1. Chapter 7
Microbial Genetics

2. The Structure and Replication of Genomes
Genetics
Study of inheritance and inheritable traits as expressed in an organism’s genetic material
Genes: specific sequences of nucleotides that code for polypeptides or RNA molecules.
Genome is the sum of all the genetic material in a cell or virus.
Includes its genes and nucleotide sequences
Prokaryotic and eukaryotic cells use DNA as their genetic material;
Some viruses use DNA, and other viruses use RNA.
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3. The structure of nucleic acids-overview
Nucleic acids: Polymers of nucleotides
Nucleotides are composed of:
a phosphate
a pentose sugar (ribose or deoxyribose)
one of five nitrogenous bases (guanine, cytosine, thymine, adenine, or uracil).

4. DNA
The two strands of DNA are held together by hydrogen bonds between complementary bases of nucleic acids called base pairs (bp).
Adenine bonds with thymine, and guanine bonds with cytosine.
One end of a DNA strand is called the 5' end
The other end of the strand is called the 3' end
The two strands are oriented in opposite directions to each other:
One strand runs in a 3' to 5' direction, whereas the other runs in a 5' to 3' direction.
The lengths of DNA molecules are expressed in base pairs.
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5. The Structure of Prokaryotic Genomes
Both bacterial and archaeal genomes consist of one or two chromosomes,
Prokaryotic chromosomes are circular molecules of DNA associated with protein and RNA molecules,
Localized in the nucleoid region
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6. May contain one or more extrachromosomal DNA molecules called plasmids,
Plasmids contain genes that functions such as: regulate nonessential life
Fertility factors – bacterial conjugation
Resistance factors antimicrobials, heavy metals,
Bacteriocin factors - destruction of competing bacteria
Virulence plasmids - pathogenicity.
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7. The Structure of Eukaryotic Genomes
Nuclear chromosomes
Have more than one chromosome per cell
Chromosomes are linear and sequestered within nucleus
Eukaryotic cells are often diploid (two chromosome copies)
Eukaryotic chromosomes contain proteins called histones, arranged as nucleosomes (beads of DNA) that interact with other proteins to form chromatin fibers
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8. The Structure of Eukaryotic Genomes contd.
Extrachromosomal DNA in mitochondria, chloroplasts, and plasmids.
Resemble chromosomes of prokaryotes
Only code for about 5% of RNA and proteins
Some fungi and protozoa carry plasmids
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9. DNA Replication
The concept: A cell separates the two original strands and uses each strand as a template for the synthesis of a new complementary strand. The process is:
semiconservative because each daughter DNA molecule is composed of one original strand and one new strand.
Anabolic polymerization process that requires monomers and energy
Triphosphate deoxyribonucleotides serve both functions
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10. Semiconservative model of DNA replication
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11. The Structure and Replication of Genomes
Initial processes in replication
Bacterial DNA replication begins at the origin
DNA polymerase replicates DNA only 5 to 3
Because strands are antiparallel, new strands are synthesized differently
Leading strand synthesized continuously
Lagging strand synthesized discontinuously
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12. The Structure and Replication of Genomes
Other characteristics of bacterial DNA replication
Bidirectional
Topoisomerases remove supercoils in DNA molecule
DNA is methylated
Control of genetic expression
Initiation of DNA replication
Protection against viral infection
Repair of DNA
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13. The Structure and Replication of Genomes
DNA Replication
Replication of eukaryotic DNA
Similar to bacterial replication
Some differences
Uses four DNA polymerases
Thousands of replication origins
Shorter Okazaki fragments
Plant and animal cells methylate only cytosine bases
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14. The Relationship Between Genotype and Phenotype:
The genotype of an organism is the actual set of genes in its genome, whereas the phenotype is the physical and functional traits expressed by those genes, such as the presence of flagella.
Genotype determines phenotype; however, not all genes are active at all times
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15. The Central Dogma The Transfer of Genetic Information Transcription
Information in DNA is copied as RNA
Translation
Polypeptides synthesized from RNA
Central dogma of genetics
DNA transcribed to RNA
RNA translated to form polypeptides
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16. The Events in Transcription
Synthesis of RNA from the genetic code. Polymerized by RNA polymerase
Begins at the promoter region of DNA and ends at the terminator region.
Other proteins may assist in termination, or it may depend solely on the nucleotide sequence of the transcribed RNA.
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17. Cells transcribe four main types of RNA from DNA:
RNA primer molecules for DNA polymerase to use during DNA replication.
Messenger RNA (mRNA) molecules, which carry genetic information from chromosomes to ribosomes
Ribosomal RNA (rRNA) molecules, which combine with ribosomal polypeptides to form ribosomes, the organelles that synthesize polypeptides
Transfer RNA (tRNA) molecules, which deliver amino acids to the ribosomes
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18. Three steps
Initiation
Elongation
Termination
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19. Prokaryotic Vs Eukaryotic Transcription
Prokaryotic Transcription
Eukaryotic Transcription
Prokaryotic transcription occurs in the cytosol.
Prokaryotes use only type of RNA polymerase
mRNA is not processed before translation
Okazaki fragments are larger in prokaryotes
Eukaryotic cells transcribe RNA in the nucleus
Eukaryotes have three types of nuclear RNA polymerase and multiple transcription factors
Eukaryotic cells process mRNA before translation. RNA processing involves capping, polyadenylation, and splicing.
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20. mRNA Processing in Eukaryotes
Capping,
Polyadenylation, and
Splicing
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21. Translation
Process where ribosomes use genetic information of nucleotide sequences to synthesize polypeptides
Understanding how four DNA nucleotides can specify the 20 different amino acids commonly found in proteins requires an understanding of the genetic code.
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22. The Genetic Code
The genetic code is the complete set of triplets of mRNA nucleotides called codons that code for specific amino acids.
These bind to complementary anticodons on tRNA.
The code is redundant; that is, more than one codon is associated with all the amino acids except methionine and tryptophan.
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23. The genetic code
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24. Translation Participants in translation Messenger RNA Transfer RNA
Ribosomes and ribosomal RNA:
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25. Prokaryotic mRNA
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26. tRNA
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27. rRNA
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28. The A site accommodates a tRNA delivering an amino acid.
The smaller subunit of a ribosome is shaped to accommodate three codons at one time. Each ribosome also has three binding sites that are named for their function:
The A site accommodates a tRNA delivering an amino acid.
The P site holds a tRNA and the growing polypeptide.
Discharged tRNAs exit from the E site.
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29. Three Stages of Translation
Prokaryotic translation proceeds in three stages:
Initiation – Formation of an initiation complex.
Elongation - tRNAs sequentially deliver amino acids as directed by the codons of mRNA. Ribosomal RNA in the large ribosomal subunit catalyzes peptide bond formation between the amino acid at the A site and the growing polypeptide at the P site.
Termination - does not involve tRNA; instead, proteins called release factors halt elongation. The ribosome then dissociates into its subunits.
Initiation and elongation require energy (GTP)
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30. The initiation of translation in prokaryotes
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31. The elongation stage of translation-overview

32. A polyribosome in a prokaryotic cell- overview
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33. Gene Function Translation differences in eukaryotes Translation
Initiation occurs when ribosomal subunit binds to 5 guanine cap
First amino acid is methionine rather than f-methionine
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34. Regulation of Genetic Expression
In bacteria, about 75% of genes are expressed at all times;
Other genes are regulated so that the polypeptides they encode are synthesized only when a cell has need of them.
Regulation of protein synthesis
Typically halts transcription
Can stop translation directly
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35. Halting Transcription - Operons
An operon consists of a promoter, an adjacent regulatory element called an operator, and a series of genes all either repressed or induced by one regulatory gene located elsewhere.
Inducible operons such as the lac operon are not usually transcribed and must be activated by inducers.
Repressible operons such as the trp operon are transcribed continually until deactivated by repressors
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36. Lactose Operon – An Inducible Operon
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37. Tryptophan Operon – A repressible Operon
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38. Control of translation
Genetic expression can be regulated at level of translation
Riboswitch
mRNA molecule that blocks translation of the polypeptide it encodes
Short interference RNA (siRNA)
RNA molecule complementary to a portion of mRNA, tRNA, or a gene that binds and renders the target inactive
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39. Mutations of Genes Mutation
Change in the nucleotide base sequence of a genome
Rare event
Almost always deleterious
Rarely leads to a protein that improves ability of organism to survive
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40. Mutations of Genes - Types of Mutations
Point mutations, in which just one or a few nucleotide base pairs are affected.
The most common type of mutation.
Point mutations is caused by substitutions in which a single nucleotide is substituted for another.
Outcome:
Silent Mutation
Missense Mutation
Nonsense Mutation
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41. Frameshift mutations nucleotide triplets subsequent to an insertion or deletion are displaced, creating new sequences of codons that result in vastly altered polypeptide sequences.
Caused by:
insertions and
deletions of nucleotides
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42. Mutagens Physical or chemical agents that cause mutations
Mutations can be spontaneous, or result from recombination.
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43. Radiation
Ionizing radiation - Radiation in the form of X rays and gamma rays can cause mutations.
Nonionizing radiation - ultraviolet light causes adjacent pyrimidine bases to bond to one another to form pyrimidine dimers.
The presence of dimers prevents hydrogen bonding with the nucleotides in the complementary strand, distorts the sugar-phosphate backbone, and prevents proper replication and transcription.
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44. Chemical mutagens
Nucleotide analogs - compounds that are structurally similar to normal nucleotides but, when incorporated into DNA, cause mutations
Disrupt DNA and RNA replication
Nucleotide-altering chemicals - Aflatoxins are nucleotide-altering chemicals that result in missense mutations and cancer
Result in base-pair substitutions and missense mutations
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45. Frameshift Mutation Frameshift mutagens Result in nonsense mutations

46. Frequency of Mutation Mutations are rare events
Otherwise organisms could not effectively reproduce
Mutagens increase the mutation rate by a factor of 10 to 1000 times
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47. DNA Repair Cells have numerous methods of repairing damaged DNA.
Light repair: Cells use DNA photolyase to break the bonds between adjoining pyrimidine nucleotides.
Dark repair: Enzymes repair pyrimidine dimers by cutting damaged DNA from the molecule, creating a gap that is repaired by DNA polymerase I and DNA ligase.
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48. Base-excision repair: an enzyme system excises the erroneous base and DNA polymerase I fills in the gap.
Mismatch repair: enzymes scan newly synthesized unmethylated DNA looking for mismatched bases, which they remove and replace. Once a new DNA strand is methylated, mismatch repair enzymes cannot correct any errors that remain.
When damage is so extensive that these mechanisms are overwhelmed, bacterial cells resort to an SOS response involving the production of a novel DNA polymerase capable of copying less-than-perfect DNA.
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49. Identifying Mutants, Mutagens, and Carcinogens
If a cell does not repair a mutation, it and its descendants are called mutants.
Cells normally found in nature are wild-type cells.
Methods of recognizing mutants among their wild-type neighbors include:
Positive selection, which involves selecting a mutant by eliminating wild-type phenotypes
Negative selection (also called indirect selection), a process in which a researcher attempts to culture auxotrophs which have non-wild type nutritional requirements
The Ames test, which is used to identify potential carcinogens (cancer-causing agents)
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50. Genetic Recombination and Transfer
Exchange of nucleotide sequences often mediated by homologous sequences
Recombinants
Cells with DNA molecules that contain new nucleotide sequences
Vertical gene transfer
Organisms replicate their genomes and provide copies to descendants
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51. Positive Selection
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52. Negative Selection
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53. Ames Test
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54. Genetic Recombination and Transfer
Horizontal Gene Transfer Among Prokaryotes
Horizontal gene transfer
Donor cell contributes part of genome to recipient cell
Three types
Transformation
Transduction
Bacterial conjugation
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55. Genetic Recombination and Transfer
Horizontal Gene Transfer Among Prokaryotes
Transformation
One of conclusive pieces of proof that DNA is genetic material
Cells that take up DNA are competent
Results from alterations in cell wall and cytoplasmic membrane that allow DNA to enter cell
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56. Transformation in Streptococcus pneumoniae - overview
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57. Genetic Recombination and Transfer
Horizontal Gene Transfer Among Prokaryotes
Transduction
Generalized transduction
Transducing phage carries random DNA segment from donor to recipient
Specialized transduction
Only certain donor DNA sequences are transferred
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58. Conjugation
In conjugation, a bacterium containing an F (fertility) plasmid (or F factor) forms a conjugation pilus that attaches to an F– recipient bacterium.
Plasmid genes are transferred to the recipient, which becomes F+ as a result.
Hfr (high frequency of recombination) cells result when an F plasmid integrates into a prokaryotic chromosome.
Hfr cells form conjugation pili and transfer cellular genes more frequently than normal F+ cells.
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59. Genetic Recombination and Transfer
Transposons and Transposition
Transposons
Segments of DNA that move from one location to another in the same or different molecule
Result is a kind of frameshift insertion (transpositions)
Transposons all contain palindromic sequences at each end
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60. Genetic Recombination and Transfer
Transposons and Transposition
Simplest transposons
Insertion sequences
Have no more than two inverted repeats and a gene for transposase
Complex transposons
Contain one or more genes not connected with transposition
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