Unit 1: Water and the Chemistry of Life & Nucleic Acids

Vocabulary flashcards based on lecture notes covering chemical foundations of life, properties of water, acids and bases, and nucleic acid structure.

Element

A distinct type of substance or matter where each element has atoms that contain a unique number of protons in the nucleus.

Atom

The fundamental unit of an element, made of protons, neutrons, and electrons.

Ion

An atom or molecule that carries a full charge—positive if it contains more protons than electrons, and negative if it contains more electrons than protons.

Molecule

A structure made of two or more atoms held together by covalent bonds.

Covalent bond

An attraction between two atoms based on shared electrons.

Electronegativity

The tendency for an atom's nucleus to attract the shared electrons in a covalent bond.

Polar covalent bond

An asymmetry in the position of shared electrons, due to differences in the electronegativities of the atoms involved, that creates a partial positive charge on one atom and a partial negative charge on the second atom.

Nonpolar covalent bond

Equal sharing of electrons, due to equal or roughly equal electronegativities of the atoms involved.

Hydrogen bond

An attraction between a partial positive charge on a hydrogen atom and a partial negative charge on another atom.

Hydrophilic molecule

A molecule that can readily interact with the partial charges on water.

Hydrophobic molecule

A molecule that contains mostly nonpolar covalent bonds and cannot readily interact with the partial charges on water.

Acid

An ion or molecule that releases a proton ($\text{H}^+$).

Base

An ion or molecule that acquires a proton ($\text{H}^+$).

pH scale

A method for expressing the concentration of protons in a solution—specifically, the negative of the base 10 logarithm of the proton concentration.

Nucleotide

A molecule made up of a phosphate group and a nitrogenous base bonded to a 5-carbon sugar.

Nucleic acid

A molecule made up of nucleotides linked to form a chain or strand.

Phosphodiester bond

Covalent bonds between the phosphate group on the 5′ carbon of one nucleotide and the -OH group on the 3′ carbon of a second nucleotide.

Complementary base pairing

Hydrogen bonding between A-T or A-U and G-C pairs in a nucleic acid.

Primary structure

The sequence of nucleotides in a nucleic acid, read 5′ to 3′.

Secondary structure

Formation of a double helix in DNA or a stem-and-loop structure in RNA, based on complementary base pairing.

Sugar-phosphate backbone

The "spine" of 5-carbon sugars and phosphate groups in a nucleic acid (the nitrogenous bases project from this backbone).

Antiparallel strands

Strands of DNA or RNA that align in opposite 5′ to 3′ orientation.

Monomer

A small "subunit" molecule that can be linked to another, via a covalent bond, to form a larger molecule called a polymer.

Polymer

A large molecule made up of strings of covalently bonded small molecules (monomers).