AP BIOLOGY 2019-20 January 13, 2020

Today’s Agenda (Day 85)1. HOUSEKEEPING:

2. Homework Check:

Chapter 18 Reading Guide

3. Class Activity: BEGIN: Chapter 18 PPT REVIEW

a) Section 18.1 – Bacteria respond to environmental change by regulating transcriptionb) Section 18.2 – Eukaryotic gene expression is regulated at many stagesc) Section 18.3 – Noncoding RNAs play multiple roles in controlling gene d) Section 18.4 – A program of differential gene expression leads to the different cell types in a

multicellular organismHOMEWORK:

Read Unit 3 – Chapters 17 – 21 Study for Chapters 17 & 18 Vocabulary Quiz AND Test

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

Chapter 18 – Regulation of Gene ExpressionActivator Bicoid protein Chromatin

modificationControl 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 18 READING GUIDE – January 13 Chapter 17 & 18 Vocabulary Quiz January 14 Chapter 17 & 18 Test January 16, 2020

AP BIOLOGY 2019-20 Reading Guide

Chapter 18: Regulation of Gene Expression Overview The overview for Chapter 18 introduces the idea that while all cells of an organism have all genes in the genome, not all genes are expressed in every cell. What regulates gene expression? Gene expression in prokaryotic cells differs from that in eukaryotic cells. How do disruptions in gene regulation lead to cancer? This chapter gives you a look at how genes are expressed and modulated. Concept 18.1 Bacteria often respond to environmental change by regulating transcription 1. All genes are not “on” all the time. Using the metabolic needs of E. coli, explain why not. 2. What are the two main ways of controlling metabolism in bacterial cells? 3. Feedback inhibition is a recurring mechanism throughout biological systems. In the case of E.

coli regulating tryptophan synthesis, is it positive or negative inhibition? Explain your choice. 4. What is a promoter?

5. What is the operator? What does it do? 6. What is an operon? 7. List the three components of an operon, and explain the role of each one. 8. How does a repressor protein work? 9. What are regulatory genes? 10. Distinguish between inducible and repressible operons, and describe one example of each type. 11. Label this sketch of the lac operon with the terms at right. Know the function of each structure.

12. Compare and contrast the lac operon and the trp operon. (Remember that compare means “to tell how they are similar,” and contrast means “to tell how they are different.”)

13. What happens when a repressor is bound to the operator? 14. What is CAP? How does CAP work? 15. Explain why CAP binding and stimulation of gene expression is positive regulation. 16. Describe the relationship between glucose supply, cAMP, and CAP. 17. How can both repressible and inducible operons be negative regulators? Concept 18.2 Eukaryotic gene expression can be regulated at any stage 18. Even though all cells of an organism have the same genes, there is differential gene expression. What

does this mean?

19. What percentage of the genes of a typical human cell is expressed at any given time?

20. What is the common control point of gene expression for all organisms? 21. Gene expression can be regulated by modifications of the chromatin. Distinguish between

heterochromatin and euchromatin as to their structure and activity. 22. What occurs in histone acetylation? How does it affect gene expression? 23. What is DNA methylation? What role may it play in gene expression? 24. The inactive mammalian X chromosome is heavily methylated. What is the result of this methylation?

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Inducer

Regulatory gene

Repressor

Operator

Repressor protein

mRNA

RNA polymerase

Operon

Operon genes

25. What is genomic imprinting, and how is it maintained? Give an example discussed earlier in human genetics.

26. Explain what is meant by epigenetic inheritance, and give an example of epigenetic changes discussed

in the text or in class.

27. Use the sketch below to explain how enhancers and activators interact with transcription factors to affect gene expression. Label the following elements: TATA box, promoter, gene, enhancer, activators, transcription factors, transcription initiation complex, RNA polymerase II, and DNA. Then place your explanation to the right of the figure.

EXPLANATION

28. In prokaryotes, functionally related genes are usually clustered in a single operon. What has been

found to be the case in eukaryotes? 29. Operons have not been found in eukaryotic cells, and the genes coding for the enzymes of a particular

metabolic pathway are often scattered over different chromosomes. What is a plausible mechanism for the coordination of gene expression?

30. How can alternative RNA splicing result in different proteins derived from the same initial RNA

transcript?

31. Posttranscriptional control includes regulation of mRNA degradation. Explain how this affects translation.

32. How can proteins be activated, processed, and degraded? Give an example or describe each process. 33. An article in Scientific American about proteasomes was entitled “Little Chamber of Horrors.” Explain

how proteins are targeted for degradation, and give a specific example of when this might occur.

34. How do these “little chambers of horrors” function? Annotate the sketch below to describe their action. Then explain their role in regulation of gene expression.

Concept 18.3 Noncoding RNAs play multiple roles in controlling gene expression 35. It is now known that much of the RNA that is transcribed is not translated into protein. these RNAs are

called noncoding RNAs. Read carefully to discern a crucial role played by these RNAs. What is this role?

36. One of the noncoding RNAs that regulate gene expression is microRNA. On the sketch below, follow an RNA loop, called a “hairpin,” from its creation. Explain the two modes of action of microRNAs.

Be sure to label the location of hydrogen bonds and Dicer.

Concept 18.4 A program of differential gene expression leads to the different cell types in a multicellular organism This concept deals with the regulation of gene expression in development. Animal development is also discussed in Chapter 47. 37. What three processes lead to the transformation of a zygote into the organism? 38. Explain what occurs in cell differentiation and morphogenesis. 39. Differential gene expression results from different activators in different cells. How do different sets of

activators come to be present in two cells? Explain how each of these occurs:

a. distribution of cytoplasmic determinants

b. different inductive signals

40. What is meant by determination? Explain what this means within an embryonic cell. 41. What process ensures that all the tissues and organs of an organism are in their characteristic places?

Where do the molecular cues that control this process arise? 42. What is controlled by homeotic genes? Concept 18.5 Cancer results from genetic changes that affect cell cycle control 43. What mechanism is involved in the beginning of tumor growth? Discuss oncogenes and proto

oncogenes. 44. What are three mechanisms for converting a proto-oncogene to an oncogene?

45. There seem to be two categories of genes involved in cancer: oncogenes, which code for proteins to regulate cell growth, and should not be stuck “on,” much like the accelerator in a car; and tumor-suppressor genes, which work like the brakes on a car and must function! Let’s begin with a look at the ras gene, which codes for a G protein and is an oncogene. Label the sketch below to explain how a ras mutation leads to cancer.

46. Tumor-suppressor genes help prevent uncontrolled cell growth. One that is found mutated (and

therefore nonfunctional) in more than 50% of human cancer is p53. So important is the p53 gene that it is sometimes called the “guardian angel of the genome.” Describe the double whammy that results from mutation of p53.

47. Explain the multistep model of cancer development by using the specific example of colorectal cancer. The figure below may be labeled to help in your explanation.

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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