biol 300 genetics mobile genetic elements quiz

UNLV

are transposons found in prokaryotes or in eukaryotes?

both

what are several possible mutations caused by transposons?

• insertions

• deletions (nearby information may be cut out)

• gene / promoter disruptions (when transposon is inserted)

can transposons infect other hosts other than a host in which they are found?

no, they cannot go outside of their cell (not a virus)

can transposons make copies of themselves?

yes

can transposons move from one location to another within the same genome?

yes

what are some strategies that an organism uses to deal with transposons?

• methylation (silence transposons)

• RNAi (RNA interference)

are sequences for new transposition insertion random?

no, the sequences are specific "target sequences" or can have hotspots

are transposable elements common in many organisms?

yes

why are composite transposons called "composite"?

because they can carry more than one gene (such as antibiotic resistant genes) and are flanked by IS (insertion sequences)

in mosst cases, what proteins are responsible for choosing the target sequence for transposons?

transposase

where is the gene for transposase located?

in the transposon between the inverted repeats (in the insertion sequence)

what does it mean to be "autonomous"?

the ability to function on its own

e.g. transposase contains genes needed for transcription and transposition and does not need outside help

can transposons exist in genomic dna and plasmids?

yes

can one organism have more than one type of transposons?

yes

how are the ends of IS elements different from the target sequences?

• IS elements: end with inverted terminal repeats

• target sequences: are direct repeats

what is the result of the target sequence after transposition?

• Gets replicated (copy + paste) or moves (cut + paste)

• Turns into direct repeats

why is resolvase needed in replicative transposition?

• a conintegrate is formed and needs to be resolved

  • a cointegrate allows the transposon to be replicated without leaving its original location

when a transposon is removed from one location and transposed to another, are the "cuts" precice?

no, they are rarely precise and will take nearby information and/or gene

what is the difference between replicative and nonreplicative transposition?

• Replicative: (copy + paste mechanism) where the element is duplicated and remains in orginal location and the new copy is transposed to a new site

• Nonreplicative: (cut + paste mechanism) where the element moves as a physical entitiy from one site to another without being duplicated

what is the difference between a retrovirus and other dna or rna viruses?

Retrovirus converts their ssRNA genome into dsDNA once inside of a host cell to integrate it into the host genome.

why is the dna stage necessary in the retrovirus life cycle?

Converts ssRNA into dsDNA for integrase to insert the DNA into the host genome

what is the difference between (+) and (-) strand of viral RNA?

(+) strand: message strand [coding]

(-) strand: template strand [noncoding]

what serves as a primer for RTase during retroviral infection?

• tRNA(100-200 bp long) initially

• and then primers produced by (RNA+) degredation by RNase H

what enzyme is required for the integration of a dsDNA retroviral genome into the host genome?

integrase

why can genes in a viral genome quickly become mutated?

bc there is no proofreading mechanism in reverse transcriptase

when a retrovirus integrates into DNA, does it generate extra direct repeats just a transposons do?

yes

what are the activities of RTase?

• RNA dependent DNA polymerase activity

  • ssRNA used as template to build/synthesize 1st strand of DNA

• Ribonuclease H activity

  • degrades RNA

• DNA dependent DNA polymerase activity

  • 1st strand of DNA as template to build/synthesize 2nd strand of DNA

what are retrotransposons?

genetic elements that can amplify themselves using an RNA intermediate but are not infectious

what is the difference between a retrotransposons and retrovirus?

unlike retroviruses, retrotransposons are not infectious and cannot move from cell to cell (because they don’t have the env gene which is what would make them infectious)

where is RTase encoded in LTR retrotransposons?

In the TyB in the LTR of the transposons themselves

what is VLP?

“virus like particle” that looks like a virus but is missing key genes needed for infectivity (env proteins)

if supplemented with extra enzymes, can a retrotransposons become a functional retrovirus?

yes, if it has the env gene

what are transposons?

movable dna elements found in prokaryotes and eukaryotes

can transposons be silenced?

yes, through methylation or RNAi

what is the base structure of a transposon in bacteria?

contains insertion sequence (IS) composed of the transposase gene and inverted repeats on either side

what is transposase?

enzyme that recognizes inverted repeats and excise sequence and transports to new location

what are the two types of transposons?

insertion sequences (IS) and composite transposons (Tn elements)

whar are insertion sequence?

simplest transposons, autonomous (contains genes needed for transposition). they have inverted terminal repeats

• genes: transposase

what are composte transposons and what are they composed of?

insertion sequences (identical or closely related to) and can carry other genes such as antibiotic resistance genes

• genes: transposase + can carry additional genes

• Two transposition types

  • faith of transposition

  • analogy

  • is transposase needed?

  • is resolvase needed?

  • is the initial break ss or ds?

  • is a cointegrate formed?

• 1. Replicative transposition

  • Faith: element is duplicated. One element stays put in the original location. Copied element becomes transposed to a new site

  • Analogy: Copy + Paste

  • Transposase needed? Yes

  • Resolvase needed? Yes

  • Initial break: Single-stranded

  • Cointegrate formed? Yes

• 2. Non-replicative transposition

  • Faith: Element moves as a physical entity from one site to another without being duplicated

  • Analogy: Cut + Paste

  • Transposase needed? Yes

  • Resolvase needed? No

  • Initial break: Single or double-stranded

  • Cointegrate formed? No

what is resolvase?

assist in copy and paste mechanism allows for duplication of transposon without leaving original location

• resolves cointegrate

Copy + Paste Mechanism (Replicative transposition)

Cut + Paste Mechanism (non-replicative transposition)

SINGLE STRANDED CUT

DOUBLE STRANDED CUT

what are retroviruses?

infectious virus whose genome is RNA (single or double stranded)

what is the function of retroviruses?

converts RNA to DNA inside the host cell so that it can incorporate its genome into the host genomes (permanently)

what unique enzmyes do retroviruses have?

• reverse transcriptase (converts ssRNA → DNA)

• integrase (inserts DNA into host genome)

what are gene cassettes?

genes that have the same function and located near one another

what are the three major gene cassettes?

gag, pol, and env gene cassettes

function of gag gene cassette

packaging

i.e. matrix, capsid, nucleocapsid

function of pol gene cassette

enzymes needed to process the retroviral genome into a state where it can be integrated

i.e. reverse transcriptase, integrase, and proteases

function of env gene cassette

signaling proteins

i.e. surface and transmembrane proteins

lipid bilayer

membrane (helps with fusion in our cells, important for infection)

(RT) reverse transcriptase

synthesizes dna from rna

surface proteins (SU)

proteins interacting with host

(CA) capsid

structural componenet

(PR) protease

cleaves Gag-Pol and Env

viral RNA

ORFs for gag, pol, env, and others

(NC) nucleocapsid

packaging dimer for rna

(MA) matrix

between nucleocapside and envelope

(IN) integrase

integrates provirus into genome

(TM) transmembrane

mediates virus host fusion

Structure of a retrovirus diagram

steps of retrovirual integration

1. virus attaches to membrane

2. rtase synthesizes first strand of dna

3. rtase degrades rna

4. rtase synthesizes second strand of dna

5. viral dna is integrated into host dna

6. viral dna is transcribed

7. viral rna is exported

8. viral rna is translated

9. viral rna and proteins are packed into new virus

Reverse transcription diagram

are retrotransposons able to escape from the cell?

no

how are retrotransposons related to retroviruses?

ability to transform RNA to DNA to integrate into host genome however is not infectious and does not move from organism to organism or cell to cell

why are LTR (long terminal repeats) retrotransposons noninfectious?

they lack gene cassette for membrane signaling proteins and viral envelope (env)

• they lost env which is vital for infection

difference between

• LTR (long terminal repeats) retreotransposons

• non-LTR / long-interspersed nuclear elements (LINEs)

different method of recombination than LTR as it does not encode for integrase or protease

difference between:

• Non-LTR retreotransposon or long-interspertsed nuclear elements (LINEs)

• short-interspersed nuclear elements (SINEs)

SINEs are non-autonomous and utilizes LINEs enzymatic machinery for transposition