finals - DNA binding proteins Flashcards
_____ Gene regulatory proteins that recognize and bind to specific DNA sequences and either promote or inhibit gene transcription by RNA pol
DNA-Binding Proteins
____ the two domains of DNA binding proteins
DNA binding domain and Transcription activation (inhibition) domains
(T/F) Surface of proteins are exactly complementary to surface topography of recognized DNA sequence
true
which of the ff is not an interaction made between DNA binding proteins and DNA?
a. ionic bonds
b. covalent bonds
c. hydrogen bonds
d. hydrophobic interactions
B
(T/F) each of the protein- DNA binding is strong
false
Each protein-DNA interaction is weak but typical DNA-binding protein subunit forms about 20 contacts with DNA to generate tight interaction
___ The protein motifs that mediate DNA-binding on the major groove
αhelices or βpleated sheets
which of the ff is not a major DNA-binding motif?
a. Helix-turn-helix (HTH)
b. Carboxy-terminal portion
c. Zinc fingers
d. Leucine zipper
B
this is part of HTH
which of the ff does not apply to helix-turn-helix?
a. 2 αhelices is connected by lysine in its β turn region
b. Each α helical region spans about 8 amino acids separated by 3.4 amino acid β turn
c. The amino acids of HTH motifs tend to be highly conserved among different HTH proteins
d. Found in hundreds of DNA-binding proteins in prokaryotes and eukaryotes
A
glycine is in the turn coz its small
_____ the HTH recognition helix that regulates
sequence-specific binding of protein to DNA and fits into the major groove
Carboxy-terminal portion
______ helps align or position recognition HTH along DNA
N-terminal helix
*(T/F) HTH proteins are typically polymers
false
are dimers
(T/F) regions of proteins outside HTH motif can vary considerably in structure (sequence) among different proteins and each may also contact the DNA to modulate the interaction
true
(T/F) binding region on DNA for each recognition helix of each member of the dimer is separated by exactly two turn of DNA helix
false
by one turn only! one turn = 3.4nm
which of the ff does not apply to the DNA binding by dimeric proteins?
a. recognition helices of the dimer bind symmetrically to symmetrical DNA sequences
b. each monomer forms nearly identical contacts with the DNA region
c. symmetrical interactions significantly increases the binding affinity of the proteins for the DNA
d. none of the above
D. all applies :)
(T/F) zinc finger motifs and HTHs contain amino acids plus zinc ions
false
this only applies to Zn finger motifs
which of the ff does not apply to Zn finger motifs?
a. exists as a monomer
b. can exist in clusters of direct repeats
c. Zinc ions coordinate two cysteine and two histidine residues at base of a 12 amino acid loop
d. zinc holds together an α helix and a β sheet (secondary structure)
A
either in clusters (multiple fingers) or dimeric
_____ example of molecules that have multiple Zn finger repeats
Transcription factor for RNA pol lll, TFlllA,
which of the ff does not apply to multiple zinc finger proteins?
a. Zinc fingers follow one another along the major groove
b. Multiple repeats mediates strong and specific binding to DNA
c. Number of zinc finger repeats are similar among different proteins
d. Provides a mechanism for cells to regulate the strength of DNA binding
among different transcription factors
C
it VARIES among diff proteins
*(T/F) Arginine and histidine residues in multiple Zince fingers form hydrogen bonds with guanine bases
true
(T/F) β-pleated sheet regions of zinc fingers mediate binding to major groove of the DNA
false
this is done by alpha helices
(T/F) zinc finger repeats varies among different proteins but zinc fingers have similar amino acid sequences and contact DNA bases in similar ways
true
*_____ the aa that is commonly iinvolved in the DNA-multiple zinc protein binding Interactions
arginine
*(T/F) DNA-protein interaction occurs between arginine of a DNA-binding protein and guanine in DNA which has a specific arrangement of hydrogen-bond acceptors that is
unambiguously recognized by the side chain of arginine in the major groove
true
(T/F) Dimeric zinc finger proteins are mostly of extracellular receptors
false
intracellular
(T/F) Each monomer forms a structure similar to that of HTH motif except it has two α helices that are held together by a zinc ion
true
which of the ff is not true about dimeric zinc proteins?
a. both α helices interacts with major groove
b. structure is similar to HTH proteins
c. are intracellular receptors
d. its helices are held together by zinc ions
A
only ONE of the two helices interact w/ major groove
____ is the third major type of DNA binding motif
Basic Region-Leucine Zipper Motif
BRLZM
which of the ff is not true about BRLZ motif?
a. has arginine
b. leucine residues every 6th position
c. has histidine
d. has lysine
B
leucine residues every seventh position
______ the basic aa that BRZL motif contains
Lys, arg, his
___ # of aa every one turn of α helix
3.6 aa
(T/F) all lysine residues in BRLZ motif line up on one side of α helix
false
all LEUCINE
which of the ff is not true about BRLZ motif?
a. can be homo or heterodimeric
b. leucine residues mediate hydrophobic interactions between monomers
c. leucines hold monomers together at one end
d. one side interacts with phosphate groups in the major groove
all is true