Viruses and Bacterial Genomes

Viruses

* Nearly all forms of life have viruses that
infect them
* They vary in structure, replication
methods, and their target hosts
* Much about virus origins and evolution are
unknown

Basic Structure of Viruses

* Tiny; much smaller than a bacteria
About 20-250 nanometers in diameter
* Acellular
* Nucleic acid core enclosed in a protein coat or __capsid__
* May have an outer envelope of proteins and
phospholipids derived from the host
* May contain enzymes and other additional proteins

Types of Viruses

Shapes classified into four
groups

* **Filamentous** - many plant
viruses; tobacco mosaic virus
(TMV)
* **Isometric (icosahedral)** -
poliovirus and herpesvirus
* **Enveloped** - many animal
viruses; HIV
* **Head and Tail** - infect
bacteria; bacteriophages

Viral Genomes

* Tend to be small
* Only genes that encode proteins the virus can't get
from the host
* May use __DNA or RNA__
* May be __single or double-stranded; linear or circular__
DNA viruses direct the host cell's replication of the
viral genomes to transcribe and translate into viral
proteins
* __RNA viruses__ have the enzyme **reverse transcriptase** that replicate RNA into DNA (cDNA)
* Retroviruses
* More likely to make copy errors and
mutations in RNA viruses occur more
frequently

Host Specificity

* Many viruses use __glycoproteins__ to attach to hosts
* Attach to molecules
called __viral receptors__ on
the __host cell__
* (glycoproteins on virus attach to viral receptors on host)
* Normally found on cell and
have their own function
* Viruses have evolved
means to attach to these
cell receptors for their
own replication

Viral Infections

* Viruses must attach - be taken inside -
manufacture __proteins__ and copy genome -
and find a way to escape
* Infect only certain __species__ of hosts and
only certain __cells__ within that host
* Based on receptor proteins, immune
response, and gene expression

Host Cell and Viral Infections

* Viral replication causes damaging changes to
host cells
* May change cell function or destroy cell
* Infected cells may die through __lysis__ or __apoptosis__
* Some cells may live for a period after viruses are
released, but won't function normally due to damage
* Symptoms of viral disease result from immune
response and cell damage

Steps of a Viral Infection

1. **Attachment**

* binds to specific receptor on host


2. **Entry**

* Genome may enter naked __without capsid__,
__fuse envelope with cell membrane,__ or by
__endocytosis__


3. **Replication and Assembly**

* Depends on viral genome; DNA or RNA


4. **Release of new viruses**

* Infect adjacent cells

Lytic Cycle (Bacteriophage)

* Kills the host cell by
causing it to lyse
* Injects genetic material
into host and uses it to
produce new viral
proteins and make copies
of DNA/RNA
* New viruses are
assembled and break
open (LYSE) host cell to
release new viruses

Lysogenic Cycle (Bacteriophage)

* Viral genetic material is injected into host cell
and is incorporated into host cell genome
* Now called a __**prophage**__
* Viral genome is copied every time host cell
reproduces
* __**Latency**__ - viruses exist in host cells without
causing damage or symptoms
* Viral genome eventually exits the host
genome and initiates lytic cycle
* Usually due to environmental triggers

Oncogenic Viruses

Can cause cancer by interfering with the
regulation of the host cell cycle by
interfering with genes or gene expression

* HPV and cervical cancer
* Hepatitis B and liver cancer
* T-cell leukemia and lymphomas

Vaccines and Treatment

__**Vaccinations**__ - intended to prevent outbreaks by
building immunity

* May be prepared using live viruses, killed viruses or
molecular subunits of the virus

__**Antiviral drugs**__ - used to control and reduce
symptoms

* May inhibit the virus by blocking the actions of
proteins
* Have limited success in curing viral disease

Other Strange Infections

__**Viroids**__ - tiny, naked, circular molecules of RNA
that __infect plants__

__**Prions**__ - misfolded proteins that convert normal
proteins in the __brain__ to prion version

* Causes many degenerative brain diseases
"Mad cow disease," Kuru, and Creutzfeldt-Jakob
disease
* Spread by the consumption of
meat, nervous tissue or internal
organs between members of the
same species

Bacterial Genomes

* DNA in nucleoid region; __no nucleus__
* **Single, double-stranded, circular chromosome**
* Have __no introns__
* Has an __origin of replication__
* May also contain plasmids
* Small, self-replicating, disposable circles of DNA with
small # of genes

Plasmids (circular DNA strand in bacteria)

May provide for the expression of beneficial
phenotypes, but not required for survival and
reproduction

May be exchanged between different bacteria
Examples:

* **F plasmids** - required for the production of __sex pili__
used in __**conjugation**__; bacteria either F+ or F-
Exchange of plasmid transfers the ability to conjugate
* **R plasmids** - contain genes for antibiotic resistance

Reproduction and Recombination

Reproduce by __**binary fission**__ (asexual)

* Copy DNA and split into two identical cells
Begin replication at a single __*ori site*__ and make DNA
in both directions around the circle

Genetic diversity/recombination accomplished
by:

* **Mutations**
* **Transformation** - uptake of foreign DNA; often
plasmids
* **Transduction** - gene transfer by phages
* **Conjugation** - one-way direct transfer of genes
(plasmids) between two bacteria through a pilus (pili)

Bacterial Gene Expression

Bacteria genes contain __**operons**__

* All genes needed to produce proteins in the same
biochemical pathway encoded together
* Series of genes are turned on or off together
__One promoter for the whole series__

Three parts:

* **Operator** - "on-off switch;" around promoter region and controls access of RNA polymerase
* **Promoter** - binding location for RNA polymerase
* **Genes they control** - entire sequence of DNA for
the pathway

Operon Control

**Repressors** - proteins that can bind to an operator and block RNA polymerase, preventing transcription

* Can also be regulated by %%__**corepressors**__%%, which help the repressor, %%__**inducers**__%% which, inactivate the repressors, and %%__**activators**__%%, which make it easier for RNA polymerase to bind

Operon Examples

__**trp Operon**__ - E.coli can either ingest or
make tryptophan (an amino acid)

* Have a series of five genes used to
synthesize the amino acid
* If tryptophan is present in the environment, a repressor binds and the genes are turned off (trp operon isnt needed)
* If tryptophan availability is low, transcription is initiated because the repressor dissociates (trp operon is turned on)

Operon Examples

__**lac Operon**__ - An inducible operon that
involves both activators and repressors
if glucose isn't present E. coli may use other
sugars like lactose

* The operon encodes genes need to acquire
and process __**lactose**__
* For the operon to be activated, __glucose must
be very low and lactose must be present__
* Transcribing the genes without these conditions
would be wasteful for the cell