Image credit: National Institute of General Medical Sciences.

Protein Structure: the structure of a protein that determines its function, for example, by creating binding sites of other molecules. (Brooker, 59)

Important in the ability of different proteins to interact with each other. For this (interaction) to occur, the surface of one protein must "bind" to the surface of the other. Such binding is usually very specific. The surface of one protein precisely fits into the surface of another. Five factors are critical for "protein folding" and stability: 1) “hydrogen” bonds;  2) “ionic" bonds; 3) “hydrophobic” effects; 4) “Van der Waals forces;” and 5) “disulfide bonds.” (Brooker, 54-55) "Tertiary" and "quaternary structures" depend on "amino acid" sequences, ion "concentration," "temperature," and "pH." Temperature is critical for protein structure. Proteins can unravel at high temperatures. (Norman, 6/17/09) As "polypeptides" are "synthesized" in a cell, they fold into “secondary" and tertiary structures, which (then) assemble into quaternary structures for most proteins. (Brooker, 54-55)

Peptides: “compounds” made up of chains of amino acids. (Hunt, 266) A short sequence of amino acids. (Lewis, 180) A sequence of amino acids which are the building blocks of proteins. These chains are held together by specific chemical bonds called “peptide bonds.” (Bynum, 293) Two or more amino acids linked by bonds between the "amino group" (-NH) and the "carboxyl group" (-CO). (OxfordMed)

Polypeptides: a “polymer” consisting of a chain of amino acid molecules joined by peptide bonds formed as a result of "condensation" reactions. (Indge, 214) A string of amino acids. This name comes from the fact that amino acids are connected to each other by a “peptide bond.” Some proteins are made up of only one polypeptide, while others are made up of several polypeptides folded together. (Batiza, 174) The term 'polypeptide' denotes a unit of structure. By comparison, the term 'protein' is a unit of function. The "ribosome" is the site where synthesis occurs. Once the entire polypeptide is made, it is released from the ribosome. One or more polypeptides assemble into a three-dimensional protein that performs a particular function. (Brooker, 69) Note the polypeptide chains have an "C-terminus" and an "N-terminus." (COOH) (Norman, 7/22/09)

C-Terminus: carboxyl terminus. The 3-prime (3') end (or 'terminus') of the amino acid chain. It has a free carboxyl group (COOH). (Norman, 7/22/09)

N-Terminus: nitrogen terminus. The 5-prime (5') end of the polypeptide chain that has a nitrogen atom or a 'free amino group.' Peptide bonds connect all of the amino acids of the chain together. (Norman, 7/22/09) When two or more amino acids are linked together, one end of the resulting molecule has a free amino group. (Brooker, 51) Also referred to as the "amino terminus."

Protein Subunits: the individual polypeptides in a protein (Indge, 54)

Primary Structure: chains of amino acids linked by peptide bonds. (Norman Lectures, 6/17/09) An amino acid sequence from beginning to end. The primary structures of polypeptides are determined by "genes." (Brooker, 52)

Protein Folding: as the amino acid chain grows, it folds into a three-dimensional (3-D) structure, which depends on both the chemical nature and order of the different amino acids. The 3-D structure determines the function of the protein. When there is a change in one or more amino acids, then the ability of the protein to function may be affected. The protein's function may be unchanged or it may become sluggish, hyperactive, or inactive. (NCI5, Slide 23) Folding is based on chemistry: attraction and repulsion between atoms of the proteins as well as interactions of proteins with chemicals in the immediate environment. Proteins begin to fold within a minute after the amino acid chain winds away from the ribosome. (Lewis, 191)

Conformation: shape of a protein. (Brooker, 171) Proteins fold into one or more three-dimensional shapes. Conformation is very important for "RNA" functioning. (Lewis, 191) Each of the three-dimensional structures that may be adopted by a particular molecule. (Oxford) The characteristic 3-dimensional shape of a protein, including the secondary, tertiary, and quaternary structure of the peptide chain. (MeSH)

Convoluted: folded. (RamachandranTTB, 16)

Protein Misfolding: should a protein misfold, an 'unfolded protein response' occurs in which "protein synthesis" slows or even stops, "transcription" of genes that encode other folding proteins speeds up, and proper protein folding is quickly restored. If a misfolded protein is made, it is sent out of the "ER" back into the cytoplasm to a "proteasome." A clear example of protein misfolding in a single-gene disorder is "sickle cell disease." (Lewis, 192-193) Editor's note - disorders associated with protein misfolding include "Alzheimer's disease,” "Huntington disease," “Parkinson's disease," “PKU," "prion disorders," and sickle cell disease. 

Protein Unfolding: conformational transitions of the shape of a protein to various unfolded states. (MeSH)

Quaternary Structure: hydrogen bonds between polypeptide chains. (Norman, 6/17/09) The association of two or more polypeptides to form a protein. (Brooker, G-31) Proteins composed of two or more polypeptides that each adopt a tertiary structure and then assemble with each other. (Brooker, 54)

Secondary Structure: hydrogen bonds between amino acids. (Norman Lectures, 6/17/09) A repeating folding pattern (possible because) proteins are flexible and can fold into a number of shapes. Two types are "alpha helix" and "beta sheet." Secondary structure contributes to the great strength of certain proteins, including those found in hair and hooves, those that make up the silk webs of spiders, and those found in "collagen," the chief component of "cartilage" in mammals. (Brooker, 52-53)  

Alpha-Helix: a repeating helical structure that is stabilized by hydrogen bonds. (Brooker, 52) The polypeptide backbone is twisted in a right-handed spiral to form a rigid rod-like structure held together by regular hydrogen bonding. (Lawrence)

Beta Pleated Sheet: a repeating ‘zig-zag’ shape that is created when parallel regions (of the polypeptide backbone of a protein) form hydrogen bonds. (Brooker, 53) Regular... secondary structure common in proteins, in which fully extended polypeptide chains lying adjacent to each other are held by hydrogen bonding to form a sheet structure. (Lawrence)

Tertiary Structure: disulfide bonds (sulfur to sulfur) between amino acids that contain sulfur in the “R-group.” (Norman Lectures, 6/17/09) Complex three-dimensional shapes. (Brooker, 54)