Evolution, Genetics, and Molecular Biology: Key Concepts for Biology

Evolution

A change in allele frequencies.

Adaptation

A heritable trait that increases fitness in a particular environment.

Theory

An explanation or set of hypotheses that attempt to explain a large and pervasive phenomenon, meaning they tie together a large suite of observations about how the natural world works.

Fitness

The ability to produce viable offspring.

Genetic drift

Any change that occurs in allele frequencies that is due to chance.

Founder events

One of the several types of events that can cause genetic drift. They occur when a relatively small number of individuals disperse to a new habitat and found a completely new population.

Genetic bottlenecks

One of the several types of events that can cause genetic drift. They occur when a species undergoes a large and rapid decrease in population size due to a disease epidemic, catastrophic storm, or other change.

Gene flow

An evolutionary process that changes allele frequencies through the movement of individuals and their alleles from one population to another. Homogenizes allele frequencies among populations.

Maladaptive

Leading to lower fitness.

Mutation

Any change in the sequence of DNA, and thus a change in genetic information. Introduces new alleles into population.

Deleterious mutation

A mutation or other event that lowers fitness.

Phylogenetic tree

A graphical depiction of evolutionary history, or phylogeny.

Root (of a phylogenetic tree)

The base of a tree, indicating the common ancestor of all the taxa indicated at the tips.

Node (of a phylogenetic tree)

A split where a speciation event occurs, so one species splits into two. Also represents the last common ancestor before a speciation event.

Branch (of a phylogenetic tree)

A species or other group changing through time.

Tip (of a phylogenetic tree)

The end of a branch, representing a taxon.

Taxon

A named group of organisms (plural is taxa).

Element

A distinct type of substance or matter. 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 (H+).

Base

An ion or molecule that acquires a proton (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.

Amino acids

The building blocks that connect together via covalent bonds to form proteins.

Amino group

A group of NH2 atoms; can pick up a proton to form NH3+.

Carboxyl group

A group of COOH atoms; can lose a proton to form COO-.

R-group

A highly variable group of atoms bonded to the central carbon of an amino acid.

Hydrophilic

Can readily interact with the partial charges on water.

Hydrophobic

Cannot readily interact with the partial charges on water.

Peptide bond

The covalent bond that forms between the carboxyl group of one amino acid and the amino group of another.

Protein primary structure

The sequence of amino acids, linked via peptide bonds.

Protein secondary structure

Formation of ⍺-helices and β-pleated sheets, stabilized by hydrogen bonds between backbone atoms.

Protein tertiary structure

Folding into a 3-D shape stabilized by hydrogen bonds, ionic bonds, S-S bridges, and hydrophobic interactions.

Ionic bond

An interaction that occurs when a positively charged ion is attracted to a negatively charged ion.

Hydrophobic interactions

Interactions that stabilize hydrophobic regions of molecules by minimizing their contact with water.

Protein quaternary structure

Assembly of multipart proteins from folded subunits, stabilized by hydrogen bonds, ionic bonds, S-S bridges, and hydrophobic interactions.

Denaturing

"Unfolding" or loss of 3-dimensional shape (secondary, tertiary, and quaternary structure), often via heating or changes in pH.

Electrical energy

Energy related to interactions among charged particles.

Thermal energy

The energy of motion in ions and molecules, measured as temperature.

Potential energy

Energy that is related to an object's position.

Chemical reaction

Conversion of substances (ions or molecules) into other substances via breaking and forming chemical bonds.

Free energy

The total energy available to do work—a combination of entropy and thermal and potential energy.

Energetic coupling

A phosphorylation reaction that makes a nonspontaneous reaction spontaneous, because it raises the free energy of the reactants.

Endergonic reaction

One that results in an increase in free energy; another way of referring to a nonspontaneous reaction.

Exergonic reaction

One that results in a decrease in free energy; another way of referring to a spontaneous reaction.

Activation energy

The amount of energy required to get a chemical reaction through its transition state.

Transition state

During a chemical reaction, an intermediate state where old bonds are being broken but new bonds have not yet formed.

Enzyme

A protein that catalyzes a chemical reaction.

Active site

The place on an enzyme (or ribozyme) where a reaction is catalyzed.

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).