Terms
Anti-parallel
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Refers to the orientations of the two single strands that compose a
double-stranded DNA helix. Strands are oriented such that one strand's 5'
end is directly across from the other strand's 3' end.
Complementary
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Term used to refer to the natural pairing of the nitrogen bases within DNA
and RNA. In DNA, cytosine pairs with guanine and adenine with thymine. In RNA,
the thymine is replaced with uracil, which pairs with adenine. Each member of
these pairs are said to be a "complements" of the other.
Deoxyribose
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A five-membered sugar ring that lacks a hydroxyl group at one position, and is
the sugar group for DNA.
Double-stranded helix
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A common structural motif of DNA. Two linear strands of single-stranded DNA
fold into a helical shape stabilized internally by hydrogen bonds between
complementary base pairs.
Ester bond
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In DNA, refers to the oxygen-carbon linkage between the triphosphate
group and the 5' carbon of the ribose sugar group in a
single DNA or RNA nucleotide.
Glycosidic Bond
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In DNA, refers to the nitrogen-carbon linkage between the 9' nitrogen of
purine bases or 1' nitrogen of pyrimidine bases and the 1' carbon of the
sugar group.
Helical Twist
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The angular rotation needed to get from one nucleotide to another in helical
structures.
Hydrogen Bonding
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Weak, noncovalent linkages between a donor and an acceptor which, when
lined up next to each other, have favorable electrostatic interactions. Provide
small amount of stability to DNA and RNA helices. Provide specificity of the
interactions between polynucleotide strands.
Hydrogen Bond Acceptor
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A group with at least one free lone pair of electrons. In DNA and RNA, common
acceptor groups include: carbonyls, hydroxyls, and tertiary amines.
Hydrogen Bond Donor
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A group with a free hydrogen group. In DNA and RNA, common donors include
secondary amines and hydroxyl groups.
Major groove
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In a helix, refers to the larger of the unequal grooves that are formed as a
result of the double-helical structure of DNA. As a
result of the patterns of hydrogen bonding between complementary bases of DNA,
the sugar groups stick out at 120 degree angles from each other instead of
180. The major groove is generated by the larger angular distance between
sugars.
Minor groove
-
In a helix, refers to the smaller of the unequal grooves that are formed as a
result of the double-helical structure of DNA. As a result of the patterns of
hydrogen bonding between complementary bases of DNA, the sugar groups stick
out at 120 degree angles from each other instead of 180. The minor groove is
generated by the smaller angular distance between sugars.
Nitrogen Base
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One of three components of a nucleotide, nitrogen bases come in two general
types: purines and pyrimidines. Of the four nitrogen bases, adenine and
guanine are purines, while cytosine and thymine are pyrimidines. Through
hydrogen bonding, base pairs link in a complementary nature: adenine with
thymine and guanine with cytosine, forming the double-stranded helix of DNA.
In RNA, thymine is replaced by uracil.
Nucleic Acid
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A chain of nucleotides joined together by phosphodiester bonds. Both
DNA and RNA are nucleic acids.
Nucleotide
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A five-membered sugar group with a purine or pyrimidine nitrogen
base group attached to its 1' carbon via a glycosidic bond and one or more
phosphate groups attached to its 5' carbon via an ester bond.
Phosphate Backbone
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Refers to the structural organization of the DNA double-helix in which the pyrimidine and purine basic groups face the
interior while the phosphate groups line the exterior of the helix. The
phosphate backbone carries a negative charge.
Phosphate Group
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One of three components of a nucleotide, comprised of a central phosphorous
surrounded by four oxygens. The phosphate links to the sugar group, carries
a negative charge because of the chemical interaction between phosphorous and
oxygen, and forms the exterior of the phosphate backbone.
Phosphodiester linkage
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In a polynucleotide, refers to the bond between the 3' hydroxyl of a sugar
group in a nucleotide and a phosphate group attached to the 5' carbon
of another sugar group.
Pitch
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In a helix, refers to the vertical distance traveled in one full turn (360
degrees of twist).
Primary Structure
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In DNA and RNA, refers to the linear sequence of base pairs or amino acids in a
polynucleotide chain.
Purine
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One of two categories of nitrogen base ring compounds found in DNA and RNA.
A purine is a nine-membered double ring composed of one five-membered joined to
a six membered ring containing four nitrogens. See pyrimidine.
Pyrimidine
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One of two categories of nitrogen base ring compounds found in DNA and RNA.
A six-membered ring containing two nitrogens. See purine.
Ribose
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The sugar group of RNA, a five-membered sugar ring containing one oxygen and
four carbons with one additional carbon attached to the 4' carbon in the ring
and hydroxyl groups attached to the 1', 2', 3', and 5' carbons. See
deoxyribose.
Right Hand Rule
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A trick used to quickly determine the "handedness" or orientation of a helix.
In a right-handed helix, if one extends his or her right hand and traces with
fingers along the backbone of the helix, the hand and thumb move upwards.
Rise
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In a helix, the vertical distance traveled when moving from one base pair to the
adjacent base pair.
Secondary Structure
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In DNA and RNA, the local folding patterns of a polynucleotide based on
complementary base-pairing. Common motifs include alpha helices and bet-pleated
sheets.
Sugar Group
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One of three components of a nucleotide, a five-ringed carbon sugar, either
ribose or deoxyribose in form. The sugar group bonds to the nitrogen
base and to the phosphate group.
Tertiary Structure
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In DNA and RNA, the complex three-dimensional form of a polynucleotide.
