E. coli CAP +cAMP + DNA
HTH motif
cAMP
ATATAA = consensus sequence of TATA box
start point at: Py2CA Py5
TFIID
Human TBP complexed at TATA box of DNA
G
G
C
A
TA T
A
T A
T
C
5'
3'
octamer CAAT GC TATA start point
DNA binding motif of steroid receptorsZn fingers
Other DNA binding motifsHelix-turn-helixHelix-loop-helix
Additional motif often present in transcription factorsLeucine zippers
-Cys-X2-4-Cys-X3-Phe-X5-Leu-X2-His-X3-His-
The zinc finger motif is:
C-terminalN-terminal
Zn finger fragment bound to DNA
Hormone binding and dimerization regions vary from 5-15%
C-terminal
N-terminal
finger
DNA binding
dimerization
GLUCOCORTICOID RECEPTOR FRAGMENT BOUND TO DNA
homeodomain
Helix-turn-helix binding motif
#3, C-terminal
#1, N-terminal
#3
#2
#1
bHLH DNA binding motif of transcription factor MyoD
basic region binding DNA
helix 1
helix 2
CREB-DNA complex
Leu selected in zipper domain
Arg selected in DNA-binding domain
Chains: blue = c-Fos, green = c-Jun
Residues: red = Leu, purple = Arg
Human protooncogenes c-Jun:c-Fos heterodimer
HN
N N
N
O
H2N
N
N N
N
O
H2N
HN
N N
N
OH
H2N
N
N N
N
O
HN
H
H
N N
O
O
H
HN
N N
N
O
H2N
N
N N
N
O
H2N
HN
N N
N
OH
H2N
N
N N
N
O
HN
H
H
N N
O
O
H
HN
N N
N
O
H2N
N
N N
N
O
H2N
HN
N N
N
OH
H2N
N
N N
N
O
HN
H
H
N N
O
O
H
H3C
Keto-enol tautomerization of Gua
keto form (normal)
enol form
pairing properties of enol
Point mutation, transition
pyrimidinepyrimidine
purinepurine
Point mutation, transversion
pyrimidinepurine
purinepyrimidine
GT GC + AT
GC CG, TA AT, GC TA
nonsense mutation occurs when a termination codon is generated
missense mutation occurs when a different amino acid is coded
GT GC + AT
One round of replication on mismatched strands “fixes” the mutation.
3'-G-p-G-p-G-p-G-p-G-p-G-5' 3'-G-p-G-p G-p-G-p-G-p-G-5'5'-C-p-C p-C-OH 5'-C-p-C-p-C-OH
p-C
G-p
Mechanism for frameshift mutations
ATA GCA ACC GGC CTT ACA AAT TC
ATA GCA ACC GCC TTA CAA ATT C
Change of reading frame following the location of a deletion
insertion deletion
LOCUS tRNA WILD-TYPE
codon/anticodon
SUPPRESSOR
anticodon/codon
supD(su1) Ser UCG CGA CUA UAG
supE(su2) Gln CAG CUG CUA UAG
supF(su3) Tyr UAC GUA CUA UAG
supC(su4) Tyr AAC GUA UUA UAA
supG(su5) Lys AAA UUU UUA UAA
supU(su7) Trp UGG CCA UCA UGA
U
U
G
G G
G
G
Bacterial nonsense suppressors
O
O
OOP
O
O
O
HN
O
O
OO
CH3
CH3HN
O
thymine-thymine dimer
T T