peptide bonds
Chemical bond between the carbonyl group of one amino acid and the amino group of a second amino acid
polypeptides
Linear polymer composed of multiple amino acids. Proteins are composed of one or more long polypeptide chains.
polypeptide chains
Linear polymer composed of multiple amino acids. Proteins are composed of one or more long polypeptide chains.
amino acid sequence
The order of the amino acid subunits in a protein
chain. Sometimes called the primary structure of a
protein.
polypeptide backbone
Repeating sequence of atoms (-N-C-C-) that forms the core of a protein molecule and to which the amino acid side chains are attached.
N-terminus
The end of a polypeptide chain that carries a free ?-amino group.
C-terminus
Also known as Carboxyl terminus. The end of a polypeptide chain that carries a free carboxyl group (-COOH).
side chains
Portion of an amino acid not involved in forming peptide bonds; its chemical identity gives each amino acid its unique properties.
conformation
Precise, three-dimensional shape of a protein or
other macromolecule, based on the spatial location
of its atoms in relation to one another.
alpha helix (? helix)
Folding pattern, common in many proteins, in which a single polypeptide chains twists around itself to form a rigid
beta sheet (? sheet)
Folding pattern found in many proteins in which neighboring regions of the polypeptide chain associate side by side with each other through hydrogen bonds to give a rigid, flattened structure.
helix
An elongated structure whose subunits twist in a regular fashion around a central axis, like a spiral staircase.
coiled-coil
Stable, rodlike protein structure formed when two or more alpha helices twist around each other.
primary structure.
The amino acid sequence of a protein.
secondary structure
Regular local folding patterns of a polymeric molecule. In proteins, it refers to alpha helices and beta sheets.
tertiary structure
Complete three-dimensional structure of a fully folded protein.
quaternary structure
Complete structure formed by multiple, interacting polypeptide chains within a protein molecule.
protein domain
Segment of a polypeptide chain that can fold INDEPENDENTLY into a compact stable structure and that usually carries out a specific function.
intrinsically disordered sequences
Region in a polypeptide chain that lacks a definite structure.
subunit
A monomer that forms part of a larger molecule, such as an amino acid residue in a protein or a nucleotide residue in a nucleic acid. Can also refer to a complete molecule that forms part of a larger molecule. Many proteins, for example, are composed of m
fibrous proteins
A protein with an elongated, rodlike shape, such as collagen or a keratin filament.
disulfide bonds
Covalent cross-link formed between the sulfhydryl
groups on two cysteine side chains; often used to
reinforce a secreted protein's structure or to join two
different proteins together.
ligand
General term for a molecule that binds to a specific site on a protein.
binding site
Region on the surface of a protein, typically a cavity or groove, that interacts with another molecule (a ligand) through the formation of multiple noncovalent bonds.
antibodies
Protein produced by B lymphocytes in response to a foreign molecule or invading organism. Binds to the foreign molecule or cell extremely tightly, thereby inactivating it or marking it for destruction.
antigens
Molecule or fragment of a molecule that is recognized by an antibody.
substrates
A molecule on which an enzyme acts.
transition state
Structure that forms transiently during the course of a chemical reaction; in this configuration, a molecule has the highest free energy, and is no longer a substrate, but is not yet a product.
active site
Region on a the surface on an enzyme that binds to a substrate molecule and catalyzes it chemical transformation.
feedback inhibition
A form of metabolic control in which the end product of a chain of enzymatic reactions reduces that activity of an enzyme earlier in the pathway.
allosteric
Describes a protein that can exist in multiple conformations depending on the bind of a ligand at a site other than the catalytic site; changes from one conformation to another often alter the protein's activity or ligand affinity.
protein phosphorylation
The covalent addition of a phosphate group to a side chain of a protein, catalyzed by a protein kinase; serves as a from of regulation that usually alters the activity or properties of the target protein. This type of regulation does NOT fall under the ca
protein kinase
Enzyme the catalyzes the transfer of a phosphate group from ATP to a specific amino acid side chain on a target protein.
protein phosphatase
Enzyme that catalyzes the removal of a phosphate group (dephosphorylation) from a protein, often with high specificity for the phosphorylated site.
GTP-binding proteins
Intracellular signaling protein whose activity is determined by its association with either GTP or GDP. Includes both trimeric G proteins and monemeric GTPases, such as Ras. These proteins act as molecular switches; they are in their active conformation w
motor proteins
Protein such as myosin or kinesin that uses energy derived from ATP hydrolysis to propel itself along a protein filament or polymeric molecule. Ex.The muscle motor protein myosin moves along actin filaments at 6 um/sec. during muscle contraction.
protein machines
Large assembly of protein molecules that operates as a unit to perform a complex series of biological activities, such as replicating DNA. In most, this complex series of biological activities is driven by the hydrolysis of bound activated carriers such a
chromatography
Technique used to separate the individual molecules
in a complex mixture on the basis of their size, charge,
or their ability to bind to a particular chemical group.
In a common form of the technique, the mixture
is run through a column filled with a mate
electrophoresis
Technique for separating a mixture of proteins or
DNA fragments by placing them on a polymer gel and
subjecting them to an electric field. The molecules
migrate through the gel at different speeds depending
on their size and net charge.
mass spectrometry
Technique for determining the exact mass of every peptide present in a sample of purified protein or protein mixture.
lysozyme
Enyzmes that serves the polysachharide chains that form the cell walls of bacteria; found in many secretions including saliva and tears.
globular protein
Any protein in whcih the polypeptide chain folds into a compact, rounded shape. Includes most enzymes.
nuclear magnetic resonance (NMR) spectroscopy
Technique used for determining the three-dimensional structure of a protein in solution.
X-ray crystallography
Technique used to determine the three-dimensional structure of a protein molecule by analyzing the pattern produced when a beam of X-rays is passed through an order array of the protein.
proteolytic
protein-cleaving
dimer
Two identical, folded polypeptide chains that form a symmetrical complex of two protein subunits that is held together by interactions between two identical sites.
alpha-keratin
A fibrous protein that forms a dimer,is extremely stable and found in hair, horns and nails.
collagen
An abundant fibrous protein that makes up the extracellular matrix found in animal tissues. This protein forms long overlapping arrays that help hold tissues together and add strength.
elastin
A fibrous protein formed form relatively loose and unstructured polypeptide chains that are covalently linked into a rubber-like elastic meshwork. The resulting fibers enable skin and other tissues to stretch and recoil without tearing.
hydrolase
General term for enzymes that catalyze a hydrolytic cleavage reaction.
nuclease
Breaks down nucleic acids by hydrolyzing bonds between nucleotides.
protease
Breaks down proteins by hydrolyzing peptide bonds between amino acids.
ligase
Joins two molecules together; DNA ligase joins two DNA strands together end-to-end.
isomerase
Catalyzes the rearrangement of bonds within a single molecule.
polymerase
Catalyzes polymerization reactions such as the synthesis of DNA and RNA.
kinase
Catalyzes the addition of phosphate groups to molecules. Protein kinases are important group of kinases that attach phosphate groups to proteins.
phosphatase
Catalyzes the hydrolytic removal of a phosphate group from a molecule
oxido-reductase
General name for enzymes that catalyze reactions in which one molecule is oxidized while the other is reduced. Enzymes of this type are often called oxidases, reductases, or dehydrogenases.
protein families
Present-day proteins that are grouped together together because each member has an amino acid sequence and a three-dimensional conformation that closely resemble those of the other family members.