Lecture 13 - Nucleic acid structure Flashcards
Information encoded in a DNA molecule is transcribed via
synthesis of an RNA molecule
The sequence of the RNA molecule is “read” and is translated into
the sequence of amino acids in a protein
Nucleic acids are
linear polymers built from similar units connected end to end
Nucleotide
each monomer unit
A single nucleotide consists of
a sugar, a phosphate, and one of four bases
DNA and RNA differ in
the sugar component and in one of the bases
The prefix deoxy indicates that the _____ carbon lacks oxygen
2’
The sugars in nucleic acids are linked to each other by
phosphodiester bridges
Nucleic acid backbone
The chain of sugars linked by phosphodiester bridges
Which groups join to phosphate groups
3’ and 5’ OH groups
Purine bases
adenine and guanine
Pyrimidine bases
cytosine, thymine, and uracil
Which nucleic acid is more prone to hydrolysis?
RNA
A nucleoside is a
base linked to a sugar
A nucleotide is a
base linked to a sugar and phosphate
Nucleoside units in RNA
adenosine, guanosine, cytidine, uridine
Nucleosides in DNA
deoxyadenosine, deoxyguanosine, deoxycytidine, and thymidine
Rotation about the ________ gives rise to syn and anti conformations in nucleosides
N-glycosidic bond
In nucleosides, the _____ conformation is generally favored
anti
Nucleoside triphosphates are
nucleosides joined to three phosphoryl groups
Where does the energy come from in ATP?
Energy is released from the cleavage of the triphosphate group
NADH stands for
Nicotinamide adenine dinucleotide
NADH exists in what two forms
NAD+ (oxidized), and NADH (reduced)
ACG indicates that
the unlinked 5’-P group is on A and the unlinked 3’-OH group is on G
In DNA, the 5’ end is usually attached to a
phosphate group
In DNA, the 3’ end is usually attached to a
free hydroxyl group
How is DNA or RNA written?
from 5’ to 3’
Nucleic acids carry information in the form of
a sequence of bases
The two strands of DNA base pair through
hydrogen bonds
Are chains in DNA parallel or antiparallel?
antiparallel
Which regions of DNA are more stable?
G:C rich regions (3 H-bonds compared to 2 in A:T)
The DNA double-helix is stabilized by
- Hydrogen bonds
- Base stacking interactions (vdW)
- Hydrophobic interactions
Which interaction most stabilizes DNA?
base-stacking
In a double helix, the pyrimidine and purine base lie on the
inside of the helix
The major groove in the double helix is large enough to accommodate
an alpha helix from a protein
Which alpha-helix motif interacts with DNA?
Zinc finger
Regulatory proteins (transcription factors) can recognize
the pattern of bases and H-bonding possibilities in the major groove
The Watson-Crick model of DNA is also known as the ______ helix
B-DNA
Most DNA is in the ___ form
B-DNA
B-DNA is more _____ than A-DNA
hydrated
The A-form of DNA is what shape compared to the B-form?
wider and shorter
The structural differences between B-DNA and A-DNA come from
different sugar puckerings
Dehydration of DNA drives it to the
A-form
What is unique about Z-DNA
It is left-handed
Z-DNA is a derivative of
B-DNA
Where is Z-DNA found?
In G:C rich regions
DNA molecules in human chromosomes are ______ while in bacteria and archaea they are ______
linear: circular
The most common nucleic acid secondary motif is a
hairpin-loop
