Gene Expression I
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| Lactose Operon | It is an inducer, inducer presented to the cell is 1, 6 Allolactose. It has a regulator gene and structural gene
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| Name the make up of the structural gene and the different parts | Characterized by an operon made up of a polycistronic mRNA. It has a p and o region as well as z, y and a region
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| What does the z, y and a region correspond to | z= B-galactosidase, y=permease, a=transacetylase
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| What it is function of the i gene? | i gene elaborates mRNA referred to as imRNA which is responsible for the synthesis of a transcription factor that acts as a repressor
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| What does the repressor bind to? | It binds to the o (operator) region and prevents transcription of z, y and a
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| What is a pallindromic sequence? | It is an inverted repeat, top and bottom strand are the same when read 5' to 3'
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| How does the repressor recognize the sequence? | Due to its helix-turn-helix motif. Repressor straddles DNA in G-C residues of palindromic sequence of the operating site
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| How do you turn on the lac operon? | You need a lack of deficiency in glucose (product of B-galactolose)
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| What happens to cAMP when glucose goes down? | cAMP goes up via activation of adenylyl cyclase, cAMP binds to CAP, cAMP-CAP complex facilitates the maximal binding of RNA polymerase when at the P site & o site is empty.
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| What does the binding of IPTG induce the repressor to do? | Binding of IPTG induces conformation changes in the repressor such that they no longer interact productively with DNA
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| Tryptophan operon similarities to lac operon | Encodes for repressor, polycistronic mRNA encoding for 5 cistrons A-E which give rise to 3 enzymes for trp biosynthesis, p & o sites
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| Trp operon differences to lac operon | very poor repressor (inactivated at first), followed by a sequence of nucleotides (162). In the 162 nts, there is a attenuator sequence which enables couple transcription-translation in Prokaryotes. Tryptophan rich region present.
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| What does the sequence 3/4 pairing signify? | Rho independent termination
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| How do you change a Heterochromatin to Euchromatin? | Change the status of methylation at the GC island or acetylation of the histone
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| What happens if m5C undergoes spontaneous deamination? | It gives rise to thymine which when under another round will give a AT base pair (transition mutation)
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| Methyltransferases | DNMTs (DNA methyltransferases)-uses S-Adenosyl methione as methyl donor
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| How does MSPI and HpaII check methylation status? | They are isoschizomers that recognize CCGG. MSPI can cut methylated internal C. HpaII cannot cut methylated internal C.
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| How is DNase I used to check methylation state? | In an undermethylated state, less DNase required/sensitivity to DNase I is increased
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| Euchromatin | Hypomethylated state, gene expression is robust
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| Heterochromatin | Hypermethylated state, DNA is repressed
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| Epigentetic control mechanism | Changes do not reflect changes at the level of DNA sequence
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| DNA methylating agents | One is a base, other is a deoxynucleoside. Induce a state of demethylation, put a N on position 5 instead of a C. Ex. Decitabine
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| MeCP role | Can bind to methylated CG islands referred to as CG binding protein. (recruitment of HDACs often associated). They organize chromatin into a status that is resistant to DNase I degradation.
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| E globin & Y globin methylation status at week 6 and 12 | 6 weeks= E-unmethylated promoter/maximally expressed, Y-methylated promoter/minimally expressed. 12 weeks=E becomes methylated and Y becomes unmethylated
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| Histone modification occurs at which histones | H3 and H4 more often, at the N terminus
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| Lysine 9 of H3 | Is subjected to acetylation and methylation
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| Bromo Domain | Can recognize acetylation of histones, has specific affinity for Acetyllysine
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| Chromo Domain | Can recognize methylation of histones
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| HAT | Histone acetyl transferase-consumes CoA
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| HDACs | Histone deacetylase. Trichostatin is a HDAC inhibitor
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| Describe process of methylation with lysine 9 of H3 | Recruits HP1(heterochromatin protein 1). HP1 binds to DNMT and then methylation status changes. DNA methylation does not occur randomly
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| What can DNA bind once it is methylated? | It can bind MeCP2 which can recruit HDAC & induce de-acetylation of the histone
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