AP BIOLOGY 2019-20 January 9, 2020

Today’s Agenda (Day 83)1. HOUSEKEEPING:

2. Homework Check:

Chapter 17 Vocabulary Chapter 17 Reading Guide

3. Class Activity: CONT’D: Chapter 17 – From Gene to Protein

a) Section 17.4 – Translation is the RNA-directed synthesis of a polypeptideb) Section 17.5 – Mutations of one of a few nucleotides can affect protein structure and

functionHOMEWORK:

Read Unit 3 – Chapters 17 – 21 Complete Chapter 17 Reading Guide

Chapter 17 – From Gene to Protein5' cap A site alternative

splicingaminoacyl-tRNA synthetase

anticodon Codons Deletions E site

Exons frameshift mutations

gene expression

Insertions Introns Messenger RNA

Missense(nonsense mutations)

Mutagens

Nucleotide-pair substitutions

P site Point mutation

Poly-A tail Polyribosome

Promoter Reading frame

Ribosomal RNA

Ribozymes RNA polymerase

RNA processing

RNA splicing Signal peptide

spliceosomes

TATA box Template strand

Transcription

Transcription factors

Transcription initiation complex

Transfer RNA

translation

Complete Chapter 18 VocabularyChapter 18 – Regulation of Gene Expression

Activator Bicoid protein Chromatin modification

Control elements Corepressor Cyclic AMP

Cytoplasmic determinants

Determination Differentiation DNA methylation Enhancers Histone acetylation

Inducer Inducible operon Induction Maternal effect genes

Morphogenesis Morphogens

mRNA degradation

Oncogene P53 Pattern formation

Positional information

Proto-oncogenes

Ras Regulatory gene Repressible operon

Repressor Tumor-suppressor genes

REMINDERS: Chapter 17 Reading Guide – January 9 Chapter 18 Vocabulary – January 10 Chapter 18 Notes – January 13 Chapter 17 & 18 Vocabulary Quiz January 14 Chapter 17 & 18 Test January 16, 2020

AP BIOLOGY 2019-20 Reading Guide

Chapter 17: From Gene to Protein Overview 1. What is gene expression? Concept 17.1 Genes specify proteins via transcription and translation 2. What situation did Archibald Garrod suggest caused inborn errors of metabolism? 3. Describe one example Garrod used to illustrate his hypothesis. 4. State the hypothesis formulated by George Beadle while studying eye color mutations in

Drosophila. 5. What strategy did Beadle and Tatum adopt to test this hypothesis? 6. Which organism did Beadle and Tatum use in their research? How did this organism’s nutritional

requirements facilitate this research? 7. How were Neurospora spores treated to increase the mutation rate? 8. Study Figure 17.2 carefully. On the figure below, outline the technique used to identify and isolate

mutant fungi.

9. Cite two significant findings that resulted from the research of Beadle and Tatum. 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! 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.

12. What are the monomers of DNA and RNA? Of proteins? 13. Define each of these processes that are essential to the formation of a protein:

transcription translation

14. Complete the following table to summarize each process. Template Product Synthesized Location in Eukaryotic Cell

Transcription

Translation

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. 17. How many nucleotide bases are there? ___________How many amino acids? __________ 18. How many nucleotides are required to code for these 20 amino acids? ___________________ 19. So, the language of DNA is a triplet code. How many unique triplets exist? ______________ 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? 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'

22. How many codons are there above? ________ Label one codon. 23. Describe Nirenberg’s experiment in which he identified the first codon. 24. What was the first codon–amino acid pair to be identified? __________________________ 25. Of the 64 possible codons, how many code for amino acids? _________________________ 26. What event is coded for by UAA, UAG and UGA? ________________________________ 27. What is the start codon? ____________________________________________________ 28. Why is the genetic code said to be redundant but not ambiguous?

29. Explain the concept of reading frame. 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. 32. You will 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' Æ direction. Which enzyme, DNA polymerase III or RNA polymerase, does not require a primer to begin synthesis?

33. What is a transcription unit? 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, non-template DNA, and RNA transcript. Then, to the right of the figure, name the three stages of transcription and briefly describe each stage.

35. 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. (1) (2) (3)

36. Use Figure 17.8 in your text to label the following elements of the figure below: 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.

37. What is the TATA box? How do you think it got this name? 38. What comprises a transcription initiation complex? 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 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.

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?

b. What happens at the 3' end?

41. What are three important functions of the 5' cap and poly-A tail? 42. Distinguish between introns and exons. Perhaps it will help to remember this: Exons are expressed.

43. On the figure below, label: pre-mRNA, 5' cap, poly-A tail, introns, and exons.

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.

45. You will be introduced to a number of small RNAs in this course. What type is the RNA in a snRNP? 46. Snurps band together in little snurp groups to form spliceosomes. How do spliceosomes work? 47. On the figure below, label the following: pre-mRNA, snRNPs, snRNA, protein, spliceosomes, intron,

and other proteins.

48. Study the figure and text carefully to explain how the splice sites are recognized. 49. What is a ribozyme? 50. What commonly held idea was rendered obsolete by the discovery of ribozymes? 51. What are three properties of RNA that allow it to function as an enzyme?

(1)

(2) (3)

52. What is the consequence of alternative splicing of identical mRNA transcripts?

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 Description Function mRNA

tRNA

rRNA

54. What is an anticodon?

55. Transfer RNA has two attachment sites. What binds at each site? Sketch tRNA, indicate the 2 attachment sites, and note where complementary base pairing and hydrogen bonding occur to give tRNA its shape.

56. How many different aminoacyl-tRNA synthetase are there? ____________________________ 57. Scientists expected to find one aminoacyl-tRNA synthetase per codon, but far fewer have been

discovered. How does wobble explain this? 58. Use the figure below 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.

59. Describe the structure of a eukaryotic ribosome. 60. How does a prokaryotic ribosome differ from a eukaryotic ribosome? What is the medical

significance of this difference? 61. On this 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.

62. Much like transcription, we can divide translation into three stages. List them. 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.

64. What is always the first amino acid in the new polypeptide? 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.

66. What is a release factor? By what mechanism is termination accomplished? 67. What is a polyribosome? 68. What are some of the things that will result in a final-form functional protein? 69. Describe at least three types of post-translational modifications. 70. Use the following figure to explain how proteins are targeted for the ER.

Concept 17.5 Point mutations can affect protein structure and function 71. Define a mutation in terms of molecular genetics.

72. Define point mutations. 73. What are frameshift mutations? 74. Identify two mechanisms by which frameshifts may occur. 75. What is the difference between a nonsense and missense mutation? 76. How can a base-pair substitution result in a silent mutation? 77. What are the two categories of mutagens?

78. Describe the action of difference types of chemical mutagens. Concept 17.6 Although 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. 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.

81. Finally, use this summary figure to put together all that you have learned in this chapter.

AP BIOLOGY 2019-20 Reading Guide

Chapter 19: Viruses Overview Experimental work with viruses has provided important evidence that genes are made of nucleic acids. Viruses were also important in working out the molecular mechanisms of DNA replication, transcription, and translation. Viruses have been important in the development of techniques of manipulating and transferring genes. As you learn about viruses in this chapter, you will build on the foundation necessary for an understanding of the molecular techniques of biotechnology. Concept 19.1 A virus consists of a nucleic acid surrounded by a protein coat 1. What was some early evidence of the existence of viruses? Why were they difficult

to study? 2. What was Wendell Stanley’s contribution to our knowledge of viruses? 3. What are the four forms of viral genomes? 4. What is a capsid? What are capsomeres? What different shapes may capsids

have? 5. As you see, all viruses consist of a nucleic acid enclosed in a protein coat. Some

viruses also have a membranous envelope. What are the components of a viral envelope? Which component is derived from the host cell, and which is of viral origin?

Viral Component Derived From

6. What is the role of an envelope in animal viruses? 7. For the virus shown below, label the protein capsid, tail fibers, head, tail

sheath, and genome. a. What type of virus is this? b. What does its name mean? c. What is its host? d. Is the genome of this virus DNA, or RNA?

Concept 19.2 Viruses reproduce only in host cells 8. What property of a virus determines its attachment to a host cell membrane?

9. Viruses are obligate intracellular parasites. What does this mean? 10. What is meant by host range? Distinguish between a virus with a broad host

range and one with an extremely limited host range, and give an example of each.

11. Compare the host range for the rabies virus to that of the human cold virus. 12. What components of the host cell does a virus use to reproduce itself? 13. How does a DNA virus reproduce its genome? 14. How do most RNA viruses replicate their genome? 15. On this figure of a simplified viral reproductive cycle, label arrows to show these

processes: transcription, translation, infection, replication, and self-assembly. Annotate your labels to explain the process of viral reproduction.

16. What are bacteriophages? Distinguish between virulent and temperate phages.

17. What portion of a phage enters the host cell? How does it do this? 18. What are restriction enzymes? What is their role in bacteria? 19. Why don’t restriction enzymes destroy the DNA of the bacterial cells that produce

them? 20. What are three ways bacteria may win the battle against the phages?

21. What is a prophage?

22. Since cells that have incorporated phage DNA into their genome may continue to divide and propagate the viral genome, this might be considered somewhat like the Trojan horse. What might trigger the switchover from lysogenic to lytic mode?

23. Label the following elements of the figure below: lysogenic phage, lysogenic

cycle, lytic cycle, prophage, phage DNA, bacterial chromosome, and self-assembly.

24. Describe the lytic and lysogenic modes of bacteriophage reproduction. 25. There are some general differences between bacteriophages and animal viruses.

What are two elements that nearly all animal viruses have? 26. What is a retrovirus? How do retroviruses, such as HIV, replicate their genome? 27. Here is a sketch of HIV. Label these parts: envelope, reverse transcriptase,

RNA, and capsid.

28. Compare and contrast a prophage and a provirus. Which one are you likely to carry?

29. This sketch shows the infection of a cell by HIV. Extend label lines to give a complete explanation of the process. Refer to your text Figure 19.8 for details.

30. The final section in this concept is titled “Evolution of Viruses.” From this part, describe the two possible sources of viral genomes. You will see each of these important mobile genetic elements again.

Description of the Mobile Genetic Element Plasmids

Transposons

Concept 19.3 Viruses, viroids, and prions are formidable pathogens in animals and plants 31. What are three ways that viruses make us ill? Why do we recover completely from a cold but not from polio?

32. What tools are in the medical arsenal against human viral diseases? 33. Emerging viruses such as HIV, Ebola, and SARS seem to burst upon the human scene. What are three processes that contribute to this sudden emergence? 34. The current flu pandemic is H1N1. What does this name mean?

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35. Distinguish between horizontal transmission and vertical transmission in plants. 36. How do viruses spread throughout plant bodies? 37. What is a viroid? What important lesson do they teach? Name one viroid disease.

38. Prions strike fear into carnivores everywhere. What are they? How are they transmitted? What do they do? 39. Name four diseases caused by prions. 40. What are two alarming characteristics of prions? 41. Two Nobel Prizes have been awarded for the study of prions. One went to Carlton Gajdusek, who worked with the Fore people of Papua New Guinea in the 1960s to determine the cause of a kuru epidemic. Who got the second Nobel Prize in this area, and when?

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