11. Gene Expression Flashcards
how does the type of regulation affect enzyme kinetics?
allosteric regulation affects Km
transcriptional control affects Vmax
what does every somatic cell contain?
the genetic material that codes for every cell in the organism
what is a super secondary structure?
when a DNA-binding protein attaches to DNA
pretty much, structure somewhere between secondary & tertiary protein structure
helix turn helix
a helix
b turn
b helix
MOST common DNA binding motif
as a dimer, DNA-binding proteins can do what?
DNA-binding proteins can bind to both halves of a palindrome with equal specificity
zinc finger
zinc chelates 2 or more histidine or cytosine residues
zinc binds to major groove of DNA
common motif in hormone receptors i.e. glucocorticoid
leucine zipper
leucine repeated at every 7th AA
forms a zipper structure
creates hydrophobic domain
combinatorial control
different DNA binding motifs used in combination to regulate gene expression
binding of DNA-binding protein to specific sequences
DNA-binding protein interacts with DNA, hydrogen bonds form between an R group on the protein & the major groove of the DNA in tight/high affinity bonds
what do restriction enzymes do
bind to a specific sequence on DNA & cut
MOST COMMON DNA-binding proteins
what is an operon?
a single stretch of DNA that encodes for all of the enzymes necessary to produce a given response
trp operon, when tryptophan is present?
DNA-binding protein is bound to DNA and trp operon is OFF
DNA-binding protein functions as a ______ in the trp operon
repressor
when DNA-binding protein is bound to the DNA, it blocks transcription, turning trp OFF
negative control
when binding of the protein to DNA inhibits transcription
positive control
when binding of the protein to DNA activates transcription
what is a gene activating protein?
DNA-binding protein that binds to the DNA and ACTIVATES transcription
lac operon
ON when lactose is present with no glucose (glucose is ideal energy source)
controls lactose metabolism
controlled by glucose & lactose
2 things transcription factors must do?
- bind DNA
2. bind more proteins so transactivation can occur
2 main functional domains of a transcription factor?
- DNA-binding domain
2. transactivation domain
if a transcription factor does not have a DNA-binding domain?
it must have two transactivation domains
promiscuity
ability of 1 DNA-binding domain to bind specifically to multiple different DNA sequences
what do promoters do?
give RNA pol the position and orientation info it needs in order to start transcription
what do enhancers do?
regulate transcription by either enhancing or inhibiting transcription
always palindromes
2 types of transcription factors that are enhancers?
- constitutive transcription factors
2. inducible transcription factors
inducible transcription factors
we can turn on/off
can be second messenger dependent, hormone receptors, or tissue specific
what do chromatin remodeling complexes do?
alter chromatin structure in order to form a transcription bubble
what does a transcription bubble do?
ensure only one strand is read during transcription
what can the chromatin remodeling complex do to create a transcription bubble?
- remodel nucleosomes
- remove histones from nucleosomes
- replace histones on nucleosomes
- modify histones (i.e. methylation or acetylation)
effects of eukaryotic gene repressor protein examples
- block gene activator proteins from binding to DNA via competitive DNA binding
- mask activation surface
- directly interact with the general transcription factors
- recruit chromatin remodeling complexes to close or silence the DNA
- recruit histone deacetylase (remove acetly groups that have been attached to the promoter to open up the DNA for transcription)
- recruit histone methyl transferase (which methylates & silences chromatin)
DNA-bending protein
manipulates DNA so you can get the factors to form an initiation complex
insulator sequence
between genes, prevent a transcription factor from cross-regulating genes, restricting their activity to the intended gene
barrier sequences
between genes, block heterochromatin from spreading, preventing cross-regulation
