DNA Lecture 5 Flashcards
Any regular, stable structure adopted by the nucleotides in the nucleic acid
DNA Secondary Structure
What is the shape of DNA?
Double Helix
DNA is comprised of two complementary strands of
Polydeoxyribonucleotides
What term describes how the opposite strands of DNA are arranged?
Anti-Parallel
5’—–>3’
(3’—–>5’)
In DNA, the ratio of A/T and G/C is…
1:1
How many base pairs per repeat were determined in the x-ray diffraction pattern produced by wet DNA fibers?
10 base pairs per repeat
Layer line spacing is 1/10 of the pattern repeat, 10 resides/turn
These interactions are important to double helix stability
Base stacking interactions
Base pairing is only possible if the major _____ forms are present. Other base pairs would form but they’re less favorable
Tautomeric
The fact that strands are complimentary suggested a model for DNA replication.
In the replication process, base pairs are formed through _____
Hydrogen bonding
A bonds to T through ___ H bonds
G bonds to C through ____ H honds
2
3
Each stand can act as a template for a new complimentary strand, and two new daughter DNA molecules are formed which are identical in sequence to the parent molecule
!
Are hydrophilic backbones of alternating deoxyribose and phosphate groups on the outside or inside of the double helix?
Purine and pyrimidine bases are on the outside or inside of the double helix?
Outside, facing water
Inside
The furanose ring of each deoxyribose is in the _____ endo conformation
C-2’
Hydrophobic and nearly planar rings are very close together and parallel/perpendicular to the long axis
Offset pairing of the two strands creates a major and minor ____
Perpendicular
groove
The three types of DNA are..
A-DNA
B-DNA
Z-DNA
This type of helix corresponds to the curvature of your left hand as you move along the helix in the direction of your thumb
This type is the opposite
Left Handed Helix
Right Handed Helix
The sugar phosphate backbone forms a right handed helix in ______ DNA
In _____ DNA the sugar phosphate backbone forms a left-handed helix
A and B DNA
Z DNA
Indicates the angle of rotation of one base pair relative tot he neighboring base either above or below it in the helix
If there are 10 steps per turn, then the rotation per step (base pair) is
Rotation per base
36 degrees
This corresponds to the step height per nucleotide
Helical rise per base pair
In B-DNA, the avg. rise is
In A-DNA, its
The rise corresponds mainly to the ___ of a pyrimidine or purine ring
- 33nm
- 23nm
Thickness
Defined as the distance along the helix axis corresponding to one turn
Pitch
Rotation about the C-N bonds (glycosidic bond) moves the base away from or on top of the deoxyribose ring. What is it called in both circumstances?
Anti - away from
Syn - On top of the deoxyribose ring
In all nucleotides in DNA, four of the five atoms are in a single plane.
The fifth atom (C-2’ or C-3’) is on the same side of the plan relative to the C-5’, and this is called
When the fifth atom is on the opposite side of the plan relative to the C-5’, it is called
Sugar Pucker Confirmations
Endo
Exo
The most stable structure for a random sequence DNA molecule under physiological conditions is..
It’s the form that Watson and Crick proposed
B-DNA
In this DNA form the bases lie close to the helix axis (center of the helix) and the base pairs are approximately perpendicular to the helical axis
The phosphate groups are on the surface of the helix. They will come into contact with the solvent
B-DNA
The B-form has major and minor grooves.
What do they result from?
What does this allow for B-DNA, but not A-DNA?
The glycosidic bonds between the sugars and bases in a given base pair not being directly opposite one another
B-DNA can accommodate a spine of water molecules lying in the minor groove
This type of DNA is favored in many solutions which lack water
A-DNA
What type of helix is A-DNA? Same as B-DNA.
What’s different?
Right handed
11 base pairs per turn (wider helix)
In this form of DNA, the bases come out farther from the helix axis, and the plane of the base pairs is tilted about 20 degrees with respect to the helix axis.
Does the A-form have grooves?
A-DNA
Yes and they are equal in depth
Is there evidence that A-DNA occurs in cells?
No.
This type of DNA is a left handed double helix. It is more slender and elongated
Z-DNA
How many base pair per helical turn in Z-DNA?
12
Describe the appearance of Z-DNA
Zig-Zag
Does Z-DNA have grooves?
One deep helical groove, it is the minor groove and is narrow and deep
Certain ______ sequences fold in left-handed Z-helices
Nucleotide
ex) Sequences with alternating pyrimidine and purine residues —-C&G, or 5-methyl C&G
Is Z-DNA found in the cell?
Yes, short stretches in both prokaryotes and eukaryotes
What role might the short tracts of Z-DNA play in prokaryotes and eukaryotes?
Regulation of gene expression or genetic recombination
Structural variations have been detected with larger chromosomes which are sequence dependent, and the function and metabolism of DNA segments in their vicinity may be affected
When ______ or more _____ residues appear sequentially in one strand, bends occur. This may be important for ________
4 or more adenine strands
It may be important for protein binding
A word or phrase that is spelled identically when read forwards or backwards, and is applied to regions of DNA with inverted repeats of base sequence
What structures can result?
Palindromes
Hairpin or cruciform
When an inverted repeat occurs within each individual strand of DNA, a _____ is formed
Mirror Repeat
In this type of position/pairing, the N-7, O6 and N6 of purines, the atoms that participate in hydrogen bonding are called
The non-Watson-Crick pairing is called
What can result?
Hoogsten positions
Hoosten Pairing
Triplex DNAs
Four DNA strands can also pair to form a _____ if a very high proportion of____ residues is present
Tetraplex; guanine
This type of DNA is found in polypyrimidine or polypurine tracts that also incorporate a mirror repeat
H-DNA
