amino acids
linked together by peptide bonds, carboxyl group of one amino acid covalently binds to nitrogen of another, molecule of water generated during condensation, contains c-terminus and n-terminus
peptide bond
the chemical bond that forms between the carboxyl group of one amino acid and the amino group of another amino acid, primary linkage of all proteins
polypeptide chain
amino acids linked together to form protein
polypeptide backbone
the chain of atoms containing repeating peptide bonds that runs through a protein molecule and to which the amino acid side chains are attached
side chain
Another term for R-group; variable grp of an amino acid that differs w/ each and determines the unique characteristics of a particular amino acid. also attached to the alpha carbon; may be polar, hydrophillic, or hydrophobic, non-polar
alpha helix
common folding pattern of protein, The The NN-HH of every peptide bond is hydrogen-bonded bonded to the C=O of a to the C=O of a
neighboring peptide bond located four amino acids away in the same chain, structure of DNA
beta sheet
One form of the secondary structure of proteins in which the polypeptide chain folds back and forth, or where two regions of the chain lie parallel to each other and are held together by hydrogen bonds.
secondary structure
The second level of protein structure; the regular local patterns of coils or folds of a polypeptide chain.
non-covalent bonds
help proteins form, three types: hydrogen bonds, electrostatic attractions, van der Waals attractions
hydrogen bonds
hydrogen sandwiched between electron-attracting atoms (oxygen or nitrogen)
electrostatic attractions
attraction between charged groups
van der Waals attractions
attraction between two atoms at very short distance
conformation
protein's unique shape that determines its function
prion protein
can adopt abnormal, denatured form, aggregation occurs leading to diseases that disrupt brain function
protein aggregation
Aggregation of misfolded proteins
protein denaturation
when proteins are subject to heat, acid or other conditions that disturb their stability; protein uncoils, loses its shape, and loses its function
disulfide bond
help stabilize a favored protein conformation, covalent bonds between two cystesine side chains, major stabilizer
protein domain
- any segment of a polypeptide chain that can fold
independently into a compact compact stable structure
secondary structure
alpha helices and beta sheets
protein subunits
pack to form filament, tube or spherical shell; ie. actin filament
binding site
Region on the surface of a protein, typically a cavity or groove, that is complementary in shape to, and forms multiple noncovalent bonds with, a second molecule (the ligand), place where protein can form dimer with identical compound, requires specific l
ligand
specific molecule that binds non-covalently with a protein, at the binding site
antibody
any of a large variety of proteins normally present in the body or produced in response to an antigen which it neutralizes, thus producing an immune response; y shaped with two binding sites for antigen, held together by disulfide bonds
antigen
A protein that, when introduced in the blood, triggers the production of an antibody
enzyme
any of several complex proteins that are produced by cells and act as catalysts in specific biochemical reactions, catalyze covalent bond breakage and/or formation (ie. Pepsin)
motor protein
A protein that interacts with cytoskeletal elements and other cell components, producing movement of the whole cell or parts of the cell. (myosin), allosteric, driven by ATP
protein kinase
transfers a phosphate from ATP to an Amino acid side chain, phosphorylating the protein
protein phosphatase
An enzyme that removes phosphate groups from proteins, often functioning to reverse the effect of a protein kinase.
GTP-binding protein
form molecular switches, hydrolysis of GTP causes protein to change conformation rendering the protein inactive, an allosteric protein whose conformation and activity are determined by its association with either GTP or GDP. Includes many proteins involve
allosteric
The binding of a regulatory molecule to a protein at one site that affects the function of the protein at a diferent site
active site
the part of an enzyme or antibody where the chemical reaction occurs
electrophoresis
Method of separating serum proteins by electrical charge
proteomics
the branch of genetics that studies the full set of proteins encoded by a genome
x-ray crystallography
A technique that depends on the diffraction of an X-ray beam by the individual atoms of a crystallized molecule to study the three-dimensional structure of the molecule.
chromatography
a process used for separating mixtures by virtue of differences in absorbency; types used for protein studying-gel filtration, affinity and ion-exchange chromatography
structure protein
provides cell with shape and structure (actin filaments)
transport protein
carries other ions and molecules (hemoglobin carries oxygen)
storage protein
protein that provides a source of amino acids for developing plants and animals
signal protein
carries signals from cell to cell (insulin---glucose levels)
receptor protein
detects signal and transmits it to the cell's machinery (insulin receptor)
gener regulatory protein
binds to DNA to turn off certain genes or turn them on (transcriptional factors)
feedback inhibition
regulates the flow through biosynthetic pathways, triggers conformation change. A method of metabolic control in which the end product of a metabolic pathway acts as an inhibitor of an enzyme within that pathway.