Chapter 14 Active Reading Guide- AP BIOLOGY PDF

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Chapter 14 Active Reading Guide- AP BIOLOGYChapter 14 Active Reading Guide- AP BIOLOGYChapter 14 Active Reading Guide- AP BIOLOGYChapter 14 Active Reading Guide- AP BIOLOGY...

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Sinead Carty Name: ________________________________________________

AP Biology

Chapter 14 Active Reading Guide 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, it took over 5 hours to write 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? The process by which DNA directs the synthesis of proteins, includes two stages: transcription and translation

Section 1 2. What situation did Archibald Garrod suggest caused “inborn errors of metabolism”? Garrod suggested that genes dictate phenotypes through enzymes that catalyze specific chemical reactions. A person's inability to make a particular enzyme. Genes dictate phenotypes through enzymes that catalyze specific chemical reactions in the cell

3. Describe one example Garrod used to illustrate his hypothesis. Hereditary condition called alkaptonuria where urine is black because it contains the chemical alkapton which darken upon exposure to air. Most people have an enzyme that metabolizes alkapton, whereas people with alkaptonuria have inherited an inability to make that enzyme. -linking genes to enzymes require understanding that cells synthesize and degrade molecules in a series of steps, a metabolic pathway

4. State the hypothesis formulated by George Beadle while studying eye color mutations in Drosophila. -each of the various mutations of affecting eye color blocks pigment synthesis at a specific step by preventing the production of the enzyme -showed that genes control the production of enzymes and that the enzymes are related to traits

5. What strategy did Beadle and Tatum adopt to test this hypothesis? They bombarded Neurospora with x-rays and then looked among the survivors for mutants that differed in their nutritional needs from the wild-type mold

Wild-type Neurospora. 6. Which organism did Beadle and Tatum use in their research? _________________ How did this organism’s nutritional requirements facilitate this research? It can survive in the lab on a moist support medium called agar, mixed with only inorganic salts, glucose, and the vitamin biotin

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7. How were Neurospora spores treated to increase the mutation rate? They allowed them to grow on a complete growth medium, which consisted of a minimal medium supplemented with all 20 amino acids and a few other nutrients

8. Cite two significant findings that resulted from the research of Beadle and Tatum. 1. The function of a gene is to dictate the production of a specific enzyme 2. Not all proteins are enzymes

9. What revision of detail (but not of basic principle) did this hypothesis undergo as more information was gained? Write this restatement and then highlight it. This is an important concept! Not all proteins are enzymes. Many proteins are constructed from two or more different polypeptide chains, and each polypeptide is specified by its own gene

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. 10. From the first paragraph in this section, find three ways in which RNA differs from DNA. RNA contains ribose instead of deoxyribose 1. ________________________________________________________________ Has the nitrogenous base Uracil instead of Thymine 2. ________________________________________________________________

Consists of a single strand 3. ________________________________________________________________ the 4 types of nucleotides

11. What are the monomers of DNA and RNA? ________________________________ amino acids Of proteins? ______________________________

12. Define each of these processes that are essential to the formation of a protein: transcription: The synthesis of RNA under the direction of DNA

translation: the synthesis of a polypeptide, which occurs uner the direction of mRNA

13. Complete the following table to summarize each process. Template Product Synthesized Location in the Eukaryotic Cell Transcription DNA nucleus RNA Translation

polypeptide

mRNA

cytoplasm

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Primary Transcript 14. In eukaryotes, what is the pre-mRNA called? _________________________

15. Write the central dogma of molecular genetics, as proclaimed by Francis Crick, in the box below. cells are governed by a molecular chain of command with a directional flow of genetic information. DNA>RNA->Protein

4 20 16. How many nucleotide bases are there? _____ How many amino acids? _____ 3 17. How many nucleotides are required to code for these 20 amino acids? _____

64 18. So, the language of DNA is a triplet code. How many unique triplets exist? _____

19. DNA is double-stranded, but for each protein, only one of these two strands is used The template strand to produce an mRNA transcript. What is the coding strand called? _____________ 20. 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' 4 21. How many codons are there above? _____ Label one codon.

22. Describe Nirenberg’s experiment in which he identified the first codon. Nirenberg synthesized an artificial mRNA by linking identical RNA nucleotides containing Uracil as their base. No matter where this message started or stopped, it could contain only one codon in repetition: UUU

UUU 23. What was the first codon–amino acid pair to be identified? ____________________ 61 24. Of the 64 possible codons, how many code for amino acids? _____ stop signals 25. What event is coded for by UAA, UAG, and UGA? _____ AUG 26. What is the start codon? _____

27. Why is the genetic code said to be redundant but not ambiguous? Because there are codons that specify the same amino acids but none of them ever specify any other amino acid

28. Explain the concept of reading frame. The triplet grouping of ribonucleotides used by the translation machinery during polypeptide synthesis

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29. 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 14.7 in your text... and no question to answer here!

Section 2 30. Name the enzyme that uses the DNA template strand to transcribe a new mRNA strand. RNA Polymerase

31. Recall from Chapter 13 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

32. What is a transcription unit? The stretch of DNA that is transcribed into and RNA molecule

33. Figure 14.8 in your text will require a bit of study. Name the three stages of transcription and briefly describe each stage. 1

2

3

Initiation : It occurs when the enzyme RNA polymerase binds to a region of a gene called the promoter. This signals the DNA to unwind so the enzyme can ‘‘read’’ the bases in one of the DNA strands. now makes a strand of mRNA with a complementary sequence of bases Elongation is the addition of nucleotides to the mRNA strand. RNA polymerase reads the unwound DNA strand and builds the mRNA molecule, u complementary base pairs. A small amount of time where when the newly formed RNA is bound to the unwound DNA. During this process, an ade (A) in the DNA binds to an uracil (U) in the RNA. Termination is the ending of transcription, and occurs when RNA polymerase crosses a stop (termination) sequence in the gene. The mRNA strand is complete, and it detaches from DNA.

34. Let’s 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. The promoter of a gene includes the transcription start poin 1. ________________________________________________________________ typically extends for several dozen more nucleotide pairs upstream from the start point. 2. ________________________________________________________________ RNA polymerase binds in a precise location and orientation on the promoter 3. ________________________________________________________________

35. Use Figure 14.9 in your text to explain the three stages of initiation. "initiator" tRNA carrying the amino acid methionine binds to a special site on the small subunit of the ribosome

1. ________________________________________________________________ The mRNA is also loaded on, and positioned so that the initiation codon (usually AUG) is base paired with the 2. anticodon of the initiator tRNA. _ The large subunit then binds to the small subunit. The resulting complex of ribosome, mRNA, and methionine-bearing

3. _initiator tRNA is called an initiation complex. Formation of this complex also requires a number of helper proteins called initiation factors.

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36. What is the TATA box? How do you think it got this name? A DNA sequence in eukaryotic promotors crucial in forming the transcription initiation complex

37. What comprises a transcription initiation complex? Transcription factors and RNA polymerase bound to a promoter

38. Now it is time to put all of the elements of transcription together. Write a short 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. A promoter, often including a TATA box in eukaryotes, establishes where RNA synthesis is initiated. Beginning at the start point on the template strand, RNA synthesis is catalyzed by RNA polymerase, which links together RNA nucleotides complementary to a DNA template strand. The RNA transcript runs 5' to 3', the reverse of the template. Transcription factors help eukaryotic RNA polymerase recognize promoter sequences, forming a transcription initiation complex. Transcription follows the same base-pairing rules as DNA replication, except that in RNA, uracil substitutes for thymine. The three stages of transcription are initiation, elongation, and termination. The mechanisms of termination are different in bacteria and eukaryotes. In bacteria, transcription proceeds through a terminator sequence in DNA. In eukaryotes, RNA pol II transcribes a specific signal sequence, which codes for a termination signal.

Section 3 39. 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? Receives a 5' cap

b. What happens at the 3' end? An enzyme adds 50 to 205 more adenine nucleotides forming a poly-A tai

40. What are three important functions of the 5' cap and poly-A tail? They facilitate the export of the mature mRNA from the nucleus 1. ________________________________________________________________ They help protect the mRNA from degradation by hydrolytic enzymes 2. ________________________________________________________________ They help ribosomes attach to the 5' end of the mRNA once the mRNA reaches the cytoplasm 3. ________________________________________________________________

41. Distinguish between introns and exons. Perhaps it will help to remember this: Exons are expressed. The noncoding segments of nucleic acid that lie between coding regions are called intervening sequences or introns. The other regions are exons because they are eventually expressed.

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42. What are snRNPs? What two types of molecules make up a snRNP? Small nuclear ribonucleoproteins that recognize splice sites. Made up of RNA & protein molecules

43. You will be introduced to a number of small RNAs in this course. What type is the RNA in a snRNP? Small Nuclear RNA

44. SnRNPs band together in little groups to form spliceosomes. How do spliceosomes work? They interact with certain sites along an intron, relaxing the intron and joining together the two exons that flanked the intron

45. Study the figure and text carefully to explain how the splice sites are recognized. snRNPs form a spliceosome on a pre-mRNA molecule. snRNA base-pairs with nucleotides at specific sites along the intron

46. What is a ribozyme? RNA molecules that function as enzymes

47. What commonly held idea was rendered obsolete by the discovery of ribozymes? All biological catalysts are proteins

48. What are three properties of RNA that allow it to function as an enzyme? Because RNA is single-stranded, a region of an RNA molecule may base pair with a complementary region elsewhere in the same molecule 1. ________________________________________________________________ Some of the bases in RNA contain functional groups that may participate in catalysis 2. ________________________________________________________________ The ability of RNA to hydrogen bond with other nucleic acid molecules adds specificity to its catalytic activity 3. ________________________________________________________________

49. What is the consequence of alternative splicing of identical mRNA transcripts? A single gene can encode more than one kind of polypeptide

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50. Three types of RNA are needed for protein synthesis. Complete the chart below. Type of RNA

Description

Function

mRNA

messenger : messenger RNA, single stranded

carries genetic material from the DNA to the protein-synthesizing machinery of the cell

tRNA

transfer RNA, about 75 nucleotides long; folds into a clover-leaf shape

transfers amino acids from the cytoplasmic pool of amino acids to a growing polypeptide in a ribosome

ribosomal RNA

together with proteins, makes up ribosomes, the most abundant type of RNA

rRNA

51. What is an anticodon? At the end of tRNA, a cleotide triplet which base-pairs with a complementary codon on mRNA/ a nucleotide triplet at one end of a tRNA molecule that base-pairs with a particular complementary codon on an mRNA molecule

52. 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. Page 337 is really good at showing this. A specific anticodon binds at one end of tRNA, and a corresponding amino acid at the other end.

20 53. How many different aminoacyl-tRNA synthetases are there? _____

54. 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.

55. Explain the process of a specific amino acid being joined to a tRNA. Be sure to use the words aminoacyl-tRNA synthetase, ATP, amino acid, and tRNA. Linkage of the tRNA and amino acid is an endergonic process that occurs at the expense of ATP. The ATP loses two phosphate groups, becoming AMP.

56. Describe the structure of a eukaryotic ribosome. consists of a large subunit and a small subunit, each made up of proteins and one or more rRNAs

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57. 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

58. Explain the functions of the A, P, and E sites on a ribosome. The peptidyl-tRNA binding site holds the tRNA carrying the growing polypeptide chain, while the aminoacyl-tRNA binding site holds the tRNA carrying the next amino acid to be added to the chain. Discharged tRNAs leave the ribosome from the exit site

59. Much like transcription, we can divide translation into three stages. List them. Translation, the synthesis of a polypeptide chain, can be divided into three stages analogous to those of transcription: initiation, elongation, and termination.

60. 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 initiation stage of translation brings together mRNA, a tRNA bearing the first amino acid of the polypeptide, and the two subunits of a ribosome. First, 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 with the anticodon UAC base-pairs with the start codon, AUG. This tRNA carries the amino acid methionine. The arrival of a large ribosomal subunit completes the initiation complex. Proteins called initiation factors are required to bring all the translation components together. Hydrolysis of GTP provides the 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.

Methionine 61. What is always the first amino acid in the new polypeptide? ___________________

62. Now, summarize the events of elongation. Include these components: mRNA, A site, tRNA, codon, anticodon, ribozyme, P site, and E site. 1. 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.) 2. An initiator tRNA, within the anticodon UAC, base-pairs with the start codon, AUG. 3. This tRNA carries the amino acid methionine (Met). 4. The arrival of a large ribosomal subunit completes the initiative compl...