Ch. 18: The Genetics of

Viruses and Bacteria

I. IntroA. Bacteria and viruses are the simplest

biological systems. Most protein synthesis research was done on bacteria.

B. Bacteria and viruses are also of interestso that we can better understand the diseases they cause.

C. Bacteria are prokaryotic organisms, and aremuch smaller and simpler than eukaryotes.D. Viruses are smaller and simpler still, lacking

the structure and most metabolic machinery in cells.

-Viruses are made up of nucleic acids and a protein coat.

II. The Genetics of VirusesA. Researchers discovered viruses by studying

a plant disease.1. In 1883, Adolf Mayer studied tobacco

mosaic disease.a. This disease causes stunted growth

and mottled plant leaves in tobacco plant.

b. Mayer found that the disease was infectious when he sprayed sap from diseased leaves onto healthy plants and caused healthy plants to become diseased.

2. He said that a bacteria caused thedisease until Dimitri Ivanovsky demonstrated that the sap was still infectious even after passing through a filter designed to remove bacteria.

3. In 1897, Martinus Beijerinck showed thatsap from one generation could infect a second generation of plants – he showedthat the pathogen had heredity.a. Beijerinck also determined that the

pathogen could reproduce only within a host.

4. In 1935, Wendell Stanley crystallized the pathogen, the tobacco mosaic virus (TMV).

B. A virus is a genome enclosed in a protectivecoat.

1. Since cells cannot be crystallized, Stanley’s crystallization of viruses was anindicator that viruses are not made up ofcells.

2. Viruses are infectious particles made upof nucleic acids encased in a protein coat,and sometimes a membranous envelope. 3. Viruses range in size from 20nm to barely

resolvable under a light microscope.

4. Viral nucleic acids can be:-double-stranded DNA -single-stranded DNA-double-stranded RNA -single-stranded RNA

depending on the specific type of virus.5. Some viruses only have a few genes,

while others have hundreds.6. The capsid: the protein shella. Capsids are built from a large number

of protein subunits called capsomeres.

b. The tobacco mosaic virus has over1,000 copies of the same proteinto make the capsid.

c. An adenovirushas 252 identical proteins arranged into a polyhedral capsid - as an

icosahedron.

d. Some viruses have viral envelopes thatare membranes derived from a hostcell.

e. They can also have viral proteins andglycoproteins.

f. The most complex capsids are foundon the phages that infect bacteria.

-The T-even phages that infect E. coli have a 20-sided capsid head that encloses their DNA and protein tail piece that attaches the phage to the host and injects the phage DNA inside.

C. Viruses can only reproduce within a host:overview

1. Viruses are obligate intracellular parasites; they can only reproduce within a host cell.

2. They can only infect a limited range ofhosts.

a. They lack enzymes and ribosomes.

3. Some viruses identify host cells by a “lock-and-key” fit between proteins on the outside of virus and specific receptor molecules on the host’s surface ORsome viruses have a wide range of hosts(ex. Rabies virus).

4. Most viruses target specific tissues.Example: Human cold viruses infect only the cells lining the upper respiratory tract.The AIDS virus binds only to certain white blood cells.

5. Infection begins when the viral nucleicacid is inserted into the host.

6. Once inside, the viral genome takes overits host, reprogramming the cell to copy viral nucleic acid and manufacture proteins from the viral genome.

7. The nucleic acid molecules

and capsomeres then self-assemble into viral particles and exit the cell.

D. Phages reproduce using lytic and lysogeniccycles

1. The lytic cycle: the phage reproductive cycle culminates in the death of the host.

a. Virulent phages reproduce only by alytic cycle.

b. Some bacteria have defense mechanisms against viruses:

-Some bacterial mutants have receptors sites that are no longer recognized by a particular type of phage.-Some bacteria produce restriction nucleases that recognize and cut up foreign DNA.

2. Lysogenic cycle: the phage genome replicates without destroying the host cell.a. Temperate phages, like phage

lambda, use both lytic and lysogenic cycles.

b. In the lysogenic cycle, the viral DNA molecule, during the lysogenic cycle, is

incorporated by genetic recombination into a specific site on the host cell’s chromosome.

c. At this stage, the phage is called aprophage, and one of its genes codes for a protein that represses most other prophage genes to “silent” the genome.

d. Each time the bacterial cell divides,it will replicates its own DNA, includingthe viral DNA. Each time the bacteriadivides, it will pass on the viral DNA to the daughter cells.

e. Sometimes the viral genome exits the bacterial chromosome and initiates a lytic cycle.

This switch from lysogenic to lytic may be initiated by an environmental trigger.

The prophage in a lysogenic cycle will exit the bacteria genome and cause a lytic cycle.

E. Animal viruses are diverse in their modes of infection and replication.1. Viruses differ in

the type of nucleic acid they have.

2. They also differon the presenceor absence of a protein capsid.

3. Viruses with an outer envelope use theenvelope to enter a host cell.

a. Glycoproteins on the envelope bind to specific receptors on the host’s membrane.

b. The envelope fuses with the host’s membrane, transporting the capsid and viral genome inside.

c. The viral genome duplicates and directsthe host’s protein synthesis machinery to synthesize capsomeres with free ribosomes & glycoproteins with bound ribosomes.

d. After the capsid and viral genome self-assemble, they bud from the host cell covered with an envelope derived from the host’s cell membrane, including viral glycoproteins.

These viruses do not always kill the host.

4. Some viruses have envelopes that are not derived from plasma membrane.

a. The herpesvirus is derived from the nuclear envelope of the host.

b. The herpesvirus has double-stranded DNA and they reproduce within the cell nucleus using viral and cellular enzymes to replicate and transcribe their DNA.

c. Their DNA can be incorporated intohost DNA. When they do, they arecalled a provirus.

d. The provirus remains latent within the nucleus until triggered by stress to leave the genome and initiate active viral production.

F. Viruses that have RNA as genetic material:1. Some viruses have single-stranded RNA

(class IV), the genome acts as mRNA and is translated directly.

2. In other cases, (class V), the RNA genome serves as a template for mRNA and for a complementary RNA (to makemore of the RNA genome).

3. All viruses that require RNA -> RNA synthesis to make mRNA use a viral enzyme that is packaged with the genome inside the capsid.

4. Retroviruses (class IV) have the most complicated reproductive cycles:

a. These viruses carry an enzyme, reverse transcriptase, which transcribes DNA from an RNA template.

b. The newly made DNA is then insertedinto the animal genome as a provirus.Proviruses never leave the host genome, unlike prophages.

c. The host’s RNA polymerase transcribes the viral DNA into more RNA molecules.

The RNA strands can serve as mRNA for viral proteins, or as genomes for new virus particles released from the cell.

d. HIV (Human immunodeficiency virus (HIV), the virus that causes AIDS (acquired immunodeficiency syndrome) is a retrovirus.

-viral envelope w/ glycoproteins-a capsid-two identical RNA strands-two reverse transcriptase enzymes

How does HIV infect a white blood cell?

1. HIV fuses with host cell membrane.

2. Reverse transcriptasesynthesizes a complementary DNAstrand to the viral RNA.

3. Reverse transcriptasesynthesizes a secondDNA strand complementary to thefirst DNA strand.

4. The new double strand DNA is incorporated as aprovirus into the host DNA.

5. Proviral genes are transcribed into RNA.

6. The RNA serves as mRNA for translationof HIV proteins. It is also used as genomesfor the next generation of viruses.

7. Capsids are assembledaround viral genomes and reverse transcriptase molecules.8. The viruses bud off the

host cell.

G. Causes and prevention of viral diseases inanimals:

1. Some viruses cause animal cell lysosomes to release their hydrolytic enzymes, thus destroying the cell.2. Some viral proteins are toxic to cells.3. Some viruses cause the cell to produce

toxins that can kill the cell.

4. Viral damage can be permanent (poliocauses nerve damage) or temporary (the cold virus).

5. Many temporary symptoms, such as fever, aches, and inflammation is due tothe body’s own efforts at defending itselfagainst infection.

6. Vaccines are harmless variants or derivatives of pathogens that stimulate the immune system to act against an actual pathogen.a. The first vaccine was developed in the

late 1700s by Edward Jenner to fight smallpox.

b. He found that milkmaids who were exposed to cowpox (milder and similar to smallpox) were resistant tosmallpox.

c. In 1796, Jenner infected a farmboy with cowpox. Later, the boy was exposed to smallpox and seemed toresist the disease.

d. Because cowpox is so similar to small-pox, an exposure to cowpox causes the immune system to react vigorously against smallpox.e. Vaccines can prevent disease, but they

cannot treat or cure disease.f. Antibiotics only work against bacteria.

They work by inhibiting bacterial enzymes. Viruses have few or no enzymes.

g. However, AZT inhibits HIV reproductionby interfering with reverse transcript-ase. Acyclovir inhibits herpesvirusDNA synthesis.

H. Emerging viruses:1. HIV (1980’s)2. New strains of the influenza (flu) virus3. Ebola (fever, severe bleeding)

The causes of these viruses:-Mutations-spread from one species to another (3/4 of new human viruses come from other animal species – Ex. Hantavirus comes from deer mice)-spread from a small population to the rest of the world (HIV from Africa)

I. Some viruses cause cancer:1. First to discover this was Peyton Rous

when in 1911, he discovered that a virus causes cancer in chickens.2. Tumor viruses: retrovirus, papovavirus,

adenovirus, and herpesvirus types.3. Hepatitis B can cause liver cancer.4. Epstein-Barr virus, which causes

infectious mononucleosis, has been linked to several types of cancer in parts of Africa, notably Burkitt’s lymphoma.5. Papilloma viruses are associated with

cervical cancers.6. The HTLV-1 retrovirus causes a type of

adult leukemia.

7. Viruses may carry oncogenes that trigger cancerous characteristics in cells.(Oncogenes = genes that causes cancer.)

-Viruses can also turn on proto-oncogenes (genes that code for growth factors that regulate the cell cycle).

J. Viroids and Prions:1. Viroids are small pieces of circular

RNA that infect plants. These viroids can stunt plant growth.2. Prions are infectious proteins that spread

a disease.

a. Prions cause several degenerative brain diseases including scrapie in sheep, “mad cow disease”, and Creutzfeldt-Jacob disease in humans.b. Scientists hypothesize that prions are

forms brain proteins that are misfolded.

c. They can convert a normal protein into the prion version, creating a chain reaction that increases their numbers.

K. Virus evolution:1. Because viruses need cells to survive, it

is thought that they evolved after cells.2. It is hypothesized that viruses originated

from fragments of cellular nucleic acids that could move from one cell to another.3. Viruses probably came from plasmids

and transposons.a. Plasmids are small, circular DNA

molecules found in bacteria and yeastthat are separate from chromosomes.

b. Transposons are DNA segments that can move from one location to another within a cell’s genome.

III. The Genetics of BacteriaA. The short generation span of bacteria help

them to adapt to changing environments.1. Bacteria are very adaptable.

2. Bacteria have a circular double strand ofDNA.

a. In E. coli, the chromosomal DNA consists of about 4.6 million nucleotide pairs with about 4,300 genes.

b. Tight coiling of the DNA results in adense region called the nucleoid.

3. In addition to the chromosome, bacteriahave plasmids, which are smaller circlesof DNA.

a. Plasmids have a few genes on them.

4. Bacteria divide by binary fission. The chromosome replicates from a single origin of replication.

5. Bacteria replicate very rapidly:-under optimal conditions, a population of E. coli can double in 20 minutes, and producing a colony of 107 to 108 bacteria in as little as 12 hours.

-In the human colon, E. coli reproduces rapidly enough to replace the 2 x 1010 bacteria lost each day in feces.

• Most of the bacteria in a colony are genetically identical to the parent cell.

• However, the spontaneous mutation rate of E. coli is 1 x 10-7 mutations per gene per cell division.

There are ~2,000 bacteria in the human colon that have a mutation in that gene per day.

B. Genetic recombination produces new strainsof bacteria.

1. In addition to mutations, genetic recombination can add to the diversity ofbacteria. 2. Recombination in bacteria is defined as

the combining of DNA from two individuals into a single genome.

3. This recombination has 3 processes:-transformation-transduction-conjugation

a. Transformation: is the alteration of a bacterial cell’s genotype by the uptake of naked, foreign DNA from the surrounding environment.

-For example, harmless Streptococcus pneumoniae bacteria can be transformed to pneumonia-causing cells.-Many bacterial species have surface proteins that are specialized for the uptake of naked DNA.They will only uptake DNA from aclosely related bacteria.

b. Transduction: occurs when a phage carries bacterial genes from one host cell to another.1. General transduction: a small piece

of the host cell’s degraded DNA is packaged within a capsid, rather than the phage genome.

2. Specialized transduction: occurs via a temperate phage.When the prophage viral genome exits the host chromosome, it some-times takes with it a small region of adjacent bacterial DNA.This bacterial DNA will be injected along with the viral DNA when the virus infects another bacteria.

-Both transduction types use a phage as a vector to transfer genes between bacteria.

c. Conjugation: transfers genetic material between two bacterial cells that are temporarily joined.

1.One cell (“male”) donates DNA and its “mate” (“female”) receives the genes.

2.A sex pilus from the male initially joins the two cells and creates a cytoplasmic bridge between cells.

3.The “maleness” is the ability to form a sex pilus and donate DNA is the result from an F factor, a section of the bacterial chromosome or as a plasmid.4.Plasmids, including the F plasmid, are small, circular, self-replicating DNA molecules.5.Episomes, like the F plasmid, can undergo reversible incorporation into the cell’s chromosome.6.Plasmids generally benefit the bacteria. They usually have only a few genes.

7.The F plasmid consists of about 25 genes, most required for the production of sex pilli.8.Cells with an F plasmid are called F+ and they pass this condition to their offspring.9.Cells lacking the F plasmid are called F-, and they function as DNA recipients.When an F+ and F- cells meet, the F+ cell will give the F- cell a copy of the F plasmid.

10.The F plasmid can integrate into the bacterial chromosome. The resulting cell is called an Hfr cell and it acts as a male during conjugation.

-The Hfr bacterial DNA will replicate (at arrowhead) and will be transferred to the F- cell. Most of the time, the conjugation bridge is destroyed before the entire chromosome and F plasmid can be transferred.

Recombination between homologous frag-ments take place and the DNA not part ofthe resulting chromosome is degraded.

C. R Plasmid: The drug resistance plasmid.1. Genes on the R plasmid codes for

enzymes that specifically destroy certain antibiotics, like tetracycline or ampicillin.

2. R plasmids also contain genes that codefor sex pili, allowing for R plasmids to be

transferred from bacteria to bacteria.When a bacterial population is exposed to an antibiotic, individuals with the R plasmid will survive and increase in the overall population.

D. Transposons: piece of DNA that can move from one location to another in a cell’s genome.

1. Transposons can bring multiple copies for antibiotic resistance into a single R plasmid by moving genes to that location from different plasmids.

Explanation for multiple resistance genes on a single R plasmid.

2. Two types of transposon movement:a. “Cut-and-paste transposition” – when a

transposon “jumps” from one locationto another location on the genome.

b. “Replicative transposons:” transposon replicates and its copy inserts elsewherein the genome.

3. Insertion sequences: The simplest bacterial transposon, an insertion sequence, consists only of the DNA necessary for the act of transposition.

a. The only gene in the sequence codes for an enzyme called transposase, which catalyzes movement of the transposon.

b. Tranposase recognizes the inverted repeats as the edges of the transposon.

c. Transposase cuts the transposon from its initial site and inserts it into the target site.

d. Gaps in the DNA strands are filled in by DNA polymerase, creating direct repeats, and then DNA ligase seals the old and new material. Insertion sequences cause mutations when they happen to land within the coding sequence of a gene or within a DNA region that regulates gene expression.

4. Composite transposons (complex transposons): include extra genes sand-wiched between two insertion sequences.

Composite transposons may help bacteria adapt to new environments.

5. Transposons were first discovered in the 1940’s byBarbara McClintock who studied color changes in maize (corn) kernels. She hypothesized that the changes in kernel color only made sense if mobile genetic element moved from other locations in the genome to the genes for kernel color.

When transposons moved next to genes for kernal color, they either activated or inactivated those genes.

E. The control of gene expression enables individual bacteria to adjust their metabolism to environmental change.

1. Cells can regulate which genes are expressed. Cells can adjust the activity of enzymes by feedback inhibition.

2. In 1961, Francois Jacob and Jacques Monod proposed the operon model for the control of gene expression in bacteria.The operon model consists of 3 parts:a.The genes the operon controls.b.A promoter region where RNA poly-

merase binds to.c.An operator region between the

promotor and the first gene which acts as an “on-off switch”.

3. The Operon Model:a. If there is no repressor, the operon is

turned on and the genes will be expressed.

b. However, if a repressor protein, a product of a regulatory gene, binds to the operator, it can prevent transcription of the operon’s genes.

c. Regulatory genes are continuously expressed at low rates.

d. Many repressors contain allosteric siteswhere molecules bind to activate it.

Ex.: Tryptophan acts as a corepressor, activating the repressor so that the operon is turned off. At low levels of tryptophan, most of the repressors are inactivated, and the operon is on.

When the operon is on, the genes areturned on. The tryp operon contains genes that code for enzymes that makethe amino acid tryptophan.Important!: How is this an example of feedback inhibition?

e. The tryp operon is an example of a repressible operon. In contrast, thereare inducible operons; operons that areturned on when molecules react withthe regulatory protein.

-In inducible operons, an inducer mole- cule binds to the repressor and inactivates it, turning on the operon.

f. An example of an inducible operon:the lac operon.-Contains genes for enzymes that help metabolize lactose sugar.-In the absence of lactose, the operon is turned off as the repessor binds to the operator.

-When lactose is present, allolactase, an isomer of lactose, binds to the repressor, inactivating it.

-Inducible enzymes usually function in catabolic pathways, digesting nutrients to simpler molecules (lac operon).-Repressible enzymes generally function in anabolic pathways, synthesizing end products (tryp operon).