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Definition
| analysis of the relations (in structure and sequence) of the genome sequences of two or more species |
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Definition
-genes that share a significant level of sequence identity
-most closely related genes (similarity in DNA and amino acid sequences)
-genes chard specific amount of sequence identity |
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| -specific gene inherited by a common ancestor |
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Definition
-genes that are related by gene-duplication events
i.e. fetal hemoglobin compared to adult hemoglobin |
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Definition
is a major mechanism through which new genetic material is generated during molecular evolution. It can be defined as any duplication of a region of DNA that contains a gene. Gene duplications can arise as products of several types of errors in DNA replication and repair machinery as well as through fortuitous capture by selfish genetic elements. Common sources of gene duplications include ectopic homologous recombination, retrotransposition event, aneuploidy, polyploidy, and replication slippage
Why gene duplication?
-more protein produced
-1 copy might not function -> from psuedogene
-other recombination events may cause duplicated gene to move away |
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Definition
-method used to analyze the expression of all genes in a genome
-able to look at expression of all genes at the same time, and whether or not genes are being expressed in a tissue/how much they are being expressed
-mRNA from cells of interest on glass plate - use fluorescent cDNA with reverse transcriptase as probe -> hybridizes to mRNA (color shows where expressed)
-can replace a Northern Blot - unless no microarray exists - then make Northern Blot |
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| Chromatin immunoprecipitation (ChIP) assay |
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Definition
- a type of immunoprecipitation experimental technique used to investigate the interaction between proteins and DNA in the cell.
-method used to map where proteins (i.e. transcription factors) bind to DNA sequences in a genome
-make an antibody from purified protein so that we can see where antibodies bind to find out where the proteins bind to in the genome, and then the sequence of where it binds
-(used to find where transcription factors bind)
-adding antibody after letting transcription factor bind to DNA precipitates that transcription factor out
-we then find sequences on the genome that are close to proximity of where this TF binds - so now we will know where it binds |
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Definition
-used instead of mouse knockout
-(used to eliminate viruses)
1. double strand RNA -> b/c single stranded degrades too quickly
2. Break into small pieces using "Dicer"
3. Pieces Bind to RISC
-can be a simple mechanism to "turn off" a gene |
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| Green Fluorescent Protein (GFP) |
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Definition
| -used to mark a reporter gene -> to use RNAi all you need is a means to get a transgene expressed in an organism -> this expression can be scene by marking that gene with GFP |
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| When to use DNA microarray |
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Definition
-replaces Northern Blot & RTPCR
-can find issues in different levels of expression using these (healthy vs. sick)
-same tissue -> expression before and after some treatment
-find expression of different tissues |
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Definition
-search for mRNA in cell with matching sequence and destroy it
1. grabs a hold of one of the strand of RNA
2. RISC complex can use that small piece of RNA as a guide
3. it scans the mRNA and if it finds a match it destroys that target |
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Term
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Definition
-the method in which a whole genome is sequenced on beads
-single strands immobilized on individual brands -> amplified by PCR but still attached to beads
-each bead contains many identical DNA fragments and is deposited individually into small wells in a device that hosts the sequencing reactions
-DNA polymerase, a particular dNTP, and 2 enzymes pass through each well -> light is made and that indicates the dNTP was added to the new strand, so that dNTP added is known and therefore the corresponding base in the template strand is known
-if there is more light for one type of base - two were added
-ability to sequence an amazing amount in a short amount of time at a very low price |
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