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BIO 325 > chapter 8 notecards > Flashcards

chapter 8 notecards Flashcards

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Biology 101 flashcards
1
Q

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:

A

nucleosome
histone octamer
H3, H4, H2A H2B

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2
Q

nucleic acid is a ________

the unit is a _________

A

polynucleotide

nucleotide

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3
Q

functions of nucleotide

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

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

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4
Q 
nucleic acid functions
-storage of genetic info (\_\_)
-transmission of genetic info (\_\_)
-processing of genetic info (\_\_\_)
protein synthsis (\_\_\_ and \_\_\_)
A

DNA
mRNA
ribozymes
tRNA and rRNA

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5
Q

nucleotide consists of

A

nitrogenous base
pentose
phosphate

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6
Q

nucleoside consists of

A

nitrogenous base

pentose

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7
Q

nucleo base consists of

A

nitrogenous base

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8
Q

the second building block of all nucleic acids is the _______ of either oxy or deoxy ribose sugar

A

furanose
oxy has two OH
deoxy only has one in middle of ring

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9
Q

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 _____

A 
N-glycosidic bond
anomeric, B
N1
N9
stable
pyrimadines
acid
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10
Q

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

A

NH

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11
Q

phosphorylation of sugars is a result of an ___________

A

esterifcation reaction

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12
Q

phosphoester bond is present between _____ and _____

A

phosphate and pentose sugar

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13
Q

adding a phosphate is simply a ________ to form a ________

A

condensation

phospho anhydride

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14
Q

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

A

OH group
3’ and 5’
phosphodiester linkage

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15
Q

one phosphate group can be attached by a phosphoester to _______

A

two hydroxyls

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16
Q

phosphorlyation of organic compounds

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

A

nucleophilic attacks

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17
Q

hydrolysis of a phosphoester bond in _________ can be coupled to the creation of a phosphodiester bond between two nucleotides
and the same for _____

A

nucleoside triphosphate

RNA

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18
Q 
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 \_\_\_
A 
phosphodiester linkages
negatively
stable
enzymes (DNAase)
unstable
few years
a few hours
linear
5 to 3
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19
Q

properties of nucleotides

A

light absorbance

hydrogen bond formation

20
Q

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

A

260 nm

21
Q 
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
A

alternating pattern
major and minor groove
T
C

22
Q

franklin and wilkins

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

helix

phosphate sugar backbone

23
Q 
watson crick model of B DNA
- anti \_\_\_\_\_
\_\_\_\_\_, \_\_\_\_\_, \_\_\_\_\_ interactions
-bases are \_\_\_\_\_ to the phosphate backbone
\_\_\_\_\_ bonding
\_\_\_\_ pairing
A 
antiparalell
ionic, hydrophobic, van der wall
perpendicular
hydrogen 
base
24
Q

the backbone of alternating pentose and phosphate groups in both types of nucleic acid is highly ____

A

polar

25
Q

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 _______

A 
base composition
5 --> 3' direction
weakly, aromatic, double bond
insolujble
ionized, solubility
planer
planer with slight pucker
van der walls and dipole dipole interaction
26
Q

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 ____)

A 
water
hydrogen
stacked
inside
away
hydrophobic interactions
3.4
3.6
27
Q

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)

A

other strand
parental single stranded DNA
complimentary daughter strand
semi conservative

28
Q

___ form is more common in solution containing less water

___ is the usual conformation of DNA

A

A

B

29
Q

right handed
C3 endo sugar pucker conformation
anti glcosyl bond conformation

A

A form

30
Q

right handed
c2 endo
anti

A

B form

31
Q 
left handed
c2 endo for \_\_\_\_\_
c3 endo for \_\_\_\_\_\_
anti for \_\_\_\_\_
syn \_\_\_\_\_
A 
z form
pyrmindines
purines
pyrimidines
purines
32
Q

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

A

seven different bonds
six
4

33
Q

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 (________)

A 
DNA synthesis
5-methylcytosine
N6-methyladenosine
epigenetic
prokaryotes
eukaryotes
34
Q

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

A

palindromes

35
Q

has a symmetric sequence within each strand

superimposing one repeat on the other requires only a single 180 degree rotation about the vertical axis

A

mirror repeat

36
Q

when only a single DNA (or RNA) strand is involved the structure is called

A

hairpin

37
Q

when both strands of a duplex DNA are involved, it is called a

A

cruciform

38
Q 
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
A 
intact
intact
broken
separated
lost
increases
high temp, or change in pH
annealing
39
Q

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 __

A 
heat denaturation of DNA
melting point
pH and ionic strength and on the size and base composition
base composition
Tm
40
Q

very slow reactions
large number of residues
the net effect is significant 100C–> U
-events/day in a mammalian cell

A

deamination

41
Q

N-glycosidic bond is hydrolyzed

significant for purines:10,000 purines lost/day in a mammalian cell

A

depurination

42
Q

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 _________

A

abasic site or an AP site

43
Q

induces dimerization of pyrimidines; this may be the main mechanism for _____

A

UV light

skin cancers

44
Q

causes ring opening and strand breaking

these are difficult to fix

A

ionizing radiation

x rays and gamma rays

45
Q

accumulation of mutations is linked to

A

aging and carcinogenesis

BIO 325 (11 decks)

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