Chapter 19 Microbial Models: The Genetics of Viruses and Bacteria.
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Transcript of Chapter 19 Microbial Models: The Genetics of Viruses and Bacteria.
![Page 1: Chapter 19 Microbial Models: The Genetics of Viruses and Bacteria.](https://reader036.fdocuments.in/reader036/viewer/2022062517/56649e875503460f94b8b655/html5/thumbnails/1.jpg)
• Chapter 19• Microbial Models: The
Genetics of Viruses and Bacteria
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Viral structure
• Virus: “poison” (Latin); infectious particles consisting of a nucleic acid in a protein coat
• Capsid; (viral envelopes); DNA or RNA
• Bacteriophages (phages)
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Viral reproduction: Lytic Cycle• Host range: infection of a
limited range of host cells (receptor molecules on the surface of cells)
• The lytic cycle: 1- attachment 2- injection 3- hydrolyzation 4- assembly 5- release
• Results in death of host cell• Virulent virus (phage
reproduction only by the lytic cycle)
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Viral reproduction: Lysogenic Cycle
• Genome replicated w/o destroying the host cell
• Genetic material of virus becomes incorporated into the host cell DNA (prophage DNA)
• Temperate virus (phages capable of using the lytic and lysogenic cycles)
• May give rise to lytic cycle
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RNA viruses
• Retroviruses: transcribe DNA from an RNA template (RNA--->DNA)
• Reverse transcriptase (catalyzing enzyme)
• HIV--->AIDS
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Viroids and Prions
• Viroids: tiny, naked circular RNA that infect plants; do not code for proteins, but use cellular enzymes to reproduce; stunt plant growth
• Prions: “infectious proteins”; “mad cow disease”; trigger chain reaction conversions; a transmissible protein
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Bacterial genetics
• Nucleoid: region in bacterium densely packed with DNA (no membrane)
• Plasmids: small circles of DNA
• Reproduction: binary fission (asexual)
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Bacterial DNA-transfer processes
• Transformation: genotype alteration by the uptake of naked, foreign DNA from the environment (Griffith expt.)
• Transduction: phages that carry bacterial genes from 1 host cell to another
•generalized - random transfer of host cell chromosome
•specialized - incorporation of prophage DNA into host chromosome
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Conjugation
direct transfer of genetic material; cytoplasmic bridges; pili; sexual
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Bacterial Plasmids• Small, circular, self-replicating DNA separate from the bacterial
chromosome• F (fertility) Plasmid: codes for the production of sex pili (F+ or F-)• R (resistance) Plasmid: codes for antibiotic drug resistance
• Transposons: transposable genetic element; piece of DNA that can move from one location to another in a cell’s genome (chromosome to plasmid, plasmid to plasmid, etc.); “jumping genes”
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Operons, I• Repressible (trp operon): • tryptophan (a.a.) synthesis • promoter: RNA polymerase binding
site; begins transcription • operator: controls access of RNA
polymerase to genes (tryptophan not present)
• repressor: protein that binds to operator and prevents attachment of RNA polymerase - coded from a regulatory gene (tryptophan present - acts as a corepressor)
• transcription is repressed – when tryptophan binds to a
regulatory protein
Unit of genetic function consisting of coordinately related clusters of genes with related functions (transcription unit)
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Operons, II
• Inducible (lac operon): - lactose metabolism
• lactose not present: repressor active, operon off; no transcription for lactose enzymes
• lactose present: repressor inactive, operon on; inducer molecule inactivates protein repressor (allolactose)
• Transcription is stimulated when inducer binds to a regulatory protein
Unit of genetic function consisting of coordinately related clusters of genes with related functions (transcription unit)
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• Chapter 19 • The Organization and
Control of Eukaryotic Genomes
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Chromatin• Def: complex of DNA and proteins• DNA Packing
•histone protein (+ charged amino acids - phosphates of DNA are - charged)
• Nucleosome •”beads on a string”; basic unit of DNA
packing• Heterochromatin
•highly condensed interphase DNA (can not be transcribed)
• Euchromatin•less compacted interphase DNA
(can be transcribed)
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Molecular Biology of Cancer
• Oncogene •cancer-causing genes
• Proto-oncogene •normal cellular genes
• How? 1-movement of DNA; chromosome fragments that have rejoined incorrectly 2-amplification; increases the number of copies of proto-oncogenes
3-proto-oncogene point mutation; protein product more active or more resistant to degradation
• Tumor-suppressor genes •changes in genes that prevent uncontrolled cell growth (cancer growth stimulated by the absence of suppression)
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• Chapter 20 and 21
BioTechnology & Genomics
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O.J. Simpson capital murder case,1/95-9/95
• Odds of blood in Ford Bronco not being R. Goldman’s:• 6.5 billion to 1
• Odds of blood on socks in bedroom not being N. Brown-Simpson’s:• 8.5 billion to 1
• Odds of blood on glove not being from R. Goldman, N. Brown-Simpson, and O.J. Simpson:
• 21.5 billion to 1• Number of people on planet earth:
• 6.1 billion• Odds of being struck by lightning in the U.S.:
• 2.8 million to 1• Odds of winning the Illinois Big Game lottery:
• 76 million to 1 • Odds of getting killed driving to the gas station to buy a lottery ticket
• 4.5 million to 1• Odds of seeing 3 albino deer at the same time:
• 85 million to 1• Odds of having quintuplets:
• 85 million to 1• Odds of being struck by a meteorite:
• 10 trillion to 1
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Recombinant DNA
• Definition: DNA in which genes from 2 different sources are linked
• Genetic engineering: direct manipulation of genes for practical purposes
• Biotechnology: manipulation of organisms or their components to perform practical tasks or provide useful products
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Bacterial plasmids in gene cloning
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DNA Cloning
• Restriction enzymes (endonucleases):in nature, these enzymes protect bacteria from intruding DNA; they cut up the DNA (restriction); very specific
• Restriction site:recognition sequence for a particular restriction enzyme
• Restriction fragments:segments of DNA cut by restriction enzymes in a reproducable way
• Sticky end:short extensions of restriction fragments
• DNA ligase: enzyme that can join the sticky ends of DNA fragments
• Cloning vector: DNA molecule that can carry foreign DNA into a cell and replicate there (usually bacterial plasmids)
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Steps for eukaryotic gene cloning
• Isolation of cloning vector (bacterial plasmid) & gene-source DNA (gene of interest)
• Insertion of gene-source DNA into the cloning vector using the same restriction enzyme; bind the fragmented DNA with DNA ligase
• Introduction of cloning vector into cells (transformation by bacterial cells)
• Cloning of cells (and foreign genes)• Identification of cell clones carrying
the gene of interest
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DNA Analysis & Genomics
• PCR (polymerase chain reaction)
• Gel electrophoresis• Restriction fragment
analysis (RFLPs)• Southern blotting• DNA sequencing• Human genome project
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Polymerase chain reaction (PCR)
• Amplification of any piece of DNA without cells (in vitro)
• Materials: heat, DNA polymerase, nucleotides, single-stranded DNA primers
• Applications: fossils, forensics, prenatal diagnosis, etc.
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DNA Analysis
• Gel electrophoresis: separates nucleic acids or proteins on the basis of size or electrical charge creating DNA bands of the same length
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Restriction fragment analysis
• Restriction fragment length polymorphisms (RFLPs)• Southern blotting: process that reveals sequences and the
RFLPs in a DNA sequence• DNA Fingerprinting
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Southern Blotting• Southern blotting: process that reveals sequences and the RFLPs in a DNA sequence
• Southern blotting is a laboratory technique used to detect a specific DNA sequence in a blood or tissue sample. A restriction enzyme is used to cut a sample of DNA into fragments that are separated using gel electrophoresis. The DNA fragments are transferred out of the gel to the surface of a membrane. The membrane is exposed to a DNA probe labeled with a radioactive or chemical tag. If the probe binds to the membrane, then the probe sequence is present in the sample.
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Southern Blotting
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DNA Sequencing
• Determination of nucleotide sequences (Sanger method, sequencing machine)
• Genomics: the study of genomes based on DNA sequences
• Human Genome Project
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Practical DNA Technology Uses
• Diagnosis of disease• Human gene therapy• Pharmaceutical products
(vaccines)• Forensics• Animal husbandry (transgenic
organisms)• Genetic engineering in plants• Ethical concerns?
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GENOMICS
AP Biology Chap 21
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• Genomes – set of genes and their interactions
• Bioinformatics – computational methods of gene analysis
- NCBI National Center Biotechnology Information – database of DNA sequences and proteins (proteomes)
NCBI HomePage
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• The most ambitious mapping project to date has been the sequencing of the human genome
• Officially begun as the Human Genome Project in 1990, the sequencing was largely completed by 2003
• The project had three stages:– Genetic (or linkage) mapping
– Physical mapping
– DNA sequencing
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Fig. 21-2-4
Cytogenetic map
Genes locatedby FISH
Chromosomebands
Linkage mapping1
2
3
Geneticmarkers
Physical mapping
Overlappingfragments
DNA sequencing
Fluorescence In Situ Hybridization
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• A linkage map (genetic map) maps the location of several thousand genetic markers on each chromosome
• A genetic marker is a gene or other identifiable DNA sequence
• Recombination frequencies are used to determine the order and relative distances between genetic markers
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Fig. 21-3-3
Cut the DNAinto overlappingfragments short enoughfor sequencing
1
2
3
4
Clone the fragmentsin plasmid or phagevectors.
Sequence eachfragment.
Order thesequences intoone overallsequencewith computer software.
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• A complete haploid set of human chromosomes consists of 3.2 billion base pairs
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By summer 2007, genomes had been sequenced for 500 bacteria, 45 archaea, and 65 eukaryotes including vertebrates, invertebrates, and plants
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What do we know?
• Humans have 20,488 genes• With alternate gene splicing, we can make
75,000 polypeptides• Genomes of most bacteria and archaea range
from 1 to 6 million base pairs (Mb); genomes of eukaryotes are usually larger
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• Free-living bacteria and archaea have 1,500 to 7,500 genes
• Unicellular fungi have from about 5,000 genes and multicellular eukaryotes from 40,000 genes
• Number of genes is not correlated to genome size
• Humans and other mammals have the lowest gene density, or number of genes, in a given length of DNA
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Table 21-1
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About the human genome…
• Only 1.5% codes for proteins, rRNA and tRNA• The rest is used for • regulatory sequences and introns 24% • pseudogenes (nonfunctioning genes) 15% • repetitive DNA 59%
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Fig. 21-7Exons (regions of genes coding for proteinor giving rise to rRNA or tRNA) (1.5%)
RepetitiveDNA thatincludestransposableelementsand relatedsequences(44%)
Introns andregulatorysequences(24%)
UniquenoncodingDNA (15%)
RepetitiveDNAunrelated totransposableelements (15%)
L1sequences(17%)
Alu elements(10%)
Simple sequenceDNA (3%)
Large-segmentduplications (5–6%)
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Repetitive DNA• 44% transposable elements (jumping genes) • - Transposons - cut and paste (ex Alu in
primates)• - Most of these are retrotransposons –
cut, copy to RNA, RT to DNA, and paste (ex Line1 or L1)
• 15% – large segment and simple sequence DNA• - small ones STR - Short Tandem Repeats
often used in centromeres and telomeres
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Fig. 21-9
TransposonNew copy of transposon
Insertion
Transposonis copied
Mobile transposon
DNA ofgenome
(a) Transposon movement (“copy-and-paste” mechanism)
RetrotransposonNew copy of
retrotransposon
Insertion
Reversetranscriptase
RNA
(b) Retrotransposon movement
Animation Quiz 5 - Transposons: Shifting Segments of the Genome
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“Jumping Genes”
• The first evidence for wandering DNA segments came from geneticist Barbara McClintock’s breeding experiments with Indian corn
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Fig. 21-8
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Genes
• Many eukaryotic genes are present in one copy per haploid set of chromosomes
• More than ½ occur in multigene families – such as for RNA products and hemoglobin
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Fig. 21-10
DNARNA transcripts
Nontranscribedspacer Transcription unit
18S
28S
5.8S 28S
5.8S
rRNA
18S
DNA
(a) Part of the ribosomal RNA gene family
Heme
Hemoglobin
-Globin
-Globin
-Globin gene family -Globin gene family
Chromosome 16 Chromosome 11
2
12 1
G A
AdultFetusEmbryoFetus
and adultEmbryo
(b) The human -globin and -globin gene families
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Genomic Evolution
• Duplication of chromosome sets (polyploidy)• Chromosome alteration – duplications,
inversions• Exon shuffling• Transposons
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• Humans have 23 pairs of chromosomes, while chimpanzees have 24 pairs
• Following the divergence of humans and chimpanzees from a common ancestor, two ancestral chromosomes fused in the human line
Why weAre
Smarter!
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• The rate of duplications and inversions seems to have accelerated about 100 million years ago
• This coincides with when large dinosaurs went extinct and mammals diversified
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How transposons affect genomes
• Multiple copies may facilitate crossing-over• Insertion may block protein sequence• Insertion may affect promoters• Insertion may carry new genes to an area• May create new sites for alternative splicing in
RNA
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Fig. 21-12
Transposableelement
Gene
Nonsisterchromatids
Crossover
Incorrect pairingof two homologsduring meiosis
and
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Comparing evolutionary developmental processes
“evo-devo”• Homeobox – 180 nucleotides that regulate
gene expression during development• Found in many organisms, both inverts and
verts• Called “hox genes” in mammals• You should read “Our Inner Fish”!
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Fig. 21-17
Adultfruit fly
Fruit fly embryo(10 hours)
Flychromosome
Mousechromosomes
Mouse embryo(12 days)
Adult mouse
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• Sometimes small changes in regulatory sequences of certain genes lead to major changes in body form.
• For example, variation in Hox gene expression controls variation in leg-bearing segments of crustaceans and insects
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for example, flies with feet in place of antennae.