BIOCH 200 Unit 3 - Protein Structure (Terms)

Zwitterion

A molecule that contains an equal number of positively and negatively charged functional groups, thus having a net neutral charge despite being charged

Chiral Molecule

A molecule that cannot be superimposed on its mirror image

Amino Acid Side Chain

A distinct R group attached to an amino acid that determines the amino acid’s overall chemical properties

Hydrophobic/Nonpolar Side Chain

An amino acid side chain classification that describes uncharged, nonpolar side chains which lack reactive functional groups and have mainly hydrocarbon side chains

Polar Side Chain

An amino acid side chain classification that describes uncharged, polar side chains at pH 7 which are reactive due to the presence of functional groups and an electronegative atom

Charged Side Chain

An amino acid side chain classification that describes charged, polar side chains at pH 7 that are reactive due to the presence of ions

Ionizable

A property in which a group or molecule can pick up and give up protons at a reasonable pH range, giving them a pKa between 1 and 14

Cystine

A hydrophobic molecule made of 2 cysteine residues joined via a disulphide bond/bridge

Aspartic Acid

The fully protonated form of the amino acid aspartate, found at pH 1

Glutamic Acid

The fully protonated form of the amino acid glutamate, found at pH 1

Peptide Bond

A covalent, neutral amide bond formed through dehydration that joins amino acids together from the carboxyl group of one to the amino group of the other

Dipeptide

Two amino acids joined together by one peptide bond, consisting of 2 amino acid residues

Oligopeptides/Peptides

General term for a larger than countable number of amino acids (<40) or synthetic peptides

Polypeptide

A long chain of amino acids (>40) usually produced naturally

Protein

A polypeptide or more than 1 polypeptide with a biological function

C (Carboxyl) Terminus

The right end of polypeptide which contains the carboxyl group of the amino acid residue

N (Amino) Terminus

The left end of polypeptide which contains the amino group of the amino acid residue

Primary Polypeptide Structure

The sequence of amino acids in a polypeptide which determines its unique backbone, joined by peptide bonds

Polypeptide Backbone

The rigid structure in a polypeptide including the alpha carbons on the amino acid residues and all atoms involved in the peptide bond

Secondary Polypeptide Structure

Local irregular and regular substructures of the polypeptide backbone created from folding of the polypeptide

Regular Secondary Structure

A type of secondary structure with a fixed backbone conformation regardless of amino acid composition that forms the specific shape even with varying amino acid sequences

Irregular Secondary Structure

A type of secondary structure with its own unique backbone conformation dependent on its sequence that differs between each specific case it is needed

Alpha Helix

A regular secondary polypeptide structure that is a right handed twist made by an average of 12-13 residues

Beta Sheet

A regular secondary polypeptide structure that is a sheet formed from 5 beta strands 3-10 amino acids long in an extended conformation arranged side by side, joined by loops

Loop

An irregular secondary polypeptide structure neither in extended or helix conformation that is variable in size and shape, with a unique structure depending on its amino sequence

Parallel Beta Sheet

A beta sheet in which all beta strands run parallel to one another, forming slightly bent H-bonds between strands

Antiparallel Beta Sheet

A beta sheet in which all beta strands run antiparallel alternating to one another, forming straight H-bonds between strands in a slightly more stable conformation

Mixed Beta Sheet

A beta sheet in which there are a mix of parallel and antiparallel strands

Tertiary Structure

Arrangement of all atoms in a single polypeptide in 3D space, including the position of secondary structures in relation to one another, the positions of amino acid sidechains, and prosthetic groups

Prosthetic Groups

A nonprotein component of a protein that is permanently tightly bound to a protein, providing structure and reactive groups that amino acids are incapable of fulfilling due to their lack of reactivity

Fibrous Proteins

A tertiary structure class of protein that forms a long protein filament insoluble in aqueous solutions

Globular Proteins

A tertiary structure class of protein that folds into compact structures soluble in aqueous solutions

Ion Pairs/Salt Bridges

Electrostatic interactions between closely charged formal charged groups in proteins

Domain

A polypeptide segment that has folded into a single structural unit with a hydrophobic core with its own function to perform

Motif

A short region of a polypeptide comprised of a common grouping of secondary structural elements with a recognizable, pattern 3D shape

Beta-Alpha-Beta Motif

A motif found in proteins that is comprised of an alpha helix sandwiched between two beta sheets

Greek Key

A motif found in proteins that is comprised of an antiparallel beta sheet that is oriented such that the “first” strand to the left is connected to the “last” strand on the right

Coordination Bond

A covalent bond in which 1 atom donates both electrons of the bond

Zinc Fingers

A prosthetic group comprised of a single Zn²⁺ ion coordinated by 2 Cys and 2 His residues

Quaternary Structure

The overall structure of proteins with more than one polypeptide chain based on its number and type of subunits

Protein Subunit

A singular polypeptide chain that is a part of a protein comprised of multiple polypeptide chains

Oligomer

A protein with more than one polypeptide chain, which has quaternary structure

Monomer

A protein with only one polypeptide chain, which does not have quarternary structure