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| observation of genes. Phenotype expresses genotype. |
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| gene that produces the same phenotype in the organism whether or not its allele identical |
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| Of or relating to a trait that is expressed only when the determining allele is present in the homozygous condition. |
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| Co-dominance occurs when the contributions of both alleles are visible in the phenotype. In the ABO example, the IA and IB alleles are co-dominant in producing the AB blood group phenotype, in which both A- and B-type antigens are made. |
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ability to see any aspect of genotype at phenotypic level.
No gene acts independently.
the proportion of individuals carrying a particular variation of a gene (allele or genotype) that also express an associated trait (phenotype) |
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| A mutation that results in reduced or abolished protein function. |
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normal gene turns itself on rather than another gene turning it on.
Gain-of-function mutations,which are much less common, confer an abnormal activity on a protein. |
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| normal copy, mutated copy. mutated copy fucks up the other. Now normal copies can't work. |
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need two functioning copies to survive. if only one, then it is not enough for the protein. Lethal.
ccurs when a diploid organism only has a single functional copy of a gene (with the other copy inactivated by mutation) and the single functional copy of the gene does not produce enough of a gene product (typically a protein) to bring about a wild-type condition, leading to an abnormal or diseased state. It is responsible for some but not all autosomal dominant disorders.
Haploinsufficiency is therefore an example of incomplete or partial dominance, as a heterozygote (with one mutant and one normal allele) displays a phenotypic effect. |
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| changes in the codon but codon still codes for the same amino acid. |
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| specifies for different amino acids. |
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| changes the codon to a stop codon. |
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| insertion or deletion of bases other than 3. changes the protein encoded for that point on. Generally leads to a non-functioning protein. |
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subunits are often held by hydrophobic ends. hydrophobic interaction is weaker at lower temperatures and proteins therefore fail to assemble.
protein wont grow at lower temps. |
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protein folds properly at low temperatures, but unfolds at high temperatures. therefore making the protein inactive. if protein is essential, a miss-sense mutation will occur.
rarer then high temp sensitivity. |
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| mutations whose affects depend on the environment. |
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| genetic recombination. formation of haploids from diploids. when gametes are formed. |
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| division of eukaryotic cell into two daughter cells with identical sets of chromosomes. |
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| reproductive cells. gametes merge to make zygotes |
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| cell formed by union of sperm and egg which develops into a new individual. |
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| A gene related to a second gene by descent from a common ancestral DNA sequence. |
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| genes in different species that evolved from a common ancestral gene by speciation. |
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| genes related by duplication within a genome. Orthologs retain the same function in the course of evolution, whereas paralogs evolve new functions, even if these are related to the original one. |
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| special case of paralogy resulting from polyploidy. Homeologous chromosomes are created through chromosome duplication events, specifically with meiosis I and polyploidy. |
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| a polyploid individual or strain having a chromosome set composed of two or more chromosome sets derived more or less complete from different species |
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| an individual or strain whose chromosome complement consists of more than two complete copies of the genome of a single ancestral species |
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method for testing whether two mutations occur in the same gene or in different genes.
if fail to compliment, mutants are in the same gene.
essential for mapping genomes through recombination. If on different chromosomes, they will separate differently. watch recombinant percentage. if on same chromosome you will get 50 cM to 50 cM. |
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| Recombination frequency (θ) is the frequency that a single chromosomal crossover will take place between two genes during meiosis. A centimorgan (cM) is a unit that describes a recombination frequency of 1%. In this way we can measure the genetic distance between two loci, based upon their recombination frequency. |
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the further the genes are apart, the more the recombination theory.
the closer they are to one another the less the recombination frequency. |
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| if a restriction enzyme that generates sticky ends is used, the vector and insert will have matching overhangs. |
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| if a restriction enzyme that generates blunt ends is used, ligation is more difficult and T4 ligase must be used. |
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| the covalent linking of two ends of DNA molecules using DNA ligase |
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| circular, non-essential bit of bacterial DNA. transmissible. carry resistance to antibiotics. used to clone fragments of DNA. limitations: they have a max size of 14-15,000 base pairs. |
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| used as vectors. like plasmids, but can hold a higher amount of base pairs for transmission--20,000 bp. They are DNA like crazy. |
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| hybrid of plasmid and virus vectors. (lambda phage and plasmid). problem: there are multiple copies per cell. 45,000 bases pairs read. |
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| yeast artificial chromosomes. Easy to clone. 300,000-1,000,000 base pairs. problem: they are fairly unstable, and highly recombinagenic. |
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| bacterial artificial chromosome. restricted origin. 1 copy per cell instead of multiple. |
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| allows you to cut out chromosome. DNA inserted into a shuttle vector can be tested or manipulated in two different cell types. The main advantage of these vectors is they can be manipulated in E. coli then used in a system which is more difficult or slower to use (e.g. yeast, other bacteria). |
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for copied DNA. is a combination of cloned cDNA (complementary DNA) fragments inserted into a collection of host cells.
cDNA is produced from fully transcribed mRNA found in the nucleus and therefore contains only the expressed genes of an organism. |
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| express sequence tags. way to get partial info for all other genes. sequence the 5 prime end. |
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serial analysis of gene expression.
make fragments of cDNAs. lumps, clone, and tag. less time consuming. |
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| high input, quick results. 10 gb comes back. |
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| ability to seperate molcules based on size and charge. we care about size. b/c DNA is negatively charged, the DNA goes through the gel to positive bottom end. for bigger fragments use argarose gell. for small fragments use polymethacrylimide gel. |
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| hybridization fundamentals |
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| used to make clones. would never use this for a genomic library, instead we use bacteria phages and filter arrays. |
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Polymerase chain reaction. developed from DNA that could withstand over 95 degree temps. steps are:
anneal primers
elongate primers
repeat step one and two and gain excess primer. now have 4 copies.
repeat!
very temp specific process, heat up in the beginning for denaturation.
efficient for under 2,000 base pairs. |
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| RT-PCR (reverse transcription-polymerase chain reaction) is the most sensitive technique for mRNA detection and quantitation currently available. Compared to the two other commonly used techniques for quantifying mRNA levels, Northern blot analysis and RNase protection assay, RT-PCR can be used to quantify mRNA levels from much smaller samples. In fact, this technique is sensitive enough to enable quantitation of RNA from a single cell. |
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| quantitative pcr. Quantitative PCR is a method used to detect relative or absolute gene expression level. All qPCR involves the use of fluorescence to detect the threshold cycle (Ct) during PCR when the level of fluorescence gives signal over the background and is in the linear portion of the amplified curve. allows us to see how much of a gene is being expressed and where. |
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| sanger termination sequencing |
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| the key principle of the Sanger method was the use of dideoxynucleotide triphosphates (ddNTPs) as DNA chain terminators. extension is initiated at a specific site on the template DNA by using a short oligonucleotide 'primer' complementary to the template at that region. The oligonucleotide primer is extended using a DNA polymerase, an enzyme that replicates DNA. An alternative to the labelling of the primer is to label the terminators instead, commonly called 'dye terminator sequencing'. The major advantage of this approach is the complete sequencing set can be performed in a single reaction, rather than the four needed with the labeled-primer approach. give each base a color based on its wave length. |
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| a DNA sequencing method based on chemical modification of DNA and subsequent cleavage at specific bases. Maxam–Gilbert sequencing rapidly became more popular, since purified DNA could be used directly, while the initial Sanger method required that each read start be cloned for production of single-stranded DNA. Though sanger then improved his method more and this one lost followers. |
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| capillary electrophoresis |
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| used to separate ionic species by their charge and frictional forces and hydrodynamic radius. |
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| garbage DNA. repeats slow things down. |
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| 4-6,000 bases length read. $4,000 cost per run. .5Gbases total. |
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100 read length. total bases read: 10-20 Gbases.
$10,000 per run |
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read length- 75
total bases-20-30 gbases
$10,000 per run
reads sequences 3 times, so practically no error. |
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| detect and quantify all RNAs in a tissue. |
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| detect transcription factor binding sites. chemically crosslink DNA where they are bound, then remove transcription factor. Tell where transcription is bound. |
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| the study of metagenomes, genetic material recovered directly from environmental samples. ex: ocean sea water. many of the organisms in the water are uncultivatable in the lab. |
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| 3rd generation sequencing |
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dye tagged gamma phosphates
no DNA preparation needed.
bases are colored.
able to translate a single molecule. |
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| createa single opening in membrane. measure resistance across the pore. watch what base fall through. no polymerase needed. are able to watch proteins assemble. |
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1. Cleave with restriction enzyme
2. gel electrophoresis
3a. capillary action transfers DNA from gel to nitrocellulose
3b.transfer gel image onto gel
4. hybridize with labeled DNA or RNA probe. |
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1. Cleave with restriction enzyme
2. gel electrophoresis
3a. capillary action transfers DNA from gel to nitrocellulose
3b.transfer gel image onto gel
4. hybridize with labeled DNA or RNA probe.
this process transfers DNA. |
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to study gene expression by detection of RNA (or isolated mRNA) in a sample.Northern blotting involves the use of electrophoresis to separate RNA samples by size, and detection with a hybridization probe complementary to part of or the entire target sequence. The term 'northern blot' actually refers specifically to the capillary transfer of RNA from the electrophoresis gel to the blotting membrane.
this process transfers DNA. |
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| the more similar the restriction fragment, the more similar the organism. |
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staining with a probe.
tissue are all relatively in tact. allows us to determine in what tissue a gene is being expressed and at what time in development. |
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| A microarray works by exploiting the ability of a given mRNA molecule to bind specifically to, or hybridize to, the DNA template from which it originated. By using an array containing many DNA samples, scientists can determine, in a single experiment, the expression levels of hundreds or thousands of genes within a cell by measuring the amount of mRNA bound to each site on the array. With the aid of a computer, the amount of mRNA bound to the spot. |
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| cluster genes who follow same time course. creating heat maps. red is down, green is up. allows us to find the origin of glycolysis. |
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| bacterial expression vector |
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| expression of proteins through bacterial cells. if you starve for lactose, then the protein won't be expressed. |
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| used if protein won't be expressed in a bacterial host. |
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in order to analyze the long term impact of altered gene or protein expression investigators typically utilize stable transfection protocols to develop stable cell lines.
a vector is created w/an animal promoter and an animal selectable marker. can only be expressed in animal cells. problem: high chance for rearrangement and cant tell where genome is going. |
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to analyze the short term impact of altered gene or protein expression.
studied the short term production of RNA in 24 hours. take plasmid that does not have a specified gene, replicated and moved into the nucleus but not into the chromosome. all cells will engage in transient transfection. more useful when trying to study a specific promoted. |
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| pronuclear injection for transgenics. |
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1. inject foreign DNA into one of the pronuclei.
2. tranfer injected eggs into foster mother.
3. about 10-30% of the offspring will contain the foreign DNA in chromosomes of all their tissues and germ line.
breed mice expressing foreign DNA to propagate through the germ line. |
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| ES (embryonic stem cells) |
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| a mouse with a particular gene knocked out in all cells for that gene |
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| demonstrates that you can contruct a reporter gene. fusion occurs at tip. |
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| site specific gene knock out. in either specific time or tissue. |
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a system within living cells that takes part in controlling which genes are active and how active they are.
There are two types:
knock out, and knock down.
can only be done in vitro. |
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| rid of part or all of a gene. so no more function. |
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| RNA interference. expression is not completely lost. 10%-20% function. easier to do. degrades or represses. |
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Created by backwards slippage.
DNA differs among people. repeated sequences themselves are the same from person to person, however the number of times it is repeated tends to vary (VNTR). which is why it can be used for paternity testing. Not all SSR's are variable between people, but the amount of times the SSR is repeated (VNTR) is variable. |
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| 20-50 base pairs. the mini and micro differ by the size of the repeat structure. satellite DNA are apart of the centromere. |
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| located at the centromere. Repeated sequenced in DNA. can occur at diffferent lengths. non-coding. |
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they are pre-existing genetic material, either RNA (retrotransposons) and DNA (dna transposons) which only cut and pastes. They code for nothing except for themselves, also known as selfish DNA.
retrotransposons have RNA as an intermediate. Retrotransposons only copy and paste. |
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| retrotransposons can spread and leave LTR sequences. |
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| if inserted into essential DNA, it causes death. only does copy and paste, not cut and paste. two different types LTR and Non LTR retrotransposons. |
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| are a type of retrotransposon. non-LTR retrotransposon. |
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| SINES are non-LTR retrotransposons. Short interspersed repetitive elements. Alu is most common type. presence of Alu repeat can cause unequal crossing over and therefore be dangerous or give rise to new function. The danger is why it is linked to cancer and diseases. Alu is useful marker when transferring DNA from species to species. |
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| Endosymbiont origin of mito and chloroplast |
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| they were own bacteria, but they joined and as time went by it became impossible to live outside the cell. |
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| difference between Mitochondria and Human Genome |
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Mito:
circular, not associated with histones.
much closer related to bacteria. Maternally inherited.
tubular network-a network that is in a state of motion.
Human: all linear and associted with histones. |
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| Mitochondrial vs. Nuclear encoded proteins |
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| membrane bound transport proteins are assembled from all types of producers, some stricly mito, some strictly nuclear, some both. all RNA's are variable, but rRNA is always encoded in the mito. Why important: useful for phylogenetics...BUT WHY CARRYE. HAHA |
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| a nuclear encoded mitochondrial mutation DNA polymerase |
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| exact same age btwn mice. but the other is aging faster bc DNA polymerase is errored. accumulation of damaged mDNA creates aging. if we repaired mitchondiral issues we could extend life. |
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| is transcribed by a nuclear encoded RNA polymerase composed of two subunits. has sigma factor. |
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| is transcribed by a chloroplast-encoded RNA polymerase. much larger. lacks sigma factor. |
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