Term
|
Definition
| the strand opposite to the template strand |
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Term
|
Definition
| – 3-nucleotide sequences within the mRNA that specify particular amino acids. Sequence within mRNA determines sequence within polypeptide (mRNA). Where the genetic information is coded within mRNA |
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Term
|
Definition
| determines transcriptional start site, and produces a basal level of transcription. Composed of TATA box and Transcriptional start site. |
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Term
|
Definition
| stores information in genes |
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Term
|
Definition
| – similar to bacterial, but more complex. 3 RNA polymerase subunits, and 3 RNA polymerases – RNA pol I, RNA pol II, and RNA pol III. |
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Term
|
Definition
| Temporary copy of a gene that contains information to make a polypeptide. Identical to DNA sequence except for substitution of Uracil for Thymine. |
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Term
|
Definition
| 17 bases long, is where the RNA polymerase attaches to – opened at the TATA box. Behind, DNA rewinds into double helix. RNA synthesis rate is 43 nucleotides per second. |
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Term
|
Definition
| – part of a functional protein that contributes to an organism’s traits |
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Term
|
Definition
| of RNA polymerase II, and 5 general transcription factors (TFIID, TFIIB, TFIIF, TFIIE, TFIIH[acts as helicase]), and a mediator |
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Term
|
Definition
| TATA box that is the -10 sequence of the promoter region |
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Term
|
Definition
| Site for RNA polymerase to bind to (DNA). Recognised by Transcription Factors. Eukaryotes – 3 features in common for structural genes – regulatory elements, TATA box, Transcriptional start site. |
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Term
|
Definition
| affect binding of RNA polymerase to the promoter: Enhancers and Silencers |
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Term
|
Definition
| sites for binding of regulatory proteins which influence transcription rates (DNA) Recognized by Transcription Factors. |
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Term
|
Definition
| making of DNA copies that are transmitted from cell to cell and from parent to offispring |
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Term
| ρ independent termination |
|
Definition
| termination of translation facilitated by 2 RNA sequences - stem loop, and U rich sequence behind stem loop. As the RNA polymerase is paused at the stem loop, the U can’t hold on, |
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Term
|
Definition
| site for binding of ribosome. Signals region where transcription will start. _Eukaryotes – looks for start codon in mRNA (mRNA) |
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|
Term
| RNA polymerase - what direction does it travel in? synthesize in? |
|
Definition
| travels 3’-5’, synthesizing RNA 5’-3’ |
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Term
|
Definition
| Transcribes rRNA genes (except for 5S rRNA) (eukaryotic) |
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Term
|
Definition
| Transcribes structural genes (thus mRNA), transcribes some snRNA (eukaryotic). Form preinitiation complex with the General transcription factors. |
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Term
|
Definition
| all tRNA genes and 5S rRNA gene (eukaryotic) |
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Term
| RNA polymerase holoenzyme |
|
Definition
| binds loosely to DNA and scans until it recognizes -10 and -35 squences of the promoter region. |
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Term
|
Definition
|
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Term
|
Definition
|
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Term
|
Definition
| specifies the first amino acid in a sequence formylmehionine in bacteria, or methionine in eukaryotes. (mRNA) |
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Term
|
Definition
| encode polypeptides – must encode in the proper cell at the proper time and in the right amounts |
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Term
|
Definition
| – specifies the end of polypeptide synthesis (mRNA) |
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Term
|
Definition
| end of RNA synthesis when RNA-DNA hybrid of open complex is forced to separate. In bacteria, is either ρ dependant or ρ independent. |
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Term
|
Definition
| Signal for end of transcription (DNA) |
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Term
|
Definition
| the strand that is physically transcribed |
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Term
|
Definition
| Produces an RNA copy of a gene. Does not alter the structure of DNA. Has 3 stages: Initiation, Elongation, Termination, which are protein-DNA interactions, like RNA polymerase |
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Term
|
Definition
| – protein that binds to DNA to regulate action of RNA polymerase |
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Term
|
Definition
| Production of a polypeptide using information in mRNA |
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Term
|
Definition
| cDNA provides info for transcription of mRNA, which provides the template to make a polypeptide. |
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|
Term
| 5’ capping / 3’ polyA tailing |
|
Definition
| RNA modification of mRNA transcripts. |
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|
Term
| ATP dependent chromatin remodelling |
|
Definition
| – energy of ATP is used to alter structure of nucleosomes and make DNA more accessible. Can significantly alter gene expression. |
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|
Term
|
Definition
|
|
Term
|
Definition
| the covalent addition of 7-methyl guanosine to the 5’ end of an mRNA. Happens when pre-mRNA is being synthesized by RNA pol II. 3 step process: de-phosphorylation, hyldrolyzation, methylation. Cap structure then recognized by cap-binding proteins. |
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|
Term
| Covalent Modification of Histones |
|
Definition
| – amino terminals of the histones are modified (acetylation, phosphorylation, methylation) |
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Term
|
Definition
|
|
Term
|
Definition
| – non-coding, intervening sequences. Can be visualized by denaturing dsDNA and mixed with complementary mRNA. The 2 hybridize. If present, forms r-loops where introns are. Bound by specific sequences recognized by the spliceosome. Gives benefit of alternative splicing. |
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|
Term
|
Definition
| a structure made of DNA wound around histone octamers – tight wrapping inhibits function of RNA pol I – fixed by loosening of chromatin structure through Covalent modification of histones or ATOP dependent chromatin remodeling |
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|
Term
|
Definition
| gene expression should be collinear (DNA=RNA=polypeptide), but euk. Structural genes are not always. Exons are interrupted by introns – entire gene product froduced during transcription, but introns are later excised, and exons are spliced. |
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|
Term
|
Definition
| the excision of introns from transcribed product. Can be done by group-1 inttron splicing, group 2 intron splicing, or by a spliceosome, Groud 1 and 2 self-splice, and does not req. aid of enzymes. RNA is its orn Ribozyme. |
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Term
|
Definition
| small nuclear RNA and a set of proteins. |
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Term
|
Definition
| complex that splices pre-mRNA, composed of snRNPs |
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Term
|
Definition
| addition of adenine nucleotides to 3’ ends. PolyA tail not encoded in gene sequence. Added after transcription of the gene. |
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Term
|
Definition
| cutting precursor rRNA and tRNA into individual parts. A form of modification |
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Term
|
Definition
| if nonpolar and charged – hydrophilic = surface dwellers |
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Term
|
Definition
| when there are several codons that encode the same amino acid |
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Term
|
Definition
| Accellerate chemical reactions within a cell. |
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Term
|
Definition
| synthesize molecules and macromolecules |
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Term
|
Definition
| Break down large molecules into small ones (energy!) |
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Term
|
Definition
the dictionary used for translation of mRNA into peptides. Deciphered by the production of synthetic mRNA with polynucleotide phosphorylase in a cell free system, to which mRNA ribosomes and tRNA – AA are addedin in specific ratios (other methods too)
• UUU – phenylalanine
• AAA – Lysine
• GGG – glycine
• CCC - Proline |
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|
Term
|
Definition
| lead to synthesis of proteins |
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|
Term
| One gene-one polypeptide theory |
|
Definition
| not all proteins are enzymes like in beadle and tatum’s experiments |
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|
Term
| Polypeptide Chain directionality? |
|
Definition
| has directionality (5’ 3’): stuck together by peptide bonds. First exposed amino acid group = N-terminal, Last amino acid has exposed carboxy terminal = Cterminal – C& N condense |
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Term
|
Definition
| defines cell characteristics. Perform variety of functions. Key proteins are enzymes |
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Term
|
Definition
| Set by the start codon, is the 3 codons that are being interpereted as a word. |
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Term
|
Definition
| nearly universal in all species |
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Term
|
Definition
| AUG (sometimes GUG or UUG in translation initiation) |
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Term
|
Definition
|
|
Term
|
Definition
| caries amino acid and recognizes triplet RNA sequences |
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Term
|
Definition
| the 3rd position in a codon |
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|
Term
|
Definition
| that tRNA just look for complementary codon |
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|
Term
| Aminoacyl-tRNA synthetases |
|
Definition
| enzymes that attach amino acids to tRNA (Charging). 1 per amino acid. Catalyze 2 step rxn btwn Amino acid, tRNA and ATP. Very accurate as anti-codon and tRNA are used for recog. |
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Term
|
Definition
| translation and transcription happen at the same time. = Polysome |
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|
Term
|
Definition
| mRNA that is undergoing both transcription and translation |
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|
Term
| Recognition between tRNA and mRNA |
|
Definition
| anticodon in tRNA recognizes complementary codon in mRNA |
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Term
|
Definition
| recognize stop codons, 3d structure similar to tRNAs – BACTERIAL: RF1 (UAA, UAG), RF2 (UAA, UGA) RF3 (binds to GTP and helps facilitate termination) EUKARYOTIC: eRF (recognizes all 3 stop codons) |
|
|
Term
| Ribosomal Functional Sites |
|
Definition
APE, 5’ – 3’ direction
Peptidyl sit
Aminoacyl site
Exit Site |
|
|
Term
|
Definition
| – macromolecular complex across whose surface translation occurs. Bacteria have 1 type ([30s: 16s] [50s; 23s + 5s]), Eukaryotes have 2 (cytoplasm & mitochondria/chloroplasts) ([40s; 18s][60s; 5s, 28s, 5.8s]). Composed of a Large and small subunit formed of proteins and rRNA |
|
|
Term
|
Definition
| – ribosomal binding site 9 nucleotides long – complementary to sequence in 16sRNA. Binding occurs through hydrogen bonds |
|
|
Term
| Translation Elongation stage |
|
Definition
| addition of amino acids to polypeptide chain. Very fast (faster in bact). Ribosome catalyzes itself via peptidyltransferase in the 50s subunit |
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|
Term
| Translation Initiation Stage |
|
Definition
| Bacteria: initiation complex formed by mRNA, initiation tRNA – tRNAfmet (IF3, IF2) and ribosomal subunits. Initiator tRNA recognizes start codon in mRNA – shine dalgarno sequence Eukaryotes: similar, except that eukaryotic Initiation Factors are required (eIFs). tRNAmet looks for 1st AUG after 5’ cap. |
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|
Term
| Translation Termination Stage |
|
Definition
| when stop codon is reached- codons recognized by release factors |
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|
Term
|
Definition
| – 2ndry structure = cloverleaf = 3 stem-loops, acceptor stem, and 3’ single strand region (ACC). 3rdry = more folding. Often contain modified nucleotides on top of AUGC |
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|
Term
|
Definition
| occurs in 3rd position, is tolerance for certain mismatches. |
|
|
Term
|
Definition
| bind to DNA and increase transcription |
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|
Term
|
Definition
| RNA strand complimentary to mRNA. |
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|
Term
|
Definition
| viruses that infect bacteria. Termed λ phage. Has 2 life cycles – Lytic and lysogenic. Which is chosen depends on cellylar proteases cll easily degraded by proteases, and whether or not they’re produced depends on environmental conditions |
|
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Term
|
Definition
| 48,503 nucleotides long, circular - see notes........... |
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Term
|
Definition
| antiterminator needed for lytic cycle. Also permits transcription through PR. |
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Term
|
Definition
|
|
Term
|
Definition
|
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Term
|
Definition
| promoter for λ repressor during establishment of lysogenic cycle |
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Term
|
Definition
|
|
Term
|
Definition
| – if Cro binds here, inhibits transcription from PRM in leftward direction. Prevents expression of cl gene and λ repressor, low level of transcription in rightward direction enabling transcription of O, P, and Q genes needed for the replication of λ DNA |
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Term
|
Definition
| inhibits transcription from PL |
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|
Term
|
Definition
| λ cl repressor binds to operators and inhibits expression of genes req. for lytic cycle. Also activates Prm |
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Term
|
Definition
| enough λ repressor to maintain lysogenic cycle |
|
|
Term
|
Definition
| – controls large operon encoding proteins necessary fpr assembly of Phage coat, packaging of DNA, and lysis of bacterial cell. |
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Term
|
Definition
| antiterminator. Binds to RNA polymerase and prevents transcriptional termination |
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Term
|
Definition
| protein helps stabilize cll activator protein |
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|
Term
|
Definition
|
|
Term
|
Definition
|
|
Term
|
Definition
| = integrase. Integrates λ DNA into bacterial chromosome |
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|
Term
| • Regulator of late genes |
|
Definition
| late promoters for the lytic cycle. |
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|
Term
| Bacteriophacge RNA transcripts |
|
Definition
| encode 2 proteins – N and cro. |
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Term
|
Definition
| regulates catabolite repression of lac operon – produced by ATP by adenylyl cyclase, which is inhibited by glucose. Binds to CAP |
|
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Term
|
Definition
| Catabolite Activator Protein – activarot protein to which cAMP binds |
|
|
Term
| Catabolite repression in lac operon |
|
Definition
| - if exposed to lactose and glucose, glc used first, with catabolite repression preventing lac operon from functioning. Regulated by cAMP. Glc = cAMP inhibition = lac inhibition |
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|
Term
| Covalent Modification of proteins |
|
Definition
| some modifications are irreversible, while acetylations, phosphorylation, and methylation are transient |
|
|
Term
|
Definition
| sequential use of 2 sugars by a bacterium |
|
|
Term
|
Definition
| regulates the activity of metabolic enzymes where the final product of a polypeptide pathway inhibits an enzyme that acts early in the pathway. |
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Term
|
Definition
| binds to lac repressor and inactivates it |
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|
Term
|
Definition
can be regulated by repressor protein mechanism (lac repressor protein and allolactase as inducer) or activator protein mechanism
• Lac I – inducer
• Lac P –
• Lac O –
• Lac Z – β-galactosidase
• Lac Y – Lactose permease
• Lac A – Galactoside transacetylase |
|
|
Term
| Lactose present no glc in lac operon |
|
Definition
| – lacI induced, lac repressor inactivated |
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|
Term
| No lacto, no glc lac operon |
|
Definition
| lac repressor active, cAMP active |
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|
Term
|
Definition
| lac induced, repressor inactivated, no cAMP inhibition |
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|
Term
|
Definition
| lac repressor active, no cAMP inhibition |
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|
Term
|
Definition
| λ DNA integrates into host chromosome (prophage) copied by DNA sometimes can be excised (induction), but rare. TEMPERATE stage when the going is thoughll and clll complex accumulates to high levels, lysogenic cycle prevails. |
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Term
|
Definition
| phage binds to cell, injects its DNA, uses cell toolkit to produce many new phages host DNA degraded cell lyses and releases new phages to attack new cells. VIRULENT stage – when things are great |
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Term
|
Definition
| regulation by repressor proteins |
|
|
Term
|
Definition
| group of structural genes under the control of 1 promotor which encodes polucistronic mRNA for 2 + structural genes. – allows for coordinated regulation of proteins with common functions. Has different regions: promoter, terminator, structural genes, operator. |
|
|
Term
|
Definition
| . of bases that provides a binding site for a regulatory |
|
|
Term
|
Definition
| – regulation by activator proteins |
|
|
Term
| Posttranslational regulation |
|
Definition
| – after translation usually via feedback inhibition, or by control of protein function by covalent modification of their structure. |
|
|
Term
|
Definition
| – signals the beginning of transcription |
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Term
|
Definition
| Bind to DNA and inhibit transcription – Negative control |
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Term
|
Definition
| Bind to DNA and inhibit transcription – Negative control |
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Term
|
Definition
|
|
Term
|
Definition
| specifies end of transcription. |
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|
Term
| Trancscriptional regulation |
|
Definition
| usually happens at transcription initiation. Increases or decreases rate of RNA synthesis uses repressors for negative control, and activators for positive control |
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Term
|
Definition
| can be through transcription, or through antisense RNA. Antisense RNA binds to mRNA so it cant be translated. |
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Term
|
Definition
| 1000-2000 nucleotides long, with high number of CpG sites. Unmethylated in housekeeping genes. Maybe be methylated in tissue specific genes to silence, change binding of TFs, or recruit factors leading to compaction of chromatin. |
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|
Term
|
Definition
| cAMP Response Element-Binding. RTF. Gets activated in response to cell-signalling molecules that cause an increase in cAMP. Recognizes response element with concensus seq. 5’-TGACGTCA-3’. Binds to DNA and stimulates transcription. If unphosphorylated it can still bind to DNA, but not activate the RNA pol. |
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Term
|
Definition
| – infreq. And highly regulated event. |
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Term
|
Definition
| – converts hemi-methylated to fully methylated DNA. Efficient and routine event. |
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Term
|
Definition
| change in chromatin structure. Carried out by DNA methhyltransferase. Silences gene. Eg. abnormal methylation of tumor suppressor gene= bad. Heritable. |
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|
Term
|
Definition
| – necessary to ensure (1) expression of genes in an accurate pattern during development (2) differences between distinct cell types. Influences = regulatory transcription factors, compaction level of chromatin during transcription, DNA methylation (inhibits), Durign RNA processing: Alternative splicing, RNA editing. During Translation: Small RNAs (miRNA) silence translation of mRNA. Phosporylation of TFs, Protein binding to 5’ end Posttranslational: feedback inhibition, covalent modifications |
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|
Term
| General transcription factors: |
|
Definition
| req for binding of RNA pol. To core promoter and for its progression to elongation stage. Necessary for basal transcription. |
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Term
|
Definition
| . influence nutrient metabolism in most cells. Promote glc use, fat metabol, protein breakdown. |
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Term
|
Definition
| inc. estrogen and testosterone. Infl. Growth and fn of the gonads |
|
|
Term
|
Definition
| assists in recognition of base sequence between DNA and RTF |
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Term
|
Definition
| – formed by 2 different transcription factors |
|
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Term
|
Definition
| formed by two identical TFs |
|
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Term
|
Definition
| causes zipping up by protein dimerization - DNA binding protein |
|
|
Term
|
Definition
| – activator protein interacts with it, enables RNA polymerase to form preinitiation complex |
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|
Term
| Regulatory transcription factors |
|
Definition
| regulate the rate of transcription of nearby genes. Influence ability of RNA pol to begin transcription of a particular gene. Recognize regulatory elements (respose/control/regulatory elements)located near core promoter. Binding of RTFs affects transcription of associated gene. Is either an Activator binding to an enhancer, or a repressor binding to a silencer. Are usually orientation independent/bidirectional. Have domains that have specific functions eg DNA binding or molecule binding.. eg. helix-turn-helixm leucine zipper, zinc finger. Usually do not bind directly to RNA pol. But through TFIID or Mediator. Modulated by binding of small effector molecule, protein protein interactions, or covalent modification. |
|
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Term
|
Definition
| – RTFs that respond to steroids. Hormone binds to TFs. EG glucocorticoids and Gonadocorticoids |
|
|
Term
|
Definition
| when bound activates transcription |
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|
Term
|
Definition
| charge interactions allow binding - DNA binding protein |
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|
Term
|
Definition
| biological advantage, when pre-mRNA can be spliced in more than one way. In most cases, large sections of coding regions are the same resulting in 2 alt. versions. Degree of splicing varies greatly among different species. Eg how smooth vs striated muscle cells are produced. Not random – involves splicing factors which choose splice sites. |
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|
Term
|
Definition
| can silence exp. of certain genes. - RNAi |
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|
Term
|
Definition
| directs addition or deletion of Uracils in trypanosomes. Eg also, human ApoB mRNA = CAA UAA. Amyotrophic lateral sclerosis (ALS) |
|
|
Term
| Iron Response Element (IRE) |
|
Definition
| found in 5’ UTR in ferritin mRNA and in 3’ UTR in transferring receptor mRNA |
|
|
Term
| Iron regulatory protein (IRP) |
|
Definition
| regulates iron assimilation by influencing ferritin mRNA and transferring receptor mRNA. Binds to IRE. When high iron on Ferritin receptor, binds to iron and releases. Ferritin protein synthesized. Low iron on Transferring: stays bound, stabilizing mRNA, and Transferrin is synthesized high, binds to iron and mRNA is degraded. |
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|
Term
|
Definition
| varies considerably – can be regulated so its half life is lengthened or shortened, influencing mRNA concentration. Length of polyAtail affects this. Recognized by polyA-binding protein. Over cell life, poly-A tail shortened. When too short, cannot be recognized anymore, and is degraded. Also affected by destabilizing elements: found esp. in mRNAs that have short half lives. Can be found anywhere on the mRNA, but are most common at 3’ end btwn codon and polyAtailEg. AU rich element (ARE) |
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|
Term
|
Definition
|
|
Term
|
Definition
| change in nucleotide seq. of RNA molecule. Involves additions/deletions/conversions of bases. Can generate start or stop codons, or change coding seq of polypeptide. |
|
|
Term
|
Definition
| form of gene regulation that can offer defence against viruses and plays roles in silencing transposable elements. |
|
|
Term
| RNA induced silencing complex |
|
Definition
| RISC. Formed by dicer forming a siRNA (ds) – recognized by protein that forms RISC, forming to (SS). siRNA then binds to mRNA and is degraded or just prevents translation |
|
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Term
|
Definition
| - recognizes 5’ and 3’ splice sites and removes the intron. |
|
|
Term
|
Definition
| choose splicing sites eg. sr proteins modulate ability of spliceosomes to recog. or choose splice sites. Happens by inhibition of spliceosome recognition, or enhancement of spliceosome recognition. |
|
|
Term
|
Definition
| at their C-terminal end have domain rich in serine (S) and arginine (R). At N terminal end, have RNA binding domain. |
|
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Term
|
Definition
|
|
Term
|
Definition
| antibiotic resistance to host cell |
|
|
Term
|
Definition
|
|
Term
|
Definition
| complementary DNA, made from RNA by reverse transcriptase. Used because no introns, therefore useful for protein expression |
|
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Term
|
Definition
| splices 2 DNA fragments together with a covalent bond –type of restriction enzyme. |
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Term
|
Definition
isolating and making many copies of a gene usually involve chromosomal DNA (source of segment of interest) and Vector DNA (Carrier of segment to be cloned- can replicate independently of host chromosomal DNA). Common vectors are Plasmids and Viruses. Plasmids can have selectable markers.
Steps - confer resistance to antibiotics via ampR, and make sure that they can encode β-galactosidase for identification
- mix with e-coli permeable to plasmid
- plate on media w/ x-gal (blue if cleaved by βgalatosidase), ampicillin and IPTG (induces lacZ). WHITE = competent, blue – non-competent
Produces an enormous amount of copies of a gene |
|
|
Term
|
Definition
| cell that harbours a vector |
|
|
Term
| Recombinant DNA molecules |
|
Definition
| – chimera of 2 DNA fragments from different sources |
|
|
Term
| Restriction endonucleases / restriction enzymes |
|
Definition
| – bind and cleave at specific locations. Natural role involves protection from invasion by foreign DNA. Typically palindromic. Sometimes ends are sticky, sometimes blunt. |
|
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Term
|
Definition
| – way of examining locations of restriction sites. – cut with various restriction enzymes, then run out on gel. compare sizes. Or by sequencing. |
|
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Term
|
Definition
| process of obtaining smaller clones from a larger chromosomal DNA insert |
|
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Term
|
Definition
| – single tube sequencing, and each dideoxyribonucleotide has a diff. colour fluorescent label attached. Loaded into single lane of gel. Identified by spec. |
|
|
Term
| Denaturing-annealing-synthesis |
|
Definition
| cycle used in PCR to synthesis DNA # cycles = 2x X increase. |
|
|
Term
|
Definition
|
|
Term
|
Definition
| DNA probe technique to clone a specific gene – identified by transferring some of a colony to an x-ray film, treating it and identifying |
|
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Term
|
Definition
| when starting material is RNA. Represents expressed genes. |
|
|
Term
|
Definition
| collection of thousands of different cloned fragments of DNA from cutting up genome of an organism. |
|
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Term
|
Definition
| to study binding of proteins to sites on DNA |
|
|
Term
| Dideoxy sequencing method |
|
Definition
| PCR DNA, clone target DNA into vector nd isolate ssDNA (if dsDNA used, must be denatured at beginning of exp.). dideoxy added so that growing DNA strand can no longer grow aka chain termination – known to be ATG or C. Then run out on acrylamide gel. |
|
|
Term
|
Definition
| used to study binding of proteins to sites on DNA. Binding of protein to a frag of DNA retards its rate of movement through a gel aka band shift assay |
|
|
Term
|
Definition
| – a DNA library when starting material is chromosomal DNA. Contains genes, introns, junk DNA, and regulatory stuff |
|
|
Term
|
Definition
technique for copying DNA w/o host cell and vectors Starting material =
• Template DNA
• Oligonucleotide primers (complementary to seq flanking DNA frag.)
• dNTPs –deoxynucleoside triphosphates
• Taq polymerase – Thermus aquaticus |
|
|
Term
|
Definition
| identifies specific RNA within a mix of many RNA molecules |
|
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Term
|
Definition
| reverse transcriptase PCR – used to quantify amount of RNA in cells. RNA isolated from sample, mixed with reverse transcriptase and a 3’ primer to gen. sscDNA which is used as a template for conventional PCR |
|
|
Term
|
Definition
| detects presence of a particular gene seq within many. Can determine copy number of a gene, can detect small gene deletions, gene families and homologous genes among diff species. |
|
|
Term
|
Definition
| identifies specific proteins within mixtures of many protein molecules via antibodies |
|
|
Term
|
Definition
| # copies of an allele in pop / tot. # all alleles for that gene in a pop. |
|
|
Term
|
Definition
|
|
Term
|
Definition
| all alleles of every gene in a population |
|
|
Term
|
Definition
| # individuals w/ genotype in pop / tot # individuals in pop |
|
|
Term
| Hardy-Weinberg equation / equilibrium theory |
|
Definition
calc. that relates allele and genotype freq. in a pop. In uilibrium = allele and genotype freq. do not change over course of many generations
p2+2pq+q2 where p = dom allele freq, q = recessive allele freq
does not apply if:
• new mutations
• genetic drift
• migration
• nat. selection
• not random mating
can be applied to 3+ alleles by (p+q+r…)2 = 1. tested by χ2 test |
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Definition
| – a subpopulation more likely to breed with each other. Usually separated by geographic barriers |
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Definition
| exists predominantly as a single allele. 99% |
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Definition
| traits display variation within a population. Eg Happyface spider. At DNA level: due to 2+ alleles that influence phenotype (gen var….) also used to desc. a gene that exists as 2+ alleles in a population. |
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Definition
| – a group of individuals of the same species that occupy the same region and can interbreed |
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Term
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Definition
| central issue = genetic variation- extent, why, and how it changes |
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Term
| Single-nucleotide polymorphism |
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Definition
| SNP – account for 90% of var btwn people. |
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Definition
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Term
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Definition
| – individuals do not mate randomly |
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Definition
– nat selection that favours the maintenance of 2+ alleles. Pop not evolving toward allele fixation. Can occur b/c of heterozygote advantage, or because a species occupies a region that contains heterogeneous environments.
Selection coefficient = s = 1-W
eg sicklecell/malaria, cystic fibrosis, tay-sach disease. |
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Term
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Definition
| when a population is reduced dramatically by nat. disaster randomly eliminating individuals. |
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Term
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Definition
| recipient pop of migration. Can calc new allelic freq. if we know original allelic freq of donor and recip pops, and the proportion of conglomerate pop that is due to migrants. ΔpC = m(pD – pR). ΔPC = change in allele freq in conglomerate pop. PD is allele freq. in donor pop. PR in orig. recipient pop. M = proportion of migrants that make up conglomerate pop……m=# donor individuals in cong / total # individuals in conglomerate. |
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Definition
| relative likelihood that a phenotype will survive and contribute to the gene pool of the next generation. Gene with highest reproductive ability = 1.0. other genes set relative to that. Can be due to fittest phenotype being more likely to survive, mate, or is more fertile. |
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Term
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Definition
| jumping genes about 1 500 bp. Can move about in the genome. 11 in atlantic salmon. Simlar seq. in other fish. Burst of transposon seq. coincides with speciation time, possibly from reorginizing the genome or parasites spreading transposons? |
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Term
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Definition
| nat. selection that favours survival or one extreme phenotype that is better adapted to survive an environmental condition. Affects hardy-weinberg eq. and allele freq. by favouring the extreme phenotype. In next gen, HW eq. will be p2WAA, 2pqWAa, q2Waa.. do not add up to 1, but the mean fitness value = Wbar. Solve by dividing both sides by Wbar.. Eg = DDT resistance in insects. |
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Definition
| nat. selection that favours survival of 2+ different phenotypes. Caused by fitness values that vary in different environments. Eg. snail that lives in woods and open fields. Migration maintains balance of polymorphisms. |
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Term
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Definition
| when an exon and flanking introns are inserted into a gene. May involve duplication and rearrangement. Results in novel genes with additional fnctnl domains. May be promoted by transposable elements, can be caused by nonhomologous double crossovers. |
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Term
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Definition
| – beak length depends on expression of calmodulin gene – high levels = long pointy beaks. Low levels = more robust beaks. Depth depends on Bmp4 (bone morphogenic protein 4, transcription factor) high exp = deep and broad. |
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Term
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Definition
| small group of individuals separates from a larger pop and establishes a colony in a new loc. Founding pop is expected to have less gen var than original pop. Will also have allelic freq. that may differ markedly from the original pop. |
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Term
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Definition
| random changes in allele freq due to chance fluctuations. Favours loss or fixation of an allele. Smaller pops, allele freq. fluctuates a lot from gen to gen. Isolated populations are more susceptible to drift. Eg. Bottleneck effect and founder effect. |
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Definition
| xchng of gen material among different species. Common phenomenon – prokaryotic cell may be taken up by eukaryotic cell, bacterial conjugation, viral transfer. Eg salmonidae |
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Definition
| mating btwn genetically related individuals. Small gene pool. |
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Term
| Inbreeding coefficient (F) |
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Definition
| quantification of degrwee of relatedness. Measures change that homozygosity is due to common ancestor. |
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Term
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Definition
| – changes in a population’s gene pool from generation to generation. Affects allelic frequencies. Driven by mutation, genetic drift, migration, natural selection, non-random mating |
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Definition
| – btwn 2 different established populations. New pop is a conglomerate |
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Definition
| probability that a gene will be altered by a new mutation = # of new mutations in a given gene per generation. Usually around 10-5 – 10-6. Increased by mutagens. |
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Definition
| the source of genetic variation. Changes in DNA sequence. Random and low rates. Can be beneficial, neutral, or deleterious. Last two far more likely than beneficial. U = rate of Aa. After 1 generation, increase in a = Δq = u∙p. Many generations = (1-u)t = Pt / P0 where t = # generations and p are allelic freq. |
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Term
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Definition
Darwin and Russel – most adapted individuals survive and pass on gene. Related to mating efficiency and fertility, as well as differential survival.
• Withing a pop there is allelic var. arising from var. factors such as mutations causing differences in DNA seq. Distinct alleles encode proteins of differing fns.
• Some alleles may encode proteins that enhance an individual’s survival or reproductive capacity
• Individuals with beneficial alleles are more likely to survive and reproduce.
• Over many generations, allele freq. of many different genes may change through nat. selection.
Occurs on phenotypes. Operates by directional selection, stabilizing selection, disruptive selection, or balancing |
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Term
| Negative assortative mating |
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Definition
| individuals with dissimilar phenotypes mate preferentially |
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Term
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Definition
| happens! Violated freq. in human pops. Wrt phenotypes: Assortative matin, Positive assortative mating, negative assortative mating. Wrt genotypes – inbreeding and outbreeding |
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Term
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Definition
| mating between genetically unrelated individuals |
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Term
| Positive assortative mating |
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Definition
| – occurs when individuals with dissimilar phenotypes mate preferentially. |
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Term
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Definition
| sex. Reproduction, prokaryotic gene transfer, DNA mutations, chromosome structure changes. |
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Term
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Definition
| nat. selection that favours the survival or individuals with intermediate phenotypes. Tends to decrease genetic diversity. Eg laying eggs. Too many eggs drains resources to care for young. Too few does not contribute to next gen. |
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Term
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Definition
| – when species have become geographically separated from each other – geological or founder effect |
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Term
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Definition
| – single species transformed into different sp. over many generations |
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Term
| Biological species concept |
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Definition
| species is a group of individuals whose members can interbreed to produce viable fertile offspring. |
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Term
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Definition
| single species divided into 2+ species….most common form of speciation c an be allopatric, parapatric, or sympatric |
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Term
| Ecological species concept |
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Definition
| each species occupies an ecological niche. Unique set of habitat resources .Nice overlap results in competition. Competing individuals likely to be of same species. |
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Term
| Evolutionary developmental biology |
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Definition
| (EVO-DEVO) role of developmental genes in the evolution of new species – embryonic development |
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Term
| Evolutionary species concept |
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Definition
| – derived from single distinct lineage. Based on pathway that led to species. Want to look at the relationships between species. |
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Term
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Definition
| + copies of homologous genes within the genome of a single organism. |
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Term
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Definition
| – each new sp. evolves continuously over long spans of time |
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Term
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Definition
| where 2 pops can interbreed. Geneflow here must be limited for speciation to occur. |
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Term
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Definition
| derived from the same ancestor orthologous or paralogous eg humans vs horses – α globin and β globin genes are othologues between humans and horses. But human α globin and β globin genes are paralogs. Orthologues more similar than paralogues. |
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Term
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Definition
| relatively large changes in form and function that are sufficient to produce new species and higher taxa. |
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Term
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Definition
| changes in gene pool wrt. Particular alleles over measurable periods of time |
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Term
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Definition
| molecular changes in gen material that underlie the phenotypic changes assoc. with evolution. |
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Term
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Definition
| homolgous genes found in diff sp. |
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Term
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Definition
| homologous genes found within a single sp. from gene duplication. |
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Term
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Definition
| sp. not completely geographically separated eg mountain range, or a species is sedentary. |
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Term
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Definition
| prevents development of viable individual after fertilization. |
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Term
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Definition
| prevents formation of a zygote |
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Term
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Definition
| diagram that desc. phylogeny of a species. Based on morph, phys, biochem, behaviour, DNA |
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Term
| Phylogenic species concept |
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Definition
| members of a single species are identified by having a unique combination of char. Traits. |
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Term
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Definition
| seq. of events involved in evodevo of sp, or group of sp. |
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Term
| Punctuate equilibrium (punk-eek) |
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Definition
| species exist unchanged for many generations, with short periods of rapid evolution. |
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Term
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Definition
| formation of new species via evolution Anagenesis or cladogenesis. Can be fast or slow. Not constant Gradualism or punctuated equilibrium (punk-eek) |
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Term
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Definition
| group of organisms w/ distinct set of attributes – may exist in 2+ distinct pops that are evolving slowly into diff. species. Can be defined by morphological traits, ability to interbreed, evolutionary lineages, ecological factors. Depends on species in question. |
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Term
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Definition
| – occurs when members of a species initially occupy same habitat within same range. Eg polyploidy in plants leads to reproductive isolation |
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Term
| Cladistic approach to phylogenetic tree |
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Definition
| groups consist of single common ancestor and all its descendants. Shared traits are ancestral (primitive) |
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Term
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Definition
| – compares development of species to understand ancestral relationships and developmental mechanisms that bring about evo change. Esp. master control genes eg. webbed feet of ducks vs claws of chickens – BMP4 causes cell death, while gremlin prevents is. Gremlin expressed in ducks. Eg eyes and pax6 |
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Term
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Definition
| – a measure of evo time. Constant rate of neutral mutations = number of mutations propotional to separation time. Assumes nucleotide differences assumed to be mostly due to neutral mutations, and assumes linear relationship. |
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Term
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Definition
do not affect phenotype of organism, therefore not acted on by nat. selection. ..survival of the luckiest, non-darwinian evo.
• For each protein, rate of evo in terms of amino acid subs. Is approx. constant wrt neutral substituations.
• During evo, proteins that are fn less important will accumulate amino acid substitutions more rapidly that important proteins
• Amino acid substitutions that do not disrupt existing structure and function occur more freq. in evolution than disruptive aminon changes.
• Gene duplication must always precede the emergence of a gene having a new fn.
• Selective elimination of definitely deleterious mutations and random fixation of selectively neutral or very slightly deleterious alleles occur far more freq. in evo than Darwinian selection of advantageous mutants |
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Term
| Neutral theory of evolution |
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Definition
| kimura –most gen. var obtained in nat pops is due to accumulation of neutral mutations. |
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Term
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Definition
| principal of least astonishment |
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Term
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Definition
| – trait shared by group of organisms, but not distant common ancestor. |
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Term
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Definition
| delineate proteins on gel with spots – then correlated with protein. Cut out from gel, purify, protease treat it, then do tandem mass spec. MALDI-TOF |
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Term
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Definition
| – extract info within gen. seq. using a mathematical approach |
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Term
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Definition
| – identifying genes whose pattern of expression strongly correlates with each other. |
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Definition
| elucidate roles of genetic sequences in a given seq. |
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Term
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Definition
| dotted with many small DNA seq. frags, corresponding to known genes. Allows study of whole genome under different enviro conditions. |
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Term
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Definition
| entire collection of proteins an organism can make. Much larger than genome. Largersize related to alternative splicing, RNA editing, and posttans. Covalent mod. Proteins produced depends on cell type, stage of development, and enviro. Conditions. |
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Definition
| understand fn roles of proteins |
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Term
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Definition
| basic local alignment search tool. When 2+ geneti c sequences are multiple seq. alignment |
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Term
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Definition
| nucleotide sequence w/o stop codons. |
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