alpha helix
Common folding pattern in proteins, in which a linear sequence of amino acids folds into a right-handed helix stabilized by internal hydrogen bonding between backbone atoms
beta sheet
Common structural motif in proteins in which different sections of the polypeptide chain run alongside each other, joined together by hydrogen bonding between atoms of the polypeptide backbone
binding site
Region on the surface of one molecule (usually a protein or nucleic acid) that can interact with another molecule through noncovalent bonding
coiled-coil
Especially stable rodlike protein structure formed by two or more alpha helices coiled around each other
primary structure
Linear sequence of monomer units in a polymer, such as the amino acid sequence of a protein
protein
The major macromolecular constituents of cells. A linear polymer of amino acids linked together by peptide bonds in a specific sequence
protein domain
Portion of a protein that has a tertiary structure of its own. Larger proteins are generally composed of several domains, each connected to the next by short flexible regions of polypeptide chain. Homologous _____ are recognized in many different proteins
protein subunit
An individual protein chain in a protein composed of more than one chain
quaternary structure
Three-dimensional relationship of the different polypeptide chains in a multisubunit protein or protein complex
secondary structure
Regular local folding pattern of a polymeric molecule; in proteins, alpha-helices and beta-sheets
side chain
The part of an amino acid that differs between amino acid types. The _____ give each type of amino acid its unique physical and chemical properties
tertiary structure
Complex three-dimensional form of a folded polymer chain, especially a protein or RNA molecule
active site
Region of an enzyme surface to which a substrate molecule binds in order to undergo a catalyzed reaction
allosteric protein
Change in a protein's conformation brought about by the binding of a regulatory ligand (at a site other than the protein's catalytic site), or by covalent modification. The change in conformation alters the activity of the protein and can form the basis o
antibody
Protein produced by B cells in response to a foreign molecule or invading microorganism. Binds tightly to the foreign molecule or cell, inactivating it or marking it for destruction by phagocytosis or complement-induced lysis
antigen
A molecule that can induce an adaptive immune response or that can bind to an antibody or T cell receptor
catalyst
Substance that can lower the activation energy of a reaction (thus increasing its rate), without itself being consumed by the reaction
coenzyme
Small molecule tightly associated with an enzyme that participates in the reaction that the enzyme catalyzes, often by forming a covalent bond to the substrate. Examples include biotin, NAD+, ...
equilibrium constant
Ratio of forward and reverse rate constants for a reaction. Equal to the association or affinity constant (Ka) for a simple binding reaction (A+B<-->AB)
enzyme
Protein that catalyzes a specific chemical reaction
feedback inhibition
The process in which a product of a reaction feeds back to inhibit a previous reaction in the same pathway
GTP-binding protein (GTPase)
An enzyme that converts GTP to GDP. ____ fall into two large families. Large trimeric G proteins are composed of three different subunits and mainly couple GPCRs to enzymes or ion channels in the plasma membrane. Small monomeric ______ consist of a single
ligand
Any molecule that binds to a specific site on a protein or other molecule
lysozyme
Enzyme that catalyzes the cutting of polysaccharide chains in the cell walls of bacteria
motor protein
Protein that uses energy derived from nucleoside triphosphate hydrolysis to propel itself along a linear track (protein filament or other polymeric molecule)
protein kinase
Enzyme that transfers the terminal phosphate group of ATP to one or more specific amino acids (serine, threonine, or tyrosine) of a target protein
protein tyrosine phosphatase
Enzyme that removes phosphate groups from phosphorylated tyrosine residues on proteins
proteomics
Study of all the proteins, including all the covalently modified forms of each, produced by a cell, tissue, or organism. _____ often investigates changes in this larger set of proteins in 'the proteome' - caused by changes in the environment or by extrace
scaffold protein
Protein that binds groups of intracellular signaling proteins into a signaling complex, often anchoring the complex at a specific location in the cell
SCF ubiquitin ligase
Family of ubiquitin ligases formed as a complex of several different proteins. One is involved in regulating the eucaryotic cell cycle, directing the destruction of inhibitors of S-Cdks in late G1 and thus promoting the activation of S-Cdks and DNA replic
substrate
Molecule on which an enzyme acts
transition state
Structure that forms transiently in the course of a chemical reaction and has the highest free energy of any reaction intermediate. Its formation is a rate-limiting step in the reaction