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CH112 > nucleic acids part 2 > Flashcards

nucleic acids part 2 Flashcards

1
Q

how are polynucleotides directional ?

A

they have a 3’ end and a 5’ with no phosphate group attached. The phosphate at top is 5’ and C3 is 3’.

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2
Q

how are the phosphate groups described and what does this mean?

A

they are deprotonated at a physiological pH meaning they are negatively charged. This is called a polyanion

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3
Q

what is DNA’s molecular structure ?

A

it is an antiparallel double helix , the backbone is made up of 2 sugar phosphate chains.

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4
Q

whats the 3 major forms of double helical DNA ?

A

a, B and Z

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5
Q

explain Chagraff’s rules

A

it was a study carried out , when DNA was hydrolysed and analysed the resulting base pairs showed that DNA had equal pairs of A=T and G=C.

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6
Q

explain NMR and x-ray data

A

this determines the correct tautomeric forms of the bases were present.

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7
Q

x-ray diffraction

A

this reveals DNA is helical

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8
Q

what is the most common form of DNA ?

A

B DNA ( beta)

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9
Q

what conditions lead to the most stable from of B DNA

A

high humidity as found in aqueous environments such as the human body , also alkali metals such as Na+

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10
Q

why are alkali metals needed for B-DNA ?

A

they react with the negatively charged phosphates found on the sugar phosphate backbone.

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11
Q

what does right handed DNA mean ?

A

this means that when looking down the central axis the sugar phosphate turns in a clockwise direction.

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12
Q

why are grooves found in the B-DNA ?

A

due to the deoxyribose rings not stacking flat.

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13
Q

whats the characteristics of A-DNA ?

A

similar to B-DNA as it is a right handed antiparallel double helix , however it is wider and flatter so looked like a squashed B-DNA

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14
Q

how many bases are found in a turn of A-DNA compared to B-DNA?

A

fit more bases in a turn of A-DNA

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15
Q

why is crystal formation favoured in A-DNA ?

A

the aromatic base pairs are closer together

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16
Q

what about the plane of tilt of the bases ?

A

they are on a tilt of 20 degrees and therefore there is a central helix cavity

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17
Q

characteristics of Z-DNA?

A

this is a left handed antiparallel double helix . It has a zig zag of sugar phosphate backbone

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18
Q

when does Z-DNA tend to form ?

A

when there’s a high concentration of cations

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19
Q

how is DNA denatured or separated ?

A

a solution of native DNA is heated , once the specific melting temperature (TM) is reached the double helix separates

20
Q

what conformation do the separated strands make ?

A

A random coil

21
Q

what happens to the viscosity when DNA is denatured?

A

it decreases

22
Q

what happens the absorbance of DNA when denatured ?

A

increases

23
Q

What happens to the aromatic bases when DNA is denatured ?

A

they undergo electron transitions with there pi electrons. The bases no longer stack and their absorbance is higher.

24
Q

what is the hyper-chromic shift ?

A

this is when the absorbance of DNA increases

25
Q

what base pair , A=t G=C has a higher TM and why ?

A

G=C as it has 3 hydrogen bonds so needs more energy than A=T which has 2 hydrogen bonds.

26
Q

what name is given to DNA that is cooled rapidly ?

A

quenching

27
Q

whats the probability of the base pair sequence being 100% the same after quenching?

A

zero

28
Q

what is annealing ?

A

this is when DNA is repeatedly cooled and heated

29
Q

what is local breathing ?

A

this is when small sections of DNA separate then reform

30
Q

what can local breathing lead to ?

A

unwanted reactions as electrophilic chemicals colud bind to the nucleophilic bases

31
Q

name 2 tertiary structures of DNA ?

A

circular DNA and super coiled DNA

32
Q

what is circular DNA ?

A

this is when a covalent bond forms between the 3’ and 5’ of the same strand of DNA

33
Q

where is circular DNA most common ?

A

viruses and bacteria

34
Q

what is superhelical DNA or supercoiled DNA ?

A

this is when a circular DNA is coiled even further

35
Q

what does supercoiled DNA interact favourable with and what does this form?

A

histone proteins to form a complex called chromatin

36
Q

what can the energy present within supercoiled DNA go towards ?

A

biological processes

37
Q

what is a topoisomer ?

A

this is when molecules have the same chemical and stereoisomer bonds but have different topologies

38
Q

what is a topology ?

A

this is when a molecule is stretched , crumpled or twisted

39
Q

when will DNA work correctly ?

A

when it is in its correct topology

40
Q

what are topoisomerases ?

A

these are enzymes that convert DNA from one topology to another

41
Q

what is a type 1A topoisomerase ?

A

this is an enzyme that unwinds DNA by one turn

42
Q

when can chemicals that prevent topoisomerases working correctly be used ?

A

as antibiotics and cancer chemotherapy drugs

43
Q

why is RNA a single strand ?

A

due to the presence of the hydroxyl group at the 2’ position which causes repulsion and prevents a double helix forming

44
Q

does RNA have intramolecular or intermolecular base pairs ?

A

intramolecular

45
Q

how come the RNA strand can twist and fold ?

A

due to the intra strand base pairing

CH112 (14 decks)

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