chapter 8 notecards Flashcards
the fundamental unit of chromatin is a ________, which is made up of 147 base pairs of DNA wrapped around a _________
2 copies of histone, 4 types:
nucleosome
histone octamer
H3, H4, H2A H2B
nucleic acid is a ________
the unit is a _________
polynucleotide
nucleotide
functions of nucleotide
- energy for ________ (__)
- enzyme ____ (___)
- signal _____ (___)
metabolism (ATP)
cofactors (NAD+)
transduction (cAMP)
nucleic acid functions -storage of genetic info (\_\_) -transmission of genetic info (\_\_) -processing of genetic info (\_\_\_) protein synthsis (\_\_\_ and \_\_\_)
DNA
mRNA
ribozymes
tRNA and rRNA
nucleotide consists of
nitrogenous base
pentose
phosphate
nucleoside consists of
nitrogenous base
pentose
nucleo base consists of
nitrogenous base
the second building block of all nucleic acids is the _______ of either oxy or deoxy ribose sugar
furanose
oxy has two OH
deoxy only has one in middle of ring
in nucleotides the pentose ring is attached to the nuclease via _________
the bond is formed to the _ ____ of the sugar in __ configuration
the bond is formed
-to position ___ in pyrimadines
-to position ____ in purines
this bond is quite _____ toward hydrolysis, especially in ________
bond cleavage is catalyzed by _____
N-glycosidic bond anomeric, B N1 N9 stable pyrimadines acid
the bases of RNA and DNA: only one of the ___ of the ring is available for glycosidic bond formation
NH
phosphorylation of sugars is a result of an ___________
esterifcation reaction
phosphoester bond is present between _____ and _____
phosphate and pentose sugar
adding a phosphate is simply a ________ to form a ________
condensation
phospho anhydride
phosophorlyation is possible on any __ but is most common on positions _______
called ________
OH group
3’ and 5’
phosphodiester linkage
one phosphate group can be attached by a phosphoester to _______
two hydroxyls
phosphorlyation of organic compounds
the phosphorus atom in phosphate groups is an easy target for _________
nucleophilic attacks
hydrolysis of a phosphoester bond in _________ can be coupled to the creation of a phosphodiester bond between two nucleotides
and the same for _____
nucleoside triphosphate
RNA
polynucleotides covalent bonds formed via \_\_\_\_\_\_\_ linkages - \_\_\_\_\_ charged backbone DNA backbone is fairly \_\_\_\_\_ - hydrolysis accelerated by \_\_\_\_\_\_ (\_\_\_\_) RNA back bone is \_\_\_\_\_\_ -in water, RNA lasts for \_\_\_\_\_ -in cells, mRNA is degraded in a \_\_\_\_\_ they are \_\_\_\_\_\_ polymers we read the sequence \_\_ to \_\_\_
phosphodiester linkages negatively stable enzymes (DNAase) unstable few years a few hours linear 5 to 3
properties of nucleotides
light absorbance
hydrogen bond formation
for mixtures of nucleotides, wavelength of ____ is used for absorption measurements
these measurements can be utilized to quantify the concentration of nucleic acids in a solutio
260 nm
road to double helix watson and crick - missing layer means \_\_\_\_\_\_\_\_ -hydrogen bonding A pairs with G pairs with watson, crick,, and wilkins shared 1962 nobel peace prize franklin died in 1958
alternating pattern
major and minor groove
T
C
franklin and wilkins
- cross means ____
- diamonds mean that the ________ is outside
- calculated helical perameters
helix
phosphate sugar backbone
watson crick model of B DNA - anti \_\_\_\_\_ \_\_\_\_\_, \_\_\_\_\_, \_\_\_\_\_ interactions -bases are \_\_\_\_\_ to the phosphate backbone \_\_\_\_\_ bonding \_\_\_\_ pairing
antiparalell ionic, hydrophobic, van der wall perpendicular hydrogen base
the backbone of alternating pentose and phosphate groups in both types of nucleic acid is highly ____
polar
complementarity of strands in the DNA double helix
the base-paired anti-parallel strands differ in _______
they also differ in sequence when each chain is read in the
______
bases are ___ basic, ____, partial _____
hydrophobic, relatively _____
-at alkaline/acidc pH, they are _____ and increased _____
-pyrimidine –> _
purine –> ______
base stacking: hydrophobic base stacking also include ____ and _______
base composition 5 --> 3' direction weakly, aromatic, double bond insolujble ionized, solubility planer planer with slight pucker van der walls and dipole dipole interaction
how is the DNA duplex held together:
charged backbone faces _____
bases are _____ bonded and are ______ on top of another base
bases are clusters ____ the helix, ____ from the water (_______)
the distance between bases is ____A(distance between closely approaching atoms is ____)
water hydrogen stacked inside away hydrophobic interactions 3.4 3.6
the sequence of bases in one strand precisely determines the sequence of the ______
if strands are separated then the other strand can be precisely generated using the ______ as a template
the preexisting or parent strands become separated and each is thee template for biosynthesis of a _
replication in this way is _________ (one parental and one newly synthesized DNA)
other strand
parental single stranded DNA
complimentary daughter strand
semi conservative
___ form is more common in solution containing less water
___ is the usual conformation of DNA
A
B
right handed
C3 endo sugar pucker conformation
anti glcosyl bond conformation
A form
right handed
c2 endo
anti
B form
left handed c2 endo for \_\_\_\_\_ c3 endo for \_\_\_\_\_\_ anti for \_\_\_\_\_ syn \_\_\_\_\_
z form pyrmindines purines pyrimidines purines
the conformation of a nucleotide in DNA is affected by rotation about _________
___ of the bonds rotate freely
the limited rotation about bond __ gives rise to ring pucker, in which one of the atoms in the five membered furanose ring is out of plane described by the other 4
this conformation is __ or ___ depending on whether the atom is displaced to the same side of the ___ or to the opposite side
seven different bonds
six
4
minor nucleosides in DNA
modification is done after _________
_________ is common in eukaryotes, also found in bacteria
__________ is common in bacteria, not eukaryotes
________: way to mark your own DNA so that cells can degrade foreign DNA (_____)
way to mark which genes should be active (________)
DNA synthesis 5-methylcytosine N6-methyladenosine epigenetic prokaryotes eukaryotes
twofold symmetry
in order to superimpose one repeat on the other, it must be rotated 180 degrees about the horizontal axis and then 180 about the vertical axis as shown by the colored arrows
palindromes
has a symmetric sequence within each strand
superimposing one repeat on the other requires only a single 180 degree rotation about the vertical axis
mirror repeat
when only a single DNA (or RNA) strand is involved the structure is called
hairpin
when both strands of a duplex DNA are involved, it is called a
cruciform
DNA Denaturation -covalent bonds are \_\_\_\_\_ genetic code is \_\_\_\_\_ hydrogen bonds are \_\_\_\_\_ - two strands \_\_\_\_\_\_ base stacking is \_\_\_\_ -UV absorbance \_\_\_\_\_\_\_ denaturation can be induced by: denaturation may be reversible by
intact intact broken separated lost increases high temp, or change in pH annealing
the denaturation or melting curves of two DNA specimens
the temperature at the midpoint of the transition (tm) is the _______
it depends on ___________ o the dNA
the midpoint of melting tm depends on _______
-high concentration gradient increases ___
____ depends on DNA length
-longer DNA has higher __
-important for short DNA
-high salt increases __
heat denaturation of DNA melting point pH and ionic strength and on the size and base composition base composition Tm
very slow reactions
large number of residues
the net effect is significant 100C–> U
-events/day in a mammalian cell
deamination
N-glycosidic bond is hydrolyzed
significant for purines:10,000 purines lost/day in a mammalian cell
depurination
loss of pyrimidines via a similar reaction occurs, but much more slowly
the resulting lesion, in which the deoxyribose is present but the base is not, is called an _________
abasic site or an AP site
induces dimerization of pyrimidines; this may be the main mechanism for _____
UV light
skin cancers
causes ring opening and strand breaking
these are difficult to fix
ionizing radiation
x rays and gamma rays
accumulation of mutations is linked to
aging and carcinogenesis
