Ch 19 The Genetics of Viruses and Bacteria

Ch. 19 – The Genetics of Viruses and Bacteria Big Idea 3; Essential Knowledge 3. C. 3

What you must know: • The components of a virus. • The differences between lytic and lysogenic cycles. • How viruses can introduce genetic variation into host organisms. • Mechanisms that introduce genetic variation into viral populations.

Intro to Virus’s • Rich Skrenta – a 15 year old high school student (back in the 1980’s) created the first infectious computer virus • If there’s no computer, there’s no computer virus • Viruses are the same way - if there’s no cell, there’s no virus, which is why they aren’t really considered living

Bacteria vs. Viruses Bacteria Prokaryotic cell Most are free-living (some parasitic) Relatively large size Antibiotics used to kill bacteria Virus Not a living cell (genes packaged in protein shell) Intracellular parasite 1/1000 size of bacteria (SOME are large) Vaccines used to prevent viral infection Antiviral treatment

Viruses Very small (<ribosomes) Components = nucleic acid + capsid ◦ Nucleic acid: DNA or RNA (double or single-stranded) ◦ Capsid: protein shell A capsid can have various structures ◦ Some viruses also have viral envelopes that surround capsid

Viral Structure cont. • Viral envelopes, which are derived from the host cell’s membrane, contain a combination of viral and host cell molecules • Looks similar to the membrane of your cell (also made out of lipids), so it’s easier for it to attach or fuse not recoginzed as being different from the cell it’s infecting)

Viruses Limited host range ◦ Entry = attach to host cell membrane receptors through capsid proteins or glycoproteins on viral envelope (animal) ◦ Eg. human cold virus (rhinovirus) upper respiratory tract (mouth & nose) Reproduce quickly within host cells Can mutate easily ◦ RNA viruses: no error-checking mechanisms

Overview • We will be talking about different types of viruses: • Bacteriophages or Phages (infect bacteria) • RNA or Retroviruses (infect animals)

Bacteriophage Virus that infects bacterial cells

Viral Structure cont. • Bacteriophages, also called phages, are viruses that infect bacteria • They have the most complex capsids found among viruses • Phages have an elongated capsid head that encloses their DNA • A protein tailpiece attaches the phage to the host and injects the phage DNA inside • E. coli and its viruses are called model systems because of their frequent use by researchers in studies that reveal broad biological principles

Simplified viral replicative cycle

Origin theories Cellular – used to be part of cells Regressive – used to be cells that regressed (chlamydia used to be able to live on its own) Coevolution – evolved with cells (like insects and plants)

The Discovery of Viruses: Scientific Inquiry • Tobacco mosaic disease stunts growth of tobacco plants and gives their leaves a mosaic coloration • In the late 1800 s, researchers hypothesized that a particle smaller than bacteria caused the disease (at first they thought it was another bacteria smaller than others) • In 1935, Wendell Stanley confirmed this hypothesis by crystallizing the infectious particle, now known as tobacco mosaic virus (TMV) – first known virus to be crystalized

Reproductive Cycles of Phages • Bacteriaphages are the best understood of all viruses • Phages have two reproductive mechanisms: the lytic cycle and the lysogenic cycle

Viral Reproduction Lytic Cycle: ◦ Use host machinery to replicate, assemble, and release copies of virus ◦ Virulent phages: phages Cells die through lysis or apoptosis Lysogenic (Latent) Cycle: ◦ DNA incorporated into host DNA and replicated along with it ◦ Bacteriophage DNA = prophage ◦ Animal virus DNA = provirus ◦ UV radiation, chemicals: lysogenic lytic cycle ◦ Temperate Phage: Phage uses both methods of replication

The Lytic Cycle • The lytic cycle is a phage reproductive cycle that culminates in the death of the host cell • The lytic cycle produces new phages and digests the host’s cell wall, releasing the progeny viruses • Bacteria have defenses against phages, including restriction enzymes that recognize and cut up certain phage DNA

The Lytic Cycle cont. Bacteriaphage injects its genetic material into a bacteria As the cell makes copies of its DNA, it uses DNA polymerase to make a copy of the viral DNA It then uses RNA polymerase and ribosomes to make proteins (basically goes through transcription and translation) Once the genetic material (protein) is completed, they lyse the cell and the viruses erupt from the cell Head to more cells to make copies of themselves Creates a viral outbreak

The Lysogenic Cycle • • The lysogenic cycle replicates the phage genome without destroying the host Injects the DNA into the host, it becomes a part of the DNA or genetic material of the cell, so every time the cell makes a copy of itself, it copies the viral DNA – The viral DNA molecule is incorporated by genetic recombination into the host cell’s chromosome – Doesn’t make actual viruses, but it copies the genetic material • This integrated viral DNA is known as a prophage • Every time the host divides, it copies the phage DNA and passes the copies to daughter cells Jumps to the lytic cycle when conditions are right – Ex – chicken pox; Eventually immune system will shut it down, but it remains in the infected cells, which causes shingles – Ex – cold sores Phages that use both the lytic and lysogenic cycles are called temperate phages • •

Lytic Cycle vs. Lysogenic Cycle

Lysogenic cycle cont. • When bacteriaphages enter the lysogenic cycle, they can change the virulence of the bacteria • Ex – cholera (causes diahrrea and dehydration) – caused by a bacteria that’s been around for 1000’s of years; on it’s own, it’s not very toxic, but once it’s infected by a specific virus (CTX virus) it becomes highly virulent and leads to cholera outbreaks • Can be prevented by cleaning the water supply

• https: //www. youtube. com/watch? v=Rpj 0 em. E GSh. Q

Reproductive Cycles of Animal Viruses • Two key variables in classifying viruses that infect animals: – DNA or RNA? – Single-stranded or double-stranded?

RNA/Retrovirus -Background info • • Has RNA instead of DNA Single-stranded Has an envelope Reverse transcriptase is an enzyme used to generate complementary DNA (c. DNA) from an RNA template, a process termed reverse transcription. (does the opposite of transcription – has RNA and makes DNA out of it)

• • RNA/Retrovirus Once inside the cytoplasm, the virus uses its own reverse transcriptase enzyme to produce DNA from it’s RNA genome (the reverse of the usual pattern – thus the word retro) The new DNA is then incorporated into the host cell genome by an integrase enzyme The newly made viral DNA that is integrated into the host genome is called a provirus The host cell treats the viral DNA as part of its own genome, using RNA polymerase to translate and transcribe the proviral DNA into RNA molecules, along with the cell’s own genes, producing the proteins required to make new copies of the virus. It’s hard to detect the virus until it’s infected the host (then the infection could last forever) Unlike a prophage, a provirus remains a permanent resident of the host cell The RNA molecules function both as m. RNA for synthesis of viral proteins and as genomes for new virus particles released from the cell

RNA as Viral Genetic Material • There’s not going to be a lot of error checking, so there’s a much higher error rate • Because of the higher error rate, RNA viruses have high mutation rates, but they can usually live on the mistakes that are made • HIV is the retrovirus that causes AIDS • Have genetic material plus the reverse transcriptase; the problem is we can make a vaccine but they mutate too quickly

LE 18 -9 Glycoprotein Viral envelope Capsid Reverse transcriptase RNA (two identical strands)

VIDEO: HIV LIFE CYCLE

Current Outbreaks • Zika Virus – Spread by Aedes mosquitoes (Aedes aegypti) – Major outbreak in Brazil and Latin America – Linked to birth defects (microcephaly) • Dengue Fever • Chikungunya

Zika Virus (as of Dec. 2015)

The Bacterial Genome and Its Replication (Essential knowledge 3. A. 1) • The bacterial chromosome is usually a circular DNA molecule with few associated proteins • Many bacteria also have plasmids, smaller circular DNA molecules that can replicate independently of the chromosome • Bacterial cells divide by binary fission, which is preceded by replication of the chromosome

Mutation and Genetic Recombination as Sources of Genetic Variation • Since bacteria can reproduce rapidly, new mutations quickly increase genetic diversity • More genetic diversity arises by recombination of DNA from two different bacterial cells – Bacteria need the mutations to increase their diversity because they reproduce asexually – If it weren’t for the mutations, they could be wiped out each time we use lysol, or each time a virus infected a population

Mechanisms of Gene Transfer and Genetic Recombination in Bacteria • Three processes bring bacterial DNA from different individuals together: – Transformation – Transduction – Conjugation *These are all examples of horizontal acquisition (allows for variation across species or specimens)

Transformation • Transformation is the alteration of a bacterial cell’s genotype and phenotype by the uptake of naked, foreign DNA from the surrounding environment • *We use this in genetic engineering (GMO’s)

Transduction • In the process known as transduction, phages carry bacterial genes from one host cell to another • During viral replication, sometimes the bacteriaphage will carry the bacterial genome with it, inject that into another bacteria where that bacteria can make use of it • Moves bacteria from one to the other (horizontally)

Conjugation and Plasmids • Closest thing bacteria have to sexual reproduction (usually through the transfer of a plasmid) • Conjugation is the direct transfer of genetic material between bacterial cells that are temporarily joined • The transfer is one-way: One cell (“male”) donates DNA, and its “mate” (“female”) receives the genes • Uses a sex pilus and donate DNA – Not really sex – there’s no meiosis involved, just a direct transfer of DNA

LE 18 -17 Sex pilus 5 µm

Emerging Viruses • Emerging viruses are those that appear suddenly or suddenly come to the attention of scientists • Severe acute respiratory syndrome (SARS) recently appeared in China • Ebola (different strands, vary in virulence) • Outbreaks of “new” viral diseases in humans are usually caused by existing viruses that expand their host territory The SARS-causing agent is a coronavirus like this one (colorized TEM), so named for the “corona” of glyco-protein spikes protruding form the envelope.

Vaccines • Vaccine: weakened virus or part of pathogen that triggers immune system response to prevent infection – Ex. HPV, MMR, Hep. A, Flu shot • Antiviral Drugs: block viral replication after infection – Ex. Tamiflu (influenza), AZT (HIV)

Viroids and Prions: The Simplest Infectious Agents • Viroids are circular RNA molecules that infect plants and disrupt their growth • Prions –Misfolded, infectious proteins that cause misfolding of normal proteins – slow-acting (incubate for at LEAST 10 years before symptoms develop), virtually indestructible (heating doesn’t kill them) infectious proteins that cause brain diseases in mammals (ex – mad cow) – No known cure – Ex. scrapie (sheep), mad cow disease (BSE), Creutzfeldt-Jakob disease (humans), kuru (humans – New Guinea)

LE 18 -13 Prion Original prion Many prions Normal protein New prion