7 Microbial Genetics.

7 Microbial Genetics

The Structure and Replication of Genomes
Genetics Study of inheritance and inheritable traits as expressed in an organism's genetic material Genome The entire genetic complement of an organism Includes its genes and nucleotide sequences

The Structure of Prokaryotic Genomes Prokaryotic chromosomes Main portion of DNA, along with associated proteins and RNA Prokaryotic cells are haploid (single chromosome copy) Typical chromosome is circular molecule of DNA in nucleoid

Figure 7.2 Bacterial genome.
Nucleoid Bacterium Chromosome Plasmid

The Structure of Prokaryotic Genomes Plasmids Small molecules of DNA that replicate independently Not essential for normal metabolism, growth, or reproduction Can confer survival advantages Many types of plasmids Fertility factors Resistance factors Bacteriocin factors Virulence plasmids

The Structure of Eukaryotic Genomes Nuclear chromosomes Typically have more than one chromosome per cell Chromosomes are linear and sequestered within nucleus Eukaryotic cells are often diploid (two chromosome copies)

Figure 7.3 Eukaryotic nuclear chromosomal packaging.
10 nm Nucleosome Active (loosely packed) Histones Linker DNA Inactive (tightly packed) DNA 10 nm 30 nm 700 nm 1400 nm Nucleosomes Chromatin fiber Euchromatin and heterochromatin Highly condensed, duplicated chromosome of dividing nucleus

The Structure of Eukaryotic Genomes Extranuclear DNA of eukaryotes DNA molecules of mitochondria and chloroplasts Resemble chromosomes of prokaryotes Only code for about 5% of RNA and proteins Some fungi and protozoa carry plasmids

DNA Replication Key to replication is complementary structure of the two strands Replication is semiconservative New DNA composed of one original and one daughter strand Anabolic polymerization process that requires monomers and energy Triphosphate deoxyribonucleotides serve both functions

DNA Replication 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

Figure 7.6b-c DNA replication.
Primase 3 1 3 Replication fork 2 5 Leading strand P P Triphosphate nucleotide + RNA primer Synthesis of leading strand Replication fork Triphosphate nucleotide Okazaki fragment Lagging strand RNA primer 6 7 3 5 8 10 9 DNA ligase Primase DNA polymerase III DNA polymerase I Synthesis of lagging strand

DNA Replication Other characteristics of bacterial DNA replication Bidirectional Gyrases and topoisomerases remove supercoils in DNA DNA is methylated Control of genetic expression Initiation of DNA replication Protection against viral infection Repair of DNA

Figure 7.7 The bidirectionality of DNA replication in prokaryotes.
Origin Parental strand Replication forks Daughter strand Replication proceeds in both directions Termination of replication

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

Gene Function The Relationship Between Genotype and Phenotype Genotype
Set of genes in the genome Phenotype Physical features and functional traits of the organism

Gene Function The Transfer of Genetic Information Transcription
Information in DNA is copied as RNA Translation Polypeptides synthesized from RNA DNA transcribed to RNA RNA translated to form polypeptides

Figure 7.8 The central dogma of genetics.

Gene Function The Events in Transcription
Five types of RNA transcribed from DNA RNA primers mRNA rRNA tRNA Regulatory RNA Occur in nucleoid of prokaryotes Three steps Initiation Elongation Termination

Gene Function The Events in Transcription
Transcriptional differences in eukaryotes RNA transcription occurs in the nucleus Transcription also occurs in mitochondria and chloroplasts Three types of RNA polymerases Numerous transcription factors mRNA processed before translation Capping Polyadenylation Splicing

Gene Function Translation
Process in which ribosomes use genetic information of nucleotide sequences to synthesize polypeptides

Figure 7.12 The genetic code.

Gene Function Translation Participants in translation Messenger RNA
Transfer RNA Ribosomes and ribosomal RNA

Promoter Gene 1 Gene 2 Gene 3 Terminator 3 5 Template DNA strand
Figure A single prokaryotic mRNA can code for several polypeptides. Promoter Gene 1 Gene 2 Gene 3 Terminator 3 5 Template DNA strand Transcription Start codon AUG Start codon AUG Start codon AUG UAA UAG UAA 5 3 mRNA Ribosome binding site (RBS) Stop codon RBS Stop codon RBS Stop codon Untranslated mRNA Translation Polypeptide 1 Polypeptide 2 Polypeptide 3

Gene Function Translation Three stages of translation
Initiation Elongation Termination All stages require additional protein factors Initiation and elongation require energy (GTP)

mRNA Ribosomes Polypeptides mRNA Ribosomes Polypeptides Direction of
Figure In prokaryotes a polyribosome—one mRNA and many ribosomes and polypeptides. mRNA Ribosomes Polypeptides mRNA Ribosomes Polypeptides Direction of transcription

Gene Function Translation Stages of translation Termination
Release factors recognize stop codons Modify ribosome to activate ribozymes Ribosome dissociates into subunits Polypeptides released at termination may function alone or together

Translation: The Process
PLAY Translation: The Process

Gene Function Translation Translation differences in eukaryotes
Initiation occurs when ribosomal subunit binds to 5′ guanine cap First amino acid is methionine rather than f-methionine Ribosomes can synthesize polypeptides into the cavity of the rough endoplasmic reticulum

Gene Function Regulation of Genetic Expression
Most genes are expressed at all times Other genes transcribed and translated when cells need them Allows cell to conserve energy Regulation of polypeptide synthesis Can stop translation directly

Gene Function Regulation of Genetic Expression
Nature of prokaryotic operons An operon consists of a promoter and a series of genes Controlled by a regulatory element called an operator

Operons: Overview PLAY Operons: Overview

Gene Function Regulation of Genetic Expression Control of translation
Regulatory RNAs can regulate translation of polypeptides microRNAs Bind complementary mRNA and inhibit its translation RNA molecule complementary to a portion of mRNA, tRNA, or DNA that binds and renders the target inactive Riboswitch RNA molecule that changes shape to help regulate translation

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

Mutations of Genes Types of Mutations Point mutations
One base pair is affected Substitutions and frameshift mutations Frameshift mutations Nucleotide triplets after the mutation are displaced

Mutations of Genes Mutagens Radiation Ionizing radiation
Nonionizing radiation Chemical mutagens Nucleotide analogs Disrupt DNA and RNA replication Nucleotide-altering chemicals Result in base-pair substitutions and missense mutations Frameshift mutagens Result in nonsense mutations

Figure 7.27 The action of a frameshift mutagen.

Mutations of Genes 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

Figure 7.28 DNA repair mechanisms.
Visible light Thymine dimer T = T G A C A G A C T T A C T G A A T C T G A A T Light-activated repair enzyme Light repair Cut DNA polymerase I and ligase repair the gap T = T T = T Repair enzyme A C A G A C A C G C G A C T T A C C T G A A T G C T G A A T G C T G A A T G Dark repair Base excision repair enzymes remove incorrect nucleotide DNA polymerase I and ligase repair gap G G C T T A G C G T G G C T T A C G T G G C T T A T C G T C C G A A T A G C A C C G A A T A G C A C C G A A T A G C A Base-excision repair Mismatch repair enzyme removes incorrect segment Mutated DNA (incorrect nucleotide pair) DNA polymerase III correctly repairs the gap T T A C C T T A G C G T G C G T C C T A G C G T G G A T C G C A G G A T C G C A G G A T C G C A Mismatch repair

Mutations of Genes Identifying Mutants, Mutagens, and Carcinogens
Descendants of a cell that does not repair a mutation Wild types Cells normally found in nature Methods to recognize mutants Positive selection Negative (indirect) selection

Medium lacking histidine Colony of revertant (his+) Salmonella
Figure The Ames test. Experimental tube Control tube Liver extract Suspected mutagen Liver extract Culture of his– Salmonella Medium lacking histidine Incubation Colony of revertant (his+) Salmonella No growth

Genetic Recombination and Transfer
Exchange of nucleotide sequences often occurs between homologous sequences Recombinants Cells with DNA molecules that contain new nucleotide sequences Vertical gene transfer Organisms replicate their genomes and provide copies to descendants

Horizontal Gene Transfer Among Prokaryotes Horizontal gene transfer Donor cell contributes part of genome to recipient cell Three types Transformation Transduction Bacterial conjugation

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

Figure 7.33 Transformation of Streptococcus pneumoniae.
Observations of Streptococcus pneumoniae Griffith's experiment: In vitro transformation X X Living strain R X X X Heat-treated dead cells of strain S X X X + Heat-treated dead cells of strain S Live cells Injection DNA broken into pieces Capsule Mouse dies Injection DNA fragment from strain S Living strain R Heat-treated dead cells of strain S Some cells take up DNA from the environment and incorporate it into their chromosomes Injection X X X X Mouse dies Mouse lives Culture of Streptococcus from dead mouse Transformed cells acquire ability to synthesize capsules Strain R live cells (no capsule) Injection Living cells with capsule (strain S) Mouse lives

phages that incorporate phage DNA and, mistakenly, some host DNA.
Figure Transduction. Bacteriophage Host bacterial cell (donor cell) Bacterial chromosome 1 Phage injects its DNA. 2 Phage enzymes degrade host DNA. Phage DNA Phage with donor DNA (transducing phage) 3 Cell synthesizes new phages that incorporate phage DNA and, mistakenly, some host DNA. Transducing phage Recipient host cell 4 Transducing phage injects donor DNA. Transduced cell 5 Donor DNA is incorporated into recipient’s chromosome by recombination. Inserted DNA

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

Figure 7.37 Transposition. Plasmid with transposon Transposon DNA
Jumping transposons. Transposons move from one place to another on a DNA molecule. Replicating transposons. Transposons may replicate while moving, resulting in more transposons in the cell. Transposons can move onto plasmids. Transposons moving onto plasmids can be transferred to another cell.

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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