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49 Cards in this Set

  • Front
  • Back
secondary structures in DS-DNA
sugar-P backbone outside
bases (h-bonding)
right-twist closes the gaps bw bp to 3.4A
"canonical" bp
A=T and G-C (have 3)
G:C rich regions are stable
watson-crick base pairs
All H bonds in both bp are straight with H pointing in direction of acceptor N or O
Linear H bonds are strongest
Major and minor grooves
tops of the bases line the floor of the major grooves
major groove is large enought to accomodate an alpha helix
recognized by regulatory proteins
bases in bp
not directly across the axis but displaced, leads to diff sizes grooves in the cylindrical column.
minor groove
bp edges nearest to the glycosidic bond to form the interior surface
propeller twist
+=CW rotation
propellar:allows greater overlap of bases w/i same strand and reduces the area of contact bw bases and h2o
propeller twested bp
H bonds bw bases are ditorted by the motion
Structural properties
A double helix
short and broad
right handed
Structural properties
B double helix
long and thin
right handed
~10 bp per turn
Structural properties
C double helix
(shaded on side that its handed) left=up?
elongated and slim
left handed
anti at C, syn at G
in G:C regions
G is syn
C is anti,but flip 180 degree
G:C preserved in transition from B to Z form
Deoxyguanosine is B and in Z
B:anti always

Z:bond rotates to adopt syn
DNA denature/renature
duplex abs<UV then ss
DNA @ 80+ degree, UV abs increases by 30-40% (denature)
Hyperchromic shift (unwind)
stacked bp abs less light
low T=low abs, reestablish stack
Right handed DNA
topologically restrained
turn R is CW and create turn
turn L is CCW and release turn
L= neg supercoiled R= opp
melting temperature Tm
dependent on G+C
Hyperchromic shift
pneumonococcus 38%
Ecoli 52%
low %=higher on graph
Tm vs Relative G+C content
Tm increases if ionic strength is raised at constant ph7. High ion strength neutralizes the repulsion bw the P residues of complementaries
Thermal denaturation/re
nucleation phase of rnx is a 2nd-order depending on sequence alignment.
process is slow, unzip is fast
denature/renature process
native DNA-->(heat)
denatured DNA-->(nucleation)2
low T,reassociation-->(zip)1
renatured DNA
Hypochromic shift
(reassociation of denatured DNA from sources)
all same [] of (nucleo/L)
[DNA]:filled to same pt (cup)
[nucleo]:compare size (tip)
small=more[]ed=anneal rapidly
Densities(g/ml) vs G:C content
GC>AT buoyant density
single linear line with sources falling on it
tertiary structure DNA
duplex: 10 bp per turn
circular:<or> 10bp (supercoil)
cruciforms: in palindromic reg
neg supercoil:promote cruciform
enzymes or gyrases can introduce or remove supercoils
DNA supercoiling
sprial:coil circle
interwind: wraps itself
long,linear:loops are restrained
linking number
(supercoils in tertiary)
change L=Lk-Lko (relaxed)
change T=Tk-TKo (#turns in last)
change W=Wk-Wko (Wko always 0)bc relaxed DNA is never supercoiled
400 bp circular DNA
400/10=40 turns in relaxed with no writhe
strained:neg bc change in L is (-), 40 to 36
DNA gyrase
negative supercoils
for each coil added W subtract 1 (neg), T remains
strained rules
supertwisted: subtract # additional loops from W
dirupted bp:subtract of previous # of loops from T, W will most likely =0
action of bacterial DNA gyrase
1.cross duplex DNA
2.gyrase binds to crossover
3.recognize + sense of cross
4.breaks both strands
5.rejoins into opp config
*changes + to -
DNA gyrase (topoisomerase II)
contains 2 neg supercoils as consequence of action
A subunits cut duplex, DNA pass thru ends, ends religated, duplex released from enzyme.
DNA gyrase
uses ATP from hydrolysis to intruduce negative supercoils
Topology change
is enzymatically mediated by topoisomerase, which changes the linking #
DNA around histones
writhe=loop, circle
wrapping DNA around a protein spool stablizes conformation and is neg
cruciform structure
(palindromic sequence)
self-complementary inverted repeats arrange to form H bonded loops
taking out turns increases the SS character of DNA
Eukaryotic chromosomes
human DNA is 2m (length)
packed in nucleus 5um
100,000x compression by wrapping DNA around spools called nucleosomes and packing into helical filaments
chromatin, consists of histone and nonhistone chromosomal proteins
histone=ocatmer structure
nonhistone=gene expression reg
chromosome structure
base pairs per turn, pack :
double helix: 10, 1
beads on string, 80, 6-7
solenoid: 1200, ~40
loops: 60,000 , 680
miniband:~1.1e6, 1.2e4
chromosome: 18 loops/miniband, 1.2e4
can NA be chemically synthesized
yes by genes, first one synthesized was gene for insulin
Secondary and tertiary for RNA
extensive H bond creat 4 double helical domains, 3 capped by loops, 1 by stem.
phenylalanine tRNA is L shaped
tRNA molecule
clover leaf structure
aa becomes covalently attached to accepting stem.
Left=D loop Right=TC loop
bottom=anticodon top=acceptor
sequence of acceptor stem
aa linked to 3'-OH end by ester bond
acceptor stem is at very 3'end has sequence CCA
tRNA continued
secondary stabilized by H bond
usual bases stabilize tertiary L-shape
ribos have big and small subs
make up 2/3 ribo
high intrastrand leads to extensive bp-ing
secondary is conserved and sequence isn't
determining the primary structure of NA
sanger:chain termination
max,gilbert:base-specific cleavage
autoradiography:xrays see radioactive isotopes in NA's
DNA replication
double helical molecule
helix copied by polymerase
polymerase need template & primer
Primer: oligo pairs with end of template to form DS-DNA
Chain termination method
4 separate methods
each rxn has dATP, dGTP, dCTP, dTTP
and a dideoxynucleotide (dd)
actual chain method
1.DNA polymerase rxn
3.4 rxn with nucleoside tri-P plus 1 dd tri-P
4. electrophortogram
chain termination method
polymerase use norm nucleot
polymerase use dd, prevent growth
natural occuring nucleot lack OH @ 2' end