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Independent Study Guide - Bacterial Genetics (Chapter 8) I. Genetic change in bacteria (p. 186-187)

a. Two general mechanisms of genetic change in bacteria (figure 8.1): i. Mutation – alteration in existing DNA sequence ii. DNA transfer (horizontal gene transfer) – acquisition of DNA from another source

b. Why study bacterial genetics? i. Model system

c. Spontaneous mutations occur in all cells at a very low frequency (≈one per billion nucleotides)

i. Bacteria quickly grow to high concentrations (109/ml) in culture, making it possible to study rare occurrences

d. Terms i. Phenotype – the observable characteristics of an organism ii. Genotype – the sequence of nucleotides in the DNA of an organism iii. Wild type – characteristics similar to the organism as it occurs in nature iv. Prototroph – a strain that grows on minimal medium (glucose-salts) v. Auxotroph – a strain that lacks the ability to synthesize a nutrient; as a

consequence, that compound must be supplied in the growth medium

II. Spontaneous Mutation (section 8.2) a. Mistakes made during replication

i. Base substitution (figure 8.3) 1. Silent 2. Missense 3. Nonsense

ii. Removal or addition of nucleotides 1. Frameshift mutation (figure 8.4)

a. Generates an entirely different set of triplets b. Often, a stop codon is generated

III. Transposable elements (transposons) (p. 189; p. 207)

a. Segments of DNA that can "jump or hop" from one site to another i. Insertional inactivation of the gene in which the transposon lands ii. A transposon can insert elsewhere in the same DNA molecule, or into an entirely

different DNA molecule iii. Some transposons simply “jump or hop”; others replicate then jump

IV. Induced Mutation (section 8.3)

a. Chemical mutagens i. Chemically modify purines and pyrimidines

1. Alter the base-pairing properties 2. Example: nitrous acid strips the amino groups from nucleotides

ii. Base analogs 1. Resemble nucleotide bases; erroneously incorporated into DNA 2. Consequence of incorporation: analog base-pairs with a different

nucleotide iii. Intercalating agents

1. Insert between base-pairs, pushing nucleotides apart; extra nucleotide may then be erroneously added during replication

b. Biological mutagens i. Transposons

c. Physical mutagens i. Ultraviolet irradiation- causes formation of covalent bonds (thymine dimers)

between adjacent thymine bases ii. X rays -causes double- and single-stranded breaks in DNA

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V. DNA Repair (section 8.4) a. Repairs of errors in base incorporation

i. DNA polymerase 1. Proofreading

ii. Mismatch repair 1. removal/replacement (figure 8.10)

b. Repairs of thymine dimers i. Light repair (photoreactivation) (figure 8.11a) ii. Dark repair/Excision repair (figure 8.11b)

c. Repair of modified bases i. Glycosylase removes oxidized guanine

d. SOS system i. Induction of SOS system

1. New DNA polymerase

VI. Mutant Selection (section 8.5) a. Direct selection (figure 8.13) b. Indirect selection (replica plating) (figure 8.14)

i. Obtain auxotrophs

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c. Application of direct selection i. The Ames Test - used to narrow down list of possible carcinogens (figure 8.16)

VII. Review questions

1. Considering that mutations are rare events, why are they significant? 2. How is a missense mutation different from a nonsense mutation? 3. Which type of single base-pair change would change the amino acid sequence of the encoded

protein most significantly? 4. Can the genotype change without a change in phenotype? 5. Can the phenotype change without a change in genotype? 6. Describe the difference between a prototroph and an auxotroph. 7. What is a transposon, and how does it cause mutations? 8. How can a base substitution cause a mutation? 9. What types of mutations can base substitutions cause? 10. Explain how intercalating agents cause mutations. 11. How does UV light cause mutations? 12. How do X-rays cause mutations? 13. How are thymine dimers repaired? 14. What would the consequence be to a cell if it didn't have an SOS system? 15. What is the purpose of adding liver extract to the substance being examined in the Ames test? 16. Why is replica plating required to isolate an auxotroph from a prototrophic strain, but not the

reverse? 17. How is mutation different from horizontal gene transfer? 18. Why would it be more important for DNA polymerase, rather than RNA polymerase, to have

"proofreading" ability?