The Genetics of Viruses & Bacteria

The Genetics of Viruses & Bacteria1. What do you know about viruses?2. How big are viruses?

- small

0.25 m

Virus

Animalcell

Bacterium

Animal cell nucleus

The Genetics of Viruses & Bacteria1. What do you know about viruses?2. How big are viruses?3. What are the components of a virus?

- Nucleic acid genome- Protein capsid

18 250 mm 70–90 nm (diameter) 80–200 nm (diameter) 80 225 nm

20 nm 50 nm 50 nm 50 nm(a) Tobacco mosaic virus (b) Adenoviruses (c) Influenza viruses (d) Bacteriophage T4

RNA

RNACapsomereof capsid DNA

Capsomere

Glycoprotein Glycoprotein

Membranousenvelope

Capsid DNAHead

Tail fiber

Tail sheath

Table 18.1 Classes of Animal Viruses

The Genetics of Viruses & Bacteria1. What do you know about viruses?2. How big are viruses?3. What are the components of a virus?4. How do viruses identify appropriate cells to infect?

- Viruses bind to specific receptors- May cross species or be tissue-specific

5. What is the lytic cycle of a bacteriophage?

Figure 18.6 The lytic cycle of phage T4, a virulent phage

Attachment. The T4 phage usesits tail fibers to bind to specificreceptor sites on the outer surface of an E. coli cell.

Entry of phage DNA and degradation of host DNA.The sheath of the tail contracts,injecting the phage DNA intothe cell and leaving an emptycapsid outside. The cell’sDNA is hydrolyzed.

Synthesis of viral genomes and proteins. The phage DNAdirects production of phageproteins and copies of the phagegenome by host enzymes, usingcomponents within the cell.

Assembly. Three separate sets of proteinsself-assemble to form phage heads, tails,and tail fibers. The phage genome ispackaged inside the capsid as the head forms.

Release. The phage directs productionof an enzyme that damages the bacterialcell wall, allowing fluid to enter. The cellswells and finally bursts, releasing 100 to 200 phage particles.

12

4 3

5

Phage assembly

Head Tails Tail fibers

The Genetics of Viruses & Bacteria1. What do you know about viruses?2. How big are viruses?3. What are the components of a virus?4. How do viruses identify appropriate cells to infect?5. What is the lytic cycle of a bacteriophage?6. What is the lysogenic cycle of a bacteriophage?

Figure 18.7 The lytic and lysogenic cycles of phage , a temperate phage

Many cell divisions produce a large population of bacteria infected with the prophage.

The bacterium reproducesnormally, copying the prophageand transmitting it to daughter cells.

Phage DNA integrates into the bacterial chromosome,becoming a prophage.

New phage DNA and proteins are synthesized and assembled into phages.

Occasionally, a prophage exits the bacterial chromosome, initiating a lytic cycle.

Certain factorsdetermine whether

The phage attaches to ahost cell and injects its DNA.

Phage DNAcircularizes

The cell lyses, releasing phages.Lytic cycleis induced

Lysogenic cycleis entered

Lysogenic cycleLytic cycle

or Prophage

Bacterialchromosome

Phage

PhageDNA

The Genetics of Viruses & Bacteria1. What do you know about viruses?2. How big are viruses?3. What are the components of a virus?4. How do viruses identify appropriate cells to infect?5. What is the lytic cycle of a bacteriophage?6. What is the lysogenic cycle of a bacteriophage?7. How do retroviruses (like HIV) reproduce?

- Reverse transcriptase – RNA back to DNA- Helper T cells

Reversetranscriptase

Viral envelope

Capsid

Glycoprotein

RNA(two identicalstrands)

Figure 18.10 The reproductive cycle of HIV, a retrovirus

Vesicles transport theglycoproteins from the ER tothe cell’s plasma membrane.

7

The viral proteins include capsid proteins and reverse transcriptase (made in the cytosol) and envelope glycoproteins (made in the ER).

6

The double-stranded DNA is incorporatedas a provirus into the cell’s DNA.

4

Proviral genes are transcribed into RNA molecules, which serve as genomes for the next viral generation and as mRNAs for translation into viral proteins.

5

Reverse transcriptasecatalyzes the synthesis ofa second DNA strandcomplementary to the first.

3

Reverse transcriptasecatalyzes the synthesis of aDNA strand complementaryto the viral RNA.

2

New viruses budoff from the host cell.9

Capsids areassembled aroundviral genomes and reverse transcriptase molecules.

8

mRNA

RNA genomefor the nextviral generation

Viral RNA

RNA-DNAhybrid

DNA

ChromosomalDNA

NUCLEUSProvirus

HOST CELL

Reverse transcriptase

New HIV leaving a cell

HIV entering a cell

0.25 µm

HIV Membrane of white blood cell

The virus fuses with thecell’s plasma membrane.The capsid proteins areremoved, releasing the viral proteins and RNA.

1

The Genetics of Viruses & Bacteria1. What do you know about viruses?2. How big are viruses?3. What are the components of a virus?4. How do viruses identify appropriate cells to infect?5. What is the lytic cycle of a bacteriophage?6. What is the lysogenic cycle of a bacteriophage?7. How do retroviruses (like HIV) reproduce?8. How do “new” viruses emerge?

- Mutation of an existing virus since there is no proofreading- Spread of an existing virus from 1 host species to another- Spread of viral disease from a small isolated population

9. What is the difference between horizontal & vertical transmission?- Horizontal – 1 organism spreads to another- Vertical – 1 organism inherits disease from parent

10. What are viroids & prions?- Viroids – tiny molecules of naked, circular RNA that infect plants,

several hundred nucleotides long- Prions – infectious proteins (NO genetic material)

- Slow incubation period – at least 10 yrs- Virtually indestructible - 1997 Nobel Prize in Medicine – Stanley Prusiner

Figure 18.13 Model for how prions propagate

Prion

Normalprotein

Originalprion

Newprion

Many prions

Mad cow diseaseCreutzfeldt-Jakob disease

The Genetics of Viruses & Bacteria1. What do you know about viruses?2. How big are viruses?3. What are the components of a virus?4. How do viruses identify appropriate cells to infect?5. What is the lytic cycle of a bacteriophage?6. What is the lysogenic cycle of a bacteriophage?7. How do retroviruses (like HIV) reproduce?8. How do “new” viruses emerge?9. What is the difference between horizontal & vertical transmission?10. What are viroids & prions?11. How is bacterial DNA different from eukaryotic DNA?

Bacterial EukaryoticCircular chromosome Linear chromosomesNucleoid region NucleusNo introns (all exons) Introns & exonsTranscription coupled w/ translation Transcription & translation separate

12.How does bacterial DNA replicate its circular chromosome?- Figure 16.16

Figure 16.16 A summary of bacterial DNA replicationOverall direction of replication

Helicase unwinds theparental double helix.

Molecules of single-strand binding proteinstabilize the unwoundtemplate strands.

The leading strand issynthesized continuously in the5 3 direction by DNA pol III.

Leadingstrand Origin of replication

Laggingstrand

Laggingstrand

LeadingstrandOVERVIEW

Leadingstrand

Replication fork

DNA pol III

Primase

PrimerDNA pol III Lagging

strand

DNA pol I DNA ligase

1

2 3

Primase begins synthesisof RNA primer for fifthOkazaki fragment.

4

DNA pol III is completing synthesis ofthe fourth fragment, when it reaches theRNA primer on the third fragment, it willdissociate, move to the replication fork,and add DNA nucleotides to the 3 endof the fifth fragment primer.

5 DNA pol I removes the primer from the 5 endof the second fragment, replacing it with DNAnucleotides that it adds one by one to the 3’ endof the third fragment. The replacement of thelast RNA nucleotide with DNA leaves the sugar-phosphate backbone with a free 3 end.

6 DNA ligase bondsthe 3 end of thesecond fragment tothe 5 end of the firstfragment.

7

Parental DNA

5

3

43

21

5

3

The Genetics of Viruses & Bacteria1. What do you know about viruses?2. How big are viruses?3. What are the components of a virus?4. How do viruses identify appropriate cells to infect?5. What is the lytic cycle of a bacteriophage?6. What is the lysogenic cycle of a bacteriophage?7. How do retroviruses (like HIV) reproduce?8. How do “new” viruses emerge?9. What is the difference between horizontal & vertical transmission?10. What are viroids & prions?11. How is bacterial DNA different from eukaryotic DNA?

Bacterial EukaryoticCircular chromosome Linear chromosomesNucleoid region NucleusNo introns (all exons) Introns & exonsTranscription coupled w/ translation Transcription & translation separate

12.How does bacterial DNA replicate its circular chromosome?- Figure 16.16- Problem with circular chromosome??????- Solved – topoisomerase

Table 16.1 Bacterial DNA replication proteins and their functions

Figure 18.14 Replication of a bacterial chromosome

Replicationfork

Origin of replication

Termination of replication

The Genetics of Viruses & Bacteria1. What do you know about viruses?2. How big are viruses?3. What are the components of a virus?4. How do viruses identify appropriate cells to infect?5. What is the lytic cycle of a bacteriophage?6. What is the lysogenic cycle of a bacteriophage?7. How do retroviruses (like HIV) reproduce?8. How do “new” viruses emerge?9. What is the difference between horizontal & vertical transmission?10. What are viroids & prions?11. How is bacterial DNA different from eukaryotic DNA?12. How does bacterial DNA replicate its circular chromosome?13. Can bacterial cells do genetic recombination?

- 3 (4) ways- Transformation – uptake of external DNA by a cell – Griffith - Transduction – phage transfers bacterial DNA- Conjugation – bacterial sex – direct transfer of genetic material- (Transposons)

Figure 18.16 Generalized transduction

Phage DNA

Donorcell

Recipientcell

A+ B+

A+ B+

A+

A+ B–

A– B–

A+

Recombinant cell

Crossingover

Phage infects bacterial cell that has alleles A+ and B+

Host DNA (brown) is fragmented, and phage DNA and proteins are made. This is the donor cell.

A bacterial DNA fragment (in this case a fragment withthe A+ allele) may be packaged in a phage capsid.

Phage with the A+ allele from the donor cell infects a recipient A–B– cell, and crossing over (recombination)between donor DNA (brown) and recipient DNA(green) occurs at two places (dotted lines).

The genotype of the resulting recombinant cell (A+B–) differs from the genotypes of both the donor (A+B+) and the recipient (A–B–).

1

2

3

4

5

Figure 18.17 Bacterial conjugation

Sex pilus 1 m

Figure 18.18 Conjugation and recombination in E. coli

1 A cell carrying an F plasmid(an F+ cell) can form amating bridge with an F– celland transfer its F plasmid.

A single strand of the F plasmid breaks at a specific point (tip of blue arrowhead) and begins tomove into the recipient cell. As transfer continues, the donor plasmid rotates(red arrow).

2DNA replication occurs inboth donor and recipientcells, using the single parental strands of the F plasmid as templates to synthesize complementary strands.

3The plasmid in the recipient cell circularizes. Transfer and replication result in a compete F plasmid in each cell. Thus, both cells are now F+.

4

F Plasmid Bacterial chromosome

Bacterial chromosomeF– cell

F+ cell

F+ cell

F+ cell Hfr cell

F factorThe circular F plasmid in an F+ cellcan be integrated into the circularchromosome by a single crossoverevent (dotted line).

1The resulting cell is called an Hfr cell (for High frequency of recombination).

2

Since an Hfr cell has all the F-factor genes, it can form a mating bridge with an F– cell and transfer DNA.

3A single strand of the F factorbreaks and begins to move through the bridge. DNA replication occurs in both donor and recipient cells, resulting in double-stranded DNA

4The location and orientation of the F factor in the donor chromosome determine the sequence of gene transfer during conjugation. In this example, the transfer sequence for four genes is A-B-C-D.

5 The mating bridgeusually breaks well before the entire chromosome and the rest of the F factor are transferred.

6

Two crossovers can result in the exchange of similar (homologous) genes between the transferred chromosome fragment (brown) and the recipient cell’s chromosome (green).

7The piece of DNA ending up outside thebacterial chromosome will eventually be degraded by the cell’s enzymes. The recipient cell now contains a new combination of genes but no F factor; it is a recombinant F– cell.

8

Temporarypartialdiploid

Recombinant F–

bacterium

Conjugation and transfer of an F plasmid from an F+ donor to an F– recipient

(a)

Conjugation and transfer of part of the bacterial chromosome from an Hfr donor to an F– recipient, resulting in recombination

(b)

A+B+ C+

D+

F– cell A–B–

C–

D–

A–B–

C–

D– D–

A–

C–B– D–

A–

C–

B–

A+

B+C+D+A+

B+C+D+A+B+

D+C+

A+

A+

B+

A–B–

C–

D–

A–B+

C–

D–

A+

B+ B–

A+

A+

B+

F+ cell

Mating bridge

Plasmid – extra-chromosomal, small, circular, self-replicating DNA

Figure 18.19 Transposable genetic elements in bacteria

(a) Insertion sequences, the simplest transposable elements in bacteria, contain a single gene that encodes transposase, which catalyzes movement within the genome. The inverted repeats are backward, upside-down versions of each other; only a portion is shown. The inverted repeat sequence varies from one type of insertion sequence to another.

(b) Transposons contain one or more genes in addition to the transposase gene. In the transposon shown here, a gene for resistance to an antibiotic is located between twin insertion sequences. The gene for antibiotic resistance is carried along as part of the transposon when the transposon is inserted at a new site in the genome.

Insertion sequence

Transposase geneInvertedrepeat

Invertedrepeat

Inverted repeats Transposase gene

Insertion sequence

Insertion sequence

Antibioticresistance gene

Transposon

3

5

3

5

5

3

5

3

A T C C G G T…

T A G G C C A …

A C C G G A T…

T G G C C T A …

- Happy Thanksgiving!!!!- Have a safe & happy holiday break!!- Present pictographs when we come back - Test Tuesday- Review sessions Monday after school & Tuesday at 7

The Genetics of Viruses & Bacteria1. What do you know about viruses?2. How big are viruses?3. What are the components of a virus?4. How do viruses identify appropriate cells to infect?5. What is the lytic cycle of a bacteriophage?6. What is the lysogenic cycle of a bacteriophage?7. How do retroviruses (like HIV) reproduce?8. How do “new” viruses emerge?9. What is the difference between horizontal & vertical transmission?10. What are viroids & prions?11. How is bacterial DNA different from eukaryotic DNA?12. How does bacterial DNA replicate its circular chromosome?13. Can bacterial cells do genetic recombination? 14. How are metabolic pathways regulated?

- Inhibition of enzyme activity – protein level- Inhibition of transcription – mRNA level

Figure 18.20 Regulation of a metabolic pathway

(a) Regulation of enzyme activity

Enzyme 1

Enzyme 2

Enzyme 3

Enzyme 4

Enzyme 5

Regulationof geneexpression

Feedbackinhibition

Tryptophan

Precursor

(b) Regulation of enzyme production

Gene 2

Gene 1

Gene 3

Gene 4

Gene 5

–

–

The Genetics of Viruses & Bacteria1. What do you know about viruses?2. How big are viruses?3. What are the components of a virus?4. How do viruses identify appropriate cells to infect?5. What is the lytic cycle of a bacteriophage?6. What is the lysogenic cycle of a bacteriophage?7. How do retroviruses (like HIV) reproduce?8. How do “new” viruses emerge?9. What is the difference between horizontal & vertical transmission?10. What are viroids & prions?11. How is bacterial DNA different from eukaryotic DNA?12. How does bacterial DNA replicate its circular chromosome?13. Can bacterial cells do genetic recombination? 14. How are metabolic pathways regulated?

- Inhibition of enzyme activity – protein level- Inhibition of transcription – mRNA level

15.What is an operon?- A cluster of genes whose products function in a common pathway &

are regulated together- Repressible – usually on – tryptophan – trp operon - anabolic- Inducible – usually off – lactose – lac operon - catabolic

Figure 18.21 The trp operon: regulated synthesis of repressible enzymes

(a) Tryptophan absent, repressor inactive, operon on. RNA polymerase attaches to the DNA at the promoter and transcribes the operon’s genes.

Genes of operon

Inactiverepressor

Protein

Operator

Polypeptides that make upenzymes for tryptophan synthesis

Promoter

Regulatorygene

RNA polymerase

Start codon Stop codon

Promoter

trp operon

5

3mRNA 5

trpDtrpE trpC trpB trpAtrpRDNA

mRNA

E D C B A

DNA

mRNA

Protein

Tryptophan(corepressor)

Active repressor

No RNA made

Tryptophan present, repressor active, operon off. As tryptophanaccumulates, it inhibits its own production by activating the repressor protein.

(b)

Figure 18.22 The lac operon: regulated synthesis of inducible enzymes

DNA

mRNA

ProteinActiverepressor

RNApolymerase

NoRNAmade

lacZlacl

Regulatorygene

Operator

Promoter

Lactose absent, repressor active, operon off. The lac repressor is innately active, and inthe absence of lactose it switches off the operon by binding to the operator.

(a)

5

3

mRNA 5'

DNA

mRNA

Protein

Allolactose(inducer)

Inactiverepressor

lacl lacz lacY lacA

RNApolymerase

Permease Transacetylase-Galactosidase

5

3

(b) Lactose present, repressor inactive, operon on. Allolactose, an isomer of lactose, derepresses the operon by inactivating the repressor. In this way, the enzymes for lactose utilization are induced.

mRNA 5

lac operon

Pictographs – a fun and creative representation of the process below

Remember each group member must write a paragraph explaining how each symbol relates to the actual biological process.

DNA replicationTranscriptionTranslationMutationstrp operonlac operon