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Viruses occupy the boundary between the living and nonliving worlds. At the very edge of life, and arguably beyond it, lie a variety of genetic elements that might or might not be classified as viruses.
There are cellular versions of viral __. Many eukaryotic genomes contain multiple copies of sequences, called __, that are able to __.
move from place to place in the genome by a process that involves an RNA intermediate
Retrotransposition begins with __
Then what happens?
synthesis of an RNA copy of the sequence by the normal process of transcription
The transcript is then copied into double-stranded DNA, which initially exists as an independent molecule outside the genome, possibly back into the same chromosome, occupied by the original unit, or possibly into a different chromosome
Retrotransposition and replication of a viral retroelement have very similar meochanisms, the only difference being that __
the RNA molecule that initiates retrotransposition is transcribed from an endogenous sequence, whereas the one that initiates replication of viral retroelement comes from outside the cell
RNA trnasposons can be classified into two types, those that have __ and those that __
__ are also possessed by __ and these __ and __ are members of the same superfamily of elements
- long terminal repeats (LTRs)
- do not
- Long terminal repeats
- viral retrelements
- viruses and the endogenous LTR retrotransposons
The first LTR retrotransposon to be discovered was the __ sequence of yeast, which is 6.3 kb in length and has a copy number of 25 to 35 in most S. cerevisiae genomes
There are several types of Ty element in yeast genomes. The most abundant of these, __, is similar to the __ of the fruit fly
These elements are therefore now called the __.
- copia retrotransposon
- Ty1/copia family
Ty1/copia retrotransposon and viral retroelement are similar. Why?
Each Ty1/copia element contains two genes, called TyA and TyB in east, which are similar to the gag and pol genes of a viral retroelement
TyB codes for a __
Ty1/copia retrotransposon lacks an equivalent of the __, the one that codes for the __.
- polyprotein that includes the reverse transcriptase that plays the central role in transposition of a Ty1/copia element
- viral env gene
- viral coat proteins
This means that Ty1/copia retrotransposons cannot __. They do however, __
- form infectious virus particles and therefore cannot escape from their host cell
- form viruslike particles consisting of the RNA and DNA copies of the retrotransposon attached to core proteins derived from the TyA polyprotein
In contrast, the members of the second family of LTR retrotransposons, called __, do have an equivalent of the __gene and at least some of these can form infectious viruses.
__ make up substantial parts of many eukaryotic genomes, and are particularly abundant in the larger plant genomes
They make up an important component of __ and __, but in humans and other mammals all the __ appear to be __ rather than true __.
These sequences are called __, and with a copy number of approx. 240,000 they make up 4.7% of the human genome
- LTR retrotransposons
- invertebrate and some vertebrate genomes
- LTR elements
- decayed viral retroelements
- endogenous retroviruses (ERVs)
Human __are 6-11 kb in length and have copies of the __.
Although most contain mutations or deletions that do what, a few members of the __ group have functional sequences.
- gag, pol, and env genes
- inactivate one or more of these genes
__(4)__are all probably beyond the edge of life
Satellite RNAs, virusoids, viroids, and prions
Satellite RNAs (virusoids) are __
RNA molecules 320-400 nucleotides in length, each containing a single gene or a very small number of genes
What can't satellite RNAs do?
cannot construct their own capsids; instead, they move from cell to cell within the capsids of helper viruses
Difference between satellite and virusoid?
a satellite virus shares a capsid with the genome of the helper virus whereas a virusoid RNA molecule becomes encapsidated on its own.
Both satellite RNAs and virusoids are __.
generally looked on as parasites of their helper viruses, although there appear to be a few ases where the helper cannot replicate without the satellite RNA or virusoid
RNA molecules of 240-375 nucleotides that contain no genes. They never become encapsidated, spreading instead from cell to cell as naked RNA
infectious, disease-causing particles that contain no nucleic acid. The normal version of the prion protein, called PrPC, is coded by a mammalian nuclear gene and synthesized in the brain, although its function is unknown.
PrpC vs. PrpSC
PrPC is easily digested by proteases, whereas the infectious version, PrPSC, has a more highly Beta-sheeted structre that is resistant to proteases and forms fibrillary aggregates that are seen in infected tissues
Once inside the cell, what does PrPSC do?
PrPSC molecules are able to convert newly synthesized PrPC proteins into the infectious form, resulting in the disease state.
Transfer of one or more of these PrPSC proteins to a new animal results in...?
accumulation of new PrPSC proteins in the brain of that animal, transmitting the disease