Ch 4 - Protein Structure and Function Flashcards
active site
region on the surface of an enzyme that binds to a substrate molecule and catalyzes its chemical transformation
allosteric
describes a protein that can exist in multiple conformations depending on the binding of a molecule (ligand) at a site other than the catalytic site; such changes from one conformation to another often alter the protein’s activity or ligand affinity
α helix (alpha helix)
folding pattern, common in many proteins, in which a single polypeptide chain twists around itself to form a rigid cylinder stabilized by hydrogen bonds between every fourth amino acid
amino acid sequence
the order of the amino acid subunits in a protein chain. sometimes called the primary structure of a protein
antibody
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
antigen
molecule or fragment of a molecule that is recognized by an antibody
β sheet (beta sheet)
folding pattern found in many proteins in which neighbouring regions of the polypeptide chain associate side-by-side with each other through hydrogen bonds to give a rigid flattened structure
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
C-terminus
the end of a polypeptide chain that carries a free carboxyl group (-COOH)
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 material that binds the desired molecule, and it is then eluted from the column with a solvent gradient.
coenzyme
small molecule that binds tightly to an enzyme and helps it to catalyze a reaction
coiled-coil
stable, rodlike protein structure formed when two or more α helices twist repeatedly around each other
conformation
precise, three-dimensional shape of a protein or other macromolecule based on the spatial location of its atoms in relation to one another
cryoelectron microscopy (cryo-EM)
technique for observing the detailed structure of a macromolecule at very low temperatures after freezing native structures in ice
disulfide bond
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
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
enzyme
a protein that catalyzes a specific chemical reaction
feedback inhibition
a form of metabolic control in which the end product of a chain of enzymatic reactions reduces the activity of an enzyme early in the pathway
fibrous protein
a protein with an elongated, rodlike shape, such as collagen or a keratin filament
globular protein
any protein in which the polypeptide folds into a compact, rounded shape. includes most enzymes
GTP -binding protein
intracellular signaling protein whose activity is determined by its association with either GTP or GDP. includes both trimeric G proteins and monomeric GTPases, such as Ras
helix
an elongated structure whose subunits twist in a regular fashion around a central axis, like a spiral staircase
intracellular condensate
a large aggregate of phase-separated macromolecules that creates a region with a special biochemistry without the use of an encapsulating membrane
intrinsically disordered-sequence
region in a polypeptide chain that lacks a definite structure
ligand
general term for a small molecule that binds to a specific site on a macromolecule
lysozyme
enzyme that severs the polysaccharide chains that form the cell walls of bacteria; found in many secretions including saliva and tears, where it serves as an antibiotic
mass spectrometry
sensitive technique that enables the determination of the exact mass of all the molecules in a complex mixture
Michaelis constant (Km)
the concentration of substrate at which an enzyme works at half its maximum velocity; serves as a measure of how tightly the substrate is bound
motor protein
protein such as myosin or kinesin that uses energy derived from the hydrolysis of a tightly bound ATP molecule to propel itself along a protein filament or polymeric molecule
nuclear magnetic resonance (NMR) spectroscopy
technique used for determining the three-dimensional structure of a protein in solution
N-terminus
the end of a polypeptide chain that carries a free α-amino group
peptide bond
covalent chemical bond between the carbonyl group of one amino acid and the amino group of a second amino acid.
polypeptide, polypeptide chain
linear polymer composed of multiple amino acids. proteins are composed of one or more polypeptide chains.
primary structure
the amino acid sequence of a protein
protein domain
segment of a polypeptide chain that can fold into a compact, stable structure and that often carries out a specific function.
protein family
a group of polypeptides that share a similar amino acid sequence or three-dimensional structure, reflecting a common evolutionary origin. individual members often have related but distinct functions, such as kinases that phosphorylate different target proteins
protein
macromolecule built from amino acids, that provides cells with their shape and structure and performance most of their activities
protein machine
assembly of protein molecules that operates as a cooperative unit to perform a complex series of biological activities, such as replicating DNA
protein kinase
enzyme that 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 from a protein, often with high specificity for the phosphorylated site
protein phosphorylation
the covalent addition of a phosphate group to a side chain of a protein, catalyzed by a protein kinase; serves as a form of regulation that usually alter the activity or properties of the target protein
quaternary structure
complete structure formed by multiple, interacting polypeptide chains that form a larger protein molecule
scaffold protein
protein with multiple binding sites for other macromolecules, holding them in a way that speeds up their functional interactions
secondary structure
regular local folding pattern of a polymeric molecule. in proteins, it refers to α helices and β sheets
side chain
portion of an amino acid not involved in forming peptide bonds; its chemical identity gives each amino acid unique properties
substrate
a molecule on which an enzyme acts to catalyze a chemical reaction
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, as composed of multiple polypeptide chains, each of which is called a protein subunit
tertiary structure
complete three-dimensional structure of a fully folded protein
transition state
transient structure that forms during the course of a chemical reaction; in this configuration, a molecule has the highest free energy; it is no longer the substrate, but it is not yet the product
turnover number
the maximum number of substrate molecules that an enzyme can convert into product per second
Vmax
the maximum rate of an enzymatic reaction, reached when the active sites of all of the enzyme molecules in a sample are fully occupied by substrate
x-ray crystallography
technique used to determine the three-dimensional structure of a protein molecule by analyzing the diffraction pattern produced when a beam of x-rays is passed through an ordered array of the protein
