Flashcards in ch 7.1 Deck (60):
What are some different techniques used to determine DNA and proteins?
Gel mobility shift
size exclusion chromatography
DNA foot printing
What is gel mobility shift used for?
To find the sequence of the protein binding DNA preference
What is size exclusion chromatography used for?
To find the DNA binding preference of regulatory protein
what is affinity chromatography used for?
protein binding to a specific DNA sequence
How do you find a specific DNA sequence from a binding protein?
What is DNA foot printing?
1) label one strand with p53
2) mix one strand with protein that binds to that site and one with out
3) add nucleases to the mixture of both strands
4) run on a gel
5) the protein protects the posphodiester bonds so if compare strands DNA sequence is determined
how is tryptophan synthesized?
tryptophan prescence shuts off promoter
trytophan absence shuts on promoter
How many enzymes synthesize tryptophan?
five enzymes all transcribed from a single promoter
What is the tryptophan operator?
regulatory element that lies in the promoter region
it recognizes the the repressor protein
What is the repressor protein for tryptophan?
a helix turn helix protein
What does the repressor blocks?
access to the promoter by RNA poly
When is the promoter in tryptophan active?
When there is tryptophan present, the tryptophan binds to repressor and activates the repressor. the repressor then binds to the promoter and prevents trancription of enzymes
how does tryptophan bind to the repressor?
it binds to two of the helices in the repressor and increases the distance
What is negative control?
when a DNA binding protein turns off transcription
What is positive control?
when regulatory protein binds to promoter for transcription
What is the repressor for the LAC operon?
What is the activator for the LAC operon?
CAP (catabolite activator protein)
What are the three genes of the LAC operon?
What does lacZ for?
it makes the beta -galactosidase for converting glucose into galactose
What is lacY for?
What is lac A for?
What does CAP allow for?
use alternative carbon in the absence of glucose
What happens in a no lactose condition?
lac repressor is bound
gene is off
what happens in a lactose presence condition?
lac repressor is removed
What happens when glucose is present?
cAMP is not bound to CAP
LAC operon is off
How operators does the LAC operon have?
How many operators can a repressor bind?
simultaneous binding strengthens overall repression
How does one repressor binds to a major and auxiliary operator?
What is the gene control region?
regulatory protein binding sequences spread over a large stretch of DNA in eukaryotes
How many regulatory proteins does the human genome encode for?
What does eukaryotic cells need to begin trancription?
gene regulatory proteins
What do activators promote?
The assembly of RNA poly and general transcription factors at transcription start point
Activators bind to DNA enhancer sequences
What do activators attract to the promoter?
attract and position transcription factors, mediators and RNA poly
What do activators also help modify?
chromatin structures (histone modifications, nucleosome remodeling:remova; and replacement)
Eukaryotes does repressors compete for binding to DNA binding sites with polymerase?
What are ways that repressor will block activator?
overlap in binding site
masking activator surface
blocking assembly of transcription factors
recruit remodeling complex (turn chromatin into transcription silence)
recruits methyl transferase
What are ways to regulate gene regulator proteins?
addition of second subunit
stimulation of nuclear entry
release from membrane
Where is the beta globin gene exclusively expressed at?
red blood cell
on the chromosome as a cluster.
What does cluster of globin contain?
adult globin genes
each has its on set of regulatory gens
What is a locus controlled region?
long stretch of DNA that controls every gene of the globin gene
located far upstream from gene cluster it controls
How do locus controlled regions bring regulatory proteins in proximity of genes it controls?
looping DNA occurs for transcription
What does LCR have to prevent the spread of heterochromatin?
What is the difference in gene control in eukaryotes and prokaryotes?
bacteria has one operon that controls many genes
eukaryote genes has their own operator
What can turn a switch on and off in eukaryotes?
despite being controlled by a combination of regulatory genes, a single regulatory gene can turn a switch off and on
What is methylated in mammal DNA?
Cytosine at CG in DNA
CG in promoters in actively transcribed genes remains unmethylated
What methylates the cytosine?
CPG methylase (methyl transferase)
When are CG in promoters methylated?
when the promoter is off
turns to nonmethylated when the promoter is on
How is cytosine methylated?
after replication what recognizes the unmethylated C strand?
What recruits the DNA methylase?
histone modyfying reader writer complex
What is genomic imprinting?
expression of a gene is depended on if it is inherited from mother or father
What is prader-willis syndrome?
What is angelmann syndrome?
What is RNA editing?
changes in RNA after transcription
in what was RNA editing first discovered?
trypanosoms -large number of Uracils were incorporated into the gene
What inserts Uracils into the RNA in trypanosoms?
5` end complementary to region of transcript to be edited
What is ADAR?
Adenisine deaminase acting on RNA
they deaminates Adenine to inosine
What is the structure for ADAR binding?
as secondary hairpin
What edit deaminates C to U apolioprotein B?
liver does not express editing enzyme