Lecture 28: Nucleic Acids Flashcards by Ryley Tegler

DNA: where are bases? backbone?

bases: center of helix
backbone: outside

How well did you know this?

Not at all

Perfectly

stability of double helix structure due to what?

BASE STACKING

NOT base bonding

How well did you know this?

Not at all

Perfectly

base pairing

done by hydrogen bonding between pairs

this adds little stability

How well did you know this?

Not at all

Perfectly

form of RNA double helicies

A form

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

How well did you know this?

Not at all

Perfectly

what pairs with what?

G-C

A-T

How well did you know this?

Not at all

Perfectly

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

5’TGCCGAT3’

start from BACK because ANTIPARALLEL

How well did you know this?

Not at all

Perfectly

what is base PAIRING important for?

SPECIFICITY

not stability

How well did you know this?

Not at all

Perfectly

how is DNA written?

ALWAYS 5’ to 3’

How well did you know this?

Not at all

Perfectly

how do bases associate in hydrophobic environments?

by hydrophobic interactions

How well did you know this?

Not at all

Perfectly

Base Stacking

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

How well did you know this?

Not at all

Perfectly

Stacks

aromatic rings, parallel ring systems above and bellow

interact by van der Waals interactions

How well did you know this?

Not at all

Perfectly

how many hydrogen bonds between AT?

How well did you know this?

Not at all

Perfectly

how many hydrogen bonds between GC?

How well did you know this?

Not at all

Perfectly

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

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

How well did you know this?

Not at all

Perfectly

stacking

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)

How well did you know this?

Not at all

Perfectly

WHY is C over G stronger than A over T?

idk!

How well did you know this?

Not at all

Perfectly

why is it base stacking not pairing?

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

How well did you know this?

Not at all

Perfectly

Thymine vs. Uracil

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)

How well did you know this?

Not at all

Perfectly

Why does RNA contain U but DNA contains T?

spontaneous deamination of cytosine makes uracil

this happens constantly

How well did you know this?

Not at all

Perfectly

Why can’t we have U in DNA?

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

How well did you know this?

Not at all

Perfectly

How do we avoid the problems with uracil in DNA?

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

How well did you know this?

Not at all

Perfectly

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

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

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

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

how do A and B forms differ?

A is more squished down

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

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

Hybridizing through base pairing

determined by base PAIRING not stacking

naturation and renaturation

heated up, unravelling, getting back together

Unravelling...

relative to the STACK

what's cool about nucleic acid helix separation?

doesn't break covalent bonds | only non-covalent weak interactions are disrupted (van der Waals and hydrogen bonds)

What is more/less stable?

GC stacks more stable than AT

review slide 11

Using spectroscopy to determine number of strands

measure absorbance of nucleotide bases | use wavelength of 260nm, you can distinguish bases

absorbance for double stranded/signle stranded

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

what does "cooperativity of transition" mean?

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

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

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

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?

half of small DNA molecules are double stranded, half are double stranded b/c they are small molecs (long molecs would cause "bubbles"

What affects the "melting temperature" (Tm) (the transition temp)

base composition salt (NaCl), length of complementary sequence

What happens if we change ratios of Gs and Cs?

Tm increases with inc precentage of G-C content | b/c G-C base stacking interactions are more stable in double helix

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

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

How does length affect Tm

lower temp needed for shorter strand | but really only matters if under 70

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

melts quicker if shorter (up to a certain length)

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

NO! you want so salt in there

Salt content of cell... how does Tm get affacted?

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

why is it bad to store DNA in water?

there are no ions!!! DNA way less stable why? at low salt, we barely shiled the phosphates

DNA palindromes

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

RNA single and double stranded regions

RNA is frequently base paired to make double strands

Transfer RNA

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

Protein binding

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

most common H bond donors:

``` Asn Gln Glu Lys Arg ```

weak interactions for protein binding often come from...

glutamine and adenine

proteins are usually in what form

helix | because can donate R goups

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

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

Lac repressor

protein dimer binds to DNA | causes formation of DNA loop to inhibit transcription