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BIOL 3051 (macromolecules) > Nucleic Acids > Flashcards

Nucleic Acids Flashcards

(48 cards)

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1
Q

DNA

A

deoxy-ribonucleic acid

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2
Q

nucleotide and examples

A

pentose sugar + nitrogenous base + phosphate

CTU (pyramidines) AG (purines)

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3
Q

what type of bond does the ribose sugar - nitrogenous base make

A

B-glycosidic bond

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4
Q

nucleoside

A

pentose sugar + nitrogenous base

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5
Q

what direction is DNA synthesized in

A

5’P ———– 3’OH

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6
Q

what direction do DNA strands run in

A

antiparallel

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7
Q

DNA DIMENSIONS

diameter =
each turn of the helix =
distance between each bp =
minor groove =
major groove =
sugar pucker of deoxyribose =

A
  • 20 Å = 2 nm
  • 34 Å = 3.4 nm
  • 3.4 Å = 0.34 nm
  • 6 Å = 0.6 nm
  • 12 Å = 1.2 nm
  • C2 endo sugar pucker
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8
Q

are bases placed in a anti or syn conformation with the sugar

A

anti = limits steric hindrance between base and sugar

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9
Q

chargaffs rule and why it is so important

A

[A] = [T] [C]=[G]
- arrangement maintains complementarity and uniform structure of DNA double helix

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10
Q

watson and crick bond stability

A

A/T = 2 H bonds
C/G = 3 H bonds

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11
Q

what 2 things lead to the stability of DNA double helix

A

-base stacking interactions between adjacent bases
- H bonding interactions between sugar-base

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12
Q

what conformation leads to the B form DNA sugar pucker

A

C2 endo (C2 is above the plane)

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13
Q

C2 endo sugar pucker refers to what form of nucleic acid

A

B form DNA

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14
Q

what conformation leads to the A form DNA sugar pucker

A

C3 endo (C3 is above the plane)

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15
Q

syn base conformation =
anti base conformation =

A

= base is directly above the sugar = not favoured
= base is beside the sugar = favoured

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16
Q

structure of a tetraplex

A
  • 4 guanine residues aligned in a square through h bonding
  • hoogsteen edge + watson&crick edge interacts
  • stabilized by K+ ions in between each tetraplex
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17
Q

3 conformations of dsDNA

A

A form = shorter, wider, right handed twists
B form = regular DNA, right handed twists
Z form = zigzag arrangement, left handed twists

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18
Q

how can dna have a triple helix

A

through Hoogsteen base pairing of a third helix that binds to the double helix

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19
Q

Hoogsteen base pairing

A

syn A / anti T syn G / anti C
A/T + T G/C + C

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20
Q

what is the hoogsteen edge

Study These Flashcards
A

the edge that H bonds from both pyramidine + imazidole rings

21
Q

what is the watson&crick edge

Study These Flashcards
A

the edge that H honds from only the pyramidine ring

22
Q

Key differences between RNA and DNA

Study These Flashcards
A

RNA = single stranded DNA = double stranded
RNA = uses a U instead of a T
RNA = OH on C2 of ribose DNA = H on C2
RNA = G/U and A/U base pairing

23
Q

RNA STRUCTURE

primary =
secondary =
tertiary =
quaternary =

Study These Flashcards
A

primary = original sequence of nts
secondary = intramolecular base pairing of nts
tertiary = intramolecular folding of structure
quaternary = intermolecular interactions

24
Q

examples of RNA seconday structures

Study These Flashcards
A

bulges, internal loops, stems/hairpins, junctions

25
examples of RNA tertiary structures
psuedoknots = discontinuous base pairing among the rna strand kissing hairpins = 2 hairpin loops base pairing
26
stabilizing forces of RNA
- hydrophobic stacking interactions, van ders wals interactions, pi-pi interactions between aromatic bases - hydrogen bonding - electrostatic interactions between phosphate (-) and metals (Mg2+, Na+, K+)
27
what is the function of metals such as Mg2+ in RNA
they stabilize the RNA A form helix by fitting really well and are involved in catalytic activities ex. hammerhead ribozyme
28
GNRA tetraloop (hairpin loops secondary structure)
4-base hairpin loops G = guanine N = any base R = A/G (purine) A = adenine h bonding between G/A (2 bonds)
29
UNCG tetraloop (hairpin looks secondary structure)
4-base hairpin loops U = urucil N = any base C = cytosine G = guanine h bonding between U/G
30
what type of metals stabilize the bends in bulges (secondary structure)
Mg2+ stabilizes the bends in bulges and Ca2+ can stabilize the overall structure
31
Hammerhead Ribozyme (tertiary structure) function = structure of ribozyme = Ions involved = ph dependant =
function = catalyzes the cleavage of phosphodiester bonds in RNA structure = made of 3 stem loops, stems 1&3 have base pairing at the cleavage site 2 Mg2+ ions aid in the attack of the 2'OH attacking the 3'P for cleavage ph between 5-8
32
unusual dna structures
m-dna (metal dna), ring expanded bases, non standard bases (nanotech)
33
what is M-dna
metal- dna - dna + divalent metal ions (Co2+, Ni2+, Zn2+) placed in the middle of dna - widens dna helix
34
what are ring expanded bases
bases are expanded through the addition of a benzene ring expanded base1 + reg base 2 = hydrogen bonding ex. expanded A + T = 2 h bonds ex. expanded G + C = 3 h bonds - widens the dna helix and makes it more stable than normal dna helix
35
what are non standard bases and why are they used
-artificial nucleobases that are inserted within the a-helix in between the standard bases through the use of metal ion coordination - used to increase the information storage of DNA by addition of artifical nucleobases that can carry more genetic contents (info) and can be used for nanotech
36
dna origami
matching multiple ssDNA through base pairing in order to make a defined dsDNA structure
37
types of drugs x DNA interactions
1. intercalating agents (EtBr) 2. groove binders (Netropsin) 3. alkylating agents (Mechloroethamine) 4. chain cutters (Bleomycin (BLM)) 5. chain terminators
38
INTERCALATING AGENTS function and example = structure = binding forces
function = EtBr, fits in between bps in the dna helix and therefore disrupts the dna structure hence, distrupting transcriptional processes structure = flat planar aromatic structure binding = by Van der Wals base stacking as well as electrostatic interactions ((+) on the ends of EtBr/ (-) P)
39
GROOVE BINDERS function and example = structure = binding forces =
function = Netropsin/DAPI, non-covalently bind to the major/minor grooves of dna minor groove binders are more common structure = cresent shaped molecules binding = by H bonding as well as electrostatic interactions ((+) on the ends of Netropsin/ (-) P)
40
ALKYLATING AGENTS function and example = structure = binding forces =
function = Mechloroethamine (Nitrogen Musturd), agents that introduce alkyl groups to dna therefore disrupt the structure by making DNA stand cuts and prevent replication from happening, used for anticancer drug theraphy structure = highly electrophilic compounds that form covalent bonds with DNA
41
CHAIN CUTTERS function and example = Site of cleavage =
function= BLM, intercalating agents that cut the DNA chain of cancer cells through free radical mediated scission by using Fe2+ as a cofactor. The indroduced radical then reacts with O2 to mediate the scission, used for anticancer drug theraphy site of cleavage = cleaves 4'H or 5'H
42
intermolecular interactions between Protiens-DNA
1. stacking interactions - dna bases + aromatic protien side chains (rare) 2. water mediated H bonding 3. electrostatic interactions - Lys/Arg + P
43
dna binding proteins bind to specific bps in a _________ _________ manner through the ______ groove usually
sequence specific major
44
what and where are the 3 aa-base interactions that only involve 2 H bonds
1. Arg - GC (major groove) 2. Gln - AT (major groove) 3. Asn - GC (minor groove)
45
PROTEIN-DNA COMPLEXES (MAJOR GROOVE) Lambda Repressor motifs = aa-base interaction = binding forces =
motifs = HTH motif between helix 2 and helix 3, helix 3 is found in the major groove aa-base interaction = Gln-AT in the major groove binding forces = H bonding from 5 P's + aa's throughout the protein , electrostatic interactions from P - 2Lys
46
PROTEIN-DNA COMPLEXES (MINOR GROOVE) Mu Repressor motifs = binding site =
motifs = winged HTH motif binding site = unstructured domain/tail binds to the minor groove of DNA
47
3 protein-RNA recognition features
1. proteins recognize the shape of RNA and not the sequence 2. protiens bind to the single stranded regions of RNA such as loops and bulges 3. Adaptive binding is common as binding changes the structure of the entire protein-RNA complex
48
RNA BINDING PROTEINS BIV TAR TAT (Arg rich) structure = binding forces =
structure = forms B-hairpin loop stucture that binds to the major groove of RNA and widens it binding forces = electrostatic interactions between Lys/Arg + RNA

BIOL 3051 (macromolecules) (3 decks)

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