Chapter 11 Structure Of Nucleic Acids

Front 1

secondary structures in DS-DNA

Back 1

sugar-P backbone outside
bases (h-bonding)
right-twist closes the gaps bw bp to 3.4A

Front 2

"canonical" bp

Back 2

A=T and G-C (have 3)
G:C rich regions are stable

Front 3

watson-crick base pairs

Back 3

All H bonds in both bp are straight with H pointing in direction of acceptor N or O
Linear H bonds are strongest

Front 4

Major and minor grooves

Back 4

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

Front 5

bases in bp

Back 5

not directly across the axis but displaced, leads to diff sizes grooves in the cylindrical column.

Front 6

minor groove

Back 6

bp edges nearest to the glycosidic bond to form the interior surface

Front 7

propeller twist
+=CW rotation

Back 7

propellar:allows greater overlap of bases w/i same strand and reduces the area of contact bw bases and h2o

Front 8

propeller twested bp

Back 8

H bonds bw bases are ditorted by the motion

Front 9

Structural properties
A double helix

Back 9

short and broad
right handed
DNA:RNA
anti

Front 10

Structural properties
B double helix

Back 10

long and thin
right handed
~10 bp per turn
anti

Front 11

Structural properties
C double helix
(shaded on side that its handed) left=up?

Back 11

elongated and slim
left handed
anti at C, syn at G

Front 12

Z-DNA

Back 12

in G:C regions
G is syn
C is anti,but flip 180 degree
G:C preserved in transition from B to Z form

Front 13

Deoxyguanosine is B and in Z

Back 13

B:anti always

Z:bond rotates to adopt syn

Front 14

DNA denature/renature

Back 14

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

Front 15

Right handed DNA

Back 15

topologically restrained
turn R is CW and create turn
turn L is CCW and release turn
L= neg supercoiled R= opp

Front 16

melting temperature Tm
dependent on G+C

Back 16

Hyperchromic shift
pneumonococcus 38%
Ecoli 52%
low %=higher on graph

Front 17

Tm vs Relative G+C content

Back 17

Tm increases if ionic strength is raised at constant ph7. High ion strength neutralizes the repulsion bw the P residues of complementaries

Front 18

Thermal denaturation/re

Back 18

nucleation phase of rnx is a 2nd-order depending on sequence alignment.
process is slow, unzip is fast

Front 19

denature/renature process

Back 19

native DNA-->(heat)
denatured DNA-->(nucleation)2
low T,reassociation-->(zip)1
renatured DNA

Front 20

Hypochromic shift
(reassociation of denatured DNA from sources)

Back 20

all same [] of (nucleo/L)
[DNA]:filled to same pt (cup)
[nucleo]:compare size (tip)
small=more[]ed=anneal rapidly

Front 21

Densities(g/ml) vs G:C content

Back 21

GC>AT buoyant density
thermodynamic
single linear line with sources falling on it

Front 22

tertiary structure DNA

Back 22

duplex: 10 bp per turn
circular:<or> 10bp (supercoil)
cruciforms: in palindromic reg
neg supercoil:promote cruciform

Front 23

topoisomerases

Back 23

enzymes or gyrases can introduce or remove supercoils

Front 24

DNA supercoiling

Back 24

sprial:coil circle
interwind: wraps itself
long,linear:loops are restrained

Front 25

linking number
writhe
twist
(supercoils in tertiary)

Back 25

L=T+W
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

Front 26

400 bp circular DNA

Back 26

400/10=40 turns in relaxed with no writhe
strained:neg bc change in L is (-), 40 to 36

Front 27

DNA gyrase

Back 27

negative supercoils
relaxed=W=O
for each coil added W subtract 1 (neg), T remains

Front 28

strained rules

Back 28

supertwisted: subtract # additional loops from W
dirupted bp:subtract of previous # of loops from T, W will most likely =0

Front 29

action of bacterial DNA gyrase

Back 29

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 -

Front 30

DNA gyrase (topoisomerase II)

Back 30

contains 2 neg supercoils as consequence of action
A subunits cut duplex, DNA pass thru ends, ends religated, duplex released from enzyme.

Front 31

DNA gyrase

Back 31

uses ATP from hydrolysis to intruduce negative supercoils

Front 32

Topology change

Back 32

is enzymatically mediated by topoisomerase, which changes the linking #

Front 33

DNA around histones
twist=turn
writhe=loop, circle

Back 33

wrapping DNA around a protein spool stablizes conformation and is neg

Front 34

cruciform structure
(palindromic sequence)

Back 34

self-complementary inverted repeats arrange to form H bonded loops
taking out turns increases the SS character of DNA

Front 35

Eukaryotic chromosomes

Back 35

human DNA is 2m (length)
packed in nucleus 5um
100,000x compression by wrapping DNA around spools called nucleosomes and packing into helical filaments

Front 36

nucleosome

Back 36

chromatin, consists of histone and nonhistone chromosomal proteins
histone=ocatmer structure
nonhistone=gene expression reg

Front 37

chromosome structure
base pairs per turn, pack :

Back 37

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

Front 38

can NA be chemically synthesized

Back 38

yes by genes, first one synthesized was gene for insulin

Front 39

Secondary and tertiary for RNA

Back 39

extensive H bond creat 4 double helical domains, 3 capped by loops, 1 by stem.
phenylalanine tRNA is L shaped

Front 40

tRNA molecule
R=purine
Y=pyrimidine

Back 40

clover leaf structure
aa becomes covalently attached to accepting stem.
Left=D loop Right=TC loop
bottom=anticodon top=acceptor

Front 41

sequence of acceptor stem

Back 41

aa linked to 3'-OH end by ester bond
acceptor stem is at very 3'end has sequence CCA

Front 42

tRNA continued

Back 42

secondary stabilized by H bond
usual bases stabilize tertiary L-shape

Front 43

rRNA

Back 43

ribos have big and small subs
make up 2/3 ribo
high intrastrand leads to extensive bp-ing

Front 44

rRNA

Back 44

secondary is conserved and sequence isn't

Front 45

determining the primary structure of NA

Back 45

sanger:chain termination
max,gilbert:base-specific cleavage
autoradiography:xrays see radioactive isotopes in NA's

Front 46

DNA replication

Back 46

double helical molecule
helix copied by polymerase
polymerase need template & primer
Primer: oligo pairs with end of template to form DS-DNA

Front 47

Chain termination method

Back 47

4 separate methods
each rxn has dATP, dGTP, dCTP, dTTP
and a dideoxynucleotide (dd)

Front 48

actual chain method

Back 48

1.DNA polymerase rxn
2.dideoxynucleotide
3.4 rxn with nucleoside tri-P plus 1 dd tri-P
4. electrophortogram

Front 49

chain termination method

Back 49

polymerase use norm nucleot
polymerase use dd, prevent growth
natural occuring nucleot lack OH @ 2' end