KH 05 Flashcards
Proteins perform an extraordinarily diverse array of activities both inside and outside cells, yet most of these diverse functions are based on the ability of proteins to engage in a common activity, which is?
Binding. Proteins bind to one another, to other macromolecules, to small molecules, and to ions.
How do we call the molecule to which a protein binds?
Its ligand
In some cases, ligand-binding changes the _____ of the protein.
conformation. This ligand-induced conformational change is integral to the mechanism of action of many proteins.
What are the 2 properties that are of primary importance in ligand-binding?
Specificity and affinity
What is specificity?
The ability of a protein to bind only one particular ligand, even in the presence of a vast excess of irrelevant molecules.
What is affinity?
The tightness, or strength of binding, expressed as dissociation constant (Kd). The stronger the interaction, the lower the Kd.
What is binding?
An interaction between complementary molecular surfaces.
Protein binding specificity arises from numerous interactions which are individually _____, but, if numerous, collectively _____.
weak, strong
What are antibodies?
Antibodies are proteins that circulate in the blood and are made by the immune system in response to antigens, which are usually macromolecules present in infectious agents. They bind to the antigen’s epitope.
How are antibodies shaped?
Antibodies are Y-shaped molecules, often formed from two identical longer, or heavy, chains and two identical shorter, or light, chains. Near the end of each arm are six highly variable loops, called complementarity-determining regions (CDRs), which form the antigen-binding sites. The sequences of these six loops are highly variable in amino acid sequence among antibodies, generating unique complementary ligand-binding sites that make them specific for different epitopes.
What are enzymes?
Enzymes are an extremely diverse class of catalytically active proteins whose ligands include the substrates of the reactions they catalyze .
Where does substrate binding and reaction catalysis occcur?
At the enzyme’s active site.
What does substrate specificity arise from?
The substrate binding site
The substrate, and the substrate binding site interact at _____ molecular surfaces.
complementary
An active site consists of two functionally important regions: the _____ site, which recognizes and binds the substrate or substrates, and the _____ site, which carries out the chemical reaction once the substrate has bound.
substrate-binding, catalytic
What is the Vmax (maximal velocity)?
The maximal rate of catalysis given saturating amounts of substrate. Depends on the amount of enzyme and how fast it can work – the turnover number.
What is the Km (Michaelis constant)?
The substrate concentration that supports a rate of catalysis equal to one-half of the Vmax. Depends on, and is a measure of, the affinity of enzyme-substrate
binding.
What is the turnover number?
Enzymatic cycles per second at top speed.
What is an example of enzyme substrate-binding and catalytic site details?
The serine protease trypsin
What do proteases do in polypeptides?
They hydrolyze peptide bonds.
What is the family of proteases whose catalytic mechanism involves a serine residue in the catalytic site?
The serine proteases
What are proteases?
Enzymes that perform proteolysis (break down proteins into smaller polypeptides or single amino acids).
Protein folding brings “distant” amino acids into _____.
proximity
What is an enzyme that has a 2-step catalytic mechanism involving 3 amino acid side chains
Asp-102, His-57, and Ser-195 (N.B., not closely positioned in linear protein sequence)?
Trypsin
What 2 things can enzyme pH optima reflect?
- Active site acid-base chemistry
- Sensitivity of overall protein conformation to charge distribution
How many different active sites does the mammalian fatty acid synthase polypeptide have?
It has 7 active sites that catalyze sequential steps in fatty acid synthesis.
What is the allosteric effect?
The binding of a ligand at one site on a protein can lead to conformational changes that affect the binding of another ligand molecule at a different site.
What is an example of the allosteric effect?
The nature of the ligand bound to the nucleotide-binding domain of the molecular chaperone Hsp70, i.e., ATP versus ADP, affects the conformation of the substrate-binding domain, which changes its interactions with the misfolded “client” protein.
A major manifestation of allosteric effects is in _____ _____ in regulatory proteins in response to ligand binding or post-translational modification.
conformational switches
What does “allostery” refer to?
It refers to any change in a protein’s tertiary or quaternary structure, or in both, induced by the noncovalent binding of a ligand.
Non-covalent binding of ___ and ___ are widely used as allosteric switches to control protein activity
(important in cellular signal transduction pathways)
Ca++, GTP
What do allosteric switches do?
Allosteric switches turn the activity of many different proteins on or off by binding to them non-covalently.
What is phosphorylation?
The addition of a phosphate group to a molecule.
What is dephosphorylation?
The removal of a phosphate group to a molecule.
Phosphorylation is catalyzed by enzymes called _____ _____.
protein kinases
Dephosphorylation is catalyzed by enzymes called _____ _____.
protein phosphatases
Phosphorylation of amino acid side chains,
a rapidly reversible _____ modification of protein structure.
covalent!
What is an example of post-translational modification?
Modification of protein conformation and activity through
phosphorylation and dephosphorylation
What is frequently used in cellular signal transduction pathways?
Phosphorylation and dephosphorylation
How many different protein kinases does the human genome encode?
More than 500. Many are specific for just one, or a few, specific target proteins.
Frequently the target of a kinase or a phosphatase is another kinase or phosphatase, creating a “_____” effect.
cascade. Such kinase cascades permit amplification of a signal and many levels of fine-tuning.
The Nobel Prize in Physiology or Medicine 1992 was awarded jointly to Edmond H. Fischer and Edwin G. Krebs. What was their discovery?
They were awarded the Nobel Prize for their discoveries concerning reversible protein phosphorylation as a
biological regulatory mechanism.
