chapter 8 notecards Flashcards by Desiree Namou

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

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nucleic acid is a ________

the unit is a _________

polynucleotide

nucleotide

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functions of nucleotide

energy for ________ (__)
enzyme ____ (___)
signal _____ (___)

metabolism (ATP)
cofactors (NAD+)
transduction (cAMP)

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nucleic acid functions
-storage of genetic info (\_\_)
-transmission of genetic info (\_\_)
-processing of genetic info (\_\_\_)
protein synthsis (\_\_\_ and \_\_\_)

DNA
mRNA
ribozymes
tRNA and rRNA

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nucleotide consists of

nitrogenous base
pentose
phosphate

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nucleoside consists of

nitrogenous base

pentose

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nucleo base consists of

nitrogenous base

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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

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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

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the bases of RNA and DNA: only one of the ___ of the ring is available for glycosidic bond formation

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phosphorylation of sugars is a result of an ___________

esterifcation reaction

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phosphoester bond is present between _____ and _____

phosphate and pentose sugar

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adding a phosphate is simply a ________ to form a ________

condensation

phospho anhydride

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phosophorlyation is possible on any __ but is most common on positions _______
called ________

OH group
3’ and 5’
phosphodiester linkage

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one phosphate group can be attached by a phosphoester to _______

two hydroxyls

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phosphorlyation of organic compounds

the phosphorus atom in phosphate groups is an easy target for _________

nucleophilic attacks

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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

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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

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properties of nucleotides

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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

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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

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alternating pattern
major and minor groove
T
C

franklin and wilkins

cross means ____
diamonds mean that the ________ is outside
calculated helical perameters

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helix

phosphate sugar backbone

watson crick model of B DNA
- anti \_\_\_\_\_
\_\_\_\_\_, \_\_\_\_\_, \_\_\_\_\_ interactions
-bases are \_\_\_\_\_ to the phosphate backbone
\_\_\_\_\_ bonding
\_\_\_\_ pairing

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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 ____

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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

chapter 8 notecards Flashcards

(45 cards)