DNA Stucture Flashcards
What is a monomeric unit of dna made of
The sugar, phosphate attached to it and the base attached to it
What is dna
Form of linear information where the sequence of based characterizes the nucleic acid
What is the sugar of the monomeric unit
It’s an aldopentose in furanose form (5 membered ring
What diff in ribonucleic acid (RNA) compared to deoxy (DNA)
RNA has 2 prime oh on the sugar
DNA has 2’ H
Where does the phosphate group link in dna/rna
The 3’ oh of one and the 5 oh of the other
What is the diretionality of dna
Read from the 5 prime to the 3’ end
3’ is where the oh group is
Which is more stable DNA or RNA and why
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
What are the purines
Adenine and guanine
What are the pyrimidine
Cytosine thymine (in rna thymine is replace with uracil)
Which nitrogen’s of the Purine and pyramids form the glycosidic bond with the sugar of the backbone
N9 of the purine
N1 of the pyrimidine
Structures of bases memorize
Okay
What is a nucleotide
The monomeric unit of dna/RNA
the base, the Pentose sugar, and 1 or more phosphate groups
What type of bond it is between the sugar and the phosphate in a nucleotide
An ester linkage
What is a nucleoside
Only the base and the Pentose sugars (no phosphates)
If a nucleoside has one phosphate group it’s called:
Nucleoside monophophate
If the base attached is adenine this would be AMP
If an rna nucleoside has adenine as a base what is it named
Adenosine
All types of adenosines (atp, amp, adp) are called adenylates
If a DNA nucleoside has adenine as a base what is it named
Deoxyadenosine
All types of theses (datp,damp,dadp) are called deoxyadenylates
What is the distance between stacked bases in the double helix
3.4A
How many A in one full turn
How many bases per turn
Of the double helix
34A
10.4
What is the width of the double helix
20A
What degreee rotation is it in the double helix between each base
36 degrees
What is the direction of the double helix
Right handed,
Opposites directionality on each strand (one is 5-3 other is 3-5)
Bases are nearly _____ to the axis of the helix
Perpendicular
How many h bond between GC
AT
3
2
Why do purine pair with pyrimidines
To keep a uniform diameter of the helix
What are the four types of base pairin
Watson crick
Reverse Watson crick
Wobble base pairs
Hoogsteen
Why does reverse Watson crick happen
Because of the 180 degree rotation of a base in rna or dna ends
Why does wobble base pairing happen
Tautomerization (makes it pair with something else)
Why does hoogsteen happen
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
Why are bases inside the helix
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
Why are bases stacked
They attract each other by vander wall
This gives stability of the helix through non covalent interactions
What is the energy per vanderwall interaction of stacked bases
2.4kj/mol
What is the major and minor groove of dna
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
What are the major and minor grooves lined by
H bond donors and accpetors the are unique to each base pair
They allow the base pair to be accessed by other protiens
What are the three forms of dna
B
A
Z
What are the B and a forms of dna
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
What is the z form of DNA
It’s left handed and specific protiens bind only to this form
This means it’s biologically significant
If circular dna is unwound what forms can it take
Negative superhelix (unwound by three right hand turns)
Unwound circle (unwound two times)
Is supercoiled dna larger or smaller than telexed circular dna
What does this mean
Smaller
Travels further in gel
What are nucleosome
Histone octamers with +200bp of dna wrapped around them
How much dna is packaged into how many chromosome
What is the diameter of the nucleus they’re packed in
3.6m
46
5 micrometers
What are histones made of
Argenine and lysine (basic) residues
What are nucleosomes compacted into
By what factor
Chromatin
Form left handed helical structures
By a factor of 7
What is the diameter of a histon octamer
100A
How does rna fold
Why is this Important
Into complex structure, It can create stem loops
Its structures let it act as a catalyst. Ex. Ribozymes where AGC are all linked together
