DNA Structure Flashcards
What is the name of a nucleotide?
2’-deoxyadenosine 5’-monophosphate
What do nucleotides comprise of?
a base, a sugar, and phosphate
What do nucleosides comprise of?
base+sugar
What are the functions of nucleotides?
energy storage (ATP), enzymatic co-factors (NAD, NADPH)
What sugar does RNA have?
ribose
What is the structure of ribose?
five carbon atoms
What sugar does DNA have?
deoxyribose
What is the structure of deoxyribose?
lacks hydroxyl group at 2’ carbon
What is a glycosidic bond?
in DNA/RNA, the base is attached to the 1’ carbon
What joins the nucleotides together into a linear strand?
3’ and 5’ positions will form covalent bonds
What are two types of bases in DNA and RNA?
purines and pyrimidines
What are purines?
adenina, guanine
What are pyrimidines?
cytosine, thymine, and uracil
What is the nucleoside form of adenine?
adenosine
What is the nucleoside form of guanine?
guanosine
What is the nucleoside form of cytosine?
cytidine
What is the nucleoside form of thymine?
thymidine
What is the nucleoside form of uracil?
uridine
How do purines make glycosidic bonds?
through the 9 position of the base to the 1’ carbon of the sugar
How do pyrimidines make glycosidic bonds?
through the 1 position of the base to the 1’ carbon of the sugar
What is the backbone of DNA or RNA?
repeating of sugar and phosphate
How are nucleotides joined?
a phosphodiester bond between the 3’ hydroxyl of one sugar and the phosphate attached to the 5’ hydroxyl of the next sugar
How are nucleic acid strands asymmetric?
one end has an exposed 3’ hydroxyl, the other end has an exposed 5’ phosphate
What are nucleic acid sequences written?
in the 5’ to 3’ direction (the DNA strand to the right has the sequence: ATGC)
How do DNA strands associate?
via non-covalent hydrogen bonds to form double-stranded DNA
How many H-bonds bond A and T?
2 H-bonds
How many H-bonds bond C and G?
3 H-bonds
What type of base pairs are AT and GC?
Watson-Crick base pairs
Why are strands complementary?
the sequence of one strand dictates the sequence of the other strand
What direction are two strands?
antiparallel - one strand runs from 5’ to 3’ while the other runs 3’ to 5’
What is the most energetically favorable formation of double stranded DNA?
two strands to wind around one another in a right-handed double helix
What is the orientation of hydrophobic bases in the center of DNA?
cluster, away from the aqueous cellular environment
What is the orientation of hydrophilic sugar-phosphate backbone?
on the outside
What are base pairs?
planar molecules that are perpendicular to the axis of the helix and form a stack in the interior of the helix
What stabilizes the helix of DNA?
Van der Waals interactions between p-orbitals of the bases
What is the diameter of the helix?
~20 A
T or F: A-T and G-C base pairs have similar widths
true
What is the predominant configuration of DNA?
B-DNA
What is the frequency of B-DNA?
repeats every 10.5 base pairs, and base pairs are 3.4 A apart
What is the structure of B-DNA?
the helix forms a major groove (~13 A) and a minor groove (~9 A) accessible from the outside of the molecule
What governs the interactions between DNA and other molecules?
the shape and size of the major and minor groove
What nucleotides lead to more flexibility?
regions rich in A-T
T or F: the sequence of bases in DNA can influence structure
true
What exposes the genetic information in DNA?
major and minor grooves
What are exposed in the major and minor grooves of the DNA helix?
chemical groups of the bases
What do each base pair have?
a characteristic set of groups that is available for interaction
T or F: DNA-binding proteins recognize specific DNA sequences through the major and minor grooves by separating the two DNA strands
false, without separating the two DNA strands
What does B-DNA represent?
the prototypical or most common DNA conformation
What is A-DNA?
a right-handed helix with 11 base pairs per turn; grooves are more evenly sized. the A conformation can be induced by DNA binding proteins
What is Z-DNA?
a left-handed helix, favored by methylation of cytosine torsional stress, and high salt concentrations. its biological significance is unclear
How do DNA relieve tension?
twists into supercoils
What are relaxed DNA?
open, uncoiled circular DNA
What induces supercoiling?
untwisting or overtwisting
What initiates the overwinding or underwinding of a closed circular DNA molecule?
at least one strand of DNA must be cut, and the strands twisted relative to each other, and re-ligated together
Why does DNA supercoil?
- changes the number of bases per turn
- restores the preferred number of bases per turn
T or F: supercoiling can be positive or negative
true
When do linear segments of DNA supercoil?
if one end is immobile
What creates negative supercoils?
unwinding the DNA helix of a constrained DNA molecule creates negative supercoiling to compensate for the strain on the molecule
When do supercoils release?
if one of the DNA strands is cut or otherwise free to rotate
What are the names of supercoiled structures?
toroidal or interwound (plectonemic)
What stabilizes the structure of DNA?
stabilized by complementary base-pairing and the combination of many weak, non-covalent interactions
What makes DNA less reactive and more stable compared with RNA?
the absence of hydroxyl
Why can one strand carry the entire code necessary to restore the other strand?
complementary base-pairing
How can two strands be separated?
held together only by non-covalent interactions
How is base information chemically readable?
in the major and minor grooves even without separating the two strands
What is supercoiling due to?
due to over- or under-winding which are caused by molecular mechanisms of replication and transcription
What is linkage number?
the number of times one strand of DNA wraps round the other
How often does B-DNA wrap around each other?
every 10.5 base pairs
T or F: linkage number can change in a closed circular DNA
false
What is twist?
the number of turns in a fragment of DNA (+1 per 360 twist)
How often does B-DNA twist?
+1 for each repeat of the double helix
What does a positive number denote in twist?
a right-handed helix
What does a negative number denote in a twist?
a left-handed helix
What is writhe?
a supercoiling of closed circular DNA or constrained linear DNA
What is the writhe of a relaxed plasmid?
zero
What is the writhe of a positively coiled DNA?
Wr > 0
What is the writhe of a negatively coiled DNA?
Wr < 0
What is the formula for linking number?
Lk = Tw + Wr
