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BIOL 3051 (macromolecules) > Nucleic Acids > Flashcards

Nucleic Acids Flashcards

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

A

the edge that H bonds from both pyramidine + imazidole rings

21
Q

what is the watson&crick edge

A

the edge that H honds from only the pyramidine ring

22
Q

Key differences between RNA and DNA

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 =

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

A

bulges, internal loops, stems/hairpins, junctions

25
Q

examples of RNA tertiary structures

A

psuedoknots = discontinuous base pairing among the rna strand

kissing hairpins = 2 hairpin loops base pairing

26
Q

stabilizing forces of RNA

A
  • 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
Q

what is the function of metals such as Mg2+ in RNA

A

they stabilize the RNA A form helix by fitting really well and are involved in catalytic activities ex. hammerhead ribozyme

28
Q

GNRA tetraloop (hairpin loops secondary structure)

A

4-base hairpin loops

G = guanine
N = any base
R = A/G (purine)
A = adenine

h bonding between G/A (2 bonds)

29
Q

UNCG tetraloop (hairpin looks secondary structure)

A

4-base hairpin loops

U = urucil
N = any base
C = cytosine
G = guanine

h bonding between U/G

30
Q

what type of metals stabilize the bends in bulges (secondary structure)

A

Mg2+ stabilizes the bends in bulges and Ca2+ can stabilize the overall structure

31
Q

Hammerhead Ribozyme (tertiary structure)

function =
structure of ribozyme =
Ions involved =
ph dependant =

A

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
Q

unusual dna structures

A

m-dna (metal dna), ring expanded bases, non standard bases (nanotech)

33
Q

what is M-dna

A

metal- dna
- dna + divalent metal ions (Co2+, Ni2+, Zn2+) placed in the middle of dna
- widens dna helix

34
Q

what are ring expanded bases

A

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
Q

what are non standard bases and why are they used

A

-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
Q

dna origami

A

matching multiple ssDNA through base pairing in order to make a defined dsDNA structure

37
Q

types of drugs x DNA interactions

A
  1. intercalating agents (EtBr)
  2. groove binders (Netropsin)
  3. alkylating agents (Mechloroethamine)
  4. chain cutters (Bleomycin (BLM))
  5. chain terminators
38
Q

INTERCALATING AGENTS

function and example =
structure =
binding forces

A

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
Q

GROOVE BINDERS

function and example =
structure =
binding forces =

A

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
Q

ALKYLATING AGENTS

function and example =
structure =
binding forces =

A

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
Q

CHAIN CUTTERS

function and example =
Site of cleavage =

A

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
Q

intermolecular interactions between
Protiens-DNA

A
  1. stacking interactions - dna bases + aromatic protien side chains (rare)
  2. water mediated H bonding
  3. electrostatic interactions - Lys/Arg + P
43
Q

dna binding proteins bind to specific bps in a _________ _________ manner through the ______ groove usually

A

sequence specific
major

44
Q

what and where are the 3 aa-base interactions that only involve 2 H bonds

A
  1. Arg - GC (major groove)
  2. Gln - AT (major groove)
  3. Asn - GC (minor groove)
45
Q

PROTEIN-DNA COMPLEXES (MAJOR GROOVE)

Lambda Repressor

motifs =
aa-base interaction =
binding forces =

A

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
Q

PROTEIN-DNA COMPLEXES (MINOR GROOVE)

Mu Repressor

motifs =
binding site =

A

motifs = winged HTH motif

binding site = unstructured domain/tail binds to the minor groove of DNA

47
Q

3 protein-RNA recognition features

A
  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
Q

RNA BINDING PROTEINS

BIV TAR TAT (Arg rich)

structure =
binding forces =

A

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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