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Molecules and Medicine > Nucleic Acids > Flashcards

Nucleic Acids Flashcards

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Organic Chemistry 101 flashcards
1
Q

What are nucleic acids composed off

A

4 or heterocyclic bases

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2
Q

what are the 2 pyrimidne bases

A

cytosine thymine

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3
Q

what are the 2 purine bases

A

adenine guanine

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4
Q

what do heterocylic base attach to form a nucleoside

A

5 memebered sugar unit

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5
Q

at what positions do phosphate linkages form

A

3’ and 5’

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6
Q

what is the uncommon base

A

uracil and it is a replacement for thymine

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7
Q

describe an A - Dna helix

A

RNA RNA and RNA DNA Helix with a short wide shape

deep narrow major grove with a wide shallow minor groove

base pair tilted to helix axis

c3’ endo

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8
Q

describe a B - DNA helix

A

DNA DNA with a narrow longer helix

Wide major groove

Narrow minor groove

base pair perpedicular to helix axis

c2’ endo

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9
Q

describe a Z - DNA helix

A

left handed

narrow long helix

narrow deep minor group

alternating anti syn conformation

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10
Q

what are the different ways a drug molecule can interact

A

intercalating agents

topoisomerism poisons

alkylating agents

chain cutters

chain terminators

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11
Q

describe how a DNA forms a protein

A 
DNA replicates
Transcription
RNA
Translation
Protein
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12
Q

what are intercalating agnets

A

contain planar or heteroaromatic structures which fit between the DNA base pairs

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13
Q

what are intercalating agents held in place by

A

van der waals interactions

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14
Q

what is doxorubicin

A

highly effective anti cancer drug

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15
Q

what does doxorubicin do

A

intercalates with DNA

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16
Q

how does doxuribicin intercalate with DNA

A

approaches from the minor groove and intercalates using the planar tricyclic structure

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17
Q

what does doxorubicin do

A

hinders the normal action of topoisomerase II, an enzyme involved in replication.

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18
Q

what is doxorubicin referred to

A

inhibit the enzyme so is referred to as a poison

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19
Q

what is super coiling

A

dna must be coiled int oa more compact structure to fit into the nucleus

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20
Q

what does super coiling require

A

super coiling requries one stretch of DNA to cross over another and this process is catalysed by topoisomerase enzymes

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21
Q

what is doxorubicins effect on super coiling

A

stablises the enzyme DNA complex and hinders the process

22
Q

what do non intercolating poisons do

A

fluroquinolones can interact with the DNA enzyme complex and inhibit biological function

The binding site for the drug appears only after DNA has been cleaved by the topoisomerase enzyme.

Planar core will stack through Van der Waals interactions, substituents at C6 and C7 positions can bind to the enzyme.

Carbonyl oxygen can form H-bonds with DNA.

23
Q

what is an alkylating agent

A

highly electrophilic molecule which will react with necleophilic groups within the heterocyclic DNA bases

24
Q

what can alkylating agents form

A

inter or intra strand crosslink

25
Q

what do interstand crosslinks do

A

disrupt replication and transcription by hindering separation of strands

26
Q

what do intrastrand crosslinks do

A

mask DNA structure from enzymes involved in replication and transcription

27
Q

what are the downside of alkylating agents

A

lack selectivity

28
Q

how do alkylating agents act as anti cancer

A

they reduce toxicity by formation of the active species during metabolism

29
Q

what is one of the most widely used anticancer drugs in medicine

A

cis platin

30
Q

what happens when cis platin enters the cellular environment

A

chlroide substituents are dispalaced by water

active species then forms intrastrand crosslinks in regions contraining adjacent guanine bases

attachement of the drug is thought to disturb the hydrogen bonding between the heterocyclic bases resulting in local unwinding of the helix

very lowselectivity for cancer cells causes high toxicity of drug

31
Q

what are chain cutters

A

these drugs will cleave DNA and prevent the enzyme DNA ligase from repairing the damage

thought to work through a radical mechanism resulting in oxidative cleavage of the DNA structure

32
Q

what do chain terminators do

A

inhibit DNA replication by acting as false substrate

33
Q

what do chain terminateors lack

A

functional groups requriered for further chain growth so incorporation into a growing DNA chain will reuslt in termination

34
Q

what are chain terminators used for

A

antiviral drugs

treatment of HIV targeting reverse transcriptase

35
Q

what does stabilisation of the gene helix

A

stabilisation of the double helix will inhibit the processes involved in transcription and ultimately protein synthesis

36
Q

what are the two modes of action of antisense therapy

A

steric block

cleavage by RNaaseH

37
Q

what are the optimal characteristics of RNA

A 
duplex stability
specificity
nuclease stability
cellular uptake
toxicity
38
Q

what does a too short chain mean

A

lead to targetting of other regions of RNA

39
Q

what does a too long chain mean

A

mismatched sequences

40
Q

what is the ideal chain length

A

20-25 bases

41
Q

what shows the greatest therapeutic potential

A

requires continueous stretch of DNA bases of 6-10 residues

42
Q

what does modification require

A

requires continuous stretch of DNA bases of 6-10 residues containing a phosphodiester or phosphothioate linkage

43
Q

what form of linkage are more resistant to nuclease degradation

A

phosphothiaote linkage

44
Q

what do 2nd generation antisense drugs use

A

a gapmer principle

45
Q

2nd generation antisense

A

Core region of phosphorothioate linkages are flanked by regions containing other modification.
They enhance the stability of DNA:RNA duplex, and therefore modifications that induce the C3’-endo sugar pucker are desired.
Also enhancement of nuclease stability is a consideration.
These modifications can also be used for the steric block approach.

46
Q

what can small RNA molecules present in the cell be used to control

A

gene expression and protect against viruses

47
Q

what are micro RNA

A

small double stranded RNA molecules are produced from larger RNA sequences by the dicer enzyme

48
Q

what are micro RNA produced from

A

larger RNA sequences by the dicer enzyme

49
Q

describe RNA INTERFERANCE

A

The miRNA then binds to a complex of enzymes known as RISC (RNA inducing silencing complex).
In the RISC complex one strand is discarded to produce the small interfering RNA sequence (siRNA).
This binds to a complementary mRNA and induces cleavage of the mRNA.

50
Q

Key points of RNA interference

A

dsRNA cleaved by Dicer to give miRNA.
Loading into RISC complex gives siRNA.
Recognition of mRNA by active RISC complex.
Cleavage of mRNA results in inhibition of protein synthesis.
Cleavage of viral RNA halts attack.

51
Q

what do siRNA do

A

silence target gene

52
Q

what is antigene therapy

A

similar to antisense approach but targets the DNa double helix rather than the RNA

Conventional drugs that target DNA have low selectivity for the target sequence

targeting of the DNA base pair will provide increased specificity

Molecules and Medicine (23 decks)

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