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Bchem 393 > DNA Stucture > Flashcards

DNA Stucture Flashcards

1
Q

What is a monomeric unit of dna made of

A

The sugar, phosphate attached to it and the base attached to it

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2
Q

What is dna

A

Form of linear information where the sequence of based characterizes the nucleic acid

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3
Q

What is the sugar of the monomeric unit

A

It’s an aldopentose in furanose form (5 membered ring

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4
Q

What diff in ribonucleic acid (RNA) compared to deoxy (DNA)

A

RNA has 2 prime oh on the sugar

DNA has 2’ H

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5
Q

Where does the phosphate group link in dna/rna

A

The 3’ oh of one and the 5 oh of the other

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6
Q

What is the diretionality of dna

A

Read from the 5 prime to the 3’ end

3’ is where the oh group is

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7
Q

Which is more stable DNA or RNA and why

A

DNA because the 2’ Oh in rna can act as a nucleophile

This means it can hydrolyze its phosphodiester bond/backbone and is prone to degredation

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8
Q

What are the purines

A

Adenine and guanine

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9
Q

What are the pyrimidine

A

Cytosine thymine (in rna thymine is replace with uracil)

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10
Q

Which nitrogen’s of the Purine and pyramids form the glycosidic bond with the sugar of the backbone

A

N9 of the purine

N1 of the pyrimidine

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11
Q

Structures of bases memorize

A

Okay

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12
Q

What is a nucleotide

A

The monomeric unit of dna/RNA

the base, the Pentose sugar, and 1 or more phosphate groups

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13
Q

What type of bond it is between the sugar and the phosphate in a nucleotide

A

An ester linkage

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14
Q

What is a nucleoside

A

Only the base and the Pentose sugars (no phosphates)

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15
Q

If a nucleoside has one phosphate group it’s called:

A

Nucleoside monophophate

If the base attached is adenine this would be AMP

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16
Q

If an rna nucleoside has adenine as a base what is it named

A

Adenosine

All types of adenosines (atp, amp, adp) are called adenylates

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17
Q

If a DNA nucleoside has adenine as a base what is it named

A

Deoxyadenosine

All types of theses (datp,damp,dadp) are called deoxyadenylates

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18
Q

What is the distance between stacked bases in the double helix

A

3.4A

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19
Q

How many A in one full turn

How many bases per turn

Of the double helix

A

34A

10.4

20
Q

What is the width of the double helix

A

20A

21
Q

What degreee rotation is it in the double helix between each base

A

36 degrees

22
Q

What is the direction of the double helix

A

Right handed,

Opposites directionality on each strand (one is 5-3 other is 3-5)

23
Q

Bases are nearly _____ to the axis of the helix

A

Perpendicular

24
Q

How many h bond between GC

AT

A

3

2

25
Q

Why do purine pair with pyrimidines

A

To keep a uniform diameter of the helix

26
Q

What are the four types of base pairin

A

Watson crick

Reverse Watson crick

Wobble base pairs

Hoogsteen

27
Q

Why does reverse Watson crick happen

A

Because of the 180 degree rotation of a base in rna or dna ends

28
Q

Why does wobble base pairing happen

A

Tautomerization (makes it pair with something else)

29
Q

Why does hoogsteen happen

A

Rotation around the c1 of the sugar to N of the base glycosidic bond

This rotates the base

This make it anti and syn

In Watson crick the bases are anti anti

30
Q

Why are bases inside the helix

A

The hydrophobic effect where the hydrophobic interactions of the base move them away from water

The more polar part of dna are on the outside

This add stability to the helix

31
Q

Why are bases stacked

A

They attract each other by vander wall

This gives stability of the helix through non covalent interactions

32
Q

What is the energy per vanderwall interaction of stacked bases

A

2.4kj/mol

33
Q

What is the major and minor groove of dna

A

The glycosidic bond to the backbone between opposite bases (base pairs) arent completely across from each other

The major groove (12A) is where the distance between glycosidic bond it larger

Minor (6A) is where the distance is shorter

34
Q

What are the major and minor grooves lined by

A

H bond donors and accpetors the are unique to each base pair

They allow the base pair to be accessed by other protiens

35
Q

What are the three forms of dna

A

B
A
Z

36
Q

What are the B and a forms of dna

A

B is where the bases are perpendicular to the back bond

A is where they are not, this is normally seen in dna rna hybrids. Caused by the rna 2’ oh causing hindrance

Both still right handed helix

37
Q

What is the z form of DNA

A

It’s left handed and specific protiens bind only to this form

This means it’s biologically significant

38
Q

If circular dna is unwound what forms can it take

A

Negative superhelix (unwound by three right hand turns)

Unwound circle (unwound two times)

39
Q

Is supercoiled dna larger or smaller than telexed circular dna

What does this mean

A

Smaller

Travels further in gel

40
Q

What are nucleosome

A

Histone octamers with +200bp of dna wrapped around them

41
Q

How much dna is packaged into how many chromosome

What is the diameter of the nucleus they’re packed in

A

3.6m

46

5 micrometers

42
Q

What are histones made of

A

Argenine and lysine (basic) residues

43
Q

What are nucleosomes compacted into

By what factor

A

Chromatin

Form left handed helical structures

By a factor of 7

44
Q

What is the diameter of a histon octamer

A

100A

45
Q

How does rna fold

Why is this Important

A

Into complex structure, It can create stem loops

Its structures let it act as a catalyst. Ex. Ribozymes where AGC are all linked together

Bchem 393 (31 decks)

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