BIOCH 200 Unit 2 - Nucleic Acids (Terms)

Pyrimidine Base

A class of nitrogenous base that contains 1 6-membered ring and 2 nitrogen molecules

Purine Base

A class of nitrogenous base that contains 2 rings: 1 6-membered ring and 1 5 membered ring, as well as 4 nitrogen molecules

Uracil

Thymine

Cytosine

Adenine

Guanine

Resonance

Delocalized electrons in molecules where the bonding cannot be expressed by a single lewis structure, occurring in systems with certain lone pairs or double bonds

Ribose Sugar

A pentose sugar consisting of 4 hydroxyl groups (OH at C2’) typically used to create RNA

Deoxyribose Sugar

A pentose sugar consisting of 3 hydroxyl groups (missing OH at C2’) typically used to create DNA

Nucleoside

A nitrogenous base (commonly purine or pyrimidine) linked to a 5-carbon sugar

Phosphoester Linkage

A linkage between a phosphate group and a hydroxyl group that creates a P-O bond

Phosphoester

A functional group consisting of a linkage P-O bond as well as a phosphate

Nucleotide

A nitrogenous base (commonly purine or pyrimidine) linked to a 5-carbon sugar linked to one or more phosphates (nucleoside + phosphates)

Nucleic Acid

Polymers of nucleotides, comprised of multiple nucleotides linked by 3’-5’ phosphodiester bonds

Phosphodiester Linkage

A linkage between a phosphate group and a hydroxyl group that creates two phosphoester bonds, forming a C-O-P-O-C bond chain

Phosphodiester

A functional group consisting of two P-O linkages to make a C-O-P-O-C bond chain

Phosphoanhydride Linkage

A linkage between two phosphate groups that creates a P-O-P bond

Phosphoanhydride

A functional group consisting of two P-O bonds adjacent to one another (POP), where each phosphorus is a phosphate group

Nucleic Acid Backbone

The polar and uniformly negatively charged backbone of DNA and RNA that consists of only the phosphate and sugar molecules

Mononucleotide

A single nucleotide not connected to any others with a pentose sugar, one nitrogenous base, and one phosphate

Dinucleotide

Two nucleotides connected to one another by their phosphate groups with two pentose sugars, two nitrogenous bases, and two phosphates

Enzymatic Hydrolysis

A method of hydrolyzing phosphodiester bonds occurring in DNA and RNA through which a phosphodiesterase regulates the specific, controlled breaking of a bond in the nucleic acid to turn it into nucleotides

Phosphodiesterase

An enzyme found in DNA and RNA that catalyzes the breakage of phosphodiester bonds in nucleic acids

Alkaline Hydrolysis

A method of hydrolyzing phosphodiester bonds occurring in only RNA through which the hydroxide ion facilitates bond breakage of a nucleic acid in basic conditions to turn it into nucleotides

DNA Primary Structure

The sequence of nucleotide residues that make up a nucleic acid

Double Helix

The secondary structure of DNA comprised of chains connected through hydrogen bonds between the bases

Chargaff’s Rule

The rule that applies only to dsDNA stating that the number of purines is equal to the number of pyrmidines in an organism, with differing AT/CG ratios in each species (%A = %T, %C = %G)

Watson-Crick Base Pair

Specific hydrogen bonding interactions between nitrogenous base pairs (A/T, C/G) based on the amino and carbonyl groups on the bases

Base Stacking Interactions

The major stabilizing force of secondary DNA structure that arises from the stacking of nitrogenous bases comprised of hydrophobic interactions and van der waals forces

DNA Groove

A section of exposed bases between the two helical strands of DNA comprised of bases that are not involved in Watson-Crick pairs in which proteins can bind

Compelmentarity

A property of DNA strands in which antiparallel strands are able to perfectly bond with one another due to containing complementary bases in the correct order

DNA Melting

Denaturation of the base stacking interactions and hydrogen bonds between double stranded DNA via the addition of heat

Midpoint of Melting (T_m)

The midpoint of a DNA melting curve in which the DNA sample is comprised of 50% ssDNA (denatured) and 50% dsDNA (not denatured), which is characteristic of the base composition of the DNA

Hyperchromicity

A property of a DNA melting curve that indicates high relative absorbance, characteristic of ssDNA

Hypochromicity

A property of a DNA melting curve that indicates low relative absorbance, characteristic of dsDNA

Hyperchromic Shift

A descriptor of a DNA melting curve that indicates a shift from low to high relative absorbance, characteristic of melting (dsDNA → ssDNA)

Hypochromic Shift

A descriptor of a DNA melting curve that indicates a shift from high to low relative absorbance, characteristic of renaturation (ssDNA → dsDNA)

Denaturation

The breaking of non-covalent bonds in an organic molecule, which is sometimes reversible

Degradation

The breaking of covalent bonds in an organic molecule, which is always irreversible

Renaturation

The reformation of a denatured organic molecule so that it regains its original conformation

Nucleation

An action in the process of DNA renaturation that occurs slowly (rate depends on complexity of DNA) in which the 2 ends of DNA are lined up together

Zippering

An action in the process of DNA renaturation that occurs quickly in which the lined up DNA base pairs are able to hydrogen bond to another to restore original conformation

pK_a

The acidity of a molecule in solution, used to represent the strength of a weak acid in which the smaller, the stronger

pH

The acidity of a solution in which an acidic molecule resides, measuring the acidity of the solution itself

DNA Hybridization

The mixing of two different denatured DNA samples that undergo renaturation to form a duplex mix, containing one strand from one sample and one from the other

Intrastrand Base Pairing

Base pairing of nitrogenous bases within the same nucleic acid strand through folding of the strand, occurring in RNA and DNA

Interstrand Base Pairing

Base pairing of nitrogenous bases from different nucleic acid strands through Watson Crick base pairs, occurring in DNA