| what is a transposon (transposable element) ? | A DNA sequence able to insert itself (or a copy of itself) at a new location in the genome without having any sequence relationship with the target locus. |
| what are retroviruses? | An RNA virus with the ability to convert its sequence into DNA by reverse transcription. |
| what is a retrotransposon (retroposon) ? | -A transposon that mobilizes via an RNA form; the DNA element is transcribed into RNA, and then reverse-transcribed into DNA, which is inserted at a new site in the genome. It does not have an infective (viral) form.
-they contain long terminal repeats (LTRs) are referred to as retrotransposons, while non-LTR-containing retrotransposons are referred to as retroposons. |
| what is an insertion sequence (IS) ? | -is a transposon that codes for the enzyme(s) needed for transposition flanked by short inverted terminal repeats.
-The target site at which an insertion sequence is inserted is duplicated during the insertion process to form two repeats in direct orientation at the ends of the transposon (direct repeats). |
| what's a transposase? | -The enzyme activity involved in insertion of transposon at a new site.
-The length of the direct repeat is 5 to 9 bp and is characteristic for any particular insertion sequence. |
| how does Transposition Occur? | Most transposons use a common mechanism in which staggered nicks are made in target DNA, the transposon is joined to the protruding ends, and the gaps are filled |
| what are determines if transposition is replicative or nonreplicative ? | The order of events and exact nature of the connections between transposon and target DNA determines it. |
| what are resolvases? | The enzyme activity involved in site-specific recombination between two copies of a transposon that has been duplicated. |
| what's composite transposons (Tn)? | Transposable elements consisting of two IS elements (which can be the same or different) and the DNA sequences between the IS elements; the non-IS sequences often include gene(s) conferring antibiotic resistance. |
| what the Replicative Transposition Proceeds through a Cointegrate? | -Replication of a strand transfer complex generates a cointegrate, which is a fusion of the donor and target replicons.
-The cointegrate has two copies of the transposon, which lie between the original replicons. |
| what regenerates the original replicons? what is a recombination reaction? | -Recombination between the transposon copies regenerates the original replicons, but the recipient has gained a copy of the transposon.
-The recombination reaction (resolution) is catalyzed by a resolvase coded by the transposon. |
| what does Nonreplicative Transposition result in? | Nonreplicative transposition results if a crossover structure is nicked on the unbroken pair of donor strands and the target strands on either side of the transposon are ligated. |
| what are the two pathways of nonreplicative transposition ? | they differ according to whether the first pair of transposon stands are joined to the target before the second pair are cut (Tn5), or whether all four strands are cut before joining to the target (Tn10). |
| what are Superfamilies of transposons ? what do they have? | Superfamilies of transposons are defined by the sequence of the transposase.
Transposon families have both autonomous and nonautonomous members. |
| what are Transposon families autonomous and nonautonomous members? | -Autonomous transposons code for proteins that enable them to transpose, they have changes of phase, when their properties alter in association with changes in the state of methylation.
-Nonautonomous transposons cannot catalyze transposition, but they can transpose when an autonomous element provides the necessary proteins. |
| what are Ac (activator) element and Ds element ? | -Ac (activator) element – an autonomous transposable element in maize.
-Ds element – Dissociation element; a nonautonomous transposable element in maize, related to the autonomous Activator (Ac) element. |
| What is hybrid dysgenesis? | The inability of certain strains of D. melanogaster to interbreed, because the hybrids are sterile (although otherwise they may be phenotypically normal). |
| What are P elements? | transposons that are carried in P strains of Drosophila melanogaster, but not in M strains. |
| When is transposition activated in hybrid dygensis? | When a P male is crossed with an M female, transposition is activated.
•The insertion of P elements at new sites in these crosses inactivates many genes and makes the cross infertile. |
| Why are P elements are activated in the germline of P male × M female crosses? | because a tissue-specific splicing event removes one intron, which generates the coding sequence for the transposase. |
| What does the P element produce? | The P element also produces a repressor of transposition, which is inherited maternally in the cytoplasm.
•The presence of the repressor explains why M male × P female crosses remain fertile. |
| How is Hybrid dysgenesis determined? | determined by the interactions between P elements in the genome and repressors in the cytotype. |
| How many copies of its genome does retroviruses have? | A retrovirus has two copies of its genome of single-stranded RNA. |
| What’s an integrated provirus? | An integrated provirus is a double-stranded DNA sequence. |
| How does a retrovirus generate a provirus? | A retrovirus generates a provirus by reverse transcription of the retroviral genome. |
| What is reverse transcriptase? | An enzyme that uses single-stranded RNA as a template to synthesize a complementary DNA strand. |
| What is integrase? | An enzyme that is responsible for a site-specific recombination that inserts one molecule of DNA into another. |
| What are the three genes in a typical retrovirus? | A typical retrovirus has three genes: gag, pol, and env.
•Gag and Pol proteins are translated from a full-length transcript of the genome.
•Translation of Pol requires a frameshift by the ribosome.
•Env is translated from a separate mRNA that is generated by splicing. |
| What processes Each of the three protein products ? | Each of the three protein products is processed by proteases to give multiple proteins. |
| How are the genes of the retrovirus are expressed? | The genes of the retrovirus are expressed as polyproteins that are processed into individual products |
| what is present at each end of the viral RNA? | A short sequence (R) is repeated at each end of the viral RNA, so the 5′ and 3′ ends are R-U5and U3-R, respectively. |
| What is A plus strand virus? | A virus with a single-stranded nucleic acid genome whose sequence directly codes for the protein products. |
| What does the Retroviral RNA end with? | Retroviral RNA ends in direct repeats (R), the free linear DNA ends in LTRs, and the provirus ends in LTRs shortened by two bases each. |
| When does Reverse transcriptase start synthesis? | Reverse transcriptase starts synthesis when a tRNA primer binds to a site 100 to 200 bases from the 5′ end.
•When the enzyme reaches the end, the 5′-terminal bases of RNA are degraded, exposing the 3′ end of the DNA product.
•The exposed 3′ end of the DNA product base pairs with the 3′ terminus of another RNA genome. |
| The organization of pro viral DNA in a chromosome is similar to what? | The organization of proviral DNA in a chromosome is the same as a transposon, with the provirus flanked by short direct repeats of a sequence at the target site. |
| How is the Linear DNA inserted into the host chromosomes? | Linear DNA is inserted directly into the host chromosome by the retroviral integrase enzyme.
•Two base pairs of DNA are lost from each end of the retroviral sequence during the integration reaction. |
| How does LTR retrotransposons mobilize? | via an RNA that is similar to retroviral RNA, but does not form an infectious particle. |
| What are long-interspersed nuclear elements (LINEs)? | Retroelements can be divided into LTR retrotransposons, non-LTR retroposons and the nonautonomous SINEs. |
| What are short-interspersed elements (SINEs)? | A major class of short (<500 bp) nonautonomous retrotransposons that occupy ~13% of the human genome. |
| What are Alu element? | One of a set of dispersed, related sequences, each ~300 bp long, in the human genome (members of the SINE family). |
| What are the four types of transposable elements? | Four types of transposable elements constitute almost half of the human genome. |
| How does retroelements that lack LTRs, or retroposons, integrate? | Although retroelements that lack LTRs, or retroposons, also transpose via reverse transcriptase, they employ a distinct method of integration and are phylogenetically distinct from both retroviruses and LTR retrotransposons. |
| Can Other elements that were generated by an RNA-mediated transposition event code transposition enzymes? | they do not themselves code for enzymes that can catalyze transposition. |
| How abundant are retro elements in the human genome? | Retroelements constitute almost half of the human genome. |
| What are Ty transposons? | Ty transposons are retrotransposons (with a reverse transcriptase activity) that transpose via an RNA intermediate.
Ty transposons have a similar organization to endogenous retroviruses. |
| What does a A major part of repetitive DNA in mammalian genomes consist of? | A major part of repetitive DNA in mammalian genomes consists of repeats of a single family organized like transposons and derived from RNA polymerase III transcripts. |
