Chapter 16: The Molecular Basis of InheritanceConcept 16.1 DNA is the genetic material 1. What are the two chemical components of chromosomes? 2. Distinguish between the virulent and nonvirulent strains of Streptococcus pneumoniae studied by Frederick Griffith.

3. Summarize the experiment in which Griffith became aware that hereditary information could be transmitted between two organisms in an unusual manner.

4. Define transformation.5. What did Oswald Avery determine to be the transforming factor? ___________ Explain his experimental approach.

6. Sketch a T2 bacteriophage and label its head, tail sheath, tail fiber, and DNA.

7. How did Hershey and Chase “label” viral DNA and viral protein so that they could be distinguished? Explain why they chose each radioactive tag in light of the chemical composition of DNA and protein.

8. Describe the means by which Hershey and Chase established that only the DNA of a phage enters an E. coli cell.

9. What are Chargaff’s rules?

10. List the three components of a nucleotide.11. Who built the first model of DNA and shared the 1962 Nobel Prize for discovery of its structure? 12. What was the role of Rosalind Franklin in the discovery of the double helix? 13. Distinguish between the structure of pyrimidines and purines. Explain why adenine bonds only to thymine.

14. Given that the DNA of a certain fly species consists of 27.3% adenine and 22.5% guanine, use Chargaff’s rules to deduce the percentages of thymine and cytosine. ______________________

15. Name the five nitrogenous bases, and put a checkmark in the correct column for each base. Also indicate if the base is found in DNA (D), RNA (R), or both (B).

Nitrogenous base purine pyrimidine D, R, or B Pairs with…1.2.3.4.5.

16. Describe the structure of DNA relative to each of the following: a. components of the backbone ____________________ b. components of the “rungs”_____________________

17. Explain what is meant by 5' and 3' ends of the nucleotide.

18. What do we mean when we say the two strands of DNA are antiparallel?

Concept 16.2 Many proteins work together in DNA replication and repair 19. What is the semiconservative model of replication?

20. Use the figure to the right to explain how Meselson and Stahl confirmed the semiconservative mechanism of DNA replication.

21. Define the origins of replication. 22. Distinguish between the leading and the lagging strands during DNA replication.

23. What is the direction of synthesis of the new strand? ____--> _____24. What are Okazaki fragments? How are they welded together?

25. Make a sketch of a chromosome and label the telomeres.

26. Explain role of telomerase.

27. Why cancer cells immortal, but most body cells are have a limited life span?

Chapter 17: From Gene to Protein1. What is gene expression?

Concept 17.1 Genes specify proteins via transcription and translation 2. State the hypothesis formulated by George Beadle while studying eye color mutations in Drosophila.

3. What strategy did Beadle and Tatum adopt to test this hypothesis?

4. Which organism did Beadle and Tatum use in their research?

5. Cite two significant findings that resulted from the research of Beadle and Tatum. a.b.

Basic Principles of Transcription and Translation 6. From the first paragraph in this section, find three ways in which RNA differs from DNA.

a.b.c.

7. What are the monomers of DNA and RNA? Of proteins?8. Define each of these processes that are essential to the formation of a protein: transcription translation 9. Complete the following table to summarize each process.

Template Product synthesized Location in eukaryotic cell

TranscriptionTranslation

10. Write the central dogma of molecular genetics, as proclaimed by Francis Crick?

11. How many nucleotide bases are there? _______________ How many amino acids? __________ 12. How many nucleotides are required to code for these 20 amino acids? ___________________ 13. So, the language of DNA is a triplet code. How many unique triplets exist? ______________

14. 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? _____________________________________________

15. 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'

16. How many codons are there above? ________ Label one codon. 17. Of the 64 possible codons, how many code for amino acids? _________________________ 18. What event is coded for by UAA, UAG and UGA? ________________________________ 19. What is the start codon? ____________________________________________________ 20. Explain the concept of reading frame.

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 21. Name the enzyme that uses the DNA template strand to transcribe a new mRNA strand. ___________________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' direction.22. Which enzyme, DNA polymerase III or RNA polymerase, does not require a primer to begin synthesis?

23. What is the TATA box? How do you think it got this name?

24. What comprises a transcription initiation complex?

Concept 17.3 Eukaryotic cells modify RNA after transcription 25. 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?

26. What are three important functions of the 5' cap and poly-A tail?

27. Distinguish between introns and exons. Perhaps it will help to remember this: Exons are expressed.

28. Snurps band together in little snurp groups to form spliceosomes. How do spliceosomes work?

29. On the figure to the right, label the following: pre-mRNA, snRNPs, snRNA, protein, spliceosomes, intron, and other proteins.

30. What is a ribozyme?

31. What are three properties of RNA that allow it to function as an enzyme? (1) (2) (3)

32. 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 look33. What is an anticodon?

34. 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.

35. How many different aminoacyl-tRNA synthetases are there? ____________________________ 36. How does a prokaryotic ribosome differ from a eukaryotic ribosome? What is the medical significance of this

difference?37. Much like transcription, we can divide translation into three stages. List them.

a.b.c.

38. 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.

39. What is always the first amino acid in the new polypeptide? ________________________40. Use the figure below to summarize the events of elongation. Include these components: mRNA, A site, tRNA,

codon, anticodon, ribozyme, P site, and E site.

41. By what mechanism is termination accomplished? 42. Describe at least three types of post-translational modifications.

43. Use the following figure to explain how proteins are targeted for the ER.

Concept 17.5 Point mutations can affect protein structure and function 44. Define a mutation in terms of molecular genetics.

45. What are the two categories of mutagens?

Concept 17.6 Although gene expression differs among the domains of life, the concept of a gene is universal 46. Describe two important ways in which bacterial and eukaryotic gene expression differ.

47. 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.

Chapter 18: Regulation of Gene Expression

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. 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.

3. What is a promoter? 4. What is the operator? What does it do?

5. What is an operon?

6. List the three components of an operon, and explain the role of each one. a.b.c.

7. How does a repressor protein work?

8. What are regulatory genes?

9. Distinguish between inducible and repressible operons, and describe one example of each type.

10. Sketch the lac operon with the terms at right. Know the function of each structure.

11. 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.”)

12. What happens when a repressor is bound to the operator?

Concept 18.2 Eukaryotic gene expression can be regulated at any stage 13. Even though all cells of an organism have the same genes, there is differential gene expression. What does this

mean?

14. What is the common control point of gene expression for all organisms?

15. Gene expression can be regulated by modifications of the chromatin. Distinguish between heterochromatin and euchromatin as to their structure and activity.

16. Explain what is meant by epigenetic inheritance, and give an example of epigenetic changes discussed in the text or in class.

17. How can alternative RNA splicing result in different proteins derived from the same initial RNA transcript?

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

19. How can proteins be activated, processed, and degraded? Give an example or describe each process. a. Activated:b. Processed:c. degraded:

20. 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.

Concept 18.3 Noncoding RNAs play multiple roles in controlling gene expression 21. It is now known that much of the RNA that is transcribed is not translated into protein. These RNAs are called

noncoding RNAs. What is the role of noncoding RNAs?

Concept 18.4 A program of differential gene expression leads to the different cell types in a multicellular organism 22. What three processes lead to the transformation of a zygote into the organism?

23. Explain what occurs in:a. cell differentiation:

b. Morphogenesis:

24. 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

25. What is meant by determination? Explain what this means within an embryonic cell.

26. What process ensures that all the tissues and organs of an organism are in their characteristic places?

a. Where do the molecular cues that control this process arise?

27. What is controlled by homeotic genes?

Chapter 19: Viruses

Concept 19.1 A virus consists of a nucleic acid surrounded by a protein coat 1. What are the four forms of viral genomes?

2. What is a capsid?3. What are capsomeres? 4. What different shapes may capsids have? 5. 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 to the right, 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. Compare the host range for the rabies virus to that of the human cold virus.

11. What components of the host cell does a virus use to reproduce itself?

12. How does a DNA virus reproduce its genome?

13. How do most RNA viruses replicate their genome?

14. What are bacteriophages?

15. Distinguish between virulent and temperate phages.

16. What portion of a phage enters the host cell? How does it do this?

17. What are restriction enzymes? What is their role in bacteria?

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

19. What is a prophage?

20. 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?

28. Describe the lytic and lysogenic modes of bacteriophage reproduction.

29. What is a retrovirus? How do retroviruses, such as HIV, replicate their genome?

30. Here is a sketch of HIV. Label these parts: envelope, reverse transcriptase, RNA, and capsid.

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

32. Fill in the following table:

Description of the mobile genetic element

PlasmidTransposons

Chapter 20: Biotechnology

Concept 20.1 DNA cloning yields multiple copies of a gene or other DNA segment 1. Plasmids are important in biotechnology. Give a full and complete definition of plasmid.

2. The production of multiple copies of a single gene is called ____________________________.3. Using Figure 20.2, label and explain the four steps in this preview of gene cloning.

4. Read the description of restriction enzymes on page 398 carefully. Then draw and explain each step of Figure 20.3. When you finish, you should have recreated Figure 20.3

5. What is a cloning vector?

6. Explain why the plasmid is engineered with ampR and lacZ.

7. After transformation has occurred, why are some colonies blue?

8. Why are some colonies white? Why is this important?

9. The polymerase chain reaction (PCR) is a Nobel Prize–winning idea that is used by scientists to amplify DNA, particularly when the quantity of DNA is very small or contaminated. Explain the three initial steps that occur in cycle 1 of PCR.

10. How many molecules will be produced by four PCR cycles?

Concept 20.2 DNA technology allows us to study the sequence, expression, and function of a gene 11. ____________________ is a technique used to separate nucleic acids or proteins that differ in size or electrical

charge.12. Why is the DNA sample to be separated by gel electrophoresis always loaded at the cathode or negative end of

the power source? 13. Explain why shorter DNA molecules travel farther down the gel than larger molecules.

Chapter 21: Genomes and Their EvolutionConcept 21.5 Duplication, rearrangement, and mutation of DNA contribute to genome evolution

14. What is the evolutionary significance of the relationship between the genes on human chromosome 16 and those same blocks of genes on mouse chromosomes 7, 8, 16, and 17?

15. A good summary of several processes involved in genomic evolution can be found in the globin gene families. Label and explain these processes as described in Figure 21.13.

16. Using the concept of a protein domain in your answer, explain why exon shuffling could lead to a novel protein.

17. What is the purpose of a Southern blot?

18. What two techniques discussed earlier in this chapter are used in performing a Southern blot?

21. In working toward the general idea of how DNA sequencing was mechanized, look at Figure 20.12 to answer the following general questions about the dideoxy chain termination method for sequencing DNA.

a. Why does a dideoxyribonucleotide terminate a growing DNA strand? (You may need to refer to Figure 16.14, as suggested in the text, to answer this question).

b. Why are the four nucleotides in DNA each labeled with a different color of fluorescent tag?

19. Use unlabeled Figure 20.15 to explain the four steps of DNA microarray assays.

22. Explain how microarrays are used in understanding patterns of gene expression in normal and cancerous tissue.