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BIOL 308 Molecular Biology > Nucleic Acid Structure and Hybridization > Flashcards

Nucleic Acid Structure and Hybridization Flashcards

1
Q

covalent bonds

A
  • strong! share e-
  • can be polar or nonpolar
  • polar covalent bonds (partial +/- charges) allow hydrogen bonds
  • don’t change in water
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2
Q

noncovalent: ionic

A
  • big difference in EN
  • transfer of e-
  • WEAK in water
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3
Q

noncovalent: hydrogen bonds

A
  • weak
  • polarity: H atom covalently attached to very EN atom (N, O, P; donors, D) has partial +ve charge
  • partially +ve H can be attracted by another EN atom (acceptor, A), forming a weak H bond
  • weak in water
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4
Q

noncovalent: Van der Waals interactions (AKA ____?)

A

london dispersion forces (LDF)
- between all types of molecules (polar and non-polar)
- cause is transient, unequal movement and dist. of e- = formation of temporary dipoles
- dipole of one molecule -> helps arrange another dipole of second molecule
- too close - repulsion; also decreases w/ distances
- works well if few atoms of a molecule are at same distance from few atoms of other molecule (esp complementary fit)

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5
Q

noncovalent: hydrophobic interactions

A
  • polar and nonpolar regions of molecules have differing affinities (hydrophilic/hydrophobic)
  • hydrophobic groups are subject to van der waals
  • individually weak, but usually lots between molecules/parts of molecules
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6
Q

Hbonds and van der waals?

A

individually weak, strong together

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7
Q

in water: interactions/bonds strength ranking?

A

covalent > ionic > hydrogen bonds > van der waals

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8
Q

nitrogenous bases

A

purines (2 rings) A,G (mnemonic (GAP2)
pyrimidine (1 ring) C,T,U

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9
Q

nucleic acid structure

A
  • nitrogenous bases
  • ribose sugars
  • phosphate group (PO4^-2)
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10
Q

ribose sugars, carbon diffs (RNA/DNA), monomer, polymer

A
  • 3’ C always has hydroxyl group, where monomers are added during replication
  • 2’C: DNA has H, RNA has OH
  • monomer: deoxyribonucleotides, ribonucleotides
  • polymer: DNA, RNA
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11
Q

phosphate group

A

PO4^-2
- why DNA always negatively charged

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12
Q

what does “nucleoside” include?

A

pentose sugar
nitrogenous base
NO phosphates

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13
Q

what does “nucleotide” include?

A

nucleoside (sugar + base) + phosphate

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14
Q

nucleotide options (3):

A

nucleoside monophosphate
nucleoside diphosphate
nucleoside triphosphate

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15
Q

naming nucleoside vs nucleotide (DNA vs RNA)

A

nucleoside:
- DNA: deoxyadenosine, deoxyguanosine, deoxycytidine, deoxythymidine, deoxynucleoside
- RNA: adenosine, guanosine, cytidine, uridine, nucleoside

nucleotide: (may contain fewer phosphates)
- DNA: deoxyadenosine 5’-triphosphate (dATP) etc, deoxynucleoside 5’-triphosphate (dNTP)
- RNA: adenosine 5’-triphosphate (ATP), etc, nucleoside 5’-triphosphate (NTP)

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16
Q

where does phosphodiester link DNA molecules together

A

3’ OH
5’ phosphate

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17
Q

reading direction for DNA?

A

5’ to 3’

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18
Q

nucleotide functions (4)

A
  • informational molecules (DNA/RNA)
  • high energy molecules (ATP/GTP)
  • in coenzymes that act as cofactors for metabolic enzymes (CoA - AMP)
  • regulatory/signaling molecules (cyclic AMP/GTP)
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19
Q

what is Chargaff’s rule?

A

purines = # pyrimidines
G=C, A=T

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20
Q

How and who - DNA structure discovery

A

X-ray diffraction
Rosalind Franklin
- irradiate crystallized DNA with x-ray and capture on film
- dark bars = phosphate backbone
- X pattern = helical structure

21
Q

DNA is a ___-handed double helix

A

right!

22
Q

DNA bases are ___nm apart? and ___ to each other

A

0.34nm apart, and parallel to each other
(anti-parallel chains)

23
Q

major vs minor grooves?

A

major grooves have more space for binding proteins

24
Q

One complete turn (DNA) means? how many nucleotides, what exact length?

A
  • one minor groove to next minor groove
  • every 10 nucleotides
  • 3.4 nm in length (10 x 0.34nm = 3.4nm)
25
Q

1 angstrom = ?

A

0.1 nm

26
Q

Major and minor grooves characteristics

A
  • binding sites for factors (regulatory, trans)
  • each factor recognizes specific nucleotide sequence on DNA
  • each nucleotide sequence “exposes” specific, unique distribution of acceptors and donors (like a code)
    – minor groove patterns are more similar (AT vs TA, not AT vs GC) than major groves
27
Q

forces that help form DNA double helix (5)

A

rigid phosphate backbone
- overall -ve
stacking interactions
- van der waals between bases
hydrophobic interactions
- highly -ve phosphate backbone “outside” vs nonpolar (hydrophobic) bases “inside
ionic interactions
- salts (+ve ions) stabilize phosphate backbone (DNA shielding)
H bonding
- complementary base pairing, not most energetically significant

28
Q

forms of DNA (3), which one is normal?

A

B-DNA - normal DNA, right-handed helix
A-DNA - right- handed helix
Z-DNA - left-handed helix

29
Q

unusual forms of DNA (2)

A
  • slipped (tandem repeats) or cruciform (inverted repeats) can form if there are REPEATED DNA seq; internal complementarity
  • slipping is ss loop
  • cruciform is four-way junction
30
Q

what level of structure is a cruciform?

A

secondary structure

31
Q

triple helix DNA? AKA?

A

Hoogsteen base pairs
- formed when purines make up one strand and pyrimidines the other, then a THIRD strand can be added (binds to major groove of existing two strands

32
Q

how is chromosomal DNA a dynamic structure?

A
  • localized structural polymorphisms (chemically identical molecules with different structures)
    – constant
    – DNA seq
    – local env
  • allows for recognition of DNA:
    – gene expression
    – DNA repair
  • B-DNA, A-DNA, Z-DNA can all exist together
33
Q

two sequences that are not complementary will _____

A

not hybridize

34
Q

if strands from native double helix (same original ds) reform a ds: _____
if strands from diff double helices (diff orig. ds) form a ds: _____

A
  • renaturation
  • hybridization
35
Q

factors that denature DNA

A
  • heat
  • low ionic strength; promotes repulsion between -ve phosphate backbones (low salt)
  • high pH; stripping of H+ shared between EN centers (NaOH)
  • agents that influence H bonds
  • agents that enhance solubility of hydrophobic substances
36
Q

What are 2 good conditions for denaturation?

A

high heat, low salt (high stringency)

37
Q

2 agents that influence H-bonds (covalent modifications)

A
  • modify EN centers and block formation of H-bonds (formaldehyde, glyoxal)
38
Q

2 agents that influence H-bonds (competition)

A
  • have functional groups that can form H-bonds with EN centers (urea, formamide)
39
Q

how to monitor DNA denaturation?

A

examine change in properties when strands separate:
- viscosity - rarely used (hard)
- absorbance (260 nm) - common in lab

40
Q

absorption spectrophotometry

A

dsDNA absorption increasing = denaturation
Tm = melting temperature (temp at which 50% DNA is denatured usually used)

higher than Tm, approach complete denaturation

higher GC, higher Tm

41
Q

why ssDNA increases absorption during absorption spectrophotometry?

A
  • stacking of molecules is disturbed
  • not strands coming apart, just bases unstacking
42
Q

absorbance changes depending on stacking of purines and pyrimidine (ss and ds): 2 terms

A
  • in ds, bases are stacked and absorbance is lower (HYPOCHROMIC)
  • in ss, bases are unstacked and absorbance increases (HYPERCHROMIC)
43
Q

___ regions separate first during denaturation

A

AT

44
Q

Tm of DNA increases by ___deg C with every __% increase in GC content under normal conditions

A

0.4 deg C
1% increase

45
Q

higher salt = ____ Tm
why?

A

higher Tm
salt stabilizes DNA

46
Q

what is renaturation? aka?

A

recombination of two complementary ssDNA
hybridization

47
Q

what does renaturation depend on? (6)

A
  • DNA conc - complementary strands have to find each other
  • salt conc - ionic conditions - mask repulsion forces of phosphate backbone
  • temp - 20-25 deg C below Tm
  • time (reaction time)
  • size of DNA fragment
  • complexity - simple seq renature faster
48
Q
A

BIOL 308 Molecular Biology (14 decks)

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