Nucleic Acids: The Biochemistry of DNA and RNA

Flashcards covering the structural components, nomenclature, functions, and physical properties of nucleotides and nucleic acids based on the lecture material.

Nucleobase

A nitrogenous base that is a derivative of pyrimidine or purine, characterized as nitrogen-containing heteroaromatic and planar or almost-planar molecules.

Nucleoside

A molecule consisting of a nitrogenous base and a pentose sugar.

Nucleotide

A molecule consisting of a nitrogenous base, a pentose sugar, and a phosphate group.

ATP

Adenosine triphosphate, which provides energy for metabolism.

$$NAD^+$$

Nicotinamide adenine dinucleotide, which functions as an enzyme cofactor.

cAMP

Cyclic adenosine monophosphate, which functions in signal transduction.

Ribozymes

Nucleic acids that function in the processing of genetic information.

Purines

A class of nucleobases that includes Adenine and Guanine.

Pyrimidines

A class of nucleobases that includes Cytosine, Thymine (found in DNA), and Uracil (found in RNA).

$\beta$-D-ribofuranose

The specific pentose sugar found in RNA.

$\beta$-2'-deoxy-D-ribofuranose

The specific pentose sugar found in DNA.

Sugar pucker

The different conformations of the pentose sugar ring, including C-2' endo, C-3' endo, C-3' exo, and C-2' exo.

N-glycosidic bond

A single bond attaching the pentose ring to the nucleobase at the anomeric 1' carbon in a $\beta$ configuration; it forms at position N1 in pyrimidines and N9 in purines.

Phosphate Group

A negatively charged group at neutral pH, typically attached to the 5' position of the pentose sugar in nucleotides.

Deoxyadenylate

Also known as deoxyadenosine 5'-monophosphate; symbols include A, dA, and dAMP.

Guanylate

Also known as guanosine 5'-monophosphate; symbols include G and GMP.

UV Absorption of Nucleotides

Nucleotides absorb ultraviolet light around $250-270\,\text{nm}$ due to $\pi \rightarrow \pi^*$ electronic transitions.

Molar extinction coefficient ($\epsilon_{260}$) of AMP

$$15,400\,M^{-1}cm^{-1}$$

Molar extinction coefficient ($\epsilon_{260}$) of CMP

$$7,500\,M^{-1}cm^{-1}$$

Syn and Anti Conformations

The relative orientations of the nucleobase and the pentose sugar around the N-glycosidic bond, such as syn-Adenosine or anti-Adenosine.