Biochemistry: Chemistry of Nucleic Acids

Flashcards covering the foundational concepts of nucleic acid chemistry, including DNA and RNA structures, nucleotide building blocks, and helical variations.

Nucleic acids

Essential biomolecules that store and transmit genetic information.

Deoxyribonucleic acid (DNA)

A macromolecule that carries genetic information from generation to generation.

Ribonucleic acids (RNAs)

Single-stranded nucleic acids made from transcribing DNA.

Nucleotides

The monomeric units of the nucleic acids composed of a nitrogenous base, a pentose sugar, and phosphate.

Phosphodiester bonds

The bonds that hold nucleotides together at the $3'$ and $5'$ positions.

Pentoses

Five-carbon sugars where atoms are given a dash or prime numbering (e.g. $5'$) to distinguish them from atoms in the nitrogenous base rings.

Purines

A class of heterocyclic nitrogenous bases that includes Adenine and Guanine.

Pyrimidines

A class of heterocyclic nitrogenous bases that includes Cytosine, Thymine, and Uracil.

Heterocyclic

Chemical structures, such as purines and pyrimidines, whose rings contain at least one atom that is not carbon, specifically nitrogen.

Phosphate

A chemical group with the formula $PO_4$ that serves as a building block for nucleotides.

Nucleoside

The structure formed by the covalent linkage of a nitrogenous base to a pentose sugar.

Nucleotide (Chemical Definition)

The structure formed by an ester linkage of a phosphate group to a nucleoside.

Polyribonucleotide

A polymer of nucleotides involving ribose sugar, commonly known as RNA.

Polydeoxyribonucleotide

A polymer of nucleotides involving deoxyribose sugar, commonly known as DNA.

$5'$ end

The terminus of a nucleic acid strand that bears a phosphate group.

$3'$ end

The terminus of a nucleic acid strand that bears a hydroxyl group.

Nucleic acid polarity

The directional nature of a nucleic acid sequence, typically written in the $5'$ to $3'$ direction.

Complementary strands

The relationship between two DNA strands where Adenine corresponds to Thymine and Guanine corresponds to Cytosine.

Adenine-Thymine (A-T) linkage

A base pair held together by two hydrogen bonds.

Guanine-Cytosine (G-C) linkage

A base pair held together by three hydrogen bonds.

Genes

The fundamental units of genetic information, as characterized by the Avery-MacLeod-McCarty Experiment.

Watson-Crick structure

The secondary structure of DNA, consisting of two independent chains coiled into a double helix.

Anti-parallel

The orientation feature of DNA where the two polynucleotide chains run in opposite directions.

DNA Supercoiling

The twisting of the DNA molecule beyond its relaxed state.

Relaxed state DNA

A state where a DNA strand circles the axis of the double helix once every $10.4$ base pairs.

Positive Supercoiling

DNA twisted in the direction of the helix so that bases are held more tightly together.

Negative Supercoiling

DNA twisted in the opposite direction of the helix so that bases come apart more easily.

Topoisomerases

Enzymes that introduce negative supercoiling and relieve twisting stresses during transcription and replication.

Hydrophobic effect

A phenomenon that stabilizes the DNA double helix which is not influenced by the DNA sequence.

B-form DNA

The common, right-handed helix form of DNA with a smooth backbone.

Z-form DNA

A left-handed helix form of DNA with an irregular backbone and a deep minor groove.

A-form DNA

A right-handed helix favored in low water conditions, common for RNA, featuring a deeper minor groove and shallow major groove.

Messenger RNA (mRNA)

A major type of RNA that participates directly in protein synthesis.

Ribonucleases

RNA molecules that are capable of catalyzing chemical reactions.

Transfer RNA (tRNA)

One of the three major types of RNA involved in the process of protein synthesis.