Term
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Definition
| first, select the desired gene. Next, cut two DNA molecules with specific restriction enzymes into fragments. Next, splice the fragments together into the desired combination. Finally, introduce DNA into living cell for replication. |
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Term
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Definition
| condition in which cells within an organism have a different genetic make-up; can be due to methylation, inactivation, somatic mutation, or proximity to heterochromatin; arise from a single zygote during embryogenesis. |
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Term
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Definition
| genetic variation within an individual organism originate from more than one zygote |
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Term
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Definition
| condition where a percentage of cells in a woman's body have only one x chromosome, depending on how early in embryogenesis the nondisjunction occured; symptoms of complete turner syndrome are milder |
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Term
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Definition
| an organism containing an artificially inserted foreign piece of DNA |
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Term
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Definition
| process by which fragments of different sizes and elctrochemical properties are separated by thier migration through an electrically charged gel |
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Term
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Definition
| protein that recognizes a short, specific nucleotide sequence and binds to and cuts only at that site; a bacterium is immune to its own restriction enzymes |
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Term
| Polymerase Chain Reaction |
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Definition
| allows rapid amplification and multiplication of a specific DNA sequence; |
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Term
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Definition
| bacgteria that easily take up foreign DNA |
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Term
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Definition
| method of transformation; dissolve cell wall, electrical pulse to create channels, and regrowth of cell wall |
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Term
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Definition
| transformation method; projectiles shot at high velocity; promising in use for live organisms |
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Term
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Definition
| inject DNA directly into the nucleus using a tiny pipette |
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Term
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Definition
| uesd for transformation; must be small, have unique restriction sites, have an origin of replication, and have markers |
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Term
| Yeast Artificial Chromosome |
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Definition
| modified plasmid that contains a yeast centromere and a yeast origin of replication; can carry relatively large pieces of DNA to be inserted into eukaryotic cells |
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Term
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Definition
| causitive agent of gall tumors in plants; can be used as a vector to introduce foreign genes into dicot plants |
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Term
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Definition
| gene inserted next to the gene of interest that is easily recognizable in the phenotype, used as another indication as to whether the gene of interest is also working |
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Term
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Definition
| reporter gene that gives the organism bioluminesence when expressed |
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Term
| three scenarios if gene is actually inserted |
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Definition
| duplication, gene replacement and ectopic integration |
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Term
| overview of eukaryotic genomes |
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Definition
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Term
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Definition
| family of genes which codes for a particular type of protein or product; found throughout genome in different locations |
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Term
| tandem gene family arrays |
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Definition
| genes which code for a product needed in great quantities that are arranged in adjacent repeats along the chromosome |
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Term
| non-coding functional sequence |
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Definition
| gene that does not code for a protein or product but which serves a definite function; ex) telomere sequences |
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Term
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Definition
| derived from the bacterium Thermus aquaticus; enzyme commonly used in PCR reactions because it is very heat tolerant which enables it to withstand the heat required to denature the DNA |
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Term
| Highly repetitive centromerit DNA |
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Definition
| tandem repeats in the untranscribed heterochromatin flanking the centromeres; function unknown |
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Term
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Definition
| variable number tandem repeats; highly variable among individuals; used as DNA fingerprints in forensics |
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Term
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Definition
| multiple copies of DNA sequences found throughout the genome that can excise themselves and move to other parts of the genome |
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Term
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Definition
| collection of cloned restirction fragments from an organism's genome; goal is to have all of the genes |
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Term
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Definition
| collection of DNA clones reconstructed from the mRNA molecules, using reverse transcriptase; advantage is that the cDNA can actually be translated into a functional protein, but it doesn't include the regulatory sequences |
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Term
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Definition
| cloning vectors that contain the regularly required elements for gene expression such as the promoter region |
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Term
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Definition
| sequencing technique that uses special modified nucleotides called dideoxynucleotide triphosphates; they lack the 3' and 2' hydroxyl groups, thus DNA synthesis is blocked at the point of addition of the dideoxy of that specific nucleotide; creates a set of DNA fragments that have the same starting point but different end points b/c of using four separate cocktails that have normal nucleotides and are spiked with a different dideoxy nucleotide; the strands are then marked and separated by gel electrophoresis; the sequence can now be read by reading up the gel |
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Term
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Definition
| a radioactively labeled nucleic acid fragment of known sequence that allows precise location of a complementary DNA sequence. |
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Term
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Definition
| getting an imprint of DNA molecules on a membrane by using the membrane to blot the gel after electrophoresis; the DNA is denatured first and then the membrane is hybridized with labeled probe; an autoradiograph will reveal the presence of any bands that are complemetary to the probe |
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Term
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Definition
| similar technique to southern blot, but used to dterct a specific RNA molecule; one application os to determine if a gene is transcribed in a certain tissue or under certain environmental conditions |
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Term
| functional complementation |
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Definition
| technique used to locate a gene of interest through its ability to restore the wild-type phenotype to a mutant; create a DNA library, introduce samples to the mutant, and use the transformed ones to recover and clone the wild type gene |
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Term
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Definition
| used in in vitro mutagenesis; complementary sequence to the gene of interest; a mutation is induced and then is taken up by a phage vector and introduced into a bacterium for further study |
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Term
| Restriction Fragment Length Polymorphism. |
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Definition
The presence of various forms of a particular restriction fragment within a species; important because:
heterozygosity of restriction fragments within a single individual can be used as a genetic marker.
RFLPs in related individuals can be used as a marker (as in mapping!) for diagnosing disorders which might be related to that RFLP's location.
Evolutionary history of related species can be studied by examination of the RFLPs of the species. A measure of the total RFLP difference can be used as an index of evolutionary divergence from a common ancestor. |
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Term
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Definition
this is the transfection of germ cells with "desired" genes, and it does have evolutionary consequences. Not only is a person carrying a deleterious allele cured, but some of his/her gametes might also be "cured"--meaning the end to the heritability of the particular disorder by that individual's offspring.
Problem: transfection fragments often insert haphazardly (ectopically, i.e., not in its usual locus) which means not only that normal gene function could be disrupted |
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Term
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Definition
| This targets only the affected body cells, and has no direct evolutionary consequences. Only some somatic cells are transfected--enough to effect a cure or confer effective function. (Note that unless one transfects a one-celled embryo, gene therapy cannot correct genetic errors in every cell of the body. Hence, this type of therapy is useful only for disorders that are highly tissue-specific and treatable if some functional cells are present. |
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Term
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Definition
| a sequence of genes adjacent to one another on DNA that are under the collective control of an operator and promoter |
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Term
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Definition
| region of the DNA where RNA polymerase attaches during transcription |
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Term
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Definition
| located just upstream of the promoter; sequence of DNA where an enzyme can attach |
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Term
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Definition
| operon that is induced when a product to be catabolized enters the cell; ex) lac operon |
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Term
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Definition
| repressed when the products of an operon saturate the cell; ex) tryp operon |
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Term
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Definition
| activator binds in order for transcription to take place |
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Term
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Definition
| repressor binds to DNA to stop transcription |
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Term
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Definition
| systems act to reduce the amount of protein produced but do not shut the gene down completely |
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Term
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Definition
protein produced by one of the genes on the lac operon; acts upon lactose (its substrate) to catabolize lactose into glucose and galactose OR isomerize lactose into allolactose. |
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Term
| beta galactoside permease |
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Definition
| another enzyme produced by a gene on the lac operon; facilitates transfer of lactose into the cell and concentrates it |
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Term
| beta galctoside acetyl transferase |
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Definition
| acetylates galactoside sugars (other than lactose) that may be in the cell, preventing Beta galactosidase from breaking them down; waste of resources/time and byproducts could be toxic |
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Term
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Definition
| operates under negative control: when lactose is present, some of it spontaneously isomerizes to allolactose which binds to the allosteric binding site of the repressor. This causes the repressor to come off the promoter/opertor, and this the genes can be transcribed to produce the enzymes for lactose catabolism |
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Term
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Definition
| characteristic of gene expression which results in constant, unregulated production of a product |
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Term
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Definition
| Also can operate under positive control: when glucose concentration is low, CAP protein binds to cAMP to form a complex which then binds to the cap site just upstream of the lac operon; it acts as a super-inducer of the lac operon; but when the glucose concentration increases, the cAMP decreases so there is not enough of the complex to bind, and so the cell basically ignores any lactose present |
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Term
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Definition
-
- When there is arabinose in the cell, it binds to the AraC protein, forming a complex that binds to the araI site.
- In addition, the same cAMP-CAP compex that operates in the lac operon must bind to the araI site.
In this configuration, RNA polymerase is attracted to the operon, and begins transcription |
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Term
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Definition
| low concentration of arabinose, AraC protein now has affinity for araI and araO; the protein fold the DNA just upstream of the operator, binding araI and araO and forming a hairpin loop; not attractive to RNA polymerase, ergo no transcription |
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Term
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Definition
| under normal circumstances, the cell is in constant need of tryptophan and so the operator remains unbound; but with the excess of trp, it binds to an R protein and this complex binds to the operator and prevents RNA polymerase from binding |
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Term
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Definition
gene expression that controls function at the translation level;
The mRNA leader transcript transcribed from this region has four complementary regions (think: velcro) which can bind together in various ways to form stem loops.
The particular configuration of the attenuator transcript determines whether the trp operon is turned "on" or "off |
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Term
| translational control in prokaryotes |
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Definition
| unusually fast degradation of an mRNA transcript; RNA/RNA hybridization; differential ribosomal binding efficiency; codon preference; codon response |
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Term
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Definition
| when prokaryote is starved for amino acids; there are extra tRNAs floating around and a naked one goes to an empty A site where it idles, an stringent factor recognizes it and produces a nucleoside phosphate: guanosine tetraphosphate (3'ppGpp5') ; most likely this sends the cell into a state of suspended animation |
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Term
| prokaryotes vs eukaryotes: gene expression |
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Definition
pro: activators and repressors act on operators; 1000 genes; always on; unpackaged; Pribnow box; one RNA polymerase; no post-transcriptional modification
euK: activators work on enhancers (its position has a profound effect on regulation) and repressors work on silencers; 20-30,000 genes; always off; packaged as chromatin-histone octamers-nucleosomes; TATA or Hogness box; three RNA polymerases; post-transcriptional modification |
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Term
| three classes of control elements in eukaryotes |
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Definition
| core promoter; cis and trans acting binding sequences; enhancers and silencers |
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Term
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Definition
| short sequence of DNA that acts as a binding site for a protein with an affintiy for that sequence; bound protein acts only on DNA sequences on the same molecule; include short consensus sequences, located close to initiation site, can be in enhancer and promoter, serves as a regulator b/c has affinity for protein that binds to it |
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Term
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Definition
| DNA sequence that codes for a protein that controls the expression of the gene from a different location by binding to its cis-acting element; enzymes that interact with RNA polymerase, stabilize initiation complex, may bind to some promoters and act as positive regulators |
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Term
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Definition
to modulate transcription, regulatory proteins possess one or more of these:
- recognizes a DNA regulatory sequence
-interacts with proteins of transcriptional apparatus
-interacts with proteins bound to nearby regulatory sequences- cooperatively regulate transcription
-influences chromatin condensation
-sensor of physiological conditions w/in cell |
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Term
| promoters and promoter proximal elements |
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Definition
| comprise the large RNA polymerase II complex; bound by transcription factors that affect the expression of many genes; mutations at these sites have dramatic effects on transcription- level is usually reduced |
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Term
| cis-acting regulatory sequences and enhancers |
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Definition
| may be located a considerable distance from the gene promoters; bound by transcription factors that control the regualtion of a smaller subset of genes; often will only act in one or a few cell types in a multi-cellular organism |
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Term
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Definition
| turns a gene on; the mRNA binding protein for which it has an affinity is the activator; when an activator binds to this, RNA polymerase is more highly attracted to it |
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Term
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Definition
| turns the gene off or reduces rate of transcription; the mRNA binding protein for which it has affinity is called the repressor and when attached, RNA polymerase cannot attach and transcription can't take place |
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Term
| nucleosome and eukaryotic gene expression |
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Definition
| proximity of a gene's promoter to nucleosome histones may affect how readily it is transcribed; may block RNA polymerase attachment to TATA box |
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Term
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Definition
| changes in winding of chromatin/nuclesome around DNA due to gene activity or with developmental stage; DNA molecule can be moved to free the promoter and regulatory sequences or conversely if it needs to be turned off, it can be rewound so that repressors can reach it |
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Term
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Definition
| amino-terminal tails stick out and can be modified in various ways; tails have lysine residues that are readily modified by enzymes- attach acetyl and methyl groups or ubiquitinate or phosphorylate; These modifications are often reversible, and may be involved in a particular gene's ability to be expressed or shut down in different generations of the cell. |
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Term
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Definition
| modifications to the histone tail; can take many forms and contains alot of information (44 lysine residues available for modification) |
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Term
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Definition
| level can cause DNA to slide along the nucleosome and wind in a different pattern than the previous "incarnation" and affect affinity of associated DNA for regualtory proteins |
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Term
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Definition
| large complex composed of multiple regualtory proteins bound to binding sites in an enhancer that has varying affinity for RNA polymerase, depending on size and composition; the highest level of transcription occurs when a certain number of reg. proteins are bound in a specific way and this depends on the physiological environment of the cell; can recruit additional co-activators and facilitate chromatin remodeling |
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Term
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Definition
| these non-coding regions at the end and beginning of mRNA can have mutations in them that result in higher than normal translation in the ORF region; vertain sequences can also promote rapid degradation or just slower translation |
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Term
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Definition
-splicesome can perform alternative splicing
-mRNA associated with snRNPs cannot leave the nucleus
-transcript control: number of transcripts allowed to leave nucleus and enter cytoplasm controlled |
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Term
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Definition
| the specific amino acid present at the N-(amino) terminal signals the lifespan to the proteases |
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Term
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Definition
| the number of regions rich in the amino acids P, E, S, and T signal to the proteases the lifespan; areas rich in these aa's have a lifespan of 2 minutes or less |
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Term
| genomic/parental imprinting |
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Definition
| gene inherited from either parent has been permanently inactivated and is passed on this way to the offspring; generally highly methylated genes; |
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Term
| maternal/ paternal imprinting / monoallelic |
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Definition
during gamete formation, DNA is methylated differently between the sexes in genes that exhibit imprinting
1) allele from mom is inativated; only dad's is expressed
2) allele from dad is inactivated; only mom's is expressed
inheritance is called _______ |
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Term
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Definition
| product of this gene is required for normal growth; however, maternal allele was silenced and so only paternal allele inherited; if there was a mutation in the maternal allele, no effect; but if the mutation was in the paternal allele, then the mouse would express dwarfism |
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Term
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Definition
| exhibits inprinting inheritance; mutation in the FMR1 gene; inherited mental impairment- connections to autism |
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Term
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Definition
| characterized by mental retardation, decreased muscle tone, short stature, emotional lability and an insatiable appetite; example of genomic imprinting; caused by the absence of segment 11-13 on the paternally derived chromosome 15. Certain genes in this region are normally suppressed on the maternal chromosome, so, for normal development to occur, they must be expressed on the paternal chromosome. When these paternally derived genes are absent or disrupted, the _____ phenotype results. When this same segment is missing from the maternally derived chromosome 15, a completely different disease, Angelman syndrome, arises |
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Term
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Definition
| altered expression of genes carried by translocation or inversion mutations; ex) can affect rate of translation and transcription |
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Term
| positron effect variegation |
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Definition
| if a gene is translocated from an area highly transcribed to an area of muted transcription, the gene's transcription may be at an abnormally slow rate; if gene is translocated to area very close to heterochromatin, it may not be always included in the heterochromatic complex because the start and end points may shift from cell to cell; this causes phenotypic variation among cell fields in tissue and popualtion; ex) drosophila- sometimes an inversion in a chromosome causes the gene for eye color comes close to a region of heterochromatin, which results in the gene being inactivated and so the eye is variegated red and white |
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Term
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Definition
| females have the potential to produce twice the amount of X product as males but this mechanism prevents this: barr body has many epigenetic marks of heterochromatin; exhibit epigenetic inheritance: A cell's daughter cell will have all the same X chromsomes inactivated, though in any given organim one X or the other is randomly inactivated in any cell line.; results in mosaic expression: active allele in any given cell line will be expressed regardless of dominance/recessiveness |
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Term
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Definition
| activity of a particular allele is reduced when inherited with a paramutagenic allele at the same locus |
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Term
| anthocyanin pigment in corn |
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Definition
B= normal color, b= no pigment, B' = reduced pigment production; is paramutagenic to the B allele
may involve gene silencing by siRNA |
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Term
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Definition
| rapid change to respond to rapid environmental change; epigenetics |
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Term
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Definition
| revert to ancestral trait |
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Term
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Definition
-most common
-narrow and more elongated
-backbone smooth
-wide major groove easily accessible to polypeptides affecting transcription
-conformation of actively transcribed genes
-kinks=where transcription factors bind (?) |
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Term
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Definition
-RNA/DNA hybrids and double-stranded RNA most forms
-shorter, greater diameter
-base-pair H bonds slanted
-major groove deep and narrow- less accessible to proteins affecting transcription
-genes transcribed at lower rate
-laboratory phenom |
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Term
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Definition
-helix spirals to left
-zig-zag backbone
-narrow minor groove
-shallow major groove
-helix even more narrow and elongated
-some research suggests that this conformation is necessary for a gene to be transcriptionally active
-when cytosine is methylated, it is stable in vitro b/c it protects from action of endonucleases
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Term
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Definition
| cell has ability to develop into any type of cell ; the zygote and possibly to first few cells in the cleavage of deuterostomes are the only true ones |
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Term
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Definition
| can develop into any cell type except the extra-embryonic membranes: amnion, chorion, allantosis: types are embryonic stem cells (somatic), germ cells (germ line) amd carcinoma (found in teratocarcinmomas) |
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Term
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Definition
| can develop into many types of cells, but not as many as pluri and toti; usually give rise to a particular type ex) hematopoietic cell=blood cells |
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Term
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Definition
| group of adjacent, structurally and functionally related genes |
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Term
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Definition
| a group of cells which cooperate and signal to each other to decide the final position of the dividing, developing cells |
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Term
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Definition
| the cell divsion and decision-making that results in the final diversity and the final fate of all the blastomeres in an embryo; can occur by assymmetric division and then the daughter cells receive different regulatory instructions |
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Term
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Definition
| one cell secretes a substance which binds to the outside or inside of a substance which triggers a pathway for signal transduction |
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Term
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Definition
mouth forms first; Annelida, Mollusca, Anthropoda
cell fate determined early- determinate cleavage |
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Term
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Definition
anus forms first; Chordata, Hemichordata, Echinodermata
cell fate determined late in development; indeterminate cleavage |
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Term
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Definition
| characteristics of both males and females; cleavage determined early usually - butterflies with one wing female coloring and one wing males coloring |
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Term
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Definition
serially repeated structures; ex) abs, vertebral column
mutations with misplaced body parts often occurred here; its a sympleisomorphy linking all bilaterian coelomates |
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Term
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Definition
changes in the identity of segments and the appendages
loss-of-function= inactivation of homeotic gene
gain-of-function= activation of homeotic gene |
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Term
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Definition
| homeotic genes that control segment identity; eight loci |
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Term
| Drosophila gene complexes |
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Definition
eight loci in two groups on chromosome 3;
Bithorax= 3 Hox genes
Antennapedia=5 Hox genes
Arranged in same spatial order as the segments they affect on the body |
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Term
| localizing mRNA transcripts |
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Definition
cDNA of gene of interest transcribed in vitro with labeled nucleotides; new probe is complementary to mRNA and so will hybridize when injected into embryo- localization of production
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Term
| localizing expressed proteins |
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Definition
| insert cDNA into bacterium and allow it to produce the proteins; inject these to a vertebrate host, which will produce antibodies; antibodies injected into embryos will bind to the proteins where they are being expressed; special dyes will reveal the location |
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Term
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Definition
| segment common to all hox genes; encodes a protein domain, the homeodomain, 60 amino acids long and similar in sequence among the eight Hox genes; similar enough to hybridize; NOT mutation friendly! |
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Term
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Definition
Hox genes demonstrate this; typical of transcription factors; Hox proteins bind directly to DNA regulatory elements- activation or repression
Basically, they encode genes that affect the transcription of other genes |
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Term
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Definition
| multi-nucleate mass of cytoplasm formed by some organisms in early development; plasma membranes do not form until 13th mitotic division; nuclei migrate to outer edge, membrane invaginates and encircles individual nuclei to form blastoderm of embryonic cells around the central mass= yolk, few nuclei |
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Term
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Definition
genes whose products are provided by the female parent to her eggs; effect on offspring soley dependent on genotype of the mother
set up anterior-posterior axis polarity and dorsoventral axis polarity |
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Term
| maternally/zygotically required |
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Definition
1) active in ovum; encoded by momma's genome
2) active in zygote; encoded by offspring's genome (expected mendelian rations) |
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Term
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Definition
| affect development of a contiguous block of segments |
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Term
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Definition
| control the proper development of adjacent segments (pairs) |
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Term
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Definition
| affect individual segments' polarity |
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Term
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Definition
| substance governing the pattern of tissue development, and the positions of the various specialized cell types within a tissue. It spreads from a localized source and forms a concentration gradient across a developing tissue |
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Term
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Definition
| earliest genes turned on in system are gap; second are pair-rule; third are segment-polarity |
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Term
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Definition
bicoid (bcd) and hunchback (hb) encode transcription factors; start out heavily concentrated at anterior pole; HB-M less conc but distributed farther to posterior pole
bcd responsible to cascade leading to differentiation between head, thorax and abdomen
hb-m: product of nos gene prevents translation; conc greatest at posterior of embryo (+ microtubules); prevents translation less and less as you travel towards anterior |
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Term
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Definition
| also triggered by maternal effect genes; dl encodes DL which acts as a transcription factorin the nucleus but is bound in cytoplasm by CACT; gradient starts to develop after fertilization and most found highly in the NUCLEI of cells at the midline of what will become the ventral side of the embryo, and in the CYTOPLASM of the more dorsal cells. |
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Term
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Definition
When the SPZ ligand is bound to the TOLL receptor, a signal transduction pathway opens.
· This signal transduction (through two other proteins called TUB and PLL) phosphorylates the DL-CACT complex.
· Phosphorylation causes DL and CACT to lose affinity for one another, and they separate.
· Free and single again (and most highly concentrated at the ventral midline) the DL proteins are now able to enter the nuclei near the ventral midline.
· Here, DL serves as a transcription factor to turn on genes that direct cells to take on the characteristics of "ventral" cells. |
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Term
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Definition
| product at the beginning of the developmental cascade can set entire process in motion or turn it off |
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Term
| fruit fly- master regulatory switch |
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Definition
left off= male
switched on = female
turned on or off by activity of sex lethal gene
X/A >= 1 female
X/A< 0.5 male |
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