Microbial Genetics Notes

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Learning Objectives	Check Your Understanding
8-1    Define genetics, genome, chromosome, gene, genetic code, genotype, phenotype, and genomics.	Give a clinical application of genomics.
8-2    Describe how DNA serves as genetic information.	Why is the base pairing in DNA important?
8-3    Describe the process of DNA replication.	Describe DNA replication, including the functions of DNA gyrase, DNA ligase, and DNA polymerase.
8-4    Describe protein synthesis, including transcription, RNA processing, and translation.	What is the role of the promoter, terminator, and mRNA in transcription?
8-5    Compare protein synthesis in prokaryotes and eukaryotes.	How does mRNA production in eukaryotes differ from the process in prokaryotes?
8-6    Define operon.	Use the following metabolic pathway to answer the questions that follow it.              enzyme a            enzyme b Substrate A ® Intermediate B ® End-product C a. If enzyme a is inducible and is not being synthesized at present, a (1) _____ protein must be bound tightly to the (2) _____ site. When the inducer is present, it will bind to the (3) _____ so that (4) _____ can occur. b. If enzyme a is repressible, end-product C, called a (1) _____, causes the (2) _____ to bind to the (3) _____. What causes derepression?
8-7    Explain pre-transcriptional regulation of gene expression in bacteria.	What is the role of cAMP in regulating gene expression?
8-8    Explain post-transcriptional regulation of gene expression.	How does miRNA stop protein synthesis?
8-9    Classify mutations by type.	How can a mutation be beneficial?
8-10  Describe two ways mutations can be repaired.	How can mutations be repaired?
8-11  Describe the effect of mutagens on the mutation rate.	How do mutagens affect the mutation rate?
8-12  Outline the methods of direct and indirect selection of mutants.	How would you isolate an antibiotic-resistant bacterium? An antibiotic-sensitive bacterium?
8-13  Identify the purpose of and outline the procedure for the Ames test.	What is the principle behind the Ames test?
8-14  Differentiate horizontal and vertical gene transfer.	Differentiate horizontal and vertical gene transfer.
8-15  Compare the mechanisms of genetic recombination in bacteria.	Compare conjugation between the following pairs: F + ´ F –, Hfr ´ F –.
8-16  Describe the functions of plasmids and transposons.	What types of genes do plasmids carry?
8-17  Discuss how genetic mutation and recombination provide material for natural selection to act upon.	Natural selection means that the environment favors survival of some genotypes. From where does diversity in genotypes come?

New in This Edition

• A new Big Picture feature, addressing genetics, has been added.

    Key Concepts:

1. DNA expression leads to cell function via the production of proteins.
2. DNA expression can be controlled by operons.
3. Mutations alter DNA sequences.
4. DNA mutations can change bacterial function.

• The central dogma of genetics is described.
• Mutation and gene transfers are now included in a new section.

Chapter Summary

Structure and Function of the Genetic Material (pp. 204–214)

ASM 4.2: Although the central dogma is universal in all cells, the processes of replication, transcription, and translation differ in Bacteria, Archaea, and Eukaryotes.

1. Genetics is the study of what genes are, how they carry information, how their information is expressed, and how they are replicated and passed to subsequent generations or other organisms.
2. DNA in cells exists as a double-stranded helix; the two strands are held together by hydrogen bonds between specific nitrogenous base pairs: AT and CG.
3. A gene is a segment of DNA, a sequence of nucleotides, that encodes a functional product, usually a protein.
4. The DNA in a cell is duplicated before the cell divides, so each offspring cell receives the same genetic information.

Genotype and Phenotype (p. 204)

5. Genotype is the genetic composition of an organism, its entire complement of DNA.
6. Phenotype is the expression of the genes: the proteins of the cell and the properties they confer on the organism.

DNA and Chromosomes (pp. 204–205)

7. The DNA in a chromosome exists as one long double helix associated with various proteins that regulate genetic activity.
8. Genomics is the molecular characterization of genomes.

  

The Flow of Genetic Information (p. 205)

9. Following cell division, each offspring cell receives a chromosome that is virtually identical to the parent’s.
10. Information contained in the DNA is transcribed into RNA and translated into proteins.

DNA Replication (pp. 205–209)

11. During DNA replication, the two strands of the double helix separate at the replication fork, and each strand is used as a template by DNA polymerases to synthesize two new strands of DNA according to the rules of nitrogenous base pairing.
12. The result of DNA replication is two new strands of DNA, each having a base sequence complementary to one of the original strands.
13. Because each double-stranded DNA molecule contains one original and one new strand, the replication process is called semiconservative.
14. DNA is synthesized in one direction designated 5¢ ® 3¢. At the replication fork, the leading strand is synthesized continuously and the lagging strand discontinuously.
15. DNA polymerase proofreads new molecules of DNA and removes mismatched bases before continuing DNA synthesis.

     

RNA and Protein Synthesis (pp. 209–214)

16. During transcription, the enzyme RNA polymerase synthesizes a strand of RNA from one strand of double-stranded DNA, which serves as a template.
17. RNA is synthesized from nucleotides containing the bases A, C, G, and U, which pair with the bases of the DNA strand being transcribed.
18. RNA polymerase binds the promoter; transcription begins at AUG; the region of DNA that is the end point of transcription is the terminator; RNA is synthesized in the 5¢ ® 3¢ direction.
19. Translation is the process in which the information in the nucleotide base sequence of mRNA is used to dictate the amino acid sequence of a protein.
20. The mRNA associates with ribosomes, which consist of rRNA and protein.
21. Three-base segments of mRNA that specify amino acids are called codons.
22. The genetic code refers to the relationship among the nucleotide base sequence of DNA, the corresponding codons of mRNA, and the amino acids for which the codons code.
23. Specific amino acids are attached to molecules of tRNA. Another portion of the tRNA has a base triplet called an anticodon.
24. The base pairing of codon and anticodon at the ribosome results in specific amino acids being brought to the site of protein synthesis.
25. The ribosome moves along the mRNA strand as amino acids are joined to form a growing polypeptide; mRNA is read in the 5¢ ® 3¢ direction.
26. Translation ends when the ribosome reaches a stop codon on the mRNA.

  

The Regulation of Bacterial Gene Expression (pp. 214–218)

ASM 4.3: The regulation of gene expression is influenced by external and internal molecular cues and/or signals.

1. Regulating protein synthesis at the gene level is energy-efficient because proteins are synthesized only as they are needed.
2. Constitutive enzymes produce products at a fixed rate. Examples are genes for the enzymes in glycolysis.

Pre-transcriptional Control (pp. 214–217)

3. When cells are exposed to a particular end-product, the synthesis of enzymes related to that product is repressed.
4. In the presence of certain chemicals (inducers), cells synthesize more enzymes. This process is called induction.
5. In bacteria, a group of coordinately regulated structural genes with related metabolic functions, plus the promoter and operator sites that control their transcription, are called an operon.
6. In the operon model for an inducible system, a regulatory gene codes for the repressor protein.
7. When the inducer is absent, the repressor binds to the operator, and no mRNA is synthesized.
8. When the inducer is present, it binds to the repressor so that it cannot bind to the operator; thus, mRNA is made, and enzyme synthesis is induced.
9. In repressible systems, the repressor requires a corepressor in order to bind to the operator site; thus, the corepressor controls enzyme synthesis.
10. Transcription of structural genes for catabolic enzymes (such as β-galactosidase) is induced by the absence of glucose. Cyclic AMP and CRP must bind to a promoter in the presence of an alternative carbohydrate.
11. Methylated nucleotides are not transcribed in epigenetic control.

    

Post-transcriptional Control (pp. 217–218)

12. MicroRNAs combine with mRNA; the resulting double-stranded RNA is destroyed.

Changes in Genetic Material (pp. 218–225)

ASM 4.1: Genetic variations can impact microbial functions (e.g., in biofilm formation, pathogenicity, and drug resistance).

ASM 1.2: Mutations and horizontal gene transfer, and the immense variety of microenvironments, have selected for a huge diversity of microorganisms.

1. Mutations and horizontal gene transfer can change a bacterium’s genotype.

Mutation (p. 219)

2. A mutation is a change in the nitrogenous base sequence of DNA; that change causes a change in the product coded for by the mutated gene.
3. Many mutations are neutral, some are disadvantageous, and others are beneficial.

Types of Mutations (pp. 219–220)

4. A base substitution occurs when one base pair in DNA is replaced with a different base pair.
5. Alterations in DNA can result in missense mutations (which cause amino acid substitutions) or nonsense mutations (which create stop codons).
6. In a frameshift mutation, one or a few base pairs are deleted or added to DNA.
7. Spontaneous mutations occur without the presence of any mutagen.

   

Mutagens (pp. 220–223)

8. Mutagens are agents in the environment that cause permanent changes in DNA.
9. Chemical mutagens include base-pair mutagens, nucleoside analogs, and frameshift mutagens.
10. Ionizing radiation causes the formation of ions and free radicals that react with DNA; base substitutions or breakage of the sugarphosphate backbone results.
11. Ultraviolet (UV) radiation is nonionizing; it causes bonding between adjacent thymines.

  

The Frequency of Mutation (p. 223)

12. Mutation rate is the probability that a gene will mutate when a cell divides; the rate is expressed as 10 to a negative power.
13. Mutations usually occur randomly along a chromosome.
14. A low rate of spontaneous mutations is beneficial in providing the genetic diversity needed for evolution.

Identifying Mutants (pp. 223)

15. Mutants can be detected by selecting or testing for an altered phenotype.
16. Positive selection involves the selection of mutant cells and the rejection of nonmutated cells.
17. Replica plating is used for negative selection—to detect, for example, auxotrophs that have nutritional requirements not possessed by the parent (nonmutated) cell.

Identifying Chemical Carcinogens (pp. 223–225)

18. The Ames test is a relatively inexpensive and rapid test for identifying possible chemical carcinogens.
19. The test assumes that a mutant cell can revert to a normal cell in the presence of a mutagen and that many mutagens are carcinogens.

Genetic Transfer and Recombination (pp. 225–233)

ASM 1.4: The traditional concept of species is not readily applicable to microbes due to asexual reproduction and the frequent occurrence of horizontal gene transfer.

1. Genetic recombination, the rearrangement of genes from separate groups of genes, usually involves DNA from different organisms; it contributes to genetic diversity.
2. In crossing over, genes from two chromosomes are recombined into one chromosome containing some genes from each original chromosome.
3. Vertical gene transfer occurs during reproduction when genes are passed from an organism to its offspring.
4. Horizontal gene transfer in bacteria involves a portion of the cell’s DNA being transferred from donor to recipient.
5. When some of the donor’s DNA has been integrated into the recipient’s DNA, the resultant cell is called a recombinant.

   

Transformation in Bacteria (pp. 226–228)

6. During this process, genes are transferred from one bacterium to another as “naked” DNA in solution.

Conjugation in Bacteria (pp. 228–229)

7. This process requires contact between living cells.
8. One type of genetic donor cell is an F ⁺; recipient cells are F ^–. F cells contain plasmids called F factors; these are transferred to the F ^– cells during conjugation.

     

Transduction in Bacteria (pp. 229–230)

9. In this process, DNA is passed from one bacterium to another in a bacteriophage and is then incorporated into the recipient’s DNA.
10. In generalized transduction, any bacterial genes can be transferred.

Plasmids and Transposons (pp. 230–233)

11. Plasmids are self-replicating circular molecules of DNA carrying genes that are not usually essential for the cell’s survival.
12. There are several types of plasmids, including conjugative plasmids, dissimilation plasmids, plasmids carrying genes for toxins or bacteriocins, and resistance factors.
13. Transposons are small segments of DNA that can move from one region to another region of the same chromosome or to a different chromosome or a plasmid.
14. Complex transposons can carry any type of gene, including antibiotic-resistance genes, and are thus a natural mechanism for moving genes from one chromosome to another.

Genes and Evolution (p. 233)

ASM 1.2: Mutations and horizontal gene transfer, and the immense variety of microenvironments have selected for a huge diversity of microorganisms.

1. Diversity is the precondition for evolution.
2. Genetic mutation and recombination provide a diversity of organisms, and the process of natural selection allows the growth of those best adapted to a given environment.

 

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