Kapitel 4 Flashcards
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.
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 either binds or lets through the desired molecule.
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.
beta sheet (β sheet)
The end of a polypeptide chain that carries a free carboxyl group (–COOH).
C-terminus (carboxyl terminus)
Region in a polypeptide chain that lacks a definite structure.
intrinsically disordered sequence
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 ordered array of the protein.
X-ray crystallography
A collection of macromolecules that are bound to each other by noncovalent bonds to form a large structure with a specific function.
complex
Technique for determining the exact mass of every peptide present in a sample of purified protein or protein mixture.
mass spectrometry
in vitro
Term used by biochemists to describe a process that takes place in an isolated cell-free extract. Also used by cell biologists to refer to cells growing in culture - as opposed to in an organism.
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.
See protein kinase
kinase
A group of polypeptides that shares 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 family
nuclear magnetic resonance (NMR) spectroscopy
Technique used for determining the three-dimensional structure of a protein in solution.
side chain
Portion of an amino acid not involved in forming peptide bonds; its chemical identity gives each amino acid its unique properties.
protein family
A group of polypeptides that shares 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.
coiled-coil
Stable - rodlike protein structure formed when two or more α helices twist around each other.
fibrous protein
A protein with an elongated - rodlike shape - such as collagen or a keratin filament.
antiparallel
Describes two similar structures arranged in opposite orientations - such as the two strands of a DNA double helix.
proteomics
The large-scale study of the structure and function of proteins.
specificity
Selective affinity of one molecule for another that permits the two to bind or react - even in the presence of a vast excess of unrelated molecular species.
Large assembly of protein molecules that operates as a unit to perform a complex series of biological activities - such as replicating DNA.
protein machine
In an intact cell or organism. (Latin for “in life.”)
in vivo
Portion of an amino acid not involved in forming peptide bonds; its chemical identity gives each amino acid its unique properties.
side chain
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.
disulfide bond
Protein such as myosin or kinesin that uses energy derived from ATP hydrolysis to propel itself along a protein filament or polymeric molecule.
motor protein
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.
Enzyme that severs the polysaccharide chains that form the cell walls of bacteria; found in many secretions including saliva and tears.
lysozyme
Describes two similar structures arranged in opposite orientations - such as the two strands of a DNA double helix.
antiparallel
Region on the surface of an enzyme that binds to a substrate molecule and catalyzes its chemical transformation.
active site
antigen
Molecule or fragment of a molecule that is recognized by an antibody.
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 alters the activity or properties of the target protein.
protein phosphorylation
A protein with an elongated - rodlike shape - such as collagen or a keratin filament.
fibrous protein
quaternary structure
Complete structure formed by multiple - interacting polypeptide chains within a protein molecule.
Complete structure formed by multiple - interacting polypeptide chains within a protein molecule.
quaternary structure
The end of a polypeptide chain that carries a free α-amino group.
N-terminus (amino terminus)
General term for a molecule that binds to a specific site on a protein.
ligand
ligand
General term for a molecule that binds to a specific site on a protein.
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.
antibody
helix
An elongated structure whose subunits twist in a regular fashion around a central axis - like a spiral staircase.
Regular local folding pattern of a polymeric molecule. In proteins - it refers to α helices and βsheets.
secondary structure
denature
To cause a dramatic change in the structure of a macromolecule by exposing it to extreme conditions - such as high heat or harsh chemicals. Usually results in the loss of biological function.
Enzyme that catalyzes the transfer of a phosphate group from ATP to a specific amino acid side chain on a target protein.
protein kinase
secondary structure
Regular local folding pattern of a polymeric molecule. In proteins - it refers to α helices and βsheets.
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.
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; changes from one conformation to another often alter the protein’s activity or ligand affinity.
allosteric
in vivo
In an intact cell or organism. (Latin for “in life.”)
The order of the amino acid subunits in a protein chain. Sometimes called the primary structure of a protein.
amino acid sequence
lysozyme
Enzyme that severs the polysaccharide chains that form the cell walls of bacteria; found in many secretions including saliva and tears.
beta sheet (β 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.
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.
electrophoresis
An elongated structure whose subunits twist in a regular fashion around a central axis - like a spiral staircase.
helix
intrinsically disordered sequence
Region in a polypeptide chain that lacks a definite structure.
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 alters the activity or properties of the target protein.
To cause a dramatic change in the structure of a macromolecule by exposing it to extreme conditions - such as high heat or harsh chemicals. Usually results in the loss of biological function.
denature
Segment of a polypeptide chain that can fold into a compact stable structure and that usually carries out a specific function.
protein domain
N-terminus (amino terminus)
The end of a polypeptide chain that carries a free α-amino group.
protein domain
Segment of a polypeptide chain that can fold into a compact stable structure and that usually carries out a specific function.
mass spectrometry
Technique for determining the exact mass of every peptide present in a sample of purified protein or protein mixture.
The large-scale study of the structure and function of proteins.
proteomics
Molecule or fragment of a molecule that is recognized by an antibody.
antigen
tertiary structure
Complete three-dimensional structure of a fully folded protein.
Complete three-dimensional structure of a fully folded protein.
tertiary structure
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.
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.
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.
transition state
active site
Region on the surface of an enzyme that binds to a substrate molecule and catalyzes its chemical transformation.
peptide bond
Chemical bond between the carbonyl group of one amino acid and the amino group of a second amino acid.
chaperone protein
Molecule that steers proteins along productive folding pathways - helping them to fold correctly and preventing them from forming aggregates inside the cell.
Linear polymer composed of multiple amino acids. Proteins are composed of one or more long polypeptide chains.
polypeptide; polypeptide chain
polypeptide; polypeptide chain
Linear polymer composed of multiple amino acids. Proteins are composed of one or more long polypeptide chains.
The amino acid sequence of a protein.
primary structure
protein kinase
Enzyme that catalyzes the transfer of a phosphate group from ATP to a specific amino acid side chain on a target protein.
Molecule that steers proteins along productive folding pathways - helping them to fold correctly and preventing them from forming aggregates inside the cell.
chaperone protein
complex
A collection of macromolecules that are bound to each other by noncovalent bonds to form a large structure with a specific function.
A molecule composed of two structurally similar subunits.
dimer
Small discrete region of a structure; in a protein - a segment that folds into a compact and stable structure. In a membrane - a region of the bilayer with a characteristic lipid and protein composition.
domain
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; changes from one conformation to another often alter the protein’s activity or ligand affinity.
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.
feedback inhibition
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.
alpha helix (α helix)
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.
binding site
dimer
A molecule composed of two structurally similar subunits.
Any protein in which the polypeptide chain folds into a compact - rounded shape. Includes most enzymes.
globular protein
primary structure
The amino acid sequence of a protein.
sulfhydryl group (–SH - thiol)
Chemical group containing sulfur and hydrogen found in the amino acid cysteine and other molecules. Two can join together to produce a disulfide bond.
domain
Small discrete region of a structure; in a protein - a segment that folds into a compact and stable structure. In a membrane - a region of the bilayer with a characteristic lipid and protein composition.
Enzyme that catalyzes the removal of a phosphate group from a protein - often with high specificity for the phosphorylated site.
protein phosphatase
Stable - rodlike protein structure formed when two or more α helices twist around each other.
coiled-coil
motor protein
Protein such as myosin or kinesin that uses energy derived from ATP hydrolysis to propel itself along a protein filament or polymeric molecule.
globular protein
Any protein in which the polypeptide chain folds into a compact - rounded shape. Includes most enzymes.
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.
polypeptide backbone
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 either binds or lets through the desired molecule.
chromatography
C-terminus (carboxyl terminus)
The end of a polypeptide chain that carries a free carboxyl group (–COOH).
Technique used for determining the three-dimensional structure of a protein in solution.
nuclear magnetic resonance (NMR) spectroscopy
Term used by biochemists to describe a process that takes place in an isolated cell-free extract. Also used by cell biologists to refer to cells growing in culture - as opposed to in an organism.
in vitro
alpha helix (α 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.
protein machine
Large assembly of protein molecules that operates as a unit to perform a complex series of biological activities - such as replicating DNA.
Selective affinity of one molecule for another that permits the two to bind or react - even in the presence of a vast excess of unrelated molecular species.
specificity
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 ordered array of the protein.
Chemical bond between the carbonyl group of one amino acid and the amino group of a second amino acid.
peptide bond
Chemical group containing sulfur and hydrogen found in the amino acid cysteine and other molecules. Two can join together to produce a disulfide bond.
sulfhydryl group (–SH - thiol)
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.
