World of Viruses

• nucleic acids: carry genetic information
• proteins: enzymatic and structural
• lipids: structure and energy; delineate inside of cell with outside

Yes, RNA. 

RNA can do all of the same things as NAs, proteins, and lipids

• RNAs can store information
• RNAs can fold and have enzymatic activity
• Through base pair binding, they can have more ordered structures

It is believed that RNA can behave as self-replicating molecules. Before we had modern cells, we had RNA that catalyzed certain cells. 

Today, nothing that is alive only has RNA. Everything alive on earth has cells and different macromolecules. But, some RNA viruses don't have any DNA. They have RNA as a genetic material

Then: RNA makes RNA, which continues to make more RNA

• Now: DNA makes RNA, which makes protein
• It is information storage--> information storage/ information transmitter--> function

the RNA world

Viroids and RNA viruses

RNA world

Transposable elements: it is a gene that is capable of moving itself around within a genome. Some make copies of themselves; some excise themselves, with the use of a transposon enzyme, and end up somewhere else

ex: domesticated grasses

When you move genetic elements around, you change the gene or interrupt it, thus altering the structure and function of proteins. This allows for the devleopment of diversity.

A transposon gene gone rogue will turn itself into a virus. If the transposon was on all the time and didn't care about the host genome, it will replicate itself and become viral.

Evolved in terms of pathogen size. 

For a long time, it was known that even the largest virus was simpler than the smallest bacterial cell.

Small and medium-sized DNA viruses

we are now finding viruses that are turning the information on its head. 

Ex: chlamydia is one of the smallest bacteria with a smallgenome. Pandoravirus, on the other hand, is more than twice the sie of a known living bacterium. Its' actually larger than some bacteria and infects single celled organisms

All viruses have a capsid. Nucleic acid alone is not a virus. it needs a covering. 


There are one or a small number of proteins that fit together to fit and protect the genome to give it a higher order structure

The capsid can have a lipid envelope covering it

Capsid+ nucleic acid= virion

package viral genomes and transmit them to a new host cell

rigid, symmetrical container composed of viral protein

capsid with enclosed genome

complete, infectious virus particle possibly including an envelope

Efficiency

Viruses are small and have small genomes with limited genes

They work on borrowed time since speed is of the essence. Many viral capsids are made of one or a small number of proteins and have self-assembly capabilities to eliminate the need for a lot of energy and time

simple, symmetrical packages

• genomic economy
• self-assembly
• identical subunits

composed of many copies of identical subunits

can assemble spontaneously

give the capsid symmetry

• shape= the geometry of its outline
• symmetry= rotational and translational operations that describe it

• icosahedral
• helical

• icosahedrom= a shape with 20 triangular faces/ a 3D polygon made out of these triangles
• icosahedral capsids have 5-fold, 3-fold, and 2-fold rotational axes

• repeating subunits with identical interactions
• repeating subnits interactions in a quasi-equivalent manner

the greater the ability to stretch the capsid structure while keeping it regular and symmetrical

Quasi-equivalent icosahedral structures are composed of subunits present in multiples of 60 (60 x T)

T= triangulation number= total number of subunits that make of the virus

The simples virus has a T of 1. So, 60 subunits make up the capsid

Their capsids contain two types of structural subunits: hexons and pentons

Different than t numbers

icosahedral symmetry

• helical symmetry
• organized as helical tubes composed of identical, repeating subunits that rotate around endlessly, protecting genetic material that is on the inside

• cellular membranes 
• lipid bilayers (with the same composition as the cell membrane from which they were derived) and viral glycoproteins (from host ER that virus uses to get inside others)

adopt a variety of shapes

by a process called budding

• - viral glycoproteins are inserted into membrane
• - nucleocapsids associate with glycoprotiens and get wrapped in membrane

• Some form and then pull their genes in
• Some form around genes
• Some make scaffold/intermediate proteins, which assist with formation of pro-capsid and are not in the final, mature virion

• size, shape, and complexity of capsid
• genomic composition

direct incorporation of viral genomes into virions/ some viruses don't care which genes are incorporated. Otehrs are very specific

core proteins

budding/ interactions between viral proteins

• envelope like; wormlike; on the inside, its RNA genome is protected by a nucleocapsid protein 
• Other nucleocapsids are used to protect the RNA; it also signals when to step in and out of the life cycle stages

Picornavirus

Flavivirus

some can give you diseases like polio

They are naked, unenveloped viruses with RNA and a protein shell.

very stable

viruses that give you Yellow Fever, etc

They almost look exactly like picornaviruses. They have a capacity to select their genes