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Biochem 385 Unit 3 > Lecture 28: Nucleic Acids > Flashcards

Lecture 28: Nucleic Acids Flashcards

1
Q

DNA: where are bases? backbone?

A

bases: center of helix
backbone: outside

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2
Q

stability of double helix structure due to what?

A

BASE STACKING

NOT base bonding

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3
Q

base pairing

A

done by hydrogen bonding between pairs

this adds little stability

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4
Q

form of RNA double helicies

A

A form

stems and loops (heleices and signel stranded RNA that arent base paired)

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5
Q

what pairs with what?

A

G-C

A-T

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6
Q

If one DNA strand has sequence 5’ATCGGCA3’, what is sequence of COMPLIMENTARY strand?

A

5’TGCCGAT3’

start from BACK because ANTIPARALLEL

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7
Q

what is base PAIRING important for?

A

SPECIFICITY

not stability

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8
Q

how is DNA written?

A

ALWAYS 5’ to 3’

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9
Q

how do bases associate in hydrophobic environments?

A

by hydrophobic interactions

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10
Q

Base Stacking

A 
chemistry and attractions for each other
van der Waals interactions
hydrophobic interactions (shielding from water=attraction)
stability of helix
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11
Q

Stacks

A

aromatic rings, parallel ring systems above and bellow

interact by van der Waals interactions

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12
Q

how many hydrogen bonds between AT?

A

2

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13
Q

how many hydrogen bonds between GC?

A

3

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14
Q

Why is it wrong that GC bonds are stronger than AT bonds?

A

really, its Gs stacked on Cs are much stronger than As stacked on Ts

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15
Q

stacking

A

need two base pairs in a row:

C-G
G-C
=-61 kJ/mol (inverse is only -40)

A-T
T-A
-16 kJ/mol inverse is -27.5)

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16
Q

WHY is C over G stronger than A over T?

A

idk!

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17
Q

why is it base stacking not pairing?

A

It can’t be hydrogen bonding because energy is different for G on C than it is for C on G (also for As and Ts)
same number of hydrogen bonds, but different energies

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18
Q

Thymine vs. Uracil

A

both pyrimidines that pair with adenine (purine)
DNA has A-T
RNA hybrids with DNA have (RNA)U-A(DNA) or (DNA)A-T(DNA)

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19
Q

Why does RNA contain U but DNA contains T?

A

spontaneous deamination of cytosine makes uracil

this happens constantly

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20
Q

Why can’t we have U in DNA?

A

if we had uracil in DNA, it would be really easy for G-C pairs in DNA double helix to mutate to TA after TWO rounds of replication

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21
Q

How do we avoid the problems with uracil in DNA?

A

enzymes evolved to quickly remove uracil from DNA b/c it doesn’t belong
Us NOT ALLOWED IN DNA!!!!!!!

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22
Q

why does it take 2 rounds of rep for a mutation from GC to TA?

A

at first: the C won’t pair with the U
first round, it will just put an A with the U instead of the C
second round: then we get put a T with the A

23
Q

the three forms of DNA helix: A, B, Z

A

all same sequence, just differing interactions
B is most common
best for stability and stacking and shielding

24
Q

how do A and B forms differ?

A

A is more squished down

25
Q

stacking: why are stacks between same base pairs (C-G vs G-C for example)?

A

stacking is more stable due to HOW its stacked, how top of one interacts with bottom of other

26
Q

Hybridizing through base pairing

A

determined by base PAIRING not stacking

27
Q

naturation and renaturation

A

heated up, unravelling, getting back together

28
Q

Unravelling…

A

relative to the STACK

29
Q

what’s cool about nucleic acid helix separation?

A

doesn’t break covalent bonds

only non-covalent weak interactions are disrupted (van der Waals and hydrogen bonds)

30
Q

What is more/less stable?

A

GC stacks more stable than AT

31
Q

review slide 11

A

review slide 11

32
Q

Using spectroscopy to determine number of strands

A

measure absorbance of nucleotide bases

use wavelength of 260nm, you can distinguish bases

33
Q

absorbance for double stranded/signle stranded

A

low absorbance for double stranded (bases inside) (but increases as it unravels)
high absorbance for single stranded (bases stick out)

34
Q

what does “cooperativity of transition” mean?

A

LOOK THIS UP!
It is an in-between state of pulling apart/denaturation. The midpoint of the S curve is the point where it goes from being wound to completely denaturing

35
Q

what is the significance of the sigmoidal curve on the graph?

A

DNA is well ordered at low temp, it opens up as temp incs

when we get to critical temp, the DNA just pulls apart b/c stacking can no longer hold it together

36
Q

What is the composition of the DNA pool at 85 degrees celcius. Are most DNA strands 50% single stranded, or are 50% of the strands completely single stranded and 5o% of the strands completely double stranded?

A

half of small DNA molecules are double stranded, half are double stranded

b/c they are small molecs (long molecs would cause “bubbles”

37
Q

What affects the “melting temperature” (Tm) (the transition temp)

A

base composition
salt (NaCl),
length of complementary sequence

38
Q

What happens if we change ratios of Gs and Cs?

A

Tm increases with inc precentage of G-C content

b/c G-C base stacking interactions are more stable in double helix

39
Q

Is the localized Tm affected by the specific DNA sequence? Explain answer in terms of base stacking nrgs

(ex CAGTCTGA vs. ATTAGCCG)

how is this biologically useful

A

Yes
As and Ts at the bottom, pulls apart faster in this part in second strand
The more GC, the higher the temperature needs to be to pull it apart. The second would pull apart faster b/c there is lower stacking energy for AT/TA.

biologically useful if you want a bubble and want a protein to sneak in

40
Q

How does length affect Tm

A

lower temp needed for shorter strand

but really only matters if under 70

41
Q

Length of DNA only affects Tm for DNA fragments less than about 70 bp. Why?

A

melts quicker if shorter (up to a certain length)

42
Q

Considering that DNA forms a helix in pure water, do you want to store DNA in water?

A

NO! you want so salt in there

43
Q

Salt content of cell… how does Tm get affacted?

A

Sodium ions neutralize negative charges and STABILIZE the helix
so more salt=higher temp needed to break it down

44
Q

why is it bad to store DNA in water?

A

there are no ions!!!
DNA way less stable

why? at low salt, we barely shiled the phosphates

45
Q

DNA palindromes

A 
evolutionarily selected for functions 
2-fold symmetry 
self complimentary and form hairpins
repeat self 
uses for sequence, not structure
46
Q

RNA single and double stranded regions

A

RNA is frequently base paired to make double strands

47
Q

Transfer RNA

A

adaptor in protein synth
folds to complex tertiary strucutre, about half nucleotides are paired
some modified tRNA bases

48
Q

Protein binding

A

bind to DNA using sequence specific fasion
critical in gene regulation
required for DNA replication, repair, and recombination

protein affinity is really high
involve non-covalent weak interactions

49
Q

most common H bond donors:

A 
Asn
Gln
Glu
Lys
Arg
50
Q

weak interactions for protein binding often come from…

A

glutamine and adenine

51
Q

proteins are usually in what form

A

helix

because can donate R goups

52
Q

Why are the protein binding interactions to bases called “specific” and those to the sugar phosphate backbone “non-specific”?

A

backbone is all phosphates: neg charges, so any pos charge can interact with it. same all the way
bases: Specific!
important b/c protein stops at base it wants, and its wobbly, so it binds to the phosphate to lock into place

53
Q

Lac repressor

A

protein dimer binds to DNA

causes formation of DNA loop to inhibit transcription

Biochem 385 Unit 3 (11 decks)

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