bacterial and eukaryotic gene expression differ. 1. Transcription is terminated differently in bacteria and eukaryotes. 2. In the absence of a nucleus, bacterial cells can simultaneously transcribe and translate the same gene, and the newly made protein can quickly diffuse to its site of function. The eukaryotic cells nuclear envelope segregates transcription from translation and provides a compartment for extensive RNA processing. This processing state includes additional steps whose regulation can help coordinate the eukaryotic cells elaborate activities. 80. What is a gene? It used to be simply stated that one gene codes for one polypeptide. That definition has now been modified. Write below the broader molecular definition in use today. A gene is a region of DNA that can be expressed to produce a final functional product that is either a polypeptide or an RNA molecule. 81. Finally, use this summary figure to put together all that you have learned in this chapter. See page 348 in your text for the labeled figure. Testing Your Understanding Answers Now you should be ready to test your knowledge. Place your answers here: 1. b 2. d 3. a 4. a 5. b 6. d 7. e

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