agry lab quiz 2

the locus corresponding to the TTG1 gene is Arabidopsis is AT5G24520. on which chromosome is this gene located on?

chromosome 5

what are introns

(int)ragenic regi(ons) that are noncoding nucleotide sequences of DNA

what are exons

(ex)pressed regi(ons) that are coding nucleotide sequences of DNA

what are GO terms

Gene Ontology, terms are used to predict information about a gene product by using computational model of biological systems

what are the differences and similarities between gDNA, mRNA< cDNA, and CDS

-gDNA is the genomic DNA, this includes the promoter, 5’ UTR, introns, exons, and 3’ UTR sequences

-mRNA is messenger RNA, this includes the 5’ CAP, 5’UTR, spliced exons, 3’ UTR, and poly A tail. this molecule is transcribed from gDNA and modified

-cDNA is the complementary DNA, this molecule is derived from mRNA using reverse transcriptase and is more stable to work with than RNA

-CDS = coding sequence, and represents the nucleotides that are translated into a protein

what mutant phenotypes do you expect to see this semester

-GL2 is important for trichome development, seed oil content, root hair formation, and anthocyanin biosynthesis. likely to have changes in these features such as deformed trichomes, changes in seed coat composition

-SUB is important in plant development (floral shape, stem development, cell shape, trichome development), sub mutants will likely have deformed flowers, altered fertility, abnormal trichomes, unusual stems

what is an operon

a cluster of structural genes along with their regulatory regions, such as the lac operon

what is a reporter gene? list 3 examples

reporter genes are used to provide some info about an organism to a researcher, they encode for a visible or detectable gene product.

ex: lacZ, GFP, GUS, blue fluorescent protein, cyan fluorescent protein, yellow fluorescent protein, and dsRED

what is the GUS assay and why are they used in plant experiments

-tests for the enzyme B glucuronidase

-X-gluc is cleaved by B-glucuronidase to produce blue pigment, which indicated the GUS gene is expressed and active

-the gusA gene is endogenous to bacteria, but not plants—> easy to detect form the background in plants

what modifications are made to Agrobacterium to make it a useful tool for plant transformation

the tumor inducing genes are removed from the Ti plasmid and replaced with the recombinant DNA for integration into the host genome

what are some characteristics of prokaryotic gene expression

have a small genome and no nucleoid envelope barrier —> no transcription and translation occur at the same time or place. they have operon and the typically have polycistronic mRNA

what are some characteristics of eukaryotic gene expression

-large genomes

-monocistronic mRNA with each gene having its own promoter element and enhancer elements

-no operons

-nuclear envelope (transcription occurs in nucleus and translation occurs in cytoplasm)

-transcription is influenced by chromatin structure, DNA methylation, transcription factors, post-transcriptional processing and regulation and translation/post-translational regulation

what is forward genetics

a mutant phenotype is observed —> find genetic basis of the phenotype

what is reverse genetics

seeks to find what phenotype arisse as a result of particular genetic sequences

what is a hybrid tomato

created by crossing two inbred tomato plants, commonly used for commercial tomato production

what is a heirloom tomato

are varieties developed and stabilized through self pollination over several generations

name 3 examples of genes that control tomato fruit colors

-PSY1- mutants are yellow

-CRTISO- mutants are orange

-LCYM- mutants are dark red

-SGR1- appear brown or rusty due to higher levels of chlorophyll

-DEL and ROS1- appear purple due to transcription factors from snapdragon

what is the Dwarf Tomato Breeding Project

established to increase the diversity of dwarf tomato varieties, an example of a citizen scientist project—> volunteers grow and stabilize crosses

which transgenes were used to create the Purple Tomato, and why are they only expressed in the tomato fruit

-DEL and ROS1- controlled by the fruit tissue specific E8 promoter from tomato, only fruit tissues have increased levels of anthocyanin making them purple

how do you prepare 1xTAE from a stock solution of 50xTAE

C1V1=C2V2

500/50= 10mL (50xTAE) + 490mL water

what is the role of detergent in DNA extraction

disrupt cellular membranes, releasing nucleic acids

what is the role of salt in DNA extractions

used to shield neutralize DNA

s negative charge, decreasing its solubility

what is the role of alcohol in DNA extractions

precipitate DNA out

what method did you use to extract genomic DNA and why

kit based DNeasy because it reduces the amount of toxic reagent used

why is guanidine hydrochloride used in the QIAGEN DNeasy plant mini kit method

used to denature proteins as well as disrupt hydrogen bonding between water molecules

used in this silica-based DNA isolation method to disrupt cells, deactivate any residual nucleases and facilitate DNA binding to the silica column

why is it important to ensure all the ethanol is completely removed from the DNeasy Mini spin column before eluting your DNA

DNA is NOT soluble in ethanol—> it will not elute off the column if the alcohol content is too high