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| Genes encoding proteins with corresponding functions. |
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| Homologes that stem from gene duplication in the same genome. |
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| Homologous genes that evolved from a common ancestral gene by speciation, often retaining the same function. |
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| The Gene Ontology (GO) provides a framework and set of concepts for describing the functions of gene products from all organisms. |
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| Development of unique characteristics that separate fom the ancestral traits, often as an adaptation to environmental stress. |
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| Genes encoding proteins with corresponding functions. |
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| Homologes that stem from gene duplication in the same genome. |
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| Homologous genes that evolved from a common ancestral gene by speciation, often retaining the same function. |
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| The Gene Ontology (GO) provides a framework and set of concepts for describing the functions of gene products from all organisms. |
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| Development of unique characteristics that separate fom the ancestral traits, often as an adaptation to environmental stress. |
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| Groups of homolog genes that are likely to have similar function. |
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| The duplication of any region of DNA that contains a gene. |
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| Self-stabilizing region of a protein that folds independantly from the rest of the protein. This includes the secondary structures such as alpha helixes and beta sheets. |
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| The minimal gene set required to support a living cell. |
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| Genes with paralogs that can do the same function. |
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| Genes that are not requiredd for the cell function. |
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| Two mutations that are viable by themselves but cause lethality when present in both duplicate hommologes. |
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| Genome duplication / Polyploiody |
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Definition
| Heritable condition of posessing more than two complete sets of chromosomes. Mostly prevalent in plants, fish, and amphibians. |
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| DNA that structurally resembles a gene, but is incapable of encoding a protein. Often the result of gene duplication. When duplication occurs, the gene can lose a gene function such as binding sites, promoters, or enhancers. |
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| Having more than two complete chromosome sets from the same species. |
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| Having more than two complete chromosome sets from different species. |
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| Complete set of proteins expressed by an organism, cell, or organelle. |
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| The entire genetic content of a cell. |
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| Protein-coding mRNA, non-coding RNA (tRNA, rRNA) in an organism, cell, or organelle. |
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| The spliceosome is a large RNA-protein complex that catalyses the removal of introns from nuclear pre-mRNA. |
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| Vertebrate genomes have undergone at least two rounds of whole genome duplication. |
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| The epigenome consists of chemical compounds that modify, or mark, the genome in a way that tells it what to do, where to do it, and when to do it. |
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| The process by which a polyploid returns to diploidy. |
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| Synteny defines the presence of two or more genes on the same chromosome of a given species. |
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| The result of reverse transcription and integration of mRNA transcripts. |
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| The result of either incomplete duplicationn or second-copy mutations in functional genes. |
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| When RNA is translated and integrated to DNA. |
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| DNA transposons move from one genomic location to another by a cut-and-paste mechanism. They are powerful forces of genetic change and have played a significant role in the evolution of many genomes. As genetic tools, DNA transposons can be used to introduce a piece of foreign DNA into a genome. |
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| Gene silencing is generally defined as an epigenetic modification of gene expression leading to inactivation of previously active individual genes or larger chromosome regions. |
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| No repetitive DNA in prokaryotes. Repetitive DNA is composed of tandem, repeated sequences of from two to several thousand base pairs and is estimated to constitute about 30% of the genome. Many of these sequences are localized in centromeres and telomeres, but they are also dispersed throughout the genome. |
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| Moderately repeated sequences |
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Definition
| Moderately repetitive sequences are found as dispersed segments among unrelated, often single-copy DNA sequences throughout the genome, while simple-sequence DNAs occur in long tandemly repeated clusters, frequently at the centromeric or telomeric regions of chromosomes. |
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| Satellite DNA (satDNA) is the highly repetitive DNA consisting of short sequences repeated a large number of times. It carries a variable AT-rich repeat unit that often forms arrays up to 100 Mb. The monomer length of satDNA sequences ranges from 150 to 400 bp in the majority of plants and animals. |
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| Cesium chloride (CsCl) is a dense salt that exhibits the ability to form a linear gradient when ultracentrifugation g-forces are applied to a homogeneous suspension. |
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| An error during pairing and crossing over events that leads one strand to receive a duplication and the other to receive a deletion as the writing machinery starts at the wrong site. |
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| Polymerase detatches during replication which results in either a duplication or deletion based on where the polymerase reattatches. |
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| Heterochromatin is a tightly packed form of DNA or condensed DNA, which comes in multiple varieties. These varieties lie on a continuum between the two extremes of constitutive heterochromatin and facultative heterochromatin. Both play a role in the expression of genes. |
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| Euchromatin (also called "open chromatin") is a lightly packed form of chromatin that is enriched in genes, and is often (but not always) under active transcription. Euchromatin stands in contrast to heterochromatin, which is tightly packed and less accessible for transcription. |
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| Interspersed repetitive DNA is found in all eukaryotic genomes. They differ from tandem repeat DNA in that rather than the repeat sequences coming right after one another, they are dispersed throughout the genome and nonadjacent. |
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| The ability for organisms to inherit the epigenetic traits from their ancestors up to several generations back. See chimpanzee vs human example, where we have a ~1% SNP divergence, ~3% indels, and <1% amino acid difference, yet are so different from one another. |
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Definition
| Single Nucleotide Polymorphism |
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| A karyotype is an individual's complete set of chromosomes. The term also refers to a laboratory-produced image of a person's chromosomes isolated from an individual cell and arranged in numerical order. A karyotype may be used to look for abnormalities in chromosome number or structure. |
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| A different name for non-coding RNA |
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| Transfer RNA (tRNA) is a small RNA molecule that plays a key role in protein synthesis. Transfer RNA serves as a link (or adaptor) between the messenger RNA (mRNA) molecule and the growing chain of amino acids that make up a protein. |
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| Ribosomal ribonucleic acid (rRNA) is a type of non-coding RNA which is the primary component of ribosomes, essential to all cells. rRNA is a ribozyme which carries out protein synthesis in ribosomes. |
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Definition
| Small interfering RNA (siRNA) is a class of double-stranded RNA (20-24bp) that acts in the RNA interference pathway, by interfering with the expression of genes with complementary nucleotide sequence to that of siRNA, inducing mRNA degradation. |
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Definition
| Endoribonuclease-prepared small interfering RNA. esiRNA is a type of RNA interference (RNAi) reagent used in molecular biology research to silence specific genes. It is typically generated by in vitro transcription of a DNA template that contains the target gene sequence, followed by digestion with a specific endoribonuclease to produce short, double-stranded RNA molecules. |
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| Circular RNA (circRNA) is a type of RNA molecule with a covalently closed loop structure, formed through back-splicing during pre-mRNA splicing. CircRNAs play roles in gene regulation by acting as microRNA sponges and interacting with RNA-binding proteins, and they have been implicated in various biological processes and diseases. |
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| Piwi-interacting RNAs (piRNAs) are a class of small RNA molecules, typically 24-31 nucleotides long, that play a crucial role in the regulation of transposons (mobile genetic elements) in the germline cells. PiRNAs interact with Piwi proteins, forming complexes that are involved in maintaining genome stability by suppressing transposon activity. These molecules are primarily found in the cells that give rise to eggs and sperm, contributing to the integrity of the germline genome and protecting it from transposon-induced mutations. |
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Definition
| Long non-coding RNAs (lncRNAs) are RNA molecules exceeding 200 nucleotides that do not code for proteins. They play diverse regulatory roles in cellular processes, such as gene expression and chromatin structure, contributing significantly to the complexity of cellular regulation. |
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Definition
| "LincRNA" stands for "long intergenic non-coding RNA." LincRNAs are a subtype of long non-coding RNAs (lncRNAs) that are transcribed from regions between protein-coding genes, known as intergenic regions. Like other lncRNAs, lincRNAs play diverse roles in cellular processes, contributing to gene regulation and various biological functions in the cell. |
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Definition
| tRNA isoacceptors are distinct tRNA molecules that recognize the same amino acid but have different anticodon sequences. These variations in the anticodon allow them to pair with different synonymous codons during protein synthesis. This redundancy in the genetic code contributes to the accuracy and flexibility of the translation process. |
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| tRNA isodecoders are different tRNA molecules that share the same anticodon but can recognize different codons coding for the same amino acid during protein synthesis. This redundancy in the genetic code contributes to the adaptability and robustness of the translation process. |
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| Guide RNA (gRNA) typically refers to a type of RNA molecule that guides the Cas9 protein in CRISPR (Clustered Regularly Interspaced Short Palindromic Repeats) gene-editing technology. In the context of CRISPR, gRNAs are designed to be complementary to specific target DNA sequences, guiding the Cas9 enzyme to the precise location in the genome for gene modification. |
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| Catalytic RNA refers to RNA molecules that exhibit catalytic activity, meaning they can accelerate chemical reactions. One well-known example is ribozymes, which are RNA molecules capable of catalyzing specific biochemical reactions. The discovery of catalytic RNA challenged the traditional view that only proteins could serve as biological catalysts, highlighting the diverse roles that RNA molecules can play in cellular processes. |
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| The hammerhead ribozyme is a small catalytic RNA molecule that can cleave phosphodiester bonds in RNA. It adopts a distinctive secondary structure resembling a hammerhead, with three double-stranded regions radiating from a central loop. The hammerhead ribozyme is known for its ability to catalyze the site-specific cleavage of RNA, and it has been used in molecular biology and biotechnology for RNA engineering and gene regulation applications. |
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Definition
| Adenosine deamination involves the removal of an amino group from adenosine, converting it to inosine. This process is catalyzed by enzymes like ADAR and is a key mechanism in RNA editing, influencing the coding properties of RNA molecules. |
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Definition
| Cytidine deamination is the process of removing an amino group from the nucleotide cytidine, resulting in the conversion of cytidine to uridine. This reaction is catalyzed by enzymes such as APOBEC proteins and AID (activation-induced cytidine deaminase). Cytidine deamination is a crucial step in various biological processes, including RNA editing and antibody diversification in the immune system. |
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| Self-splicing involves RNA molecules autonomously removing their own introns through intramolecular catalysis, without requiring external enzymes. This process, exemplified by group I introns, provides insights into the self-regulatory capabilities of RNA and contributes to our understanding of RNA processing and evolution. |
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Definition
| Indel mutation that disrupts the normal reading frame of 3 bp. |
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| RNA modification refers to the chemical alterations that occur in RNA molecules after transcription. These modifications can include additions, deletions, or substitutions of specific nucleotides, and they play crucial roles in various cellular processes. RNA modifications contribute to the regulation of gene expression, RNA stability, and the functional diversity of RNA molecules, impacting cellular functions and responses to environmental cues. |
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Definition
| A riboswitch is a segment of a messenger RNA (mRNA) molecule that can directly bind to small molecules, typically metabolites or ions, and regulate gene expression based on the concentration of these molecules. The binding of the small molecule induces a conformational change in the riboswitch, leading to either the activation or repression of gene expression. Riboswitches are found in the non-coding regions of mRNA and serve as a unique type of RNA-based regulatory element in controlling cellular responses to changing environmental conditions. |
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Definition
| Dicer is an enzyme involved in the process of RNA interference (RNAi) and microRNA (miRNA) biogenesis. It plays a key role in the generation of small RNA molecules, specifically small interfering RNAs (siRNAs) and miRNAs, which are essential for the regulation of gene expression. Dicer processes long double-stranded RNA or precursor miRNA molecules into short, functional RNA duplexes, initiating the RNA interference pathway and influencing post-transcriptional gene silencing. |
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Definition
| Drosha is a nuclear enzyme involved in microRNA biogenesis, responsible for cleaving long primary miRNA transcripts into precursor miRNAs. This processed form is later further modified in the cytoplasm to produce mature miRNAs, which play essential roles in post-transcriptional gene regulation. |
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Term
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Definition
| AGO proteins, or Argonaute proteins, are central to RNA interference and microRNA pathways, forming the core of the RNA-induced silencing complex (RISC). They bind small RNA molecules, such as miRNAs or siRNAs, guiding RISC to complementary target RNAs and facilitating gene regulation through mRNA cleavage or translational repression. |
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Term
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Definition
| The RISC complex, or RNA-induced silencing complex, is a multiprotein complex involved in RNA interference (RNAi) and microRNA (miRNA) pathways. It includes key components such as Argonaute proteins (AGOs) and small RNA molecules (such as miRNAs or siRNAs). The RISC complex plays a crucial role in post-transcriptional gene regulation by binding to these small RNAs and guiding the complex to complementary target RNAs, resulting in mRNA cleavage or translational repression. |
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Definition
| Backsplicing is a process in molecular biology where the 3' end of an exon is covalently joined to the 5' end of the same or another exon during RNA splicing. This non-canonical splicing event results in the formation of circular RNA (circRNA) molecules. Backsplicing can occur in both protein-coding and non-coding genes, contributing to the diversity of RNA transcripts and potentially playing regulatory roles in gene expression. |
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Term
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Definition
| RNA interference (RNAi) is a cellular process that regulates gene expression through small RNA molecules, such as siRNAs and miRNAs, guiding the RNA-induced silencing complex (RISC) to target mRNAs. This mechanism results in mRNA degradation or translational repression, providing a powerful tool for gene silencing in research and potential therapeutic applications. |
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Definition
| Ribozymes are RNA molecules with catalytic activity, meaning they can function as enzymes to facilitate specific chemical reactions. These catalytic RNAs play a role in various cellular processes, such as RNA splicing, self-cleavage, and other reactions. |
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Definition
| Sequence complementarity is the specific matching of nucleotide bases between two strands of DNA or RNA, with adenine pairing with thymine (or uracil in RNA) and guanine pairing with cytosine. This principle underlies key biological processes like replication, transcription, and RNA interactions. |
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Definition
| A DNA sequence element that can move from one location on the genome to another. |
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Definition
| Move via RNA intermediate using reverse traanscriptase. |
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Term
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Definition
ACGCGCG ... CGCGCGT
TGCGCGC ... GCGCGCA |
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Term
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Definition
ACGCGCG ... ACGCGCG
TGCGCGC ... TGCGCGC |
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Term
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Definition
When a transposon (jumping gene) lands in DNA, it creates a short copy of the landing spot next to itself.
Like a parked mobile home leaving a duplicate of its parking space.
Helps scientists see where transposons have jumped.
Key points:
Happens with transposon movement.
Short, repeated sequence near the transposon.
Useful for studying mobile DNA. |
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Term
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Definition
A record skipping: The same pattern repeats right after another.
In DNA, a sequence of bases is copied and pasted next to itself.
Can be short or long, with or without spacer DNA between them.
Key points:
Two or more identical DNA sequences appear close together.
Common in genes, viruses, and repetitive regions of the genome.
Play a role in gene regulation, DNA repair, and evolution. |
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Term
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Definition
Transposon makes a copy during movement, unlike cut-and-paste types.
Creates a cointegrate with two transposons and the original DNA.
More frequent in bacteria than other organisms. |
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Definition
A self-sufficient mover: A piece of DNA that can jump around the genome by itself.
No help needed: Carries the instructions (protein) to cut, copy, and paste itself elsewhere.
Independent contractor: Unlike others who need partners, this one does the job solo.
Key points:
Encodes the transposase enzyme for movement.
Can jump and multiply without relying on other elements.
Common in both bacteria and eukaryotes. |
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Definition
Offspring problems: Sterility, mutations, and other issues in certain crosses within the same species (e.g., fruit flies).
Culprit: Transposable elements (jumping genes) going wild, especially when parents have different versions.
Think of it as: Incompatible roommates messing up the house (genome).
Key points:
Happens in certain intraspecific crosses involving transposable elements.
Causes reproductive issues and genetic instability.
Linked to piRNA pathway dysfunction in germline cells. |
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Term
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Definition
Instructions for the mobile element to:
Copy itself (reverse transcriptase gene).
Integrate into the new location (integrase gene).
Key points:
Found in retroviruses and retrotransposons.
Flanks the mobile element's genes.
Crucial for its mobility and replication. |
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Term
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Definition
Giant protein: Contains several smaller proteins stuck together.
Multi-tool kit: Cleaved into individual protein tools later.
Saves space: One gene makes many proteins.
Common in viruses: Efficient way to pack a punch. |
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Definition
Enzyme jumps "templates" during DNA copying, creating "repeat" errors.
Used in research to tag or amplify specific DNA sections.
Can happen naturally, causing mutations and genetic diversity. |
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Term
| Sleeping beauty transposon |
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Definition
| The Sleeping Beauty transposon system is a synthetic DNA transposon designed to introduce precisely defined DNA sequences into the chromosomes of vertebrate animals for the purposes of introducing new traits and to discover new genes and their functions. It is a Tc1/mariner-type system, with the transposase resurrected from multiple inactive fish sequences |
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Definition
| SINEs and LINEs are short and long interspersed retrotransposable elements, respectively, that invade new genomic sites using RNA intermediates. SINEs and LINEs are found in almost all eukaryotes (although not in Saccharomyces cerevisiae) and together account for at least 34% of the human genome. |
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Definition
A virus with RNA as its genetic material, unlike most viruses which use DNA.
It carries a special enzyme called reverse transcriptase that does the opposite of normal transcription:
Reads its RNA backwards to make DNA.
Inserts that DNA into the host cell's DNA, hijacking the cell's machinery. |
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Definition
Happens when two autonomous transposons (ones with their own movement machinery) interact.
Each transposon cuts the DNA and inserts itself, but instead of separate insertions, they join at their insertion sites.
This creates a single molecule with two transposon copies and the original DNA in between.
Cointegrates are unstable and often resolve (break apart) later, but they can be useful for studying transposon movement and evolution. |
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Term
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Definition
Mobile DNA element using RNA to "jump" locations.
Two types: LTR (like retroviruses) and non-LTR.
Impacts genes, can cause mutations or contribute to diversity.
Examples: LINE-1 (human), Alu (human). |
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Definition
Viral DNA permanently integrated into the host cell's genome.
Not immediately infectious, but can produce new infectious viruses upon reactivation.
Examples: HIV, some oncoviruses (cancer-causing viruses).
Significance: Can contribute to chronic infections, genetic instability, and tumor development. |
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Definition
An inactive transposon, like a fossilized dinosaur: stuck in the genome but no longer mobile.
Evidence of past transposon activity: it tells us a transposon was once there and potentially jumped around.
Can be intact or degraded: some retain their original structure, while others have accumulated many changes.
Key points:
Result of accumulated mutations: mutations disable the transposon's movement machinery.
Common in genomes: they can make up a significant portion of some genomes.
Useful for studying evolution: help track transposon movement and diversity over time. |
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Term
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Definition
Transposon (mobile DNA) in fruit flies (Drosophila).
Causes hybrid dysgenesis: sterility and other issues in certain crosses.
Encodes its own "transposase" enzyme for movement.
Two key features:
Target site duplication: creates a short copy next to itself after insertion.
Autonomous: doesn't rely on other elements for movement. |
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Definition
Two main activities:
Cleaves (cuts) both viral and host DNA.
Joins the viral DNA into the host DNA.
Essential for viral replication: Without integrase, viruses cannot establish successful infections.
Targeted by drugs: Many antiviral drugs inhibit integrase to prevent HIV replication. |
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Definition
Gene with the potential to cause cancer when mutated or overexpressed.
Imagine it as a gas pedal:
Normal gene helps cell growth, like a properly adjusted pedal.
Oncogene acts like a stuck pedal, causing uncontrolled cell division (cancer). |
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Term
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Definition
| An Alu element is a short stretch of DNA originally characterized by the action of the Arthrobacter luteus (Alu) restriction endonuclease. Alu elements are the most abundant transposable elements, containing over one million copies dispersed throughout the human genome. Alu elements were thought to be selfish or parasitic DNA, because their sole known function is self reproduction. However, they are likely to play a role in evolution and have been used as genetic markers. |
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Term
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Definition
Long Interspersed Nuclear Element 1
Most active autonomous (replicates on its own) non-LTR retrotransposon in humans.
Makes up about 17% of the human genome.
Copies and inserts itself into new locations, potentially disrupting genes and causing mutations.
Structure:
~6,000 base pairs long.
Two open reading frames (ORFs) for proteins involved in its movement (ORF0, ORF1/ORF2).
Flanking untranslated regions (UTRs) and target site duplications (TSDs). |
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Term
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Definition
| Processed pseudogenes are copies of messenger RNAs that have been reverse transcribed into DNA and inserted into the genome using the enzymatic activities of active L1 elements. |
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